bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021‒02‒14
eighty-four papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing.
  2. The IMiD target CRBN determines HSP90 activity toward transmembrane proteins essential in multiple myeloma.
  3. Mitochondria autophagy: a potential target for cancer therapy.
  4. Inflammatory cell-derived CXCL3 promotes pancreatic cancer metastasis through a novel myofibroblast-hijacked cancer escape mechanism.
  5. Beyond Autophagy: The Expanding Roles of ATG8 Proteins.
  6. Senescent cells and the incidence of age-related diseases.
  7. Mitophagy receptor FUNDC1 is regulated by PGC-1α/NRF1 to fine tune mitochondrial homeostasis.
  8. Whole-genome doubling confers unique genetic vulnerabilities on tumour cells.
  9. Distinct roles of UVRAG and EGFR signaling in skeletal muscle homeostasis.
  10. Fueling the cytoskeleton - links between cell metabolism and actin remodeling.
  11. Mitochondrial dynamics links PINCH-1 signaling to proline metabolic reprogramming and tumor growth.
  12. Preclinical Models of Pancreatic Ductal Adenocarcinoma and Their Utility in Immunotherapy Studies.
  13. Regulation of PRKN-Independent Mitophagy.
  14. IRF3 reduces adipose thermogenesis via ISG15-mediated reprogramming of glycolysis.
  15. Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts.
  16. TFEB-mediated lysosomal biogenesis and lysosomal drug sequestration confer resistance to MEK inhibition in pancreatic cancer.
  17. Mitophagy in tumorigenesis and metastasis.
  18. STING activated tumor-intrinsic type I IFN signaling promotes CXCR3 dependent antitumor immunity in pancreatic cancer.
  19. The distinct roles of calcium in rapid control of neuronal glycolysis and the tricarboxylic acid cycle.
  20. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives.
  21. Integrated spatial genomics reveals global architecture of single nuclei.
  22. Stress-induced nuclear condensation of NELF drives transcriptional downregulation.
  23. Suppression of p16 alleviates the senescence-associated secretory phenotype.
  24. Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation.
  25. Metabolic profiles of regulatory T cells in the tumour microenvironment.
  26. Differential mitochondrial gene expression in adipose tissue following weight loss induced by diet or bariatric surgery.
  27. Non-genetic evolution drives lung adenocarcinoma spatial heterogeneity and progression.
  28. S100A14 promotes progression and gemcitabine resistance in pancreatic cancer.
  29. Fueling Cell Invasion through Extracellular Matrix.
  30. From bench to bedside: updates in basic science, translational and clinical research on muscle fatigue in cancer cachexia.
  31. Biomolecular Condensates and Their Links to Cancer Progression.
  32. Inhibition of Mitochondrial Dynamics Preferentially Targets Pancreatic Cancer Cells with Enhanced Tumorigenic and Invasive Potential.
  33. Metabolic adaptation to hypoxia: do worms and cancer cells share common metabolic responses to hypoxic stress?
  34. Lactate in contemporary biology: A phoenix risen1.
  35. The nuclear envelope: target and mediator of the apoptotic process.
  36. The Adhesome Network: Key Components Shaping the Tumour Stroma.
  37. Shaping human telomeres: from shelterin and CST complexes to telomeric chromatin organization.
  38. The glucose-dependent insulinotropic polypeptide (GIP) regulates body weight and food intake via CNS-GIPR signaling.
  39. Mitochondrial dynamics in cancer stem cells.
  40. Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway.
  41. Heterogeneity in Metastatic Potential of Cancer Cells Is Revealed En Masse.
  42. Applications of CRISPR Genome Editing to Advance the Next Generation of Adoptive Cell Therapies for Cancer.
  43. The Golgi microtubules regulate single cell durotaxis.
  44. Demographic perspectives on the rise of longevity.
  45. Mutations in the RAS/MAPK pathway drive replication repair deficient hypermutated tumors and confer sensitivity to MEK inhibition.
  46. Lysosome biology in autophagy.
  47. Cancer risk in normal-weight individuals with metabolic obesity: A narrative review.
  48. Assessing Autophagy in Muscle Stem Cells.
  49. The therapeutic potential of renin-angiotensin system inhibitors in the treatment of pancreatic cancer.
  50. Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit.
  51. Regulation of biomolecular condensate dynamics by signaling.
  52. The Increasing Proportion of Early-Stage Pancreatic Cancer between 2004-2013: A SEER Analysis.
  53. Telomere Length as a Marker of Biological Age: State-of-the-Art, Open Issues, and Future Perspectives.
  54. Immune profiling and immunotherapeutic targets in pancreatic cancer.
  55. Cutting edge: Metabolic immune reprogramming, reactive oxygen species, and cancer.
  56. Cost-Effective Trap qPCR Approach to Evaluate Telomerase Activity: an Important Tool for Aging, Cancer, and Chronic Disease Research.
  57. DNA- and telomere-damage does not limit lifespan: evidence from rapamycin.
  58. Transcriptome analysis of the procession from chronic pancreatitis to pancreatic cancer and metastatic pancreatic cancer.
  59. Sensing and Signaling of Methionine Metabolism.
  60. Standing at the Crossroads.
  61. Mouse model of colorectal cancer: orthotopic co-implantation of tumor and stroma cells in cecum and rectum.
  62. shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data.
  63. Targeting and Reprograming Cancer-Associated Fibroblasts and the Tumor Microenvironment in Pancreatic Cancer.
  64. A Malignant Case of Arrested Development: Cancer Cell Dormancy Mimics Embryonic Diapause.
  65. The NANOTUMOR consortium - towards the Tumor Cell Atlas.
  66. Weight loss with exercise improves muscle architecture and progenitor cell populations compared to weight loss alone in mice with preneoplastic colorectal lesions.
  67. Regulation of ATR-dependent DNA damage response by nitric oxide.
  68. Overexpression of TopBP1, a canonical ATR/Chk1 activator, paradoxically hinders ATR/Chk1 activation in cancer.
  69. Transient phases of OXPHOS inhibitor resistance reveal underlying metabolic heterogeneity in single cells.
  70. Malignant subclone drives metastasis of genetically and phenotypically heterogenous cell clusters through fibrotic niche generation.
  71. Tumour-regulated anorexia preceding cachexia.
  72. Hyperglycemia Promotes Pancreatic Cancer Initiation and Progression by Activating the Wnt/β-Catenin Signaling Pathway.
  73. DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks.
  74. Leveraging Single-Cell Approaches in Cancer Precision Medicine.
  75. Gain-of-function p53 protein transferred via small extracellular vesicles promotes conversion of fibroblasts to a cancer-associated phenotype.
  76. Inhibition of Stearoyl-CoA Desaturase Induces the Unfolded Protein Response in Pancreatic Tumors and Suppresses Their Growth.
  77. Fabrication of a microfluidic device for studying the combinatorial effect of physical and chemical cues on cell migration.
  78. Solid tumours hijack the histone variant network.
  79. Mitochondrial outer membrane permeabilization at the single molecule level.
  80. Proteogenomic and metabolomic characterization of human glioblastoma.
  81. Intratumoral heterogeneity in cancer progression and response to immunotherapy.
  82. Mechanism of gating and partial agonist action in the glycine receptor.
  83. Tissue-Specific Landscape of Metabolic Dysregulation during Ageing.
  84. Divide and conquer acoustic diversity.
  1. Nat Cancer. 2020 ;1 653-664
    The serine hydroxymethyltransferase-2 (SHMT2) initiates lymphoma development through epigenetic tumor suppressor silencing.
    Sara Parsa, Ana Ortega-Molina, Hsia-Yuan Ying, Man Jiang, Matt Teater, Jiahui Wang, Chunying Zhao, Ed Reznik, Joyce P Pasion, David Kuo, Prathibha Mohan, Shenqiu Wang, Jeannie M Camarillo, Paul M Thomas, Neeraj Jain, Javier Garcia-Bermudez, Byoung-Kyu Cho, Wayne Tam, Neil L Kelleher, Nicholas Socci, Ahmet Dogan, Elisa De Stanchina, Giovanni Ciriello, Michael R Green, Sheng Li, Kivanc Birsoy, Ari M Melnick, Hans-Guido Wendel.
      Cancer cells adapt their metabolic activities to support growth and proliferation. However, increased activity of metabolic enzymes is not usually considered an initiating event in the malignant process. Here, we investigate the possible role of the enzyme serine hydroxymethyltransferase-2 (SHMT2) in lymphoma initiation. SHMT2 localizes to the most frequent region of copy number gains at chromosome 12q14.1 in lymphoma. Elevated expression of SHMT2 cooperates with BCL2 in lymphoma development; loss or inhibition of SHMT2 impairs lymphoma cell survival. SHMT2 catalyzes the conversion of serine to glycine and produces an activated one-carbon unit that can be used to support S-adenosyl methionine synthesis. SHMT2 induces changes in DNA and histone methylation patterns leading to promoter silencing of previously uncharacterized mutational genes, such as SASH1 and PTPRM. Together, our findings reveal that amplification of SHMT2 in cooperation with BCL2 is sufficient in the initiation of lymphomagenesis through epigenetic tumor suppressor silencing.
    DOI:  https://doi.org/10.1038/s43018-020-0080-0
  2. Mol Cell. 2021 Feb 03. pii: S1097-2765(20)30988-6. [Epub ahead of print]
    The IMiD target CRBN determines HSP90 activity toward transmembrane proteins essential in multiple myeloma.
    Michael Heider, Ruth Eichner, Jacob Stroh, Volker Morath, Anna Kuisl, Jana Zecha, Jannis Lawatscheck, Kheewoong Baek, Anne-Kathrin Garz, Martina Rudelius, Friedrich-Christian Deuschle, Ulrich Keller, Simone Lemeer, Mareike Verbeek, Katharina S Götze, Arne Skerra, Wolfgang A Weber, Johannes Buchner, Brenda A Schulman, Bernhard Kuster, Vanesa Fernández-Sáiz, Florian Bassermann.
      The complex architecture of transmembrane proteins requires quality control (QC) of folding, membrane positioning, and trafficking as prerequisites for cellular homeostasis and intercellular communication. However, it has remained unclear whether transmembrane protein-specific QC hubs exist. Here we identify cereblon (CRBN), the target of immunomodulatory drugs (IMiDs), as a co-chaperone that specifically determines chaperone activity of HSP90 toward transmembrane proteins by means of counteracting AHA1. This function is abrogated by IMiDs, which disrupt the interaction of CRBN with HSP90. Among the multiple transmembrane protein clients of CRBN-AHA1-HSP90 revealed by cell surface proteomics, we identify the amino acid transporter LAT1/CD98hc as a determinant of IMiD activity in multiple myeloma (MM) and present an Anticalin-based CD98hc radiopharmaceutical for MM radio-theranostics. These data establish the CRBN-AHA1-HSP90 axis in the biogenesis of transmembrane proteins, link IMiD activity to tumor metabolism, and nominate CD98hc and LAT1 as attractive diagnostic and therapeutic targets in MM.
    Keywords:  CD98hc; CRBN; HSP90; IMiDs; LAT1; chaperones; multiple myeloma; protein quality control; radio-theranostics; ubiquitin
    DOI:  https://doi.org/10.1016/j.molcel.2020.12.046
  3. J Drug Target. 2021 Feb 08. 1-16
    Mitochondria autophagy: a potential target for cancer therapy.
    Yu-Han Qiu, Tian-Shu Zhang, Xiao-Wei Wang, Meng-Yan Wang, Wen-Xia Zhao, Hui-Min Zhou, Cong-Hui Zhang, Mei-Lian Cai, Xiao-Fang Chen, Wu-Li Zhao, Rong-Guang Shao.
      Mitophagy is a selective form of macroautophagy in which dysfunctional and damaged mitochondria can be efficiently degraded, removed and recycled through autophagy. Selective removal of damaged or fragmented mitochondria is critical to the functional integrity of the entire mitochondrial network and cells. In past decades, numerous studies have shown that mitophagy is involved in various diseases; however, since the dual role of mitophagy in tumour development, mitophagy role in tumour is controversial, and further elucidation is needed. That is, although mitophagy has been demonstrated to contribute to carcinogenesis, cell migration, ferroptosis inhibition, cancer stemness maintenance, tumour immune escape, drug resistance, etc. during cancer progression, many research also shows that to promote cancer cell death, mitophagy can be induced physiologically or pharmacologically to maintain normal cellular metabolism and prevent cell stress responses and genome damage by diminishing mitochondrial damage, thus suppressing tumour development accompanying these changes. Signalling pathway-specific molecular mechanisms are currently of great biological significance in the identification of potential therapeutic targets. Here, we review recent progress of molecular pathways mediating mitophagy including both canonical pathways (Parkin/PINK1- and FUNDC1-mediated mitophagy) and noncanonical pathways (FKBP8-, Nrf2-, and DRP1-mediated mitophagy); and the regulation of these pathways, and abovementioned pro-cancer and pro-death roles of mitophagy. Finally, we summarise the role of mitophagy in cancer therapy. Mitophagy can potentially be acted as the target for cancer therapy by promotion or inhibition.
    Keywords:  LC3; Mitophagy; PINK1; cancer; parkin
    DOI:  https://doi.org/10.1080/1061186X.2020.1867992
  4. Gut. 2021 Feb 10. pii: gutjnl-2020-322744. [Epub ahead of print]
    Inflammatory cell-derived CXCL3 promotes pancreatic cancer metastasis through a novel myofibroblast-hijacked cancer escape mechanism.
    Xiaoting Sun, Xingkang He, Yin Zhang, Kayoko Hosaka, Patrik Andersson, Jing Wu, Jieyu Wu, Xu Jing, Qiqiao Du, Xiaoli Hui, Bo Ding, Ziheng Guo, An Hong, Xuan Liu, Yan Wang, Qing Ji, Rudi Beyaert, Yunlong Yang, Qi Li, Yihai Cao.
      OBJECTIVE: Pancreatic ductal adenocarcinoma (PDAC) is the most lethal malignancy and lacks effective treatment. We aimed to understand molecular mechanisms of the intertwined interactions between tumour stromal components in metastasis and to provide a new paradigm for PDAC therapy.DESIGN: Two unselected cohorts of 154 and 20 patients with PDAC were subjected to correlation between interleukin (IL)-33 and CXCL3 levels and survivals. Unbiased expression profiling, and genetic and pharmacological gain-of-function and loss-of-function approaches were employed to identify molecular signalling in tumour-associated macrophages (TAMs) and myofibroblastic cancer-associated fibroblasts (myoCAFs). The role of the IL-33-ST2-CXCL3-CXCR2 axis in PDAC metastasis was evaluated in three clinically relevant mouse PDAC models.
    RESULTS: IL-33 was specifically elevated in human PDACs and positively correlated with tumour inflammation in human patients with PDAC. CXCL3 was highly upregulated in IL-33-stimulated macrophages that were the primary source of CXCL3. CXCL3 was correlated with poor survival in human patients with PDAC. Mechanistically, activation of the IL-33-ST2-MYC pathway attributed to high CXCL3 production. The highest level of CXCL3 was found in PDAC relative to other cancer types and its receptor CXCR2 was almost exclusively expressed in CAFs. Activation of CXCR2 by CXCL3 induced a CAF-to-myoCAF transition and α-smooth muscle actin (α-SMA) was uniquely upregulated by the CXCL3-CXCR2 signalling. Type III collagen was identified as the CXCL3-CXCR2-targeted adhesive molecule responsible for myoCAF-driven PDAC metastasis.
    CONCLUSIONS: Our work provides novel mechanistic insights into understanding PDAC metastasis by the TAM-CAF interaction and targeting each of these signalling components would provide an attractive and new paradigm for treating pancreatic cancer.
    Keywords:  chemokines; interleukins; macrophages; myofibroblasts; pancreatic cancer
    DOI:  https://doi.org/10.1136/gutjnl-2020-322744
  5. Trends Biochem Sci. 2021 Feb 05. pii: S0968-0004(21)00006-2. [Epub ahead of print]
    Beyond Autophagy: The Expanding Roles of ATG8 Proteins.
    Jose L Nieto-Torres, Andrew M Leidal, Jayanta Debnath, Malene Hansen.
