bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021‒02‒28
eighty-five papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation.
  2. The major cap-binding protein eIF4E regulates lipid homeostasis and diet-induced obesity.
  3. mTORC1 activity is supported by spatial association with focal adhesions.
  4. Lipid and glucose metabolism in white adipocytes: pathways, dysfunction and therapeutics.
  5. Inflammation promotes adipocyte lipolysis via IRE1 kinase.
  6. Should I bend or should I grow: the mechanisms of droplet-mediated autophagosome formation.
  7. Self-assembly of multi-component mitochondrial nucleoids via phase separation.
  8. Nuclear sensing of breaks in mitochondrial DNA enhances immune surveillance.
  9. Homology-directed repair protects the replicating genome from metabolic assaults.
  10. Causes and consequences of micronuclei.
  11. Potential Roles of Muscle-Derived Extracellular Vesicles in Remodeling Cellular Microenvironment: Proposed Implications of the Exercise-Induced Myokine, Irisin.
  12. A Quantitative Paradigm for Decision-Making in Precision Oncology.
  13. BLOC1S1/GCN5L1/BORCS1 is a critical mediator for the initiation of autolysosomal tubulation.
  14. Loss of optineurin drives cancer immune evasion via palmitoylation-dependent IFNGR1 lysosomal sorting and degradation.
  15. Protein products of nonstop mRNA disrupt nucleolar homeostasis.
  16. Mitochondrial clearance: mechanisms and roles in cellular fitness.
  17. Functional antagonism of chromatin modulators regulates epithelial-mesenchymal transition.
  18. A unique subset of glycolytic tumour-propagating cells drives squamous cell carcinoma.
  19. Dichloroacetate reverses sepsis-induced hepatic metabolic dysfunction.
  20. Specialised endocytic proteins regulate diverse internalisation mechanisms and signalling outputs in physiology and cancer.
  21. Age-associated mitochondrial complex I deficiency is linked to increased stem cell proliferation rates in the mouse colon.
  22. Facilitative lysosomal transport of bile acids alleviates ER stress in mouse hematopoietic precursors.
  23. Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms.
  24. Sulfur sequestration promotes multicellularity during nutrient limitation.
  25. Liver homeostasis is maintained by midlobular zone 2 hepatocytes.
  26. Body Composition and Response and Outcome of Neoadjuvant Treatment for Pancreatic Cancer.
  27. Comprehensive analysis of single cell ATAC-seq data with SnapATAC.
  28. Links between mitochondrial retrograde response and mitophagy in pathogenic cell signalling.
  29. SEC24A facilitates colocalization and calcium flux between endoplasmic reticulum and mitochondria.
  30. Gut microbiome pattern reflects healthy ageing and predicts survival in humans.
  31. Fibronectin fibril alignment is established upon initiation of extracellular matrix assembly.
  32. DNA hypomethylating agents increase activation and cytolytic activity of CD8+ T cells.
  33. In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer.
  34. Cell-type Specific Adaptive Signaling Responses to KRASG12C inhibition.
  35. The Common Germline TP53-R337H Mutation is Hypomorphic and Confers Incomplete Penetrance and Late Tumor Onset in a Mouse Model.
  36. p53 induces ARTS to promote mitochondrial apoptosis.
  37. Asparagine couples mitochondrial respiration to ATF4 activity and tumor growth.
  38. Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
  39. Protein kinase C fusion proteins are paradoxically loss-of-function in cancer.
  40. Targeting eIF4A Dependent Translation of KRAS Signaling Molecules.
  41. Murine neonatal ketogenesis preserves mitochondrial energetics by preventing protein hyperacetylation.
  42. Pro-Tumoral Functions of Autophagy Receptors in the Modulation of Cancer Progression.
  43. One-carbon metabolism in cancer cells: a critical review based on a core model of central metabolism.
  44. Autophagy Paradox of Cancer: Role, Regulation, and Duality.
  45. Neuronal autophagy controls the axonal endoplasmic reticulum to regulate neurotransmission in healthy neurons.
  46. High mRNA expression of LY6 gene family is associated with overall survival outcome in pancreatic ductal adenocarcinoma.
  47. Incidence and Risk of Pancreatic Cancer in Patients with a New Diagnosis of Chronic Pancreatitis.
  48. FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity.
  49. Cell Volume Regulation in Immune Cell Function, Activation and Survival.
  50. Aging and rejuvenation - a modular epigenome model.
  51. Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues.
  52. Depletion of H3K36me2 recapitulates epigenomic and phenotypic changes induced by the H3.3K36M oncohistone mutation.
  53. The foggy world(s) of p63 isoform regulation in normal cells and cancer.
  54. 5-Fluorouracil efficacy requires anti-tumor immunity triggered by cancer-cell-intrinsic STING.
  55. TARGETING CELL-INTRINSIC METABOLISM FOR ANTI-FIBROGENIC THERAPY.
  56. Exercise Training as Therapeutic Approach in Cancer Cachexia: A Review of Potential Anti-inflammatory Effect on Muscle Wasting.
  57. Drivers of Gene Expression Dysregulation in Pancreatic Cancer.
  58. MYB oncoproteins: emerging players and potential therapeutic targets in human cancer.
  59. Sialic acids in pancreatic cancer cells drive tumour-associated macrophage differentiation via the Siglec receptors Siglec-7 and Siglec-9.
  60. H2A.Z overexpression suppresses senescence and chemosensitivity in pancreatic ductal adenocarcinoma.
  61. PINK1/PARK2 Dependent Mitophagy Effectively Suppresses NLRP3 Inflammasome to Alleviate Acute Pancreatitis.
  62. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for Alagille syndrome.
  63. PAF remodels the DREAM complex to bypass cell quiescence and promote lung tumorigenesis.
  64. Collaborations with artists go beyond communicating the science.
  65. Underreporting of symptomatic adverse events in phase I clinical trials.
  66. Whole-body metabolic fate of branched-chain amino acids.
  67. Identifying molecular features that are associated with biological function of intrinsically disordered protein regions.
  68. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis.
