bims-ectoca Biomed News
on Epigenetic control of tolerance in cancer
Issue of 2021‒10‒03
thirty-two papers selected by
Ankita Daiya
BITS Pilani
  1. Histone Deacetylases in the Control of Epidermal Homeostasis: From Chromatin Biology toward Therapy.
  2. Vorinostat (SAHA) and Breast Cancer: An Overview.
  3. Single-Cell Omics in Dissecting Immune Microenvironment of Malignant Gliomas-Challenges and Perspectives.
  4. Histone Deacetylases and Immediate Early Genes: Key Players in Psychostimulant-Induced Neuronal Plasticity.
  5. Targeting Histone Modifications in Breast Cancer: A Precise Weapon on the Way.
  6. Tagmentation-based single-cell genomics.
  7. Single-cell trajectories of melanoma cell resistance to targeted treatment.
  8. Identification of Drug Resistance Genes Using a Pooled Lentiviral CRISPR/Cas9 Screening Approach.
  9. Cancer cell states and emergent properties of the dynamic tumor system.
  10. Combining histone deacetylase inhibitors (HDACis) with other therapies for cancer therapy.
  11. Niclosamide and Pyrvinium Are Both Potential Therapeutics for Osteosarcoma, Inhibiting Wnt-Axin2-Snail Cascade.
  12. Bromodomains: A novel target for the anticancer therapy.
  13. Histone H1 mutations in lymphoma: a link(er) between chromatin organization, developmental reprogramming, and cancer.
  14. Cell stiffness predicts cancer cell sensitivity to ultrasound as a selective superficial cancer therapy.
  15. Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation.
  16. Detecting Persister Awakening Determinants.
  17. Circular RNA hsa_circ_0000073 Enhances Osteosarcoma Cells Malignant Behavior by Sponging miR-1252-5p and Modulating CCNE2 and MDM2.
  18. NSD1: A Lysine Methyltransferase between Developmental Disorders and Cancer.
  19. Mitochondrial DNA and MitomiR Variations in Pancreatic Cancer: Potential Diagnostic and Prognostic Biomarkers.
  20. A fatal affair: Circulating tumor cell relationships that shape metastasis.
  21. Current Applications and Discoveries Related to the Membrane Components of Circulating Tumor Cells and Extracellular Vesicles.
  22. Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states.
  23. Overexpression of the Ubiquitin Specific Proteases USP43, USP41, USP27x and USP6 in Osteosarcoma Cell Lines: Inhibition of Osteosarcoma Tumor Growth and Lung Metastasis Development by the USP Antagonist PR619.
  24. The Nucleus/Mitochondria-Shuttling LncRNAs Function as New Epigenetic Regulators of Mitophagy in Cancer.
  25. Ferroptosis and Cancer: Complex Relationship and Potential Application of Exosomes.
  26. From Hit Seeking to Magic Bullets: The Successful Union of Epigenetic and Fragment Based Drug Discovery (EPIDD + FBDD).
  27. Comprehensive characterization genetic regulation and chromatin landscape of enhancer-associated long non-coding RNAs and their implication in human cancer.
  28. Ultrasound and Transcriptomics Identify a Differential Impact of Cisplatin and Histone Deacetylation on Tumor Structure and Microenvironment in a Patient-Derived In Vivo Model of Gastric Cancer.
  29. Improved HDAC Inhibition, Stronger Cytotoxic Effect and Higher Selectivity against Leukemias and Lymphomas of Novel, Tricyclic Vorinostat Analogues.
  30. From the Evasion of Degradation to Ubiquitin-Dependent Protein Stabilization.
  31. Combining repurposed drugs to treat colorectal cancer.
  32. Chromatin accessibility associates with protein-RNA correlation in human cancer.
  1. J Invest Dermatol. 2021 Sep 23. pii: S0022-202X(21)01445-7. [Epub ahead of print]
    Histone Deacetylases in the Control of Epidermal Homeostasis: From Chromatin Biology toward Therapy.
    Vladimir A Botchkarev, Andrey A Sharov.
      Histone deacetylases (HDACs) induce gene repression and modify the activity of nonhistone proteins. In a new article in the Journal of Investigative Dermatology, Zhu et al. (2021) demonstrate essential roles for HDAC1/2 in maintaining keratinocyte proliferation and survival in adult epidermis and basal cell carcinoma, thus providing a rationale for using HDAC inhibitors for the treatment of hyperproliferative and neoplastic skin disorders.
    DOI:  https://doi.org/10.1016/j.jid.2021.06.021
  2. Cancers (Basel). 2021 Sep 19. pii: 4700. [Epub ahead of print]13(18):
    Vorinostat (SAHA) and Breast Cancer: An Overview.
    Anna Wawruszak, Lidia Borkiewicz, Estera Okon, Wirginia Kukula-Koch, Syeda Afshan, Marta Halasa.
      Vorinostat (SAHA), an inhibitor of class I and II of histone deacetylases, is the first histone deacetylase inhibitor (HDI) approved for the treatment of cutaneous T-cell lymphoma in 2006. HDIs are promising anticancer agents that inhibit the proliferation of many types of cancer cells including breast carcinoma (BC). BC is a heterogeneous disease with variable biological behavior, morphological features, and response to therapy. Although significant progress in the treatment of BC has been made, high toxicity to normal cells, serious side effects, and the occurrence of multi-drug resistance limit the effective therapy of BC patients. Therefore, new active agents which improve the effectiveness of currently used regimens are highly needed. This manuscript analyzes preclinical and clinical trials data of SAHA, applied individually or in combination with other anticancer agents, considering different histological subtypes of BC.
    Keywords:  breast cancer; epigenetics; histone acetylation; histone deacetylase inhibitor (HDI); histone deacetylases (HDACs); suberoylanilide hydroxamic acid; targeted therapy; vorinostat (SAHA)
    DOI:  https://doi.org/10.3390/cancers13184700
  3. Cells. 2021 Aug 31. pii: 2264. [Epub ahead of print]10(9):
    Single-Cell Omics in Dissecting Immune Microenvironment of Malignant Gliomas-Challenges and Perspectives.
    Bozena Kaminska, Natalia Ochocka, Pawel Segit.
