bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2020–11–08
sixty-nine papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells.
  2. Autophagic receptor p62 protects against glycation-derived toxicity and enhances viability.
  3. Neurons Release Serine to Support mRNA Translation in Pancreatic Cancer.
  4. Inhibition of LTβR signalling activates WNT-induced regeneration in lung.
  5. Autophagy-independent function of lipidated LC3 essential for TFEB activation during the lysosomal damage responses.
  6. eIF4E S209 phosphorylation licenses Myc-and stress-driven oncogenesis.
  7. Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer.
  8. Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.
  9. Antibody-mediated activation of the FGFR1/Klothoβ complex corrects metabolic dysfunction and alters food preference in obese humans.
  10. Multi-Tissue Acceleration of the Mitochondrial Phosphoenolpyruvate Cycle Improves Whole-Body Metabolic Health.
  11. Pyruvate Kinase Controls Signal Strength in the Insulin Secretory Pathway.
  12. Regulation and inhibition of the DNA sensor cGAS.
  13. New Horizons: Novel Approaches to Enhance Healthspan Through Targeting Cellular Senescence and Related Aging Mechanisms.
  14. Metabolic determinants of cellular fitness dependent on mitochondrial reactive oxygen species.
  15. Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast.
  16. Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines.
  17. A Blueprint for Characterizing Senescence.
  18. Roles of mitochondria in the hallmarks of metastasis.
  19. DNA Damage and Mitochondria in Cancer and Aging.
  20. Perivascular mesenchymal cells control adipose-tissue macrophage accrual in obesity.
  21. Early-Life Body Adiposity and the Breast Tumor Transcriptome.
  22. Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome.
  23. Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation.
  24. Epigenetic and transcriptional control of the epidermal growth factor receptor (EGFR) regulates the tumor immune microenvironment in pancreatic cancer.
  25. Genomic control of metastasis.
  26. The dialogue between the ubiquitin-proteasome system and autophagy: implications in ageing.
  27. Tumor Mutational Burden as a Predictive Biomarker in Solid Tumors.
  28. Combinatorial expression of GPCR isoforms affects signalling and drug responses.
  29. Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design.
  30. TCA cycle signalling and the evolution of eukaryotes.
  31. Age-related loss of gene-to-gene transcriptional coordination among single cells.
  32. Screening for Pancreatic Ductal Adenocarcinoma: Are We Asking the Impossible?
  33. Rapamycin-mediated mouse lifespan extension: Late-life dosage regimes with sex-specific effects.
  34. CRISPR pioneers win Nobel prize.
  35. The paradox-breaking panRAF plus SRC family kinase inhibitor, CCT3833, is effective in mutant KRAS-driven cancers.
  36. Loss of metabolic plasticity underlies metformin toxicity in aged Caenorhabditis elegans.
  37. Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.
  38. NMDAR in cultured astrocytes: Flux-independent pH sensor and flux-dependent regulator of mitochondria and plasma membrane-mitochondria bridging.
  39. Cellular Control of Viscosity Counters Changes in Temperature and Energy Availability.
  40. A Nuclear Stress Pathway that Parallels Cytoplasmic Stress Granule Formation.
  41. Metastasis is a highly stressful process.
  42. Loss of ARID1A promotes epithelial-mesenchymal transition and sensitizes pancreatic tumors to proteotoxic stress.
  43. Pheno-RNA, a method to associate genes with a specific phenotype, identifies genes linked to cellular transformation.
  44. Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity.
  45. Phase I Basket Study of Taselisib, an Isoform-Selective PI3K Inhibitor, in Patients with PIK3CA-Mutant Cancers.
  46. Loss of sympathetic innervation to islets of Langerhans in canine diabetes and pancreatitis is not associated with insulitis.
  47. Injury triggers fascia fibroblast collective cell migration to drive scar formation through N-cadherin.
  48. Genome-wide detection of DNA double-strand breaks by in-suspension BLISS.
  49. Organic fluorescent probes for monitoring autophagy in living cells.
  50. Obesity and Pancreatic Cancer: A Matched-Pair Survival Analysis.
  51. Mutant p53 oncogenicity - dominant-negative or gain-of-function?
  52. Therapeutics Targeting Mutant KRAS.
  53. The Endothelium: An Active Regulator of Lipid and Glucose Homeostasis.
  54. Anti-mullerian hormone as a serum biomarker for risk of chemotherapy-induced amenorrhea.
  55. Lipids and membrane-associated proteins in autophagy.
  56. Regulation of Mitochondrial Ca2+ Uptake.
  57. Mitochondrial disorders of the oxphos system.
  58. Broad genic repression domains signify enhanced silencing of oncogenes.
  59. The fluorescence toolbox for visualizing autophagy.
  60. Protein phase separation and its role in tumorigenesis.
  61. Genetic profiling of protein burden and nuclear export overload.
  62. Small molecules as potent biphasic modulators of protein liquid-liquid phase separation.
  63. Cancer and climate change.
  64. Hair graying with aging in mice carrying oncogenic RET.
  65. The anti-malarial drug atovaquone potentiates platinum-mediated cancer cell death by increasing oxidative stress.
  66. Ceramides in Metabolism: Key Lipotoxic Players.
  67. BELLINI: a renaissance for an era of precision therapy in multiple myeloma.
  68. MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.
  69. PALB2 Variants: Protein Domains and Cancer Susceptibility.
  1. Cell Metab. 2020 Oct 28. pii: S1550-4131(20)30550-7. [Epub ahead of print]
    Functional Genomics In Vivo Reveal Metabolic Dependencies of Pancreatic Cancer Cells.
    Xiphias Ge Zhu, Aleksey Chudnovskiy, Lou Baudrier, Benjamin Prizer, Yuyang Liu, Benjamin N Ostendorf, Norihiro Yamaguchi, Abolfozl Arab, Bernardo Tavora, Rebecca Timson, Søren Heissel, Elisa de Stanchina, Henrik Molina, Gabriel D Victora, Hani Goodarzi, Kıvanç Birsoy.
      Pancreatic ductal adenocarcinoma (PDAC) cells require substantial metabolic rewiring to overcome nutrient limitations and immune surveillance. However, the metabolic pathways necessary for pancreatic tumor growth in vivo are poorly understood. To address this, we performed metabolism-focused CRISPR screens in PDAC cells grown in culture or engrafted in immunocompetent mice. While most metabolic gene essentialities are unexpectedly similar under these conditions, a small fraction of metabolic genes are differentially required for tumor progression. Among these, loss of heme synthesis reduces tumor growth due to a limiting role of heme in vivo, an effect independent of tissue origin or immune system. Our screens also identify autophagy as a metabolic requirement for pancreatic tumor immune evasion. Mechanistically, autophagy protects cancer cells from CD8+ T cell killing through TNFα-induced cell death in vitro. Altogether, this resource provides metabolic dependencies arising from microenvironmental limitations and the immune system, nominating potential anti-cancer targets.
    Keywords:  cancer metabolism; in vivo CRISPR screen; pancreatic cancer; tumor immune evasion
    DOI:  https://doi.org/10.1016/j.cmet.2020.10.017
  2. Aging Cell. 2020 Nov 04. e13257
    Autophagic receptor p62 protects against glycation-derived toxicity and enhances viability.
    Gemma Aragonès, Kalavathi Dasuri, Opeoluwa Olukorede, Sarah G Francisco, Carol Renneburg, Caroline Kumsta, Malene Hansen, Shun Kageyama, Masaaki Komatsu, Sheldon Rowan, Jonathan Volkin, Michael Workman, Wenxin Yang, Paula Daza, Diego Ruano, Helena Dominguez-Martín, José Antonio Rodríguez-Navarro, Xue-Liang Du, Michael A Brownlee, Eloy Bejarano, Allen Taylor.
      Diabetes and metabolic syndrome are associated with the typical American high glycemia diet and result in accumulation of high levels of advanced glycation end products (AGEs), particularly upon aging. AGEs form when sugars or their metabolites react with proteins. Associated with a myriad of age-related diseases, AGEs accumulate in many tissues and are cytotoxic. To date, efforts to limit glycation pharmacologically have failed in human trials. Thus, it is crucial to identify systems that remove AGEs, but such research is scanty. Here, we determined if and how AGEs might be cleared by autophagy. Our in vivo mouse and C. elegans models, in which we altered proteolysis or glycative burden, as well as experiments in five types of cells, revealed more than six criteria indicating that p62-dependent autophagy is a conserved pathway that plays a critical role in the removal of AGEs. Activation of autophagic removal of AGEs requires p62, and blocking this pathway results in accumulation of AGEs and compromised viability. Deficiency of p62 accelerates accumulation of AGEs in soluble and insoluble fractions. p62 itself is subject to glycative inactivation and accumulates as high mass species. Accumulation of p62 in retinal pigment epithelium is reversed by switching to a lower glycemia diet. Since diminution of glycative damage is associated with reduced risk for age-related diseases, including age-related macular degeneration, cardiovascular disease, diabetes, Alzheimer's, and Parkinson's, discovery of methods to limit AGEs or enhance p62-dependent autophagy offers novel potential therapeutic targets to treat AGEs-related pathologies.
    Keywords:  aging; autophagy; glycative stress; p62; proteotoxicity
    DOI:  https://doi.org/10.1111/acel.13257
  3. Cell. 2020 Oct 28. pii: S0092-8674(20)31322-2. [Epub ahead of print]
    Neurons Release Serine to Support mRNA Translation in Pancreatic Cancer.
    Robert S Banh, Douglas E Biancur, Keisuke Yamamoto, Albert S W Sohn, Beth Walters, Miljan Kuljanin, Ajami Gikandi, Huamin Wang, Joseph D Mancias, Robert J Schneider, Michael E Pacold, Alec C Kimmelman.
      Pancreatic ductal adenocarcinoma (PDAC) tumors have a nutrient-poor, desmoplastic, and highly innervated tumor microenvironment. Although neurons can release stimulatory factors to accelerate PDAC tumorigenesis, the metabolic contribution of peripheral axons has not been explored. We found that peripheral axons release serine (Ser) to support the growth of exogenous Ser (exSer)-dependent PDAC cells during Ser/Gly (glycine) deprivation. Ser deprivation resulted in ribosomal stalling on two of the six Ser codons, TCC and TCT, and allowed the selective translation and secretion of nerve growth factor (NGF) by PDAC cells to promote tumor innervation. Consistent with this, exSer-dependent PDAC tumors grew slower and displayed enhanced innervation in mice on a Ser/Gly-free diet. Blockade of compensatory neuronal innervation using LOXO-101, a Trk-NGF inhibitor, further decreased PDAC tumor growth. Our data indicate that axonal-cancer metabolic crosstalk is a critical adaptation to support PDAC growth in nutrient poor environments.
    Keywords:  mRNA translation; metabolic crosstalk; neurons; pancreatic cancer; serine
    DOI:  https://doi.org/10.1016/j.cell.2020.10.016
  4. Nature. 2020 Nov 04.
    Inhibition of LTβR signalling activates WNT-induced regeneration in lung.
    Thomas M Conlon, Gerrit John-Schuster, Danijela Heide, Dominik Pfister, Mareike Lehmann, Yan Hu, Zeynep Ertüz, Martin A Lopez, Meshal Ansari, Maximilian Strunz, Christoph Mayr, Chiara Ciminieri, Rita Costa, Marlene Sophia Kohlhepp, Adrien Guillot, Gizem Günes, Aicha Jeridi, Maja C Funk, Giorgi Beroshvili, Sandra Prokosch, Jenny Hetzer, Stijn E Verleden, Hani Alsafadi, Michael Lindner, Gerald Burgstaller, Lore Becker, Martin Irmler, Michael Dudek, Jakob Janzen, Eric Goffin, Reinoud Gosens, Percy Knolle, Bernard Pirotte, Tobias Stoeger, Johannes Beckers, Darcy Wagner, Indrabahadur Singh, Fabian J Theis, Martin Hrabé de Angelis, Tracy O'Connor, Frank Tacke, Michael Boutros, Emmanuel Dejardin, Oliver Eickelberg, Herbert B Schiller, Melanie Königshoff, Mathias Heikenwalder, Ali Önder Yildirim.
      Lymphotoxin β-receptor (LTβR) signalling promotes lymphoid neogenesis and the development of tertiary lymphoid structures1,2, which are associated with severe chronic inflammatory diseases that span several organ systems3-6. How LTβR signalling drives chronic tissue damage particularly in the lung, the mechanism(s) that regulate this process, and whether LTβR blockade might be of therapeutic value have remained unclear. Here we demonstrate increased expression of LTβR ligands in adaptive and innate immune cells, enhanced non-canonical NF-κB signalling, and enriched LTβR target gene expression in lung epithelial cells from patients with smoking-associated chronic obstructive pulmonary disease (COPD) and from mice chronically exposed to cigarette smoke. Therapeutic inhibition of LTβR signalling in young and aged mice disrupted smoking-related inducible bronchus-associated lymphoid tissue, induced regeneration of lung tissue, and reverted airway fibrosis and systemic muscle wasting. Mechanistically, blockade of LTβR signalling dampened epithelial non-canonical activation of NF-κB, reduced TGFβ signalling in airways, and induced regeneration by preventing epithelial cell death and activating WNT/β-catenin signalling in alveolar epithelial progenitor cells. These findings suggest that inhibition of LTβR signalling represents a viable therapeutic option that combines prevention of tertiary lymphoid structures1 and inhibition of apoptosis with tissue-regenerative strategies.