  69. Pancreatic ductal adenocarcinoma in the era of precision medicine.
  70. Common Weight Loss Surgeries' Benefits Sustained at Year 7.
  71. Energy-dependent protein folding: modeling how a protein folding machine may work.
  72. The crosstalk between HIFs and mitochondrial dysfunctions in cancer development.
  73. Clonal expansion in non-cancer tissues.
  74. Re-defining synthetic lethality by phenotypic profiling for precision oncology.
  75. Human-specific polymorphic pseudogenization of SIGLEC12 protects against advanced cancer progression.
  76. Ca2+ as the prime trigger of aerobic glycolysis in astrocytes.
  77. T cell circuits that sense antigen density with an ultrasensitive threshold.
  78. POMC neuronal heterogeneity in energy balance and beyond: an integrated view.
  79. Discovery of Metastatic Regulators using a Rapid and Quantitative Intravital Chick Chorioallantoic Membrane Model.
  80. Computational Screening of Biological Phase-separating Proteins.
  81. Applying genomic and transcriptomic advances to mitochondrial medicine.
  82. Autophagy in Acute Pancreatitis: Organelle Interaction and microRNA Regulation.
  83. A nomogram of preoperative predictors for occult metastasis in patients with PDAC during laparoscopic exploration.
  84. OncoTree: A Cancer Classification System for Precision Oncology.
  85. Integrating Quantitative Approaches in Cancer Research and Oncology.
  1. Elife. 2021 Feb 23. pii: e63270. [Epub ahead of print]10
    Dissecting phenotypic transitions in metastatic disease via photoconversion-based isolation.
    Yogev Sela, Jinyang Li, Paola Kuri, Allyson Merrell, Ning Li, Chris Lengner, Pantelis Rompolas, Ben Z Stanger.
      Cancer patients often harbor occult metastases, a potential source of relapse that is targetable only through systemic therapy. Studies of this occult fraction have been limited by a lack of tools with which to isolate discrete cells on spatial grounds. We developed PIC-IT, a photoconversion-based isolation technique allowing efficient recovery of cell clusters of any size - including single-metastatic cells - which are largely inaccessible otherwise. In a murine pancreatic cancer model, transcriptional profiling of spontaneously arising microcolonies revealed phenotypic heterogeneity, functionally reduced propensity to proliferate and enrichment for an inflammatory-response phenotype associated with NF-κB/AP-1 signaling. Pharmacological inhibition of NF-κB depleted microcolonies but had no effect on macrometastases, suggesting microcolonies are particularly dependent on this pathway. PIC-IT thus enables systematic investigation of metastatic heterogeneity. Moreover, the technique can be applied to other biological systems in which isolation and characterization of spatially distinct cell populations is not currently feasible.
    Keywords:  cancer biology; mouse
    DOI:  https://doi.org/10.7554/eLife.63270
  2. Nat Metab. 2021 Feb;3(2): 244-257
    The major cap-binding protein eIF4E regulates lipid homeostasis and diet-induced obesity.
    Crystal S Conn, Haojun Yang, Harrison J Tom, Kenji Ikeda, Juan A Oses-Prieto, Hieu Vu, Yasuo Oguri, Supna Nair, Ryan M Gill, Shingo Kajimura, Ralph J DeBerardinis, Alma L Burlingame, Davide Ruggero.
      Obesity is a global epidemic leading to increased mortality and susceptibility to comorbidities, with few viable therapeutic interventions. A hallmark of disease progression is the ectopic deposition of lipids in the form of lipid droplets in vital organs such as the liver. However, the mechanisms underlying the dynamic storage and processing of lipids in peripheral organs remain an outstanding question. Here, we show an unexpected function for the major cap-binding protein, eIF4E, in high-fat-diet-induced obesity. In response to lipid overload, select networks of proteins involved in fat deposition are altered in eIF4E-deficient mice. Specifically, distinct messenger RNAs involved in lipid metabolic processing and storage pathways are enhanced at the translation level by eIF4E. Failure to translationally upregulate these mRNAs results in increased fatty acid oxidation, which enhances energy expenditure. We further show that inhibition of eIF4E phosphorylation genetically-and by a potent clinical compound-restrains weight gain following intake of a high-fat diet. Together, our study uncovers translational control of lipid processing as a driver of high-fat-diet-induced weight gain and provides a pharmacological target to treat obesity.
    DOI:  https://doi.org/10.1038/s42255-021-00349-z
  3. J Cell Biol. 2021 May 03. pii: e202004010. [Epub ahead of print]220(5):
    mTORC1 activity is supported by spatial association with focal adhesions.
    Yoana Rabanal-Ruiz, Adam Byron, Alexander Wirth, Ralitsa Madsen, Lucia Sedlackova, Graeme Hewitt, Glyn Nelson, Julian Stingele, Jimi C Wills, Tong Zhang, André Zeug, Reinhard Fässler, Bart Vanhaesebroeck, Oliver D K Maddocks, Evgeni Ponimaskin, Bernadette Carroll, Viktor I Korolchuk.
      The mammalian target of rapamycin complex 1 (mTORC1) integrates mitogenic and stress signals to control growth and metabolism. Activation of mTORC1 by amino acids and growth factors involves recruitment of the complex to the lysosomal membrane and is further supported by lysosome distribution to the cell periphery. Here, we show that translocation of lysosomes toward the cell periphery brings mTORC1 into proximity with focal adhesions (FAs). We demonstrate that FAs constitute discrete plasma membrane hubs mediating growth factor signaling and amino acid input into the cell. FAs, as well as the translocation of lysosome-bound mTORC1 to their vicinity, contribute to both peripheral and intracellular mTORC1 activity. Conversely, lysosomal distribution to the cell periphery is dispensable for the activation of mTORC1 constitutively targeted to FAs. This study advances our understanding of spatial mTORC1 regulation by demonstrating that the localization of mTORC1 to FAs is both necessary and sufficient for its activation by growth-promoting stimuli.
    DOI:  https://doi.org/10.1083/jcb.202004010
  4. Nat Rev Endocrinol. 2021 Feb 24.
    Lipid and glucose metabolism in white adipocytes: pathways, dysfunction and therapeutics.
    Pauline Morigny, Jeremie Boucher, Peter Arner, Dominique Langin.
      In mammals, the white adipocyte is a cell type that is specialized for storage of energy (in the form of triacylglycerols) and for energy mobilization (as fatty acids). White adipocyte metabolism confers an essential role to adipose tissue in whole-body homeostasis. Dysfunction in white adipocyte metabolism is a cardinal event in the development of insulin resistance and associated disorders. This Review focuses on our current understanding of lipid and glucose metabolic pathways in the white adipocyte. We survey recent advances in humans on the importance of adipocyte hypertrophy and on the in vivo turnover of adipocytes and stored lipids. At the molecular level, the identification of novel regulators and of the interplay between metabolic pathways explains the fine-tuning between the anabolic and catabolic fates of fatty acids and glucose in different physiological states. We also examine the metabolic alterations involved in the genesis of obesity-associated metabolic disorders, lipodystrophic states, cancers and cancer-associated cachexia. New challenges include defining the heterogeneity of white adipocytes in different anatomical locations throughout the lifespan and investigating the importance of rhythmic processes. Targeting white fat metabolism offers opportunities for improved patient stratification and a wide, yet unexploited, range of therapeutic opportunities.