      Single-cell technologies allow precise identification of tumor composition at the single-cell level, providing high-resolution insights into the intratumoral heterogeneity and transcriptional activity of cells in the tumor microenvironment (TME) that previous approaches failed to capture. Malignant gliomas, the most common primary brain tumors in adults, are genetically heterogeneous and their TME consists of various stromal and immune cells playing an important role in tumor progression and responses to therapies. Previous gene expression or immunocytochemical studies of immune cells infiltrating TME of malignant gliomas failed to dissect their functional phenotypes. Single-cell RNA sequencing (scRNA-seq) and cytometry by time-of-flight (CyTOF) are powerful techniques allowing quantification of whole transcriptomes or >30 protein targets in individual cells. Both methods provide unprecedented resolution of TME. We summarize the findings from these studies and the current state of knowledge of a functional diversity of immune infiltrates in malignant gliomas with different genetic alterations. A precise definition of functional phenotypes of myeloid and lymphoid cells might be essential for designing effective immunotherapies. Single-cell omics studies have identified crucial cell subpopulations and signaling pathways that promote tumor progression, influence patient survival or make tumors vulnerable to immunotherapy. We anticipate that the widespread usage of single-cell omics would allow rational design of oncoimmunotherapeutics.
    Keywords:  glioma associated microglia/macrophages; glioma heterogeneity; immunosuppression; immunotherapy; malignant gliomas; mass cytometry; single-cell RNA sequencing; tumor infiltrating lymphocytes
    DOI:  https://doi.org/10.3390/cells10092264
  4. Neurotox Res. 2021 Sep 28.
    Histone Deacetylases and Immediate Early Genes: Key Players in Psychostimulant-Induced Neuronal Plasticity.
    Veronica Bisagno, Jean Lud Cadet.
      IEGs play a critical functional role of in molecular, cellular, and behavioral alterations induced by psychostimulants. IEGs appear to have specific chromatin structures that may contribute to the rapid activation of their transcription. HDAC enzymes regulate reversible acetylation of lysine residues of histones and non-histone proteins. Dysregulation of HDACs has been proposed to modulate the establishment and maintenance of aberrant transcriptional programs and behaviors associated with cognitive dysfunctions and drug addiction. In this mini-review we focus our attention on recent discoveries concerning networks of protein-protein interactions for the two classes of HDAC protein family members that are highly expressed in neurons, class I and IIa HDACs. Because dynamic histone acetylation appears to be critical to IEG expression in the brain, we discuss the role of these epigenetic regulators on IEG expression induced by cocaine and methamphetamine intake.
    Keywords:  Addiction; Epigenetic; Histone deacetylases; Immediate early genes; Psychostimulant
    DOI:  https://doi.org/10.1007/s12640-021-00420-3
  5. Front Cell Dev Biol. 2021 ;9 736935
    Targeting Histone Modifications in Breast Cancer: A Precise Weapon on the Way.
    Wei Li, Hao Wu, Shiyao Sui, Qin Wang, Shouping Xu, Da Pang.
      Histone modifications (HMs) contribute to maintaining genomic stability, transcription, DNA repair, and modulating chromatin in cancer cells. Furthermore, HMs are dynamic and reversible processes that involve interactions between numerous enzymes and molecular components. Aberrant HMs are strongly associated with tumorigenesis and progression of breast cancer (BC), although the specific mechanisms are not completely understood. Moreover, there is no comprehensive overview of abnormal HMs in BC, and BC therapies that target HMs are still in their infancy. Therefore, this review summarizes the existing evidence regarding HMs that are involved in BC and the potential mechanisms that are related to aberrant HMs. Moreover, this review examines the currently available agents and approved drugs that have been tested in pre-clinical and clinical studies to evaluate their effects on HMs. Finally, this review covers the barriers to the clinical application of therapies that target HMs, and possible strategies that could help overcome these barriers and accelerate the use of these therapies to cure patients.
    Keywords:  acetylation; breast cancer; epi-drugs; histone modification; methylation
    DOI:  https://doi.org/10.3389/fcell.2021.736935
  6. Genome Res. 2021 Oct;31(10): 1693-1705
    Tagmentation-based single-cell genomics.
    Andrew C Adey.
      It has been just over 10 years since the initial description of transposase-based methods to prepare high-throughput sequencing libraries, or "tagmentation," in which a hyperactive transposase is used to simultaneously fragment target DNA and append universal adapter sequences. Tagmentation effectively replaced a series of processing steps in traditional workflows with one single reaction. It is the simplicity, coupled with the high efficiency of tagmentation, that has made it a favored means of sequencing library construction and fueled a diverse range of adaptations to assay a variety of molecular properties. In recent years, this has been centered in the single-cell space with a catalog of tagmentation-based assays that have been developed, covering a substantial swath of the regulatory landscape. To date, there have been a number of excellent reviews on single-cell technologies structured around the molecular properties that can be profiled. This review is instead framed around the central components and properties of tagmentation and how they have enabled the development of innovative molecular tools to probe the regulatory landscape of single cells. Furthermore, the granular specifics on cell throughput or richness of data provided by the extensive list of individual technologies are not discussed. Such metrics are rapidly changing and highly sample specific and are better left to studies that directly compare technologies for assays against one another in a rigorously controlled framework. The hope for this review is that, in laying out the diversity of molecular techniques at each stage of these assay platforms, new ideas may arise for others to pursue that will further advance the field of single-cell genomics.
    DOI:  https://doi.org/10.1101/gr.275223.121
  7. Cancer Biol Med. 2021 Oct 01. pii: j.issn.2095-3941.2021.0267. [Epub ahead of print]
    Single-cell trajectories of melanoma cell resistance to targeted treatment.
    Maria Schmidt, Lena Sünke Mortensen, Henry Loeffler-Wirth, Corinna Kosnopfel, Knut Krohn, Hans Binder, Manfred Kunz.
      OBJECTIVE: Cellular heterogeneity is regarded as a major factor affecting treatment response and resistance in malignant melanoma. Recent developments in single-cell sequencing technology have provided deeper insights into these mechanisms.METHODS: Here, we analyzed a BRAFV600E-mutant melanoma cell line by single-cell RNA-seq under various conditions: cells sensitive to BRAF inhibition with BRAF inhibitor vemurafenib and cells resistant to BRAF inhibition with vemurafenib alone or vemurafenib in combination with the MEK1/2 inhibitors cobimetinib or trametinib. Dimensionality reduction by t-distributed stochastic neighbor embedding and self-organizing maps identified distinct trajectories of resistance development clearly separating the 4 treatment conditions in cell and gene state space.