      The ATG8 family proteins are critical players in autophagy, a cytoprotective process that mediates degradation of cytosolic cargo. During autophagy, ATG8s conjugate to autophagosome membranes to facilitate cargo recruitment, autophagosome biogenesis, transport, and fusion with lysosomes, for cargo degradation. In addition to these canonical functions, recent reports demonstrate that ATG8s are also delivered to single-membrane organelles, which leads to highly divergent degradative or secretory fates, vesicle maturation, and cargo specification. The association of ATG8s with different vesicles involves complex regulatory mechanisms still to be fully elucidated. Whether individual ATG8 family members play unique canonical or non-canonical roles, also remains unclear. This review summarizes the many open molecular questions regarding ATG8s that are only beginning to be unraveled.
    Keywords:  GABARAP; LC3; LC3-associated phagocytosis; multivesicular bodies; non-canonical autophagy; unconventional secretion
    DOI:  https://doi.org/10.1016/j.tibs.2021.01.004
  6. Aging Cell. 2021 Feb 08. e13314
    Senescent cells and the incidence of age-related diseases.
    Itay Katzir, Miri Adler, Omer Karin, Netta Mendelsohn-Cohen, Avi Mayo, Uri Alon.
      Age-related diseases such as cancer, cardiovascular disease, kidney failure, and osteoarthritis have universal features: Their incidence rises exponentially with age with a slope of 6-8% per year and decreases at very old ages. There is no conceptual model which explains these features in so many diverse diseases in terms of a single shared biological factor. Here, we develop such a model, and test it using a nationwide medical record dataset on the incidence of nearly 1000 diseases over 50 million life-years, which we provide as a resource. The model explains incidence using the accumulation of senescent cells, damaged cells that cause inflammation and reduce regeneration, whose level rise stochastically with age. The exponential rise and late drop in incidence are captured by two parameters for each disease: the susceptible fraction of the population and the threshold concentration of senescent cells that causes disease onset. We propose a physiological mechanism for the threshold concentration for several disease classes, including an etiology for diseases of unknown origin such as idiopathic pulmonary fibrosis and osteoarthritis. The model can be used to design optimal treatments that remove senescent cells, suggeting that treatment starting at old age can sharply reduce the incidence of all age-related diseases, and thus increase the healthspan.
    Keywords:  age-related disease; aging; cancer; cellular senescence; diabetes; electronic medical records; fibrosis; idiopathic pulmonary fibrosis; incidence rate; mathematical model; osteoarthritis
    DOI:  https://doi.org/10.1111/acel.13314
  7. EMBO Rep. 2021 Feb 08. e50629
    Mitophagy receptor FUNDC1 is regulated by PGC-1α/NRF1 to fine tune mitochondrial homeostasis.
    Lei Liu, Yanjun Li, Jianing Wang, Di Zhang, Hao Wu, Wenhui Li, Huifang Wei, Na Ta, Yuyuan Fan, Yujiao Liu, Xiaohui Wang, Jun Wang, Xin Pan, Xudong Liao, Yushan Zhu, Quan Chen.
      Mitophagy is an essential cellular autophagic process that selectively removes superfluous and damaged mitochondria, and it is coordinated with mitochondrial biogenesis to fine tune the quantity and quality of mitochondria. Coordination between these two opposing processes to maintain the functional mitochondrial network is of paramount importance for normal cellular and organismal metabolism. However, the underlying mechanism is not completely understood. Here we report that PGC-1α and nuclear respiratory factor 1 (NRF1), master regulators of mitochondrial biogenesis and metabolic adaptation, also transcriptionally upregulate the gene encoding FUNDC1, a previously characterized mitophagy receptor, in response to cold stress in brown fat tissue. NRF1 binds to the classic consensus site in the promoter of Fundc1 to upregulate its expression and to enhance mitophagy through its interaction with LC3. Specific knockout of Fundc1 in BAT results in reduced mitochondrial turnover and accumulation of functionally compromised mitochondria, leading to impaired adaptive thermogenesis. Our results demonstrate that FUNDC1-dependent mitophagy is directly coupled with mitochondrial biogenesis through the PGC-1α/NRF1 pathway, which dictates mitochondrial quantity, quality, and turnover and contributes to adaptive thermogenesis.
    Keywords:  adaptive thermogenesis; brown adipose tissue; mitochondrial biogenesis; mitophagy
    DOI:  https://doi.org/10.15252/embr.202050629
  8. Nature. 2021 Jan 27.
    Whole-genome doubling confers unique genetic vulnerabilities on tumour cells.
    Ryan J Quinton, Amanda DiDomizio, Marc A Vittoria, Kristýna Kotýnková, Carlos J Ticas, Sheena Patel, Yusuke Koga, Jasmine Vakhshoorzadeh, Nicole Hermance, Taruho S Kuroda, Neha Parulekar, Alison M Taylor, Amity L Manning, Joshua D Campbell, Neil J Ganem.
      Whole-genome doubling (WGD) is common in human cancers, occurring early in tumorigenesis and generating genetically unstable tetraploid cells that fuel tumour development1,2. Cells that undergo WGD (WGD+ cells) must adapt to accommodate their abnormal tetraploid state; however, the nature of these adaptations, and whether they confer vulnerabilities that can be exploited therapeutically, is unclear. Here, using sequencing data from roughly 10,000 primary human cancer samples and essentiality data from approximately 600 cancer cell lines, we show that WGD gives rise to common genetic traits that are accompanied by unique vulnerabilities. We reveal that WGD+ cells are more dependent than WGD- cells on signalling from the spindle-assembly checkpoint, DNA-replication factors and proteasome function. We also identify KIF18A, which encodes a mitotic kinesin protein, as being specifically required for the viability of WGD+ cells. Although KIF18A is largely dispensable for accurate chromosome segregation during mitosis in WGD- cells, its loss induces notable mitotic errors in WGD+ cells, ultimately impairing cell viability. Collectively, our results suggest new strategies for specifically targeting WGD+ cancer cells while sparing the normal, non-transformed WGD- cells that comprise human tissue.
    DOI:  https://doi.org/10.1038/s41586-020-03133-3
  9. Mol Metab. 2021 Feb 06. pii: S2212-8778(21)00025-9. [Epub ahead of print] 101185
    Distinct roles of UVRAG and EGFR signaling in skeletal muscle homeostasis.
    Min Jeong Kim, Daniella Febbraro, Sofia Farkona, Taylor Gillmore, Joe Eun Son, Romario Regeenes, Huntley H Chang, Evan Pollock-Tahiri, Jiaqi Yang, Yoo Jin Park, Tharini Sivasubramaniyam, Soo Jung Oh, Punit Saraon, Igor Stagljar, Jonathan V Rocheleau, Chi-Chung Hui, Isabella Caniggia, Zhenyu Hao, Tak W Mak, Ana Konvalinka, Minna Woo.
      OBJECTIVE: Autophagy is a physiological self-eating process that can promote cell survival or activate cell death in eukaryotic cells. In skeletal muscle, it is important in the maintenance of muscle mass and function that is critical to sustain mobility and regulate metabolism. UV radiation resistance-associated gene (UVRAG) regulates early stages of autophagy and autophagosome maturation, while also playing a key role in endosomal trafficking. This study investigated the essential in vivo role of UVRAG in skeletal muscle biology.METHODS: To determine the role of UVRAG in skeletal muscle in vivo, we generated muscle specific UVRAG knock-out mice using the cre-loxP system driven by Myf6 promoter that is exclusively expressed in skeletal muscle. Myf6- Cre+ UVRAGfl/fl (M-UVRAG-/-) mice were compared to littermate Myf6-Cre+ UVRAG+/+ (M-UVRAG+/+) controls under basal conditions on normal chow diet. Body composition, muscle function and mitochondria morphology were assessed in muscles of WT and KO mice at 24 weeks of age.
    RESULTS: M-UVRAG-/- mice developed accelerated sarcopenia and impaired muscle function compared to M-UVRAG+/+ littermates at 24 weeks of age. Interestingly, these mice displayed improved glucose tolerance and increased energy expenditure likely related to up-regulated Fgf21, a marker of muscle dysfunction. Skeletal muscle of M-UVRAG-/- mice showed altered mitochondrial morphology with increased mitochondrial fission, as well as EGFR accumulation reflecting defects in endosomal trafficking. To determine whether increased EGFR signaling had a causal role in muscle dysfunction, mice were treated with an EGFR inhibitor, gefitinib, which partially restored markers of muscle and mitochondrial deregulation. Conversely, constitutively active EGFR transgenic expression in UVRAG deficient muscle led to further detrimental effects with non-overlapping distinct defects in muscle function, with EGFR activation affecting muscle fiber type whereas UVRAG deficiency impaired mitochondrial homeostasis.
    CONCLUSIONS: Our results show that both UVRAG and EGFR signaling are critical in the maintenance of muscle mass and function with distinct mechanisms in the differentiation pathway.
    Keywords:  EGFR; Fgf21; UVRAG; mitochondrial dynamics; skeletal muscle
    DOI:  https://doi.org/10.1016/j.molmet.2021.101185
  10. J Cell Sci. 2021 Feb 08. pii: jcs248385. [Epub ahead of print]134(3):
    Fueling the cytoskeleton - links between cell metabolism and actin remodeling.
    Gillian DeWane, Alicia M Salvi, Kris A DeMali.
      Attention has long focused on the actin cytoskeleton as a unit capable of organizing into ensembles that control cell shape, polarity, migration and the establishment of intercellular contacts that support tissue architecture. However, these investigations do not consider observations made over 40 years ago that the actin cytoskeleton directly binds metabolic enzymes, or emerging evidence suggesting that the rearrangement and assembly of the actin cytoskeleton is a major energetic drain. This Review examines recent studies probing how cells adjust their metabolism to provide the energy necessary for cytoskeletal remodeling that occurs during cell migration, epithelial to mesenchymal transitions, and the cellular response to external forces. These studies have revealed that mechanotransduction, cell migration, and epithelial to mesenchymal transitions are accompanied by alterations in glycolysis and oxidative phosphorylation. These metabolic changes provide energy to support the actin cytoskeletal rearrangements necessary to allow cells to assemble the branched actin networks required for cell movement and epithelial to mesenchymal transitions and the large actin bundles necessary for cells to withstand forces. In this Review, we discuss the emerging evidence suggesting that the regulation of these events is highly complex with metabolism affecting the actin cytoskeleton and vice versa.
    Keywords:  Actin; Cytoskeleton; Force; Mechanotransduction
    DOI:  https://doi.org/10.1242/jcs.248385
  11. Cell Stress. 2020 Dec 10. 5(2): 23-25
    Mitochondrial dynamics links PINCH-1 signaling to proline metabolic reprogramming and tumor growth.
    Ling Guo, Chuanyue Wu.
      Proline metabolism is critical for cellular response to microenvironmental stress in living organisms across different kingdoms, ranging from bacteria, plants to animals. In bacteria and plants, proline is known to accrue in response to osmotic and other stresses. In higher organisms such as human, proline metabolism plays important roles in physiology as well as pathological processes including cancer. The importance of proline metabolism in physiology and diseases lies in the fact that the products of proline metabolism are intimately involved in essential cellular processes including protein synthesis, energy production and redox signaling. A surge of protein synthesis in fast proliferating cancer cells, for example, results in markedly increased demand for proline. Proline synthesis is frequently unable to meet the demand in fast proliferating cancer cells. The inadequacy of proline or "proline vulnerability" in cancer may provide an opportunity for therapeutic control of cancer progression. To this end, it is important to understand the signaling mechanism through which proline synthesis is regulated. In a recent study (Guo et al., Nat Commun 11(1):4913, doi: 10.1038/s41467-020-18753-6), we have identified PINCH-1, a component of cell-extracellular matrix (ECM) adhesions, as an important regulator of proline synthesis and cancer progression.
    Keywords:  PINCH-1; cell-extracellular matrix adhesion; fibrosis; mitochondrial dynamics; proline metabolism; tumor growth
    DOI:  https://doi.org/10.15698/cst2021.02.241
  12. Cancers (Basel). 2021 Jan 25. pii: 440. [Epub ahead of print]13(3):
    Preclinical Models of Pancreatic Ductal Adenocarcinoma and Their Utility in Immunotherapy Studies.
    Thao N D Pham, Mario A Shields, Christina Spaulding, Daniel R Principe, Bo Li, Patrick W Underwood, Jose G Trevino, David J Bentrem, Hidayatullah G Munshi.
      The advent of immunotherapy has transformed the treatment landscape for several human malignancies. Antibodies against immune checkpoints, such as anti-PD-1/PD-L1 and anti-CTLA-4, demonstrate durable clinical benefits in several cancer types. However, checkpoint blockade has failed to elicit effective anti-tumor responses in pancreatic ductal adenocarcinoma (PDAC), which remains one of the most lethal malignancies with a dismal prognosis. As a result, there are significant efforts to identify novel immune-based combination regimens for PDAC, which are typically first tested in preclinical models. Here, we discuss the utility and limitations of syngeneic and genetically-engineered mouse models that are currently available for testing immunotherapy regimens. We also discuss patient-derived xenograft mouse models, human PDAC organoids, and ex vivo slice cultures of human PDAC tumors that can complement murine models for a more comprehensive approach to predict response and resistance to immunotherapy regimens.
    Keywords:  genetically-engineered mouse models; human tumor slice cultures; immunotherapy; murine models; organoids; pancreatic cancer; patient-derived xenografts
    DOI:  https://doi.org/10.3390/cancers13030440
  13. Autophagy. 2021 Feb 11.
    Regulation of PRKN-Independent Mitophagy.
    Petra Terešak, Ana Lapao, Nemanja Subic, Patricia Boya, Zvulun Elazar, Anne Simonsen.
      Mitochondria are dynamic, multifunctional cellular organelles that play a fundamental role in maintaining cellular homeostasis. Keeping the quality of mitochondria in check is of essential importance for functioning and survival of the cells. Selective autophagic clearance of flawed mitochondria, a process termed mitophagy, is one of the most prominent mechanisms through which cells maintain a healthy mitochondrial pool. The best-studied pathway through which mitophagy is exerted is the PINK1-PRKN pathway. However, an increasing number of studies have shown an existence of alternative pathways, where different proteins and lipids are able to recruit autophagic machinery independently of PINK1 and PRKN. The significance of PRKN-independent mitophagy pathways is reflected in various physiological and pathophysiological processes, but many questions regarding the regulation and the interplay between these pathways remain open. Here we review the current knowledge and recent progress made in the field of PRKN-independent mitophagy. Particularly we focus on the regulation of various receptors that participate in targeting impaired mitochondria to autophagosomes independently of PRKN.
    Keywords:  autophagy receptors; mitochondria; mitochondrial dysfunction; mitophagy; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2021.1888244
  14. J Clin Invest. 2021 Feb 11. pii: 144888. [Epub ahead of print]
    IRF3 reduces adipose thermogenesis via ISG15-mediated reprogramming of glycolysis.
    Shuai Yan, Manju Kumari, Haopeng Xiao, Christopher Jacobs, Shihab Kochumon, Mark Jedrychowski, Edward Chouchani, Rasheed Ahmad, Evan D Rosen.
      Adipose thermogenesis is repressed in obesity, reducing the homeostatic capacity to compensate for chronic overnutrition. Inflammation inhibits adipose thermogenesis, but little is known about how this occurs. Here we show that the innate immune transcription factor IRF3 is a strong repressor of thermogenic gene expression and oxygen consumption in adipocytes. IRF3 achieves this by driving expression of the ubiquitin-like modifier ISG15, which becomes covalently attached to glycolytic enzymes, thus reducing their function and decreasing lactate production. Lactate repletion is able to restore thermogenic gene expression, even when the IRF3-ISG15 axis is activated. Mice lacking ISG15 phenocopy mice lacking IRF3 in adipocytes, as both have elevated energy expenditure and are resistant to diet-induced obesity. These studies provide a deep mechanistic understanding of how the chronic inflammatory milieu of adipose tissue in obesity prevents thermogenic compensation for overnutrition.
    Keywords:  Adipose tissue; Innate immunity; Metabolism
    DOI:  https://doi.org/10.1172/JCI144888
  15. Nat Commun. 2021 Feb 12. 12(1): 970
    Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts.
    Rebecca E Graff, Taylor B Cavazos, Khanh K Thai, Linda Kachuri, Sara R Rashkin, Joshua D Hoffman, Stacey E Alexeeff, Maruta Blatchins, Travis J Meyers, Lancelote Leong, Caroline G Tai, Nima C Emami, Douglas A Corley, Lawrence H Kushi, Elad Ziv, Stephen K Van Den Eeden, Eric Jorgenson, Thomas J Hoffmann, Laurel A Habel, John S Witte, Lori C Sakoda.