    DOI:  https://doi.org/10.1038/s41574-021-00471-8
  5. J Biol Chem. 2021 Feb 19. pii: S0021-9258(21)00213-1. [Epub ahead of print] 100440
    Inflammation promotes adipocyte lipolysis via IRE1 kinase.
    Kevin P Foley, Yong Chen, Nicole G Barra, Mark Heal, Kieran Kwok, Akhilesh K Tamrakar, Wendy Chi, Brittany M Duggan, Brandyn D Henriksbo, Yong Liu, Jonathan D Schertzer.
      Obesity associates with inflammation, insulin resistance and higher blood lipids. It is unclear if immune responses facilitate lipid breakdown and release from adipocytes via lipolysis in a separate way from hormones or adrenergic signals. We found that an ancient component of ER stress, inositol-requiring protein 1 (IRE1), discriminates inflammation-induced adipocyte lipolysis versus lipolysis from adrenergic or hormonal stimuli. Our data show that inhibiting IRE1 kinase activity was sufficient to block adipocyte-autonomous lipolysis from multiple inflammatory ligands, including bacterial components, certain cytokines, and thapsigargin-induced ER stress. IRE1-mediated lipolysis was specific for inflammatory triggers since IRE1 kinase activity was dispensable for isoproterenol and cAMP-induced lipolysis in adipocytes and mouse adipose tissue. IRE1 RNase activity was not associated with inflammation-induced adipocyte lipolysis. Inhibiting IRE1 kinase activity blocked NF-κB activation, interleukin-6 secretion, and adipocyte-autonomous lipolysis from inflammatory ligands. Inflammation-induced lipolysis mediated by IRE1 occurred independently from changes in insulin signaling in adipocytes, suggesting that inflammation can promote IRE1-mediated lipolysis independent of adipocyte insulin resistance. We found no role for canonical unfolded protein responses or ABL kinases in linking ER stress to IRE1-mediated lipolysis. Adiponectin-Cre-mediated IRE1 knockout in mice showed that adipocyte IRE1 was required for inflammatory ligand-induced lipolysis in adipose tissue explants and that adipocyte IRE1 was required for approximately half of the increase in blood triglycerides after a bacterial endotoxin-mediated inflammatory stimulus in vivo. Together, our results show that IRE1 propagates an inflammation-specific lipolytic program independent from hormonal or adrenergic regulation. Targeting IRE1 kinase activity may benefit metabolic syndrome and inflammatory lipid disorders.
    Keywords:  ER stress; adipocyte; cytokine; endocrinology; immunometabolism; inflammation; lipid; lipolysis; metabolic syndrome; obesity
    DOI:  https://doi.org/10.1016/j.jbc.2021.100440
  6. Autophagy. 2021 Feb 25. 1-3
    Should I bend or should I grow: the mechanisms of droplet-mediated autophagosome formation.
    Sebastian W Schultz, Jaime Agudo-Canalejo, Haruka Chino, Simona M Migliano, Chieko Saito, Ikuko Koyama-Honda, Harald Stenmark, Andreas Brech, Noboru Mizushima, Roland L Knorr, Alexander I May.
      Phase-separated droplets with liquid-like properties can be degraded by macroautophagy/autophagy, but the mechanism underlying this degradation is poorly understood. We have recently derived a physical model to investigate the interaction between autophagic membranes and such droplets, uncovering that intrinsic wetting interactions underlie droplet-membrane contacts. We found that the competition between droplet surface tension and the increasing tendency of growing membrane sheets to bend determines whether a droplet is completely engulfed or isolated in a piecemeal fashion, a process we term fluidophagy. Intriguingly, we found that another critical parameter of droplet-membrane interactions, the spontaneous curvature of the membrane, determines whether the droplet is degraded by autophagy or - counterintuitively - serves as a platform from which autophagic membranes expand into the cytosol. We also discovered that the interaction of membrane-associated LC3 with the LC3-interacting region (LIR) found in the autophagic cargo receptor protein SQSTM1/p62 and many other autophagy-related proteins influences the preferred bending directionality of forming autophagosomes in living cells. Our study provides a physical account of how droplet-membrane wetting underpins the structure and fate of forming autophagosomes.
    Keywords:  Autophagy; condensate; droplet; isolation membrane; membrane; p62; phase separation; piecemeal autophagy; wetting
    DOI:  https://doi.org/10.1080/15548627.2021.1887548
  7. EMBO J. 2021 Feb 23. e107165
    Self-assembly of multi-component mitochondrial nucleoids via phase separation.
    Marina Feric, Tyler G Demarest, Jane Tian, Deborah L Croteau, Vilhelm A Bohr, Tom Misteli.
      Mitochondria contain an autonomous and spatially segregated genome. The organizational unit of their genome is the nucleoid, which consists of mitochondrial DNA (mtDNA) and associated architectural proteins. Here, we show that phase separation is the primary physical mechanism for assembly and size control of the mitochondrial nucleoid (mt-nucleoid). The major mtDNA-binding protein TFAM spontaneously phase separates in vitro via weak, multivalent interactions into droplets with slow internal dynamics. TFAM and mtDNA form heterogenous, viscoelastic structures in vitro, which recapitulate the dynamics and behavior of mt-nucleoids in vivo. Mt-nucleoids coalesce into larger droplets in response to various forms of cellular stress, as evidenced by the enlarged and transcriptionally active nucleoids in mitochondria from patients with the premature aging disorder Hutchinson-Gilford Progeria Syndrome (HGPS). Our results point to phase separation as an evolutionarily conserved mechanism of genome organization.
    Keywords:  TFAM; biomolecular condensate; genome organization; mitochondrial genome; phase separation
    DOI:  https://doi.org/10.15252/embj.2020107165
  8. Nature. 2021 Feb 24.
    Nuclear sensing of breaks in mitochondrial DNA enhances immune surveillance.
    Marco Tigano, Danielle C Vargas, Samuel Tremblay-Belzile, Yi Fu, Agnel Sfeir.
