bims-myxlip Biomed News
on Myxoid liposarcoma
Issue of 2020–12–20
102 papers selected by
Laura Mannarino
  1. A Phase 1b Study Evaluating the Safety, Tolerability, and Immunogenicity of CMB305, a Lentiviral-Based Prime-Boost Vaccine Regimen, in Patients with Locally Advanced, Relapsed, or Metastatic Cancer Expressing NY-ESO-1.
  2. Treatment options in unresectable soft tissue and bone sarcoma of the extremities and pelvis - a systematic literature review.
  3. PD-1 blockade using pembrolizumab in adolescent and young adult patients with advanced bone and soft tissue sarcoma.
  4. Anti-Angiogenic Agents in Management of Sarcoma Patients: Overview of Published Trials.
  5. Factors associated with 30-day soft tissue complications following upper extremity sarcoma surgery.
  6. Tumor-on-a-chip platforms to study cancer-immune system crosstalk in the era of immunotherapy.
  7. Adjuvant and neoadjuvant chemotherapy for soft tissue sarcomas: JCOG Bone and Soft Tissue Tumor Study Group.
  8. Germline Variation and Somatic Alterations in Ewing Sarcoma.
  9. Epigenetic Analysis in Ewing Sarcoma.
  10. Harmine and Piperlongumine Revert TRIB2-Mediated Drug Resistance.
  11. A single institutional experience treating adipocytic tumors: incidence, disease-related outcomes, and the clinical significance of MDM2 analysis.
  12. Regulation of PD-L1 Expression by NF-κB in Cancer.
  13. Systems Biology Analysis for Ewing Sarcoma.
  14. Phagocytic function of tumor-associated macrophages as a key determinant of tumor progression control: a review.
  15. Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy.
  16. Metabolic Regulation of Epigenetic Modifications and Cell Differentiation in Cancer.
  17. Comprehensive analysis of immune infiltration and gene expression for predicting survival in patients with sarcomas.
  18. External validation and adaptation of a dynamic prediction model for patients with high-grade extremity soft tissue sarcoma.
  19. Trabectedin overcomes doxorubicin-resistance, counteracts tumor-immunosuppressive reprogramming of monocytes and decreases xenograft growth in Hodgkin lymphoma.
  20. Molecular Approaches to Diagnosis in Ewing Sarcoma: Targeted RNA Sequencing.
  21. SWI/SNF complex mutations promote thyroid tumor progression and insensitivity to redifferentiation therapies.
  22. Tissue Preservation and FFPE Samples: Optimized Nucleic Acids Isolation in Ewing Sarcoma.
  23. Emerging Need of Today: Significant Utilization of Various Databases and Softwares in Drug Design and Development.
  24. Emerging Autophagy Functions Shape the Tumor Microenvironment and Play a Role in Cancer Progression - Implications for Cancer Therapy.
  25. Molecular Approaches to Diagnosis in Ewing Sarcoma: RT-PCR.
  26. p38β (MAPK11) mediates gemcitabine-associated radiosensitivity in sarcoma experimental models.
  27. Bioinformatics Identification of the Expression and Clinical Significance of E2F Family in Endometrial Cancer.
  28. No Easy Way Out for EZH2: Its Pleiotropic, Noncanonical Effects on Gene Regulation and Cellular Function.
  29. MicroRNA-381-A Key Transcriptional Regulator: Its Biological Function and Clinical Application Prospects in Cancer.
  30. Ewing Sarcoma PDX Models.
  31. Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma.
  32. Genetically Engineered Mouse Model in Ewing Sarcoma.
  33. A feed-forward regulatory loop in adipose tissue promotes signaling by the hepatokine FGF21.
  34. Essential functions of miR-125b in cancer.
  35. Long non-coding RNAs as the regulators and targets of macrophage M2 polarization.
  36. Bone marrow mesenchymal stem cells derived miRNA-130b enhances epithelial sodium channel by targeting PTEN.
  37. Progress and Promises of Epigenetic Drugs and Epigenetic Diets in Cancer Prevention and Therapy: A Clinical Update.
  38. Lipid Metabolism and Resistance to Anticancer Treatment.
  39. Recurrent FOS rearrangement in proliferative fasciitis/proliferative myositis.
  40. Defective FXR-SHP Regulation in Obesity Aberrantly Increases miR-802 Expression, Promoting Insulin Resistance and Fatty Liver.
  41. A Novel Tool to Predict Early Death in Uterine Sarcoma Patients: A Surveillance, Epidemiology, and End Results-Based Study.
  42. Resection outcomes for primary and local recurrent retroperitoneal liposarcoma patients.
  43. Main Repositories and Databases Used in Ewing Sarcoma Research.
  44. Energy metabolism during osteogenic differentiation: the role of Akt.
  45. Extracellular Matrix-Related Six-lncRNA Signature as a Novel Prognostic Biomarker for Bladder Cancer.
  46. Current and future landscape of poly (ADP-ribose) polymerase inhibition resistance.
  47. HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation.
  48. Mitophagy-mediated adipose inflammation contributes to type 2 diabetes with hepatic insulin resistance.
  49. Metabolic response as assessed by 18 F-fluorodeoxyglucose positron emission tomography-computed tomography does not predict outcome in patients with intermediate- or high-risk rhabdomyosarcoma: A report from the Children's Oncology Group Soft Tissue Sarcoma Committee.
  50. Ewing Sarcoma-Specific (Re)expression Models.
  51. G-Quadruplex loops regulate PARP-1 enzymatic activation.
  52. MiR-125b-2 knockout increases high-fat diet-induced fat accumulation and insulin resistance.
  53. Western Blot Analysis in Ewing Sarcoma.
  54. New Actors Driving the Epithelial-Mesenchymal Transition in Cancer: The Role of Leptin.
  55. ELABELA ameliorates hypoxic/ischemic-induced bone mesenchymal stem cell apoptosis via alleviation of mitochondrial dysfunction and activation of PI3K/AKT and ERK1/2 pathways.
  56. The Role of Calcium Signaling in Regulation of Epithelial-Mesenchymal Transition.
  57. Epidrug Repurposing: Discovering New Faces of Old Acquaintances in Cancer Therapy.
  58. Development of a miRNA-controlled dual-sensing system and its application for targeting miR-21 signaling in tumorigenesis.
  59. Novel approaches to glycomimetic design: Development of small molecular weight lectin antagonists.
  60. Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses.
  61. Analysis of Regulatory DNA Sequences by Dual-Luciferase Reporter Assays in Ewing Sarcoma.
  62. Tumor Microenvironment Uses a Reversible Reprogramming of Mesenchymal Stromal Cells to Mediate Pro-tumorigenic Effects.
  63. Emerging trends in chromatin remodeler plasticity in mesenchymal stromal cell function.
  64. Histone acylation marks respond to metabolic perturbations and enable cellular adaptation.
  65. The role of Schlafen 11 (SLFN11) as a predictive biomarker for targeting the DNA damage response.
  66. Post-translational modifications of EZH2 in cancer.
  67. HDAC Inhibition Increases HLA Class I Expression in Uveal Melanoma.
  68. NAD+ Metabolism Regulates Preadipocyte Differentiation by Enhancing α-Ketoglutarate-Mediated Histone H3K9 Demethylation at the PPARγ Promoter.
  69. MiR-4310 induced by SP1 targets PTEN to promote glioma progression.
  70. PPARγ S273 Phosphorylation Modifies the Dynamics of Coregulator Proteins Recruitment.
  71. New Roles for Fusobacterium nucleatum in Cancer: Target the Bacteria, Host, or Both?
  72. The Molecular Mechanisms Underlying Mitochondria-Associated Endoplasmic Reticulum Membrane-Induced Insulin Resistance.
  73. CBX2 depletion inhibits the proliferation, invasion and migration of gastric cancer cells by inactivating the YAP/β-catenin pathway.
  74. Toll-like Receptors as a Potential Drug Target for Diabetes Mellitus and Diabetes-associated Complications.
  75. Natural Compounds That Target DNA Repair Pathways and Their Therapeutic Potential to Counteract Cancer Cells.
  76. Long non-coding RNA MEG3 promotes autophagy and apoptosis of nasopharyngeal carcinoma cells via PTEN up-regulation by binding to microRNA-21.
  77. Macrophages and brown adipocytes cross-communicate to modulate a thermogenic program following methamphetamine exposure.
  78. PKM2-Induced the Phosphorylation of Histone H3 Contributes to EGF-Mediated PD-L1 Transcription in HCC.
  79. Analysis of Migration and Invasion in Ewing Sarcoma.
  80. Liquid Biopsies in Ewing Sarcoma.
  81. Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer.
  82. Exosomes: Critical mediators of tumour microenvironment reprogramming.
  83. Immune Adaptation of Colorectal Cancer Stem Cells and Their Interaction With the Tumor Microenvironment.
  84. SPATA4 improves aging-induced metabolic dysfunction through promotion of preadipocyte differentiation and adipose tissue expansion.
  85. DNA damage alters nuclear mechanics through chromatin reorganization.
  86. Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses.
  87. CCAAT/Enhancer Binding Protein β Promotes Muscle Stem Cell Quiescence through Regulation of Quiescence-Associated Genes.
  88. Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials.
  89. DNA Sensing in Mismatch Repair-Deficient Tumor Cells Is Essential for Anti-tumor Immunity.
  90. BET-Inhibitor I-BET762 and PARP-Inhibitor Talazoparib Synergy in Small Cell Lung Cancer Cells.
  91. CD47 differentially regulates white and brown fat function.
  92. Tumor Growth Analysis of Ewing Sarcoma Cell Lines Using Subcutaneous Xenografts in Mice.
  93. Different expression of lipid metabolism-related genes in Shandong black cattle and Luxi cattle based on transcriptome analysis.
  94. The Role of Non-Coding RNAs in Controlling Cell Cycle Related Proteins in Cancer Cells.
  95. A Machine Learning Approach for Tracing Tumor Original Sites With Gene Expression Profiles.
  96. Induction of HOX genes by HCV infection via impairment of histone H2A monoubiquitination.
  97. Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology.
  98. Differential modulation of GR signaling and HDACs in the development of resilient/vulnerable phenotype and antidepressant-like response of vorinostat.
  99. SLFN11 informs on standard of care and novel treatments in a wide range of cancer models.
  100. Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications.
  101. Over expression of PTEN induces apoptosis and prevents cell proliferation in breast cancer cells.
  102. Targeted therapy of TERT-rearranged neuroblastoma with BET bromodomain inhibitor and proteasome inhibitor combination therapy.
  1. Oncoimmunology. 2020 Nov 19. 9(1): 1847846
    A Phase 1b Study Evaluating the Safety, Tolerability, and Immunogenicity of CMB305, a Lentiviral-Based Prime-Boost Vaccine Regimen, in Patients with Locally Advanced, Relapsed, or Metastatic Cancer Expressing NY-ESO-1.
    Neeta Somaiah, Sant P Chawla, Matthew S Block, John C Morris, Khanh Do, Joseph W Kim, Mihaela Druta, Kamalesh K Sankhala, Patrick Hwu, Robin L Jones, Sacha Gnjatic, Seunghee Kim-Schulze, Kevin Tuballes, Mahlet Yishak, Hailing Lu, Adam Yakovich, Jan Ter Meulen, Michael Chen, Richard T Kenney, Chet Bohac, Seth M Pollack.
      Preclinical data suggest that a "prime-boost" vaccine regimen using a target-expressing lentiviral vector for priming, followed by a recombinant protein boost, may be effective against cancer; however, this strategy has not been evaluated in a clinical setting. CMB305 is a prime-boost vaccine designed to induce a broad anti-NY-ESO-1 immune response. It is composed of LV305, which is an NY-ESO-1 expressing lentiviral vector, and G305, a recombinant adjuvanted NY-ESO-1 protein. This multicenter phase 1b, first-in-human trial evaluated CMB305 in patients with NY-ESO-1 expressing solid tumors. Safety was examined in a 3 + 3 dose-escalation design, followed by an expansion with CMB305 alone or in a combination with either oral metronomic cyclophosphamide or intratumoral injections of a toll-like receptor agonist (glucopyranosyl lipid A). Of the 79 patients who enrolled, 81.0% had sarcomas, 86.1% had metastatic disease, and 57.0% had progressive disease at study entry. The most common adverse events were fatigue (34.2%), nausea (26.6%), and injection-site pain (24.1%). In patients with soft tissue sarcomas, a disease control rate of 61.9% and an overall survival of 26.2 months (95% CI, 22.1-NA) were observed. CMB305 induced anti-NY-ESO-1 antibody and T-cell responses in 62.9% and 47.4% of patients, respectively. This is the first trial to test a prime-boost vaccine regimen in patients with advanced cancer. This approach is feasible, can be delivered safely, and with evidence of immune response as well as suggestion of clinical benefit.
    Keywords:  G305; LV305; NY-ESO-1; immunotherapy; lentivirus; myxoid liposarcoma; prime-boost; synovial sarcoma; vaccine
    DOI:  https://doi.org/10.1080/2162402X.2020.1847846
  2. EFORT Open Rev. 2020 Nov;5(11): 799-814
    Treatment options in unresectable soft tissue and bone sarcoma of the extremities and pelvis - a systematic literature review.
    Maria Anna Smolle, Joanna Szkandera, Dimosthenis Andreou, Emanuela Palmerini, Marko Bergovec, Andreas Leithner.
      In patients with metastatic or unresectable soft tissue and bone sarcoma of extremities and pelvis, survival is generally poor. The aim of the current systematic review was to analyse recent publications on treatment approaches in patients with inoperable and/or metastatic sarcoma.Original articles published between 1st January 2011 and 2nd May 2020, using the search terms 'unresectable sarcoma', 'inoperability AND sarcoma', 'inoperab* AND sarcoma', and 'treatment AND unresectable AND sarcoma' in PubMed, were potentially eligible. Out of the 839 initial articles (containing 274 duplicates) obtained and 23 further articles identified by cross-reference checking, 588 were screened, of which 447 articles were removed not meeting the inclusion criteria. A further 54 articles were excluded following full-text assessment, resulting in 87 articles finally being analysed.Of the 87 articles, 38 were retrospective (43.7%), two prospective (2.3%), six phase I or I/II trials (6.9%), 22 phase II non-randomized trials (27.6%), nine phase II randomized trials (10.3%) and eight phase III randomized trials (9.2%). Besides radio/particle therapy, isolated limb perfusion and conventional chemotherapy, novel therapeutic approaches, including immune checkpoint inhibitors and tyrosine kinase inhibitors were also identified, with partially very promising effects in advanced sarcomas.Management of inoperable, advanced or metastatic sarcomas of the pelvis and extremities remains challenging, with the optimal treatment to be defined individually. Besides conventional chemotherapy, some novel therapeutic approaches have promising effects in both bone and soft tissue subtypes. Considering that only a small proportion of studies were randomized, the clinical evidence currently remains moderate and thus calls for further large, randomized clinical trials. Cite this article: EFORT Open Rev 2020;5:799-814. DOI: 10.1302/2058-5241.5.200069.
    Keywords:  advanced sarcoma; inoperable sarcoma; novel therapeutics; treatment approach
    DOI:  https://doi.org/10.1302/2058-5241.5.200069
  3. Cancer Rep (Hoboken). 2020 Dec 13. e1327
    PD-1 blockade using pembrolizumab in adolescent and young adult patients with advanced bone and soft tissue sarcoma.
    Tahlia Scheinberg, Anna Lomax, Martin Tattersall, David Thomas, Geoff McCowage, Michael Sullivan, Rooshdiya Karim, Peter P Luk, Annabelle Mahar, Fiona Bonar, Vivek A Bhadri.
       BACKGROUND: Sarcomas represent 10%-15% of cancers in adolescent and young adult (AYA) patients, and survival for those with metastatic disease or relapse is poor. Immunotherapy with checkpoint inhibition has improved outcomes in multiple tumor types, but data in advanced sarcomas, particularly within the AYA population, are limited.
    AIM: We aim to evaluate response and toxicity for AYA patients with sarcoma treated with pembrolizumab.
    METHODS AND RESULTS: We retrospectively reviewed AYA patients with advanced bone and soft tissue sarcoma who received self-funded pembrolizumab between May 2015 and January 2019. Eighteen patients were identified. One patient with Ewing sarcoma had a sustained complete response to therapy. Two patients with alveolar soft part sarcoma received a clinical benefit from pembrolizumab: one had a radiological partial response with an excellent clinical response and one patient achieved stable disease. Four patients died of disease prior to first scheduled assessment and thus were not evaluable. The remaining eleven patients had progressive disease.
    CONCLUSION: The role of immunotherapy in AYA sarcoma warrants further investigation. Biomarkers of response need to be further evaluated in order to guide patient selection.
    Keywords:  adolescent; bone neoplasms; immunotherapy; sarcoma; young adult
    DOI:  https://doi.org/10.1002/cnr2.1327
  4. Front Oncol. 2020 ;10 594445
    Anti-Angiogenic Agents in Management of Sarcoma Patients: Overview of Published Trials.
    Pierre-Yves Cren, Loïc Lebellec, Thomas Ryckewaert, Nicolas Penel.
      We reviewed all fully published clinical trials assessing anti-angiogenic agents in sarcoma patients (last issue, January 13, 2020). Anti-angiogenic macromolecules (e.g., bevacizumab or ombrabulin) provide disappointing results. Many multikinase inhibitors have been assessed with non-randomized phase II trials with limited samples and without stratification according to histological subtypes, therefore interpretation of such trials is very challenging. On the contrary, pazopanib, regorafenib, and sorafenib have been assessed using double-blind placebo-controlled randomized phase II or phase III trials. Compared to placebo, sorafenib demonstrates activity in desmoid-type fibromatosis patients. Based on results of phase 3 trial, pazopanib had obtained approval for treatment of pretreated non-adipocytic soft tissue sarcoma. Regorafenib is currently assessed in several clinical settings and provides significant improvement of progression-free survival in pre-treated non-adipocytic soft tissue sarcoma and in advanced pretreated osteosarcoma. Multikinase inhibitors are a breakthrough in sarcoma management. Many trials are ongoing. Nevertheless, predictive factors are still missing.
    Keywords:  Choi criteria; clinical trial; multikinase inhibitor; non-adipocytic soft tissue sarcoma; sarcoma
    DOI:  https://doi.org/10.3389/fonc.2020.594445
  5. J Surg Oncol. 2020 Dec 17.
    Factors associated with 30-day soft tissue complications following upper extremity sarcoma surgery.
    Yannick A J Hoftiezer, Jonathan Lans, Brian B Freniere, Kyle R Eberlin, Neal C Chen, Santiago A Lozano-Calderón.
       BACKGROUND AND OBJECTIVES: The incidence of soft tissue complications following sarcoma surgery in the upper extremity is reportedly high. Therefore, this study assessed the National Surgical Quality Improvement Program (NSQIP) database to identify independent risk factors, while also reporting the incidence of soft tissue complications in the first 30 days after surgery.
    METHODS: A total of 620 patients that underwent surgical treatment for upper extremity sarcoma were included from the NSQIP database. Soft tissue complications were defined as surgical site infection, wound dehiscence, or soft-tissue related reoperations. Clinically relevant patient and treatment characteristics were selected and analyzed.
    RESULTS: The 30-day soft tissue complication rate was 4.7%. In the multivariable analysis, higher body mass index (p = .047) and longer operative times (p = .002) were independently associated with soft tissue complications.
    CONCLUSIONS: Higher body mass index and longer operative times are risk factors for soft tissue complications following upper extremity sarcoma surgery. The soft-tissue complication rate following resection of upper extremity tumors is low in this national cohort, possibly due to the relatively small tumor size and low prevalence of radiotherapy.
    Keywords:  orthopedic oncology; predictors; sarcoma; soft tissue complications; upper extremity
    DOI:  https://doi.org/10.1002/jso.26311
  6. Lab Chip. 2020 Dec 14.
    Tumor-on-a-chip platforms to study cancer-immune system crosstalk in the era of immunotherapy.
    Stefania Parlato, Giulia Grisanti, Giorgia Sinibaldi, Giovanna Peruzzi, Carlo Massimo Casciola, Lucia Gabriele.
      Immunotherapy is a powerful therapeutic approach able to re-educate the immune system to fight cancer. A key player in this process is the tumor microenvironment (TME), which is a dynamic entity characterized by a complex array of tumor and stromal cells as well as immune cell populations trafficking to the tumor site through the endothelial barrier. Recapitulating these multifaceted dynamics is critical for studying the intimate interactions between cancer and the immune system and to assess the efficacy of emerging immunotherapies, such as immune checkpoint inhibitors (ICIs) and adoptive cell-based products. Microfluidic devices offer a unique technological approach to build tumor-on-a-chip reproducing the multiple layers of complexity of cancer-immune system crosstalk. Here, we seek to review the most important biological and engineering developments of microfluidic platforms for studying cancer-immune system interactions, in both solid and hematological tumors, highlighting the role of the vascular component in immune trafficking. Emphasis is given to image processing and related algorithms for real-time monitoring and quantitative evaluation of the cellular response to microenvironmental dynamic changes. The described approaches represent a valuable tool for preclinical evaluation of immunotherapeutic strategies.
    DOI:  https://doi.org/10.1039/d0lc00799d
  7. Jpn J Clin Oncol. 2020 Dec 14. pii: hyaa231. [Epub ahead of print]
    Adjuvant and neoadjuvant chemotherapy for soft tissue sarcomas: JCOG Bone and Soft Tissue Tumor Study Group.
    Kazuhiro Tanaka, Toshifumi Ozaki.