      Even distinct cancer types share biological hallmarks. Here, we investigate polygenic risk score (PRS)-specific pleiotropy across 16 cancers in European ancestry individuals from the Genetic Epidemiology Research on Adult Health and Aging cohort (16,012 cases, 50,552 controls) and UK Biobank (48,969 cases, 359,802 controls). Within cohorts, each PRS is evaluated in multivariable logistic regression models against all other cancer types. Results are then meta-analyzed across cohorts. Ten positive and one inverse cross-cancer associations are found after multiple testing correction. Two pairs show bidirectional associations; the melanoma PRS is positively associated with oral cavity/pharyngeal cancer and vice versa, whereas the lung cancer PRS is positively associated with oral cavity/pharyngeal cancer, and the oral cavity/pharyngeal cancer PRS is inversely associated with lung cancer. Overall, we validate known, and uncover previously unreported, patterns of pleiotropy that have the potential to inform investigations of risk prediction, shared etiology, and precision cancer prevention strategies.
    DOI:  https://doi.org/10.1038/s41467-021-21288-z
  16. Cell Death Discov. 2020 Mar 11. 6(1): 12
    TFEB-mediated lysosomal biogenesis and lysosomal drug sequestration confer resistance to MEK inhibition in pancreatic cancer.
    Ben Zhao, Laura Dierichs, Jiang-Ning Gu, Marija Trajkovic-Arsic, Ralf Axel Hilger, Konstantinos Savvatakis, Silvia Vega-Rubin-de-Celis, Sven-Thorsten Liffers, Samuel Peña-Llopis, Diana Behrens, Stephan Hahn, Jens T Siveke, Smiths S Lueong.
      Oncogenic KRAS mutations are encountered in more than 90% of pancreatic ductal adenocarcinomas. MEK inhibition has failed to procure any clinical benefits in mutant RAS-driven cancers including pancreatic ductal adenocarcinoma (PDAC). To identify potential resistance mechanisms underlying MEK inhibitor (MEKi) resistance in PDAC, we investigated lysosomal drug accumulation in PDAC models both in vitro and in vivo. Mouse PDAC models and human PDAC cell lines as well as human PDAC xenografts treated with the MEK inhibitor trametinib or refametinib led to an enhanced expression of lysosomal markers and enrichment of lysosomal gene sets. A time-dependent, increase in lysosomal content was observed upon MEK inhibition. Strikingly, there was a strong activation of lysosomal biogenesis in cell lines of the classical compared to the basal-like molecular subtype. Increase in lysosomal content was associated with nuclear translocation of the Transcription Factor EB (TFEB) and upregulation of TFEB target genes. siRNA-mediated depletion of TFEB led to a decreased lysosomal biogenesis upon MEK inhibition and potentiated sensitivity. Using LC-MS, we show accumulation of MEKi in the lysosomes of treated cells. Therefore, MEK inhibition triggers lysosomal biogenesis and subsequent drug sequestration. Combined targeting of MEK and lysosomal function may improve sensitivity to MEK inhibition in PDAC.
    DOI:  https://doi.org/10.1038/s41420-020-0246-7
  17. Cell Mol Life Sci. 2021 Feb 13.
    Mitophagy in tumorigenesis and metastasis.
    Logan P Poole, Kay F Macleod.
      Cells use mitophagy to remove dysfunctional or excess mitochondria, frequently in response to imposed stresses, such as hypoxia and nutrient deprivation. Mitochondrial cargo receptors (MCR) induced by these stresses target mitochondria to autophagosomes through interaction with members of the LC3/GABARAP family. There are a growing number of these MCRs, including BNIP3, BNIP3L, FUNDC1, Bcl2-L-13, FKBP8, Prohibitin-2, and others, in addition to mitochondrial protein targets of PINK1/Parkin phospho-ubiquitination. There is also an emerging link between mitochondrial lipid signaling and mitophagy where ceramide, sphingosine-1-phosphate, and cardiolipin have all been shown to promote mitophagy. Here, we review the upstream signaling mechanisms that regulate mitophagy, including components of the mitochondrial fission machinery, AMPK, ATF4, FoxOs, Sirtuins, and mtDNA release, and address the significance of these pathways for stress responses in tumorigenesis and metastasis. In particular, we focus on how mitophagy modulators intersect with cell cycle control and survival pathways in cancer, including following ECM detachment and during cell migration and metastasis. Finally, we interrogate how mitophagy affects tissue atrophy during cancer cachexia and therapy responses in the clinic.
    Keywords:  AMPK; ATF4; Autophagy; BCL2-L-13; BNIP3/BNIP3L; Cachexia; DRP1; Electron transport chain; FUNDC1; Fission; FoxOs; LC3/GABARAP; Metabolism; Metastasis; Mitochondria; Mitohormesis; Mitophagy; NAD+; PARP; PINK1/Parkin; ROS; Respiration; Sirtuins; UPRmt
    DOI:  https://doi.org/10.1007/s00018-021-03774-1
  18. Cell Mol Gastroenterol Hepatol. 2021 Feb 03. pii: S2352-345X(21)00024-2. [Epub ahead of print]
    STING activated tumor-intrinsic type I IFN signaling promotes CXCR3 dependent antitumor immunity in pancreatic cancer.
    Emily P Vonderhaar, Nicholas S Barnekow, Donna McAllister, Laura McOlash, Mahmoud Abu Eid, Matthew J Riese, Vera L Tarakanova, Bryon D Johnson, Michael B Dwinell.
      BACKGROUND AND AIMS: Pancreatic ductal adenocarcinoma (PDA) is a lethal chemoresistant cancer that exhibits early metastatic spread. The highly immuno-suppressive PDA tumor microenvironment renders patients resistant to emerging immune-targeted therapies. Building from our prior work we evaluated Stimulator of Interferon Genes (STING) agonist activation of PDA cell interferon-αβ-receptor (IFNAR) signaling in systemic antitumor immune responses.METHODS: PDA cells were implanted subcutaneously to wild-type, IFNAR- or CXCR3-knock-out mice. Tumor growth was monitored and immune responses comprehensively profiled.
    RESULTS: Human and mouse STING agonist ADU-S100 reduced local and distal tumor burden and activated systemic tumor reactive antitumor immune responses in PDA-bearing mice. Effector T cell infiltration and inflammatory cytokine and chemokine production, including IFN-dependent CXCR3-agonist chemokines, were elevated while suppressive immune populations were decreased in treated tumors. Intratumoral STING agonist treatment also generated inflammation in distal non-injected tumors and peripheral immune tissues. STING agonist treatment of type I IFN-responsive PDA tumors engrafted to IFNAR-/- recipient mice was sufficient to contract tumors and stimulate local and systemic T cell activation. Tumor regression and CD8+ T cell infiltration were abolished in PDA-engrafted to CXCR3-/- mice treated with STING agonist.
    CONCLUSION: These data indicate that STING agonists promote T cell infiltration and counteract immune suppression in locally treated and distant tumors. Tumor-intrinsic type I IFN signaling initiated systemic STING-mediated antitumor inflammation and required CXCR3 expression. STING-mediated induction of systemic immune responses provides an approach to harness the immune system to treat primary and disseminated pancreatic cancers.
    Keywords:  Antitumor Immunity; Flow Immunophenotyping; Tumor Microenvironment; Tumor-intrinsic IFNAR signaling
    DOI:  https://doi.org/10.1016/j.jcmgh.2021.01.018
  19. Elife. 2021 Feb 08. pii: e64821. [Epub ahead of print]10
    The distinct roles of calcium in rapid control of neuronal glycolysis and the tricarboxylic acid cycle.
    Carlos Manlio Díaz-García, Dylan J Meyer, Nidhi Nathwani, Mahia Rahman, Juan Ramón Martínez-François, Gary Yellen.
      When neurons engage in intense periods of activity, the consequent increase in energy demand can be met by the coordinated activation of glycolysis, the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation. However, the trigger for glycolytic activation is unknown and the role for Ca2+ in the mitochondrial responses has been debated. Using genetically encoded fluorescent biosensors and NAD(P)H autofluorescence imaging in acute hippocampal slices, here we find that Ca2+ uptake into the mitochondria is responsible for the buildup of mitochondrial NADH, probably through Ca2+ activation of dehydrogenases in the TCA cycle. In the cytosol, we do not observe a role for the Ca2+/calmodulin signaling pathway, or AMPK, in mediating the rise in glycolytic NADH in response to acute stimulation. Aerobic glycolysis in neurons is triggered mainly by the energy demand resulting from either Na+ or Ca2+ extrusion, and in mouse dentate granule cells, Ca2+ creates the majority of this demand.
    Keywords:  brain metabolism; mitochondrial calcium; mitochondrial calcium uniporter; mouse; neuronal glycolysis; neuroscience
    DOI:  https://doi.org/10.7554/eLife.64821
  20. Mol Cell Proteomics. 2020 Dec 07. pii: S1535-9476(20)35130-6. [Epub ahead of print]20 100016
    Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives.
    Alison Barbara Ross, Julian David Langer, Marko Jovanovic.
      In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
    Keywords:  Dynamic SILAC; Mass spectrometry; Protein degradation; Protein synthesis; Proteome turnover; Proteomics; pSILAC
    DOI:  https://doi.org/10.1074/mcp.R120.002190
  21. Nature. 2021 02;590(7845): 344-350
    Integrated spatial genomics reveals global architecture of single nuclei.
    Yodai Takei, Jina Yun, Shiwei Zheng, Noah Ollikainen, Nico Pierson, Jonathan White, Sheel Shah, Julian Thomassie, Shengbao Suo, Chee-Huat Linus Eng, Mitchell Guttman, Guo-Cheng Yuan, Long Cai.
      Identifying the relationships between chromosome structures, nuclear bodies, chromatin states and gene expression is an overarching goal of nuclear-organization studies1-4. Because individual cells appear to be highly variable at all these levels5, it is essential to map different modalities in the same cells. Here we report the imaging of 3,660 chromosomal loci in single mouse embryonic stem (ES) cells using DNA seqFISH+, along with 17 chromatin marks and subnuclear structures by sequential immunofluorescence and the expression profile of 70 RNAs. Many loci were invariably associated with immunofluorescence marks in single mouse ES cells. These loci form 'fixed points' in the nuclear organizations of single cells and often appear on the surfaces of nuclear bodies and zones defined by combinatorial chromatin marks. Furthermore, highly expressed genes appear to be pre-positioned to active nuclear zones, independent of bursting dynamics in single cells. Our analysis also uncovered several distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states. Using clonal analysis, we show that the global levels of some chromatin marks, such as H3 trimethylation at lysine 27 (H3K27me3) and macroH2A1 (mH2A1), are heritable over at least 3-4 generations, whereas other marks fluctuate on a faster time scale. This seqFISH+-based spatial multimodal approach can be used to explore nuclear organization and cell states in diverse biological systems.
    DOI:  https://doi.org/10.1038/s41586-020-03126-2
  22. Mol Cell. 2021 Jan 28. pii: S1097-2765(21)00016-2. [Epub ahead of print]
    Stress-induced nuclear condensation of NELF drives transcriptional downregulation.
    Prashant Rawat, Marc Boehning, Barbara Hummel, Fernando Aprile-Garcia, Anwit S Pandit, Nathalie Eisenhardt, Ashkan Khavaran, Einari Niskanen, Seychelle M Vos, Jorma J Palvimo, Andrea Pichler, Patrick Cramer, Ritwick Sawarkar.
      In response to stress, human cells coordinately downregulate transcription and translation of housekeeping genes. To downregulate transcription, the negative elongation factor (NELF) is recruited to gene promoters impairing RNA polymerase II elongation. Here we report that NELF rapidly forms nuclear condensates upon stress in human cells. Condensate formation requires NELF dephosphorylation and SUMOylation induced by stress. The intrinsically disordered region (IDR) in NELFA is necessary for nuclear NELF condensation and can be functionally replaced by the IDR of FUS or EWSR1 protein. We find that biomolecular condensation facilitates enhanced recruitment of NELF to promoters upon stress to drive transcriptional downregulation. Importantly, NELF condensation is required for cellular viability under stressful conditions. We propose that stress-induced NELF condensates reported here are nuclear counterparts of cytosolic stress granules. These two stress-inducible condensates may drive the coordinated downregulation of transcription and translation, likely forming a critical node of the stress survival strategy.
    Keywords:  CDK9; RNA polymerase II; SUMO; heat shock; negative elongation factor (NELF); pausing; phase separation; proteostasis; transcriptional condensates; transcriptional stress response
    DOI:  https://doi.org/10.1016/j.molcel.2021.01.016
  23. Aging (Albany NY). 2021 Feb 06. 13
    Suppression of p16 alleviates the senescence-associated secretory phenotype.
    Raquel Buj, Kelly E Leon, Marlyn A Anguelov, Katherine M Aird.
      Oncogene-induced senescence (OIS) is characterized by increased expression of the cell cycle inhibitor p16, leading to a hallmark cell cycle arrest. Suppression of p16 in this context drives proliferation, senescence bypass, and contributes to tumorigenesis. OIS cells are also characterized by the expression and secretion of a widely variable group of factors collectively termed the senescence-associated secretory phenotype (SASP). The SASP can be both beneficial and detrimental and affects the microenvironment in a highly context-dependent manner. The relationship between p16 suppression and the SASP remains unclear. Here, we show that knockdown of p16 decreases expression of the SASP factors and pro-inflammatory cytokines IL6 and CXCL8 in multiple models, including OIS and DNA damage-induced senescence. Notably, this is uncoupled from the senescence-associated cell cycle arrest. Moreover, low p16 expression in both cancer cell lines and patient samples correspond to decreased SASP gene expression, suggesting this is a universal effect of loss of p16 expression. Together, our data suggest that p16 regulates SASP gene expression, which has implications for understanding how p16 modulates both the senescent and tumor microenvironment.
    Keywords:  LMNB1; inflammation; interleukin-6; interleukin-8; melanoma
    DOI:  https://doi.org/10.18632/aging.202640
  24. Genome Med. 2021 Feb 10. 13(1): 23
    Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation.
    Daniela Mancarella, Christoph Plass.
      Epigenetic alterations are associated with normal biological processes such as aging or differentiation. Changes in global epigenetic signatures, together with genetic alterations, are driving events in several diseases including cancer. Comparative studies of cancer and healthy tissues found alterations in patterns of DNA methylation, histone posttranslational modifications, and changes in chromatin accessibility. Driven by sophisticated, next-generation sequencing-based technologies, recent studies discovered cancer epigenomes to be dominated by epigenetic patterns already present in the cell-of-origin, which transformed into a neoplastic cell. Tumor-specific epigenetic changes therefore need to be redefined and factors influencing epigenetic patterns need to be studied to unmask truly disease-specific alterations. The underlying mechanisms inducing cancer-associated epigenetic alterations are poorly understood. Studies of mutated epigenetic modifiers, enzymes that write, read, or edit epigenetic patterns, or mutated chromatin components, for example oncohistones, help to provide functional insights on how cancer epigenomes arise. In this review, we highlight the importance and define challenges of proper control tissues and cell populations to exploit cancer epigenomes. We summarize recent advances describing mechanisms leading to epigenetic changes in tumorigenesis and briefly discuss advances in investigating their translational potential.
    Keywords:  Cancer; Cell-of-origin; Epigenetic signatures; Epigenetic therapy; Epigenomics; Oncohistones; Precision oncology; Tumor subclassification
    DOI:  https://doi.org/10.1186/s13073-021-00837-7
  25. Cancer Immunol Immunother. 2021 Feb 12.
    Metabolic profiles of regulatory T cells in the tumour microenvironment.
    Disha Rao, Fabienne Verburg, Kathrin Renner, Daniel S Peeper, Ruben Lacroix, Christian U Blank.
      Metabolic reprogramming of cancer cells generates a tumour microenvironment (TME) characterised by nutrient restriction, hypoxia, acidity and oxidative stress. While these conditions are unfavourable for infiltrating effector T cells, accumulating evidence suggests that regulatory T cells (Tregs) continue to exert their immune-suppressive functions within the TME. The advantages of Tregs within the TME stem from their metabolic profile. Tregs rely on oxidative phosphorylation for their functions, which can be fuelled by a variety of substrates. Even though Tregs are an attractive target to augment anti-tumour immune responses, it remains a challenge to specifically target intra-tumoral Tregs. We provide a comprehensive review of distinct mechanistic links and pathways involved in regulation of Treg metabolism under the prevailing conditions within the tumour. We also describe how these Tregs differ from the ones in the periphery, and from conventional T cells in the tumour. Targeting pathways responsible for adaptation of Tregs in the tumour microenvironment improves anti-tumour immunity in preclinical models. This may provide alternative therapies aiming at reducing immune suppression in the tumour.