      Mitochondrial DNA double-strand breaks (mtDSBs) are toxic lesions that compromise the integrity of mitochondrial DNA (mtDNA) and alter mitochondrial function1. Communication between mitochondria and the nucleus is essential to maintain cellular homeostasis; however, the nuclear response to mtDSBs remains unknown2. Here, using mitochondrial-targeted transcription activator-like effector nucleases (TALENs)1,3,4, we show that mtDSBs activate a type-I interferon response that involves the phosphorylation of STAT1 and activation of interferon-stimulated genes. After the formation of breaks in the mtDNA, herniation5 mediated by BAX and BAK releases mitochondrial RNA into the cytoplasm and triggers a RIG-I-MAVS-dependent immune response. We further investigated the effect of mtDSBs on interferon signalling after treatment with ionizing radiation and found a reduction in the activation of interferon-stimulated genes when cells that lack mtDNA are exposed to gamma irradiation. We also show that mtDNA breaks synergize with nuclear DNA damage to mount a robust cellular immune response. Taken together, we conclude that cytoplasmic accumulation of mitochondrial RNA is an intrinsic immune surveillance mechanism for cells to cope with mtDSBs, including breaks produced by genotoxic agents.
    DOI:  https://doi.org/10.1038/s41586-021-03269-w
  9. Dev Cell. 2021 Feb 22. pii: S1534-5807(21)00069-1. [Epub ahead of print]56(4): 461-477.e7
    Homology-directed repair protects the replicating genome from metabolic assaults.
    Kumar Somyajit, Julian Spies, Fabian Coscia, Ufuk Kirik, Maj-Britt Rask, Ji-Hoon Lee, Kai John Neelsen, Andreas Mund, Lars Juhl Jensen, Tanya T Paull, Matthias Mann, Jiri Lukas.
      Homology-directed repair (HDR) safeguards DNA integrity under various forms of stress, but how HDR protects replicating genomes under extensive metabolic alterations remains unclear. Here, we report that besides stalling replication forks, inhibition of ribonucleotide reductase (RNR) triggers metabolic imbalance manifested by the accumulation of increased reactive oxygen species (ROS) in cell nuclei. This leads to a redox-sensitive activation of the ATM kinase followed by phosphorylation of the MRE11 nuclease, which in HDR-deficient settings degrades stalled replication forks. Intriguingly, nascent DNA degradation by the ROS-ATM-MRE11 cascade is also triggered by hypoxia, which elevates signaling-competent ROS and attenuates functional HDR without arresting replication forks. Under these conditions, MRE11 degrades daughter-strand DNA gaps, which accumulate behind active replisomes and attract error-prone DNA polymerases to escalate mutation rates. Thus, HDR safeguards replicating genomes against metabolic assaults by restraining mutagenic repair at aberrantly processed nascent DNA. These findings have implications for cancer evolution and tumor therapy.
    Keywords:  BRCA1/2; cancer evolution; genome instability; homology-directed repair; hypoxia; nascent DNA degradation; reactive oxygen species; replication stress; ribonucleotide reductase; translesion DNA synthesis
    DOI:  https://doi.org/10.1016/j.devcel.2021.01.011
  10. Curr Opin Cell Biol. 2021 Feb 18. pii: S0955-0674(21)00004-1. [Epub ahead of print]70 91-99
    Causes and consequences of micronuclei.
    Ksenia Krupina, Alexander Goginashvili, Don W Cleveland.
      Micronuclei are small membrane-bounded compartments with a DNA content encapsulated by a nuclear envelope and spatially separated from the primary nucleus. Micronuclei have long been linked to chromosome instability, genome rearrangements, and mutagenesis. They are frequently found in cancers, during senescence, and after genotoxic stress. Compromised integrity of the micronuclear envelope delays or disrupts DNA replication, inhibits DNA repair, and exposes micronuclear DNA directly to cytoplasm. Micronuclei play a central role in tumorigenesis, with micronuclear DNA being a source of complex genome rearrangements (including chromothripsis) and promoting a cyclic GMP-AMP synthase (cGAS)-mediated cellular immune response that may contribute to cancer metastasis. Here, we discuss recent findings on how micronuclei are generated, what the consequences are, and what cellular mechanisms can be applied to protect against micronucleation.
    DOI:  https://doi.org/10.1016/j.ceb.2021.01.004
  11. Front Cell Dev Biol. 2021 ;9 634853
    Potential Roles of Muscle-Derived Extracellular Vesicles in Remodeling Cellular Microenvironment: Proposed Implications of the Exercise-Induced Myokine, Irisin.
    Samuel Darkwah, Eun Jeong Park, Phyoe Kyawe Myint, Atsushi Ito, Michael G Appiah, Gideon Obeng, Eiji Kawamoto, Motomu Shimaoka.
      Extracellular vesicles (EVs) have emerged as key players of intercellular communication and mediate crosstalk between tissues. Metastatic tumors release tumorigenic EVs, capable of pre-conditioning distal sites for organotropic metastasis. Growing evidence identifies muscle cell-derived EVs and myokines as potent mediators of cellular differentiation, proliferation, and metabolism. Muscle-derived EVs cargo myokines and other biological modulators like microRNAs, cytokines, chemokines, and prostaglandins hence, are likely to modulate the remodeling of niches in vital sites, such as liver and adipose tissues. Despite the scarcity of evidence to support a direct relationship between muscle-EVs and cancer metastasis, their indirect attribution to the regulation of niche remodeling and the establishment of pre-metastatic homing niches can be put forward. This hypothesis is supported by the role of muscle-derived EVs in findings gathered from other pathologies like inflammation and metabolic disorders. In this review, we present and discuss studies that evidently support the potential roles of muscle-derived EVs in the events of niche pre-conditioning and remodeling of metastatic tumor microenvironment. We highlight the potential contributions of the integrin-mediated interactions with an emerging myokine, irisin, to the regulation of EV-driven microenvironment remodeling in tumor metastasis. Further research into muscle-derived EVs and myokines in cancer progression is imperative and may hold promising contributions to advance our knowledge in the pathophysiology, progression and therapeutic management of metastatic cancers.
    Keywords:  extracellular vesicles; homing niche; integrins; irisin; muscle; myokines; tissue microenvironment; tumor metastasis
    DOI:  https://doi.org/10.3389/fcell.2021.634853
  12. Trends Cancer. 2021 Feb 23. pii: S2405-8033(21)00020-0. [Epub ahead of print]
    A Quantitative Paradigm for Decision-Making in Precision Oncology.
    Dalit Engelhardt, Franziska Michor.
      The complexity and variability of cancer progression necessitate a quantitative paradigm for therapeutic decision-making that is dynamic, personalized, and capable of identifying optimal treatment strategies for individual patients under substantial uncertainty. Here, we discuss the core components and challenges of such an approach and highlight the need for comprehensive longitudinal clinical and molecular data integration in its development. We describe the complementary and varied roles of mathematical modeling and machine learning in constructing dynamic optimal cancer treatment strategies and highlight the potential of reinforcement learning approaches in this endeavor.