    RESULTS: Trajectories associated with resistance to single-agent treatment involved cell cycle, extracellular matrix, and de-differentiation programs. In contrast, shifts detected in double-resistant cells primarily affected translation and mitogen-activated protein kinase pathway reactivation, with a small subpopulation showing markers of pluripotency. These findings were validated in pseudotime analyses and RNA velocity measurements.
    CONCLUSIONS: The single-cell transcriptomic analyses reported here employed a spectrum of bioinformatics methods to identify mechanisms of melanoma resistance to single- and double-agent treatments. This study deepens our understanding of treatment-induced cellular reprogramming and plasticity in melanoma cells and identifies targets of potential relevance to the management of treatment resistance.
    Keywords:  Melanoma; single-cell transcriptome sequencing; treatment response
    DOI:  https://doi.org/10.20892/j.issn.2095-3941.2021.0267
  8. Methods Mol Biol. 2021 ;2381 227-242
    Identification of Drug Resistance Genes Using a Pooled Lentiviral CRISPR/Cas9 Screening Approach.
    Evan M Kerek, Christopher R Cromwell, Basil P Hubbard.
      In addition to advancing the development of gene-editing therapeutics, CRISPR/Cas9 is transforming how functional genetic studies are carried out in the lab. By increasing the ease with which genetic information can be inserted, deleted, or edited in cell and organism models, it facilitates genotype-phenotype analysis. Moreover, CRISPR/Cas9 has revolutionized the speed at which new genes underlying a particular phenotype can be identified through its application in genomic screens. Arrayed high-throughput and pooled lentiviral-based CRISPR/Cas9 screens have now been used in a wide variety of contexts, including the identification of essential genes, genes involved in cancer metastasis and tumor growth, and even genes involved in viral response. This technology has also been successfully used to identify drug targets and drug resistance mechanisms. Here, we provide a detailed protocol for performing a genome-wide pooled lentiviral CRISPR/Cas9 knockout screen to identify genetic modulators of a small-molecule drug. While we exemplify how to identify genes involved in resistance to a cytotoxic histone deacetylase inhibitor, Trichostatin A (TSA), the workflow we present can easily be adapted to different types of selections and other types of exogenous ligands or drugs.
    Keywords:  CRISPR/Cas9; CRISPR/Cas9 pooled lentiviral screen; Cytotoxic drug; Drug resistance mechanisms; Drug selection; Epigenetic drugs; Gene editing; Genome engineering; Genome-wide knockout screen; Trichostatin A (TSA)
    DOI:  https://doi.org/10.1007/978-1-0716-1740-3_13
  9. Genome Res. 2021 Oct;31(10): 1719-1727
    Cancer cell states and emergent properties of the dynamic tumor system.
    Dalia Barkley, Anjali Rao, Maayan Pour, Gustavo S França, Itai Yanai.
      Phenotypic heterogeneity within malignant cells of a tumor is emerging as a key property of tumorigenesis. Recent work using single-cell transcriptomics has led to the identification of distinct cancer cell states across a range of cancer types, but their functional relevance and the advantage that they provide to the tumor as a system remain elusive. We present here a definition of cancer cell states in terms of coherently and differentially expressed gene modules and review the origins, dynamics, and impact of states on the tumor system as a whole. The spectrum of cell states taken on by a malignant population may depend on cellular lineage, epigenetic history, genetic mutations, or environmental cues, which has implications for the relative stability or plasticity of individual states. Finally, evidence has emerged that malignant cells in different states may cooperate or compete within a tumor niche, thereby providing an evolutionary advantage to the tumor through increased immune evasion, drug resistance, or invasiveness. Uncovering the mechanisms that govern the origin and dynamics of cancer cell states in tumorigenesis may shed light on how heterogeneity contributes to tumor fitness and highlight vulnerabilities that can be exploited for therapy.
    DOI:  https://doi.org/10.1101/gr.275308.121
  10. Eur J Med Chem. 2021 Sep 04. pii: S0223-5234(21)00674-7. [Epub ahead of print]226 113825
    Combining histone deacetylase inhibitors (HDACis) with other therapies for cancer therapy.
    Mengjiao Zhou, Minjian Yuan, Meng Zhang, Chenyi Lei, Omer Aras, Xiaohong Zhang, Feifei An.
      Histone deacetylases (HDACs) play an important role in regulating the expression of genes involved in tumorigenesis and tumor maintenance, and hence they have been considered as key targets in cancer therapy. As a novel category of antitumor agents, histone deacetylase inhibitors (HDACis) can induce cell cycle arrest, apoptosis, and differentiation in cancer cells, ultimately combating cancer. Although in the United States, the use of HDACis for the treatment of certain cancers has been approved, the therapeutic efficacy of HDACis as a single therapeutic agent in solid tumorshas been unsatisfactory and drug resistance may yet occur. To enhance therapeutic efficacy and limit drug resistance, numerous combination therapies involving HDACis in synergy with other antitumor therapies have been studied. In this review, we describe the classification of HDACs. Moreover, we summarize the antitumor mechanism of the HDACis for targeting key cellular processes of cancers (cell cycle, apoptosis, angiogenesis, DNA repair, and immune response). In addition, we outline the major developments of other antitumor therapies in combination with HDACis, including chemotherapy, radiotherapy, phototherapy, targeted therapy, and immunotherapy. Finally, we discuss the current state and challenges of HDACis-drugs combinations in future clinical studies, with the aim of optimizing the antitumor effect of such combinations.
    Keywords:  Cancer; Combination therapies; Histone deacetylases inhibitors; Histone deacetylations
    DOI:  https://doi.org/10.1016/j.ejmech.2021.113825
  11. Cancers (Basel). 2021 Sep 15. pii: 4630. [Epub ahead of print]13(18):
    Niclosamide and Pyrvinium Are Both Potential Therapeutics for Osteosarcoma, Inhibiting Wnt-Axin2-Snail Cascade.
    Young Yi, Young Mi Woo, Kyu Ho Hwang, Hyun Sil Kim, Sang Hyeong Lee.