      The standard therapy for all localized soft tissue sarcomas is surgical resection of the tumor. For patients with soft tissue sarcomas who are at high risk for recurrence and/or metastasis, perioperative chemotherapy is a potential treatment option. Adriamycin plus ifosfamide is currently the most promising chemotherapy regimen for localized soft tissue sarcomas. Randomized controlled trials and meta-analyses of adjuvant postoperative chemotherapy for soft tissue sarcomas have suggested that adjuvant chemotherapy may provide an advantage, however small, compared with surgery alone. On the other hand, recent randomized trials have demonstrated the efficacy of neoadjuvant preoperative chemotherapy using full-dose anthracycline plus ifosfamide for high-risk soft tissue sarcomas and showed survival benefits in patients with large, deep-seated and high-grade soft tissue sarcomas of the trunk and extremities. In this review, adjuvant and neoadjuvant chemotherapies for soft tissue sarcomas and future perspectives are discussed.
    Keywords:  adjuvant chemotherapy; localized; neoadjuvant chemotherapy; soft tissue sarcoma
    DOI:  https://doi.org/10.1093/jjco/hyaa231
  8. Methods Mol Biol. 2021 ;2226 3-14
    Germline Variation and Somatic Alterations in Ewing Sarcoma.
    Mitchell J Machiela, Thomas G P Grünewald.
      Ewing sarcoma (EwS) is a rare bone or soft tissue tumor that occurs early in life and as such genetic variation is a major contributor to EwS risk. To date, genetic investigations have identified key somatic mutations and germline variants of importance for EwS risk. While substantial progress is being made in uncovering the genetic etiology of EwS, considerable gaps in knowledge remain. Herein, we provide a summary of methodological approaches for future genomic investigations of EwS. We anticipate this recommended analytical framework for germline and somatic investigations, along with genomic data from growing EwS case series, will aid in accelerating new genomic discoveries in EwS and expand knowledge of the genetic architecture of EwS.
    Keywords:  EWSR1-FLI1; Ewing sarcoma; Genetics; Germline variants; SNPs; Somatic mutations; Translocation
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_1
  9. Methods Mol Biol. 2021 ;2226 285-302
    Epigenetic Analysis in Ewing Sarcoma.
    Jeremy M Simon, Nicholas C Gomez.
      Ewing sarcoma is a highly malignant tumor characterized by a chromosomal translocation that modifies the activity of an ETS family transcription factor. The most prevalent translocation product, EWSR1-FLI1, exploits a permissive and unique chromatin environment of stem cells, and transforms them into an oncogenic state through alterations to gene expression and gene regulatory programs. Though the transformation ability of, and subsequent reliance on EWSR1-FLI1 had been previously described, the advent of genome-wide sequencing technologies allowed for the specific identification of genomic loci and genes targeted by EWSR1-FLI1. Furthermore, the characterization of the chromatin environment in these, and other, cell types could not have been accomplished without the computational and statistical methods that enable large-scale data analysis. Here, we outline in detail the tools and steps needed to analyze genome-wide transcription factor binding and histone modification data (chromatin immunoprecipitation, ChIP-seq), as well as chromatin accessibility data (assay for transposase-accessible chromatin, ATAC-seq) from Ewing sarcoma cells. Our protocol includes a compilation of data quality control metrics, trimming of adapter sequences, reference genome alignment, identification of enriched sites ("peaks") and motifs, as well as annotation and visualization, using real-world data. These steps should provide a platform on which molecular biologists can build their own analytical pipelines to aid in data processing, analysis, and interpretation.
    Keywords:  ATAC-Seq; Bioinformatics; ChIP-seq; EWSR1-FLI1; Epigenetics; Ewing sarcoma; H3K27ac; Next-generation sequencing
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_22
  10. Cancers (Basel). 2020 Dec 09. pii: E3689. [Epub ahead of print]12(12):
    Harmine and Piperlongumine Revert TRIB2-Mediated Drug Resistance.
    Susana Machado, Andreia Silva, Ana Luísa De Sousa-Coelho, Isabel Duarte, Inês Grenho, Bruno Santos, Victor Mayoral-Varo, Diego Megias, Fátima Sánchez-Cabo, Ana Dopazo, Bibiana I Ferreira, Wolfgang Link.
      Therapy resistance is responsible for most relapses in patients with cancer and is the major challenge to improving the clinical outcome. The pseudokinase Tribbles homologue 2 (TRIB2) has been characterized as an important driver of resistance to several anti-cancer drugs, including the dual ATP-competitive PI3K and mTOR inhibitor dactolisib (BEZ235). TRIB2 promotes AKT activity, leading to the inactivation of FOXO transcription factors, which are known to mediate the cell response to antitumor drugs. To characterize the downstream events of TRIB2 activity, we analyzed the gene expression profiles of isogenic cell lines with different TRIB2 statuses by RNA sequencing. Using a connectivity map-based computational approach, we identified drug-induced gene-expression profiles that invert the TRIB2-associated expression profile. In particular, the natural alkaloids harmine and piperlongumine not only produced inverse gene expression profiles but also synergistically increased BEZ235-induced cell toxicity. Importantly, both agents promote FOXO nuclear translocation without interfering with the nuclear export machinery and induce the transcription of FOXO target genes. Our results highlight the great potential of this approach for drug repurposing and suggest that harmine and piperlongumine or similar compounds might be useful in the clinic to overcome TRIB2-mediated therapy resistance in cancer patients.
    Keywords:  BEZ235; FOXO; TRIB2; cancer; drug resistance; harmine; piperlongumine
    DOI:  https://doi.org/10.3390/cancers12123689
  11. Orthop Rev (Pavia). 2020 Nov 24. 12(3): 8818
    A single institutional experience treating adipocytic tumors: incidence, disease-related outcomes, and the clinical significance of MDM2 analysis.
    Saule Tamkus, Charles A Gusho, Matthew W Colman, Ira Miller, Steven Gitelis, Alan T Blank.
      Adipocytic tumors exist either as a benign or malignant form. The benign variant, lipoma, is composed of normal fat tissue. Lipomas typically develop from superficial fat cells beneath the skin or mucous membranes. Liposarcoma, the malignant counterpart, often develops in deeper tissues and is the most commonly diagnosed Soft Tissue Sarcoma (STS), comprising at least 20% of adult STS. However, malignant tumors of fatty origin exist as a spectrum of diagnoses, each carrying a unique risk of recurrence, metastasis, and longterm survival. The World Health Organization classifies liposarcomas into five categories: i) Atypical Lipomatous Tumors/Well Differentiated (ALT/WD); Ii) Dedifferentiated (ALT/DD); Iii) Myxoid; Iv) Round cell; and v) Pleomorphic. Lipomatous tumors often exhibit different immunohistochemical patterns. Benign lipomas are distinguished by the absence of Murine Double-Minute 2 (MDM2) amplification. Similarly, ALT/WD, classically defined as a low-grade and locally aggressive tumor, demonstrates consistent patterns of MDM2 amplification. Some studies suggest 10% of ALT/WD progress to the highgrade DD form, with others report a dedifferentiation rate of as high as 20% for primary ALT/WD based on location. The ALT/DD subtype is aggressive and has a high capacity to metastasize. While the mechanism of pathogenesis of ALT/DD metastasis is unknown, previous studies suggest that increased MDM2 amplification may play a role. This study sought to evaluate a single institutional experience treating the entire spectrum of lipomatous tumors and describe utilization patterns of MDM2 testing. The group hypothesized: i) Atypical Lipomatous Tumors (ALT), which include ALT/DD and ALT/WD, would exhibit a higher rate of local recurrence than lipomas with no significantly increased incidence of metastases; and ii) at least 50% of our MDM2 testing of ALT would prove positive for the MDM2 overamplification. This study retrospectively reviewed 105 cases (66 lipomas, 27 ALTs, 12 liposarcomas) of patients who underwent lipomatous tumor excision at our institution from 2013 to 2017. Twenty-five tumors (6 lipomas, 18 ALT, 1 liposarcoma) were tested for MDM2 amplification. Three of the tested tumors recurred (2 ALT, 1 liposarcoma), and each exhibited MDM2 overamplification. Five tumors (5 liposarcoma) developed late metastases. These data suggest that although ALT is associated with a higher rate of local recurrence, metastases are quite rare. Additionally, the data demonstrate a high rate of positive MDM2 testing (76%) based on clinical and imaging characteristics of the tumors.
    Keywords:  Liposarcoma; MDM2; atypical lipomatous tumor; lipoma
    DOI:  https://doi.org/10.4081/or.2020.8818
  12. Front Immunol. 2020 ;11 584626
    Regulation of PD-L1 Expression by NF-κB in Cancer.
    Fabrizio Antonangeli, Ambra Natalini, Marina Chiara Garassino, Antonio Sica, Angela Santoni, Francesca Di Rosa.
      Immune checkpoints are inhibitory receptor/ligand pairs regulating immunity that are exploited as key targets of anti-cancer therapy. Although the PD-1/PD-L1 pair is one of the most studied immune checkpoints, several aspects of its biology remain to be clarified. It has been established that PD-1 is an inhibitory receptor up-regulated by activated T, B, and NK lymphocytes and that its ligand PD-L1 mediates a negative feedback of lymphocyte activation, contributing to the restoration of the steady state condition after acute immune responses. This loop might become detrimental in the presence of either a chronic infection or a growing tumor. PD-L1 expression in tumors is currently used as a biomarker to orient therapeutic decisions; nevertheless, our knowledge about the regulation of PD-L1 expression is limited. The present review discusses how NF-κB, a master transcription factor of inflammation and immunity, is emerging as a key positive regulator of PD-L1 expression in cancer. NF-κB directly induces PD-L1 gene transcription by binding to its promoter, and it can also regulate PD-L1 post-transcriptionally through indirect pathways. These processes, which under conditions of cellular stress and acute inflammation drive tissue homeostasis and promote tissue healing, are largely dysregulated in tumors. Up-regulation of PD-L1 in cancer cells is controlled via NF-κB downstream of several signals, including oncogene- and stress-induced pathways, inflammatory cytokines, and chemotherapeutic drugs. Notably, a shared signaling pathway in epithelial cancers induces both PD-L1 expression and epithelial-mesenchymal transition, suggesting that PD-L1 is part of the tissue remodeling program. Furthermore, PD-L1 expression by tumor infiltrating myeloid cells can contribute to the immune suppressive features of the tumor environment. A better understanding of the interplay between NF-κB signaling and PD-L1 expression is highly relevant to cancer biology and therapy.
    Keywords:  T cells; epithelial-mesenchymal transition; immune checkpoint inhibitors; inflammation; non-small-cell-lung cancer; tissue homeostasis; tumor associated macrophages; tumor immunity
    DOI:  https://doi.org/10.3389/fimmu.2020.584626
  13. Methods Mol Biol. 2021 ;2226 303-333
    Systems Biology Analysis for Ewing Sarcoma.
    Marianyela Petrizzelli, Jane Merlevede, Andrei Zinovyev.
      Ewing sarcoma (EwS) is a highly aggressive pediatric bone cancer that is defined by a somatic fusion between the EWSR1 gene and an ETS family member, most frequently the FLI1 gene, leading to expression of a chimeric transcription factor EWSR1-FLI1. Otherwise, EwS is one of the most genetically stable cancers. The situation when the major cancer driver is well known looks like a unique opportunity for applying the systems biology approach in order to understand the EwS mechanisms as well as to uncover some general mechanistic principles of carcinogenesis. A number of studies have been performed revealing the direct and indirect effects of EWSR1-FLI1 on multiple aspects of cellular life. Nevertheless, the emerging picture of the oncogene action appears to be highly complex and systemic, with multiple reciprocal influences between the immediate consequences of the driver mutation and intracellular and intercellular molecular mechanisms, including regulation of transcription, epigenome, and tumoral microenvironment. In this chapter, we present an overview of existing molecular profiling resources available for EwS tumors and cell lines and provide an online comprehensive catalogue of publicly available omics and other datasets. We further highlight the systems biology studies of EwS, involving mathematical modeling of networks and integration of molecular data. We conclude that despite the seeming simplicity, a lot has yet to be understood on the systems-wide mechanisms connecting the driver mutation and the major cellular phenotypes of this pediatric cancer. Overall, this chapter can serve as a guide for a systems biology researcher to start working on EwS.
    Keywords:  Cancer systems biology; Data integration; EWSR1-FLI1; Ewing sarcoma; Mathematical modeling; Network; Omics data
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_23
  14. J Immunother Cancer. 2020 Dec;pii: e001408. [Epub ahead of print]8(2):
    Phagocytic function of tumor-associated macrophages as a key determinant of tumor progression control: a review.
    Marc Lecoultre, Valérie Dutoit, Paul R Walker.
      Tumor-associated macrophage (TAM) phagocytic activity is emerging as a new mechanism to harness for cancer treatment. Currently, many approaches are investigated at the preclinical level and some modalities have now reached clinical trials, including the targeting of the phagocytosis inhibitor CD47. The rationale for increasing TAM phagocytic activity is to improve innate anticancer immunity, and to promote T-cell mediated adaptive immune responses. In this context, a clear understanding of the impact of TAM phagocytosis on both innate and adaptive immunity is critical. Indeed, uncertainties persist regarding the capacity of TAM to present tumor antigens to CD8 T cells by cross-presentation. This process is critical for an optimal cytotoxic T-cell immune response and can be mediated by dendritic cells but also potentially by macrophages. In addition, the engulfment of cancer cells affects TAM functionality, as apoptotic cell uptake (a process termed efferocytosis) promotes macrophage anti-inflammatory functions. Because of the abundance of TAM in most solid tumors and the common use of apoptosis inducers such as radiotherapy to treat patients with cancer, efferocytosis potentially affects the overall immune balance within the tumor microenvironment (TME). In this review, we will discuss how cancer cell phagocytosis by TAM impacts antitumor immunity. First, we will focus on the potential of the phagocytic activity of TAM per se to control tumor progression. Second, we will examine the potential of TAM to act as antigen presenting cells for tumor specific CD8 T cells, considering the different characteristics of this process in the tumor tissue and at the molecular level. Finally, we will see how phagocytosis and efferocytosis affect TAM functionality and how these mechanisms impact on antitumor immunity. A better understanding of these aspects will enable us to better predict and interpret the consequences of cancer therapies on the immune status of the TME. Future cancer treatment regimens can thereby be designed to not only impact directly on cancer cells, but also to favorably modulate TAM phagocytic activity to benefit from the potential of this central immune player to achieve more potent therapeutic efficacy.
    Keywords:  antigen presentation; immunity; innate; macrophages; phagocytosis; tumor microenvironment
    DOI:  https://doi.org/10.1136/jitc-2020-001408
  15. Nat Commun. 2020 12 17. 11(1): 6410
    Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy.
    Amy J Wisdom, Yvonne M Mowery, Cierra S Hong, Jonathon E Himes, Barzin Y Nabet, Xiaodi Qin, Dadong Zhang, Lan Chen, Hélène Fradin, Rutulkumar Patel, Alex M Bassil, Eric S Muise, Daniel A King, Eric S Xu, David J Carpenter, Collin L Kent, Kimberly S Smythe, Nerissa T Williams, Lixia Luo, Yan Ma, Ash A Alizadeh, Kouros Owzar, Maximilian Diehn, Todd Bradley, David G Kirsch.
      Immunotherapy fails to cure most cancer patients. Preclinical studies indicate that radiotherapy synergizes with immunotherapy, promoting radiation-induced antitumor immunity. Most preclinical immunotherapy studies utilize transplant tumor models, which overestimate patient responses. Here, we show that transplant sarcomas are cured by PD-1 blockade and radiotherapy, but identical treatment fails in autochthonous sarcomas, which demonstrate immunoediting, decreased neoantigen expression, and tumor-specific immune tolerance. We characterize tumor-infiltrating immune cells from transplant and primary tumors, revealing striking differences in their immune landscapes. Although radiotherapy remodels myeloid cells in both models, only transplant tumors are enriched for activated CD8+ T cells. The immune microenvironment of primary murine sarcomas resembles most human sarcomas, while transplant sarcomas resemble the most inflamed human sarcomas. These results identify distinct microenvironments in murine sarcomas that coevolve with the immune system and suggest that patients with a sarcoma immune phenotype similar to transplant tumors may benefit most from PD-1 blockade and radiotherapy.
    DOI:  https://doi.org/10.1038/s41467-020-19917-0
  16. Cancers (Basel). 2020 Dec 16. pii: E3788. [Epub ahead of print]12(12):
    Metabolic Regulation of Epigenetic Modifications and Cell Differentiation in Cancer.
    Pasquale Saggese, Assunta Sellitto, Cesar A Martinez, Giorgio Giurato, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Claudio Scafoglio.
      Metabolic reprogramming is a hallmark of cancer, with consistent rewiring of glucose, glutamine, and mitochondrial metabolism. While these metabolic alterations are adequate to meet the metabolic needs of cell growth and proliferation, the changes in critical metabolites have also consequences for the regulation of the cell differentiation state. Cancer evolution is characterized by progression towards a poorly differentiated, stem-like phenotype, and epigenetic modulation of the chromatin structure is an important prerequisite for the maintenance of an undifferentiated state by repression of lineage-specific genes. Epigenetic modifiers depend on intermediates of cellular metabolism both as substrates and as co-factors. Therefore, the metabolic reprogramming that occurs in cancer likely plays an important role in the process of the de-differentiation characteristic of the neoplastic process. Here, we review the epigenetic consequences of metabolic reprogramming in cancer, with particular focus on the role of mitochondrial intermediates and hypoxia in the regulation of cellular de-differentiation. We also discuss therapeutic implications.
    Keywords:  cancer epigenetics; cancer metabolism; cell differentiation in cancer; mitochondrial metabolism
    DOI:  https://doi.org/10.3390/cancers12123788
  17. Aging (Albany NY). 2020 Dec 09. 12
    Comprehensive analysis of immune infiltration and gene expression for predicting survival in patients with sarcomas.
    Hongmin Chen, Yijiang Song, Chuangzhong Deng, Yanyang Xu, Huaiyuan Xu, Xiaojun Zhu, Guohui Song, Qinglian Tang, Jinchang Lu, Jin Wang.
      Tumor microenvironments are strongly related to tumor development, and immune-infiltrating cells and immune-related molecules are potential prognostic markers. However, the shortcomings of traditional measurement methods limit the accurate evaluation of various components in tumor microenvironments. With the rapid advancement of Next-Generation RNA Sequencing technology, dedicated and in-depth analyses of immune filtration within the tumor microenvironment has been achieved. In this study, we combined the bioinformatics analysis methods ESTIMATE, CIBERSORT, and ssGSEA to characterize the immune infiltration of sarcomas and to identify specific immunomodulators of different pathological subtypes. We further extracted a functional enrichment of significant immune-related genes related to improved prognosis, including NR1H3, VAMP5, GIMAP2, GBP2, HLA-E and CRIP1. Overall, the immune microenvironment is an important prognostic determinant of sarcomas and may be a potential resource for developing effective immunotherapy.
    Keywords:  immune checkpoint; sarcoma; tumor-infiltrating immune cells
    DOI:  https://doi.org/10.18632/aging.202229
  18. J Surg Oncol. 2020 Dec 17.
    External validation and adaptation of a dynamic prediction model for patients with high-grade extremity soft tissue sarcoma.
    PERSARC Study Group
       BACKGROUND AND OBJECTIVES: A dynamic prediction model for patients with soft tissue sarcoma of the extremities was previously developed to predict updated overall survival probabilities throughout patient follow-up. This study updates and externally validates the dynamic model.
    METHODS: Data from 3826 patients with high-grade extremity soft tissue sarcoma, treated surgically with curative intent were used to update the dynamic PERsonalised SARcoma Care (PERSARC) model. Patients were added to the model development cohort and grade was included in the model. External validation was performed with data from 1111 patients treated at a single tertiary center.
    RESULTS: Calibration plots show good model calibration. Dynamic C-indices suggest that the model can discriminate between high- and low-risk patients. The dynamic C-indices at 0, 1, 2, 3, 4, and 5 years after surgery were equal to 0.697, 0.790, 0.822, 0.818, 0.812, and 0.827, respectively.
    CONCLUSION: Results from the external validation show that the dynamic PERSARC model is reliable in predicting the probability of surviving an additional 5 years from a specific prediction time point during follow-up. The model combines patient-, treatment-specific and time-dependent variables such as local recurrence and distant metastasis to provide accurate survival predictions throughout follow-up and is available through the PERSARC app.
    Keywords:  dynamic prediction; external validation; landmark analysis; soft tissue sarcoma; survival
    DOI:  https://doi.org/10.1002/jso.26337
  19. Cancer Lett. 2020 Dec 13. pii: S0304-3835(20)30665-0. [Epub ahead of print]
    Trabectedin overcomes doxorubicin-resistance, counteracts tumor-immunosuppressive reprogramming of monocytes and decreases xenograft growth in Hodgkin lymphoma.
    Naike Casagrande, Cinzia Borghese, Andrea Favero, Cristina Vicenzetto, Donatella Aldinucci.
      Classical Hodgkin lymphoma (cHL) tumor cells are surrounded by a protective tumor microenvironment (TME). Trabectedin, an anticancer drug targeting both tumor cells and TME, demonstrated a potent antitumor activity against Hodgkin Reed Sternberg (HRS) cells. It was cytotoxic against cHL cell lines, including the doxorubicin-resistant clones, with subnanomolar IC50 values, and inhibited clonogenic growth and heterospheroid cell viability. It induced necroptosis, caused DNA damage, G2/M cell cycle arrest, and increased reactive oxygen species production. It reduced HRS cell secretion of CCL5, M-CSF, IL-6, IL-13 and TARC, and inhibited migration. Conditioned medium from trabectedin-treated HRS cells was less chemoattractive toward monocytes, mesenchymal stromal cells and lymphocytes, and less effective in educating monocytes to become immunosuppressive macrophages. These monocytes expressed lower levels of indoleamine 2,3-dioxygenase-1, CD206 and PD-L1, secreted lower amounts of IL-10, TARC, and TGF-β, and were less able to inhibit the growth of activated lymphocytes. In vivo, trabectedin inhibited by >75% the growth of cHL murine xenografts with minimal weight loss; tumors of trabectedin-treated mice had fewer TAMs and less angiogenesis. Altogether, this study offers a preclinical rationale for trabectedin use as a new therapeutic option in relapsed/refractory cHL patients.