    Keywords:  machine learning; mathematical modeling; personalized medicine; treatment optimization
    DOI:  https://doi.org/10.1016/j.trecan.2021.01.006
  13. Autophagy. 2021 Feb 25.
    BLOC1S1/GCN5L1/BORCS1 is a critical mediator for the initiation of autolysosomal tubulation.
    Kaiyuan Wu, Allen Seylani, Jing Wu, Xufeng Wu, Christopher K E Bleck, Michael N Sack.
      The mechanisms orchestrating recycling of lysosomes through autophagic lysosome reformation (ALR) is incompletely understood. Previous data show that genetic depletion of BLOC1S1/GCN5L1/BORCS1 increases autolysosome (AL) accumulation. We postulated that this phenotype may manifest due to perturbed ALR. We explored this in control and bloc1s1 liver-specific knockout (LKO) mouse hepatocytes, showing that in response to nutrient-deprivation LKO's fail to initiate ALR due to blunted lysosomal tubulation. As kinesin motor proteins and the intracellular cytoskeleton are requirements for tubular formation from ALs, we explored the interaction of BLOC1S1 with motor proteins and cytoskeletal factors. BLOC1S1 interacts with the ARL8B-KIF5B (GTPase and kinesin motor protein) complex to recruit KIF5B to ALs. Furthermore, BLOC1S1 interacts with the actin nucleation promoting factor WHAMM, which is an essential structural protein in the initiation of lysosomal tubulation (LT). Interestingly, the genetic reintroduction of BLOC1S1 rescues LT in LKO hepatocytes, but not when KIF5B is concurrently depleted. Finally, given the central role of MTORC1 signaling in ALR initiation, it was interesting that MTORC1 activity was increased despite the absence of LT in LKO hepatocytes. Concurrently, inhibition of MTORC1 abolished BLOC1S1 reconstitution-mediated rescue of LT in LKO hepatocytes. Taken together these data demonstrate that the functional interaction of BLOC1S1 with the kinesin binding complex and the actin cytoskeleton are a requirement for LT which, in parallel with MTORC1 signaling, initiate lysosome recycling via ALR.
    Keywords:  Autophagic lysosome reformation; GCN5L1; MTORC1; autophagy; hepatocyte; lysosomal tubulation; lysosome
    DOI:  https://doi.org/10.1080/15548627.2021.1894759
  14. Cancer Discov. 2021 Feb 24. pii: candisc.1571.2020. [Epub ahead of print]
    Loss of optineurin drives cancer immune evasion via palmitoylation-dependent IFNGR1 lysosomal sorting and degradation.
    Wan Du, Fang Hua, Xiong Li, Jian Zhang, Shasha Li, Weichao Wang, Jiajia Zhou, Weimin Wang, Peng Liao, Yijian Yan, Gaopeng Li, Shuang Wei, Sara Grove, Linda Vatan, Witold Zgodzinski, Marek Majewski, Grzegorz Wallner, Haoyan Chen, Ilona Kryczek, Jing-Yuan Fang, Weiping Zou.
      Mutations in IFN- and MHC-signaling genes endow immunotherapy resistance. Colorectal cancer patients infrequently exhibit IFN- and MHC-signaling gene mutations, and are generally resistant to immunotherapy. In exploring the integrity of the IFN- and MHC-signaling in colorectal cancer, we found that optineurin was a shared node between the two pathways, and predicted colorectal cancer patient outcome. Loss of optineurin occurred in early stage human colorectal cancer. Immunologically, optineurin deficiency attenuated IFNGR1 and MHC-I expression, impaired T cell-immunity, and diminished immunotherapy efficacy in murine cancer models and cancer patients. Mechanistically, IFNGR1 was S-palmitoylated on Cys122, and AP3D1 bound with and sorted palmitoylated-IFNGR1 to lysosome for degradation. Unexpectedly, optineurin interacted with AP3D1 to prevent palmitoylated-IFNGR1 lysosomal sorting and degradation - thereby maintaining IFNy- and MHC-I-signaling integrity. Furthermore, pharmacologically targeting IFNGR1-palmitoylation stabilized IFNGR1, augmented tumor immunity, and sensitized checkpoint therapy. Thus, loss of optineurin drives immune evasion and intrinsic immunotherapy resistance in colorectal cancer.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1571
  15. Cell Stress Chaperones. 2021 Feb 22.
    Protein products of nonstop mRNA disrupt nucleolar homeostasis.
    Zoe H Davis, Laura Mediani, Francesco Antoniani, Jonathan Vinet, Shuangxi Li, Simon Alberti, Bingwei Lu, Alex S Holehouse, Serena Carra, Onn Brandman.
      Stalled mRNA translation results in the production of incompletely synthesized proteins that are targeted for degradation by ribosome-associated quality control (RQC). Here we investigated the fate of defective proteins translated from stall-inducing, nonstop mRNA that escape ubiquitylation by the RQC protein LTN1. We found that nonstop protein products accumulated in nucleoli and this localization was driven by polylysine tracts produced by translation of the poly(A) tails of nonstop mRNA. Nucleolar sequestration increased the solubility of invading proteins but disrupted nucleoli, altering their dynamics, morphology, and resistance to stress in cell culture and intact flies. Our work elucidates how stalled translation may affect distal cellular processes and may inform studies on the pathology of diseases caused by failures in RQC and characterized by nucleolar stress.
    Keywords:  LTN1; Nonstop mRNA; Nucleolus; Phase separation; Protein quality control; Ribosome-associated quality control (RQC)
    DOI:  https://doi.org/10.1007/s12192-021-01200-w
  16. FEBS Lett. 2021 Feb 22.
    Mitochondrial clearance: mechanisms and roles in cellular fitness.
    Mashun Onishi, Koji Okamoto.
      Mitophagy is one of the selective autophagy pathways that catabolizes dysfunctional or superfluous mitochondria. Under mitophagy-inducing conditions, mitochondria are labeled with specific molecular landmarks that recruit the autophagy machinery to the surface of mitochondria, enclosed into autophagosomes, and delivered to lysosomes (vacuoles in yeast) for degradation. As damaged mitochondria are the major sources of reactive oxygen species, mitophagy is critical for mitochondrial quality control and cellular health. Moreover, appropriate control of mitochondrial quantity via mitophagy is vital for the energy supply-demand balance in cells and whole organisms, cell differentiation, and developmental programs. Thus, it seems conceivable that defects in mitophagy could elicit pleiotropic pathologies such as excess inflammation, tissue injury, neurodegeneration, and ageing. In this review, we will focus on the molecular basis and physiological relevance of mitophagy, and potential of mitophagy as a therapeutic target to overcome such disorders.