    DOI:  https://doi.org/10.1038/s41586-020-2882-8
  5. Autophagy. 2020 Nov 05.
    Autophagy-independent function of lipidated LC3 essential for TFEB activation during the lysosomal damage responses.
    Shuhei Nakamura, Shiori Akayama, Tamotsu Yoshimori.
      Lysosomes are digestive organelles in cells containing many hydrolases, and also serve as a signaling hub to integrate intracellular and extracellular inputs; therefore, the integrity of lysosomes is critical for cellular homeostasis. Many agents and conditions can damage lysosomal membranes, which lead to leakage of lysosomal acidic contents into the cytosol thus becoming harmful for cells. Accordingly, cells have developed several defense systems to cope with damaged lysosomes, but underlying mechanisms of each system and their cross-talks are unclear. In our recent study, we found that a master transcription factor regulating autophagy and lysosomal biogenesis, TFEB (transcription factor EB) is activated during lysosomal damage, and this activation depends on an autophagy-independent function of lipidated LC3, which localizes on lysosomes. We further showed that this regulatory mechanism is essential to prevent the progression of the crystal nephropathy that accompanies lysosomal damage.
    Keywords:  Autophagy; LC3; TFEB; TRPML1; lysosome
    DOI:  https://doi.org/10.1080/15548627.2020.1846292
  6. Elife. 2020 Nov 02. pii: e60151. [Epub ahead of print]9
    eIF4E S209 phosphorylation licenses Myc-and stress-driven oncogenesis.
    Hang Ruan, Xiangyun Li, Xiang Xu, Brian J Leibowitz, Jingshan Tong, Lujia Chen, Luoquan Ao, Wei Xing, Jianhua Luo, Yanping Yu, Robert E Schoen, Nahum Sonenberg, Xinghua Lu, Lin Zhang, Jian Yu.
      To better understand a role of eIF4E S209 in oncogenic translation, we generated EIF4ES209A/+ heterozygous knockin (4EKI) HCT 116 human colorectal cancer (CRC) cells. 4EKI had little on total eIF4E levels, cap binding or global translation, while markedly reduced HCT 116 cell growth in spheroids and mice, and CRC organoid growth. 4EKI strongly inhibited Myc and ATF4 translation, the integrated Stress Response (ISR)-dependent glutamine metabolic signature, AKT activation and proliferation in vivo. 4EKI inhibited polyposis in ApcMin/+ mice by suppressing Myc protein and AKT activation. Furthermore, p-eIF4E was highly elevated in CRC precursor lesions in mouse and human. p-eIF4E cooperated with mutant KRAS to promote Myc and ISR-dependent glutamine addiction in various CRC cell lines, characterized by increased cell death, transcriptomic heterogeneity and immune suppression upon deprivation. These findings demonstrate a critical role of eIF4E S209-dependent translation in Myc and stress-driven oncogenesis and as a potential therapeutic vulnerability.
    Keywords:  cancer biology; human; mouse
    DOI:  https://doi.org/10.7554/eLife.60151
  7. Cell Metab. 2020 Oct 28. pii: S1550-4131(20)30551-9. [Epub ahead of print]
    Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer.
    Douglas E Biancur, Kevin S Kapner, Keisuke Yamamoto, Robert S Banh, Jasper E Neggers, Albert S W Sohn, Warren Wu, Robert T Manguso, Adam Brown, David E Root, Andrew J Aguirre, Alec C Kimmelman.
      Pancreatic ductal adenocarcinoma (PDA) is a deadly cancer characterized by complex metabolic adaptations that promote survival in a severely hypoxic and nutrient-limited tumor microenvironment (TME). Modeling microenvironmental influences in cell culture has been challenging, and technical limitations have hampered the comprehensive study of tumor-specific metabolism in vivo. To systematically interrogate metabolic vulnerabilities in PDA, we employed parallel CRISPR-Cas9 screens using in vivo and in vitro systems. This work revealed striking overlap of in vivo metabolic dependencies with those in vitro. Moreover, we identified that intercellular nutrient sharing can mask dependencies in pooled screens, highlighting a limitation of this approach to study tumor metabolism. Furthermore, metabolic dependencies were similar between 2D and 3D culture, although 3D culture may better model vulnerabilities that influence certain oncogenic signaling pathways. Lastly, our work demonstrates the power of genetic screening approaches to define in vivo metabolic dependencies and pathways that may have therapeutic utility.
    Keywords:  cancer cell signaling; metabolism; nutrient crosstalk; pancreatic cancer; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cmet.2020.10.018
  8. Mol Cell. 2020 Nov 05. pii: S1097-2765(20)30729-2. [Epub ahead of print]80(3): 452-469.e9
    Zmat3 Is a Key Splicing Regulator in the p53 Tumor Suppression Program.
    Kathryn T Bieging-Rolett, Alyssa M Kaiser, David W Morgens, Anthony M Boutelle, Jose A Seoane, Eric L Van Nostrand, Changyu Zhu, Shauna L Houlihan, Stephano S Mello, Brian A Yee, Jacob McClendon, Sarah E Pierce, Ian P Winters, Mengxiong Wang, Andrew J Connolly, Scott W Lowe, Christina Curtis, Gene W Yeo, Monte M Winslow, Michael C Bassik, Laura D Attardi.
      Although TP53 is the most commonly mutated gene in human cancers, the p53-dependent transcriptional programs mediating tumor suppression remain incompletely understood. Here, to uncover critical components downstream of p53 in tumor suppression, we perform unbiased RNAi and CRISPR-Cas9-based genetic screens in vivo. These screens converge upon the p53-inducible gene Zmat3, encoding an RNA-binding protein, and we demonstrate that ZMAT3 is an important tumor suppressor downstream of p53 in mouse KrasG12D-driven lung and liver cancers and human carcinomas. Integrative analysis of the ZMAT3 RNA-binding landscape and transcriptomic profiling reveals that ZMAT3 directly modulates exon inclusion in transcripts encoding proteins of diverse functions, including the p53 inhibitors MDM4 and MDM2, splicing regulators, and components of varied cellular processes. Interestingly, these exons are enriched in NMD signals, and, accordingly, ZMAT3 broadly affects target transcript stability. Collectively, these studies reveal ZMAT3 as a novel RNA-splicing and homeostasis regulator and a key component of p53-mediated tumor suppression.
    Keywords:  CRISPR screen; Mdm4; RBP; RNAi screen; Zmat3; alternative splicing; hepatocellular carcinoma; lung adenocarcinoma; p53; tumor suppression
    DOI:  https://doi.org/10.1016/j.molcel.2020.10.022
  9. Proc Natl Acad Sci U S A. 2020 Nov 02. pii: 202012073. [Epub ahead of print]
    Antibody-mediated activation of the FGFR1/Klothoβ complex corrects metabolic dysfunction and alters food preference in obese humans.
    Amos Baruch, Chin Wong, Leslie W Chinn, Anjali Vaze, Junichiro Sonoda, Thomas Gelzleichter, Shan Chen, Nicholas Lewin-Koh, Linda Morrow, Suresh Dheerendra, Richard Boismenu, Johnny Gutierrez, Eric Wakshull, Maria E Wilson, Puneet S Arora.
      Fibroblast growth factor 21 (FGF21) controls metabolic organ homeostasis and eating/drinking behavior via FGF receptor 1/Klothoβ (FGFR1/KLB) complexes expressed in adipocytes, pancreatic acinar cells, and the nervous system in mice. Chronic administration of recombinant FGF21 or engineered variants improves metabolic health in rodents, nonhuman primates, and humans; however, the rapid turnover of these molecules limits therapeutic utility. Here we show that the bispecific anti-FGFR1/KLB agonist antibody BFKB8488A induced marked weight loss in obese cynomolgus monkeys while elevating serum adiponectin and the adipose expression of FGFR1 target genes, demonstrating its action as an FGF21 mimetic. In a randomized, placebo-controlled, single ascending-dose study in overweight/obese human participants, subcutaneous BFKB8488A injection caused transient body weight reduction, sustained improvement in cardiometabolic parameters, and a trend toward reduction in preference for sweet taste and carbohydrate intake. These data suggest that specific activation of the FGFR1/KLB complex in humans can be used as therapy for obesity-related metabolic defects.
    Keywords:  FGF21 receptor activation; food preference; metabolism; obesity; weight loss
    DOI:  https://doi.org/10.1073/pnas.2012073117
  10. Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30539-8. [Epub ahead of print]32(5): 751-766.e11
    Multi-Tissue Acceleration of the Mitochondrial Phosphoenolpyruvate Cycle Improves Whole-Body Metabolic Health.
    Abudukadier Abulizi, Rebecca L Cardone, Romana Stark, Sophie L Lewandowski, Xiaojian Zhao, Joelle Hillion, Lingjun Ma, Raghav Sehgal, Tiago C Alves, Craig Thomas, Charles Kung, Bei Wang, Stephan Siebel, Zane B Andrews, Graeme F Mason, Jesse Rinehart, Matthew J Merrins, Richard G Kibbey.
      The mitochondrial GTP (mtGTP)-dependent phosphoenolpyruvate (PEP) cycle couples mitochondrial PEPCK (PCK2) to pyruvate kinase (PK) in the liver and pancreatic islets to regulate glucose homeostasis. Here, small molecule PK activators accelerated the PEP cycle to improve islet function, as well as metabolic homeostasis, in preclinical rodent models of diabetes. In contrast, treatment with a PK activator did not improve insulin secretion in pck2-/- mice. Unlike other clinical secretagogues, PK activation enhanced insulin secretion but also had higher insulin content and markers of differentiation. In addition to improving insulin secretion, acute PK activation short-circuited gluconeogenesis to reduce endogenous glucose production while accelerating red blood cell glucose turnover. Four-week delivery of a PK activator in vivo remodeled PK phosphorylation, reduced liver fat, and improved hepatic and peripheral insulin sensitivity in HFD-fed rats. These data provide a preclinical rationale for PK activation to accelerate the PEP cycle to improve metabolic homeostasis and insulin sensitivity.
    Keywords:  anaplerosis; cataplerosis; fatty liver; human islets; insulin resistance; insulin secretion; mitochondrial GTP; mitochondrial PEPCK; phosphoenolpyruvate cycle; pyruvate kinase
    DOI:  https://doi.org/10.1016/j.cmet.2020.10.006
  11. Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30540-4. [Epub ahead of print]32(5): 736-750.e5
    Pyruvate Kinase Controls Signal Strength in the Insulin Secretory Pathway.
    Sophie L Lewandowski, Rebecca L Cardone, Hannah R Foster, Thuong Ho, Evgeniy Potapenko, Chetan Poudel, Halena R VanDeusen, Sophia M Sdao, Tiago C Alves, Xiaojian Zhao, Megan E Capozzi, Arnaldo H de Souza, Ishrat Jahan, Craig J Thomas, Craig S Nunemaker, Dawn Belt Davis, Jonathan E Campbell, Richard G Kibbey, Matthew J Merrins.
      Pancreatic β cells couple nutrient metabolism with appropriate insulin secretion. Here, we show that pyruvate kinase (PK), which converts ADP and phosphoenolpyruvate (PEP) into ATP and pyruvate, underlies β cell sensing of both glycolytic and mitochondrial fuels. Plasma membrane-localized PK is sufficient to close KATP channels and initiate calcium influx. Small-molecule PK activators increase the frequency of ATP/ADP and calcium oscillations and potently amplify insulin secretion. PK restricts respiration by cyclically depriving mitochondria of ADP, which accelerates PEP cycling until membrane depolarization restores ADP and oxidative phosphorylation. Our findings support a compartmentalized model of β cell metabolism in which PK locally generates the ATP/ADP required for insulin secretion. Oscillatory PK activity allows mitochondria to perform synthetic and oxidative functions without any net impact on glucose oxidation. These findings suggest a potential therapeutic route for diabetes based on PK activation that would not be predicted by the current consensus single-state model of β cell function.
    Keywords:  K(ATP) channel; anaplerosis; biosensor imaging; insulin secretion; metabolic flux; metabolic oscillations; oxidative phosphorylation; phosphoenolpyruvate cycle; pyruvate kinase; β cell metabolism
    DOI:  https://doi.org/10.1016/j.cmet.2020.10.007
  12. EMBO Rep. 2020 Nov 05. e51345
    Regulation and inhibition of the DNA sensor cGAS.
    Jonny Hertzog, Jan Rehwinkel.
      Cell-autonomous sensing of nucleic acids is essential for host defence against invading pathogens by inducing antiviral and inflammatory cytokines. cGAS has emerged in recent years as a non-redundant DNA sensor important for detection of many viruses and bacteria. Upon binding to DNA, cGAS synthesises the cyclic dinucleotide 2'3'-cGAMP that binds to the adaptor protein STING and thereby triggers IRF3- and NFκB-dependent transcription. In addition to infection, the pathophysiology of an ever-increasing number of sterile inflammatory conditions in humans involves the recognition of DNA through cGAS. Consequently, the cGAS/STING signalling axis has emerged as an attractive target for pharmacological modulation. However, the development of cGAS and STING inhibitors has just begun and a need for specific and effective compounds persists. In this review, we focus on cGAS and explore how its activation by immunostimulatory DNA is regulated by cellular mechanisms, viral immune modulators and small molecules. We further use our knowledge of cGAS modulation by cells and viruses to conceptualise potential new ways of pharmacological cGAS targeting.
    Keywords:  DNA sensing; STING; cGAMP; cGAS; inhibitor
    DOI:  https://doi.org/10.15252/embr.202051345
  13. J Clin Endocrinol Metab. 2020 Nov 06. pii: dgaa728. [Epub ahead of print]
    New Horizons: Novel Approaches to Enhance Healthspan Through Targeting Cellular Senescence and Related Aging Mechanisms.