    Keywords:  Acidity; Hypoxia; Metabolism; Nutrient depletion; Oxidative stress; Treg
    DOI:  https://doi.org/10.1007/s00262-021-02881-z
  26. J Clin Endocrinol Metab. 2021 Feb 09. pii: dgab072. [Epub ahead of print]
    Differential mitochondrial gene expression in adipose tissue following weight loss induced by diet or bariatric surgery.
    Birgitta W van der Kolk, Maheswary Muniandy, Dorota Kaminska, Marcus Alvarez, Arthur Ko, Zong Miao, Armand Valsesia, Dominique Langin, Maija Vaittinen, Mirva Pääkkönen, Riikka Jokinen, Sanna Kaye, Sini Heinonen, Kirsi A Virtanen, Daniel P Andersson, Ville Männistö, Wim H Saris, Arne Astrup, Mikael Rydén, Ellen E Blaak, Päivi Pajukanta, Jussi Pihlajamäki, Kirsi H Pietiläinen.
      CONTEXT: Mitochondria are essential for cellular energy homeostasis, yet their role in subcutaneous adipose tissue (SAT) during different types of weight-loss interventions remains unknown.OBJECTIVE: Investigate how SAT mitochondria change following diet-induced and bariatric surgery-induced weight-loss interventions in four independent weight-loss studies.
    DESIGN/SETTING: The DiOGenes study is a European multicenter dietary intervention with an 8-week low caloric diet (LCD; 800 kcal/d; n=261) and 6-month weight maintenance (n=121) period. The Kuopio Obesity Surgery study (KOBS) is a Roux-en-Y gastric bypass (RYGB) surgery study (n=172) with a 1-year follow-up. We associated weight-loss percentage with global and 2210 mitochondria-related RNA transcripts in linear regression analysis adjusted for age and sex. We repeated these analyses in two studies. The Finnish CRYO study has a 6-week LCD (800-1000 kcal/d; n=19) and a 10.5-month follow-up. The Swedish DEOSH study is a RYGB surgery study with a 2-year (n=49) and 5-year (n=37) follow-up.
    RESULTS: Diet-induced weight loss led to a significant transcriptional downregulation of oxidative phosphorylation (DiOGenes; Ingenuity Pathway Analyses (IPA) z-scores: -8.7 following LCD, -4.4 following weight maintenance; CRYO: IPA z-score: -5.6, all p<0.001), while upregulation followed surgery-induced weight loss (KOBS: IPA z-score: 1.8, p<0.001; in DEOSH: IPA z-scores: 4.0 following 2 years, 0.0 following 5 years). We confirmed an upregulated oxidative phosphorylation at the proteomics level following surgery (IPA z-score: 3.2, p<0.001).
    CONCLUSIONS: Differentially regulated SAT mitochondria-related gene expressions suggest qualitative alterations between weight-loss interventions, providing insights into the potential molecular mechanistic targets for weight-loss success.
    Keywords:  Adipose tissue; bariatric surgery; diet-induced; mitochondria; transcriptomics; weight loss
    DOI:  https://doi.org/10.1210/clinem/dgab072
  27. Cancer Discov. 2021 Feb 09. pii: candisc.1274.2020. [Epub ahead of print]
    Non-genetic evolution drives lung adenocarcinoma spatial heterogeneity and progression.
    Daniele Tavernari, Elena Battistello, Elie Dheilly, Aaron S Petruzzella, Marco Mina, Jessica Sordet-Dessimoz, Solange Peters, Thorsten Krueger, David Gfeller, Nicolo Riggi, Elisa Oricchio, Igor Letovanec, Giovanni Ciriello.
      Cancer evolution determines molecular and morphological intra-tumor heterogeneity and challenges the design of effective treatments. In lung adenocarcinoma, disease progression and prognosis are associated with the appearance of morphologically diverse tumor regions, termed histologic patterns. However, the link between molecular and histological features remains elusive. Here, we generated multi-omics and spatially resolved molecular profiles of histologic patterns from primary lung adenocarcinoma, which we integrated with molecular data from >2,000 patients. The transition from indolent to aggressive patterns was not driven by genetic alterations but by epigenetic and transcriptional reprogramming reshaping cancer cell identity. A signature quantifying this transition was an independent predictor of patient prognosis in multiple human cohorts. Within individual tumors, highly multiplexed protein spatial profiling revealed co-existence of immune desert, inflamed, and excluded regions, which matched histologic pattern composition. Our results provide a detailed molecular map of lung adenocarcinoma intra-tumor spatial heterogeneity, tracing non-genetic routes of cancer evolution.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1274
  28. Pancreatology. 2021 Jan 22. pii: S1424-3903(21)00035-1. [Epub ahead of print]
    S100A14 promotes progression and gemcitabine resistance in pancreatic cancer.
    Hongwei Zhu, Wenzhe Gao, Xia Li, Li Yu, Dong Luo, Yunfei Liu, Xiao Yu.
      S100 calcium binding protein A14 (S100A14) plays an important role in the progression of several types of cancer. However, its roles in pancreatic ductal adenocarcinoma (PDAC) are largely unexplored. Here, we characterized the functional roles of S100A14 in the progression and chemoresistance of PDAC. Gene expression microarray identified that S100A14 was significantly highly expressed in four pairs of human PDAC tumor compared with corresponding non-tumor tissues genes. Quantitative reverse transcription PCR (qRT-PCR), western blotting and immunohistochemical staining (IHC) showed that S100A14 was frequently overexpressed in PDAC cell lines and tissues. Moreover, expression level of S100A14 was positively correlated to advanced cancer stages. Further, Kaplan-Meier survival analysis suggested that PDAC patients with low S100A14 expression had longer overall survival in TCGA PDAC datasets. Transient overexpressing of S100A14 promoted cell proliferation, anchorage-independent colony formation, cell migration and invasion in cell lines with low endogenous S100A14 levels, while transient silencing of S100A14 inhibited cell proliferation, anchorage-independent colony formation, cell migration and invasion in cell lines with high endogenous S100A14 levels. Persistent knockdown of S100A14 by transducing shRNAs carrying lentivirus inhibited subcutaneous tumor formation in nude mice, and sensitized the PDAC cells to gemcitabine treatment. Taken together, S100A14 exhibited oncogenic properties by promoting cell proliferation, transformation, migration and invasion, and enhanced in vivo tumor growth. More importantly, inhibition of S100A14 could effectively abrogate the cancerous properties of the PDAC cells. Our study indicated that S100A14 was a valuable target for the development of therapeutic strategy, as well as a diagnostic and prognosis biomarker for PDAC patients.
    Keywords:  Chemoresistance; Gemcitabine; Pancreatic cancer; Progression; S100A14
    DOI:  https://doi.org/10.1016/j.pan.2021.01.011
  29. Trends Cell Biol. 2021 Feb 03. pii: S0962-8924(21)00010-6. [Epub ahead of print]
    Fueling Cell Invasion through Extracellular Matrix.
    Aastha Garde, David R Sherwood.
      Cell invasion through extracellular matrix (ECM) has pivotal roles in cell dispersal during development, immune cell trafficking, and cancer metastasis. Many elegant studies have revealed the specialized cellular protrusions, proteases, and distinct modes of migration invasive cells use to overcome ECM barriers. Less clear, however, is how invasive cells provide energy, specifically ATP, to power the energetically demanding membrane trafficking, F-actin polymerization, and actomyosin machinery that mediate break down, remodeling, and movement through ECMs. Here, we provide an overview of the challenges of examining ATP generation and delivery within invading cells and how recent studies using diverse invasion models, experimental approaches, and energy biosensors are revealing that energy metabolism is an integral component of cell invasive behavior that is dynamically tuned to overcome the ECM environment.
    Keywords:  Cell invasion; adaptive ATP metabolism; extracellular matrix; glycolysis; mitochondrial localization; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.tcb.2021.01.006
  30. Curr Opin Clin Nutr Metab Care. 2021 Feb 05.
    From bench to bedside: updates in basic science, translational and clinical research on muscle fatigue in cancer cachexia.
    Katherine M Jackson, Calvin L Cole, Richard F Dunne.
      PURPOSE OF REVIEW: Cancer cachexia is a syndrome of loss of weight and muscle mass that leads to reduced strength, poor physical performance and functional impairment. Muscular fatigue is a distressing syndrome that patients with cachexia suffer from and can impair quality of life. Here, we review recent updates in muscular fatigue in cancer cachexia research with a focus on mechanisms, biomarkers and potential therapies.RECENT FINDINGS: Both in mice and humans, research has shown that muscle fatigue can be independent of muscular atrophy and can happen early in cancer development or in precachexia. Inflammatory pathways, mitochondrial dysfunction and gut microbiota have recently been studied to play an important role in muscle fatigue in preclinical models. Exercise can target these pathways and has been studied as a therapeutic intervention to improve muscle fatigue.
    SUMMARY: Heightened inflammation within muscle, altered muscle function and muscle fatigue can begin prior to clinical evidence of cachexia, making early recognition and intervention challenging. The emergence of cachexia mouse models and translational and clinical research studying muscle fatigue will hopefully lead to new therapies targeting the underlying mechanisms of cancer cachexia. Exercise will need to be tested in larger randomized studies before entering into daily practice.
    DOI:  https://doi.org/10.1097/MCO.0000000000000738
  31. Trends Biochem Sci. 2021 Feb 10. pii: S0968-0004(21)00004-9. [Epub ahead of print]
    Biomolecular Condensates and Their Links to Cancer Progression.
    Danfeng Cai, Zhe Liu, Jennifer Lippincott-Schwartz.
      Liquid-liquid phase separation (LLPS) has emerged in recent years as an important physicochemical process for organizing diverse processes within cells via the formation of membraneless organelles termed biomolecular condensates. Emerging evidence now suggests that the formation and regulation of biomolecular condensates are also intricately linked to cancer formation and progression. We review the most recent literature linking the existence and/or dissolution of biomolecular condensates to different hallmarks of cancer formation and progression. We then discuss the opportunities that this condensate perspective provides for cancer research and the development of novel therapeutic approaches, including the perturbation of condensates by small-molecule inhibitors.
    Keywords:  biomolecular condensates; cancer; cancer therapy; phase separation
    DOI:  https://doi.org/10.1016/j.tibs.2021.01.002
  32. Cancers (Basel). 2021 Feb 09. pii: 698. [Epub ahead of print]13(4):
    Inhibition of Mitochondrial Dynamics Preferentially Targets Pancreatic Cancer Cells with Enhanced Tumorigenic and Invasive Potential.
    Sarah Courtois, Beatriz de Luxán-Delgado, Laure Penin-Peyta, Alba Royo-García, Beatriz Parejo-Alonso, Petra Jagust, Sonia Alcalá, Juan A Rubiolo, Laura Sánchez, Bruno Sainz, Christopher Heeschen, Patricia Sancho.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest tumors, partly due to its intrinsic aggressiveness, metastatic potential, and chemoresistance of the contained cancer stem cells (CSCs). Pancreatic CSCs strongly rely on mitochondrial metabolism to maintain their stemness, therefore representing a putative target for their elimination. Since mitochondrial homeostasis depends on the tightly controlled balance between fusion and fission processes, namely mitochondrial dynamics, we aim to study this mechanism in the context of stemness. In human PDAC tissues, the mitochondrial fission gene DNM1L (DRP1) was overexpressed and positively correlated with the stemness signature. Moreover, we observe that primary human CSCs display smaller mitochondria and a higher DRP1/MFN2 expression ratio, indicating the activation of the mitochondrial fission. Interestingly, treatment with the DRP1 inhibitor mDivi-1 induced dose-dependent apoptosis, especially in CD133+ CSCs, due to the accumulation of dysfunctional mitochondria and the subsequent energy crisis in this subpopulation. Mechanistically, mDivi-1 inhibited stemness-related features, such as self-renewal, tumorigenicity, and invasiveness and chemosensitized the cells to the cytotoxic effects of Gemcitabine. In summary, mitochondrial fission is an essential process for pancreatic CSCs and represents an attractive target for designing novel multimodal treatments that will more efficiently eliminate cells with high tumorigenic potential.
    Keywords:  CD133; DRP1; PDAC; cancer stem cells; energy crisis; mitochondria; mitochondrial dynamics; mitochondrial fission; pancreatic cancer
    DOI:  https://doi.org/10.3390/cancers13040698
  33. Cell Death Differ. 2021 Feb 12.
    Metabolic adaptation to hypoxia: do worms and cancer cells share common metabolic responses to hypoxic stress?
    Ralf Baumeister, Coleen T Murphy, Thomas Heimbucher.
      
    DOI:  https://doi.org/10.1038/s41418-021-00741-y
  34. J Physiol. 2021 Feb 10.
    Lactate in contemporary biology: A phoenix risen1.
    George A Brooks, Jose A Arevalo, Adam D Osmond, Robert G Leija, Casey C Curl, Ashley P Tovar.
      After a Century, it's time to turn the page on understanding of lactate metabolism and appreciate that lactate shuttling is an important component of intermediary metabolism in vivo. Cell-Cell and intracellular Lactate Shuttles fulfill purposes of energy substrate production and distribution as well as cell signaling under fully aerobic conditions. Recognition of lactate shuttling came first in studies of physical exercise where the roles of driver (producer) and recipient (consumer) cells and tissues were obvious. Moreover, the presence of lactate shuttling as part of postprandial glucose disposal and satiety signaling has been recognized. Mitochondrial respiration creates the physiological sink for lactate disposal in vivo. Repeated lactate exposure from regular exercise results in adaptive processes such as mitochondrial biogenesis and other healthful circulatory and neurological characteristic such as improved physical work capacity, metabolic flexibility, learning, and memory. The importance of lactate and lactate shuttling in healthful living is further emphasized when lactate signaling and shuttling are dysregulated as occur in particular illnesses and injuries. Like a Phoenix, lactate has risen to major importance in 21st Century Biology. This article is protected by copyright. All rights reserved.
    Keywords:  exercise; fiber type; gene adaptation; gluconeogenesis; glycogenolysis; indirect pathway; lactate shuttle; lactate signaling; microbiome; muscle; postabsorptive metabolism; postprandial metabolism; satiety
    DOI:  https://doi.org/10.1113/JP280955
  35. Cell Death Discov. 2020 Apr 27. 6(1): 29
    The nuclear envelope: target and mediator of the apoptotic process.
    Liora Lindenboim, Hila Zohar, Howard J Worman, Reuven Stein.
      Apoptosis is characterized by the destruction of essential cell organelles, including the cell nucleus. The nuclear envelope (NE) separates the nuclear interior from the cytosol. During apoptosis, the apoptotic machinery, in particular caspases, increases NE permeability by cleaving its proteins, such as those of the nuclear pore complex (NPC) and the nuclear lamina. This in turns leads to passive diffusion of cytosolic apoptogenic proteins, such as caspases and nucleases, through NPCs into the nucleus and the subsequent breakdown of the NE and destruction of the nucleus. However, NE leakiness at early stages of the apoptotic process can also occur in a caspase-independent manner, where Bax, by a non-canonical action, promotes transient and repetitive localized generation and subsequent rupture of nuclear protein-filled nuclear bubbles. This NE rupture leads to discharge of apoptogenic nuclear proteins from the nucleus to the cytosol, a process that can contribute to the death process. Therefore, the NE may play a role as mediator of cell death at early stages of apoptosis. The NE can also serve as a platform for assembly of complexes that regulate the death process. Thus, the NE should be viewed as both a mediator of the cell death process and a target.
    DOI:  https://doi.org/10.1038/s41420-020-0256-5
  36. Cancers (Basel). 2021 Jan 30. pii: 525. [Epub ahead of print]13(3):
    The Adhesome Network: Key Components Shaping the Tumour Stroma.
    Pinelopi A Nikolopoulou, Maria A Koufaki, Vassiliki Kostourou.