    Keywords:  Doxorubicin; Hodgkin lymphoma; Trabectedin; Tumor associated macrophages; Tumor microenvironment
    DOI:  https://doi.org/10.1016/j.canlet.2020.12.015
  20. Methods Mol Biol. 2021 ;2226 105-116
    Molecular Approaches to Diagnosis in Ewing Sarcoma: Targeted RNA Sequencing.
    Carmen Salguero-Aranda, Juan Diaz-Martin.
      Molecular testing of pathognomonic gene fusions is mandatory for small round cell tumor diagnosis, including Ewing sarcoma which is indeed defined by a variety of chimeric genes. Reference laboratories are increasingly implementing NGS-based techniques to overcome several limitations of conventional singleplex determinations. We have been early adopters of a targeted-RNA sequencing method based on Anchored multiplex PCR, which allows assessing several fusion transcripts simultaneously with previous knowledge of only one partner gene. Here we describe in detail our protocol and tips for nucleic acid extraction, library preparation, sequencing, and reporting of gene fusions.
    Keywords:  Anchored Multiplex PCR (AMP); Ewing sarcoma; FFPE sample; Gene fusion; Nucleic acid extraction; Precision diagnostics; Targeted RNA-seq
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_8
  21. Cancer Discov. 2020 Dec 14. pii: CD-20-0735. [Epub ahead of print]
    SWI/SNF complex mutations promote thyroid tumor progression and insensitivity to redifferentiation therapies.
    Mahesh Saqcena, Luis Javier Leandro-Garcia, Jesper L V Maag, Vatche Tchekmedyian, Gnana P Krishnamoorthy, Prasanna P Tamarapu, Vera Tiedje, Vincent Reuter, Jeffrey A Knauf, Elisa de Stanchina, Bin Xu, Xiao-Hui Liao, Samuel Refetoff, Ronald Ghossein, Ping Chi, Alan L Ho, Richard P Koche, James A Fagin.
      Mutations of subunits of the SWI/SNF chromatin remodeling complexes occur commonly in cancers of different lineages, including advanced thyroid cancers. Here we show that thyroid-specific loss of Arid1a, Arid2 or Smarcb1 in mouse BrafV600E-mutant tumors promotes disease progression and decreased survival, associated with lesion-specific effects on chromatin accessibility and differentiation. As compared to normal thyrocytes, BrafV600E-mutant mouse PTCs have decreased lineage transcription factor expression and accessibility to their target DNA binding sites, leading to impairment of thyroid differentiated gene expression and radioiodine incorporation, which is rescued by MAPK inhibition. Loss of individual Swi/Snf subunits in Braf tumors leads to a repressive chromatin state that cannot be reversed by MAPK pathway blockade, rendering them insensitive to its redifferentiation effects. Our results show that SWI/SNF complexes are central to the maintenance of differentiated function in thyroid cancers, and their loss confers radioiodine refractoriness and resistance to MAPK inhibitor-based redifferentiation therapies.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0735
  22. Methods Mol Biol. 2021 ;2226 27-38
    Tissue Preservation and FFPE Samples: Optimized Nucleic Acids Isolation in Ewing Sarcoma.
    Laura Romero-Pérez, Thomas G P Grünewald.
      Different methods have been described for the preservation of biopsy or resection samples. In the routine pathology, the cheapest and most commonly used is fixation of samples in formalin and embedding in paraffin (FFPE samples). This method preserves tissue samples for a very long time and is suitable for several specialized techniques such as fluorescence in situ hybridization (FISH) and immunohistochemistry, the latter being the most frequent and often the only additional method used for establishment of final diagnosis. However, in light of the growing need of next-generation sequencing and microarray technologies that are often very helpful to establish and/or confirm diagnoses in the field of pediatric sarcoma (including Ewing sarcoma), preservation of high-quality and quantity of nucleic acids (DNA/RNA) is desirable. Herein, we describe how to ideally preserve samples, as well as how to proceed to isolate nucleic acids for successful subsequent molecular assays with a special focus on Ewing sarcoma samples.
    Keywords:  DNA; Ewing sarcoma; FFPE samples; Molecular assays; Preservation; RNA
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_3
  23. Mini Rev Med Chem. 2020 Dec 13.
    Emerging Need of Today: Significant Utilization of Various Databases and Softwares in Drug Design and Development.
    Neema Bisht, Archana N Sah, Sandeep Bisht, Himanshu Joshi.
      In drug discovery, in silico methods have become a very important part of the process. These approaches impact the entire development process by discovering and identifying new target proteins as well as designing potential ligands with a significant reduction of time and cost. Furthermore, in silico approaches are also preferred because of reduction in experimental use of animals as; in vivo testing, for safer drug design and repositioning of known drugs. Novel software based discovery and development such as direct/indirect drug design, molecular modelling, docking, screening, drugreceptor interaction, and molecular simulation studies are very important tools for the predictions of ligand-target interaction pattern, pharmacodynamics as well as pharmacokinetic properties of ligands. On the other part, the computational approaches can be numerous, requiring interdisciplinary studies and the application of advance computer technology to design effective and commercially feasible drugs. This review mainly focuses on the various databases and softwares used in drug design and development for speed up the process.
    Keywords:  Drug development process; In silico methods; computational approaches; interaction studies; potential ligands; softwares and databases.
    DOI:  https://doi.org/10.2174/1389557520666201214101329
  24. Front Oncol. 2020 ;10 606436
    Emerging Autophagy Functions Shape the Tumor Microenvironment and Play a Role in Cancer Progression - Implications for Cancer Therapy.
    Silvina Odete Bustos, Fernanda Antunes, Maria Cristina Rangel, Roger Chammas.
      The tumor microenvironment (TME) is a complex environment where cancer cells reside and interact with different types of cells, secreted factors, and the extracellular matrix. Additionally, TME is shaped by several processes, such as autophagy. Autophagy has emerged as a conserved intracellular degradation pathway for clearance of damaged organelles or aberrant proteins. With its central role, autophagy maintains the cellular homeostasis and orchestrates stress responses, playing opposite roles in tumorigenesis. During tumor development, autophagy also mediates autophagy-independent functions associated with several hallmarks of cancer, and therefore exerting several effects on tumor suppression and/or tumor promotion mechanisms. Beyond the concept of degradation, new different forms of autophagy have been described as modulators of cancer progression, such as secretory autophagy enabling intercellular communication in the TME by cargo release. In this context, the synthesis of senescence-associated secretory proteins by autophagy lead to a senescent phenotype. Besides disturbing tumor treatment responses, autophagy also participates in innate and adaptive immune signaling. Furthermore, recent studies have indicated intricate crosstalk between autophagy and the epithelial-mesenchymal transition (EMT), by which cancer cells obtain an invasive phenotype and metastatic potential. Thus, autophagy in the cancer context is far broader and complex than just a cell energy sensing mechanism. In this scenario, we will discuss the key roles of autophagy in the TME and surrounding cells, contributing to cancer development and progression/EMT. Finally, the potential intervention in autophagy processes as a strategy for cancer therapy will be addressed.
    Keywords:  cancer; epithelial-mesenchymal transition; immune system; new autophagy functions; secretion; tumor microenvironment
    DOI:  https://doi.org/10.3389/fonc.2020.606436
  25. Methods Mol Biol. 2021 ;2226 85-103
    Molecular Approaches to Diagnosis in Ewing Sarcoma: RT-PCR.
    Carlos Rodríguez-Martín, Javier Alonso.
      Ewing sarcoma is a rare and aggressive tumor that affects children and young adults. Ewing sarcomas are characterized by specific chromosomal translocations that give rise to fusion transcripts that codify for aberrant transcription factors. More than 95% of Ewing sarcoma harbor translocations that produce the fusion of the EWSR1 gene with the transcription factors FLI1 or ERG. This feature can be used to diagnose this entity unambiguously.In this chapter we describe a RT-PCR method that allows for the detection of the most frequent alterations with elevated specificity and sensitivity which is able to distinguish among the different types of fusions. The method is fast and economical, and can be carried out with the conventional equipment available in any molecular biology laboratory.
    Keywords:  EWSR1-ERG; EWSR1-FLI1; Ewing sarcoma; Molecular diagnosis; RT-PCR
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_7
  26. Radiother Oncol. 2020 Dec 10. pii: S0167-8140(20)31227-5. [Epub ahead of print]
    p38β (MAPK11) mediates gemcitabine-associated radiosensitivity in sarcoma experimental models.
    R Pascual-Serra, D M Fernández-Aroca, S Sabater, O Roche, I Andrés, M Ortega-Muelas, E Arconada-Luque, Natalia Garcia-Flores, G Bossi, B Belandia, M J Ruiz-Hidalgo, R Sánchez-Prieto.
       BACKGROUND AND PURPOSE: Gemcitabine is an antitumour agent currently used in the treatment of several types of cancer with known properties as a radiosensitizer. p38MAPK signalling pathway has been shown to be a major determinant in the cellular response to gemcitabine in different experimental models. However, the molecular mechanism implicated in gemcitabine-associated radiosensitivity remains unknown.
    MATERIALS AND METHODS: The human sarcoma cell lines A673 and HT1080, and a mouse cell line derived from a 3-methylcholanthrene induced sarcoma were used as experimental models. Modulation of p38MAPKs was performed by pharmacological approaches (SB203580) and genetic interference using lentiviral vectors coding for specific shRNAs. Viability was assessed by MTT. Gene expression was evaluated by western blot and RT-qPCR. Induction of apoptosis was monitored by caspase 3/7 activity. Response to ionizing radiation was evaluated by clonogenic assays.
    RESULTS: Our data demonstrate that chemical inhibition of p38MAPK signalling pathway blocks gemcitabine radiosensitizing potential. Genetic interference of MAPK14 (p38 α), the most abundantly expressed and best characterized p38MAPK, despite promoting resistance to gemcitabine, it does not affect its radiosensitizing potential. Interestingly, specific knockdown of MAPK11 (p38β) induces a total loss of the radiosensitivity associated to gemcitabine, as well as a marked increase in the resistance to the drug.
    CONCLUSION: The present work identifies p38β as a major determinant of the radiosensitizing potential of gemcitabine without implication of p38 α, suggesting that p38β status should be analysed in those cases in which gemcitabine is combined with ionizing radiation.
    Keywords:  Gemcitabine; MAPK11 (p38β); MAPK14 (p38 α); p38MAPK; radiosensitivity; sarcoma
    DOI:  https://doi.org/10.1016/j.radonc.2020.12.008
  27. Front Genet. 2020 ;11 557188
    Bioinformatics Identification of the Expression and Clinical Significance of E2F Family in Endometrial Cancer.
    YunZheng Zhang, Zihao Wang, Jian Ma, JiaNing Huo, YiBing Li, YuShan Wang, Hao Chen, LuHe Shan, Xiaoxin Ma.
       Background: Besides being one of the most prevalent cancers among women, incidence and mortality rates of endometrial cancer (EC) are still increasing. The E2F family of transcriptional factors is involved in cell differentiation, apoptosis, and inhibition of DNA damage response, thus affecting growth and invasion of tumor cells.
    Methods: We used multiple bioinformatics tools to explore the role of E2F family in endometrial cancer.
    Results: The expression of E2F1/2/3/7/8 was significantly upregulated in endometrial cancer tissues, converse to E2F4, which was downregulated. Methylation downregulates all E2Fs except for E2F2. Accordingly, E2F1/2/3/5/7/8 are potential diagnostic biomarkers for EC. In particular, EC patients displaying upregulated E2F1, and E2F3 expression had a worse overall survival and relapse-free survival. E2F8, E2F7, and E2F1 were the top three, most-frequently altered genes in endometrial cancer. E2F family activates apoptosis pathways, regulates cell cycle, and impairs DNA damage response pathways. Drug-sensitivity analysis demonstrated that the level of E2F2/3/8 negatively correlated with drug resistance. Meanwhile, immune infiltrations analysis revealed that E2F family is associated with recruitment of several immune cells. Enrichment analysis on its part revealed that the E2F family is mainly associated with cell cycle, sequence-specific DNA binding, nuclear transcription factor complex, PI3K-Akt signaling, and p53 signaling pathway. We also identified multiple E2Fs-associated miRNA and kinase targets in endometrial cancer.
    Conclusion: Our study revealed the unique expression signature and clinical significance of E2F family in EC, demonstrating the potential clinical utility of these transcription factors (TF) in endometrial cancer.
    Keywords:  E2Fs; bioinformatics analysis; biomarker; endometrial cancer; immune infiltration
    DOI:  https://doi.org/10.3389/fgene.2020.557188
  28. Int J Mol Sci. 2020 Dec 14. pii: E9501. [Epub ahead of print]21(24):
    No Easy Way Out for EZH2: Its Pleiotropic, Noncanonical Effects on Gene Regulation and Cellular Function.
    Jun Wang, Gang Greg Wang.
      Enhancer of zeste homolog 2 (EZH2) plays critical roles in a range of biological processes including organ development and homeostasis, epigenomic and transcriptomic regulation, gene repression and imprinting, and DNA damage repair. A widely known function of EZH2 is to serve as an enzymatic subunit of Polycomb repressive complex 2 (PRC2) and catalyze trimethylation of histone H3 lysine 27 (H3K27me3) for repressing target gene expression. However, an increasing body of evidence demonstrates that EZH2 has many "non-conventional" functions that go beyond H3K27 methylation as a Polycomb factor. First, EZH2 can methylate a number of nonhistone proteins, thereby regulating cellular processes in an H3K27me3-independent fashion. Furthermore, EZH2 relies on both methyltransferase-dependent and methyltransferase-independent mechanisms for modulating gene-expression programs and/or epigenomic patterns of cells. Importantly, independent of PRC2, EZH2 also forms physical interactions with a number of DNA-binding factors and transcriptional coactivators to context-dependently influence gene expression. The purpose of this review is to detail the complex, noncanonical roles of EZH2, which are generally less appreciated in gene and (epi)genome regulation. Because EZH2 deregulation is prevalent in human diseases such as cancer, there is increased dependency on its noncanonical function, which shall have important implications in developing more effective therapeutics.
    Keywords:  EZH2; Polycomb repressive complex; cancer; chromatin; coactivator; gene transcription; histone; methylation
    DOI:  https://doi.org/10.3390/ijms21249501
  29. Front Oncol. 2020 ;10 535665
    MicroRNA-381-A Key Transcriptional Regulator: Its Biological Function and Clinical Application Prospects in Cancer.
    Xue Zeng, Zhe Cao, Wenhao Luo, Lianfang Zheng, Taiping Zhang.
      MicroRNAs (miRNAs) are small non-coding RNA molecules that function by regulating messenger RNAs. Recent studies have shown that miRNAs play important roles in multiple processes of cancer development. MiR-381 is one of the most important miRNAs in cancer progression. MiR-381 is downregulated in some cancers and upregulated in other cancers, including glioma, epithelial sarcoma, and osteosarcoma. MiR-381 regulates epithelial-mesenchymal transition (EMT), chemotherapeutic resistance, radioresistance, and immune responses. Thus, miR-381 participates in tumor initiation, progression, and metastasis. Moreover, miR-381 functions in various oncogenic pathways, including the Wnt/β-catenin, AKT, and p53 pathways. Clinical studies have shown that miR-381 could be considered a biomarker or a novel prognostic factor. Here, we summarize the present studies on the role of miR-381 in cancer development, including its biogenesis and various affected signaling pathways, and its clinical application prospects. MiR-381 expression is associated with tumor stage and survival time, making miR-381 a novel prognostic factor.
    Keywords:  biomarker; cancer; chemotherapy; mechanisms of resistance; miR-381
    DOI:  https://doi.org/10.3389/fonc.2020.535665
  30. Methods Mol Biol. 2021 ;2226 223-242
    Ewing Sarcoma PDX Models.
    Didier Surdez, Lorena Landuzzi, Katia Scotlandi, Maria Cristina Manara.
      Ewing sarcoma (EWS) is a rare malignant pediatric tumor and patient derived xenografts (PDXs) could represent a possibility to increase the number of available models to study this disease. Compared to cell derived xenografts (CDX), PDXs are reported to better recapitulate tumor microenvironment, heterogeneity, genetic and epigenetic features and are considered reliable models for their better predictive value when comparing preclinical efficacy and treatment response in patients. In this chapter, we extensively describe a method for generating Ewing sarcoma PDX models, for their validation and molecular characterization.
    Keywords:  Ewing sarcoma; Immunodeficient mice; Patient-derived xenografts; Pediatric tumors; Preclinical models
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_18
  31. Methods Mol Biol. 2021 ;2226 265-284
    Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma.
    Gwenneg Kerdivel, Valentina Boeva.
      ChIP-seq is the method of choice for profiling protein-DNA interactions, and notably for characterizing the landscape of transcription factor binding and histone modifications. This technique has been widely used to study numerous aspects of tumor biology and led to the development of several promising cancer therapies. In Ewing sarcoma research, ChIP-seq provided important insights into the mechanism of action of the major oncogenic fusion protein EWSR1-FLI1 and related epigenetic and transcriptional changes. In this chapter, we provide a detailed pipeline to analyze ChIP-seq experiments from the preprocessing of raw data to tertiary analysis of detected binding sites. We also advise on best practice to prepare tumor samples prior to sequencing.
    Keywords:  Binding sites; ChIP-seq; Ewing sarcoma; Histone modifications; Motif analysis; Transcription factors
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_21
  32. Methods Mol Biol. 2021 ;2226 183-189
    Genetically Engineered Mouse Model in Ewing Sarcoma.
    Miwa Tanaka, Takuro Nakamura.
      Modeling Ewing sarcoma is challenging, since overexpression of EWS-FLI1 induces apoptosis and is not sufficient for tumor induction. It is therefore important to obtain the cell-of-origin of Ewing sarcoma that is tolerant of EWS-FLI1 expression. Here we describe the generation of the EWS-FLI1-expressing mouse model for Ewing sarcoma by selecting embryonic chondrogenic progenitor, eSZ cells that contain Ewing sarcoma precursors.
    Keywords:  EWS-FLI1; Embryonic superficial zone; Ewing sarcoma; Mouse model; Retrovirus-mediated gene transfer
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_14
  33. Genes Dev. 2020 Dec 17.
    A feed-forward regulatory loop in adipose tissue promotes signaling by the hepatokine FGF21.
    Myoung Sook Han, Rachel J Perry, João-Paulo Camporez, Philipp E Scherer, Gerald I Shulman, Guangping Gao, Roger J Davis.
      The cJun NH2-terminal kinase (JNK) signaling pathway is activated by metabolic stress and promotes the development of metabolic syndrome, including hyperglycemia, hyperlipidemia, and insulin resistance. This integrated physiological response involves cross-talk between different organs. Here we demonstrate that JNK signaling in adipocytes causes an increased circulating concentration of the hepatokine fibroblast growth factor 21 (FGF21) that regulates systemic metabolism. The mechanism of organ crosstalk is mediated by a feed-forward regulatory loop caused by JNK-regulated FGF21 autocrine signaling in adipocytes that promotes increased expression of the adipokine adiponectin and subsequent hepatic expression of the hormone FGF21. The mechanism of organ cross-talk places circulating adiponectin downstream of autocrine FGF21 expressed by adipocytes and upstream of endocrine FGF21 expressed by hepatocytes. This regulatory loop represents a novel signaling paradigm that connects autocrine and endocrine signaling modes of the same hormone in different tissues.
    Keywords:  FGF21; JNK; autocrine; endocrine; organ cross-talk
    DOI:  https://doi.org/10.1101/gad.344556.120
  34. Cell Prolif. 2020 Dec 17. e12913
    Essential functions of miR-125b in cancer.
    Boya Peng, Poh Ying Theng, Minh T N Le.
      MicroRNAs (miRNAs) are small and highly conserved non-coding RNAs that silence target mRNAs, and compelling evidence suggests that they play an essential role in the pathogenesis of human diseases, especially cancer. miR-125b, which is the mammalian orthologue of the first discovered miRNA lin-4 in Caenorhabditis elegans, is one of the most important miRNAs that regulate various physiological and pathological processes. The role of miR-125b in many types of cancer has been well established, and so here we review the current knowledge of how miR-125b is deregulated in different types of cancer; its oncogenic and/or tumour-suppressive roles in tumourigenesis and cancer progression; and its regulation with regard to treatment response, all of which are underlined in multiple studies. The emerging information that elucidates the essential functions of miR-125b might help support its potentiality as a diagnostic and prognostic biomarker as well as an effective therapeutic tool against cancer.
    Keywords:  biomarker; cancer; chemoresistance; miR-125b; microRNA
    DOI:  https://doi.org/10.1111/cpr.12913
  35. Life Sci. 2020 Dec 10. pii: S0024-3205(20)31648-9. [Epub ahead of print]266 118895
    Long non-coding RNAs as the regulators and targets of macrophage M2 polarization.
    Rong Dong, Bo Zhang, Biqin Tan, Nengming Lin.
      Macrophages are immune cells with high heterogeneity and plasticity. M2 polarization is one extreme of the well-established phenotypes of macrophage polarization, and involves in diverse biological processes. The polarization process is initiated at the command of numerous components. Long non-coding RNAs (lncRNAs) are RNAs longer than 200 nucleotides with limited protein-coding capacity. Recent studies have revealed a newly found subset of lncRNAs engaged in the M2 polarization and their potent and multifunctional roles in developing diseases. By interfering with specific signaling pathways and altering the active mode, acting as the sponges of microRNAs or decoys of transcription factors, lncRNAs prompted macrophages to an M2 phenotype. Further, lncRNAs can bind to the genome to regulate the chromatin dynamics or work as a platform for protein complexes tether. Exosomal lncRNAs can also orchestrate the polarization in a paracrine way. To make it easier to interpret the roles of lncRNAs in the M2 polarization, we review the reported lncRNAs according to the underlying mechanisms. Moreover, we discuss the possibilities of targeting macrophages' M2 polarization using the oligonucleotides drugs or clustered regularly interspaced palindromic repeats (CRISPR) technologies to provoke wisdom on the therapeutic strategies.