      Osteosarcoma, the most common primary bone malignancy, is typically related to growth spurts during adolescence. Prognosis is very poor for patients with metastatic or recurrent osteosarcoma, with survival rates of only 20-30%. Epithelial-mesenchymal transition (EMT) is a cellular mechanism that contributes to the invasion and metastasis of cancer cells, and Wnt signaling activates the EMT program by stabilizing Snail and β-catenin in tandem. Although the Wnt/Snail axis is known to play significant roles in the progression of osteosarcoma, and the anthelmintic agents, niclosamide and pyrvinium, have been studied as inhibitors of the Wnt pathway, their therapeutic effects and regulatory mechanisms in osteosarcoma remain unidentified. In this study, we show that both niclosamide and pyrvinium target Axin2, resulting in the suppression of EMT by the inhibition of the Wnt/Snail axis in osteosarcoma cells. Axin2 and Snail are abundant in patient samples and cell lines of osteosarcoma. The treatment of niclosamide and pyrvinium inhibits the migration of osteosarcoma cells at nanomolar concentrations. These results suggest that Axin2 and Snail are candidate therapeutic targets in osteosarcoma, and that anthelminthic agents, niclosamide and pyrvinium, may be effective for osteosarcoma patients.
    Keywords:  Axin2; Snail; Wnt; epithelial–mesenchymal transition; niclosamide; osteosarcoma; pyrvinium
    DOI:  https://doi.org/10.3390/cancers13184630
  12. Eur J Pharmacol. 2021 Sep 23. pii: S0014-2999(21)00679-8. [Epub ahead of print] 174523
    Bromodomains: A novel target for the anticancer therapy.
    Shivani Gokani, Lokesh Kumar Bhatt.
      Bromodomains are a group of structurally diverse proteins characterized as readers of post-translational modifications. They bear unique structural topology and are known to have diverse cellular functions. As epigenetic readers of histone acetylation, bromodomains appear to have both physiological and pathological implications. Among the various types of bromodomain-containing proteins, BRD2 and BRD4 proteins are expressed ubiquitously and act as critical regulators of the cell cycle in normal mammalian cells. Therefore, they are increasingly involved in the process of oncogenesis. Bromodomains are the emerging novel epigenetic targets for the treatment of cancer. Various small molecules are proposed to target the bromodomain proteins as the readers of acetyl-lysine residues. In recent years, inhibiting the interaction of acetyl-lysine residues and bromodomain proteins on chromatin has served as an interesting target to regulate the expression of various pathological genes, including BCL-2, MYC, and NF-κB. The review summarizes bromodomains as potential targets in cancer and various bromodomain inhibitors in the early stages of the clinical trial.
    Keywords:  Anticancer therapy; Bromodomain inhibitors; Bromodomain-containing proteins; Bromodomains
    DOI:  https://doi.org/10.1016/j.ejphar.2021.174523
  13. Cancer Res. 2021 Sep 27. pii: canres.2619.2021. [Epub ahead of print]
    Histone H1 mutations in lymphoma: a link(er) between chromatin organization, developmental reprogramming, and cancer.
    Alexey A Soshnev, C David Allis, Ethel Cesarman, Ari M Melnick.
      Aberrant cell fate decisions due to transcriptional misregulation are central to malignant transformation. Histones are the major constituents of chromatin, and mutations in histone-encoding genes are increasingly recognized as drivers of oncogenic transformation. Mutations in linker histone H1 genes were recently identified as drivers of peripheral lymphoid malignancy. Loss of H1 in germinal center B-cells results in widespread chromatin decompaction, redistribution of core histone modifications, and reactivation of stem cell-specific transcriptional programs. This review explores how linker histones and mutations therein regulate chromatin structure, highlighting reciprocal relationships between epigenetic circuits, and discusses the emerging role of aberrant three-dimensional chromatin architecture in malignancy.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-2619
  14. Bioeng Transl Med. 2021 Sep;6(3): e10226
    Cell stiffness predicts cancer cell sensitivity to ultrasound as a selective superficial cancer therapy.
    Eden Bergman, Riki Goldbart, Tamar Traitel, Eliz Amar-Lewis, Jonathan Zorea, Ksenia Yegodayev, Irit Alon, Sanela Rankovic, Yuval Krieger, Itay Rousso, Moshe Elkabets, Joseph Kost.
      We hypothesize that the biomechanical properties of cells can predict their viability, with Young's modulus representing the former and cell sensitivity to ultrasound representing the latter. Using atomic force microscopy, we show that the Young's modulus stiffness measure is significantly lower for superficial cancer cells (squamous cell carcinomas and melanoma) compared with noncancerous keratinocyte cells. In vitro findings reveal a significant difference between cancerous and noncancerous cell viability at the four ultrasound energy levels evaluated, with different cell lines exhibiting different sensitivities to the same ultrasound intensity. Young's modulus correlates with cell viability (R 2 = 0.93), indicating that this single biomechanical property can predict cell sensitivity to ultrasound treatment. In mice, repeated ultrasound treatment inhibits tumor growth without damaging healthy skin tissue. Histopathological tumor analysis indicates ultrasound-induced focal necrosis at the treatment site. Our findings provide a strong rationale for developing ultrasound as a noninvasive selective treatment for superficial cancers.
    Keywords:  AFM measurements; mechanical properties of cancer cells; noninvasive therapy; selective cancer therapy; superficial cancer; ultrasound
    DOI:  https://doi.org/10.1002/btm2.10226
  15. Molecules. 2021 Sep 15. pii: 5606. [Epub ahead of print]26(18):
    Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation.
    Laura Márquez-Cantudo, Ana Ramos, Claire Coderch, Beatriz de Pascual-Teresa.
      Protein degradation by the Ubiquitin-Proteasome System is one of the main mechanisms of the regulation of cellular proteostasis, and the E3 ligases are the key effectors for the protein recognition and degradation. Many E3 ligases have key roles in cell cycle regulation, acting as checkpoints and checkpoint regulators. One of the many important proteins involved in the regulation of the cell cycle are the members of the Histone Deacetylase (HDAC) family. The importance of zinc dependent HDACs in the regulation of chromatin packing and, therefore, gene expression, has made them targets for the design and synthesis of HDAC inhibitors. However, achieving potency and selectivity has proven to be a challenge due to the homology between the zinc dependent HDACs. PROteolysis TArgeting Chimaera (PROTAC) design has been demonstrated to be a useful strategy to inhibit and selectively degrade protein targets. In this review, we attempt to summarize the E3 ligases that naturally ubiquitinate HDACs, analyze their structure, and list the known ligands that can bind to these E3 ligases and be used for PROTAC design, as well as the already described HDAC-targeted PROTACs.
    Keywords:  E3-ligase; HDACs; PROTACs; drug design; proteasomal degradation
    DOI:  https://doi.org/10.3390/molecules26185606
  16. Methods Mol Biol. 2021 ;2357 197-208
    Detecting Persister Awakening Determinants.
    Dorien Wilmaerts, Jan Michiels, Natalie Verstraeten.