    Keywords:  adaptor; ageing; autophagy; inflammation; mitochondria; neurodegeneration; ubiquitin
    DOI:  https://doi.org/10.1002/1873-3468.14060
  17. Sci Adv. 2021 Feb;pii: eabd7974. [Epub ahead of print]7(9):
    Functional antagonism of chromatin modulators regulates epithelial-mesenchymal transition.
    Michela Serresi, Sonia Kertalli, Lifei Li, Matthias Jürgen Schmitt, Yuliia Dramaretska, Jikke Wierikx, Danielle Hulsman, Gaetano Gargiulo.
      Epithelial-mesenchymal transition (EMT) is a developmental process hijacked by cancer cells to modulate proliferation, migration, and stress response. Whereas kinase signaling is believed to be an EMT driver, the molecular mechanisms underlying epithelial-mesenchymal interconversion are incompletely understood. Here, we show that the impact of chromatin regulators on EMT interconversion is broader than that of kinases. By combining pharmacological modulation of EMT, synthetic genetic tracing, and CRISPR interference screens, we uncovered a minority of kinases and several chromatin remodelers, writers, and readers governing homeostatic EMT in lung cancer cells. Loss of ARID1A, DOT1L, BRD2, and ZMYND8 had nondeterministic and sometimes opposite consequences on epithelial-mesenchymal interconversion. Together with RNAPII and AP-1, these antagonistic gatekeepers control chromatin of active enhancers, including pan-cancer-EMT signature genes enabling supraclassification of anatomically diverse tumors. Thus, our data uncover general principles underlying transcriptional control of cancer cell plasticity and offer a platform to systematically explore chromatin regulators in tumor-state-specific therapy.
    DOI:  https://doi.org/10.1126/sciadv.abd7974
  18. Nat Metab. 2021 Feb;3(2): 182-195
    A unique subset of glycolytic tumour-propagating cells drives squamous cell carcinoma.
    Jee-Eun Choi, Carlos Sebastian, Christina M Ferrer, Caroline A Lewis, Moshe Sade-Feldman, Thomas LaSalle, Anna Gonye, Begona G C Lopez, Walid M Abdelmoula, Michael S Regan, Murat Cetinbas, Gloria Pascual, Gregory R Wojtkiewicz, Giorgia G Silveira, Ruben Boon, Kenneth N Ross, Itay Tirosh, Srinivas V Saladi, Leif W Ellisen, Ruslan I Sadreyev, Salvador Aznar Benitah, Nathalie Y R Agar, Nir Hacohen, Raul Mostoslavsky.
      Head and neck squamous cell carcinoma (SCC) remains among the most aggressive human cancers. Tumour progression and aggressiveness in SCC are largely driven by tumour-propagating cells (TPCs). Aerobic glycolysis, also known as the Warburg effect, is a characteristic of many cancers; however, whether this adaptation is functionally important in SCC, and at which stage, remains poorly understood. Here, we show that the NAD+-dependent histone deacetylase sirtuin 6 is a robust tumour suppressor in SCC, acting as a modulator of glycolysis in these tumours. Remarkably, rather than a late adaptation, we find enhanced glycolysis specifically in TPCs. More importantly, using single-cell RNA sequencing of TPCs, we identify a subset of TPCs with higher glycolysis and enhanced pentose phosphate pathway and glutathione metabolism, characteristics that are strongly associated with a better antioxidant response. Together, our studies uncover enhanced glycolysis as a main driver in SCC, and, more importantly, identify a subset of TPCs as the cell of origin for the Warburg effect, defining metabolism as a key feature of intra-tumour heterogeneity.
    DOI:  https://doi.org/10.1038/s42255-021-00350-6
  19. Elife. 2021 Feb 22. pii: e64611. [Epub ahead of print]10
    Dichloroacetate reverses sepsis-induced hepatic metabolic dysfunction.
    Rabina Mainali, Manal Zabalawi, David Long, Nancy Buechler, Ellen Quillen, Chia-Chi Key, Xuewei Zhu, John S Parks, Cristina Furdui, Peter W Stacpoole, Jennifer Martinez, Charles E McCall, Matthew A Quinn.
      Metabolic reprogramming between resistance and tolerance occurs within the immune system in response to sepsis. While metabolic tissues such as the liver are subjected to damage during sepsis, how their metabolic and energy reprogramming ensures survival is unclear. Employing comprehensive metabolomic, lipidomic, and transcriptional profiling in a mouse model of sepsis, we show that hepatocyte lipid metabolism, mitochondrial tricarboxylic acid (TCA) energetics, and redox balance are significantly reprogrammed after cecal ligation and puncture (CLP). We identify increases in TCA cycle metabolites citrate, cis-aconitate, and itaconate with reduced fumarate and triglyceride accumulation in septic hepatocytes. Transcriptomic analysis of liver tissue supports and extends the hepatocyte findings. Strikingly, the administration of the pyruvate dehydrogenase kinase (PDK) inhibitor dichloroacetate reverses dysregulated hepatocyte metabolism and mitochondrial dysfunction. In summary, our data indicate that sepsis promotes hepatic metabolic dysfunction and that targeting the mitochondrial PDC/PDK energy homeostat rebalances transcriptional and metabolic manifestations of sepsis within the liver.
    Keywords:  immunology; inflammation; liver; metabolism; mouse; sepsis; steatosis
    DOI:  https://doi.org/10.7554/eLife.64611
  20. Biol Cell. 2020 Dec 06.
    Specialised endocytic proteins regulate diverse internalisation mechanisms and signalling outputs in physiology and cancer.
    Giovanni Giangreco, Maria Grazia Malabarba, Sara Sigismund.
      Although endocytosis was first described as the process mediating macromolecule or nutrient uptake through the plasma membrane, it is now recognised as a critical component of the cellular infrastructure involved in numerous processes, ranging from receptor signalling, proliferation and migration to polarity and stem cell regulation. To realise these varying roles, endocytosis needs to be finely regulated. Accordingly, multiple endocytic mechanisms exist that require specialised molecular machineries and an array of endocytic adaptor proteins with cell-specific functions. This review provides some examples of specialised functions of endocytic adaptors and other components of the endocytic machinery in different cell physiological processes, and how the alteration of these functions is linked to cancer. In particular, we focus on: (i) cargo selection and endocytic mechanisms linked to different adaptors; (ii) specialised functions in clathrin-mediated versus non-clathrin endocytosis; (iii) differential regulation of endocytic mechanisms by post-translational modification of endocytic proteins; (iv) cell context-dependent expression and function of endocytic proteins. As cases in point, we describe two endocytic protein families, dynamins and epsins. Finally, we discuss how dysregulation of the physiological role of these specialised endocytic proteins is exploited by cancer cells to increase cell proliferation, migration and invasion, leading to anti-apoptotic or pro-metastatic behaviours.