      Beyond the conventional perception of solid tumours as mere masses of cancer cells, advanced cancer research focuses on the complex contributions of tumour-associated host cells that are known as "tumour microenvironment" (TME). It has been long appreciated that the tumour stroma, composed mainly of blood vessels, cancer-associated fibroblasts and immune cells, together with the extracellular matrix (ECM), define the tumour architecture and influence cancer cell properties. Besides soluble cues, that mediate the crosstalk between tumour and stroma cells, cell adhesion to ECM arises as a crucial determinant in cancer progression. In this review, we discuss how adhesome, the intracellular protein network formed at cell adhesions, regulate the TME and control malignancy. The role of adhesome extends beyond the physical attachment of cells to ECM and the regulation of cytoskeletal remodelling and acts as a signalling and mechanosensing hub, orchestrating cellular responses that shape the tumour milieu.
    Keywords:  adhesome; cancer-associated fibroblasts; endothelial cells; focal adhesion sites; immune cells; mural cells; tumour microenvironment; tumour stroma
    DOI:  https://doi.org/10.3390/cancers13030525
  37. Nat Rev Mol Cell Biol. 2021 Feb 09.
    Shaping human telomeres: from shelterin and CST complexes to telomeric chromatin organization.
    Ci Ji Lim, Thomas R Cech.
      The regulation of telomere length in mammals is crucial for chromosome end-capping and thus for maintaining genome stability and cellular lifespan. This process requires coordination between telomeric protein complexes and the ribonucleoprotein telomerase, which extends the telomeric DNA. Telomeric proteins modulate telomere architecture, recruit telomerase to accessible telomeres and orchestrate the conversion of the newly synthesized telomeric single-stranded DNA tail into double-stranded DNA. Dysfunctional telomere maintenance leads to telomere shortening, which causes human diseases including bone marrow failure, premature ageing and cancer. Recent studies provide new insights into telomerase-related interactions (the 'telomere replisome') and reveal new challenges for future telomere structural biology endeavours owing to the dynamic nature of telomere architecture and the great number of structures that telomeres form. In this Review, we discuss recently determined structures of the shelterin and CTC1-STN1-TEN1 (CST) complexes, how they may participate in the regulation of telomere replication and chromosome end-capping, and how disease-causing mutations in their encoding genes may affect specific functions. Major outstanding questions in the field include how all of the telomere components assemble relative to each other and how the switching between different telomere structures is achieved.
    DOI:  https://doi.org/10.1038/s41580-021-00328-y
  38. Cell Metab. 2021 Feb 03. pii: S1550-4131(21)00015-2. [Epub ahead of print]
    The glucose-dependent insulinotropic polypeptide (GIP) regulates body weight and food intake via CNS-GIPR signaling.
    Qian Zhang, Challa Tenagne Delessa, Robert Augustin, Mostafa Bakhti, Gustav Colldén, Daniel J Drucker, Annette Feuchtinger, Cristina Garcia Caceres, Gerald Grandl, Alexandra Harger, Stephan Herzig, Susanna Hofmann, Cassie Lynn Holleman, Martin Jastroch, Susanne Keipert, Maximilian Kleinert, Patrick J Knerr, Konxhe Kulaj, Beata Legutko, Heiko Lickert, Xue Liu, Gerd Luippold, Dominik Lutter, Emilija Malogajski, Marta Tarquis Medina, Stephanie A Mowery, Andreas Blutke, Diego Perez-Tilve, Ciro Salinno, Laura Sehrer, Richard D DiMarchi, Matthias H Tschöp, Kerstin Stemmer, Brian Finan, Christian Wolfrum, Timo D Müller.
      Uncertainty exists as to whether the glucose-dependent insulinotropic polypeptide receptor (GIPR) should be activated or inhibited for the treatment of obesity. Gipr was recently demonstrated in hypothalamic feeding centers, but the physiological relevance of CNS Gipr remains unknown. Here we show that HFD-fed CNS-Gipr KO mice and humanized (h)GIPR knockin mice with CNS-hGIPR deletion show decreased body weight and improved glucose metabolism. In DIO mice, acute central and peripheral administration of acyl-GIP increases cFos neuronal activity in hypothalamic feeding centers, and this coincides with decreased body weight and food intake and improved glucose handling. Chronic central and peripheral administration of acyl-GIP lowers body weight and food intake in wild-type mice, but shows blunted/absent efficacy in CNS-Gipr KO mice. Also, the superior metabolic effect of GLP-1/GIP co-agonism relative to GLP-1 is extinguished in CNS-Gipr KO mice. Our data hence establish a key role of CNS Gipr for control of energy metabolism.
    Keywords:  CNS; GIP; GIPR CNS KO; body weight; diet-induced obesity; food intake; glucose metabolism; incretin; type 2 diabetes
    DOI:  https://doi.org/10.1016/j.cmet.2021.01.015
  39. Cell Mol Life Sci. 2021 Feb 13.
    Mitochondrial dynamics in cancer stem cells.
    Dane T Sessions, David F Kashatus.
      Many tumors are now understood to be heterogenous cell populations arising from a minority of epithelial-like cancer stem cells (CSCs). CSCs demonstrate distinctive metabolic signatures from the more differentiated surrounding tumor bulk that confer resistance to traditional chemotherapeutic regimens and potential for tumor relapse. Many CSC phenotypes including metabolism, epithelial-to-mesenchymal transition, cellular signaling pathway activity, and others, arise from altered mitochondrial function and turnover, which are regulated by constant cycles of mitochondrial fusion and fission. Further, recycling of mitochondria through mitophagy in CSCs is associated with maintenance of reactive oxygen species levels that dictate gene expression. The protein machinery that drives mitochondrial dynamics is surprisingly simple and may represent attractive new therapeutic avenues to target CSC metabolism and selectively eradicate tumor-generating cells to reduce the risks of metastasis and relapse for a variety of tumor types.
    Keywords:  Cancer stem cells; EMT; Metabolism; Mitochondrial dynamics; Mitochondrial morphology; Signaling; Therapeutic resistance
    DOI:  https://doi.org/10.1007/s00018-021-03773-2
  40. Annu Rev Biochem. 2021 Feb 08.
    Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway.
    Benjamin M Stinson, Joseph J Loparo.
      DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-biochem-080320-110356
  41. Cancer Cell. 2021 Feb 08. pii: S1535-6108(21)00061-1. [Epub ahead of print]39(2): 148-150
    Heterogeneity in Metastatic Potential of Cancer Cells Is Revealed En Masse.
    Pavitra Viswanath, Alana L Welm.
      A new study in Nature determines metastatic tropism in xenograft mouse models. This results in a metastasis map for 21 tumor types, the utility of which is demonstrated by identifying lipid metabolism to be uniquely altered in breast cancer cell lines that metastasize to the brain.
    DOI:  https://doi.org/10.1016/j.ccell.2021.01.017
  42. Cancer Discov. 2021 Feb 09.
    Applications of CRISPR Genome Editing to Advance the Next Generation of Adoptive Cell Therapies for Cancer.
    Samantha M Fix, Amir A Jazaeri, Patrick Hwu.
      Adoptive cell therapy (ACT) for cancer shows tremendous potential; however, several challenges preclude its widespread use. These include poor T-cell function in hostile tumor microenvironments, a lack of tumor-specific target antigens, and the high cost and poor scalability of cell therapy manufacturing. Creative genome-editing strategies are beginning to emerge to address each of these limitations, which has initiated the next generation of cell therapy products now entering clinical trials. CRISPR is at the forefront of this revolution, offering a simple and versatile platform for genetic engineering. This review provides a comprehensive overview of CRISPR applications that have advanced ACT. SIGNIFICANCE: The clinical impact of ACT for cancer can be expanded by implementing specific genetic modifications that enhance the potency, safety, and scalability of cellular products. Here we provide a detailed description of such genetic modifications, highlighting avenues to enhance the therapeutic efficacy and accessibility of ACT for cancer. Furthermore, we review high-throughput CRISPR genetic screens that have unveiled novel targets for cell therapy enhancement.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1083
  43. EMBO Rep. 2021 Feb 09. e51094
    The Golgi microtubules regulate single cell durotaxis.
    Yingxue Rong, Wenzhong Yang, Huiwen Hao, Wenxu Wang, Shaozhen Lin, Peng Shi, Yuxing Huang, Bo Li, Yujie Sun, Zheng Liu, Congying Wu.
      Current understandings on cell motility and directionality rely heavily on accumulated investigations of the adhesion-actin cytoskeleton-actomyosin contractility cycles, while microtubules have been understudied in this context. Durotaxis, the ability of cells to migrate up gradients of substrate stiffness, plays a critical part in development and disease. Here, we identify the pivotal role of Golgi microtubules in durotactic migration of single cells. Using high-throughput analysis of microtubule plus ends/focal adhesion interactions, we uncover that these non-centrosomal microtubules actively impart leading edge focal adhesion (FA) dynamics. Furthermore, we designed a new system where islands of higher stiffness were patterned within RGD peptide coated polyacrylamide gels. We revealed that the positioning of the Golgi apparatus is responsive to external mechanical cues and that the Golgi-nucleus axis aligns with the stiffness gradient in durotaxis. Together, our work unveils the cytoskeletal underpinning for single cell durotaxis. We propose a model in which the Golgi-nucleus axis serves both as a compass and as a steering wheel for durotactic migration, dictating cell directionality through the interaction between non-centrosomal microtubules and the FA dynamics.
    Keywords:  Golgi; durotaxis; mechanobiology; microtubules
    DOI:  https://doi.org/10.15252/embr.202051094
  44. Proc Natl Acad Sci U S A. 2021 Mar 02. pii: e2019536118. [Epub ahead of print]118(9):
    Demographic perspectives on the rise of longevity.
    James W Vaupel, Francisco Villavicencio, Marie-Pier Bergeron-Boucher.
      This article reviews some key strands of demographic research on past trends in human longevity and explores possible future trends in life expectancy at birth. Demographic data on age-specific mortality are used to estimate life expectancy, and validated data on exceptional life spans are used to study the maximum length of life. In the countries doing best each year, life expectancy started to increase around 1840 at a pace of almost 2.5 y per decade. This trend has continued until the present. Contrary to classical evolutionary theories of senescence and contrary to the predictions of many experts, the frontier of survival is advancing to higher ages. Furthermore, individual life spans are becoming more equal, reducing inequalities, with octogenarians and nonagenarians accounting for most deaths in countries with the highest life expectancy. If the current pace of progress in life expectancy continues, most children born this millennium will celebrate their 100th birthday. Considerable uncertainty, however, clouds forecasts: Life expectancy and maximum life span might increase very little if at all, or longevity might rise much faster than in the past. Substantial progress has been made over the past three decades in deepening understanding of how long humans have lived and how long they might live. The social, economic, health, cultural, and political consequences of further increases in longevity are so significant that the development of more powerful methods of forecasting is a priority.
    Keywords:  forecasts; life expectancy; life span equality; maximum life span; mortality
    DOI:  https://doi.org/10.1073/pnas.2019536118
  45. Cancer Discov. 2021 Feb 09. pii: candisc.1050.2020. [Epub ahead of print]
    Mutations in the RAS/MAPK pathway drive replication repair deficient hypermutated tumors and confer sensitivity to MEK inhibition.
    Brittany B Campbell, Melissa A Galati, Simone C Stone, Alexandra N Riemenschneider, Melissa Edwards, Sumedha Sudhaman, Robert Siddaway, Martin Komosa, Nuno M Nunes, Liana Nobre, A Sorana Morrissy, Matthew Zatzman, Michal Zapotocky, Lazar Joksimovic, Sangeetha N Kalimuthu, David Samuel, Gary Mason, Eric Bouffet, Daniel A Morgenstern, Melyssa Aronson, Carol Durno, David Malkin, John M Maris, Michael D Taylor, Adam Shlien, Trevor J Pugh, Pamela S Ohashi, Cynthia E Hawkins, Uri Tabori.
      The RAS/MAPK pathway is an emerging targeted pathway across a spectrum of both adult and pediatric cancers. Typically, this is associated with a single, well-characterized point mutation in an oncogene. Hypermutant tumors which harbor many somatic mutations may obscure the interpretation of such targetable genomic events. We find that replication repair deficient (RRD) cancers which are universally hypermutant and affect children born with RRD cancer predisposition, are enriched for RAS/MAPK mutations (p=10-8). These mutations are not random, exist in subclones, and increase in allelic frequency over time. The RAS/MAPK pathway is activated both transcriptionally and at the protein level in patient derived RRD tumors and these tumors responded to MEK inhibition in vitro and in vivo. Treatment of patients with RAS/MAPK hypermutant gliomas reveal durable responses to MEK inhibition. Our observations suggest that hypermutant tumors may be addicted to oncogenic pathways resulting in favorable response to targeted therapies.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1050
  46. Cell Discov. 2020 Feb 11. 6(1): 6
    Lysosome biology in autophagy.
    Willa Wen-You Yim, Noboru Mizushima.
      Autophagy is a major intracellular degradation system that derives its degradative abilities from the lysosome. The most well-studied form of autophagy is macroautophagy, which delivers cytoplasmic material to lysosomes via the double-membraned autophagosome. Other forms of autophagy, namely chaperone-mediated autophagy and microautophagy, occur directly on the lysosome. Besides providing the means for degradation, lysosomes are also involved in autophagy regulation and can become substrates of autophagy when damaged. During autophagy, they exhibit notable changes, including increased acidification, enhanced enzymatic activity, and perinuclear localization. Despite their importance to autophagy, details on autophagy-specific regulation of lysosomes remain relatively scarce. This review aims to provide a summary of current understanding on the behaviour of lysosomes during autophagy and outline unexplored areas of autophagy-specific lysosome research.
    DOI:  https://doi.org/10.1038/s41421-020-0141-7
  47. Cancer Prev Res (Phila). 2021 Feb 09. pii: canprevres.0633.2020. [Epub ahead of print]
    Cancer risk in normal-weight individuals with metabolic obesity: A narrative review.
    Bethina Liu, Hugh E Giffney, Rhonda S Arthur, Thomas E Rohan, Andrew J Dannenberg.
      Obesity represents one of the most significant public health challenges worldwide. Current clinical practice relies on body mass index (BMI) to define the obesity status of an individual, even though the index has long been recognized for its limitations as a measure of body fat. In normal BMI individuals, increased central adiposity has been associated with worse health outcomes, including increased risks of cardiovascular disease and metabolic disorders. The condition leading to these outcomes has been described as metabolic obesity in the normal weight (MONW). More recent evidence suggests that MONW is associated with increased risk of several obesity-related malignancies, including postmenopausal breast, endometrial, colorectal, and liver cancers. In MONW patients, the false reassurance of a normal range BMI can lead to lost opportunities for implementing preventive interventions that may benefit a substantial number of people. A growing body of literature has documented the increased risk profile of MONW individuals and demonstrated practical uses for body composition and biochemical analyses to identify this at-risk population. In this review, we survey the current literature on MONW and cancer, summarize pathophysiology and oncogenic mechanisms, highlight potential strategies for diagnosis and treatment, and suggest directions for future research.
    DOI:  https://doi.org/10.1158/1940-6207.CAPR-20-0633
  48. Front Cell Dev Biol. 2020 ;8 620409
    Assessing Autophagy in Muscle Stem Cells.
    Silvia Campanario, Ignacio Ramírez-Pardo, Xiaotong Hong, Joan Isern, Pura Muñoz-Cánoves.
      The skeletal muscle tissue in the adult is relatively stable under normal conditions but retains a striking ability to regenerate by its resident stem cells (satellite cells). Satellite cells exist in a quiescent (G0) state; however, in response to an injury, they reenter the cell cycle and start proliferating to provide sufficient progeny to form new myofibers or undergo self-renewal and returning to quiescence. Maintenance of satellite cell quiescence and entry of satellite cells into the activation state requires autophagy, a fundamental degradative and recycling process that preserves cellular proteostasis. With aging, satellite cell regenerative capacity declines, correlating with loss of autophagy. Enhancing autophagy in aged satellite cells restores their regenerative functions, underscoring this proteostatic activity's relevance for tissue regeneration. Here we describe two strategies for assessing autophagic activity in satellite cells from GFP-LC3 reporter mice, which allows direct autophagosome labeling, or from non-transgenic (wild-type) mice, where autophagosomes can be immunostained. Treatment of GFP-LC3 or WT satellite cells with compounds that interfere with autophagosome-lysosome fusion enables measurement of autophagic activity by flow cytometry and immunofluorescence. Thus, the methods presented permit a relatively rapid assessment of autophagy in stem cells from skeletal muscle in homeostasis and in different pathological scenarios such as regeneration, aging or disease.