    Tamar Tchkonia, Allyson K Palmer, James L Kirkland.
      The elderly population is increasing faster than other segments of the population throughout the world. Age is the leading predictor for most chronic diseases and disorders, multimorbidity, geriatric syndromes, and impaired ability to recover from accidents or illnesses. Enhancing the duration of health and independence, termed healthspan, would be more desirable than extending lifespan merely by prolonging the period of morbidity toward the end of life. The geroscience hypothesis posits that healthspan can be extended by targeting fundamental aging mechanisms, rather than attempting to address each age-related disease one at a time, only so the afflicted individual survives disabled and dies shortly afterward of another age-related disease. These fundamental aging mechanisms include, among others, chronic inflammation, fibrosis, stem cell/ progenitor dysfunction, DNA damage, epigenetic changes, metabolic shifts, destructive metabolite generation, mitochondrial dysfunction, misfolded or aggregated protein accumulation, and cellular senescence. These processes appear to be tightly interlinked, as targeting any one appears to affect many of the rest, underlying our Unitary Theory of Fundamental Aging Mechanisms. Interventions targeting many fundamental aging processes are being developed, including dietary manipulations, metformin, mTOR (mechanistic target of rapamycin) inhibitors, and senolytics, which are in early human trials. These interventions could lead to greater healthspan benefits than treating age-related diseases one at a time. To illustrate these points, we focus on cellular senescence and therapies in development to target senescent cells. Combining interventions targeting aging mechanisms with disease-specific drugs could result in more than additive benefits for currently difficult-to-treat or intractable diseases. More research attention needs to be devoted to targeting fundamental aging processes.
    Keywords:   senolytics; SASP (senescence-associated secretory phenotype); geroscience hypothesis; healthspan; multimorbidity; unitary theory of fundamental aging mechanisms
    DOI:  https://doi.org/10.1210/clinem/dgaa728
  14. Sci Adv. 2020 Nov;pii: eabb7272. [Epub ahead of print]6(45):
    Metabolic determinants of cellular fitness dependent on mitochondrial reactive oxygen species.
    Hyewon Kong, Colleen R Reczek, Gregory S McElroy, Elizabeth M Steinert, Tim Wang, David M Sabatini, Navdeep S Chandel.
      Mitochondria-derived reactive oxygen species (mROS) are required for the survival, proliferation, and metastasis of cancer cells. The mechanism by which mitochondrial metabolism regulates mROS levels to support cancer cells is not fully understood. To address this, we conducted a metabolism-focused CRISPR-Cas9 genetic screen and uncovered that loss of genes encoding subunits of mitochondrial complex I was deleterious in the presence of the mitochondria-targeted antioxidant mito-vitamin E (MVE). Genetic or pharmacologic inhibition of mitochondrial complex I in combination with the mitochondria-targeted antioxidants, MVE or MitoTEMPO, induced a robust integrated stress response (ISR) and markedly diminished cell survival and proliferation in vitro. This was not observed following inhibition of mitochondrial complex III. Administration of MitoTEMPO in combination with the mitochondrial complex I inhibitor phenformin decreased the leukemic burden in a mouse model of T cell acute lymphoblastic leukemia. Thus, mitochondrial complex I is a dominant metabolic determinant of mROS-dependent cellular fitness.
    DOI:  https://doi.org/10.1126/sciadv.abb7272
  15. Elife. 2020 Nov 03. pii: e61245. [Epub ahead of print]9
    Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast.
    Tomoyuki Fukuda, Yuki Ebi, Tetsu Saigusa, Kentaro Furukawa, Shun-Ichi Yamashita, Keiichi Inoue, Daiki Kobayashi, Yutaka Yoshida, Tomotake Kanki.
      Degradation of mitochondria through mitophagy contributes to the maintenance of mitochondrial function. In this study, we identified that Atg43, a mitochondrial outer membrane protein, serves as a mitophagy receptor in the model organism Schizosaccharomyces pombe to promote the selective degradation of mitochondria. Atg43 contains an Atg8-family-interacting motif essential for mitophagy. Forced recruitment of Atg8 to mitochondria restores mitophagy in Atg43-deficient cells, suggesting that Atg43 tethers expanding isolation membranes to mitochondria. We found that the mitochondrial import factors, including the Mim1-Mim2 complex and Tom70, are crucial for mitophagy. Artificial mitochondrial loading of Atg43 bypasses the requirement of the import factors, suggesting that they contribute to mitophagy through Atg43. Atg43 not only maintains growth ability during starvation but also facilitates vegetative growth through its mitophagy-independent function. Thus, Atg43 is a useful model to study the mechanism and physiological roles, as well as the origin and evolution, of mitophagy in eukaryotes.
    Keywords:  Atg43; MIM complex; S. pombe; autophagy; cell biology; mitochondria; mitophagy; receptor
    DOI:  https://doi.org/10.7554/eLife.61245
  16. Cancer Cell. 2020 Oct 26. pii: S1535-6108(20)30539-0. [Epub ahead of print]
    Large-Scale Characterization of Drug Responses of Clinically Relevant Proteins in Cancer Cell Lines.
    Wei Zhao, Jun Li, Mei-Ju M Chen, Yikai Luo, Zhenlin Ju, Nicole K Nesser, Katie Johnson-Camacho, Christopher T Boniface, Yancey Lawrence, Nupur T Pande, Michael A Davies, Meenhard Herlyn, Taru Muranen, Ioannis K Zervantonakis, Erika von Euw, Andre Schultz, Shwetha V Kumar, Anil Korkut, Paul T Spellman, Rehan Akbani, Dennis J Slamon, Joe W Gray, Joan S Brugge, Yiling Lu, Gordon B Mills, Han Liang.
      Perturbation biology is a powerful approach to modeling quantitative cellular behaviors and understanding detailed disease mechanisms. However, large-scale protein response resources of cancer cell lines to perturbations are not available, resulting in a critical knowledge gap. Here we generated and compiled perturbed expression profiles of ∼210 clinically relevant proteins in >12,000 cancer cell line samples in response to ∼170 drug compounds using reverse-phase protein arrays. We show that integrating perturbed protein response signals provides mechanistic insights into drug resistance, increases the predictive power for drug sensitivity, and helps identify effective drug combinations. We build a systematic map of "protein-drug" connectivity and develop a user-friendly data portal for community use. Our study provides a rich resource to investigate the behaviors of cancer cells and the dependencies of treatment responses, thereby enabling a broad range of biomedical applications.
    Keywords:  biomarker; cancer signaling pathway; drug response; protein array
    DOI:  https://doi.org/10.1016/j.ccell.2020.10.008
  17. Cell. 2020 Oct 29. pii: S0092-8674(20)31396-9. [Epub ahead of print]
    A Blueprint for Characterizing Senescence.
    Ananda L Roy, Felipe Sierra, Kevin Howcroft, Dinah S Singer, Norman Sharpless, Richard J Hodes, Elizabeth L Wilder, James M Anderson.
      Given the heterogeneity of senescent cells, our knowledge of both the drivers and consequences of cellular senescence in tissues and organs remains limited, as is our understanding of how this process could be harnessed for human health. Here we identified five broad areas that would help propel the field forward.
    DOI:  https://doi.org/10.1016/j.cell.2020.10.032
  18. Br J Cancer. 2020 Nov 04.
    Roles of mitochondria in the hallmarks of metastasis.
    Adam D Scheid, Thomas C Beadnell, Danny R Welch.
      Although mitochondrial contributions to cancer have been recognised for approximately a century, given that mitochondrial DNA (mtDNA) is dwarfed by the size of the nuclear genome (nDNA), nuclear genetics has represented a focal point in cancer biology, often at the expense of mtDNA and mitochondria. However, genomic sequencing and advances in in vivo models underscore the importance of mtDNA and mitochondria in cancer and metastasis. In this review, we explore the roles of mitochondria in the four defined 'hallmarks of metastasis': motility and invasion, microenvironment modulation, plasticity and colonisation. Biochemical processes within the mitochondria of both cancer cells and the stromal cells with which they interact are critical for each metastatic hallmark. We unravel complex dynamics in mitochondrial contributions to cancer, which are context-dependent and capable of either promoting metastasis or being leveraged to prevent it at various points of the metastatic cascade. Ultimately, mitochondrial contributions to cancer and metastasis are rooted in the capacity of these organelles to tune metabolic and genetic responses to dynamic microenvironmental cues.
    DOI:  https://doi.org/10.1038/s41416-020-01125-8
  19. Carcinogenesis. 2020 Nov 04. pii: bgaa114. [Epub ahead of print]
    DNA Damage and Mitochondria in Cancer and Aging.
    Jaimin Patel, Beverly A Baptiste, Edward Kim, Mansoor Hussain, Deborah L Croteau, Vilhelm A Bohr.
      Age and DNA repair deficiencies are strong risk factors for developing cancer. This is reflected in the comorbidity of cancer with premature aging diseases associated with DNA damage repair deficiencies. Recent research has suggested that DNA damage accumulation, telomere dysfunction, and the accompanying mitochondrial dysfunction exacerbate the aging process and may increase the risk of cancer development. Thus, an area of interest in both cancer and aging research is the elucidation of the dynamic crosstalk between the nucleus and the mitochondria. In this review, we discuss current research on aging and cancer with specific focus on the role of mitochondrial dysfunction in cancer and aging as well as how nuclear to mitochondrial DNA damage signaling may be a driving factor in the increased cancer incidence with aging. We suggest that therapeutic interventions aimed at induction of autophagy and mediation of nuclear to mitochondrial signaling may provide a mechanism for healthier aging and reduced tumorigenesis.
    DOI:  https://doi.org/10.1093/carcin/bgaa114
  20. Nat Metab. 2020 Nov 02.
    Perivascular mesenchymal cells control adipose-tissue macrophage accrual in obesity.
    Bo Shan, Mengle Shao, Qianbin Zhang, Chelsea Hepler, Vivian A Paschoal, Spencer D Barnes, Lavanya Vishvanath, Yu A An, Lin Jia, Venkat S Malladi, Douglas W Strand, Olga T Gupta, Joel K Elmquist, Dayoung Oh, Rana K Gupta.
      Chronic low-grade white adipose tissue (WAT) inflammation is a hallmark of metabolic syndrome in obesity. Here, we demonstrate that a subpopulation of mouse WAT perivascular (PDGFRβ+) cells, termed fibro-inflammatory progenitors (FIPs), activate proinflammatory signalling cascades shortly after the onset of high-fat diet feeding and regulate proinflammatory macrophage accumulation in WAT in a TLR4-dependent manner. FIPs activation in obesity is mediated by the downregulation of zinc-finger protein 423 (ZFP423), identified here as a transcriptional corepressor of NF-κB. ZFP423 suppresses the DNA-binding capacity of the p65 subunit of NF-κB by inducing a p300-to-NuRD coregulator switch. Doxycycline-inducible expression of Zfp423 in PDGFRβ+ cells suppresses inflammatory signalling in FIPs and attenuates metabolic inflammation of visceral WAT in obesity. Inducible inactivation of Zfp423 in PDGFRβ+ cells increases FIP activity, exacerbates adipose macrophage accrual and promotes WAT dysfunction. These studies implicate perivascular mesenchymal cells as important regulators of chronic adipose-tissue inflammation in obesity and identify ZFP423 as a transcriptional break on NF-κB signalling.
    DOI:  https://doi.org/10.1038/s42255-020-00301-7
  21. J Natl Cancer Inst. 2020 Nov 02. pii: djaa169. [Epub ahead of print]
    Early-Life Body Adiposity and the Breast Tumor Transcriptome.
    Jun Wang, Cheng Peng, Catherine Askew, Yujing J Heng, Gabrielle M Baker, Christopher A Rubadue, Kimberly Glass, A Heather Eliassen, Rulla M Tamimi, Kornelia Polyak, Susan Hankinson.
       BACKGROUND: Cumulative epidemiologic evidence has shown that early-life adiposity is strongly inversely associated with breast cancer risk throughout life, independent of adult obesity. However, the molecular mechanisms remain poorly understood.
    METHODS: We assessed the association of early-life adiposity, defined as self-reported body size during ages 10-20 years from a validated 9-level pictogram, with the transcriptome of breast tumor (N = 835) and tumor-adjacent histologically-normal tissue (N = 663) in the Nurses' Health Studies. We conducted multivariable linear regression analysis to identify differentially expressed genes in tumor and tumor-adjacent tissue, respectively. Molecular pathway analysis using Hallmark gene sets (N = 50) was further performed to gain biological insights. Analysis was stratified by tumor estrogen receptor (ER) protein expression status (N = 673 for ER+ and 162 for ER- tumors).
    RESULTS: No gene was statistically significantly differentially expressed by early-life body size after multiple comparison adjustment. However, pathway analysis revealed several statistically significantly (FDR < 0.05) up or down regulated gene sets. In stratified analyses by tumor ER status, larger body size during ages 10-20 years was associated with decreased cellular proliferation pathways, including MYC target genes, in both ER+ and ER- tumors. In ER+ tumors, larger body size was also associated with upregulation in genes involved in TNFα/NFkB signaling. In ER- tumors, larger body size was additionally associated with downregulation in genes involved in IFNα and IFNγ immune response and PI3K/ATK/mTOR signaling; the INFγ response pathway was also downregulated in ER- tumor-adjacent tissue though at borderline statistical significance (FDR = 0.1).
    CONCLUSION: These findings provide new insights into the biological and pathological underpinnings of the early-life adiposity and breast cancer association.