    Keywords:  Cancer; Endocytosis; Exocytosis; Membrane transport; Receptor signalling
    DOI:  https://doi.org/10.1111/boc.202000129
  21. Aging Cell. 2021 Feb 24. e13321
    Age-associated mitochondrial complex I deficiency is linked to increased stem cell proliferation rates in the mouse colon.
    Craig Stamp, Julia C Whitehall, Anna L M Smith, David Houghton, Carla Bradshaw, Elizabeth A Stoll, Alasdair P Blain, Doug M Turnbull, Laura C Greaves.
      One of the hallmarks of aging is an accumulation of cells with defects in oxidative phosphorylation (OXPHOS) due to mutations of mitochondrial DNA (mtDNA). Rapidly dividing tissues maintained by stem cells, such as the colonic epithelium, are particularly susceptible to accumulation of OXPHOS defects over time; however, the effects on the stem cells are unknown. We have crossed a mouse model in which intestinal stem cells are labelled with EGFP (Lgr5-EGFP-IRES-creERT2) with a model of accelerated mtDNA mutagenesis (PolgAmut/mut ) to investigate the effect of OXPHOS dysfunction on colonic stem cell proliferation. We show that a reduction in complex I protein levels is associated with an increased rate of stem cell cycle re-entry. These changes in stem cell homeostasis could have significant implications for age-associated intestinal pathogenesis.
    Keywords:  aging; colon; complex I; mitochondria; stem cells
    DOI:  https://doi.org/10.1111/acel.13321
  22. Nat Commun. 2021 02 23. 12(1): 1248
    Facilitative lysosomal transport of bile acids alleviates ER stress in mouse hematopoietic precursors.
    Avinash K Persaud, Sreenath Nair, Md Fazlur Rahman, Radhika Raj, Brenna Weadick, Debasis Nayak, Craig McElroy, Muruganandan Shanmugam, Sue Knoblaugh, Xiaolin Cheng, Rajgopal Govindarajan.
      Mutations in human equilibrative nucleoside transporter 3 (ENT3) encoded by SLC29A3 results in anemia and erythroid hypoplasia, suggesting that ENT3 may regulate erythropoiesis. Here, we demonstrate that lysosomal ENT3 transport of taurine-conjugated bile acids (TBA) facilitates TBA chemical chaperone function and alleviates endoplasmic reticulum (ER) stress in expanding mouse hematopoietic stem and progenitor cells (HSPCs). Slc29a3-/- HSPCs accumulate less TBA despite elevated levels of TBA in Slc29a3-/- mouse plasma and have elevated basal ER stress, reactive oxygen species (ROS), and radiation-induced apoptosis. Reintroduction of ENT3 allows for increased accumulation of TBA into HSPCs, which results in TBA-mediated alleviation of ER stress and erythroid apoptosis. Transplanting TBA-preconditioned HSPCs expressing ENT3 into Slc29a3-/- mice increase bone marrow repopulation capacity and erythroid pool size and prevent early mortalities. Together, these findings suggest a putative role for a facilitative lysosomal transporter in the bile acid regulation of ER stress in mouse HSPCs which may have implications in erythroid biology, the treatment of anemia observed in ENT3-mutated human genetic disorders, and nucleoside analog drug therapy.
    DOI:  https://doi.org/10.1038/s41467-021-21451-6
  23. Cell Stem Cell. 2021 Feb 18. pii: S1934-5909(21)00051-5. [Epub ahead of print]
    Reconstructing the Lineage Histories and Differentiation Trajectories of Individual Cancer Cells in Myeloproliferative Neoplasms.
    Debra Van Egeren, Javier Escabi, Maximilian Nguyen, Shichen Liu, Christopher R Reilly, Sachin Patel, Baransel Kamaz, Maria Kalyva, Daniel J DeAngelo, Ilene Galinsky, Martha Wadleigh, Eric S Winer, Marlise R Luskin, Richard M Stone, Jacqueline S Garcia, Gabriela S Hobbs, Fernando D Camargo, Franziska Michor, Ann Mullally, Isidro Cortes-Ciriano, Sahand Hormoz.
      Some cancers originate from a single mutation event in a single cell. Blood cancers known as myeloproliferative neoplasms (MPNs) are thought to originate when a driver mutation is acquired by a hematopoietic stem cell (HSC). However, when the mutation first occurs in individuals and how it affects the behavior of HSCs in their native context is not known. Here we quantified the effect of the JAK2-V617F mutation on the self-renewal and differentiation dynamics of HSCs in treatment-naive individuals with MPNs and reconstructed lineage histories of individual HSCs using somatic mutation patterns. We found that JAK2-V617F mutations occurred in a single HSC several decades before MPN diagnosis-at age 9 ± 2 years in a 34-year-old individual and at age 19 ± 3 years in a 63-year-old individual-and found that mutant HSCs have a selective advantage in both individuals. These results highlight the potential of harnessing somatic mutations to reconstruct cancer lineages.
    Keywords:  JAK2; blood cancer; lineage tree; myeloproliferative neoplasm; single cell sequencing; stem cell dynamics
    DOI:  https://doi.org/10.1016/j.stem.2021.02.001
  24. Nature. 2021 Feb 24.
    Sulfur sequestration promotes multicellularity during nutrient limitation.
    Beth Kelly, Gustavo E Carrizo, Joy Edwards-Hicks, David E Sanin, Michal A Stanczak, Chantal Priesnitz, Lea J Flachsmann, Jonathan D Curtis, Gerhard Mittler, Yaarub Musa, Thomas Becker, Joerg M Buescher, Erika L Pearce.
      The behaviour of Dictyostelium discoideum depends on nutrients1. When sufficient food is present these amoebae exist in a unicellular state, but upon starvation they aggregate into a multicellular organism2,3. This biology makes D. discoideum an ideal model for investigating how fundamental metabolism commands cell differentiation and function. Here we show that reactive oxygen species-generated as a consequence of nutrient limitation-lead to the sequestration of cysteine in the antioxidant glutathione. This sequestration limits the use of the sulfur atom of cysteine in processes that contribute to mitochondrial metabolism and cellular proliferation, such as protein translation and the activity of enzymes that contain an iron-sulfur cluster. The regulated sequestration of sulfur maintains D. discoideum in a nonproliferating state that paves the way for multicellular development. This mechanism of signalling through reactive oxygen species highlights oxygen and sulfur as simple signalling molecules that dictate cell fate in an early eukaryote, with implications for responses to nutrient fluctuations in multicellular eukaryotes.