      For long, persistence research has focused primarily on disentangling mechanisms of persister state entry. Due to the rapid advances in the field of single-cell techniques and newly obtained insights in the persister phenotype, studying persister awakening has been unlocked and it has gained much interest in the scientific community. However, a framework on how this research should be conducted is currently lacking. Therefore, we here present a method to detect and validate genes important for persister awakening.
    Keywords:  Cell sorting; Persister; Persister awakening; Single-cell
    DOI:  https://doi.org/10.1007/978-1-0716-1621-5_13
  17. Front Cell Dev Biol. 2021 ;9 714601
    Circular RNA hsa_circ_0000073 Enhances Osteosarcoma Cells Malignant Behavior by Sponging miR-1252-5p and Modulating CCNE2 and MDM2.
    Zhijing Ren, Qinqin Yang, Jiajia Guo, Haifeng Huang, Bo Li, Zhen Yang, Xiaobin Tian.
      Objective: An increasing number of studies have demonstrated that circular RNAs (circRNAs) are involved in tumor progression. However, the role of hsa_circ_0000073 in osteosarcoma (OS) is still not fully elucidated. Methods: Quantitative reverse transcription-polymerase chain reaction or Western blot was used to detect the gene expression. GeneChip analysis, bioinformatics, luciferase reporter, and RNA immunoprecipitation assays were adopted to predict and verify the relationships between genes. Counting Kit-8 Assay, clone formation assay, wound-healing assay, transwell assays, cell cycle assays, and in vivo tumorigenesis were used to evaluate cell function. Results: hsa_circ_0000073 was highly expressed in OS cell lines and could promote OS progression, including proliferation, migration, invasion, and cell cycle in vitro as well as tumorigenesis in vivo. Mechanically, hsa_circ_0000073 could readily downregulate the expression of CCNE2 and MDM2 through miR-1252-5p. Rescue experiments validated miR-1252-5p mimics, or CCNE2/MDM2 short hairpin RNA could reverse the hsa_circ_0000073 overexpressing-induced impairment of malignant tumor behavior. Conclusion: hsa_circ_0000073 functions as a tumor promoter in OS to increase malignant tumor behavior through sponging miR-1252-5p and regulating CCNE2 and MDM2 expression, which could be a novel target for OS therapy.
    Keywords:  CCNE2; MDM2; cell cycle; hsa_circ_0000073; miR-1252-5p; osteosarcoma; proliferation
    DOI:  https://doi.org/10.3389/fcell.2021.714601
  18. Life (Basel). 2021 Aug 25. pii: 877. [Epub ahead of print]11(9):
    NSD1: A Lysine Methyltransferase between Developmental Disorders and Cancer.
    Samantha Tauchmann, Juerg Schwaller.
      Recurrent epigenomic alterations associated with multiple human pathologies have increased the interest in the nuclear receptor binding SET domain protein 1 (NSD1) lysine methyltransferase. Here, we review the current knowledge about the biochemistry, cellular function and role of NSD1 in human diseases. Several studies have shown that NSD1 controls gene expression by methylation of lysine 36 of histone 3 (H3K36me1/2) in a complex crosstalk with de novo DNA methylation. Inactivation in flies and mice revealed that NSD1 is essential for normal development and that it regulates multiple cell type-specific functions by interfering with transcriptional master regulators. In humans, putative loss of function NSD1 mutations characterize developmental syndromes, such as SOTOS, as well as cancer from different organs. In pediatric hematological malignancies, a recurrent chromosomal translocation forms a NUP98-NSD1 fusion with SET-dependent leukemogenic activity, which seems targetable by small molecule inhibitors. To treat or prevent diseases driven by aberrant NSD1 activity, future research will need to pinpoint the mechanistic correlation between the NSD1 gene dosage and/or mutational status with development, homeostasis, and malignant transformation.
    Keywords:  AML; H3K36; NSD1; NUP98-NSD1; SOTOS; cancer
    DOI:  https://doi.org/10.3390/life11090877
  19. Int J Mol Sci. 2021 Sep 07. pii: 9692. [Epub ahead of print]22(18):
    Mitochondrial DNA and MitomiR Variations in Pancreatic Cancer: Potential Diagnostic and Prognostic Biomarkers.
    Loredana Moro.
      Pancreatic cancer is an aggressive disease with poor prognosis. Only about 15-20% of patients diagnosed with pancreatic cancer can undergo surgical resection, while the remaining 80% are diagnosed with locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). In these cases, chemotherapy and radiotherapy only confer marginal survival benefit. Recent progress has been made in understanding the pathobiology of pancreatic cancer, with a particular effort in discovering new diagnostic and prognostic biomarkers, novel therapeutic targets, and biomarkers that can predict response to chemo- and/or radiotherapy. Mitochondria have become a focus in pancreatic cancer research due to their roles as powerhouses of the cell, important subcellular biosynthetic factories, and crucial determinants of cell survival and response to chemotherapy. Changes in the mitochondrial genome (mtDNA) have been implicated in chemoresistance and metastatic progression in some cancer types. There is also growing evidence that changes in microRNAs that regulate the expression of mtDNA-encoded mitochondrial proteins (mitomiRs) or nuclear-encoded mitochondrial proteins (mitochondria-related miRs) could serve as diagnostic and prognostic cancer biomarkers. This review discusses the current knowledge on the clinical significance of changes of mtDNA, mitomiRs, and mitochondria-related miRs in pancreatic cancer and their potential role as predictors of cancer risk, as diagnostic and prognostic biomarkers, and as molecular targets for personalized cancer therapy.
    Keywords:  mitochondrial genome; mitochondrial microRNAs; pancreatic cancer
    DOI:  https://doi.org/10.3390/ijms22189692
  20. iScience. 2021 Sep 24. 24(9): 103073
    A fatal affair: Circulating tumor cell relationships that shape metastasis.
    Lauren L Ozimski, David Gremmelspacher, Nicola Aceto.
      Circulating tumor cells are metastatic precursors in several cancer types. Their biology and clinical utility are subject to numerous investigations, yet one aspect that is often neglected is their entanglement with the tumor microenvironment, namely the cross talk with stromal and immune cells and their relationships with other tumor-derived components such as circulating tumor DNA and extracellular vesicles in circulation. We will focus our short review specifically on these aspects, i.e., providing some examples of the liaison that circulating tumor cells have with stromal or immune cells and illustrating their relationship with other circulating tumor derivatives such as circulating tumor DNA and extracellular vesicles.