    Keywords:  breast cancer; breast tumor; early-life adiposity; epidemiology; gene expression; gene set analysis
    DOI:  https://doi.org/10.1093/jnci/djaa169
  22. Biochem J. 2020 Nov 13. 477(21): 4085-4132
    Blackout in the powerhouse: clinical phenotypes associated with defects in the assembly of OXPHOS complexes and the mitoribosome.
    Daniella H Hock, David R L Robinson, David A Stroud.
      Mitochondria produce the bulk of the energy used by almost all eukaryotic cells through oxidative phosphorylation (OXPHOS) which occurs on the four complexes of the respiratory chain and the F1-F0 ATPase. Mitochondrial diseases are a heterogenous group of conditions affecting OXPHOS, either directly through mutation of genes encoding subunits of OXPHOS complexes, or indirectly through mutations in genes encoding proteins supporting this process. These include proteins that promote assembly of the OXPHOS complexes, the post-translational modification of subunits, insertion of cofactors or indeed subunit synthesis. The latter is important for all 13 of the proteins encoded by human mitochondrial DNA, which are synthesised on mitochondrial ribosomes. Together the five OXPHOS complexes and the mitochondrial ribosome are comprised of more than 160 subunits and many more proteins support their biogenesis. Mutations in both nuclear and mitochondrial genes encoding these proteins have been reported to cause mitochondrial disease, many leading to defective complex assembly with the severity of the assembly defect reflecting the severity of the disease. This review aims to act as an interface between the clinical and basic research underpinning our knowledge of OXPHOS complex and ribosome assembly, and the dysfunction of this process in mitochondrial disease.
    Keywords:  mitochondria; mitochondrial dysfunction; mitochondrial respiration; mutation; oxidative phosphorylation; ribosomes
    DOI:  https://doi.org/10.1042/BCJ20190767
  23. Science. 2020 Nov 05. pii: eabc5667. [Epub ahead of print]
    Structural basis of antagonizing the vitamin K catalytic cycle for anticoagulation.
    Shixuan Liu, Shuang Li, Guomin Shen, Narayanasami Sukumar, Andrzej M Krezel, Weikai Li.
      Vitamin K antagonists are widely used anticoagulants targeting vitamin K epoxide reductases (VKOR), a family of integral membrane enzymes. To elucidate their catalytic cycle and inhibitory mechanism, here we report eleven x-ray crystal structures of human VKOR and pufferfish VKOR-like with substrates and antagonists in different redox states. Substrates entering the active site in a partially oxidized state form a cysteine adduct that induces an open-to-closed conformational change, triggering reduction. Binding and catalysis is facilitated by hydrogen-bonding interactions in a hydrophobic pocket. The antagonists bind specifically to the same hydrogen-bonding residues and induce a similar closed conformation. Thus, vitamin K antagonists act through mimicking the key interactions and conformational changes required for the VKOR catalytic cycle.
    DOI:  https://doi.org/10.1126/science.abc5667
  24. Cancer Discov. 2020 Nov 06. pii: CD-20-0519. [Epub ahead of print]
    Epigenetic and transcriptional control of the epidermal growth factor receptor (EGFR) regulates the tumor immune microenvironment in pancreatic cancer.
    Jinyang Li, Salina Yuan, Robert J Norgard, Fangxue Yan, Yu H Sun, Il-Kyu Kim, Allyson J Merrell, Yogev Sela, Yanqing Jiang, Natarajan V Bhanu, Benjamin A Garcia, Robert H Vonderheide, Andrés Blanco, Ben Z Stanger.
      Although immunotherapy has revolutionized cancer care, patients with pancreatic ductal adenocarcinoma (PDA) rarely respond to these treatments, a failure that is attributed to poor infiltration and activation of T cells in the tumor microenvironment (TME). We performed an in vivo CRISPR screen and identified lysine demethylase 3A (KDM3A) as a potent epigenetic regulator of immunotherapy response in PDA. Mechanistically, KDM3A acts through Krueppel-like factor 5 (KLF5) and SMAD family member 4 (SMAD4) to regulate the expression of the epidermal growth factor receptor (EGFR). Ablation of KDM3A, KLF5, SMAD4, or EGFR in tumor cells altered the immune TME and sensitized tumors to combination immunotherapy, while treatment of established tumors with an EGFR inhibitor erlotinib prompted a dose-dependent increase in intratumoral T cells. This study defines an epigenetic-transcriptional mechanism by which tumor cells modulate their immune microenvironment and highlights the potential of EGFR inhibitors as immunotherapy sensitizers in PDA.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0519
  25. Br J Cancer. 2020 Nov 04.
    Genomic control of metastasis.
    Saroor A Patel, Paulo Rodrigues, Ludovic Wesolowski, Sakari Vanharanta.
      Metastasis remains the leading cause of cancer-associated mortality, and a detailed understanding of the metastatic process could suggest new therapeutic avenues. However, how metastatic phenotypes arise at the genomic level has remained a major open question in cancer biology. Comparative genetic studies of primary and metastatic cancers have revealed a complex picture of metastatic evolution with diverse temporal patterns and trajectories to dissemination. Whole-genome amplification is associated with metastatic cancer clones, but no metastasis-exclusive driver mutations have emerged. Instead, genetically activated oncogenic pathways that drive tumour initiation and early progression acquire metastatic traits by co-opting physiological programmes from stem cell, developmental and regenerative pathways. The functional consequences of oncogenic driver mutations therefore change via epigenetic mechanisms to promote metastasis. Increasing evidence is starting to uncover the molecular mechanisms that determine how specific oncogenic drivers interact with various physiological programmes, and what triggers their activation in support of metastasis. Detailed insight into the mechanisms that control metastasis is likely to reveal novel opportunities for intervention at different stages of metastatic progression.
    DOI:  https://doi.org/10.1038/s41416-020-01127-6
  26. Ageing Res Rev. 2020 Oct 29. pii: S1568-1637(20)30338-X. [Epub ahead of print] 101203
    The dialogue between the ubiquitin-proteasome system and autophagy: implications in ageing.
    Jia Liang Sun-Wang, Saška Ivanova, Antonio Zorzano.
      Dysregulated proteostasis is one of the hallmarks of ageing. Damaged proteins may impair cellular function and their accumulation may lead to tissue dysfunction and disease. This is why protective mechanisms to safeguard the cell proteome have evolved. These mechanisms consist of cellular machineries involved in protein quality control, including regulators of protein translation, folding, trafficking and degradation. In eukaryotic cells, protein degradation occurs via two main pathways: the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway. Although distinct pathways, they are not isolated systems and have a complementary nature, as evidenced by recent studies. These findings raise the question of how autophagy and the proteasome crosstalk. In this review we address how the two degradation pathways impact each other, thereby adding a new layer of regulation to protein degradation. We also analyze the implications of the UPS and autophagy in ageing.
    Keywords:  Ageing; UPS-autophagy crosstalk; autophagy; proteostasis; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1016/j.arr.2020.101203
  27. Cancer Discov. 2020 Nov 02.
    Tumor Mutational Burden as a Predictive Biomarker in Solid Tumors.
    Dan Sha, Zhaohui Jin, Jan Budczies, Klaus Kluck, Albrecht Stenzinger, Frank A Sinicrope.
      Tumor mutational burden (TMB), defined as the number of somatic mutations per megabase of interrogated genomic sequence, varies across malignancies. Panel sequencing-based estimates of TMB have largely replaced whole-exome sequencing-derived TMB in the clinic. Retrospective evidence suggests that TMB can predict the efficacy of immune checkpoint inhibitors, and data from KEYNOTE-158 led to the recent FDA approval of pembrolizumab for the TMB-high tumor subgroup. Unmet needs include prospective validation of TMB cutoffs in relationship to tumor type and patient outcomes. Furthermore, standardization and harmonization of TMB measurement across test platforms are important to the successful implementation of TMB in clinical practice. SIGNIFICANCE: Evaluation of TMB as a predictive biomarker creates the need to harmonize panel-based TMB estimation and standardize its reporting. TMB can improve the predictive accuracy for immunotherapy outcomes, and has the potential to expand the candidate pool of patients for treatment with immune checkpoint inhibitors.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0522
  28. Nature. 2020 Nov 04.
    Combinatorial expression of GPCR isoforms affects signalling and drug responses.
    Maria Marti-Solano, Stephanie E Crilly, Duccio Malinverni, Christian Munk, Matthew Harris, Abigail Pearce, Tezz Quon, Amanda E Mackenzie, Xusheng Wang, Junmin Peng, Andrew B Tobin, Graham Ladds, Graeme Milligan, David E Gloriam, Manojkumar A Puthenveedu, M Madan Babu.
      G-protein-coupled receptors (GPCRs) are membrane proteins that modulate physiology across human tissues in response to extracellular signals. GPCR-mediated signalling can differ because of changes in the sequence1,2 or expression3 of the receptors, leading to signalling bias when comparing diverse physiological systems4. An underexplored source of such bias is the generation of functionally diverse GPCR isoforms with different patterns of expression across different tissues. Here we integrate data from human tissue-level transcriptomes, GPCR sequences and structures, proteomics, single-cell transcriptomics, population-wide genetic association studies and pharmacological experiments. We show how a single GPCR gene can diversify into several isoforms with distinct signalling properties, and how unique isoform combinations expressed in different tissues can generate distinct signalling states. Depending on their structural changes and expression patterns, some of the detected isoforms may influence cellular responses to drugs and represent new targets for developing drugs with improved tissue selectivity. Our findings highlight the need to move from a canonical to a context-specific view of GPCR signalling that considers how combinatorial expression of isoforms in a particular cell type, tissue or organism collectively influences receptor signalling and drug responses.
    DOI:  https://doi.org/10.1038/s41586-020-2888-2
  29. J Cell Sci. 2020 Nov 05. pii: jcs250027. [Epub ahead of print]133(21):
    Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design.
    Eric C Wait, Michael A Reiche, Teng-Leong Chew.
      One of the challenges in modern fluorescence microscopy is to reconcile the conventional utilization of microscopes as exploratory instruments with their emerging and rapidly expanding role as a quantitative tools. The contribution of microscopy to observational biology will remain enormous owing to the improvements in acquisition speed, imaging depth, resolution and biocompatibility of modern imaging instruments. However, the use of fluorescence microscopy to facilitate the quantitative measurements necessary to challenge hypotheses is a relatively recent concept, made possible by advanced optics, functional imaging probes and rapidly increasing computational power. We argue here that to fully leverage the rapidly evolving application of microscopes in hypothesis-driven biology, we not only need to ensure that images are acquired quantitatively but must also re-evaluate how microscopy-based experiments are designed. In this Opinion, we present a reverse logic that guides the design of quantitative fluorescence microscopy experiments. This unique approach starts from identifying the results that would quantitatively inform the hypothesis and map the process backward to microscope selection. This ensures that the quantitative aspects of testing the hypothesis remain the central focus of the entire experimental design.
    Keywords:  Experimental design; Hypothesis; Image analysis; Microscope choice; Microscopy; Quantitative analysis
    DOI:  https://doi.org/10.1242/jcs.250027
  30. Curr Opin Biotechnol. 2020 Oct 30. pii: S0958-1669(20)30144-0. [Epub ahead of print]68 72-88
    TCA cycle signalling and the evolution of eukaryotes.
    Dylan G Ryan, Christian Frezza, Luke Aj O'Neill.
      A major question remaining in the field of evolutionary biology is how prokaryotic organisms made the leap to complex eukaryotic life. The prevailing theory depicts the origin of eukaryotic cell complexity as emerging from the symbiosis between an α-proteobacterium, the ancestor of present-day mitochondria, and an archaeal host (endosymbiont theory). A primary contribution of mitochondria to eukaryogenesis has been attributed to the mitochondrial genome, which enabled the successful internalisation of bioenergetic membranes and facilitated remarkable genome expansion. It has also been postulated that a key contribution of the archaeal host during eukaryogenesis was in providing 'archaeal histones' that would enable compaction and regulation of an expanded genome. Yet, how the communication between the host and the symbiont evolved is unclear. Here, we propose an evolutionary concept in which mitochondrial TCA cycle signalling was also a crucial player during eukaryogenesis enabling the dynamic control of an expanded genome via regulation of DNA and histone modifications. Furthermore, we discuss how TCA cycle remodelling is a common evolutionary strategy invoked by eukaryotic organisms to coordinate stress responses and gene expression programmes, with a particular focus on the TCA cycle-derived metabolite itaconate.
    DOI:  https://doi.org/10.1016/j.copbio.2020.09.014
  31. Nat Metab. 2020 Nov 02.
    Age-related loss of gene-to-gene transcriptional coordination among single cells.
    Orr Levy, Guy Amit, Dana Vaknin, Tom Snir, Sol Efroni, Peter Castaldi, Yang-Yu Liu, Haim Y Cohen, Amir Bashan.
      A long-standing model holds that stochastic aberrations of transcriptional regulation play a key role in the process of ageing. While transcriptional dysregulation is observed in many cell types in the form of increased cell-to-cell variability, its generality to all cell types remains doubted. Here, we propose a new approach for analysing transcriptional regulation in single-cell RNA sequencing data by focusing on the global coordination between the genes rather than the variability of individual genes or correlations between pairs of genes. Consistently, across very different organisms and cell types, we find a decrease in the gene-to-gene transcriptional coordination in ageing cells. In addition, we find that loss of gene-to-gene transcriptional coordination is associated with high mutational load of a specific, age-related signature and with radiation-induced DNA damage. These observations suggest a general, potentially universal, stochastic attribute of transcriptional dysregulation in ageing.