    Keywords:  Antisense oligonucleotides; CRISPR interference; Long non-coding RNAs; M2 polarization; Macrophages
    DOI:  https://doi.org/10.1016/j.lfs.2020.118895
  36. Respir Res. 2020 Dec 11. 21(1): 329
    Bone marrow mesenchymal stem cells derived miRNA-130b enhances epithelial sodium channel by targeting PTEN.
    Honglei Zhang, Yan Ding, Yapeng Hou, Yanhong Liu, Zhiyu Zhou, Hongguang Nie.
       AIMS: Acute lung injury (ALI) is a clinical syndrome with high morbidity and mortality, and severe pulmonary edema is one of the characteristics. Epithelial sodium channel (ENaC) located on the apical side of alveolar type 2 epithelial (AT2) cells is the primary rate limiting segment in alveolar fluid clearance. Many preclinical studies have revealed that mesenchymal stem cells (MSCs) based therapy has great therapeutic potential for ALI, while the role of ENaC in this process is rarely known.
    METHODS: We studied the effects of bone marrow-derived MSCs (BMSCs) on the protein/mRNA expression and activity of ENaC in primary mouse AT2 and human H441 cells by co-culture with them, respectively. Moreover, the changes of miRNA-130b in AT2 cells were detected by qRT-PCR, and we studied the involvement of phosphatase and tensin homolog deleted on chromosome ten (PTEN) and the downstream PI3K/AKT pathway in the miRNA-130b regulation of ENaC.
    RESULTS: Our results demonstrated that BMSCs could increase ENaC protein expression and function, as well as the expression level of miRNA-130b. The dual luciferase target gene assay verified that PTEN was one of the target genes of miR-130b, which showed adverse effects on the protein expression of α/γ-ENaC and PTEN in AT2 cells. Upregulating miR-130b and/or knocking down PTEN resulted in the increase of α/γ-ENaC protein level, and the protein expression of p-AKT/AKT was enhanced by miR-130b. Both α and γ-ENaC protein expressions were increased after AT2 cells were transfected with siPTEN, which could be reversed by the co-administration of PI3K/AKT inhibitor LY294002.
    CONCLUSION: In summary, miRNA-130b in BMSCs can enhance ENaC at least partially by targeting PTEN and activating PI3K/AKT pathway, which may provide a promising new direction for therapeutic strategy in ALI.
    Keywords:  Acute lung injury; Bone marrow mesenchymal stem cells; Epithelial sodium channel; miRNA-130b
    DOI:  https://doi.org/10.1186/s12931-020-01595-7
  37. Semin Cancer Biol. 2020 Dec 09. pii: S1044-579X(20)30266-2. [Epub ahead of print]
    Progress and Promises of Epigenetic Drugs and Epigenetic Diets in Cancer Prevention and Therapy: A Clinical Update.
    Priya Mondal, Jagadish Natesh, Dhanamjai Penta, Syed Musthapa Meeran.
      Epigenetic modifications are heritable yet reversible, essential for normal physiological functions and biological development. Aberrant epigenetic modifications, including DNA methylation, histone modification, and non-coding RNA (ncRNA)-mediated gene regulation play a crucial role in cancer progression. In cellular reprogramming, irregular epigenomic modulations alter cell signaling pathways and the expression of tumor suppressor genes and oncogenes, resulting in cancer growth and metastasis. Therefore, alteration of epigenetic-status in cancer cells can be used as a potential target for cancer therapy. Several synthetic epigenetic inhibitors (epi-drugs) and natural epigenetic modulatory bioactives (epi-diets) have been shown to have the potential to alter the aberrant epigenetic status and inhibit cancer progression. Further, the use of combinatorial approaches with epigenetic drugs and diets has brought promising outcomes in cancer prevention and therapy. In this article, we have summarized the epigenetic modulatory activities of epi-drugs, epi-diets, and their combination against various cancers. We have also compiled the preclinical and clinical status of these epigenetic modulators in different cancers.
    Keywords:  Cancer epigenetics; Clinical trials; Dietary bioactives; Epigenetic diets; Epigenetic drugs
    DOI:  https://doi.org/10.1016/j.semcancer.2020.12.006
  38. Biology (Basel). 2020 Dec 16. pii: E474. [Epub ahead of print]9(12):
    Lipid Metabolism and Resistance to Anticancer Treatment.
    Nicolas Germain, Mélanie Dhayer, Marie Boileau, Quentin Fovez, Jerome Kluza, Philippe Marchetti.
      Metabolic reprogramming is crucial to respond to cancer cell requirements during tumor development. In the last decade, metabolic alterations have been shown to modulate cancer cells' sensitivity to chemotherapeutic agents including conventional and targeted therapies. Recently, it became apparent that changes in lipid metabolism represent important mediators of resistance to anticancer agents. In this review, we highlight changes in lipid metabolism associated with therapy resistance, their significance and how dysregulated lipid metabolism could be exploited to overcome anticancer drug resistance.
    Keywords:  antimetabolic cooperativity; cancer drug resistance; lipid metabolism; synthetic lethality
    DOI:  https://doi.org/10.3390/biology9120474
  39. Mod Pathol. 2020 Dec 14.
    Recurrent FOS rearrangement in proliferative fasciitis/proliferative myositis.
    Naohiro Makise, Taisuke Mori, Toru Motoi, Junji Shibahara, Tetsuo Ushiku, Akihiko Yoshida.
      Proliferative fasciitis (PF) and proliferative myositis (PM) are rare benign soft tissue lesions, usually affecting the extremities of middle-aged or older adults. Presenting as poorly circumscribed masses, they histologically show bland spindle cell proliferation in a myxoid to fibrous background and a hallmark component of large epithelioid "ganglion-like" cells in various numbers, which may lead to their misdiagnosis as sarcoma. PF/PM has been long considered as reactive, akin to nodular fasciitis; however, its pathogenesis has remained unknown. In this study, we analyzed the FOS status in 6 PF/PMs (5 PFs and 1 PM). Five PF/PMs occurred in adults, all showing diffuse strong expression of c-FOS primarily in the epithelioid cells, whereas spindle cell components were largely negative. Using fluorescence in situ hybridization (FISH), all 5 c-FOS-immunopositive tumors showed evidence of FOS gene rearrangement in the epithelioid cells. RNA sequencing in 1 case detected a FOS-VIM fusion transcript, which was subsequently validated by reverse transcriptase-polymerase chain reaction, Sanger sequencing, and VIM FISH. The one pediatric PF case lacked c-FOS expression and FOS rearrangement. c-FOS immunohistochemistry was negative in 45 cases of selected mesenchymal tumor types with epithelioid components that may histologically mimic PF/PM, including pleomorphic sarcoma with epithelioid features and epithelioid sarcoma. Recurrent FOS rearrangement and c-FOS overexpression in PF/PM suggested these lesions to be neoplastic. FOS abnormality was largely restricted to the epithelioid cell population, clarifying the histological composition of at least 2 different cell types. c-FOS immunohistochemistry may serve as a useful adjunct to accurately distinguish PF/PM from mimics.
    DOI:  https://doi.org/10.1038/s41379-020-00725-2
  40. Diabetes. 2020 Dec 16. pii: db200856. [Epub ahead of print]
    Defective FXR-SHP Regulation in Obesity Aberrantly Increases miR-802 Expression, Promoting Insulin Resistance and Fatty Liver.
    Sunmi Seok, Hao Sun, Young-Chae Kim, Byron Kemper, Jongsook Kim Kemper.
      Aberrantly elevated expression in obesity of microRNAs (miRs), including miR-802, contributes to obesity-associated metabolic complications but the mechanisms underlying the elevated expression are unclear. Farnesoid-X-Receptor (FXR), a key regulator of hepatic energy metabolism, has great potential for treatment of obesity-related diseases. We examined whether a nuclear receptor cascade involving FXR and FXR-induced Small Heterodimer Partner (SHP) regulates expression of miR-802 to maintain glucose and lipid homeostasis. Hepatic miR-802 levels are increased in FXR-knockout (KO) or SHP-KO mice and are decreased by activation of FXR in a SHP-dependent manner. Mechanistically, transactivation of miR-802 by Aromatic Hydrocarbon Receptor (AHR) is inhibited by SHP. In obese mice, activation of FXR by obeticholic acid treatment reduced miR-802 levels and improved insulin resistance and hepatosteatosis, but these beneficial effects were largely abolished by overexpression of miR-802. In non-alcoholic fatty liver disease patients and obese mice, occupancy of SHP is reduced and that of AHR is modestly increased at the miR-802 promoter, consistent with elevated hepatic miR-802 expression. These results demonstrate that normal inhibition of miR-802 by FXR-SHP is defective in obesity, resulting in increased miR-802 levels, insulin resistance and fatty liver. This FXR-SHP-miR-802 pathway may present novel targets for treating type 2 diabetes and NAFLD.
    DOI:  https://doi.org/10.2337/db20-0856
  41. Front Oncol. 2020 ;10 608548
    A Novel Tool to Predict Early Death in Uterine Sarcoma Patients: A Surveillance, Epidemiology, and End Results-Based Study.
    Zixuan Song, Yizi Wang, Dandan Zhang, Yangzi Zhou.
       Background: Uterine sarcoma is a rare gynecologic tumor with a high degree of malignancy. There is a lack of effective prognostic tools to predict early death of uterine sarcoma.
    Methods: Data on patients with uterine sarcoma registered between 2004 and 2015 were extracted from the Surveillance, Epidemiology, and End Results (SEER) data. Important independent prognostic factors were identified by univariate and multivariate logistic regression analyses to construct a nomogram for total early deaths and cancer-specific early deaths.
    Results: A total of 5,274 patients with uterine sarcoma were included in this study. Of which, 397 patients experienced early death (≤3 months), and 356 of whom died from cancer-specific causes. A nomogram for total early deaths and cancer-specific early deaths was created using data on age, race, tumor size, the International Federation of Gynecology and Obstetrics (FIGO) staging, histological classification, histological staging, treatment (surgery, radiotherapy, chemotherapy), and brain metastases. On comparing the C-index, area under the curve, and decision curve analysis, the created nomogram showed better predictive power and clinical practicality than one made exclusively with FIGO staging. Calibration of the nomogram by internal validation showed good consistency between the predicted and actual early death.
    Conclusions: Nomograms that include clinical characteristics can provide a better prediction of the risk of early death for uterine sarcoma patients than nomograms only comprising the FIGO stage system. In doing so, this tool can help in identifying patients at high risk for early death because of uterine sarcoma.
    Keywords:  Epidemiology, and EndResults database; Surveillance; early death; nomograms; prognosis; uterine sarcoma
    DOI:  https://doi.org/10.3389/fonc.2020.608548
  42. Ann Transl Med. 2020 Nov;8(21): 1450
    Resection outcomes for primary and local recurrent retroperitoneal liposarcoma patients.
    Yang Yan, Shaoyou Xia, Da Teng, Shidong Hu, Songyan Li, Yufeng Wang, Xiaohui Du, Rong Li.
       Background: The clinical characteristics of primary retroperitoneal liposarcoma (PR RPLPS) and local recurrent retroperitoneal liposarcoma (LR RPLPS) cases were compared to determine the related factors involved in postoperative survival.
    Methods: A total of 90 patients who underwent surgery between 2006 and 2013 were included in this study. Clinicopathological data that was prospectively gathered was analyzed to identify factors associated with overall survival (OS) and progression-free survival (PFS).
    Results: The PR cases showed a higher complete resection rate when compared to the LR group. The LR group showed a greater number that were poorly differentiated and highly malignant. More blood loss was observed in the LR compared to the PR group. Multivariate analysis suggested that blood loss and tumor grade were prognostic factors for OS and PFS of the PR group, but extent of resection was a prognostic factor only for OS. In the LR group, the extent of resection was a significant prognostic factor associated with OS, whereas tumor grade was associated with PFS.
    Conclusions: Complete surgical resection is the most important factor for the survival of RPLPS patients. Tumor grade is an independent prognostic factor for PFS. In PR RPLPS, poor tumor classification and increased intraoperative bleeding are associated with a poor prognosis.
    Keywords:  Retroperitoneal liposarcoma (RPLPS); local recurrence; overall survival (OS); primary tumor; progression-free survival (PFS); retroperitoneal sarcoma
    DOI:  https://doi.org/10.21037/atm-20-6316
  43. Methods Mol Biol. 2021 ;2226 259-264
    Main Repositories and Databases Used in Ewing Sarcoma Research.
    Maria Debiec-Rychter.
      Within sarcomas 50 different histological subtypes exist, each with their own molecular and clinical characteristics. The combination of tumor subtype heterogeneity and often a limited number of clinical cases make detailed molecular sarcoma studies challenging, particularly when focusing on individual cohorts. However, the increasing number of publicly available genomics data opens inroads to overcome this obstacle. The international public repositories for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community create resources that are freely available for download in a variety of formats. Here, we describe the selected web resources for sarcoma genomics research. These resources support archiving of raw data, processed data, and metadata which are indexed, cross-linked, and searchable.
    Keywords:  Cancer genomics; Databases; Genomic data; Portals; Repositories
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_20
  44. Stem Cells Dev. 2020 Dec 14.
    Energy metabolism during osteogenic differentiation: the role of Akt.
    Charles Owen Smith, Roman A Eliseev.
      Osteogenic differentiation, the process by which bone marrow mesenchymal stem/stromal (a.k.a. skeletal stem) cells and osteoprogenitors form osteoblasts, is a critical event for bone formation during development, fracture repair, and tissue maintenance. Extra- and intracellular signaling pathways triggering osteogenic differentiation are relatively well known; however, the ensuing change in cell energy metabolism is less clearly defined. We and others have previously reported activation of mitochondria during osteogenic differentiation. To further elucidate the involved bioenergetic mechanisms and triggers, we tested the effect of osteogenic media containing ascorbate and β-glycerol phosphate, or various osteogenic hormones and growth factors on energy metabolism in long bone (ST2)- and calvarial bone (MC3T3-E1)-derived osteoprogenitors. We show that osteogenic media, and differentiation factors, Wnt3a and BMP2, stimulate mitochondrial oxidative phosphorylation (OxPhos) with little effect on glycolysis. The activation of OxPhos occurs acutely, suggesting a metabolic signaling change rather than protein expression change. To this end, we found that the observed mitochondrial activation is Akt-dependent. Akt is activated by osteogenic media, Wnt3a, and BMP2, leading to increased phosphorylation of various mitochondrial Akt targets, a phenomenon known to stimulate OxPhos. In sum, our data provide comprehensive analysis of cellular bioenergetics during osteoinduction in cells of two different origins (mesenchyme vs neural crest) and identify Wnt3a and BMP2 as physiological stimulators of mitochondrial respiration via Akt activation.
    DOI:  https://doi.org/10.1089/scd.2020.0141
  45. Onco Targets Ther. 2020 ;13 12521-12538
    Extracellular Matrix-Related Six-lncRNA Signature as a Novel Prognostic Biomarker for Bladder Cancer.
    Liangliang Qing, Peng Gu, Mingsheng Liu, Jihong Shen, Xiaodong Liu, Runyun Guang, Kunbin Ke, Zhuo Huang, Wenhui Lee, Hui Zhao.
       Introduction: Bladder cancer (BC) is the fourth-commones cancer and the sixth-leading cause of cancer-related death among men. However, a lack of reliable biomarkers remains a problem forprognosis and treatment of BC. lncRNAs have been shown to play important roles in various cancers, and have emerged as promising biomarkers for cancer prognosis and treatment.
    Methods: In this study, using univariate and multivariate Cox regression analysis, we examined the differential expression profiles of 1,651 lncRNAs in the TCGA BLCA cohort and created a prognostic gene signature composed of six lncRNAs (for SNHG12, MAFG- DT, ASMTL-AS1, LINC02321, LINC01322, and LINC00922), designed the SMALLL signature.
    Results: The SMALLL signature displayed significant prognostic power for overall survival for BC patients in multiple cohorts. Gene Ontology analysis showed that genes coexpressed with the SMALLL signature were associated with the extracellular matrix network, and immune cell-infiltration analysis showed that activated naïve B cells, regulatory T cells, M0 macrophages, eosinophils, resting memory CD4 T cells and resting NK cells were significantly different in high- and low-risk groups. We also confirmed differential expression of the lncRNAs of the SMALLL signature in BC tissue and paracancer normal tissue by qRT-PCR analysis. Cell-invasion and -migration experiments showed that MAFG-AS1, ASMTL-AS1, LINC02321, and LINC00922 significantly affected cell invasion and migration.
    Conclusion: Our study revealed that the lncRNA signature is an important predictive factor of prognosis and provides a promising biomarker for BC.
    Keywords:  bladder cancer; extracellular matrix; immune-cell infiltration; long noncoding RNA; prognosis; signature
    DOI:  https://doi.org/10.2147/OTT.S284167
  46. Curr Opin Obstet Gynecol. 2020 Dec 09.
    Current and future landscape of poly (ADP-ribose) polymerase inhibition resistance.
    Emily Hinchcliff, Anca Chelariu-Raicu, Shannon N Westin.
       PURPOSE OF REVIEW: To highlight relevant strategies to overcome poly(ADP-ribose) polymerase (PARP) inhibitor resistance and present key clinical trials.
    RECENT FINDINGS: The use of PARP inhibition (PARPi) for frontline maintenance offers substantial clinical benefit in patients with homologous recombination-deficient tumors. However, expanding PARPi from recurrent therapy to frontline maintenance may potentially result in more PARPi resistant tumors earlier in the treatment continuum and data for the use of PARPi after PARPi remain limited. Clinical evidence demonstrates tumors may develop resistance to PARPi through demethylation of the BRCA promoter or BRCA reversion mutations. Multiple clinical trials investigating therapeutic strategies to overcome resistance, such as combinations of PARPi with antiangiogenic drugs, PI3K/AKT/mTOR, or MEK inhibitors have already been reported and more are ongoing. Furthermore, increasing the amount of DNA damage in the tumor using chemotherapy or cell cycle inhibitors such as ATM, ATR/CHK1/WEE1 is also under exploration.
    SUMMARY: There is increasing clinical interest to identify options to enhance PARPi efficacy and overcome adaptive resistance. PARPi represent a class of drugs that have significantly impacted the treatment and maintenance of ovarian cancer; as the use of PARPi increases, better understanding of resistance mechanisms is essential.
    DOI:  https://doi.org/10.1097/GCO.0000000000000678
  47. PLoS Genet. 2020 Dec 14. 16(12): e1009162
    HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation.
    Laure Bridoux, Peyman Zarrineh, Joshua Mallen, Mike Phuycharoen, Victor Latorre, Frank Ladam, Marta Losa, Syed Murtuza Baker, Charles Sagerstrom, Kimberly A Mace, Magnus Rattray, Nicoletta Bobola.
      Gene expression programs determine cell fate in embryonic development and their dysregulation results in disease. Transcription factors (TFs) control gene expression by binding to enhancers, but how TFs select and activate their target enhancers is still unclear. HOX TFs share conserved homeodomains with highly similar sequence recognition properties, yet they impart the identity of different animal body parts. To understand how HOX TFs control their specific transcriptional programs in vivo, we compared HOXA2 and HOXA3 binding profiles in the mouse embryo. HOXA2 and HOXA3 directly cooperate with TALE TFs and selectively target different subsets of a broad TALE chromatin platform. Binding of HOX and tissue-specific TFs convert low affinity TALE binding into high confidence, tissue-specific binding events, which bear the mark of active enhancers. We propose that HOX paralogs, alone and in combination with tissue-specific TFs, generate tissue-specific transcriptional outputs by modulating the activity of TALE TFs at selected enhancers.
    DOI:  https://doi.org/10.1371/journal.pgen.1009162
  48. J Exp Med. 2021 Mar 01. pii: e20201416. [Epub ahead of print]218(3):
    Mitophagy-mediated adipose inflammation contributes to type 2 diabetes with hepatic insulin resistance.
    Feng He, Yanrui Huang, Zhi Song, Huanjiao Jenny Zhou, Haifeng Zhang, Rachel J Perry, Gerald I Shulman, Wang Min.
      White adipose tissues (WAT) play crucial roles in maintaining whole-body energy homeostasis, and their dysfunction can contribute to hepatic insulin resistance and type 2 diabetes mellitus (T2DM). However, the mechanisms underlying these alterations remain unknown. By analyzing the transcriptome landscape in human adipocytes based on available RNA-seq datasets from lean, obese, and T2DM patients, we reveal elevated mitochondrial reactive oxygen species (ROS) pathway and NF-κB signaling with altered fatty acid metabolism in T2DM adipocytes. Mice with adipose-specific deletion of mitochondrial redox Trx2 develop hyperglycemia, hepatic insulin resistance, and hepatic steatosis. Trx2-deficient WAT exhibited excessive mitophagy, increased inflammation, and lipolysis. Mechanistically, mitophagy was induced through increasing ROS generation and NF-κB-dependent accumulation of autophagy receptor p62/SQSTM1, which recruits damaged mitochondria with polyubiquitin chains. Importantly, administration of ROS scavenger or NF-κB inhibitor ameliorates glucose and lipid metabolic disorders and T2DM progression in mice. Taken together, this study reveals a previously unrecognized mechanism linking mitophagy-mediated adipose inflammation to T2DM with hepatic insulin resistance.
    DOI:  https://doi.org/10.1084/jem.20201416
  49. Cancer Med. 2020 Dec 19.
    Metabolic response as assessed by 18 F-fluorodeoxyglucose positron emission tomography-computed tomography does not predict outcome in patients with intermediate- or high-risk rhabdomyosarcoma: A report from the Children's Oncology Group Soft Tissue Sarcoma Committee.