    Keywords:  Biotechnology; Cell biology; Integrative aspects of cell biology
    DOI:  https://doi.org/10.1016/j.isci.2021.103073
  21. Cells. 2021 Aug 27. pii: 2221. [Epub ahead of print]10(9):
    Current Applications and Discoveries Related to the Membrane Components of Circulating Tumor Cells and Extracellular Vesicles.
    Luis Enrique Cortés-Hernández, Zahra Eslami-S, Bruno Costa-Silva, Catherine Alix-Panabières.
      In cancer, many analytes can be investigated through liquid biopsy. They play fundamental roles in the biological mechanisms underpinning the metastatic cascade and provide clinical information that can be monitored in real time during the natural course of cancer. Some of these analytes (circulating tumor cells and extracellular vesicles) share a key feature: the presence of a phospholipid membrane that includes proteins, lipids and possibly nucleic acids. Most cell-to-cell and cell-to-matrix interactions are modulated by the cell membrane composition. To understand cancer progression, it is essential to describe how proteins, lipids and nucleic acids in the membrane influence these interactions in cancer cells. Therefore, assessing such interactions and the phospholipid membrane composition in different liquid biopsy analytes might be important for future diagnostic and therapeutic strategies. In this review, we briefly describe some of the most important surface components of circulating tumor cells and extracellular vesicles as well as their interactions, putting an emphasis on how they are involved in the different steps of the metastatic cascade and how they can be exploited by the different liquid biopsy technologies.
    Keywords:  circulating tumor cells; extracellular vesicles; liquid biopsy
    DOI:  https://doi.org/10.3390/cells10092221
  22. Nat Genet. 2021 Sep 30.
    Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states.
    Ronan Chaligne, Federico Gaiti, Dana Silverbush, Joshua S Schiffman, Hannah R Weisman, Lloyd Kluegel, Simon Gritsch, Sunil D Deochand, L Nicolas Gonzalez Castro, Alyssa R Richman, Johanna Klughammer, Tommaso Biancalani, Christoph Muus, Caroline Sheridan, Alicia Alonso, Franco Izzo, Jane Park, Orit Rozenblatt-Rosen, Aviv Regev, Mario L Suvà, Dan A Landau.
      Single-cell RNA sequencing has revealed extensive transcriptional cell state diversity in cancer, often observed independently of genetic heterogeneity, raising the central question of how malignant cell states are encoded epigenetically. To address this, here we performed multiomics single-cell profiling-integrating DNA methylation, transcriptome and genotype within the same cells-of diffuse gliomas, tumors characterized by defined transcriptional cell state diversity. Direct comparison of the epigenetic profiles of distinct cell states revealed key switches for state transitions recapitulating neurodevelopmental trajectories and highlighted dysregulated epigenetic mechanisms underlying gliomagenesis. We further developed a quantitative framework to directly measure cell state heritability and transition dynamics based on high-resolution lineage trees in human samples. We demonstrated heritability of malignant cell states, with key differences in hierarchal and plastic cell state architectures in IDH-mutant glioma versus IDH-wild-type glioblastoma, respectively. This work provides a framework anchoring transcriptional cancer cell states in their epigenetic encoding, inheritance and transition dynamics.
    DOI:  https://doi.org/10.1038/s41588-021-00927-7
  23. Cells. 2021 Aug 31. pii: 2268. [Epub ahead of print]10(9):
    Overexpression of the Ubiquitin Specific Proteases USP43, USP41, USP27x and USP6 in Osteosarcoma Cell Lines: Inhibition of Osteosarcoma Tumor Growth and Lung Metastasis Development by the USP Antagonist PR619.
    Mélanie Lavaud, Mathilde Mullard, Robel Tesfaye, Jérôme Amiaud, Mélanie Legrand, Geoffroy Danieau, Régis Brion, Sarah Morice, Laura Regnier, Maryne Dupuy, Bénédicte Brounais-Le Royer, François Lamoureux, Benjamin Ory, Françoise Rédini, Franck Verrecchia.
      Osteosarcoma (OS) is the most common malignant bone tumor in children and teenagers. In many cases, such as poor response to treatment or the presence of metastases at diagnosis, the survival rate of patients remains very low. Although in the literature, more and more studies are emerging on the role of Ubiquitin-Specific Proteases (USPs) in the development of many cancers, few data exist regarding OS. In this context, RNA-sequencing analysis of OS cells and mesenchymal stem cells differentiated or not differentiated into osteoblasts reveals increased expression of four USPs in OS tumor cells: USP6, USP27x, USP41 and USP43. Tissue microarray analysis of patient biopsies demonstrates the nucleic and/or cytoplasmic expression of these four USPs at the protein level. Interestingly, Kaplan-Meyer analysis shows that the expression of two USPs, USP6 and USP41, is correlated with patient survival. In vivo experiments using a preclinical OS model, finally demonstrate that PR619, a USP inhibitor able to enhance protein ubiquitination in OS cell lines, reduces primary OS tumor growth and the development of lung metastases. In this context, in vitro experiments show that PR619 decreases the viability of OS cells, mainly by inducing a caspase3/7-dependent cell apoptosis. Overall, these results demonstrate the relevance of targeting USPs in OS.
    Keywords:  Osteosarcoma; PR619; Ubiquitin Specific Proteases
    DOI:  https://doi.org/10.3390/cells10092268
  24. Front Cell Dev Biol. 2021 ;9 699621
    The Nucleus/Mitochondria-Shuttling LncRNAs Function as New Epigenetic Regulators of Mitophagy in Cancer.
    Yan Li, Wei Li, Andrew R Hoffman, Jiuwei Cui, Ji-Fan Hu.
      Mitophagy is a specialized autophagic pathway responsible for the selective removal of damaged or dysfunctional mitochondria by targeting them to the autophagosome in order to maintain mitochondria quality. The role of mitophagy in tumorigenesis has been conflicting, with the process both supporting tumor cell survival and promoting cell death. Cancer cells may utilize the mitophagy pathway to augment their metabolic requirements and resistance to cell death, thereby leading to increased cell proliferation and invasiveness. This review highlights major regulatory pathways of mitophagy involved in cancer. In particular, we summarize recent progress regarding how nuclear-encoded long non-coding RNAs (lncRNAs) function as novel epigenetic players in the mitochondria of cancer cells, affecting the malignant behavior of tumors by regulating mitophagy. Finally, we discuss the potential application of regulating mitophagy as a new target for cancer therapy.