    DOI:  https://doi.org/10.1038/s42255-020-00304-4
  32. Cancer Prev Res (Phila). 2020 Nov 03. pii: canprevres.0426.2020. [Epub ahead of print]
    Screening for Pancreatic Ductal Adenocarcinoma: Are We Asking the Impossible?
    Katharine E Caldwell, Alexander P Conway, Chet W Hammill.
      Pancreatic cancer is projected to become the second leading cause of cancer-related death in the US by 2020. Because of this, significant interest and research funding has been devoted to development of a screening test to identify individuals during a prolonged asymptomatic period, however, to date, no such test has been developed. We evaluated current National Institute of Health spending and clinical trials to determine the focus of research on pancreatic cancer screening as compared to other cancer subtypes. Using statistical methodology, we determined the effects of population-based pancreatic cancer screening on overall population morbidity and mortality. Population-based pancreatic cancer screening would result in significant harm to non-diseased individuals, even in cases where a near perfect test was developed. Despite this mathematical improbability, NIH funding for pancreatic cancer demonstrates bias toward screening test development not seen in other cancer subtypes Focusing research energy on development of pancreatic screening tests is unlikely to result in overall survival benefits. Efforts to increase the number of patients who are candidates for surgery and improving surgical outcomes would result in greater population benefit.
    DOI:  https://doi.org/10.1158/1940-6207.CAPR-20-0426
  33. Aging Cell. 2020 Nov 04. e13269
    Rapamycin-mediated mouse lifespan extension: Late-life dosage regimes with sex-specific effects.
    Randy Strong, Richard A Miller, Molly Bogue, Elizabeth Fernandez, Martin A Javors, Sergiy Libert, Paul Anthony Marinez, Michael P Murphy, Nicolas Musi, James F Nelson, Michael Petrascheck, Peter Reifsnyder, Arlan Richardson, Adam B Salmon, Francesca Macchiarini, David E Harrison.
      To see if variations in timing of rapamycin (Rapa), administered to middle aged mice starting at 20 months, would lead to different survival outcomes, we compared three dosing regimens. Initiation of Rapa at 42 ppm increased survival significantly in both male and female mice. Exposure to Rapa for a 3-month period led to significant longevity benefit in males only. Protocols in which each month of Rapa treatment was followed by a month without Rapa exposure were also effective in both sexes, though this approach was less effective than continuous exposure in female mice. Interpretation of these results is made more complicated by unanticipated variation in patterns of weight gain, prior to the initiation of the Rapa treatment, presumably due to the use of drug-free food from two different suppliers. The experimental design included tests of four other drugs, minocycline, β-guanidinopropionic acid, MitoQ, and 17-dimethylaminoethylamino-17-demethoxygeldanamycin (17-DMAG), but none of these led to a change in survival in either sex.
    Keywords:  17-DMAG; MitoQ; minocycline; rapamycin; survival; β-GPA
    DOI:  https://doi.org/10.1111/acel.13269
  34. Nat Rev Drug Discov. 2020 Nov 03.
    CRISPR pioneers win Nobel prize.
    Asher Mullard.
      
    DOI:  https://doi.org/10.1038/d41573-020-00198-7
  35. Ann Oncol. 2020 Oct 29. pii: S0923-7534(20)42986-2. [Epub ahead of print]
    The paradox-breaking panRAF plus SRC family kinase inhibitor, CCT3833, is effective in mutant KRAS-driven cancers.
    G Saturno, F Lopes, I Niculescu-Duvaz, D Niculescu-Duvaz, A Zambon, L Davies, L Johnson, N Preece, R Lee, A Viros, D Holovanchuk, M Pedersen, R McLeary, P Lorigan, N Dhomen, C Fisher, U Banerji, E Dean, M G Krebs, M Gore, J Larkin, R Marais, C Springer.
       BACKGROUND: KRAS is mutated in ∼90% of pancreatic ductal adenocarcinomas (PDAC), ∼35% of colorectal cancers (CRC) and ∼20% of non-small-cell lung cancers (NSCLC). There has been recent progress in targeting G12CKRAS specifically, but therapeutic options for other mutant forms of KRAS are limited, largely because the complexity of downstream signaling and feedback mechanisms mean that targeting individual pathway components is ineffective.
    DESIGN: The protein kinases RAF and SRC are validated therapeutic targets in KRAS-mutant PDAC, CRC and NSCLC and we show that both must be inhibited to block growth of these cancers. We describe CCT3833, a new drug that inhibits both RAF and SRC which may be effective in KRAS-mutant cancers.
    RESULTS: We show that CCT3833 inhibits RAF and SRC in KRAS-mutant tumors in vitro and in vivo, and that it inhibits tumor growth at well-tolerated doses in mice. CCT3833 has been evaluated in a Phase I clinical trial (NCT02437227) and we report here that it significantly prolongs progression-free survival of a patient with a G12VKRAS spindle cell sarcoma who did not respond to a multi kinase inhibitor and therefore had limited treatment options.
    CONCLUSIONS: New drug CCT3833 elicits significant pre-clinical therapeutic efficacy in KRAS-mutant colorectal, lung and pancreatic tumor xenografts, demonstrating a treatment option for several areas of unmet clinical need. Based on these pre-clinical data, and the Phase I clinical unconfirmed response in a patient with KRAS-mutant spindle cell CCT3833 requires further evaluation in patients with other KRAS-mutant cancers.
    Keywords:  CRC; KRAS; NSCLC; PDAC; panRAF/SRC inhibitor
    DOI:  https://doi.org/10.1016/j.annonc.2020.10.483
  36. Nat Metab. 2020 Nov 02.
    Loss of metabolic plasticity underlies metformin toxicity in aged Caenorhabditis elegans.
    Lilia Espada, Alexander Dakhovnik, Prerana Chaudhari, Asya Martirosyan, Laura Miek, Tetiana Poliezhaieva, Yvonne Schaub, Ashish Nair, Nadia Döring, Norman Rahnis, Oliver Werz, Andreas Koeberle, Joanna Kirkpatrick, Alessandro Ori, Maria A Ermolaeva.
      Current clinical trials are testing the life-extending benefits of the diabetes drug metformin in healthy individuals without diabetes. However, the metabolic response of a non-diabetic cohort to metformin treatment has not been studied. Here, we show in C. elegans and human primary cells that metformin shortens lifespan when provided in late life, contrary to its positive effects in young organisms. We find that metformin exacerbates ageing-associated mitochondrial dysfunction, causing respiratory failure. Age-related failure to induce glycolysis and activate the dietary-restriction-like mobilization of lipid reserves in response to metformin result in lethal ATP exhaustion in metformin-treated aged worms and late-passage human cells, which can be rescued by ectopic stabilization of cellular ATP content. Metformin toxicity is alleviated in worms harbouring disruptions in insulin-receptor signalling, which show enhanced resilience to mitochondrial distortions at old age. Together, our data show that metformin induces deleterious changes of conserved metabolic pathways in late life, which could bring into question its benefits for older individuals without diabetes.
    DOI:  https://doi.org/10.1038/s42255-020-00307-1
  37. EMBO J. 2020 Oct 31. e105364
    Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency.
    Denisa Hathazi, Helen Griffin, Matthew J Jennings, Michele Giunta, Christopher Powell, Sarah F Pearce, Benjamin Munro, Wei Wei, Veronika Boczonadi, Joanna Poulton, Angela Pyle, Claudia Calabrese, Aurora Gomez-Duran, Ulrike Schara, Robert Ds Pitceathly, Michael G Hanna, Kairit Joost, Ana Cotta, Julia Filardi Paim, Monica Machado Navarro, Jennifer Duff, Andre Mattmann, Kristine Chapman, Serenella Servidei, Adela Della Marina, Johanna Uusimaa, Andreas Roos, Vamsi Mootha, Michio Hirano, Mar Tulinius, Manta Giri, Eric P Hoffmann, Hanns Lochmüller, Salvatore DiMauro, Michal Minczuk, Patrick F Chinnery, Juliane S Müller, Rita Horvath.
      Reversible infantile respiratory chain deficiency (RIRCD) is a rare mitochondrial myopathy leading to severe metabolic disturbances in infants, which recover spontaneously after 6-months of age. RIRCD is associated with the homoplasmic m.14674T>C mitochondrial DNA mutation; however, only ~ 1/100 carriers develop the disease. We studied 27 affected and 15 unaffected individuals from 19 families and found additional heterozygous mutations in nuclear genes interacting with mt-tRNAGlu including EARS2 and TRMU in the majority of affected individuals, but not in healthy carriers of m.14674T>C, supporting a digenic inheritance. Our transcriptomic and proteomic analysis of patient muscle suggests a stepwise mechanism where first, the integrated stress response associated with increased FGF21 and GDF15 expression enhances the metabolism modulated by serine biosynthesis, one carbon metabolism, TCA lipid oxidation and amino acid availability, while in the second step mTOR activation leads to increased mitochondrial biogenesis. Our data suggest that the spontaneous recovery in infants with digenic mutations may be modulated by the above described changes. Similar mechanisms may explain the variable penetrance and tissue specificity of other mtDNA mutations and highlight the potential role of amino acids in improving mitochondrial disease.
    Keywords:  digenic inheritance; homoplasmic tRNA mutation; mitochondrial myopathy; reversible infantile respiratory chain deficiency
    DOI:  https://doi.org/10.15252/embj.2020105364
  38. FASEB J. 2020 Nov 01.
    NMDAR in cultured astrocytes: Flux-independent pH sensor and flux-dependent regulator of mitochondria and plasma membrane-mitochondria bridging.
    Pavel Montes de Oca Balderas, Mauricio Matus Núñez, Arturo Picones, Arturo Hernández-Cruz.
      Glutamate N-methyl-D-aspartate (NMDA) receptor (NMDAR) is critical for neurotransmission as a Ca2+ channel. Nonetheless, flux-independent signaling has also been demonstrated. Astrocytes express NMDAR distinct from its neuronal counterpart, but cultured astrocytes have no electrophysiological response to NMDA. We recently demonstrated that in cultured astrocytes, NMDA at pH6 (NMDA/pH6) acting through the NMDAR elicits flux-independent Ca2+ release from the Endoplasmic Reticulum (ER) and depletes mitochondrial membrane potential (mΔΨ). Here we show that Ca2+ release is due to pH6 sensing by NMDAR, whereas mΔΨ depletion requires both: pH6 and flux-dependent NMDAR signaling. Plasma membrane (PM) NMDAR guard a non-random distribution relative to the ER and mitochondria. Also, NMDA/pH6 induces ER stress, endocytosis, PM electrical capacitance reduction, mitochondria-ER, and -nuclear contacts. Strikingly, it also produces the formation of PM invaginations near mitochondria along with structures referred to here as PM-mitochondrial bridges (PM-m-br). These and earlier data strongly suggest PM-mitochondria communication. As proof of the concept of mass transfer, we found that NMDA/pH6 provoked mitochondria labeling by the PM dye FM-4-64FX. NMDA/pH6 caused PM depolarization, cell acidification, and Ca2+ release from most mitochondria. Finally, the MCU and microtubules were not involved in mΔΨ depletion, while actin cytoskeleton was partially involved. These findings demonstrate that NMDAR has concomitant flux-independent and flux-dependent actions in cultured astrocytes.
    Keywords:  NMDAR; astrocyte; calcium; flux-independent; mitochondria; organelle communication
    DOI:  https://doi.org/10.1096/fj.202001300R
  39. Cell. 2020 Nov 03. pii: S0092-8674(20)31380-5. [Epub ahead of print]
    Cellular Control of Viscosity Counters Changes in Temperature and Energy Availability.
    Laura B Persson, Vardhaan S Ambati, Onn Brandman.
      Cellular functioning requires the orchestration of thousands of molecular interactions in time and space. Yet most molecules in a cell move by diffusion, which is sensitive to external factors like temperature. How cells sustain complex, diffusion-based systems across wide temperature ranges is unknown. Here, we uncover a mechanism by which budding yeast modulate viscosity in response to temperature and energy availability. This "viscoadaptation" uses regulated synthesis of glycogen and trehalose to vary the viscosity of the cytosol. Viscoadaptation functions as a stress response and a homeostatic mechanism, allowing cells to maintain invariant diffusion across a 20°C temperature range. Perturbations to viscoadaptation affect solubility and phase separation, suggesting that viscoadaptation may have implications for multiple biophysical processes in the cell. Conditions that lower ATP trigger viscoadaptation, linking energy availability to rate regulation of diffusion-controlled processes. Viscoadaptation reveals viscosity to be a tunable property for regulating diffusion-controlled processes in a changing environment.
    Keywords:  ATP; diffusion; glycogen; heat shock; homeostasis; phase separation; starvation; stress response; trehalose; viscosity
    DOI:  https://doi.org/10.1016/j.cell.2020.10.017
  40. iScience. 2020 Nov 20. 23(11): 101664
    A Nuclear Stress Pathway that Parallels Cytoplasmic Stress Granule Formation.
    Tyler Quoc-Thai Do, Antoine Gaudreau-Lapierre, Carmen G Palii, Virginia Maria Ferreira Resende, Denise Campuzano, Claire Simada Aeschimann, Majorie Brand, Laura Trinkle-Mulcahy.