    Keywords:  autophagy; flow cytometry; immunofluorescence; quiescence; regeneration; satellite cell; skeletal muscle; stem cell
    DOI:  https://doi.org/10.3389/fcell.2020.620409
  49. Life Sci. 2021 Feb 03. pii: S0024-3205(21)00103-X. [Epub ahead of print]270 119118
    The therapeutic potential of renin-angiotensin system inhibitors in the treatment of pancreatic cancer.
    Negar Khoshghamat, Niloufar Jafari, Vajiheh Toloue-Pouya, Shakiba Azami, Seyyedeh Helya Mirnourbakhsh, Majid Khazaei, Gordon A Ferns, Majid Rajabian, Amir Avan.
      Pancreatic cancer is among the most lethal malignancies with poor prognosis and patients become chemoresistant to current therapies, supporting further investigations to identify new therapeutic regimens in the treatment of this condition. Preclinical and clinical studies now appear to support the role of the renin-angiotensin system (RAS) in the regulation of tumor growth, angiogenesis, and metastasis in different malignancies including pancreatic cancer. These studies suggest that RAS blockers; Angiotensin-converting enzyme (ACE) inhibitors and angiotensin receptor blockers (ARBs); could have anti-carcinogenic effects and improve clinical outcomes in the management of pancreatic cancer. Here we provided an overview of ACE inhibitors and ARBs as a potential therapeutic option in the treatment of pancreatic cancer.
    Keywords:  ACE inhibitor; ARBs; Pancreatic cancer; Renin-angiotensin system inhibitor; Treatment
    DOI:  https://doi.org/10.1016/j.lfs.2021.119118
  50. EMBO J. 2021 Feb 12. e106292
    Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit.
    Victor Tobiasson, Ondřej Gahura, Shintaro Aibara, Rozbeh Baradaran, Alena Zíková, Alexey Amunts.
      Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt-EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl-carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.
    Keywords:  assembly; mitochondria; mitoribosome; translation; trypanosoma
    DOI:  https://doi.org/10.15252/embj.2020106292
  51. Curr Opin Cell Biol. 2021 Feb 09. pii: S0955-0674(21)00002-8. [Epub ahead of print]69 111-119
    Regulation of biomolecular condensate dynamics by signaling.
    Carla Garcia-Cabau, Xavier Salvatella.
      Biomolecular condensates are mesoscopic biomolecular assemblies devoid of long range order that contribute to important cellular functions. They form reversibly, are stabilized by numerous but relatively weak intermolecular interactions, and their formation can be regulated by various cellular signals including changes in local concentration, post-translational modifications, energy-consuming processes, and biomolecular interactions. Condensates formed by liquid-liquid phase separation are initially liquid but are metastable relative to hydrogels or irreversible solids that have been associated with protein aggregation diseases and are stabilized by stronger, more permanent interactions. As a consequence of this, a series of cellular mechanisms are available to regulate not only biomolecular condensation but also the physical properties of the condensates.
    Keywords:  Alternative splicing; Biomolecular condensation; Liquid-liquid phase separation; Maturation; Post-translational modifications
    DOI:  https://doi.org/10.1016/j.ceb.2021.01.002
  52. Cancer Invest. 2021 Feb 11. 1-15
    The Increasing Proportion of Early-Stage Pancreatic Cancer between 2004-2013: A SEER Analysis.
    Sven P Oman, Juan E Corral, John Stauffer, Massimo Raimondo, Kabir Mody, Michael Wallace.
      Pancreatic cancer will become the second leading cause of cancer-related death in the United States by 2030. Survival improves when it is identified at an early-stage and resected. Increasing public attention and cross-section imaging may shift detection to earlier stages. We found a small total increase in the proportion of stage I cancer relative to all stages and a significant increase compared to distant disease in the Surveillance, Epidemiology, and End Results (SEER) database. Despite this, our ability to screen and identify early-stage disease is still lacking. Additional research and population-based interventions are necessary to improve early detection.
    Keywords:  Digestive System Neoplasms; Epidemiology; Pancreas; Pancreatic Neoplasms; Public Health
    DOI:  https://doi.org/10.1080/07357907.2021.1888386
  53. Front Genet. 2020 ;11 630186
    Telomere Length as a Marker of Biological Age: State-of-the-Art, Open Issues, and Future Perspectives.
    Alexander Vaiserman, Dmytro Krasnienkov.
      Telomere shortening is a well-known hallmark of both cellular senescence and organismal aging. An accelerated rate of telomere attrition is also a common feature of age-related diseases. Therefore, telomere length (TL) has been recognized for a long time as one of the best biomarkers of aging. Recent research findings, however, indicate that TL per se can only allow a rough estimate of aging rate and can hardly be regarded as a clinically important risk marker for age-related pathologies and mortality. Evidence is obtained that other indicators such as certain immune parameters, indices of epigenetic age, etc., could be stronger predictors of the health status and the risk of chronic disease. However, despite these issues and limitations, TL remains to be very informative marker in accessing the biological age when used along with other markers such as indices of homeostatic dysregulation, frailty index, epigenetic clock, etc. This review article is aimed at describing the current state of the art in the field and at discussing recent research findings and divergent viewpoints regarding the usefulness of leukocyte TL for estimating the human biological age.
    Keywords:  age-related telomere shortening; aging-related disease; biomarker of biological age; leukocyte telomere length; mortality; telomerase
    DOI:  https://doi.org/10.3389/fgene.2020.630186
  54. Ann Transl Med. 2021 Jan;9(2): 119
    Immune profiling and immunotherapeutic targets in pancreatic cancer.
    Felicia L Lenzo, Shumei Kato, Sarabjot Pabla, Paul DePietro, Mary K Nesline, Jeffrey M Conroy, Blake Burgher, Sean T Glenn, Boris Kuvshinoff, Razelle Kurzrock, Carl Morrison.
      Background: Immunotherapeutic approaches for pancreatic ductal adenocarcinoma (PDAC) are less successful as compared to many other tumor types. In this study, comprehensive immune profiling was performed in order to identify novel, potentially actionable targets for immunotherapy.Methods: Formalin-fixed paraffin embedded (FFPE) specimens from 68 patients were evaluated for expression of 395 immune-related markers (RNA-seq), mutational burden by complete exon sequencing of 409 genes, PD-L1 expression by immunohistochemistry (IHC), pattern of tumor infiltrating lymphocytes (TILs) infiltration by CD8 IHC, and PD-L1/L2 copy number by fluorescent in situ hybridization (FISH).
    Results: The seven classes of actionable genes capturing myeloid immunosuppression, metabolic immunosuppression, alternative checkpoint blockade, CTLA-4 immune checkpoint, immune infiltrate, and programmed cell death 1 (PD-1) axis immune checkpoint, discerned 5 unique clinically relevant immunosuppression expression profiles (from most to least common): (I) combined myeloid and metabolic immunosuppression [affecting 25 of 68 patients (36.8%)], (II) multiple immunosuppressive mechanisms (29.4%), (III) PD-L1 positive (20.6%), (IV) highly inflamed PD-L1 negative (10.3%); and (V) immune desert (2.9%). The Wilcoxon rank-sum test was used to compare the PDAC cohort with a comparison cohort (n=1,416 patients) for the mean expressions of the 409 genes evaluated. Multiple genes including TIM3, VISTA, CCL2, CCR2, TGFB1, CD73, and CD39 had significantly higher mean expression versus the comparison cohort, while three genes (LAG3, GITR, CD38) had significantly lower mean expression.
    Conclusions: This study demonstrates that a clinically relevant unique profile of immune markers can be identified in PDAC and be used as a roadmap for personalized immunotherapeutic decision-making strategies.
    Keywords:  PD-L1; Precision immunotherapy; checkpoint inhibitors; immune activation; immune suppression
    DOI:  https://doi.org/10.21037/atm-20-1076
  55. J Cell Physiol. 2021 Feb 09.
    Cutting edge: Metabolic immune reprogramming, reactive oxygen species, and cancer.
    Hamid Aria, Farhoodeh Ghaedrahmati, Mazdak Ganjalikhani-Hakemi.
      A recently proposed term "immunometabolism" points to the functional intracellular metabolic changes that occur within different immune cells. Recent findings suggest that immune responses can be determined by the metabolic status of immune cells and metabolic reprogramming is an important feature of immune cell activation. Metabolic reprogramming is also well known for cancer cells and has been suggested as a major sign of cancer progression. Metabolic reprogramming of immune cells is also seen in the tumor microenvironment. In the past decade, immunometabolism has progressively become an extraordinarily vibrant and productive area of study in immunology because of its importance for immunotherapy. Understanding the immunometabolic situation of T cells and other immune cells along with the metabolic behavior of cancer cells can help us design new therapeutic approaches against cancers. Here, we have the aim to review the cutting-edge findings on the immunometabolic situation in immune and tumor cells. We discuss new findings on signaling pathways during metabolic reprogramming, its regulation, and the participation of reactive oxygen species in these processes.
    Keywords:  T cells; immunometabolism; metabolic reprogramming; reactive oxygen species; tumor cells
    DOI:  https://doi.org/10.1002/jcp.30303
  56. Clinics (Sao Paulo). 2021 ;pii: S1807-59322021000100228. [Epub ahead of print]76 e2432
    Cost-Effective Trap qPCR Approach to Evaluate Telomerase Activity: an Important Tool for Aging, Cancer, and Chronic Disease Research.
    Thalyta Nery Carvalho Pinto, Juliana Ruiz Fernandes, Liã Barbara Arruda, Alberto José da Silva Duarte, Gil Benard.
      OBJECTIVES: Telomeres are a terminal "DNA cap" that prevent chromosomal fusion and degradation. However, aging is inherent to life, and so is the loss of terminal sequences. Telomerase is a specialized reverse transcriptase encoded by self-splicing introns that counteract chromosome erosion. Telomerase activity is observed during early embryonic development, but after the blastocyst stage, the expression of telomerase reduces. The consequences of either insufficient or unrestrained telomerase activity underscore the importance of ongoing studies aimed at elucidating the regulation of telomerase activity in humans. In the present study, we aimed to standardize a simplified telomerase repeat-amplification protocol (TRAP) assay to detect telomerase activity in unstimulated and PHA-stimulated mononuclear cells.METHODS AND RESULTS: Our optimized qPCR-based can efficiently evaluate telomerase activity. Quantification of protein and DNA between unstimulated and PHA-stimulated peripheral blood mononuclear cells revealed cellular activation and cell-cycle entry. The assay also showed that relative telomerase activity is significantly different between these two conditions, supporting the applicability of the assay. Furthermore, our findings corroborated that telomerase activity decreases with age.
    CONCLUSIONS: Telomeres and telomerase are implicated in aging and development of chronic diseases and cancer; however, difficulty in accessing commercial kits to investigate these aspects is a critical constraint in health surveillance studies. Our optimized assay was successfully used to differentiate telomerase activity between unstimulated and stimulated cells, clearly showing the reactivation of telomerase upon cell activation. This assay is affordable, reproducible, and can be executed in resource-limited settings.
    DOI:  https://doi.org/10.6061/clinics/2021/e2432
  57. Aging (Albany NY). 2021 Feb 12. 13
    DNA- and telomere-damage does not limit lifespan: evidence from rapamycin.
    Mikhail V Blagosklonny.
      Failure of rapamycin to extend lifespan in DNA repair mutant and telomerase-knockout mice, while extending lifespan in normal mice, indicates that neither DNA damage nor telomere shortening limits normal lifespan or causes normal aging.
    Keywords:  antagonistic pleiotropy; hyperfunction theory; mTOR; natural selection; quasi-programmed aging
    DOI:  https://doi.org/10.18632/aging.202674
  58. Sci Rep. 2021 Feb 09. 11(1): 3409
    Transcriptome analysis of the procession from chronic pancreatitis to pancreatic cancer and metastatic pancreatic cancer.
    Jihao Tu, Zhehao Huang, Yin Wang, Meijing Wang, Zukun Yin, Xianglin Mei, Meiying Li, Lisha Li.
      Exploring the underlying mechanisms of cancer development is useful for cancer treatment. In this paper, we analyzed the transcriptome profiles from the human normal pancreas, pancreatitis, pancreatic cancer and metastatic pancreatic cancer to study the intricate associations among pancreatic cancer progression. We clustered the transcriptome data, and analyzed the differential expressed genes. WGCNA was applied to construct co-expression networks and detect important modules. Importantly we selected the module in a different way. As the pancreatic disease deteriorates, the number of differentially expressed genes increases. The gene networks of T cells and interferon are upregulated in stages. In conclusion, the network-based study provides gradually activated gene networks in the disease progression of pancreatitis, pancreatic cancer, and metastatic pancreatic cancer. It may contribute to the rational design of anti-cancer drugs.
    DOI:  https://doi.org/10.1038/s41598-021-83015-4
  59. Metabolites. 2021 Jan 31. pii: 83. [Epub ahead of print]11(2):
    Sensing and Signaling of Methionine Metabolism.
    Linda Lauinger, Peter Kaiser.
      Availability of the amino acid methionine shows remarkable effects on the physiology of individual cells and whole organisms. For example, most cancer cells, but not normal cells, are hyper dependent on high flux through metabolic pathways connected to methionine, and diets restricted for methionine increase healthy lifespan in model organisms. Methionine's impact on physiology goes beyond its role in initiation of translation and incorporation in proteins. Many of its metabolites have a major influence on cellular functions including epigenetic regulation, maintenance of redox balance, polyamine synthesis, and phospholipid homeostasis. As a central component of such essential pathways, cells require mechanisms to sense methionine availability. When methionine levels are low, cellular response programs induce transcriptional and signaling states to remodel metabolic programs and maintain methionine metabolism. In addition, an evolutionary conserved cell cycle arrest is induced to ensure cellular and genomic integrity during methionine starvation conditions. Methionine and its metabolites are critical for cell growth, proliferation, and development in all organisms. However, mechanisms of methionine perception are diverse. Here we review current knowledge about mechanisms of methionine sensing in yeast and mammalian cells, and will discuss the impact of methionine imbalance on cancer and aging.
    Keywords:  S-adenosylmethionine; aging; cancer; cell cycle; methionine; methionine/SAM sensing
    DOI:  https://doi.org/10.3390/metabo11020083
  60. Cancer Cell. 2021 Feb 08. pii: S1535-6108(21)00062-3. [Epub ahead of print]39(2): 123-124
    Standing at the Crossroads.
    Lili Tang, Javid Moslehi, Yamei Tang.
      Comorbid conditions among cancer survivors are not a stranger to oncologists, but the conditions change when the cancer therapy toolbox expands. New interdisciplinary fields are recognized. We ask clinicians from psycho-oncology, cardio-oncology, and neurology to tell us how the fields have progressed and what to expect when we are standing at the crossroads of cancer.
    DOI:  https://doi.org/10.1016/j.ccell.2021.01.018
  61. STAR Protoc. 2021 Mar 19. 2(1): 100297
    Mouse model of colorectal cancer: orthotopic co-implantation of tumor and stroma cells in cecum and rectum.
    Hiroaki Kasashima, Angeles Duran, Tania Cid-Diaz, Yu Muta, Hiroto Kinoshita, Eduard Batlle, Maria T Diaz-Meco, Jorge Moscat.
      In vivo interrogation of the functional role of genes implicated in colorectal cancer (CRC) is limited by the need for physiological models that mimic the disease. Here, we describe a protocol that provides the steps required for the orthotopic co-implantation of tumoral and stromal cells into the cecum and rectum to investigate the crosstalk between the tumor and its microenvironment. This protocol recapitulates metastases to the lymph nodes, liver, and lungs observed in human CRC. For complete details on the use and execution of this protocol, please refer to Kasashima et al. (2020).
    Keywords:  Cancer; Model organisms; Organoids
    DOI:  https://doi.org/10.1016/j.xpro.2021.100297
  62. Elife. 2021 Feb 08. pii: e57116. [Epub ahead of print]10
    shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data.
    Kenichi Shimada, John A Bachman, Jeremy L Muhlich, Timothy J Mitchison.
      Individual cancers rely on distinct essential genes for their survival. The Cancer Dependency Map (DepMap) is an ongoing project to uncover these gene dependencies in hundreds of cancer cell lines. To make this drug discovery resource more accessible to the scientific community we built an easy-to-use browser, shinyDepMap (https://labsyspharm.shinyapps.io/depmap). shinyDepMap combines CRISPR and shRNA data to determine, for each gene, the growth reduction caused by knockout/knockdown and the selectivity of this effect across cell lines. The tool also clusters genes with similar dependencies, revealing functional relationships. shinyDepMap can be used to 1) predict the efficacy and selectivity of drugs targeting particular genes; 2) identify maximally sensitive cell lines for testing a drug; 3) target hop, i.e., navigate from an undruggable protein with the desired selectivity profile, such as an activated oncogene, to more druggable targets with a similar profile; and 4) identify novel pathways driving cancer cell growth and survival.