    Douglas J Harrison, Yueh-Yun Chi, Jing Tian, Pooja Hingorani, Leo Mascarenhas, Geoffrey B McCowage, Brenda J Weigel, Rajkumar Venkatramani, Suzanne L Wolden, Torunn I Yock, David A Rodeberg, Andrea A Hayes-Jordan, Lisa A Teot, Sheri L Spunt, William H Meyer, Douglas S Hawkins, Barry L Shulkin, Marguerite T Parisi.
       BACKGROUND: Strategies to optimize management in rhabdomyosarcoma (RMS) include risk stratification to assign therapy aiming to minimize treatment morbidity yet improve outcomes. This analysis evaluated the relationship between complete metabolic response (CMR) as assessed by 18 F-fluorodeoxyglucose positron emission tomography-computed tomography (FDG-PET) imaging and event-free survival (EFS) in intermediate-risk (IR) and high-risk (HR) RMS patients.
    METHODS: FDG-PET imaging characteristics, including assessment of CMR and maximum standard uptake values (SUVmax) of the primary tumor, were evaluated by central review. Institutional reports of SUVmax were used when SUVmax values could not be determined by central review. One hundred and thirty IR and 105 HR patients had FDG-PET scans submitted for central review or had SUVmax data available from institutional report at any time point. A Cox proportional hazards regression model was used to evaluate the relationship between these parameters and EFS.
    RESULTS: SUVmax at study entry did not correlate with EFS for IR (p = 0.32) or HR (p = 0.86) patients. Compared to patients who did not achieve a CMR, EFS was not superior for IR patients who achieved a CMR at weeks 4 (p = 0.66) or 15 (p = 0.46), nor for HR patients who achieved CMR at week 6 (p = 0.75) or 19 (p = 0.28). Change in SUVmax at week 4 (p = 0.21) or 15 (p = 0.91) for IR patients or at week 6 (p = 0.75) or 19 (p = 0.61) for HR patients did not correlate with EFS.
    CONCLUSION: Based on these data, FDG-PET does not appear to predict EFS in IR or HR-RMS. It remains to be determined whether FDG-PET has a role in predicting survival outcomes in other RMS subpopulations.
    Keywords:  chemotherapy; complete metabolic response; maximum standard uptake value (SUVmax); pediatric; positron emission tomography; rhabdomyosarcoma
    DOI:  https://doi.org/10.1002/cam4.3667
  50. Methods Mol Biol. 2021 ;2226 119-138
    Ewing Sarcoma-Specific (Re)expression Models.
    Maximilian M L Knott, Florencia Cidre-Aranaz.
      Gene expression and knockdown systems are powerful tools to study the function of single genes and their pathway interaction. Plasmid transfection and viral transduction have revolutionized the field of molecular biology and paved the ground for various gene-editing strategies such as TALEN, zinc finger nucleases, and ultimately CRISPR. In Ewing sarcoma (EwS), almost as many genes are repressed by the expression of EWSR1-FLI1 as are upregulated by the fusion oncogene. Here we present a useful point-to-point protocol for the generation of transgene expression systems in EwS that allow (conditional) reexpression of a gene of interest. We provide an extensive instruction on molecular cloning, plasmid generation, viral transduction, and expression validation. Finally, we address common problems and highlight potential pitfalls, which can easily be avoided by thoughtful guidance.
    Keywords:  Enhancer; Ewing sarcoma; Fusion-driven sarcoma; Gene expression; Inducible vector; Microsatellites; Overexpression; Promoter
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_9
  51. Nucleic Acids Res. 2020 Dec 11. pii: gkaa1172. [Epub ahead of print]
    G-Quadruplex loops regulate PARP-1 enzymatic activation.
    Andrea D Edwards, John C Marecki, Alicia K Byrd, Jun Gao, Kevin D Raney.
      G-Quadruplexes are non-B form DNA structures present at regulatory regions in the genome, such as promoters of proto-oncogenes and telomeres. The prominence in such sites suggests G-quadruplexes serve an important regulatory role in the cell. Indeed, oxidized G-quadruplexes found at regulatory sites are regarded as epigenetic elements and are associated with an interlinking of DNA repair and transcription. PARP-1 binds damaged DNA and non-B form DNA, where it covalently modifies repair enzymes or chromatin-associated proteins respectively with poly(ADP-ribose) (PAR). PAR serves as a signal in regulation of transcription, chromatin remodeling, and DNA repair. PARP-1 is known to bind G-quadruplexes with stimulation of enzymatic activity. We show that PARP-1 binds several G-quadruplex structures with nanomolar affinities, but only a subset promote PARP-1 activity. The G-quadruplex forming sequence found in the proto-oncogene c-KIT promoter stimulates enzymatic activity of PARP-1. The loop-forming characteristics of the c-KIT G-quadruplex sequence regulate PARP-1 catalytic activity, whereas eliminating these loop features reduces PARP-1 activity. Oxidized G-quadruplexes that have been suggested to form unique, looped structures stimulate PARP-1 activity. Our results support a functional interaction between PARP-1 and G-quadruplexes. PARP-1 enzymatic activation by G-quadruplexes is dependent on the loop features and the presence of oxidative damage.
    DOI:  https://doi.org/10.1093/nar/gkaa1172
  52. Sci Rep. 2020 Dec 15. 10(1): 21969
    MiR-125b-2 knockout increases high-fat diet-induced fat accumulation and insulin resistance.
    Li-Min Wei, Rui-Ping Sun, Tao Dong, Jie Liu, Ting Chen, Bin Zeng, Jia-Han Wu, Jun-Yi Luo, Jia-Jie Sun, Qian-Yun Xi, Yong-Liang Zhang.
      Obese individuals are more susceptible to comorbidities than individuals of healthy weight, including cardiovascular disease and metabolic disorders. MicroRNAs are a class of small and noncoding RNAs that are implicated in the regulation of chronic human diseases. We previously reported that miR-125b plays a critical role in adipogenesis in vitro. However, the involvement of miR-125b-2 in fat metabolism in vivo remains unknown. In the present study, miR-125b-2 knockout mice were generated using CRISPR/CAS9 technology, resulting in mice with a 7 bp deletion in the seed sequence of miR-125b-2. MiR-125b-2 knockout increased the weight of liver tissue, epididymal white fat and inguinal white fat. MiR-125b-2 knockout also increased adipocyte volume in HFD-induced obese mice, while there were no significant differences in body weight and feed intake versus mice fed a normal diet. Additionally, qRT-PCR and western blot analysis revealed that the expression of the miR-125b-2 target gene SCD-1 and fat synthesis-associated genes, such as PPARγ and C/EBPα, were significantly up-regulated in miR-125b-2KO mice (P < 0.05). Moreover, miR-125b-2KO altered HFD-induced changes in glucose tolerance and insulin resistance. In conclusion, we show that miR-125b-2 is a novel potential target for regulating fat accumulation, and also a candidate target to develop novel treatment strategies for obesity and diabetes.
    DOI:  https://doi.org/10.1038/s41598-020-77714-7
  53. Methods Mol Biol. 2021 ;2226 15-25
    Western Blot Analysis in Ewing Sarcoma.
    Aruna Marchetto, Laura Romero-Pérez.
      Western blot is an experimental method used to analyze protein expression. In Ewing sarcoma, as in many other diseases, Western blot provides information about the level of protein expression in different cell conditions, in comparison with other tissues or upon induced molecular changes. Based on the specific pattern of protein expression of the tissue, as well as on the characteristics of the protein of interest, the antibodies and protocol of Western blot may be modified according to different specifications. Here we describe some of these peculiarities in frame of Ewing sarcoma field.
    Keywords:  Ewing sarcoma; Protein expression; Western blot
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_2
  54. Biomolecules. 2020 Dec 15. pii: E1676. [Epub ahead of print]10(12):
    New Actors Driving the Epithelial-Mesenchymal Transition in Cancer: The Role of Leptin.
    Monserrat Olea-Flores, Juan C Juárez-Cruz, Miriam D Zuñiga-Eulogio, Erika Acosta, Eduardo García-Rodríguez, Ana E Zacapala-Gomez, Miguel A Mendoza-Catalán, Julio Ortiz-Ortiz, Carlos Ortuño-Pineda, Napoleón Navarro-Tito.
      Leptin is a hormone secreted mainly by adipocytes; physiologically, it participates in the control of appetite and energy expenditure. However, it has also been linked to tumor progression in different epithelial cancers. In this review, we describe the effect of leptin on epithelial-mesenchymal transition (EMT) markers in different study models, including in vitro, in vivo, and patient studies and in various types of cancer, including breast, prostate, lung, and ovarian cancer. The different studies report that leptin promotes the expression of mesenchymal markers and a decrease in epithelial markers, in addition to promoting EMT-related processes such as cell migration and invasion and poor prognosis in patients with cancer. Finally, we report that leptin has the greatest biological relevance in EMT and tumor progression in breast, lung, prostate, esophageal, and ovarian cancer. This relationship could be due to the key role played by the enriched tumor microenvironment in adipose tissue. Together, these findings demonstrate that leptin is a key biomolecule that drives EMT and metastasis in cancer.
    Keywords:  EMT; cancer; epithelial markers; leptin; mesenchymal markers; signaling pathways
    DOI:  https://doi.org/10.3390/biom10121676
  55. Stem Cell Res Ther. 2020 Dec 14. 11(1): 541
    ELABELA ameliorates hypoxic/ischemic-induced bone mesenchymal stem cell apoptosis via alleviation of mitochondrial dysfunction and activation of PI3K/AKT and ERK1/2 pathways.
    Jiaying Fu, Xuxiang Chen, Xin Liu, Daishi Xu, Huan Yang, Chaotao Zeng, Huibao Long, Changqing Zhou, Haidong Wu, Guanghui Zheng, Hao Wu, Wuming Wang, Tong Wang.
       BACKGROUND: Mesenchymal stem cells (MSCs) have exerted their brilliant potential to promote heart repair following myocardial infarction. However, low survival rate of MSCs after transplantation due to harsh conditions with hypoxic and ischemic stress limits their therapeutic efficiency in treating cardiac dysfunction. ELABELA (ELA) serves as a peptide hormone which has been proved to facilitate cell growth, survival, and pluripotency in human embryonic stem cells. Although ELA works as an endogenous ligand of a G protein-coupled receptor APJ (Apelin receptor, APLNR), whether APJ is an essential signal for the function of ELA remains elusive. The effect of ELA on apoptosis of MSCs is still vague.
    OBJECTIVE: We studied the role of ELABELA (ELA) treatment on the anti-apoptosis of MSCs in hypoxic/ischemic (H/I) conditions which mimic the impaired myocardial microenvironment and explored the possible mechanisms in vitro.
    METHODS: MSCs were obtained from donated rats weighing between 80~120 g. MSCs were exposed to serum-free and hypoxic (1% O2) environments for 24 h, which mimics hypoxic/ischemic damage in vivo, using serum-containing normoxic conditions (20% O2) as a negative control. MSCs that were exposed to H/I injury with ELA processing were treated by 5 μM of ELA. Cell viability and apoptosis of MSCs were evaluated by CCK8 and flow cytometry, respectively. Mitochondrial function of MSCs was also assessed according to mitochondrial membrane potential (MMP) and ATP content. The protein expression of key kinases of the PI3K/AKT and ERK1/2 signaling pathways involving t-AKT, p-AKT, t-ERK1/2, and p-ERK1/2, as well as apoptosis-related protein expression of Bcl-2, Bax, and cleaved Caspase 3, were monitored by Western blot.
    RESULTS: We found that ELA treatment of H/I-induced MSCs improved overall cell viability, enhanced Bcl/Bax expression, and decreased Caspase 3 activity. ELA inhibited H/I-induced mitochondrial dysfunction by increasing ATP concentration and suppressing the loss of mitochondrial transmembrane potential. However, this anti-apoptotic property of ELA was restrained in APJ-silenced MSCs. Additionally, ELA treatment induced the phosphorylation of AKT and ERK, while the blockade of PI3K/AKT and ERK1/2 pathways with respective inhibitors, LY294002 and U0126, suppressed the action of ELA.
    CONCLUSION: ELA positively affected on the survival of MSCs and exhibited anti-apoptotic characteristics when exposed to hypoxic/ischemic condition in vitro. Also, the function of ELA was correlated with the APJ receptor, reduced mitochondrial damage, and activation of the PI3K/AKT and ERK1/2 signal axes.
    Keywords:  Apoptosis; ELABELA; Hypoxic/ischemic; Mesenchymal stem cells; Putative receptor protein related to the angiotensin receptor AT1 endogenous ligand
    DOI:  https://doi.org/10.1186/s13287-020-02063-1
  56. Cells Tissues Organs. 2020 Dec 14. 1-23
    The Role of Calcium Signaling in Regulation of Epithelial-Mesenchymal Transition.
    Divya Adiga, Raghu Radhakrishnan, Sanjiban Chakrabarty, Prashant Kumar, Shama Prasada Kabekkodu.
      Despite substantial advances in the field of cancer therapeutics, metastasis is a significant challenge for a favorable clinical outcome. Epithelial to mesenchymal transition (EMT) is a process of acquiring increased motility, invasiveness, and therapeutic resistance by cancer cells for their sustained growth and survival. A plethora of intrinsic mechanisms and extrinsic microenvironmental factors drive the process of cancer metastasis. Calcium (Ca2+) signaling plays a critical role in dictating the adaptive metastatic cell behavior comprising of cell migration, invasion, angiogenesis, and intravasation. By modulating EMT, Ca2+ signaling can regulate the complexity and dynamics of events leading to metastasis. This review summarizes the role of Ca2+ signal remodeling in the regulation of EMT and metastasis in cancer.
    Keywords:  Calcium channels; Calcium pumps; Calcium signal remodeling; Cancer; Epithelial to mesenchymal transition (EMT); Metastasis
    DOI:  https://doi.org/10.1159/000512277
  57. Front Oncol. 2020 ;10 605386
    Epidrug Repurposing: Discovering New Faces of Old Acquaintances in Cancer Therapy.
    Michel Montalvo-Casimiro, Rodrigo González-Barrios, Marco Antonio Meraz-Rodriguez, Vasti Thamara Juárez-González, Cristian Arriaga-Canon, Luis A Herrera.
      Gene mutations are strongly associated with tumor progression and are well known in cancer development. However, recently discovered epigenetic alterations have shown the potential to greatly influence tumoral response to therapy regimens. Such epigenetic alterations have proven to be dynamic, and thus could be restored. Due to their reversible nature, the promising opportunity to improve chemotherapy response using epigenetic therapy has arisen. Beyond helping to understand the biology of the disease, the use of modern clinical epigenetics is being incorporated into the management of the cancer patient. Potential epidrug candidates can be found through a process known as drug repositioning or repurposing, a promising strategy for the discovery of novel potential targets in already approved drugs. At present, novel epidrug candidates have been identified in preclinical studies and some others are currently being tested in clinical trials, ready to be repositioned. This epidrug repurposing could circumvent the classic paradigm where the main focus is the development of agents with one indication only, while giving patients lower cost therapies and a novel precision medical approach to optimize treatment efficacy and reduce toxicity. This review focuses on the main approved epidrugs, and their druggable targets, that are currently being used in cancer therapy. Also, we highlight the importance of epidrug repurposing by the rediscovery of known chemical entities that may enhance epigenetic therapy in cancer, contributing to the development of precision medicine in oncology.
    Keywords:  cancer; cancer therapy; drug repurposing; epidrugs; epigenetic inhibitors; epigenetics
    DOI:  https://doi.org/10.3389/fonc.2020.605386
  58. Exp Mol Med. 2020 Dec 11.
    Development of a miRNA-controlled dual-sensing system and its application for targeting miR-21 signaling in tumorigenesis.
    Yoona Seo, Sung Soo Kim, Namdoo Kim, Sungchan Cho, Jong Bae Park, Jong Heon Kim.
      MicroRNAs (miRNAs) are considered to be strong prognostic markers and key therapeutic targets in human diseases, especially cancer. A sensitive monitoring platform for cancer-associated miRNA (oncomiR) action is needed for mechanistic studies, preclinical evaluation, and inhibitor screening. In this study, we developed and systemically applied a sensitive and efficient lentivirus-based system for monitoring oncomiR actions, essentially miR-21. The specificity and sensitivity of "miRDREL" against various oncomiRs were validated by checking for tight correlations between their expression and targeting efficacy. Experiments based on the transfection of synthetic mimics and antagomir-mediated depletion of oncomiRs further confirmed the specificity of the system. Systemic application of miRDRELs to natural oncomiR targets, knockdown of key microprocessors, and physiological triggering of oncomiRs also demonstrated that the system is an effective tool for monitoring cellular oncomiR action. Importantly, molecular modeling-based screening confirmed the action of the miR-21-targeting drug ivermectin and led to the identification of a new effective derivative, GW4064, for inhibiting oncogenic DDX23-miR-21 signaling. Furthermore, proteomic-kinase inhibitor screenings identified a novel oncogenic kinome-DDX23-miR-21 axis and thus expands our understanding of miR-21 targeting therapeutics in tumorigenesis. Taken together, these data indicate that miRDREL and its versatile application have great potential in basic, preclinical studies and drug development pipelines for miRNA-related diseases, especially cancer.
    DOI:  https://doi.org/10.1038/s12276-020-00537-z
  59. Expert Opin Drug Discov. 2020 Dec 18.
    Novel approaches to glycomimetic design: Development of small molecular weight lectin antagonists.
    Vishnu C Damalanka, Amarendar Reddy Maddirala, James W Janetka.
       INTRODUCTION: The direct binding of carbohydrates or those presented on glycoproteins or glycolipids to proteins is the primary effector of many biological responses. One class of carbohydrate binding proteins, lectins are important in all forms of life. Their function in animals include regulating cell adhesion, glycoprotein synthesis, metabolism, and mediating immune system response while in bacteria and viruses a lectin-mediated carbohydrate protein interaction between host cells and the pathogen initiates pathogenesis of the infection.
    AREAS COVERED: In this review, the authors outline the structural and functional pathogenesis of lectins from bacteria, amoeba, and humans. Mimics of a carbohydrate are referred to as glycomimetics, which are much smaller in molecular weight and are devised to mimic the key binding interactions of the carbohydrate while also allowing additional contacts with the lectin. This article emphasizes the various approaches used over the past 10-15 years in the rational design of glycomimetic ligands.
    EXPERT OPINION: Medicinal chemistry efforts enabled by X-ray structural biology have identified small molecule glycomimetic lectin antagonists which have entered or are nearing clinical trials. A common theme in these strategies is the use of biaryl ring systems to emulate the carbohydrate interactions with the lectin.
    Keywords:  antibacterial; antibiotic resistance; bacterial adhesin; carbohydrate; glycomimetic; glycoside; infectious disease; lectin; structure-based drug design (SBDD); virulence factor
    DOI:  https://doi.org/10.1080/17460441.2021.1857721
  60. Sci Rep. 2020 Dec 14. 10(1): 21838
    Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses.
    Zhiqiang Du, Jeniece Regan, Elizabeth Bartom, Wei-Sheng Wu, Li Zhang, Dustin Kenneth Goncharoff, Liming Li.
      Transcriptional regulators are prevalent among identified prions in Saccharomyces cerevisiae, however, it is unclear how prions affect genome-wide transcription. We show here that the prion ([SWI+]) and mutant (swi1∆) forms of Swi1, a subunit of the SWI/SNF chromatin-remodeling complex, confer dramatically distinct transcriptomic profiles. In [SWI+] cells, genes encoding for 34 transcription factors (TFs) and 24 Swi1-interacting proteins can undergo transcriptional modifications. Several TFs show enhanced aggregation in [SWI+] cells. Further analyses suggest that such alterations are key factors in specifying the transcriptomic signatures of [SWI+] cells. Interestingly, swi1∆ and [SWI+] impose distinct and oftentimes opposite effects on cellular functions. Translation-associated activities, in particular, are significantly reduced in swi1∆ cells. Although both swi1∆ and [SWI+] cells are similarly sensitive to thermal, osmotic and drought stresses, harmful, neutral or beneficial effects were observed for a panel of tested chemical stressors. Further analyses suggest that the environmental stress response (ESR) is mechanistically different between swi1∆ and [SWI+] cells-stress-inducible ESR (iESR) are repressed by [SWI+] but unchanged by swi1∆ while stress-repressible ESR (rESR) are induced by [SWI+] but repressed by swi1∆. Our work thus demonstrates primarily gain-of-function outcomes through transcriptomic modifications by [SWI+] and highlights a prion-mediated regulation of transcription and phenotypes in yeast.
    DOI:  https://doi.org/10.1038/s41598-020-77993-0
  61. Methods Mol Biol. 2021 ;2226 139-149
    Analysis of Regulatory DNA Sequences by Dual-Luciferase Reporter Assays in Ewing Sarcoma.
    Tilman L B Hölting, Maximilian M L Knott.
      Reporter gene assays allow for examining the influence of regulatory DNA sequences on the transcription of target genes. In Ewing sarcoma, the study of these DNA sequences is especially paramount for its main driver mutation is a fusion transcription factor that binds different motifs than its wild-type constituents. Here, we describe the process of analyzing the enhancer activity of regulatory DNA sequences using transfection-based dual-luciferase reporter assays in Ewing sarcoma cell lines. To this end, we provide a protocol for cloning sequences of interest from genomic DNA into a firefly luciferase-containing plasmid, transfecting Ewing sarcoma cells with plasmids and measuring luciferase expression by luminescence. The entire procedure can be completed in 14 days.
    Keywords:  Enhancer activity; Ewing sarcoma; Fusion-driven sarcoma; Gene expression; Luciferase assay; Promoter activity; Regulatory DNA; Regulatory sequence; Reporter assays
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_10
  62. Front Cell Dev Biol. 2020 ;8 545126
    Tumor Microenvironment Uses a Reversible Reprogramming of Mesenchymal Stromal Cells to Mediate Pro-tumorigenic Effects.