      Stress adaptation is exploited by cancer cells to survive and proliferate under adverse conditions. Survival pathways induced by stress are thus highly promising therapeutic targets. One key pathway involves formation of cytoplasmic stress granules, which regulate the location, stability, and translation of specific mRNAs. Here, we describe a transcriptional stress response that is triggered by similar stressors and characterized by accumulation of RepoMan (cell division cycle associated 2) at nuclear stress foci (nucSF). Formation of these structures is reversible, and they are distinct from known nuclear organelles and stress bodies. Immunofluorescence analysis revealed accumulation of heterochromatic markers, and increased association of RepoMan with the adenylate cyclase 2 (ADCY2) gene locus in stressed cells accompanied reduced levels of ADCY2 mRNA and protein. Quantitative comparison of the RepoMan interactome in stressed vs. unstressed cells identified condensin II as a nucSF factor, suggesting their functional association in the establishment and/or maintenance of these facultative heterochromatic domains.
    Keywords:  Cell Biology; Molecular Biology; Optical Imaging; Proteomics
    DOI:  https://doi.org/10.1016/j.isci.2020.101664
  41. Cancer Metastasis Rev. 2020 Nov 06.
    Metastasis is a highly stressful process.
    Alejandro D Campos, Sara M Weis, David A Cheresh.
      
    DOI:  https://doi.org/10.1007/s10555-020-09938-y
  42. Cancer Res. 2020 Nov 06. pii: canres.3922.2019. [Epub ahead of print]
    Loss of ARID1A promotes epithelial-mesenchymal transition and sensitizes pancreatic tumors to proteotoxic stress.
    Hideo Tomihara, Federica Carbone, Luigi Perelli, Justin K Huang, Melinda Soeung, Johnathon L Rose, Frederick S Robinson, Yonathan Lissanu Deribe, Ningping Feng, Mitsunobu Takeda, Akira Inoue, Angela K Deem, Anirban Maitra, Pavlos Msaouel, Nizar M Tannir, Giulio F Draetta, Christopher A Bristow, Alessandro Carugo, Giannicola Genovese.
      Cellular de-differentiation is a key mechanism driving cancer progression. Acquisition of mesenchymal features has been associated with drug resistance, poor prognosis, and disease relapse in many tumor types. Therefore, successful targeting of tumors harboring these characteristics is a priority in oncology practice. The SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex has also emerged as a critical player in tumor progression, leading to the identification of several SWI/SNF complex genes as potential disease biomarkers and targets of anti-cancer therapies. AT-rich interaction domain-containing protein 1A (ARID1A) is a component of SWI/SNF, and mutations in ARID1A represent one of the most frequent molecular alterations in human cancers. ARID1A mutations occur in ~10% of pancreatic ductal adenocarcinomas (PDAC), but whether these mutations confer a therapeutic opportunity remains unclear. Here we demonstrate that loss of ARID1A promotes an epithelial-mesenchymal transition (EMT) phenotype and sensitizes PDAC cells to a clinical inhibitor of HSP90, NVP-AUY922, both in vitro and in vivo. While loss of ARID1A alone did not significantly affect proliferative potential or rate of apoptosis, ARID1A-deficient cells were sensitized to HSP90 inhibition, potentially by promoting the degradation of intermediate filaments driving EMT, resulting in cell death. Our results describe a mechanistic link between ARID1A defects and a quasi-mesenchymal phenotype, suggesting that deleterious mutations in ARID1A associated with protein loss exhibits potential as a biomarker for PDAC patients who may benefit by HSP90-targeting drugs treatment.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-19-3922
  43. Proc Natl Acad Sci U S A. 2020 Nov 03. pii: 202014165. [Epub ahead of print]
    Pheno-RNA, a method to associate genes with a specific phenotype, identifies genes linked to cellular transformation.
    Rabih Darwiche, Kevin Struhl.
      Cellular transformation is associated with dramatic changes in gene expression, but it is difficult to determine which regulated genes are oncogenically relevant. Here we describe Pheno-RNA, a general approach to identifying candidate genes associated with a specific phenotype. Specifically, we generate a "phenotypic series" by treating a nontransformed breast cell line with a wide variety of molecules that induce cellular transformation to various extents. By performing transcriptional profiling across this phenotypic series, the expression profile of every gene can be correlated with the strength of the transformed phenotype. We identify ∼200 genes whose expression profiles are very highly correlated with the transformation phenotype, strongly suggesting their importance in transformation. Within biological categories linked to cancer, some genes show high correlations with the transformed phenotype, but others do not. Many genes whose expression profiles are highly correlated with transformation have never been associated with cancer, suggesting the involvement of heretofore unknown genes in cancer.
    Keywords:  cancer; cellular transformation; mRNA profiling; phenotypic analysis
    DOI:  https://doi.org/10.1073/pnas.2014165117
  44. Genome Biol. 2020 Nov 04. 21(1): 271
    Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity.
    Won-Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V Negrao, Shawna M Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H Peng, Wei Lu, Ximing Tang, Chi-Wan Chow, Junya Fujimoto, Carmen Behrens, Neda Kalhor, Kazutaka Fukumura, Marcus Coyle, Rebecca Thornton, Curtis Gumbs, Jun Li, Chang-Jiun Wu, Latasha Little, Emily Roarty, Xingzhi Song, J Jack Lee, Erik P Sulman, Ganesh Rao, Stephen Swisher, Lixia Diao, Jing Wang, John V Heymach, Jason T Huse, Paul Scheet, Ignacio I Wistuba, Don L Gibbons, P Andrew Futreal, Jianhua Zhang, Daniel Gomez, Jianjun Zhang.
       BACKGROUND: Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary.
    RESULTS: We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases. Furthermore, we analyze published WES data from 35 primary NSCLC and metastasis pairs, and transcriptomic data from 4 autopsy cases with metastatic NSCLC and one metastatic lung cancer mouse model. The majority of somatic mutations are shared between primary tumors and paired distant metastases although mutational signatures suggest different mutagenesis processes in play before and after metastatic spread. Subclonal analysis reveals evidence of monoclonal seeding in 41 of 42 patients. Pathway analysis of transcriptomic data reveals that downregulated pathways in metastases are mainly immune-related. Further deconvolution analysis reveals significantly lower infiltration of various immune cell types in metastases with the exception of CD4+ T cells and M2 macrophages. These results are in line with lower densities of immune cells and higher CD4/CD8 ratios in metastases shown by IHC. Analysis of transcriptomic data from autopsy cases and animal models confirms that immunosuppression is also present in extracranial metastases. Significantly higher somatic copy number aberration and allelic imbalance burdens are identified in metastases.
    CONCLUSIONS: Metastasis is a molecularly late event, and immunosuppression driven by different molecular events, including somatic copy number aberration, may be a common characteristic of tumors with metastatic plasticity.
    Keywords:  DNA methylation; Gene expression; Genomics; Immune profiling; Lung cancer; Metastasis; Multiomics
    DOI:  https://doi.org/10.1186/s13059-020-02175-0
  45. Clin Cancer Res. 2020 Nov 04. pii: clincanres.2657.2020. [Epub ahead of print]
    Phase I Basket Study of Taselisib, an Isoform-Selective PI3K Inhibitor, in Patients with PIK3CA-Mutant Cancers.
    Komal Jhaveri, Matthew T Chang, Dejan Juric, Cristina Saura, Valentina Gambardella, Anton Melnyk, Manish R Patel, Vincent Ribrag, Cynthia X Ma, Raid Aljumaily, Philippe L Bedard, Jasgit C Sachdev, Lara Dunn, Helen H Won, John Bond, Surai Jones, Heidi M Savage, Maurizio Scaltriti, Timothy R Wilson, Michael C Wei, David M Hyman.
       PURPOSE: Somatic mutations in phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA), which encodes the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K), are found in multiple human cancers. While recurrent mutations in PIK3CA helical, regulatory, and kinase domains lead to constitutive PI3K pathway activation, other mutations remain uncharacterized. To further evaluate their clinical actionability, we designed a basket study for patients with PIK3CA-mutant cancers with the isoform-specific PI3K inhibitor, taselisib.
    PATIENTS AND METHODS: Patients were enrolled based on local PIK3CA mutation testing into 1 of 11 histology-specific cohorts and treated with taselisib at 6 mg or 4 mg daily until progression. Tumor DNA from baseline and progression (when available) was sequenced using a next-generation sequencing panel. Exploratory analyses correlating genomic alterations with treatment outcomes were performed.
    RESULTS: 166 patients with PIK3CA-mutant cancers were enrolled. The confirmed response rate was 9.0%. Activity varied by tumor type and mutant allele, with confirmed responses observed in head and neck squamous (15.4%), cervical (10.0%), and other cancers, plus tumors containing helical domain mutations. Genomic analyses identified mutations potentially associated with resistance to PI3K inhibition upfront (TP53 and PTEN) and post-progression through reactivation of the PI3K pathway (PTEN, STK11, and PIK3R1). Higher rates of dose modification occurred at higher doses of taselisib, indicating a narrow therapeutic index.
    CONCLUSIONS: Taselisib had limited activity in the tumor types tested and is no longer in development. This genome-driven study improves understanding of the activity, limitations, and resistance mechanisms of using PI3K inhibitors as monotherapy to target PIK3CA-mutant tumors.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-20-2657
  46. Sci Rep. 2020 Nov 05. 10(1): 19187
    Loss of sympathetic innervation to islets of Langerhans in canine diabetes and pancreatitis is not associated with insulitis.
    Chen Gilor, Jully Pires, Rachel Greathouse, Rebecca Horn, Mark O Huising, Stanley L Marks, Brian Murphy, Amir Kol.
      Canine diabetes mellitus (DM) affects 0.6% of the canine population and yet, its etiology is poorly understood. Most affected dogs are diagnosed as adults and are insulin-dependent. We compared pan-leukocyte and sympathetic innervation markers in pancreatic islets of adult dogs with spontaneous DM (sDM), spontaneous pancreatitis (sPanc), both (sDMPanc), toxin-induced DM (iDM) and controls. We found evidence of decreased islet sympathetic innervation but no significant infiltration of islets with leukocytes in all disease groups. We show that loss of sympathetic innervation is ongoing in canine DM and does not necessarily precede it. We further found selective loss of islet-associated beta cells in dogs with sDM and sDMPanc, suggesting that collateral damage from inflammation in the exocrine pancreas is not a likely cause of DM in these dogs. The cause of this selective loss of beta cells needs to be further elucidated but overall, our findings are not supportive of an autoimmune process as a cause of sDM in adult dogs. The loss of sympathetic innervation in sPanc in dogs that do not suffer from DM links the disease in the exocrine pancreas to a pathological process in the endocrine pancreas, suggesting pancreatitis might be a potential precursor to DM.
    DOI:  https://doi.org/10.1038/s41598-020-76091-5
  47. Nat Commun. 2020 Nov 06. 11(1): 5653
    Injury triggers fascia fibroblast collective cell migration to drive scar formation through N-cadherin.
    Dongsheng Jiang, Simon Christ, Donovan Correa-Gallegos, Pushkar Ramesh, Shruthi Kalgudde Gopal, Juliane Wannemacher, Christoph H Mayr, Valerio Lupperger, Qing Yu, Haifeng Ye, Martin Mück-Häusl, Vijayanand Rajendran, Li Wan, Juan Liu, Ursula Mirastschijski, Thomas Volz, Carsten Marr, Herbert B Schiller, Yuval Rinkevich.
      Scars are more severe when the subcutaneous fascia beneath the dermis is injured upon surgical or traumatic wounding. Here, we present a detailed analysis of fascia cell mobilisation by using deep tissue intravital live imaging of acute surgical wounds, fibroblast lineage-specific transgenic mice, and skin-fascia explants (scar-like tissue in a dish - SCAD). We observe that injury triggers a swarming-like collective cell migration of fascia fibroblasts that progressively contracts the skin and form scars. Swarming is exclusive to fascia fibroblasts, and requires the upregulation of N-cadherin. Both swarming and N-cadherin expression are absent from fibroblasts in the upper skin layers and the oral mucosa, tissues that repair wounds with minimal scar. Impeding N-cadherin binding inhibits swarming and skin contraction, and leads to reduced scarring in SCADs and in animals. Fibroblast swarming and N-cadherin thus provide therapeutic avenues to curtail fascia mobilisation and pathological fibrotic responses across a range of medical settings.
    DOI:  https://doi.org/10.1038/s41467-020-19425-1
  48. Nat Protoc. 2020 Nov 02.
    Genome-wide detection of DNA double-strand breaks by in-suspension BLISS.
    Britta A M Bouwman, Federico Agostini, Silvano Garnerone, Giuseppe Petrosino, Henrike J Gothe, Sergi Sayols, Andreas E Moor, Shalev Itzkovitz, Magda Bienko, Vassilis Roukos, Nicola Crosetto.
      sBLISS (in-suspension breaks labeling in situ and sequencing) is a versatile and widely applicable method for identification of endogenous and induced DNA double-strand breaks (DSBs) in any cell type that can be brought into suspension. sBLISS provides genome-wide profiles of the most consequential DNA lesion implicated in a variety of pathological, but also physiological, processes. In sBLISS, after in situ labeling, DSB ends are linearly amplified, followed by next-generation sequencing and DSB landscape analysis. Here, we present a step-by-step experimental protocol for sBLISS, as well as a basic computational analysis. The main advantages of sBLISS are (i) the suspension setup, which renders the protocol user-friendly and easily scalable; (ii) the possibility of adapting it to a high-throughput or single-cell workflow; and (iii) its flexibility and its applicability to virtually every cell type, including patient-derived cells, organoids, and isolated nuclei. The wet-lab protocol can be completed in 1.5 weeks and is suitable for researchers with intermediate expertise in molecular biology and genomics. For the computational analyses, basic-to-intermediate bioinformatics expertise is required.
    DOI:  https://doi.org/10.1038/s41596-020-0397-2
  49. Chem Soc Rev. 2020 Nov 06.
    Organic fluorescent probes for monitoring autophagy in living cells.