    Keywords:  cancer biology; computational biology; human; systems biology
    DOI:  https://doi.org/10.7554/eLife.57116
  63. Cancers (Basel). 2021 Feb 09. pii: 697. [Epub ahead of print]13(4):
    Targeting and Reprograming Cancer-Associated Fibroblasts and the Tumor Microenvironment in Pancreatic Cancer.
    Yoshiaki Sunami, Viktoria Böker, Jörg Kleeff.
      Pancreatic cancer is the fourth leading cause of cancer deaths in the United States both in female and male, and is projected to become the second deadliest cancer by 2030. The overall five-year survival rate remains at around 10%. Pancreatic cancer exhibits a remarkable resistance to established therapeutic options such as chemotherapy and radiotherapy, due to dense stromal tumor microenvironment. Cancer-associated fibroblasts are the major stromal cell type and source of extracellular matrix proteins shaping a physical and metabolic barrier thereby reducing therapeutic efficacy. Targeting cancer-associated fibroblasts has been considered a promising therapeutic strategy. However, depleting cancer-associated fibroblasts may also have tumor-promoting effects due to their functional heterogeneity. Several subtypes of cancer-associated fibroblasts have been suggested to exhibit tumor-restraining function. This review article summarizes recent preclinical and clinical investigations addressing pancreatic cancer therapy through targeting specific subtypes of cancer-associated fibroblasts, deprogramming activated fibroblasts, administration of mesenchymal stem cells, as well as reprogramming tumor-promoting cancer-associated fibroblasts to tumor-restraining cancer-associated fibroblasts. Further, inter-cellular mediators between cancer-associated fibroblasts and the surrounding tissue microenvironment are discussed. It is important to increase our understanding of cancer-associated fibroblast heterogeneity and the tumor microenvironment for more specific and personalized therapies for pancreatic cancer patients in the future.
    Keywords:  cancer immunotherapy; mesenchymal stem cells; pancreatic cancer; reprogramming cancer-associated fibroblasts; tumor microenvironment; tumor-promoting cancer-associated fibroblasts; tumor-restraining cancer-associated fibroblasts
    DOI:  https://doi.org/10.3390/cancers13040697
  64. Cancer Cell. 2021 Feb 08. pii: S1535-6108(21)00057-X. [Epub ahead of print]39(2): 142-144
    A Malignant Case of Arrested Development: Cancer Cell Dormancy Mimics Embryonic Diapause.
    Yu-Hsuan Lin, Hao Zhu.
      Writing in Cancer Cell and Cell, two groups investigate the nature of dormant cancer cells that persist after chemotherapy. These cells adopt a state that resembles diapause, an evolutionarily conserved adaptation used by embryos to survive inhospitable conditions. Understanding cancer diapause could uncover therapeutic strategies that reduce cancer relapse.
    DOI:  https://doi.org/10.1016/j.ccell.2021.01.013
  65. Biol Cell. 2021 Feb 07.
    The NANOTUMOR consortium - towards the Tumor Cell Atlas.
    Florent Colin, Kristine Schauer, Ali Hamiche, Pierre Martineau, Jean-Paul Borg, Jan Bednar, Guilia Bertolin, Luc Camoin, Yves Collette, Stephan Dimitrov, Isabelle Fournier, Vincent Hyenne, Marco A Mendoza-Parra, Xavier Morelli, Philippe Rondé, Izabela Sumara, Marc Tramier, Patrick Schultz, Jacky G Goetz.
      Cancer is a multi-step disease where an initital tumor progresses through critical steps shaping, in most cases, life-threatening secondary foci called metastases. The oncogenic cascade involves genetic, epigenetic, signaling pathways, intracellular trafficking and/or metabolic alterations within cancer cells. In addition, pre-malignant and malignant cells orchestrate complex and dynamic interactions with non-malignant cells and acellular matricial components or secreted factors within the tumor microenvironment that is instrumental in the progression of the disease. As our aptitude to effectively treat cancer mostly depends on our ability to decipher, properly diagnose and impede cancer progression and metastasis formation, full characterization of molecular complexes and cellular processes at play along the metastasis cascade is crucial. For many years, the scientific community lacked adapted imaging and molecular technologies to accurately dissect, at the highest resolution possible, tumor and stromal cells behavior within their natural microenvironment. In that context, the NANOTUMOR consortium is a French national multi-disciplinary workforce which aims at a providing a multi-scale characterization of the oncogenic cascade, from the atomic level to the dynamic organization of the cell in response to genetic mutations, environmental changes or epigenetic modifications. Ultimately, this program aims at identifying new therapeutic targets using innovative drug design. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1111/boc.202000135
  66. Appl Physiol Nutr Metab. 2021 Feb 12.
    Weight loss with exercise improves muscle architecture and progenitor cell populations compared to weight loss alone in mice with preneoplastic colorectal lesions.
    Sophia Roubos, Donna D'Souza, Diego Hernández-Saavedra, Guanying Xu, Nicolas Collao, Russell Emmons, Jillian Larkin, Jessica Lloyd, James J Vanhie, Yuan-Xiang Pan, Hong Chen, Michael De Lisio.
      Weight loss and exercise reduce colorectal cancer (CRC) risk in persons with obesity. Whether weight loss and exercise effect myofibre characteristics and muscle stem/progenitor cell populations in mice with preneoplastic colorectal lesions, a model of CRC risk, is unknown. To address this gap, male C57Bl/6J mice were fed a high-fat diet (HFD) to induce obesity or a control (CON) diet prior to azoxymethane injection to induce preneoplastic colorectal lesions. The HFD group was then randomized to weight loss conditions that included (1) switching to the CON diet only (HFD-SED) or switching to the CON diet with treadmill exercise training (HFD-EX). Average myofibre cross-sectional area was not different between groups. There were more smaller-sized fibers in HFD-EX (p<0.05 vs. CON), and more fibrosis in HFD-SED (p<0.05 vs. HFD-EX and CON). There was a trend for more committed (Pax7+MyoD+) myoblasts (p=0.059) and more fibro-adipogenic progenitors (FAPs) in HFD-EX (p<0.05 vs. CON). Additionally, the canonical pro-inflammatory marker p-NF-κB, was markedly reduced in the insterstitium of HFD-EX (p<0.05 vs. CON and HFD-SED). Our findings suggest that in mice with preneoplastic colorectal lesions, HFD followed by weight loss with exercise, reduces muscle fibrosis and results in a higher content of muscle stem/progenitor cells. Novelty Bullets: • Exercise improves muscle architecture in mice with preneoplastic colorectal lesion • Exercise increases fibro/adipogenic progenitors and reduces inflammatory signaling in mice with preneoplastic colorectal lesions.
    DOI:  https://doi.org/10.1139/apnm-2020-0956
  67. J Biol Chem. 2021 Feb 07. pii: S0021-9258(21)00160-5. [Epub ahead of print] 100388
    Regulation of ATR-dependent DNA damage response by nitric oxide.
    Chay Teng Yeo, Jennifer S Stancill, Bryndon J Oleson, Jamie K Schnuck, Joshua D Stafford, Aaron Naatz, Polly A Hansen, John A Corbett.
      We have shown that nitric oxide limits ataxia-telangiectasia mutated (ATM) signaling by inhibiting mitochondrial oxidative metabolism in a β-cell selective manner. In this study, we examined the actions of nitric oxide on a second DNA damage response (DDR) transducer kinase, ataxia-telangiectasia and Rad3-related protein (ATR). In β-cells and non-β-cells, nitric oxide activates ATR signaling by inhibiting ribonucleotide reductase (RNR); however, when produced at iNOS-derived (low μM) levels, nitric oxide impairs ATR signaling in a β-cell selective manner. The inhibitory actions of nitric oxide are associated with impaired mitochondrial oxidative metabolism and lack of glycolytic compensation that results in a decrease in β-cell ATP. Like nitric oxide, inhibitors of mitochondrial respiration reduce ATP levels and limit ATR signaling in a β-cell selective manner. When non-β-cells are forced to utilize mitochondrial oxidative metabolism for ATP generation their response is more like β-cells, as nitric oxide and inhibitors of mitochondrial respiration attenuate ATR signaling. These studies support a dual role for nitric oxide in regulating ATR signaling. Nitric oxide activates ATR in all cell types examined by inhibiting RNR, and in a β-cell selective manner, iNOS-derived levels of nitric oxide limit ATR signaling by attenuating mitochondrial oxidative metabolism and depleting ATP.
    DOI:  https://doi.org/10.1016/j.jbc.2021.100388
  68. J Biol Chem. 2021 Feb 05. pii: S0021-9258(21)00154-X. [Epub ahead of print] 100382
    Overexpression of TopBP1, a canonical ATR/Chk1 activator, paradoxically hinders ATR/Chk1 activation in cancer.
    Kang Liu, Joshua D Graves, Fang-Tsyr Lin, Weei-Chin Lin.
      Topoisomerase IIβ-binding protein 1 (TopBP1) is involved in cellular replication among other functions, and is known to activate ATR/Chk1 during replicative stress. TopBP1 is also expressed at high levels in many cancers. However, the impact of TopBP1 overexpression on ATR/Chk1 activation and cancer development has not been investigated. Here we demonstrate that the degree of ATR/Chk1 activation is regulated by TopBP1 in a biphasic, concentration-dependent manner in a non-transformed MCF10A cell line and several cancer cell lines, including H1299, MDA-MB468 and U2OS. At low levels, TopBP1 activates ATR/Chk1, but once TopBP1 protein accumulates above an optimal level, it paradoxically leads to lower activation of ATR/Chk1. This is due to the perturbation of ATR/TopBP1 interaction and ATR chromatin loading by excessive TopBP1. Overexpression of TopBP1 thus hinders the ATR/Chk1 checkpoint response, leading to the impairment of genome integrity as demonstrated by the cytokinesis-block micronucleus assay. In contrast, moderate depletion of TopBP1 by shRNA in TopBP1-overexpressing cancer cells enhanced ATR/Chk1 activation and S-phase checkpoint response after replicative stress. The clinical significance of these findings is supported by an association between TopBP1 overexpression and genome instability in many types of human cancer. Taken together, our study illustrates an unexpected relationship between the levels of TopBP1 and the final functional outcome, and suggests TopBP1 overexpression as a new mechanism directly contributing to genomic instability during tumorigenesis.
    Keywords:  ATR; Chk1; TopBP1; hormesis
    DOI:  https://doi.org/10.1016/j.jbc.2021.100382
  69. Cell Metab. 2021 Feb 04. pii: S1550-4131(21)00014-0. [Epub ahead of print]
    Transient phases of OXPHOS inhibitor resistance reveal underlying metabolic heterogeneity in single cells.
    Nont Kosaisawe, Breanne Sparta, Michael Pargett, Carolyn K Teragawa, John G Albeck.
      Cell-to-cell heterogeneity in metabolism plays an unknown role in physiology and pharmacology. To functionally characterize cellular variability in metabolism, we treated cells with inhibitors of oxidative phosphorylation (OXPHOS) and monitored their responses with live-cell reporters for ATP, ADP/ATP, or activity of the energy-sensing kinase AMPK. Across multiple OXPHOS inhibitors and cell types, we identified a subpopulation of cells resistant to activation of AMPK and reduction of ADP/ATP ratio. This resistant state persists transiently for at least several hours and can be inherited during cell divisions. OXPHOS inhibition suppresses the mTORC1 and ERK growth signaling pathways in sensitive cells, but not in resistant cells. Resistance is linked to a multi-factorial combination of increased glucose uptake, reduced protein biosynthesis, and G0/G1 cell-cycle status. Our results reveal dynamic fluctuations in cellular energetic balance and provide a basis for measuring and predicting the distribution of cellular responses to OXPHOS inhibition.
    Keywords:  AKT; FRET; PI3K; adenosine mono-phosphate-regulated protein kinase; electron transport chain; insulin signaling; mammalian target of rapamycin; metabolic cycle; oligomycin; oscillation; translation regulation
    DOI:  https://doi.org/10.1016/j.cmet.2021.01.014
  70. Nat Commun. 2021 02 08. 12(1): 863
    Malignant subclone drives metastasis of genetically and phenotypically heterogenous cell clusters through fibrotic niche generation.
    Sau Yee Kok, Hiroko Oshima, Kei Takahashi, Mizuho Nakayama, Kazuhiro Murakami, Hiroki R Ueda, Kohei Miyazono, Masanobu Oshima.
      A concept of polyclonal metastasis has recently been proposed, wherein tumor cell clusters break off from the primary site and are disseminated. However, the involvement of driver mutations in such polyclonal mechanism is not fully understood. Here, we show that non-metastatic AP cells metastasize to the liver with metastatic AKTP cells after co-transplantation to the spleen. Furthermore, AKTP cell depletion after the development of metastases results in the continuous proliferation of the remaining AP cells, indicating a role of AKTP cells in the early step of polyclonal metastasis. Importantly, AKTP cells, but not AP cells, induce fibrotic niche generation when arrested in the sinusoid, and such fibrotic microenvironment promotes the colonization of AP cells. These results indicate that non-metastatic cells can metastasize via the polyclonal metastasis mechanism using the fibrotic niche induced by malignant cells. Thus, targeting the fibrotic niche is an effective strategy for halting polyclonal metastasis.
    DOI:  https://doi.org/10.1038/s41467-021-21160-0
  71. Nat Cell Biol. 2021 Feb;23(2): 111-113
    Tumour-regulated anorexia preceding cachexia.
    Gang Wang, Haiying Zhang, David Lyden.
      
    DOI:  https://doi.org/10.1038/s41556-021-00635-8
  72. Anticancer Agents Med Chem. 2021 Jan 31.
    Hyperglycemia Promotes Pancreatic Cancer Initiation and Progression by Activating the Wnt/β-Catenin Signaling Pathway.
    Huiming Chen, Junfeng Zhao, Ningning Jiang, Zheng Wang, Chang Liu.
      BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal diseases, with a 5-year survival rate of less than 10% because of the limited knowledge of tumor-promoting factors and their underlying mechanism. Diabetes mellitus (DM) and hyperglycemia are risk factors for many cancers, including PDAC, that modulate multiple downstream signaling pathways, such as the wingless/integrated (Wnt)/β-catenin signaling pathway. However, whether hyperglycemia promotes PDAC initiation and progression by activating the Wnt/β-catenin signaling pathway remains unclear.METHODS: In this study, we used bioinformatics analysis and clinical specimen analysis to evaluate the activation states of the Wnt/βcatenin signaling pathway. In addition, colony formation assays, Transwell assays and wound-healing assays were used to evaluate the malignant biological behaviors of pancreatic cancer cells (PCs) under hyperglycemic conditions. To describe the effects of hyperglycemia and the Wnt/β-catenin signaling pathway on the initiation of PDAC, we used pancreatitis-driven pancreatic cancer initiation models in vivo and pancreatic acinar cell 3-dimensional culture in vitro.
    RESULTS: Wnt/β-catenin signaling pathway-related molecules were overexpressed in PDAC tissues/cells and correlated with poor prognosis in PDAC patients. In addition, hyperglycemia exacerbated the abnormal activation of β-catenin in PDAC and enhanced the malignant biological behaviors of PCs in a Wnt/β-catenin signaling pathway-dependent manner. Indeed, hyperglycemia accelerated the formation of pancreatic precancerous lesions by activating the Wnt/β-catenin signaling pathway in vivo and in vitro.
    CONCLUSION: Hyperglycemia promotes pancreatic cancer initiation and progression by activating the Wnt/β-catenin signaling pathway.
    Keywords:  Wnt/β-catenin; ancreatic ductal adenocarcinoma; hyperglycemia; pancreatic cancer; signaling pathway; tumor initiation and progression
    DOI:  https://doi.org/10.2174/1871520621666210201095613
  73. PLoS Comput Biol. 2021 Feb 11. 17(2): e1008730
    DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks.
    Pablo Rodríguez-Mier, Nathalie Poupin, Carlo de Blasio, Laurent Le Cam, Fabien Jourdan.