    Keywords:  cancer metabolism; cancer stem cells; cancer therapy; long non-coding RNA; mitochondria; mitophagy
    DOI:  https://doi.org/10.3389/fcell.2021.699621
  25. Front Cell Dev Biol. 2021 ;9 733751
    Ferroptosis and Cancer: Complex Relationship and Potential Application of Exosomes.
    Shuang Wu, Tianye Li, Weiwei Liu, Yongye Huang.
      Cell death induction has become popular as a novel cancer treatment. Ferroptosis, a newly discovered form of cell death, features regulated, iron-dependent accumulation of lipid hydroperoxides. Since this word "ferroptosis" was coined, numerous studies have examined the complex relationship between ferroptosis and cancer. Here, starting from the intrinsic hallmarks of cancer and cell death, we discuss the theoretical basis of cell death induction as a cancer treatment. We review various aspects of the relationship between ferroptosis and cancer, including the genetic basis, epigenetic modification, cancer stem cells, and the tumor microenvironment, to provide information and support for further research on ferroptosis. We also note that exosomes can be applied in ferroptosis-based therapy. These extracellular vesicles can deliver different molecules to modulate cancer cells and cell death pathways. Using exosomes to control ferroptosis occurring in targeted cells is promising for cancer therapy.
    Keywords:  apoptosis; cancer; cell death; exosomes; ferroptosis
    DOI:  https://doi.org/10.3389/fcell.2021.733751
  26. J Med Chem. 2021 Sep 30.
    From Hit Seeking to Magic Bullets: The Successful Union of Epigenetic and Fragment Based Drug Discovery (EPIDD + FBDD).
    Miguel M Vaidergorn, Flavio da Silva Emery, A Ganesan.
      We review progress in the application of fragment-based drug discovery (FBDD) to epigenetic drug discovery (EPIDD) targeted at epigenetic writer and eraser enzymes as well as reader domains over the last 15 years. The greatest successes to date are in prospecting for bromodomain binding ligands. From a diverse array of fragment hits, multiple potent and selective compounds ensued, including the oncology clinical candidates mivebresib, ABBV-744, pelabresib, and PLX51107.
    DOI:  https://doi.org/10.1021/acs.jmedchem.1c00787
  27. Brief Bioinform. 2021 Sep 28. pii: bbab401. [Epub ahead of print]
    Comprehensive characterization genetic regulation and chromatin landscape of enhancer-associated long non-coding RNAs and their implication in human cancer.
    Xin Li, Xu Pan, Hanxiao Zhou, Peng Wang, Yue Gao, Shipeng Shang, Shuang Guo, Jie Sun, Zhiying Xiong, Shangwei Ning, Hui Zhi, Xia Li.
      Long non-coding RNAs (lncRNAs) that emanate from enhancer regions (defined as enhancer-associated lncRNAs, or elncRNAs) are emerging as critical regulators in disease progression. However, their biological characteristics and clinical relevance have not been fully portrayed. Here, based on the traditional expression quantitative loci (eQTL) and our optimized residual eQTL method, we comprehensively described the genetic effect on elncRNA expression in more than 300 lymphoblastoid cell lines. Meanwhile, a chromatin atlas of elncRNAs relative to the genetic regulation state was depicted. By applying the maximum likelihood estimate method, we successfully identified causal elncRNAs for protein-coding gene expression reprogramming and showed their associated single nucleotide polymorphisms (SNPs) favor binding of transcription factors. Further epigenome analysis revealed two immune-associated elncRNAs AL662844.4 and LINC01215 possess high levels of H3K27ac and H3K4me1 in human cancer. Besides, pan-cancer analysis of 3D genome, transcriptome, and regulatome data showed they potentially regulate tumor-immune cell interaction through affecting MHC class I genes and CD47, respectively. Moreover, our study showed there exist associations between elncRNA and patient survival. Finally, we made a user-friendly web interface available for exploring the regulatory relationship of SNP-elncRNA-protein-coding gene triplets (http://bio-bigdata.hrbmu.edu.cn/elncVarReg). Our study provides critical mechanistic insights for elncRNA function and illustrates their implications in human cancer.
    Keywords:  3D genome; SNP; TF; chromatin; elncRNA; epigenome
    DOI:  https://doi.org/10.1093/bib/bbab401
  28. Pharmaceutics. 2021 Sep 16. pii: 1485. [Epub ahead of print]13(9):
    Ultrasound and Transcriptomics Identify a Differential Impact of Cisplatin and Histone Deacetylation on Tumor Structure and Microenvironment in a Patient-Derived In Vivo Model of Gastric Cancer.
    Aina Venkatasamy, Eric Guerin, Anais Blanchet, Christophe Orvain, Véronique Devignot, Matthieu Jung, Alain C Jung, Marie-Pierre Chenard, Benoit Romain, Christian Gaiddon, Georg Mellitzer.
      The reasons behind the poor efficacy of transition metal-based chemotherapies (e.g., cisplatin) or targeted therapies (e.g., histone deacetylase inhibitors, HDACi) on gastric cancer (GC) remain elusive and recent studies suggested that the tumor microenvironment could contribute to the resistance. Hence, our objective was to gain information on the impact of cisplatin and the pan-HDACi SAHA (suberanilohydroxamic acid) on the tumor substructure and microenvironment of GC, by establishing patient-derived xenografts of GC and a combination of ultrasound, immunohistochemistry, and transcriptomics to analyze. The tumors responded partially to SAHA and cisplatin. An ultrasound gave more accurate tumor measures than a caliper. Importantly, an ultrasound allowed a noninvasive real-time access to the tumor substructure, showing differences between cisplatin and SAHA. These differences were confirmed by immunohistochemistry and transcriptomic analyses of the tumor microenvironment, identifying specific cell type signatures and transcription factor activation. For instance, cisplatin induced an "epithelial cell like" signature while SAHA favored a "mesenchymal cell like" one. Altogether, an ultrasound allowed a precise follow-up of the tumor progression while enabling a noninvasive real-time access to the tumor substructure. Combined with transcriptomics, our results underline the different intra-tumoral structural changes caused by both drugs that impact differently on the tumor microenvironment.
    Keywords:  HDAC Inhibitors; SAHA; cancer immunity; cisplatin; epigenetic; gastric cancer; microenvironment; p53; transcriptomic; ultrasound
    DOI:  https://doi.org/10.3390/pharmaceutics13091485
  29. Pharmaceuticals (Basel). 2021 Aug 26. pii: 851. [Epub ahead of print]14(9):
    Improved HDAC Inhibition, Stronger Cytotoxic Effect and Higher Selectivity against Leukemias and Lymphomas of Novel, Tricyclic Vorinostat Analogues.