    Xuechen Li, Xing Liang, Junling Yin, Weiying Lin.
      As a ubiquitous degradation process in cells, autophagy plays important roles in various biological activities. However, the abnormality of autophagy is closely related to many diseases, such as aging, neurological disorder, and cancer. Thus, monitoring the process of autophagy in living cells has high significance in biological studies and diagnosis of related diseases. In order to real-time and in situ monitor the process of autophagy, various organic fluorescent probes have been explored in recent years owing to the advantages such as handy staining processes, flexible molecular design strategies, and near-nondestructive detection. However, this interesting and frontier topic has not been reviewed so far. In this tutorial review, we will focus on the latest breakthrough results of organic fluorescent probes in monitoring autophagy of living cells, especially the probe design strategies based on the several microenvironment changes of the autophagy process, and the responding mechanisms and bio-imaging applications in the autophagy process. In addition, we will discuss the shortcomings and limitations of the probes developed, such as susceptible to interference, unable to monitor the whole process, and lack of clinical applications. Finally, we will highlight some challenges and further opportunities in this field. This tutorial review may promote the development of more robust fluorescent probes to further reveal the mechanisms of autophagy, which is the basis of degradation and recycling of cell components.
    DOI:  https://doi.org/10.1039/d0cs00896f
  50. J Clin Med. 2020 Oct 31. pii: E3526. [Epub ahead of print]9(11):
    Obesity and Pancreatic Cancer: A Matched-Pair Survival Analysis.
    Patrick Téoule, Erik Rasbach, Hani Oweira, Mirko Otto, Nuh N Rahbari, Christoph Reissfelder, Felix Rückert, Emrullah Birgin.
       BACKGROUND: Morbid obesity is a risk factor for pancreatic ductal adenocarcinoma (PDAC). However, the impact of obesity on postoperative outcomes and overall survival in patients with PDAC remains a controversial topic.
    METHODS: Patients who underwent pancreatic surgery for PDAC between 1997 and 2018 were included in this study. Matched pairs (1:1) were generated according to age, gender and American Society of Anesthesiologists status. Obesity was defined according to the WHO definition as BMI ≥ 30 kg/m2. The primary endpoint was the difference in overall survival between patients with and without obesity.
    RESULTS: Out of 553 patients, a total of 76 fully matched pairs were generated. Obese patients had a mean BMI-level of 33 compared to 25 kg/m2 in patients without obesity (p = 0.001). The frequency of arterial hypertension (p = 0.002), intraoperative blood loss (p = 0.039), and perineural invasion (p = 0.033) were also higher in obese patients. Clinically relevant postoperative complications (p = 0.163) and overall survival rates (p = 0.885) were comparable in both study groups. Grade II and III obesity resulted in an impaired overall survival, although this was not statistically significant. Subgroup survival analyses revealed no significant differences for completion of adjuvant chemotherapy and curative-intent surgery.
    CONCLUSIONS: Obesity did not affect overall survival and postoperative complications in these patients with PDAC. Therefore, pancreatic surgery should not be withheld from obese patients.
    Keywords:  morbidity; mortality; obesity; pancreatic ductal adenocarcinoma; survival
    DOI:  https://doi.org/10.3390/jcm9113526
  51. Carcinogenesis. 2020 Nov 07. pii: bgaa117. [Epub ahead of print]
    Mutant p53 oncogenicity - dominant-negative or gain-of-function?
    Yan Stein, Ronit Aloni-Grinstein, Varda Rotter.
      The p53 protein is mutated in about 50% of human cancers. Aside from losing its tumor-suppressive activities, mutant p53 may acquire pro-oncogenic activity, which is facilitated by two underlying mechanisms. The first mechanism is the inhibition of co-expressed wild-type p53 (WTp53) activity, dubbed the dominant-negative effect (DNE). The second mechanism is a neomorphic pro-oncogenic activity that does not involve the inhibition of WTp53, termed gain-of-function (GOF). Throughout the years, both mechanisms were demonstrated in a plethora of in vitro and in vivo models. However, whether both account for pro-tumorigenic activities of mutant p53 and in which contexts is still a matter of ongoing debate. Here we discuss evidence for both DNE and GOF in a variety of models. These models suggest that both GOF and DNE can be relevant, but are highly dependent on the specific mutation type, genetic and cellular context and even the phenotype that is being assessed. In addition, we discuss how mutant and WTp53 might not exist as two separate entities, but rather as a continuum that may involve a balance between the two forms in the same cells, which could be tilted by various factors and drugs. Further elucidation of the factors that dictate the balance between the WT and mutant p53 states, as well as the factors that govern the impact of DNE and GOF in different cancer types, may lead to the development of more effective treatment regimens for cancer patients.
    Keywords:  Mutant p53; dominant-negative effect; gain of function (GOF); p53 conformation; p53 reactivation
    DOI:  https://doi.org/10.1093/carcin/bgaa117
  52. Annu Rev Med. 2020 Nov 02.
    Therapeutics Targeting Mutant KRAS.
    Kyaw Z Thein, Amadeo B Biter, David S Hong.
      Aberrations in rat sarcoma (RAS) viral oncogene are the most prevalent and best-known genetic alterations identified in human cancers. Indeed, RAS drives tumorigenesis as one of the downstream effectors of EGFR activation, regulating cellular switches and functions and triggering intracellular signaling cascades such as the MAPK, and PI3K pathways. Of the three RAS isoforms expressed in human cells, all of which were linked to tumorigenesis more than three decades ago, KRAS is the most frequently mutated. In particular, point mutations in KRAS codon 12 are present in up to 80% of KRAS-mutant malignancies. Unfortunately, there are no approved KRAS-targeted agents, despite decades of research and development. Recently, a revolutionary strategy to use covalent allosteric inhibitors that target a shallow pocket on the KRAS surface has provided new impetus for renewed drug development efforts, specifically against KRASG12C. These inhibitors, such as AMG 510 and MRTX849, show promise in early-phase studies. Nevertheless, combination strategies that target resistance mechanisms have become vital in the war against KRAS-mutant tumors. Expected final online publication date for the Annual Review of Medicine, Volume 72 is January 27, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-med-080819-033145
  53. Trends Cell Biol. 2020 Oct 28. pii: S0962-8924(20)30208-7. [Epub ahead of print]
    The Endothelium: An Active Regulator of Lipid and Glucose Homeostasis.
    Sana S Hasan, Andreas Fischer.
      The vascular endothelium serves as a dynamic barrier that separates blood from interstitia. Endothelial cells (ECs) respond rapidly to changes in the circulation and actively regulate vessel tone, permeability, and platelet functions. ECs also secrete angiocrine factors that dictate the function of adjacent parenchymal cells in an organ-specific manner. Endothelial dysfunction is considered as a hallmark of metabolic diseases. However, there is emerging evidence that ECs modulate the transfer of nutrients and hormones to parenchymal cells in response to alterations in metabolic profile. As such, a causal role for ECs in systemic metabolic dysregulation can be envisaged. This review summarizes recent progress in the understanding of regulated fatty acid, glucose, and insulin transport across the endothelium and discusses its pathophysiological implications.
    Keywords:  endothelium; fatty acid transport; insulin transport; metabolic homeostasis; obesity
    DOI:  https://doi.org/10.1016/j.tcb.2020.10.003
  54. J Natl Cancer Inst. 2020 Nov 07. pii: djaa160. [Epub ahead of print]
    Anti-mullerian hormone as a serum biomarker for risk of chemotherapy-induced amenorrhea.
    Kathryn J Ruddy, Daniel J Schaid, Anthony Batzler, Reena S Cecchini, Ann H Partridge, Aaron Norman, Louis Fehrenbacher, Elizabeth A Stewart, Emanuel Trabuco, Elizabeth Ginsburg, Fergus J Couch, Peter A Fasching, Celine Vachon, Patricia A Ganz.
      Anti-mullerian hormone (AMH) is a promising biomarker for ovarian reserve. In this study, we assessed AMH before and one year after initiation of adjuvant chemotherapy on NSABP/NRG Oncology B-47 in female participants aged 42 years and younger (with median age 39 years). At baseline, median AMH was 1.2 ng/mL; 13 (4.7%) values were <0.1ng/mL (the threshold for detectable levels, in the perimenopause/menopause range), and 57 values (20.6%) were less than 0.5 ng/mL. At 1 year, 215 (77.6%) were less than 0.1ng/mL, and 264 (95.3%) were less than 0.5 ng/mL. Post-chemotherapy menses were reported by 46.2% of participants. Multivariable logistic regression found that the odds of having post-chemotherapy menses increased with younger age, higher BMI, and higher pre-chemotherapy AMH, but not by trastuzumab administration or by the choice of chemotherapy (doxorubicin-cyclophosphamide followed by paclitaxel vs. docetaxel-cyclophosphamide). We conclude that higher pre-chemotherapy AMH predicts a lower risk of chemotherapy-induced amenorrhea, and that AMH one year after chemotherapy initiation is not informative in this setting because it is likely to be very low.
    Keywords:  Breast neoplasms; amenorrhea; drug therapy; toxicity
    DOI:  https://doi.org/10.1093/jnci/djaa160
  55. Protein Cell. 2020 Nov 05.
    Lipids and membrane-associated proteins in autophagy.
    Linsen Li, Mindan Tong, Yuhui Fu, Fang Chen, Shen Zhang, Hanmo Chen, Xi Ma, Defa Li, Xiaoxia Liu, Qing Zhong.
      Autophagy is essential for the maintenance of cellular homeostasis and its dysfunction has been linked to various diseases. Autophagy is a membrane driven process and tightly regulated by membrane-associated proteins. Here, we summarized membrane lipid composition, and membrane-associated proteins relevant to autophagy from a spatiotemporal perspective. In particular, we focused on three important membrane remodeling processes in autophagy, lipid transfer for phagophore elongation, membrane scission for phagophore closure, and autophagosome-lysosome membrane fusion. We discussed the significance of the discoveries in this field and possible avenues to follow for future studies. Finally, we summarized the membrane-associated biochemical techniques and assays used to study membrane properties, with a discussion of their applications in autophagy.
    Keywords:  ATG2; ESCRT; autophagy; elongation; fusion; lipid transfer; membrane-associated biochemistry assays; membrane-associated proteins; scission
    DOI:  https://doi.org/10.1007/s13238-020-00793-9
  56. Annu Rev Physiol. 2020 Nov 03.
    Regulation of Mitochondrial Ca2+ Uptake.
    Elizabeth Murphy, Charles Steenbergen.
      Mitochondria are responsible for ATP production but are also known as regulators of cell death, and mitochondrial matrix Ca2+ is a key modulator of both ATP production and cell death. Although mitochondrial Ca2+ uptake and efflux have been studied for over 50 years, it is only in the past decade that the proteins responsible for mitochondrial Ca2+ uptake and efflux have been identified. The identification of the mitochondrial Ca2+ uniporter (MCU) led to an explosion of studies identifying regulators of the MCU. The levels of these regulators vary in a tissue- and disease-specific manner, providing new insight into how mitochondrial Ca2+ is regulated. This review focuses on the proteins responsible for mitochondrial transport and what we have learned from mouse studies with genetic alterations in these proteins. Expected final online publication date for the Annual Review of Physiology, Volume 83 is February 10, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-physiol-031920-092419
  57. FEBS Lett. 2020 Nov 07.
    Mitochondrial disorders of the oxphos system.
    Erika Fernandez-Vizarra, Massimo Zeviani.
      Mitochondrial disorders are amongst the most frequent inborn errors of metabolism, their primary cause being the dysfunction of the oxidative phosphorylation system (OXPHOS). OXPHOS is composed of the electron transport chain (ETC), formed by four multimeric enzymes and two mobile electron carriers, plus an ATP synthase (also called complex V). The ETC performs the redox reactions involved in cellular respiration while generating the proton motive force used by complex V to synthesize ATP. OXPHOS biogenesis involves multiple steps, starting from the expression of genes encoded in physically separated genomes, namely the mitochondrial and nuclear DNA, to the coordinated assembly of components and cofactors building each individual complex and eventually the supercomplexes. The genetic cause underlying around half of the diagnosed mitochondrial disease cases is currently known. Many of these cases result from pathogenic variants in genes encoding structural subunits or additional factors directly involved in the assembly of the ETC complexes. Here we review the historical and most recent findings concerning the clinical phenotypes and the molecular pathological mechanisms underlying this particular group of disorders.
    Keywords:  ATP production; Mitochondrial respiratory chain; biogenesis of the respiratory chain; mitochondrial disease; mitochondrial electrochemical gradient; mitochondrial potential; mitochondrial proton pumping; oxidative phosphorylation; respiratory complex; respiratory supercomplex
    DOI:  https://doi.org/10.1002/1873-3468.13995
  58. Nat Commun. 2020 11 03. 11(1): 5560
    Broad genic repression domains signify enhanced silencing of oncogenes.
    Dongyu Zhao, Lili Zhang, Min Zhang, Bo Xia, Jie Lv, Xinlei Gao, Guangyu Wang, Qingshu Meng, Yang Yi, Sen Zhu, Alin S Tomoiaga, Min Gyu Lee, John P Cooke, Qi Cao, Kaifu Chen.