    Armel H Nwabo Kamdje, Paul F Seke Etet, Richard Simo Tagne, Lorella Vecchio, Kiven Erique Lukong, Mauro Krampera.
      The role of mesenchymal stromal cells (MSCs) in the tumor microenvironment is well described. Available data support that MSCs display anticancer activities, and that their reprogramming by cancer cells in the tumor microenvironment induces their switch toward pro-tumorigenic activities. Here we discuss the recent evidence of pro-tumorigenic effects of stromal cells, in particular (i) MSC support to cancer cells through the metabolic reprogramming necessary to maintain their malignant behavior and stemness, and (ii) MSC role in cancer cell immunosenescence and in the establishment and maintenance of immunosuppression in the tumor microenvironment. We also discuss the mechanisms of tumor microenvironment mediated reprogramming of MSCs, including the effects of hypoxia, tumor stiffness, cancer-promoting cells, and tumor extracellular matrix. Finally, we summarize the emerging strategies for reprogramming tumor MSCs to reactivate anticancer functions of these stromal cells.
    Keywords:  anticancer effects; reprogramming; stromal cells; tumor microenvironment; tumorigenic effects
    DOI:  https://doi.org/10.3389/fcell.2020.545126
  63. FASEB J. 2021 Jan;35(1): e21234
    Emerging trends in chromatin remodeler plasticity in mesenchymal stromal cell function.
    Sayan Chakraborty, Sayantani Sinha, Amitava Sengupta.
      Emerging evidences highlight importance of epigenetic regulation and their integration with transcriptional and cell signaling machinery in determining tissue resident adult pluripotent mesenchymal stem/stromal cell (MSC) activity, lineage commitment, and multicellular development. Histone modifying enzymes and large multi-subunit chromatin remodeling complexes and their cell type-specific plasticity remain the central defining features of gene regulation and establishment of tissue identity. Modulation of transcription factor expression gradient ex vivo and concomitant flexibility of higher order chromatin architecture in response to signaling cues are exciting approaches to regulate MSC activity and tissue rejuvenation. Being an important constituent of the adult bone marrow microenvironment/niche, pathophysiological perturbation in MSC homeostasis also causes impaired hematopoietic stem/progenitor cell function in a non-cell autonomous mechanism. In addition, pluripotent MSCs can function as immune regulatory cells, and they reside at the crossroad of innate and adaptive immune response pathways. Research in the past few years suggest that MSCs/stromal fibroblasts significantly contribute to the establishment of immunosuppressive microenvironment in shaping antitumor immunity. Therefore, it is important to understand mesenchymal stromal epigenome and transcriptional regulation to leverage its applications in regenerative medicine, epigenetic memory-guided trained immunity, immune-metabolic rewiring, and precision immune reprogramming. In this review, we highlight the latest developments and prospects in chromatin biology in determining MSC function in the context of lineage commitment and immunomodulation.
    Keywords:  cell differentiation; chromatin remodeling; epigenetics; gene regulation; hematopoiesis; inflammation; innate immunity; mesenchymal stem cells (MSCs); tumor microenvironment
    DOI:  https://doi.org/10.1096/fj.202002232R
  64. Exp Mol Med. 2020 Dec 11.
    Histone acylation marks respond to metabolic perturbations and enable cellular adaptation.
    Chanhee Jo, Seokjae Park, Sungjoon Oh, Jinmi Choi, Eun-Kyoung Kim, Hong-Duk Youn, Eun-Jung Cho.
      Acetylation is the most studied histone acyl modification and has been recognized as a fundamental player in metabolic gene regulation, whereas other short-chain acyl modifications have only been recently identified, and little is known about their dynamics or molecular functions at the intersection of metabolism and epigenetic gene regulation. In this study, we aimed to understand the link between nonacetyl histone acyl modification, metabolic transcriptional regulation, and cellular adaptation. Using antibodies specific for butyrylated, propionylated, and crotonylated H3K23, we analyzed dynamic changes of H3K23 acylation upon various metabolic challenges. Here, we show that H3K23 modifications were highly responsive and reversibly regulated by nutrient availability. These modifications were commonly downregulated by the depletion of glucose and recovered based on glucose or fatty acid availability. Depletion of metabolic enzymes, namely, ATP citrate lyase, carnitine acetyltransferase, and acetyl-CoA synthetase, which are involved in Ac-CoA synthesis, resulted in global loss of H3K23 butyrylation, crotonylation, propionylation, and acetylation, with a profound impact on gene expression and cellular metabolic states. Our data indicate that Ac-CoA/CoA and central metabolic inputs are important for the maintenance of histone acylation. Additionally, genome-wide analysis revealed that acyl modifications are associated with gene activation. Our study shows that histone acylation acts as an immediate and reversible metabolic sensor enabling cellular adaptation to metabolic stress by reprogramming gene expression.
    DOI:  https://doi.org/10.1038/s12276-020-00539-x
  65. Br J Cancer. 2020 Dec 16.
    The role of Schlafen 11 (SLFN11) as a predictive biomarker for targeting the DNA damage response.
    Niamh Coleman, Bingnan Zhang, Lauren A Byers, Timothy A Yap.
      The therapeutic landscape of drugs targeting the DNA damage response (DDR) is rapidly expanding; however, an urgent unmet need remains for validated predictive biomarkers of response. SLFN11 has emerged as a promising predictor of sensitivity to DNA-damaging chemotherapies, and recently, been associated with sensitivity to PARP inhibition. We discuss its use as a predictive biomarker of response for targeting the DDR.
    DOI:  https://doi.org/10.1038/s41416-020-01202-y
  66. Cell Biosci. 2020 Dec 11. 10(1): 143
    Post-translational modifications of EZH2 in cancer.
    Zhongwei Li, Minle Li, Diandian Wang, Pingfu Hou, Xintian Chen, Sufang Chu, Dafei Chai, Junnian Zheng, Jin Bai.
      Enhancer of zeste homolog 2 (EZH2), as a main component of Polycomb Repressive Complex 2, catalyzes histone H3K27me3 to silence its target gene expression. EZH2 upregulation results in cancer development and poor prognosis of cancer patients. Post-translational modifications (PTMs) are important biological events in cancer progression. PTMs regulate protein conformation and diversity functions. Recently, mounting studies have demonstrated that EZH2 stability, histone methyltransferase activity, localization, and binding partners can be regulated by PTMs, including phosphorylation, O-GlcNAcylation, acetylation, methylation and ubiquitination. However, the detailed molecular mechanisms of the EZH2-PTMs and whether other types of PTMs occur in EZH2 remain largely unclear. This review presents an overview of different roles of EZH2 modification and EZH2-PTMs crosstalk during tumorigenesis and cancer metastasis. We also discussed the therapeutic potential of targeting EZH2 modifications for cancer therapy.
    Keywords:  Cancer therapy; Crosstalk; EZH2; Post-translational modification
    DOI:  https://doi.org/10.1186/s13578-020-00505-0
  67. Cancers (Basel). 2020 Dec 09. pii: E3690. [Epub ahead of print]12(12):
    HDAC Inhibition Increases HLA Class I Expression in Uveal Melanoma.
    Zahra Souri, Aart G Jochemsen, Mieke Versluis, Annemijn P A Wierenga, Fariba Nemati, Pieter A van der Velden, Wilma G M Kroes, Robert M Verdijk, Gregorius P M Luyten, Martine J Jager.
      The treatment of uveal melanoma (UM) metastases or adjuvant treatment may imply immunological approaches or chemotherapy. It is to date unknown how epigenetic modifiers affect the expression of immunologically relevant targets, such as the HLA Class I antigens, in UM. We investigated the expression of HDACs and the histone methyl transferase EZH2 in a set of 64 UMs, using an Illumina HT12V4 array, and determined whether a histone deacetylase (HDAC) inhibitor and EZH2 inhibitor modified the expression of HLA Class I on three UM cell lines. Several HDACs (HDAC1, HDAC3, HDAC4, and HDAC8) showed an increased expression in high-risk UM, and were correlated with an increased HLA expression. HDAC11 had the opposite expression pattern. While in vitro tests showed that Tazemetostat did not influence cell growth, Quisinostat decreased cell survival. In the three tested cell lines, Quisinostat increased HLA Class I expression at the protein and mRNA level, while Tazemetostat did not have an effect on the cell surface HLA Class I levels. Combination therapy mostly followed the Quisinostat results. Our findings indicate that epigenetic drugs (in this case an HDAC inhibitor) may influence the expression of immunologically relevant cell surface molecules in UM, demonstrating that these drugs potentially influence immunotherapy.
    Keywords:  HDAC; HLA; eye diseases; immunology; inflammation; oncology; uveal melanoma
    DOI:  https://doi.org/10.3390/cancers12123690
  68. Front Cell Dev Biol. 2020 ;8 586179
    NAD+ Metabolism Regulates Preadipocyte Differentiation by Enhancing α-Ketoglutarate-Mediated Histone H3K9 Demethylation at the PPARγ Promoter.
    Keisuke Okabe, Allah Nawaz, Yasuhiro Nishida, Keisuke Yaku, Isao Usui, Kazuyuki Tobe, Takashi Nakagawa.
      Obesity has become a serious problem in public health worldwide, causing numerous metabolic diseases. Once the differentiation to mature adipocytes is disrupted, adipocyte hypertrophy and ectopic lipid accumulation leads to the inflammation in adipose tissue and systemic metabolic disorders. Intracellular metabolic state is known to change during cell differentiation and it affects the cell fate or the differentiation through epigenetic mechanism. Although the mechanism of preadipocyte differentiation has been well established, it is unknown how metabolic state changes and how it affects the differentiation in predipocyte differentiation. Nicotinamide adenine dinucleotide (NAD+) plays crucial roles in energy metabolism as a coenzyme in multiple redox reactions in major catabolic pathways and as a substrate of sirtuins or poly(ADP-ribose)polymerases. NAD+ is mainly synthesized from salvage pathway mediated by two enzymes, Nampt and Nmnat. The manipulation to NAD+ metabolism causes metabolic change in each tissue and changes in systemic metabolism. However, the role of NAD+ and Nampt in adipocyte differentiation remains unknown. In this study, we employed liquid chromatography-mass spectrometry (LC-MS)- and gas chromatography-mass spectrometry (GC-MS)-based targeted metabolomics to elucidate the metabolic reprogramming events that occur during 3T3-L1 preadipocyte differentiation. We found that the tricarboxylic acid (TCA) cycle was enhanced, which correlated with upregulated NAD+ synthesis. Additionally, increased alpha-ketoglutarate (αKG) contributed to histone H3K9 demethylation in the promoter region of PPARγ, leading to its transcriptional activation. Thus, we concluded that NAD+-centered metabolic reprogramming is necessary for the differentiation of 3T3-L1 preadipocytes.
    Keywords:  NAD+; adipocyte; alpha-ketoglutarate; demethylation; differentiation; metabolomics; nampt; preadipocyte
    DOI:  https://doi.org/10.3389/fcell.2020.586179
  69. Cancer Cell Int. 2020 Dec 17. 20(1): 567
    MiR-4310 induced by SP1 targets PTEN to promote glioma progression.
    Zhiyong Wu, Jie Luo, Tengyue Huang, Renhui Yi, Shengfeng Ding, Cheng Xie, An'qi Xu, Yu Zeng, Xizhao Wang, Ye Song, Xiaofeng Shi, Hao Long.
       BACKGROUND: miRNAs have been reported to be involved in multiple biological processes of gliomas. Here, we aimed to analyze miR-4310 and its correlation genes involved in the progression of human glioma.
    METHODS: miR-4310 expression levels were examined in glioma and non-tumor brain (NB) tissues. The molecular mechanisms of miR-4310 expression and its effects on cell proliferation, migration, and invasion were explored using 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide, Transwell chamber, Boyden chamber, and western blot analyses, as well as its effect on tumorigenesis was explored in vivo in nude mice. The relationships between miR-4310, SP1, phosphatase, and tensin homolog (PTEN) were explored using chromatin immunoprecipitation, agarose gel electrophoresis, electrophoresis mobility shift, and dual-luciferase reporter gene assays.
    RESULTS: miR-4310 expression was upregulated in glioma tissues compared to that in NB tissues. Overexpressed miR-4310 promoted glioma cell proliferation, migration, and invasion in vitro, as well as tumorigenesis in vivo. The inhibition of miR-4310 expression was sufficient to reverse these results. Mechanistic analyses revealed that miR-4310 promoted glioma progression through the PI3K/AKT pathway by targeting PTEN. Additionally, SP1 induced the expression of miR-4310 by binding to its promoter region.
    CONCLUSION: miR-4310 promotes the progression of glioma by targeting PTEN and activating the PI3K/AKT pathway; meanwhile, the expression of miR-4310 was induced by SP1.
    Keywords:  Glioma; PI3K/AKT signaling; PTEN; SP1; miR-4310
    DOI:  https://doi.org/10.1186/s12935-020-01650-9
  70. Front Endocrinol (Lausanne). 2020 ;11 561256
    PPARγ S273 Phosphorylation Modifies the Dynamics of Coregulator Proteins Recruitment.
    Marieli Mariano Gonçalves Dias, Fernanda Aparecida Heleno Batista, Thais Helena Tittanegro, André Gustavo de Oliveira, Albane Le Maire, Felipe Rafael Torres, Helder Veras Ribeiro Filho, Leonardo Reis Silveira, Ana Carolina Migliorini Figueira.
      The nuclear receptor PPARγ is essential to maintain whole-body glucose homeostasis and insulin sensitivity, acting as a master regulator of adipogenesis, lipid, and glucose metabolism. Its activation through natural or synthetic ligands induces the recruitment of coactivators, leading to transcription of target genes such as cytokines and hormones. More recently, post translational modifications, such as PPARγ phosphorylation at Ser273 by CDK5 in adipose tissue, have been linked to insulin resistance trough the dysregulation of expression of a specific subset of genes. Here, we investigate how this phosphorylation may disturb the interaction between PPARγ and some coregulator proteins as a new mechanism that may leads to insulin resistance. Through cellular and in vitro assays, we show that PPARγ phosphorylation inhibition increased the activation of the receptor, therefore the increased recruitment of PGC1-α and TIF2 coactivators, whilst decreases the interaction with SMRT and NCoR corepressors. Moreover, our results show a shift in the coregulators interaction domains preferences, suggesting additional interaction interfaces formed between the phosphorylated PPARγ and some coregulator proteins. Also, we observed that the CDK5 presence disturb the PPARγ-coregulator's synergy, decreasing interaction with PGC1-α, TIF2, and NCoR, but increasing coupling of SMRT. Finally, we conclude that the insulin resistance provoked by PPARγ phosphorylation is linked to a differential coregulators recruitment, which may promote dysregulation in gene expression.
    Keywords:  PPARgamma; Ser273 phosphorylation; coactivator; coregulator interaction; corepressor; insulin resistance; nuclear receptors
    DOI:  https://doi.org/10.3389/fendo.2020.561256
  71. Trends Cancer. 2020 Dec 09. pii: S2405-8033(20)30307-1. [Epub ahead of print]
    New Roles for Fusobacterium nucleatum in Cancer: Target the Bacteria, Host, or Both?
    Daniel J Slade.
      Fusobacterium nucleatum is an oral bacterium associated with colorectal cancer (CRC) proliferation, chemoresistance, inflammation, metastasis, and now DNA damage. While controlling F. nucleatum through antibiotics could reduce cancer severity, this article proposes additional strategies to block Fusobacterium-host interactions, as well as treatment of activated host immune and oncogenic signaling pathways in CRC.
    DOI:  https://doi.org/10.1016/j.trecan.2020.11.006
  72. Front Endocrinol (Lausanne). 2020 ;11 592129
    The Molecular Mechanisms Underlying Mitochondria-Associated Endoplasmic Reticulum Membrane-Induced Insulin Resistance.
    Han Cheng, Xiaokun Gang, Guangyu He, Yujia Liu, Yingxuan Wang, Xue Zhao, Guixia Wang.
      Mitochondria and the endoplasmic reticulum (ER) are connected at multiple sites via what are known as mitochondria-associated ER membranes (MAMs). These associations are known to play an important role in maintaining cellular homeostasis. Impaired MAM signaling has wide-ranging effects in many diseases, such as obesity, diabetes, and neurodegenerative disorders. Accumulating evidence has suggested that MAMs influence insulin signaling through different pathways, including those associated with Ca2+ signaling, lipid metabolism, mitochondrial function, ER stress responses, and inflammation. Altered MAM signaling is a common feature of insulin resistance in different tissues, including the liver, muscle, and even the brain. In the liver, MAMs are key glucose-sensing regulators and have been proposed to be a hub for insulin signaling. Impaired MAM integrity has been reported to disrupt hepatic responses to changes in glucose availability during nutritional transition and to induce hepatic insulin resistance. Meanwhile, these effects can be rescued by the reinforcement of MAM interactions. In contrast, several studies have proposed that enhanced ER-mitochondria connections are detrimental to hepatic insulin signaling and can lead to mitochondrial dysfunction. Thus, given these contradictory results, the role played by the MAM in the regulation of hepatic insulin signaling remains elusive. Similarly, in skeletal muscle, enhanced MAM formation may be beneficial in the early stage of diabetes, whereas continuous MAM enhancement aggravates insulin resistance. Furthermore, recent studies have suggested that ER stress may be the primary pathway through which MAMs induce brain insulin resistance, especially in the hypothalamus. This review will discuss the possible mechanisms underlying MAM-associated insulin resistance as well as the therapeutic potential of targeting the MAM in the treatment of type 2 diabetes.
    Keywords:  endoplasmic reticulum; endoplasmic reticulum stress; insulin resistance; mitochondria; mitochondria-associated endoplasmic reticulum membrane; type 2 diabetes
    DOI:  https://doi.org/10.3389/fendo.2020.592129
  73. Mol Med Rep. 2021 Feb;pii: 137. [Epub ahead of print]23(2):
    CBX2 depletion inhibits the proliferation, invasion and migration of gastric cancer cells by inactivating the YAP/β-catenin pathway.
    Miaomiao Zeng, Bangxue Li, Lei Yang, Quanlin Guan.
      Gastric cancer (GC) is the most common and fast‑growing malignancy of the digestive system, which has a high mortality. Chromobox homolog 2 (CBX2) has been reported to be highly expressed in cancer tissues compared with adjacent normal tissues. It has also been established that CBX2 is upregulated in GC cell lines by searching the Cancer Cell Line Encyclopedia. The aim of the present study was to investigate the biomolecular role and underlying mechanism of CBX2 in the proliferation, invasion and migration of GC cells. Short hairpin RNA‑CBX2 and yes‑associated protein (YAP) overexpression plasmids were constructed to regulate CBX2 and YAP expression, respectively. Additionally, the expression of certain mRNAs and proteins involved in the YAP/β‑catenin pathway and those associated with cell invasion were assessed by western blotting and reverse transcription‑quantitative PCR, respectively. The cellular behaviors of MFC cells were analyzed using Cell Counting Kit‑8, colony formation wound‑healing and Transwell assays. The results of the present study revealed that increased CBX2 expression was observed in GC cell lines compared with normal gastric cells. In addition, CBX2 knockdown inhibited the nuclear cytoplasm translocation of YAP, inducing its phosphorylation, and suppressing the activation of the β‑catenin signaling pathway. The results also demonstrated that CBX2 depletion inhibited the proliferation, migration and invasion of GC cells by inactivating the YAP/β‑catenin pathway. It was determined that CBX2 promoted the proliferation, invasion and migration of GC cells by activating the YAP/β‑catenin pathway, suggesting that CBX2 is involved in the pathogenesis of GC and may represent a novel target for the clinical treatment of GC.
    DOI:  https://doi.org/10.3892/mmr.2020.11776
  74. Diabetes Metab Syndr Obes. 2020 ;13 4763-4777
    Toll-like Receptors as a Potential Drug Target for Diabetes Mellitus and Diabetes-associated Complications.
    Awgichew Shewasinad Yehualashet.
      Diabetes mellitus (DM) is a chronic endocrine disease distinguished by hyperglycemia due to disturbance in carbohydrate or lipid metabolism or insulin function. To date, diabetes, and its complications, is established as a global cause of morbidity and mortality. The intended aim during the management of diabetes is to maintain blood glucose close to normal because the majority of patients have poor control of their elevated blood glucose and are highly prone to severe macrovascular and microvascular complications. To decrease the burden of the disease and its complications, scientists from various disciplines are working intensively to identify novel and promising drug targets for diabetes and its complications. Increased and ongoing investigations on mechanisms relating to diabetes and associated complications could potentially consider inflammatory cascades as a promising component of the strategy in the prevention and control of diabetes and its complications. The potential of targeting mediators of inflammation like toll-like receptors (TLRs) are part of current investigation by the scientific community. Hence, the aim of the present review is to discuss the role of TLRs as a potential drug target for diabetes and diabetes associated complications.
    Keywords:  TLR; complication; diabetes mellitus; immunity; inflammation
    DOI:  https://doi.org/10.2147/DMSO.S274844
  75. Front Oncol. 2020 ;10 598174
    Natural Compounds That Target DNA Repair Pathways and Their Therapeutic Potential to Counteract Cancer Cells.
    Francisco Alejandro Lagunas-Rangel, Rosa María Bermúdez-Cruz.
      Resistance to current cancer treatments is an important problem that arises through various mechanisms, but one that stands out involves an overexpression of several factors associated with DNA repair. To counteract this type of resistance, different drugs have been developed to affect one or more DNA repair pathways, therefore, to test different compounds of natural origin that have been shown to induce cell death in cancer cells is paramount. Since natural compounds target components of the DNA repair pathways, they have been shown to promote cancer cells to be resensitized to current treatments. For this and other reasons, natural compounds have aroused great curiosity and several research projects are being developed around the world to establish combined treatments between them and radio or chemotherapy. In this work, we summarize the effects of different natural compounds on the DNA repair mechanisms of cancer cells and emphasize their possible application to re-sensitize these cells.