      The correct identification of metabolic activity in tissues or cells under different conditions can be extremely elusive due to mechanisms such as post-transcriptional modification of enzymes or different rates in protein degradation, making difficult to perform predictions on the basis of gene expression alone. Context-specific metabolic network reconstruction can overcome some of these limitations by leveraging the integration of multi-omics data into genome-scale metabolic networks (GSMN). Using the experimental information, context-specific models are reconstructed by extracting from the generic GSMN the sub-network most consistent with the data, subject to biochemical constraints. One advantage is that these context-specific models have more predictive power since they are tailored to the specific tissue, cell or condition, containing only the reactions predicted to be active in such context. However, an important limitation is that there are usually many different sub-networks that optimally fit the experimental data. This set of optimal networks represent alternative explanations of the possible metabolic state. Ignoring the set of possible solutions reduces the ability to obtain relevant information about the metabolism and may bias the interpretation of the true metabolic states. In this work we formalize the problem of enumerating optimal metabolic networks and we introduce DEXOM, an unified approach for diversity-based enumeration of context-specific metabolic networks. We developed different strategies for this purpose and we performed an exhaustive analysis using simulated and real data. In order to analyze the extent to which these results are biologically meaningful, we used the alternative solutions obtained with the different methods to measure: 1) the improvement of in silico predictions of essential genes in Saccharomyces cerevisiae using ensembles of metabolic network; and 2) the detection of alternative enriched pathways in different human cancer cell lines. We also provide DEXOM as an open-source library compatible with COBRA Toolbox 3.0, available at https://github.com/MetExplore/dexom.
    DOI:  https://doi.org/10.1371/journal.pcbi.1008730
  74. Trends Cancer. 2021 Feb 06. pii: S2405-8033(21)00021-2. [Epub ahead of print]
    Leveraging Single-Cell Approaches in Cancer Precision Medicine.
    Aritro Nath, Andrea H Bild.
      Cancer precision medicine aims to improve patient outcomes by tailoring treatment to the unique genomic background of a tumor. However, efforts to develop prognostic and drug response biomarkers largely rely on bulk 'omic' data, which fails to capture intratumor heterogeneity (ITH) and deconvolve signals from normal versus tumor cells. These shortcomings in measuring clinically relevant features are being addressed with single-cell technologies, which provide a fine-resolution map of the genetic and phenotypic heterogeneity in tumors and their microenvironment, as well as an improved understanding of the patterns of subclonal tumor populations. Here we present recent advances in the application of single-cell technologies, towards gaining a deeper understanding of ITH and evolution, and potential applications in developing personalized therapeutic strategies.
    Keywords:  biomarkers; clonal evolution; single-cell sequencing; tumor heterogeneity; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.trecan.2021.01.007
  75. Cell Rep. 2021 Feb 09. pii: S2211-1247(21)00039-5. [Epub ahead of print]34(6): 108726
    Gain-of-function p53 protein transferred via small extracellular vesicles promotes conversion of fibroblasts to a cancer-associated phenotype.
    Shaolin Ma, Michael H McGuire, Lingegowda S Mangala, Sanghoon Lee, Elaine Stur, Wen Hu, Emine Bayraktar, Alejandro Villar-Prados, Cristina Ivan, Sherry Y Wu, Akira Yokoi, Santosh K Dasari, Nicholas B Jennings, Jinsong Liu, Gabriel Lopez-Berestein, Prahlad Ram, Anil K Sood.
      Tumor and stromal interactions consist of reciprocal signaling through cytokines, growth factors, direct cell-cell interactions, and extracellular vesicles (EVs). Small EVs (≤200 nm) have been considered critical messengers of cellular communication during tumor development. Here, we demonstrate that gain-of-function (GOF) p53 protein can be packaged into small EVs and transferred to fibroblasts. GOF p53 protein is selectively bound by heat shock protein 90 (HSP90), a chaperone protein, and packaged into small EVs. Inhibition of HSP90 activity blocks packaging of GOF, but not wild-type, p53 in small EVs. GOF p53-containing small EVs result in their conversion to cancer-associated fibroblasts. In vivo studies reveal that GOF p53-containing small EVs can enhance tumor growth and promote fibroblast transformation into a cancer-associated phenotype. These findings provide a better understanding of the complex interactions between cancer and stromal cells and may have therapeutic implications.
    Keywords:  CAFs; HSP90; Nrf2; p53; small EVs
    DOI:  https://doi.org/10.1016/j.celrep.2021.108726
  76. Pancreas. 2021 Feb 01. 50(2): 219-226
    Inhibition of Stearoyl-CoA Desaturase Induces the Unfolded Protein Response in Pancreatic Tumors and Suppresses Their Growth.
    Kaitlin Skrypek, Steven Balog, Yoshihiro Eriguchi, Kinji Asahina.
      OBJECTIVE: Pancreatic ductal adenocarcinoma is the fourth-leading cause of cancer death in the United States, and there is an urgent need for effective therapies. Stearoyl-CoA desaturase (SCD) is an enzyme localized in the endoplasmic reticulum and generates monounsaturated fatty acid from saturated fatty acid. In this study, we examined the role of SCD in pancreatic cancer.METHODS: We isolated epithelial cell adhesion molecule-positive pancreatic tumors from the Pdx1Cre;LSL-KrasG12D mouse and formed organoids in Matrigel. Using a SCD inhibitor, A939572, we tested its effects on growth and cell death in tumor organoids, tumors developed in the Pdx1Cre;LSL-KrasG12D mouse, and a human pancreatic ductal adenocarcinoma cell line, PANC-1.
    RESULTS: A939572 treatment rapidly induced degeneration of mouse tumor organoids and activated the unfolded protein response (UPR). Cotreatment of oleic acid, but not stearic acid, reduced the UPR in the organoids and rescued the inhibitory effect of the SCD inhibitor on their growth. Administration of A939572 to Pdx1Cre;LSL-KrasG12D mice caused cell death in early pancreatic tumors, but not in acini or islets. The SCD inhibitor induced the UPR in PANC-1 and suppressed their growth but did not induce cell death.
    CONCLUSIONS: The inhibition of the SCD enzyme causes an UPR and cell death in early pancreatic tumors.
    DOI:  https://doi.org/10.1097/MPA.0000000000001737
  77. STAR Protoc. 2021 Mar 19. 2(1): 100310
    Fabrication of a microfluidic device for studying the combinatorial effect of physical and chemical cues on cell migration.
    Neha Saxena, Sameer Jadhav, Shamik Sen.
      In vivo cell migration is influenced by soluble factors as well as stiffness. Current in vitro strategies mostly account for one of these two factors to study cell migration. To understand the combinatorial effect of stiffness and chemokines on cell behavior, we have developed a microfluidic model to study stiffness-dependent chemotaxis of mesenchymal stem cells (hMSCs). A detailed description of our methodology will help researchers develop microfluidic models that combine these two factors influencing cell behavior. For complete details on the use and execution of this protocol, please refer to Saxena et al. (2018).
    Keywords:  Biophysics; Cancer; Cell biology; Microscopy
    DOI:  https://doi.org/10.1016/j.xpro.2021.100310
  78. Nat Rev Cancer. 2021 Feb 10.
    Solid tumours hijack the histone variant network.
    Flávia G Ghiraldini, Dan Filipescu, Emily Bernstein.
      Cancer is a complex disease characterized by loss of cellular homeostasis through genetic and epigenetic alterations. Emerging evidence highlights a role for histone variants and their dedicated chaperones in cancer initiation and progression. Histone variants are involved in processes as diverse as maintenance of genome integrity, nuclear architecture and cell identity. On a molecular level, histone variants add a layer of complexity to the dynamic regulation of transcription, DNA replication and repair, and mitotic chromosome segregation. Because these functions are critical to ensure normal proliferation and maintenance of cellular fate, cancer cells are defined by their capacity to subvert them. Hijacking histone variants and their chaperones is emerging as a common means to disrupt homeostasis across a wide range of cancers, particularly solid tumours. Here we discuss histone variants and histone chaperones as tumour-promoting or tumour-suppressive players in the pathogenesis of cancer.
    DOI:  https://doi.org/10.1038/s41568-020-00330-0
  79. Cell Mol Life Sci. 2021 Feb 12.
    Mitochondrial outer membrane permeabilization at the single molecule level.
    Shashank Dadsena, Andreas Jenner, Ana J García-Sáez.
      Apoptotic cell death is essential for development, immune function or tissue homeostasis, and its mis-regulation is linked to various diseases. Mitochondrial outer membrane permeabilization (MOMP) is a central event in the intrinsic apoptotic pathway and essential to control the execution of cell death. Here we review current concepts in regulation of MOMP focusing on the interaction network of the Bcl-2 family proteins as well as further regulatory elements influencing MOMP. As MOMP is a complex spatially and temporally controlled process, we point out the importance of single-molecule techniques to unveil processes which would be masked by ensemble measurements. We report key single-molecule studies applied to decipher the composition, assembly mechanism and structure of protein complexes involved in MOMP regulation.
    Keywords:  Apoptosis; Bcl-2 proteins; Mitochondrial outer membrane permeabilization (MOMP); Single-molecule techniques
    DOI:  https://doi.org/10.1007/s00018-021-03771-4
  80. Cancer Cell. 2021 Feb 02. pii: S1535-6108(21)00050-7. [Epub ahead of print]
    Proteogenomic and metabolomic characterization of human glioblastoma.
    Liang-Bo Wang, Alla Karpova, Marina A Gritsenko, Jennifer E Kyle, Song Cao, Yize Li, Dmitry Rykunov, Antonio Colaprico, Joseph H Rothstein, Runyu Hong, Vasileios Stathias, MacIntosh Cornwell, Francesca Petralia, Yige Wu, Boris Reva, Karsten Krug, Pietro Pugliese, Emily Kawaler, Lindsey K Olsen, Wen-Wei Liang, Xiaoyu Song, Yongchao Dou, Michael C Wendl, Wagma Caravan, Wenke Liu, Daniel Cui Zhou, Jiayi Ji, Chia-Feng Tsai, Vladislav A Petyuk, Jamie Moon, Weiping Ma, Rosalie K Chu, Karl K Weitz, Ronald J Moore, Matthew E Monroe, Rui Zhao, Xiaolu Yang, Seungyeul Yoo, Azra Krek, Alexis Demopoulos, Houxiang Zhu, Matthew A Wyczalkowski, Joshua F McMichael, Brittany L Henderson, Caleb M Lindgren, Hannah Boekweg, Shuangjia Lu, Jessika Baral, Lijun Yao, Kelly G Stratton, Lisa M Bramer, Erika Zink, Sneha P Couvillion, Kent J Bloodsworth, Shankha Satpathy, Weiva Sieh, Simina M Boca, Stephan Schürer, Feng Chen, Maciej Wiznerowicz, Karen A Ketchum, Emily S Boja, Christopher R Kinsinger, Ana I Robles, Tara Hiltke, Mathangi Thiagarajan, Alexey I Nesvizhskii, Bing Zhang, D R Mani, Michele Ceccarelli, Xi S Chen, Sandra L Cottingham, Qing Kay Li, Albert H Kim, David Fenyö, Kelly V Ruggles, Henry Rodriguez, Mehdi Mesri, Samuel H Payne, Adam C Resnick, Pei Wang, Richard D Smith, Antonio Iavarone, Milan G Chheda, Jill S Barnholtz-Sloan, Karin D Rodland, Tao Liu, Li Ding, .
      Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis is crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification and metabolomic data on 99 treatment-naive GBMs provides insights to GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 and PLCG1) as potential switches mediating oncogenic pathway activation, as well as potential targets for EGFR-, TP53-, and RB1-altered tumors. Immune subtypes with distinct immune cell types are discovered using bulk omics methodologies, validated by snRNA-seq, and correlated with specific expression and histone acetylation patterns. Histone H2B acetylation in classical-like and immune-low GBM is driven largely by BRDs, CREBBP, and EP300. Integrated metabolomic and proteomic data identify specific lipid distributions across subtypes and distinct global metabolic changes in IDH-mutated tumors. This work highlights biological relationships that could contribute to stratification of GBM patients for more effective treatment.
    Keywords:  CPTAC; acetylome; glioblastoma; lipidome; metabolome; proteogenomics; proteomics; signaling; single nuclei RNA-seq
    DOI:  https://doi.org/10.1016/j.ccell.2021.01.006
  81. Nat Med. 2021 Feb 11.
    Intratumoral heterogeneity in cancer progression and response to immunotherapy.
    Ilio Vitale, Efrat Shema, Sherene Loi, Lorenzo Galluzzi.
      Most (if not all) tumors emerge and progress under a strong evolutionary pressure imposed by trophic, metabolic, immunological, and therapeutic factors. The relative impact of these factors on tumor evolution changes over space and time, ultimately favoring the establishment of a neoplastic microenvironment that exhibits considerable genetic, phenotypic, and behavioral heterogeneity in all its components. Here, we discuss the main sources of intratumoral heterogeneity and its impact on the natural history of the disease, including sensitivity to treatment, as we delineate potential strategies to target such a detrimental feature of aggressive malignancies.
    DOI:  https://doi.org/10.1038/s41591-021-01233-9
  82. Cell. 2021 Feb 05. pii: S0092-8674(21)00069-6. [Epub ahead of print]
    Mechanism of gating and partial agonist action in the glycine receptor.
    Jie Yu, Hongtao Zhu, Remigijus Lape, Timo Greiner, Juan Du, Wei Lü, Lucia Sivilotti, Eric Gouaux.
      Ligand-gated ion channels mediate signal transduction at chemical synapses and transition between resting, open, and desensitized states in response to neurotransmitter binding. Neurotransmitters that produce maximum open channel probabilities (Po) are full agonists, whereas those that yield lower than maximum Po are partial agonists. Cys-loop receptors are an important class of neurotransmitter receptors, yet a structure-based understanding of the mechanism of partial agonist action has proven elusive. Here, we study the glycine receptor with the full agonist glycine and the partial agonists taurine and γ-amino butyric acid (GABA). We use electrophysiology to show how partial agonists populate agonist-bound, closed channel states and cryo-EM reconstructions to illuminate the structures of intermediate, pre-open states, providing insights into previously unseen conformational states along the receptor reaction pathway. We further correlate agonist-induced conformational changes to Po across members of the receptor family, providing a hypothetical mechanism for partial and full agonist action at Cys-loop receptors.
    Keywords:  SMA; cryo-EM; gating mechanism; glycine receptor; ligand-gated ion channels; partial agonists action
    DOI:  https://doi.org/10.1016/j.cell.2021.01.026
  83. Biomolecules. 2021 Feb 07. pii: 235. [Epub ahead of print]11(2):
    Tissue-Specific Landscape of Metabolic Dysregulation during Ageing.
    Fangrong Zhang, Jakob Kerbl-Knapp, Alena Akhmetshina, Melanie Korbelius, Katharina Barbara Kuentzel, Nemanja Vujić, Gerd Hörl, Margret Paar, Dagmar Kratky, Ernst Steyrer, Tobias Madl.
      The dysregulation of cellular metabolism is a hallmark of ageing. To understand the metabolic changes that occur as a consequence of the ageing process and to find biomarkers for age-related diseases, we conducted metabolomic analyses of the brain, heart, kidney, liver, lung and spleen in young (9-10 weeks) and old (96-104 weeks) wild-type mice [mixed genetic background of 129/J and C57BL/6] using NMR spectroscopy. We found differences in the metabolic fingerprints of all tissues and distinguished several metabolites to be altered in most tissues, suggesting that they may be universal biomarkers of ageing. In addition, we found distinct tissue-clustered sets of metabolites throughout the organism. The associated metabolic changes may reveal novel therapeutic targets for the treatment of ageing and age-related diseases. Moreover, the identified metabolite biomarkers could provide a sensitive molecular read-out to determine the age of biologic tissues and organs and to validate the effectiveness and potential off-target effects of senolytic drug candidates on both a systemic and tissue-specific level.
    Keywords:  ageing; biomarker; metabolomics; tissue-specific
    DOI:  https://doi.org/10.3390/biom11020235
  84. EMBO J. 2021 Feb 08. e107531
    Divide and conquer acoustic diversity.
    Maria E Gómez-Casati, Juan D Goutman.
      Humans can recognize differences in sound intensity of up to 6 orders of magnitude. However, it is not clear how this is achieved and what enables our auditory systems to encode such a gradient. Özçete & Moser (2021) report in this issue that the key to this lies in the synaptic heterogeneity within individual sensory cells in the inner ear.
    DOI:  https://doi.org/10.15252/embj.2020107531
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