      Cancers result from a set of genetic and epigenetic alterations. Most known oncogenes were identified by gain-of-function mutations in cancer, yet little is known about their epigenetic features. Through integrative analysis of 11,596 epigenomic profiles and mutations from >8200 tumor-normal pairs, we discover broad genic repression domains (BGRD) on chromatin as an epigenetic signature for oncogenes. A BGRD is a widespread enrichment domain of the repressive histone modification H3K27me3 and is further enriched with multiple other repressive marks including H3K9me3, H3K9me2, and H3K27me2. Further, BGRD displays widespread enrichment of repressed cis-regulatory elements. Shortening of BGRDs is linked to derepression of transcription. BGRDs at oncogenes tend to be conserved across normal cell types. Putative tumor-promoting genes and lncRNAs defined using BGRDs are experimentally verified as required for cancer phenotypes. Therefore, BGRDs play key roles in epigenetic regulation of cancer and provide a direction for mutation-independent discovery of oncogenes.
    DOI:  https://doi.org/10.1038/s41467-020-18913-8
  59. Chem Soc Rev. 2020 Nov 06.
    The fluorescence toolbox for visualizing autophagy.
    Siyang Ding, Yuning Hong.
      Autophagy is an adaptive catabolic process functioning to promote cell survival in the event of inappropriate living conditions such as nutrient shortage and to cope with diverse cytotoxic insults. It is regarded as one of the key survival mechanisms of living organisms. Cells undergo autophagy to accomplish the lysosomal digestion of intracellular materials including damaged proteins, organelles, and foreign bodies, in a bulk, non-selective or a cargo-specific manner. Studies in the past decades have shed light on the association of autophagy pathways with various diseases and also highlighted the therapeutic value of autophagy modulation. Hence, it is crucial to develop effective approaches for monitoring intracellular autophagy dynamics, as a comprehensive account of methodology establishment is far from complete. In this review, we aim to provide an overview of the major current fluorescence-based techniques utilized for visualizing, sensing or measuring autophagic activities in cells or tissues, which are categorized firstly by targets detected and further by the types of fluorescence tools. We will mainly focus on the working mechanisms of these techniques, put emphasis on the insight into their roles in biomedical science and provide perspectives on the challenges and future opportunities in this field.
    DOI:  https://doi.org/10.1039/d0cs00913j
  60. Elife. 2020 Nov 03. pii: e60264. [Epub ahead of print]9
    Protein phase separation and its role in tumorigenesis.
    Shan Jiang, Johan Bourghardt Fagman, Changyan Chen, Simon Alberti, Beidong Liu.
      Cancer is a disease characterized by uncontrolled cell proliferation, but the precise pathological mechanisms underlying tumorigenesis often remain to be elucidated. In recent years, condensates formed by phase separation have emerged as a new principle governing the organization and functional regulation of cells. Increasing evidence links cancer-related mutations to aberrantly altered condensate assembly, suggesting that condensates play a key role in tumorigenesis. In this review, we summarize and discuss the latest progress on the formation, regulation, and function of condensates. Special emphasis is given to emerging evidence regarding the link between condensates and the initiation and progression of cancers.
    Keywords:  C. elegans; E. coli; S. cerevisiae; biomolecular condensate; cancer; cancer biology; human; membraneless organelle; mouse; phase separation
    DOI:  https://doi.org/10.7554/eLife.60264
  61. Elife. 2020 Nov 04. pii: e54080. [Epub ahead of print]9
    Genetic profiling of protein burden and nuclear export overload.
    Reiko Kintaka, Koji Makanae, Shotaro Namba, Hisaaki Kato, Keiji Kito, Shinsuke Ohnuki, Yoshikazu Ohya, Brenda J Andrews, Charles Boone, Hisao Moriya.
      Overproduction (op) of proteins triggers cellular defects. One of the consequences of overproduction is the protein burden/cost, which is produced by an overloading of the protein synthesis process. However, the physiology of cells under a protein burden is not well characterized. We performed genetic profiling of protein burden by systematic analysis of genetic interactions between GFP-op, surveying both deletion and temperature-sensitive mutants in budding yeast. We also performed genetic profiling in cells with overproduction of triple-GFP (tGFP), and the nuclear export signal-containing tGFP (NES-tGFP). The mutants specifically interacted with GFP-op were suggestive of unexpected connections between actin-related processes like polarization and the protein burden, which was supported by morphological analysis. The tGFP-op interactions suggested that this protein probe overloads the proteasome, whereas those that interacted with NES-tGFP involved genes encoding components of the nuclear export process, providing a resource for further analysis of the protein burden and nuclear export overload.
    Keywords:  S. cerevisiae; genetics; genomics
    DOI:  https://doi.org/10.7554/eLife.54080
  62. Nat Commun. 2020 11 04. 11(1): 5574
    Small molecules as potent biphasic modulators of protein liquid-liquid phase separation.
    W Michael Babinchak, Benjamin K Dumm, Sarah Venus, Solomiia Boyko, Andrea A Putnam, Eckhard Jankowsky, Witold K Surewicz.
      Liquid-liquid phase separation (LLPS) of proteins that leads to formation of membrane-less organelles is critical to many biochemical processes in the cell. However, dysregulated LLPS can also facilitate aberrant phase transitions and lead to protein aggregation and disease. Accordingly, there is great interest in identifying small molecules that modulate LLPS. Here, we demonstrate that 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) and similar compounds are potent biphasic modulators of protein LLPS. Depending on context, bis-ANS can both induce LLPS de novo as well as prevent formation of homotypic liquid droplets. Our study also reveals the mechanisms by which bis-ANS and related compounds modulate LLPS and identify key chemical features of small molecules required for this activity. These findings may provide a foundation for the rational design of small molecule modulators of LLPS with therapeutic value.
    DOI:  https://doi.org/10.1038/s41467-020-19211-z
  63. Lancet Oncol. 2020 Nov;pii: S1470-2045(20)30448-4. [Epub ahead of print]21(11): e519-e527
    Cancer and climate change.
    Robert A Hiatt, Naomi Beyeler.
      The acute impact of climate change on human health is receiving increased attention, but little is known or appreciated about the effect of climate change on chronic diseases, particularly cancer. This Review provides a synopsis of what is known about climate change and the exposures it generates relevant to cancer. In the context of the world's cancer burden and the probable direction we could expect to follow in the absence of climate change, this scoping review of the literature summarises the effects that climate change is having on major cancers, from environmental exposures to ultraviolet radiation, air pollution, disruptions in the food and water supply, environmental toxicants, and infectious agents. Finally, we explore the effect of climate change on the possible disruption of health systems that have been essential to cancer control practice. We conclude with potential responses and opportunities for intervention.
    DOI:  https://doi.org/10.1016/S1470-2045(20)30448-4
  64. Aging Cell. 2020 Nov 07. e13273
    Hair graying with aging in mice carrying oncogenic RET.
    Machiko Iida, Akira Tazaki, Ichiro Yajima, Nobutaka Ohgami, Nobuhiko Taguchi, Yuji Goto, Mayuko Y Kumasaka, Armelle Prévost-Blondel, Michihiro Kono, Masashi Akiyama, Masahide Takahashi, Masashi Kato.
      Hair graying is a representative sign of aging in animals and humans. However, the mechanism for hair graying with aging remains largely unknown. In this study, we found that the microscopic appearance of hair follicles without melanocyte stem cells (MSCs) and descendant melanocytes as well as macroscopic appearances of hair graying in RET-transgenic mice carrying RET oncogene (RET-mice) are in accordance with previously reported results for hair graying in humans. Therefore, RET-mice could be a novel model mouse line for age-related hair graying. We further showed hair graying with aging in RET-mice associated with RET-mediated acceleration of hair cycles, increase of senescent follicular keratinocyte stem cells (KSCs), and decreased expression levels of endothelin-1 (ET-1) in bulges, decreased endothelin receptor B (Ednrb) expression in MSCs, resulting in a decreased number of follicular MSCs. We then showed that hair graying in RET-mice was accelerated by congenitally decreased Ednrb expression in MSCs in heterozygously Ednrb-deleted RET-mice [Ednrb(+/-);RET-mice]. We finally partially confirmed common mechanisms of hair graying with aging in mice and humans. Taken together, our results suggest that age-related dysfunction between ET-1 in follicular KSCs and endothelin receptor B (Ednrb) in follicular MSCs via cumulative hair cycles is correlated with hair graying with aging.
    Keywords:  RET; age-related hair graying; endothelin; keratinocyte stem cells; melanocyte stem cells
    DOI:  https://doi.org/10.1111/acel.13273
  65. Cell Death Discov. 2020 ;6 110
    The anti-malarial drug atovaquone potentiates platinum-mediated cancer cell death by increasing oxidative stress.
    James T T Coates, Gonzalo Rodriguez-Berriguete, Rathi Puliyadi, Thomas Ashton, Remko Prevo, Archie Wing, Giovanna Granata, Giacomo Pirovano, Gillies W McKenna, Geoff S Higgins.
      Platinum chemotherapies are highly effective cytotoxic agents but often induce resistance when used as monotherapies. Combinatorial strategies limit this risk and provide effective treatment options for many cancers. Here, we repurpose atovaquone (ATQ), a well-tolerated & FDA-approved anti-malarial agent by demonstrating that it potentiates cancer cell death of a subset of platinums. We show that ATQ in combination with carboplatin or cisplatin induces striking and repeatable concentration- and time-dependent cell death sensitization in vitro across a variety of cancer cell lines. ATQ induces mitochondrial reactive oxygen species (mROS), depleting intracellular glutathione (GSH) pools in a concentration-dependent manner. The superoxide dismutase mimetic MnTBAP rescues ATQ-induced mROS production and pre-loading cells with the GSH prodrug N-acetyl cysteine (NAC) abrogates the sensitization. Together, these findings implicate ATQ-induced oxidative stress as key mediator of the sensitizing effect. At physiologically achievable concentrations, ATQ and carboplatin furthermore synergistically delay the growth of three-dimensional avascular spheroids. Clinically, ATQ is a safe and specific inhibitor of the electron transport chain (ETC) and is concurrently being repurposed as a candidate tumor hypoxia modifier. Together, these findings suggest that ATQ is deserving of further study as a candidate platinum sensitizing agent.
    Keywords:  Chemotherapy; Preclinical research
    DOI:  https://doi.org/10.1038/s41420-020-00343-6
  66. Annu Rev Physiol. 2020 Nov 06.
    Ceramides in Metabolism: Key Lipotoxic Players.
    Bhagirath Chaurasia, Scott A Summers.
      The global prevalence of metabolic diseases such as type 2 diabetes mellitus, steatohepatitis, myocardial infarction, and stroke has increased dramatically over the past two decades. These obesity-fueled disorders result, in part, from the aberrant accumulation of harmful lipid metabolites in tissues not suited for lipid storage (e.g., the liver, vasculature, heart, and pancreatic beta-cells). Among the numerous lipid subtypes that accumulate, sphingolipids such as ceramides are particularly impactful, as they elicit the selective insulin resistance, dyslipidemia, and ultimately cell death that underlie nearly all metabolic disorders. This review summarizes recent findings on the regulatory pathways controlling ceramide production, the molecular mechanisms linking the lipids to these discrete pathogenic events, and exciting attempts to develop therapeutics to reduce ceramide levels to combat metabolic disease. Expected final online publication date for the Annual Review of Physiology, Volume 83 is February 10, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-physiol-031620-093815
  67. Lancet Oncol. 2020 Oct 29. pii: S1470-2045(20)30587-8. [Epub ahead of print]
    BELLINI: a renaissance for an era of precision therapy in multiple myeloma.
    Irene Ghobrial.
      
    DOI:  https://doi.org/10.1016/S1470-2045(20)30587-8
  68. Nucleic Acids Res. 2020 Nov 06. pii: gkaa992. [Epub ahead of print]
    MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models.
    Sébastien Moretti, Van Du T Tran, Florence Mehl, Mark Ibberson, Marco Pagni.
      MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing cross-links between major public biochemistry and Genome-Scale Metabolic Network (GSMN) databases. The new release brings several improvements with respect to the quality of the reconciliation, with particular attention dedicated to preserving the intrinsic properties of GSMN models. The MetaNetX website (https://www.metanetx.org/) provides access to the full database and online services. A major improvement is for mapping of user-provided GSMNs to MXNref, which now provides diagnostic messages about model content. In addition to the website and flat files, the resource can now be accessed through a SPARQL endpoint (https://rdf.metanetx.org).
    DOI:  https://doi.org/10.1093/nar/gkaa992
  69. Trends Cancer. 2020 Oct 30. pii: S2405-8033(20)30265-X. [Epub ahead of print]
    PALB2 Variants: Protein Domains and Cancer Susceptibility.
    Thales C Nepomuceno, Marcelo A Carvalho, Amélie Rodrigue, Jacques Simard, Jean-Yves Masson, Alvaro N A Monteiro.
      Since its discovery, partner and localizer of breast cancer 2 (BRCA2) (PALB2) has emerged as a major tumor suppressor gene linked to breast cancer (BC), pancreatic cancer (PC), and ovarian cancer (OC) susceptibility. Its protein product plays a pivotal role in the maintenance of genome integrity. Here we discuss the first functional evaluation of a large set of PALB2 missense variants of uncertain significance (VUSs). Assessment of 136 VUSs interrogating a range of PALB2 biological functions resulted in the identification of 15 variants with consistent loss of function across different assays. All loss-of-function variants are located at the PALB2 coiled coil (CC) or at the WD40 domain, highlighting the importance of modular domains mechanistically involved in the DNA damage response (DDR) and pinpointing their roles in tumor suppression.
    Keywords:  PALB2; breast cancer; genetic testing; ovarian cancer; protein modular domains; susceptibility genes; tumor suppressor; variants of uncertain significance
    DOI:  https://doi.org/10.1016/j.trecan.2020.10.002
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