    Keywords:  DNA damage; chemoresistance; radioresistance; sensitization; treatment
    DOI:  https://doi.org/10.3389/fonc.2020.598174
  76. J Cell Mol Med. 2020 Dec 17.
    Long non-coding RNA MEG3 promotes autophagy and apoptosis of nasopharyngeal carcinoma cells via PTEN up-regulation by binding to microRNA-21.
    Liqiang Lin, Xiaoli Liu, Baotao Lv.
      Long non-coding RNAs (lncRNAs) have been highlighted as attractive markers for diagnosis and prognosis as well as new therapeutic targets in multiple cancers, including nasopharyngeal carcinoma (NPC). Here, we attempted to investigate the underlying regulatory role of the lncRNA maternally expressed gene 3 (MEG3) in NPC development. As determined by RT-qPCR, MEG3 expression was down-regulated in NPC cells. Online RNA crosstalk analysis predicted the binding of miR-21 to MEG3 and PTEN, respectively. MEG3 was validated to bind to miR-21 while PTEN was identified as a target of miR-21 by dual-luciferase reporter gene assay. Exogenous transfection was done to change the levels of MEG3, miR-21 and PTEN in HK-1 cells to investigate their effects on the autophagy and apoptosis of NPC cells. The results suggested that MEG3 overexpression in HK-1 cells up-regulated PTEN and down-regulated miR-21, by which MEG3 further inhibited autophagy and apoptosis ability of NPC cells. The tumour formation ability was tested after injecting the HK-1 cells into nude, mice and tumour growth was monitored. Consistently, MEG3 overexpression inhibited the tumour formation in vivo. Collectively, MEG3 promotes the autophagy and apoptosis of NPC cells via enhancing PTEN expression by binding to miR-21.
    Keywords:  apoptosis; autophagy; maternally expressed gene 3; microRNA-21; nasopharyngeal carcinoma; phosphatase and tensin homologue
    DOI:  https://doi.org/10.1111/jcmm.15759
  77. Int J Hyperthermia. 2020 ;37(1): 1368-1382
    Macrophages and brown adipocytes cross-communicate to modulate a thermogenic program following methamphetamine exposure.
    Manuel Sanchez-Alavez, Nikki Bortell, Liana Basova, Fahumiya Samad, Maria Cecilia Garibaldi Marcondes.
      Hyperthermia is a potentially lethal side-effect of Methamphetamine (Meth), a stimulant drug. Activation of non-shivering thermogenesis in brown adipose tissue (BAT) is partly responsible for Meth-induced rise in temperature, with contributing sympathetic neurotransmitters, such as norepinephrine (NE), and reactive oxygen species (ROS). However, the mechanisms controlling the development of a molecular thermogenic program in brown adipocytes (BA) following Meth are unknown. We hypothesize that Meth and NE affect BAT cells, BA and macrophages, to modify their physiology and interactions, with consequences to thermogenic genes. We also hypothesize that ROS play a critical role in signaling transcription of thermogenic genes and their regulatory components. Using primary BA and macrophage cultures, we measured Meth and NE interference with physiological and phenotypic measures that are relevant to thermogenesis in BAT. Meth caused both BA and macrophages to decrease mitochondrial maximal capacity and increase ROS. In BA, the thermogenic genes UCP1, PPARγ, PGC1α and GADD45γ were transcriptionally increased by Meth in a ROS-dependent manner. In macrophages, Meth increased oxidative stress response and caused a predominance of M2 subset markers. BA transcriptional changes in response to Meth and NE were significantly controlled by macrophages. The results suggest that BA and macrophages respond to Meth and NE, with effects on mitochondrial functions and transcription of genes involved in thermogenesis. ROS-dependent signals in BA and cellular interactions between BA and macrophages synergize to regulate the BAT environment and control critical pathways leading to Meth-hyperthermia.
    Keywords:  Methamphetamine; brown adipocytes; macrophages; thermogenesis
    DOI:  https://doi.org/10.1080/02656736.2020.1849822
  78. Front Pharmacol. 2020 ;11 577108
    PKM2-Induced the Phosphorylation of Histone H3 Contributes to EGF-Mediated PD-L1 Transcription in HCC.
    Xiao Wang, Chao Liang, Xin Yao, Ruo-Han Yang, Zhan-Sheng Zhang, Fan-Ye Liu, Wen-Qi Li, Shu-Hua Pei, Jing Ma, Song-Qiang Xie, Dong Fang.
      High expression of programmed death-ligand-1 (PD-L1) in hepatocellular carcinoma (HCC) cells usually inhibits the proliferation and functions of T cells, leading to immune suppression in tumor microenvironment. However, very little has been described regarding the mechanism of PD-L1 overexpression in HCC cells. In the present study, we found epidermal growth factor (EGF) stimulation promoted the expression of PD-L1 mRNA and protein in HCC cells. Inhibition of epidermal growth factor receptor (EGFR) could reverse EGF-induced the expression of PD-L1 mRNA and protein. Subsequently, we also observed that the phosphorylation level of Pyruvate kinase isoform M2 (PKM2) at Ser37 site was also increased in response to EGF stimulation. Expression of a phosphorylation-mimic PKM2 S37D mutant stimulated PD-L1 expression as well as H3-Thr11 phosphorylation in HCC cells, while inhibition of PKM2 significantly blocked EGF-induced PD-L1 expression and H3-Thr11 phosphorylation. Furthermore, mutation of Thr11 of histone H3 into alanine abrogated EGF-induced mRNA and protein expression of PD-L1, Chromatin immunoprecipitation (ChIP) assay also suggested that EGF treatment resulted in enhanced H3-Thr11 phosphorylation at the PD-L1 promoter. In a diethylnitrosamine (DEN)-induced rat model of HCC, we found that the expression of phosphorylated EGFR, PKM2 nuclear expression, H3-Thr11 phosphorylation as well as PD-L1 mRNA and protein was higher in the livers than that in normal rat livers. Taken together, our study suggested that PKM2-dependent histone H3-Thr11 phosphorylation was crucial for EGF-induced PD-L1 expression at transcriptional level in HCC. These findings may provide an alternative target for the treatment of hepatocellular carcinoma.
    Keywords:  Pyruvate kinase isoform M2; epidermal growth factor; hepatocellular carcinoma; histone H3; programmed death-ligand-1
    DOI:  https://doi.org/10.3389/fphar.2020.577108
  79. Methods Mol Biol. 2021 ;2226 167-179
    Analysis of Migration and Invasion in Ewing Sarcoma.
    Florencia Cidre-Aranaz.
      The metastasis is a complex, well-orchestrated process, which includes migration from the primary tumor and invasion into secondary locations as main features. In Ewing sarcoma, metastasis is the main determinant of malignancy, with ~30% of patients presenting with metastatic disease at diagnosis. Therefore, analyzing migration and invasion in different experimental settings in vitro is key to understanding this disease. Among the variety of possible techniques to study migration, this chapter described the methods of wound healing (migration in 2D) and transwell (migration through a porous membrane in response to a given stimulus). Additionally, this chapter includes a variation of the transwell protocol that allows for the analysis of cell invasion through a gel matrix in response to stimulus.
    Keywords:  Ewing sarcoma; Invasion; Migration; Transwell; Wound healing
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_13
  80. Methods Mol Biol. 2021 ;2226 39-45
    Liquid Biopsies in Ewing Sarcoma.
    Manuela Krumbholz, Markus Metzler.
      Liquid biopsies enable noninvasive therapy monitoring in patients with solid tumors. Specific serum markers such as proteins, hormones, or enzymes released from tumor cells or in response to tumor growth can be used for quantification of the tumor burden. However, only a fraction of pediatric tumors has none of these serum markers, but tumor-specific genetic alterations represent reliable alternatives. Here we describe a method for using genomic fusion sequences as liquid biopsy markers in Ewing sarcoma patients.
    Keywords:  Cell-free circulating DNA; Double-quenched probes; Droplet digital PCR; Ewing sarcoma; Genomic fusion sequences; Liquid biopsy; Serum marker
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_4
  81. Cancers (Basel). 2020 Dec 09. pii: E3695. [Epub ahead of print]12(12):
    Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer.
    Kathleen M Lucere, Megan M R O'Malley, Sarah D Diermeier.
      Recent technological advancements such as CRISPR/Cas-based systems enable multiplexed, high-throughput screening for new therapeutic targets in cancer. While numerous functional screens have been performed on protein-coding genes to date, long non-coding RNAs (lncRNAs) represent an emerging class of potential oncogenes and tumor suppressors, with only a handful of large-scale screens performed thus far. Here, we review in detail currently available screening approaches to identify new lncRNA drivers of tumorigenesis and tumor progression. We discuss the various approaches of genomic and transcriptional targeting using CRISPR/Cas9, as well as methods to post-transcriptionally target lncRNAs via RNA interference (RNAi), antisense oligonucleotides (ASOs) and CRISPR/Cas13. We discuss potential advantages, caveats and future applications of each method to provide an overview and guide on investigating lncRNAs as new therapeutic targets in cancer.
    Keywords:  CRISPR; antisense oligonucleotide (ASO); cancer; functional screening; long non-coding RNA (lncRNA); oncology; shRNA; siRNA; target identification; therapeutic target
    DOI:  https://doi.org/10.3390/cancers12123695
  82. Curr Med Chem. 2020 Dec 16.
    Exosomes: Critical mediators of tumour microenvironment reprogramming.
    Rama Rao Malla, Gugalavath Shailender, Mohammad Amjad Kamal.
      Tumour microenvironment (TME) is a resident of a variety of cells, which devoted to the heterogeneous population of the tumour. TME establishes a communication network for crosstalk and signalling between tumour cells, stroma, and other interstitial cells. The cross-communication drives the reprogramming of TME cells, which promote cancer progression and metastasis via diverse signalling pathways. Recently, TME-derived exosomes are recognized as critical communicators of TME cell reprogramming. This review addresses the role of TME-derived exosomes in the modulation of stroma, including reprogramming the stromal cells, ECM and tumour cell metabolism, as well as neoplastic transformation. Subsequently, we described the role of exosomes in pre-metastatic niche development, maintenance of stemness and tumour vasculature as well as development of drug resistance. We also explored tumour-derived exosomes in precision, including diagnosis, drug delivery, and vaccine development. We discussed the currently established bioengineered exosomes as carriers for chemotherapeutic drugs, RNAi molecules, and natural compounds. Finally, we presented tetraspanin and DNAbased precision methods for the quantification of tumour-derived exosomes. Overall, TME-derived exosome-mediated reprogramming of TME and precision strategies could illuminate the potential mechanisms for targeted therapeutic intervention.
    Keywords:  Angiogenesis; cancer stem cells; exosomes; metastasis; tumour microenvironment
    DOI:  https://doi.org/10.2174/0929867328666201217105529
  83. Front Oncol. 2020 ;10 588542
    Immune Adaptation of Colorectal Cancer Stem Cells and Their Interaction With the Tumor Microenvironment.
    Chun-Chi Lin, Tsai-Tsen Liao, Muh-Hwa Yang.
      Metastasis is the primary cause of death in colorectal cancer (CRC) patients. Emerging evidence has shown that CRC stem cells (CRCSCs) play a significant role in metastatic dissemination and tumor recurrence. However, strategies for targeting CRCSCs are limited because CRCSCs are resistant to therapeutic interventions and because the tumor microenvironment (TME) provides a supportive niche. Moreover, growing evidence highlights the critical role of CRCSCs in immune adaptation and modulation of the TME. CRCSCs escape immune surveillance by avoiding recognition by the innate immune system and shaping the TME through exosomes, cytokines, and chemokines to generate an immunosuppressive niche that facilitates cancer progression. In this review, we summarize studies investigating the immunomodulatory properties of CRCSCs and their underlying mechanisms in order to improve the efficacy of treatment strategies against advanced CRC.
    Keywords:  colorectal cancer stem cells; immune evasion; immunotherapy; metastasis; tumor microenviroment
    DOI:  https://doi.org/10.3389/fonc.2020.588542
  84. Aging Cell. 2020 Dec 13. e13282
    SPATA4 improves aging-induced metabolic dysfunction through promotion of preadipocyte differentiation and adipose tissue expansion.
    Zhongchi Li, Kang Xu, Sen Zhao, Yannan Guo, Huiling Chen, Jianquan Ni, Qingfei Liu, Zhao Wang.
      Spermatogenesis-associated protein 4 (SPATA4) is conserved across multiple species. However, the function of this gene remains largely unknown. In this study, we generated Spata4 transgenic mice to explore tissue-specific function of SPATA4. Spata4 overexpression mice displayed increased subcutaneous fat tissue compared with wild-type littermates at an old age, while this difference was not observed in younger mice. Aging-induced ectopic fat distribution, inflammation, and insulin resistance were also significantly attenuated by SPATA4. In vitro, SPATA4 promoted preadipocyte differentiation through activation of the ERK1/2 and C/EBPβ pathway and increased the expression of adipokines. These data suggest SPATA4 can regulate lipid accumulation in a tissue-specific manner and improve aging-induced dysmetabolic syndromes. Clarifying the mechanism of SPATA4 functioning in lipid metabolism might provide novel therapeutic targets for disease interventions.
    Keywords:  SPATA4; adipocyte differentiation; aging; fat redistribution
    DOI:  https://doi.org/10.1111/acel.13282
  85. Nucleic Acids Res. 2020 Dec 16. pii: gkaa1202. [Epub ahead of print]
    DNA damage alters nuclear mechanics through chromatin reorganization.
    Ália Dos Santos, Alexander W Cook, Rosemarie E Gough, Martin Schilling, Nora A Olszok, Ian Brown, Lin Wang, Jesse Aaron, Marisa L Martin-Fernandez, Florian Rehfeldt, Christopher P Toseland.
      DNA double-strand breaks drive genomic instability. However, it remains unknown how these processes may affect the biomechanical properties of the nucleus and what role nuclear mechanics play in DNA damage and repair efficiency. Here, we have used Atomic Force Microscopy to investigate nuclear mechanical changes, arising from externally induced DNA damage. We found that nuclear stiffness is significantly reduced after cisplatin treatment, as a consequence of DNA damage signalling. This softening was linked to global chromatin decondensation, which improves molecular diffusion within the organelle. We propose that this can increase recruitment for repair factors. Interestingly, we also found that reduction of nuclear tension, through cytoskeletal relaxation, has a protective role to the cell and reduces accumulation of DNA damage. Overall, these changes protect against further genomic instability and promote DNA repair. We propose that these processes may underpin the development of drug resistance.
    DOI:  https://doi.org/10.1093/nar/gkaa1202
  86. Int J Mol Sci. 2020 Dec 15. pii: E9560. [Epub ahead of print]21(24):
    Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses.
    Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano.
      The main hallmarks of cancer diseases are the evasion of programmed cell death, uncontrolled cell division, and the ability to invade adjacent tissues. The explosion of omics technologies offers challenging opportunities to identify molecular agents and processes that may play relevant roles in cancer. They can support comparative investigations, in one or multiple experiments, exploiting evidence from one or multiple species. Here, we analyzed gene expression data from induction of programmed cell death and stress response in Homo sapiens and compared the results with Saccharomyces cerevisiae gene expression during the response to cell death. The aim was to identify conserved candidate genes associated with Homo sapiens cell death, favored by crosslinks based on orthology relationships between the two species. We identified differentially-expressed genes, pathways that are significantly dysregulated across treatments, and characterized genes among those involved in induced cell death. We investigated on co-expression patterns and identified novel genes that were not expected to be associated with death pathways, that have a conserved pattern of expression between the two species. Finally, we analyzed the resulting list by HumanNet and identified new genes predicted to be involved in cancer. The data integration and the comparative approach between distantly-related reference species that were here exploited pave the way to novel discoveries in cancer therapy and also contribute to detect conserved genes potentially involved in programmed cell death.
    Keywords:  autophagy; bioinformatics; co-expression analysis; conserved expression patterns; programmed cell death
    DOI:  https://doi.org/10.3390/ijms21249560
  87. Stem Cells. 2020 Dec 16.
    CCAAT/Enhancer Binding Protein β Promotes Muscle Stem Cell Quiescence through Regulation of Quiescence-Associated Genes.
    Neena Lala-Tabbert, Hamood AlSudais, François Marchildon, Dechen Fu, Nadine Wiper-Bergeron.
      Regeneration of skeletal muscle depends on resident muscle stem cells called satellite cells that in healthy, uninjured muscle remain quiescent (non-cycling). After activation and expansion of satellite cells post-injury, satellite cell numbers return to uninjured levels and return to mitotic quiescence. Here, we show that the transcription factor CCAAT/Enhancer Binding Protein beta (C/EBPβ) is required to maintain quiescence of satellite cells in uninjured muscle. We show that C/EBPβ is expressed in quiescent satellite cells in vivo and upregulated in non-cycling myoblasts in vitro. Loss of C/EBPβ in satellite cells promotes their premature exit from quiescence resulting in spontaneous activation and differentiation of the stem cell pool. Forced expression of C/EBPβ in myoblasts inhibits proliferation by upregulation of 28 quiescence-associated genes. Further, we find that Caveolin-1 is a direct transcriptional target of C/EBPβ and is required for cell cycle exit in muscle satellite cells expressing C/EBPβ. The induction of mitotic quiescence is considered necessary for the long-term maintenance of adult stem cell populations with dysregulation driving increased differentiation of progenitors and depletion of the stem cell pool. Our findings place C/EBPβ as an important transcriptional regulator of muscle satellite cell quiescence. © AlphaMed Press 2020 SIGNIFICANCE STATEMENT: Little is known about the mechanisms regulating satellite cell quiescence. Here, Lala-Tabbert et al use an unbiased approach to show that C/EBPβ-overexpression induces expression of quiescence-associated genes in myoblasts. The authors identify Caveolin-1 as a target of C/EBPβ required for cell growth arrest in vitro. Furthermore, in vivo, C/EBPβ is required to maintain muscle satellite cell quiescence in steady state adult muscle.
    Keywords:  CCAAT-Enhancer-Binding Protein-beta; cell differentiation; cell proliferation; muscle satellite cells; myoblasts, muscle; quiescence; regeneration; skeletal
    DOI:  https://doi.org/10.1002/stem.3319
  88. Signal Transduct Target Ther. 2019 Dec 17. 4(1): 62
    Targeting epigenetic regulators for cancer therapy: mechanisms and advances in clinical trials.
    Yuan Cheng, Cai He, Manni Wang, Xuelei Ma, Fei Mo, Shengyong Yang, Junhong Han, Xiawei Wei.
      Epigenetic alternations concern heritable yet reversible changes in histone or DNA modifications that regulate gene activity beyond the underlying sequence. Epigenetic dysregulation is often linked to human disease, notably cancer. With the development of various drugs targeting epigenetic regulators, epigenetic-targeted therapy has been applied in the treatment of hematological malignancies and has exhibited viable therapeutic potential for solid tumors in preclinical and clinical trials. In this review, we summarize the aberrant functions of enzymes in DNA methylation, histone acetylation and histone methylation during tumor progression and highlight the development of inhibitors of or drugs targeted at epigenetic enzymes.
    DOI:  https://doi.org/10.1038/s41392-019-0095-0
  89. Cancer Cell. 2020 Nov 28. pii: S1535-6108(20)30598-5. [Epub ahead of print]
    DNA Sensing in Mismatch Repair-Deficient Tumor Cells Is Essential for Anti-tumor Immunity.
    Changzheng Lu, Junhong Guan, Steve Lu, Qihuang Jin, Benoit Rousseau, Tianshi Lu, Dennis Stephens, Hongyi Zhang, Jiankun Zhu, Mingming Yang, Zhenhua Ren, Yong Liang, Zhida Liu, Chuanhui Han, Longchao Liu, Xuezhi Cao, Anli Zhang, Jian Qiao, Kimberly Batten, Mingyi Chen, Diego H Castrillon, Tao Wang, Bo Li, Luis A Diaz, Guo-Min Li, Yang-Xin Fu.
      Increased neoantigens in hypermutated cancers with DNA mismatch repair deficiency (dMMR) are proposed as the major contributor to the high objective response rate in anti-PD-1 therapy. However, the mechanism of drug resistance is not fully understood. Using tumor models defective in the MMR gene Mlh1 (dMLH1), we show that dMLH1 tumor cells accumulate cytosolic DNA and produce IFN-β in a cGAS-STING-dependent manner, which renders dMLH1 tumors slowly progressive and highly sensitive to checkpoint blockade. In neoantigen-fixed models, dMLH1 tumors potently induce T cell priming and lose resistance to checkpoint therapy independent of tumor mutational burden. Accordingly, loss of STING or cGAS in tumor cells decreases tumor infiltration of T cells and endows resistance to checkpoint blockade. Clinically, downregulation of cGAS/STING in human dMMR cancers correlates with poor prognosis. We conclude that DNA sensing within tumor cells is essential for dMMR-triggered anti-tumor immunity. This study provides new mechanisms and biomarkers for anti-dMMR-cancer immunotherapy.
    Keywords:  DNA sensing; MLH1; MSI; STING; T cell infiltration; cGAS; cancer; checkpoint blockade; cytosolic DNA; mismatch repair
    DOI:  https://doi.org/10.1016/j.ccell.2020.11.006
  90. Int J Mol Sci. 2020 Dec 16. pii: E9595. [Epub ahead of print]21(24):
    BET-Inhibitor I-BET762 and PARP-Inhibitor Talazoparib Synergy in Small Cell Lung Cancer Cells.
    Francesco Paolo Fiorentino, Irene Marchesi, Christoph Schröder, Ronny Schmidt, Jun Yokota, Luigi Bagella.