    Bartosz Bieszczad, Damian Garbicz, Marta Świtalska, Marta K Dudek, Dawid Warszycki, Joanna Wietrzyk, Elżbieta Grzesiuk, Adam Mieczkowski.
      Histone deacetylase (HDAC) inhibitors are a class of drugs used in the cancer treatment. Here, we developed a library of 19 analogues of Vorinostat, an HDAC inhibitor used in lymphomas treatment. In Vorinostat, we replaced the hydrophobic phenyl group with various tricyclic 'caps' possessing a central, eight-membered, heterocyclic ring, and investigated the HDAC activity and cytotoxic effect on the cancer and normal cell lines. We found that 3 out of the 19 compounds, based on dibenzo[b,f]azocin-6(5H)-one, 11,12-dihydrodibenzo[b,f]azocin-6(5H)-one, and benzo[b]naphtho[2,3-f][1,5]diazocine-6,14(5H,13H)-dione scaffolds, showed better HDACs inhibition than the referenced Vorinostat. In leukemic cell line MV4-11 and in the lymphoma cell line Daudi, three compounds showed lower IC50 values than Vorinostat. These compounds had higher activity and selectivity against MV4-11 and Daudi cell lines than reference Vorinostat. We also observed a strong correlation between HDACs inhibition and the cytotoxic effect. Cell lines derived from solid tumours: A549 (lung carcinoma) and MCF-7 (breast adenocarcinoma) as well as reference BALB/3T3 (normal murine fibroblasts) were less susceptible to compounds tested. Developed derivatives show improved properties than Vorinostat, thus they could be considered as possible agents for leukemia and lymphoma treatment.
    Keywords:  HDAC inhibitors; Vorinostat; dibenzodiazocines; histone deacetylase; hydroxamic acid; selectivity
    DOI:  https://doi.org/10.3390/ph14090851
  30. Cells. 2021 Sep 09. pii: 2374. [Epub ahead of print]10(9):
    From the Evasion of Degradation to Ubiquitin-Dependent Protein Stabilization.
    Yamen Abu Ahmad, Avital Oknin-Vaisman, Eliya Bitman-Lotan, Amir Orian.
      A hallmark of cancer is dysregulated protein turnover (proteostasis), which involves pathologic ubiquitin-dependent degradation of tumor suppressor proteins, as well as increased oncoprotein stabilization. The latter is due, in part, to mutation within sequences, termed degrons, which are required for oncoprotein recognition by the substrate-recognition enzyme, E3 ubiquitin ligase. Stabilization may also result from the inactivation of the enzymatic machinery that mediates the degradation of oncoproteins. Importantly, inactivation in cancer of E3 enzymes that regulates the physiological degradation of oncoproteins, results in tumor cells that accumulate multiple active oncoproteins with prolonged half-lives, leading to the development of "degradation-resistant" cancer cells. In addition, specific sequences may enable ubiquitinated proteins to evade degradation at the 26S proteasome. While the ubiquitin-proteasome pathway was originally discovered as central for protein degradation, in cancer cells a ubiquitin-dependent protein stabilization pathway actively translates transient mitogenic signals into long-lasting protein stabilization and enhances the activity of key oncoproteins. A central enzyme in this pathway is the ubiquitin ligase RNF4. An intimate link connects protein stabilization with tumorigenesis in experimental models as well as in the clinic, suggesting that pharmacological inhibition of protein stabilization has potential for personalized medicine in cancer. In this review, we highlight old observations and recent advances in our knowledge regarding protein stabilization.
    Keywords:  E3 ubiquitin ligases; RNF4; STUbL; cancer; degradation; degradation-resistant tumors; degron; heterotypic-Ub chains; oncoproteins; proteasome; protein-stabilization; ubiquitin
    DOI:  https://doi.org/10.3390/cells10092374
  31. Drug Discov Today. 2021 Sep 27. pii: S1359-6446(21)00406-2. [Epub ahead of print]
    Combining repurposed drugs to treat colorectal cancer.
    Diana Duarte, Nuno Vale.
      The drug development process, especially of antineoplastic agents, has become increasingly costly and ineffective. Drug repurposing and drug combination are alternatives to de novo drug development, being low cost, rapid, and easy to apply. These strategies allow higher efficacy, decreased toxicity, and overcoming of drug resistance. The combination of antineoplastic agents is already being applied in cancer therapy, but the combination of repurposed drugs is still under-explored in pre- and clinical development. In this review, we provide a set of pharmacological concepts focusing on drug repurposing for treating colorectal cancer (CRC) and that are relevant for the application of new drug combinations against this disease.
    Keywords:  chemotherapy; colon cancer; drug combination; drug repurposing
    DOI:  https://doi.org/10.1016/j.drudis.2021.09.012
  32. Nat Commun. 2021 Sep 30. 12(1): 5732
    Chromatin accessibility associates with protein-RNA correlation in human cancer.
    Akshay Sanghi, Joshua J Gruber, Ahmed Metwally, Lihua Jiang, Warren Reynolds, John Sunwoo, Lisa Orloff, Howard Y Chang, Maya Kasowski, Michael P Snyder.
      Although alterations in chromatin structure are known to exist in tumors, how these alterations relate to molecular phenotypes in cancer remains to be demonstrated. Multi-omics profiling of human tumors can provide insight into how alterations in chromatin structure are propagated through the pathway of gene expression to result in malignant protein expression. We applied multi-omics profiling of chromatin accessibility, RNA abundance, and protein abundance to 36 human thyroid cancer primary tumors, metastases, and patient-match normal tissue. Through quantification of chromatin accessibility associated with active transcription units and global protein expression, we identify a local chromatin structure that is highly correlated with coordinated RNA and protein expression. In particular, we identify enhancers located within gene-bodies as predictive of correlated RNA and protein expression, that is independent of overall transcriptional activity. To demonstrate the generalizability of these findings we also identify similar results in an independent cohort of human breast cancers. Taken together, these analyses suggest that local enhancers, rather than distal enhancers, are likely most predictive of cancer gene expression phenotypes. This allows for identification of potential targets for cancer therapeutic approaches and reinforces the utility of multi-omics profiling as a methodology to understand human disease.
    DOI:  https://doi.org/10.1038/s41467-021-25872-1
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