      Small cell lung cancer (SCLC) is an aggressive type of lung cancer with high mortality that is caused by frequent relapses and acquired resistance. Despite that several target-based approaches with potential therapeutic impact on SCLC have been identified, numerous targeted drugs have not been successful in providing improvements in cancer patients when used as single agents. A combination of targeted therapies could be a strategy to induce maximum lethal effects on cancer cells. As a starting point in the development of new drug combination strategies for the treatment of SCLC, we performed a mid-throughput screening assay by treating a panel of SCLC cell lines with BETi or AKi in combination with PARPi or EZH2i. We observed drug synergy between I-BET762 and Talazoparib, BETi and PARPi, respectively, in SCLC cells. Combinatorial efficacy was observed in MYCs-amplified and MYCs-wt SCLC cells over SCLC cells with impaired MYC signaling pathway or non-tumor cells. We indicate that drug synergy between I-BET762 and Talazoparib is associated with the attenuation HR-DSBR process and the downregulation of various players of DNA damage response by BET inhibition, such as CHEK2, PTEN, NBN, and FANCC. Our results provide a rationale for the development of new combinatorial strategies for the treatment of SCLC.
    Keywords:  BET; BMN673; GSK-525762A; PARP; SCLC
    DOI:  https://doi.org/10.3390/ijms21249595
  91. Biol Open. 2020 Dec 16. pii: bio056747. [Epub ahead of print]9(12):
    CD47 differentially regulates white and brown fat function.
    Heather Norman-Burgdolf, Dong Li, Patrick Sullivan, Shuxia Wang.
      Mechanisms that enhance energy expenditure are attractive therapeutic targets for obesity. Previously we have demonstrated that mice lacking cd47 are leaner, exhibit increased energy expenditure, and are protected against diet-induced obesity. In this study, we further defined the physiological role of cd47 deficiency in regulating mitochondrial function and energy expenditure in both white and brown adipose tissue. We observed that cd47 deficient mice (under normal chow diet) had comparable amount of white fat mass but reduced white adipocyte size as compared to wild-type mice. Subsequent ex vivo and in vitro studies suggest enhanced lipolysis, and not impaired lipogenesis or energy utilization, contributes to this phenotype. In contrast to white adipose tissue, there were no obvious morphological differences in brown adipose tissue between wild-type and knockout mice. However, mitochondria isolated from brown fat of cd47 deficient mice had significantly higher rates of free fatty acid-mediated uncoupling. This suggests that enhanced fuel availability via white adipose tissue lipolysis may perpetuate elevated brown adipose tissue energy expenditure and contributes to the lean phenotype observed in cd47 deficient mice.
    Keywords:  Brown fat; CD47; Lipolysis; Mitochondria; White fat
    DOI:  https://doi.org/10.1242/bio.056747
  92. Methods Mol Biol. 2021 ;2226 191-199
    Tumor Growth Analysis of Ewing Sarcoma Cell Lines Using Subcutaneous Xenografts in Mice.
    Florencia Cidre-Aranaz, Shunya Ohmura.
      Subcutaneous murine xenograft models are one of the most commonly used in vivo experimental methods in the cancer research field. Due to the lack of appropriate animal models for Ewing sarcoma, subcutaneous murine xenograft models currently offer the simplest way to investigate antineoplastic effects of therapeutics or biological functions of target genes in vivo. In order to properly carry out tumor growth analysis via subcutaneous xenografts of Ewing sarcoma cells many factors should be taken into account beforehand at the planning phase of experiments. Therefore, in this chapter we describe in detail a widely used procedure for subcutaneous injection in mice, focusing on the specific characteristics of Ewing sarcoma cell lines.
    Keywords:  Ewing sarcoma; Immunocompromised mice; Subcutaneous injection; Xenografts
    DOI:  https://doi.org/10.1007/978-1-0716-1020-6_15
  93. Sci Rep. 2020 Dec 14. 10(1): 21915
    Different expression of lipid metabolism-related genes in Shandong black cattle and Luxi cattle based on transcriptome analysis.
    Ruili Liu, Xianxun Liu, Xuejin Bai, Chaozhu Xiao, Yajuan Dong.
      To provide new ideas for improving meat quality and generating new breeds of cattle, the important candidate genes affecting fat deposition in two kinds of cattle were identified. Eighteen months Shandong black cattle (n = 3) and Luxi cattle (n = 3) were randomly assigned into two environmental. The longissimus dorsi muscles of Shandong Black Cattle and Luxi Cattle were collected and analyzed by fatty acid determination, high-throughput sequencing transcriptomics, qRT-PCR expression profile and western blot. The ratio of unsaturated fatty acids to saturated fatty acids was 1.37:1 and 1.24:1 in the muscle tissues of Shandong black cattle and Luxi cattle, respectively. The results of RNA-Seq analysis revealed 1320 DEGs between the longissimus dorsi of Shandong black cattle and Luxi cattle. A total of 867 genes were upregulated, and the other 453 genes were downregulated. With GO enrichment analysis, it was found that the identified DEGs were significantly enriched in regulation of the Wnt signaling pathway, negative regulation of the Wnt signaling pathway, cAMP metabolic process, fat cell differentiation and among other functions. We found that regulation of lipolysis in adipocytes was the significant enrichment pathway of upregulated genes and downregulated genes, PPAR signaling pathway and AMPK signaling pathway are highly representative pathways of lipid metabolism in Shandong black cattle. Network analysis showed that PPARGC1A, ADCY4, ANKRD6, COL1A1, FABP4, ADIPOQ, PLIN1, PLIN2, and LIPE genes were correlated with key loci genes in multiple metabolic pathways. Meanwhile we found that FABP4 and ADIPOQ had 7 common regulatory factors in different genes, which were PLIN1, PLIN2, PPARGC1A, RXRA, PCK1, LEPR, LEP. These genes were involved in regulation of lipolysis in adipocytes, adipocytokine signaling pathway, PPAR signaling pathway. FABP4 and ADIPOQ were selected as important candidate marker genes for fat deposition based on the results.
    DOI:  https://doi.org/10.1038/s41598-020-79086-4
  94. Front Oncol. 2020 ;10 608975
    The Role of Non-Coding RNAs in Controlling Cell Cycle Related Proteins in Cancer Cells.
    Soudeh Ghafouri-Fard, Hamed Shoorei, Farhad Tondro Anamag, Mohammad Taheri.
      Cell cycle is regulated by a number of proteins namely cyclin-dependent kinases (CDKs) and their associated cyclins which bind with and activate CDKs in a phase specific manner. Additionally, several transcription factors (TFs) such as E2F and p53 and numerous signaling pathways regulate cell cycle progression. Recent studies have accentuated the role of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in the regulation of cell cycle. Both lncRNAs and miRNAs interact with TFs participating in the regulation of cell cycle transition. Dysregulation of cell cycle regulatory miRNAs and lncRNAs results in human disorders particularly cancers. Understanding the role of lncRNAs, miRNAs, and TFs in the regulation of cell cycle would pave the way for design of anticancer therapies which intervene with the cell cycle progression. In the current review, we describe the role of lncRNAs and miRNAs in the regulation of cell cycle and their association with human malignancies.
    Keywords:  cell cycle; expression; long non coding RNA; microRNA; polymorphism
    DOI:  https://doi.org/10.3389/fonc.2020.608975
  95. Front Bioeng Biotechnol. 2020 ;8 607126
    A Machine Learning Approach for Tracing Tumor Original Sites With Gene Expression Profiles.
    Xin Liang, Wen Zhu, Bo Liao, Bo Wang, Jialiang Yang, Xiaofei Mo, Ruixi Li.
      Some carcinomas show that one or more metastatic sites appear with unknown origins. The identification of primary or metastatic tumor tissues is crucial for physicians to develop precise treatment plans for patients. With unknown primary origin sites, it is challenging to design specific plans for patients. Usually, those patients receive broad-spectrum chemotherapy, while still having poor prognosis though. Machine learning has been widely used and already achieved significant advantages in clinical practices. In this study, we classify and predict a large number of tumor samples with uncertain origins by applying the random forest and Naive Bayesian algorithms. We use the precision, recall, and other measurements to evaluate the performance of our approach. The results have showed that the prediction accuracy of this method was 90.4 for 7,713 samples. The accuracy was 80% for 20 metastatic tumors samples. In addition, the 10-fold cross-validation is used to evaluate the accuracy of classification, which reaches 91%.
    Keywords:  machine learning; naive Bayes; random forest; the ability of tissue tracing; uncertain origins
    DOI:  https://doi.org/10.3389/fbioe.2020.607126
  96. J Virol. 2020 Dec 16. pii: JVI.01784-20. [Epub ahead of print]
    Induction of HOX genes by HCV infection via impairment of histone H2A monoubiquitination.
    Hirotake Kasai, Kazuki Mochizuki, Tomohisa Tanaka, Atsuya Yamashita, Yoshiharu Matsuura, Kohji Moriishi.
      Hepatitis C virus (HCV) infection causes liver pathologies, including hepatocellular carcinoma (HCC). Homeobox (HOX) gene products regulate embryonic development and are associated with tumorigenesis, although the regulation of HOX genes by HCV infection has not been clarified in detail. We examined the effect of HCV infection on HOX gene expression. In this study, HCV infection induced more than half of the HOX genes and reduced the level of histone H2A monoubiquitination on lysine (K) 119 (H2Aub), which represses HOX gene promoter activity. HCV infection also promoted proteasome-dependent degradation of RNF2, which is an E3 ligase mediating H2A monoubiquitination as a component of polycomb repressive complex 1. Since full-genomic replicon cells but not subgenomic replicon cells exhibited reduced RNF2 and H2Aub levels and induction of HOX genes, we focused on the core protein. Expression of the core protein reduced the amounts of RNF2 and H2Aub and induced HOX genes. Treatment with LY-411575, which can reduce HCV core protein expression via SPP inhibition without affecting other viral proteins, dose-dependently restored the amounts of RNF2 and H2Aub in HCV-infected cells and impaired the induction of HOX genes and production of viral particles but not viral replication. The chromatin immunoprecipitation assay results also indicated infection- and proteasome-dependent reductions in H2Aub located in HOX gene promoters. These results suggest that HCV infection or core protein induces HOX genes by impairing histone H2A monoubiquitination via a reduction in the RNF2 level.Importance Recently sustained virologic response can be achieved by direct acting antiviral therapy in most of hepatitis C patients. Unfortunately, DAA therapy does not completely eliminate a risk of HCC. Several epigenetic factors, including histone modifications, are well known to contribute to HCV-associated HCC. However, the regulation of histone modifications by HCV infection has not been clarified in detail. In this study, our data suggest that HCV infection or HCV core protein expression impairs monoubiquitination of histone H2A K119 in HOX gene promoter via destabilization of RNF2 and then induces HOX genes. Several lines of evidence suggest that the expression of several HOX genes is dysregulated in certain types of tumors. These findings reveal a novel mechanism of HCV-related histone modification and may provide information about new targets for diagnosis and prevention of HCC occurrence.
    DOI:  https://doi.org/10.1128/JVI.01784-20
  97. Curr Pharm Biotechnol. 2020 Dec 10.
    Cell free DNA as an evolving liquid biopsy biomarker for initial diagnosis and therapeutic nursing in Cancer- An evolving aspect in Medical Biotechnology.
    Suman Kumar Ray, Sukhes Mukherjee.
      Cell-free DNA (cfDNA) is present in numerous body fluids in addition to initiates generally from blood cells. It is undoubtedly the utmost promising tool among all components of liquid biopsy. Liquid biopsy is a specialized method investigating the nonsolid biological tissue by revealing of circulating cells, cell free DNA etc. that enter body fluids. Since, cancer cells disengage from compact tumors circulate in peripheral blood, evaluating blood of cancer patients holds the opportunities for capture and molecular level analysis of various tumor-derived constituents. Cell free DNA samples can deliver a significant perceptions into oncology, for instance tumor heterogeneity, instantaneous tumor development, response to therapy and treatment, comprising immunotherapy and mechanisms of cancer metastasis. Malignant growth at any phase can outhouse tumor cells in addition to fragments of neoplasticity causing DNA into circulatory system giving noble sign of mutation in the tumor at sampling time. Liquid biopsy distinguishes diverse blood based evolving biomarkers comprising circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) or cfDNA, circulating RNA (cfRNA) and exosomes. Cell free DNA are little DNA fragments found circulating in plasma or serum, just as other fluids present in our body. Cell free DNA involves primarily double stranded nuclear DNA and mitochondrial DNA, present both on a surface level and in the lumen of vesicles. The probable origins of the tumor-inferred portion of cfDNA are apoptosis or tumor necrosis, lysis of CTCs or release of DNA from the tumor cells into circulation. The evolution of innovations, refinement and improvement in therapeutics for determination of cfDNA fragment size and its distribution provide significant information related with pathological conditions of the cell, thus emerging as promising indicator for clinical output in medical biotechnology.
    Keywords:  Cell free DNA; biomarkers; cancer; circulating tumor cells; liquid biopsy; medical biotechnology.
    DOI:  https://doi.org/10.2174/1389201021666201211102710
  98. Psychoneuroendocrinology. 2020 Dec 01. pii: S0306-4530(20)30506-0. [Epub ahead of print]124 105083
    Differential modulation of GR signaling and HDACs in the development of resilient/vulnerable phenotype and antidepressant-like response of vorinostat.
    Athira K V, Abhipradnya Bipin Wahul, Kalyani Soren, Tapatee Das, Sandeep Dey, Pavan Kumar Samudrala, Arvind Kumar, Mangala Lahkar, Sumana Chakravarty.
      The present study explored the antidepressant potential of vorinostat (VOR) against chronic social defeat stress (CSDS) in mice. Since this model has the remarkable capacity to delineate the resilient and the defeated mice, we also looked for their molecular deviations. Defeated mice showed classical phenotypic alterations such as anhedonia, social avoidance, anxiety and despair. Whereas, resilient mice were immune to the development of those. Both defeated and resilient mice demonstrated marked CORT elevation in blood. Development of resilience vs. defeat to CSDS was found to be associated with the differential nuclear levels of GR, HDAC3 and HDAC6 in the hippocampus. Activation of a stress responsive adaptive mechanism involving these mediators at the nuclear level might be offering resilience while maladaptive mechanisms leading to defeat. Interestingly, an elevated hippocampal HDAC6 level in defeated mice was also observed, which was restored by VOR treatment. Further studies will be necessary to delineate the HDAC6 associated antidepressant mechanisms. As HDAC3 and HDAC6 are crucial mediators of GR signaling, further molecular studies may aid in understanding the basis of development of resilience to target MDD with new prospective.
    Keywords:  Chronic social defeat stress; Depression; Epigenetics; Glucocorticoid receptor; Histone deacetylases; Resilience
    DOI:  https://doi.org/10.1016/j.psyneuen.2020.105083
  99. Br J Cancer. 2020 Dec 18.
    SLFN11 informs on standard of care and novel treatments in a wide range of cancer models.
    Claudia Winkler, Joshua Armenia, Gemma N Jones, Luis Tobalina, Matthew J Sale, Tudor Petreus, Tarrion Baird, Violeta Serra, Anderson T Wang, Alan Lau, Mathew J Garnett, Patricia Jaaks, Elizabeth A Coker, Andrew J Pierce, Mark J O'Connor, Elisabetta Leo.
       BACKGROUND: Schlafen 11 (SLFN11) has been linked with response to DNA-damaging agents (DDA) and PARP inhibitors. An in-depth understanding of several aspects of its role as a biomarker in cancer is missing, as is a comprehensive analysis of the clinical significance of SLFN11 as a predictive biomarker to DDA and/or DNA damage-response inhibitor (DDRi) therapies.
    METHODS: We used a multidisciplinary effort combining specific immunohistochemistry, pharmacology tests, anticancer combination therapies and mechanistic studies to assess SLFN11 as a potential biomarker for stratification of patients treated with several DDA and/or DDRi in the preclinical and clinical setting.
    RESULTS: SLFN11 protein associated with both preclinical and patient treatment response to DDA, but not to non-DDA or DDRi therapies, such as WEE1 inhibitor or olaparib in breast cancer. SLFN11-low/absent cancers were identified across different tumour types tested. Combinations of DDA with DDRi targeting the replication-stress response (ATR, CHK1 and WEE1) could re-sensitise SLFN11-absent/low cancer models to the DDA treatment and were effective in upper gastrointestinal and genitourinary malignancies.
    CONCLUSION: SLFN11 informs on the standard of care chemotherapy based on DDA and the effect of selected combinations with ATR, WEE1 or CHK1 inhibitor in a wide range of cancer types and models.
    DOI:  https://doi.org/10.1038/s41416-020-01199-4
  100. Trends Biochem Sci. 2020 Dec 08. pii: S0968-0004(20)30276-0. [Epub ahead of print]
    Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications.
    Robert M Vaughan, Ariana Kupai, Scott B Rothbart.
      Chromatin functions are influenced by the addition, removal, and recognition of histone post-translational modifications (PTMs). Ubiquitin and ubiquitin-like (UBL) PTMs on histone proteins can function as signaling molecules by mediating protein-protein interactions. Fueled by the identification of novel ubiquitin and UBL sites and the characterization of the writers, erasers, and readers, the breadth of chromatin functions associated with ubiquitin signaling is emerging. Here, we highlight recently appreciated roles for histone ubiquitination in DNA methylation control, PTM crosstalk, nucleosome structure, and phase separation. We also discuss the expanding diversity and functions associated with histone UBL modifications. We conclude with a look toward the future and pose key questions that will drive continued discovery at the interface of epigenetics and ubiquitin signaling.
    Keywords:  DNA methylation; epigenetics; histones; phase separation; post-translational modifications; ubiquitin-like modifications; ubiquitination
    DOI:  https://doi.org/10.1016/j.tibs.2020.11.005
  101. Acta Biochim Pol. 2020 Dec 17.
    Over expression of PTEN induces apoptosis and prevents cell proliferation in breast cancer cells.
    Jinfeng Wu, Hong Gao, Wanyu Ge, Jie He.
      The phosphatase and tensin homolog (PTEN) is a tumor suppressor lipid phosphatase frequently mutated or deleted in breast cancer cells. Loss of PTEN is associated with aberrant activation of P13K/AKT signaling pathways, which are responsible for uncontrolled cell cycle, migration and prolonged survival. Therefore, stability and functional PTEN is essential for prevention of cancer growth and migration. In the present study, we have determined the effect of PTEN over expression in apoptosis induction and cell proliferation in breast cancer cells. We showed that PTEN over expression significantly declined the cell proliferation rate during logarithmic growth phase. Furthermore, the PTEN over expression leads to the activation of mitochondrial based intrinsic apoptosis pathways, which is confirmed by the activation and over expression of caspases 9 and caspases 3. In addition, the number of apoptotic cells are significantly more in PTEN over expressed cells, where they showed more apoptotic bodies in AO-EtBr and Hoechst 33344 staining. Finally, PTEN over expressed cells showed decreased chemo resistance as chemotherapeutic drugs kill them efficiently. Therefore, our findings suggest that tumor suppressive effect of PTEN is crucial for cancer prevention and thus PTEN might be a potential target for anti-cancer drugs.
    DOI:  https://doi.org/10.18388/abp.2020_5371
  102. Clin Cancer Res. 2020 Dec 11. pii: clincanres.3044.2020. [Epub ahead of print]
    Targeted therapy of TERT-rearranged neuroblastoma with BET bromodomain inhibitor and proteasome inhibitor combination therapy.
    Jingwei Chen, Christopher Nelson, Matthew Kwok Kei Wong, Andrew El Tee, Pei Y Liu, Ting La, Jamie I Fletcher, Alvin Kamili, Chelsea Mayoh, Christoph Bartenhagen, Toby N Trahair, Ning Xu, Nisitha Jayatilleke, Marie Wong, Hui Peng, Bernard Atmadibrata, Belamy B Cheung, Qing Lan, Tracy M Bryan, Pieter Mestdagh, Jo Vandesompele, Valérie Combaret, Valentina Boeva, Jenny Y Wang, Isabelle Janoueix-Lerosey, Mark J Cowley, Karen L MacKenzie, Alla Dolnikov, Jinyan Li, Patsie Polly, Glenn Marshall, Roger R Reddel, Murray D Norris, Michelle Haber, Matthias Fischer, Xu Dong Zhang, Hilda A Pickett, Tao Liu.
       PURPOSE: TERT gene rearrangement with transcriptional super-enhancers leads to TERT over-expression and neuroblastoma. No targeted therapy is available for clinical trials in TERT-rearranged neuroblastoma patients.
    EXPERIMENTAL DESIGN: Anticancer agents exerting the best synergistic anticancer effects with BET bromodomain inhibitors were identified by screening a US Food and Drug Administration-approved oncology drug library. The synergistic effects of the BET bromodomain inhibitor OTX015 and the proteasome inhibitor carfilzomib were examined by immunoblot and flow cytometry analysis. The anticancer efficacy of OTX015 and carfilzomib combination therapy was investigated in mice xenografted with TERT-rearranged neuroblastoma cell lines or patient-derived xenograft (PDX) tumor cells, and the role of TERT reduction in the anticancer efficacy was examined through rescue experiments in mice.
    RESULTS: The BET bromodomain protein BRD4 promoted TERT-rearranged neuroblastoma cell proliferation through up-regulating TERT expression. Screening of an approved oncology drug library identified the proteasome inhibitor carfilzomib as the agent exerting the best synergistic anticancer effects with BET bromodomain inhibitors including OTX015. OTX015 and carfilzomib synergistically reduced TERT protein expression, induced endoplasmic reticulum stress, and induced TERT-rearranged neuroblastoma cell apoptosis which was blocked by TERT over-expression and endoplasmic reticulum stress antagonists. In mice xenografted with TERT-rearranged neuroblastoma cell lines or PDX tumor cells, OTX015 and carfilzomib synergistically blocked TERT expression, induced tumor cell apoptosis, suppressed tumor progression and improved mouse survival, which was largely reversed by forced TERT over-expression.
    CONCLUSIONS: OTX015 and carfilzomib combination therapy is likely to be translated into the first clinical trial of a targeted therapy in TERT-rearranged neuroblastoma patients.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-20-3044
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