    DOI:  https://doi.org/10.1038/s41586-021-03270-3
  25. Science. 2021 Feb 26. pii: eabb1625. [Epub ahead of print]371(6532):
    Liver homeostasis is maintained by midlobular zone 2 hepatocytes.
    Yonglong Wei, Yunguan G Wang, Yuemeng Jia, Lin Li, Jung Yoon, Shuyuan Zhang, Zixi Wang, Yu Zhang, Min Zhu, Tripti Sharma, Yu-Hsuan Lin, Meng-Hsiung Hsieh, Jeffrey H Albrecht, Phuong T Le, Clifford J Rosen, Tao Wang, Hao Zhu.
      The liver is organized into zones in which hepatocytes express different metabolic enzymes. The cells most responsible for liver repopulation and regeneration remain undefined, because fate mapping has only been performed on a few hepatocyte subsets. Here, 14 murine fate-mapping strains were used to systematically compare distinct subsets of hepatocytes. During homeostasis, cells from both periportal zone 1 and pericentral zone 3 contracted in number, whereas cells from midlobular zone 2 expanded in number. Cells within zone 2, which are sheltered from common injuries, also contributed to regeneration after pericentral and periportal injuries. Repopulation from zone 2 was driven by the insulin-like growth factor binding protein 2-mechanistic target of rapamycin-cyclin D1 (IGFBP2-mTOR-CCND1) axis. Therefore, different regions of the lobule exhibit differences in their contribution to hepatocyte turnover, and zone 2 is an important source of new hepatocytes during homeostasis and regeneration.
    DOI:  https://doi.org/10.1126/science.abb1625
  26. Nutr Cancer. 2021 Feb 25. 1-10
    Body Composition and Response and Outcome of Neoadjuvant Treatment for Pancreatic Cancer.
    Kaizhou Jin, Yuan Tang, Anqi Wang, Zhiqian Hu, Chen Liu, Haiyang Zhou, Xianjun Yu.
      To assess the correlation of body composition with the response and outcome of neoadjuvant treatment (NAT) in patients with pancreatic ductal adenocarcinoma (PDAC). One hundred and nineteen PDAC patients underwent curative resection after NAT. Computed tomography scans of the third lumbar vertebra were used to assess the body composition of these patients before and after NAT. Three distinct wasting phenotypes were identified during NAT, with 51 patients (42.9%) developing muscle and fat wasting (MFW), 17 patients (14.3%) developing fat-only wasting (FW), and 51 patients (42.9%) having no wasting (NW). The response rate was higher in the NW phenotype than in the MFW and FW phenotypes (P = 0.007). In univariate and multivariate analyses, histological grade, sarcopenia before NAT, and MFW during NAT were associated with decreased overall survival (OS). Sarcopenia before NAT and MFW during NAT were associated with decreased disease-free survival (DFS). Body composition was associated with the response and outcome of patients undergoing NAT for PDAC. The response rate was higher in patients having NW during NAT. Sarcopenia before NAT and MFW during NAT were associated with decreased OS and DFS.
    DOI:  https://doi.org/10.1080/01635581.2020.1870704
  27. Nat Commun. 2021 Feb 26. 12(1): 1337
    Comprehensive analysis of single cell ATAC-seq data with SnapATAC.
    Rongxin Fang, Sebastian Preissl, Yang Li, Xiaomeng Hou, Jacinta Lucero, Xinxin Wang, Amir Motamedi, Andrew K Shiau, Xinzhu Zhou, Fangming Xie, Eran A Mukamel, Kai Zhang, Yanxiao Zhang, M Margarita Behrens, Joseph R Ecker, Bing Ren.
      Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volume of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals ~370,000 candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.
    DOI:  https://doi.org/10.1038/s41467-021-21583-9
  28. Cell Mol Life Sci. 2021 Feb 23.
    Links between mitochondrial retrograde response and mitophagy in pathogenic cell signalling.
    Daniela Strobbe, Soumya Sharma, Michelangelo Campanella.
      Preservation of mitochondrial quality is paramount for cellular homeostasis. The integrity of mitochondria is guarded by the balanced interplay between anabolic and catabolic mechanisms. The removal of bio-energetically flawed mitochondria is mediated by the process of mitophagy; the impairment of which leads to the accumulation of defective mitochondria which signal the activation of compensatory mechanisms to the nucleus. This process is known as the mitochondrial retrograde response (MRR) and is enacted by Reactive Oxygen Species (ROS), Calcium (Ca2+), ATP, as well as imbalanced lipid and proteostasis. Central to this mitochondria-to-nucleus signalling are the transcription factors (e.g. the nuclear factor kappa-light-chain-enhancer of activated B cells, NF-κB) which drive the expression of genes to adapt the cell to the compromised homeostasis. An increased degree of cellular proliferation is among the consequences of the MRR and as such, engagement of mitochondrial-nuclear communication is frequently observed in cancer. Mitophagy and the MRR are therefore interlinked processes framed to, respectively, prevent or compensate for mitochondrial defects.In this review, we discuss the available knowledge on the interdependency of these processes and their contribution to cell signalling in cancer.
    Keywords:  Cell signalling and Cancer; Mitochondrial retrograde response; Mitophagy
    DOI:  https://doi.org/10.1007/s00018-021-03770-5
  29. J Cell Sci. 2021 Feb 23. pii: jcs.249276. [Epub ahead of print]
    SEC24A facilitates colocalization and calcium flux between endoplasmic reticulum and mitochondria.
    Tamutenda Chidawanyika, Rajarshi Chakrabarti, Kathryn S Beauchemin, Henry N Higgs, Surachai Supattapone.
      A genome-wide screen recently identified SEC24A as a novel mediator of thapsigargin-induced cell death in HAP1 cells. Here, we determined the cellular mechanism and specificity of SEC24A-mediated cytotoxicity. Measurement of calcium levels using organelle-specific fluorescent indicator dyes showed that calcium efflux from endoplasmic reticulum (ER) and influx into mitochondria were significantly impaired in SEC24A knockout cells. Furthermore, SEC24A knockout cells also showed ∼44% less colocalization of mitochondria and peripheral tubular ER. Knockout of SEC24A, but not its paralogs SEC24B, SEC24C, or SEC24D, rescued HAP1 cells from cell death induced by three different inhibitors of Sarcoplasmic/Endoplasmic Reticulum Ca2+ ATPase (SERCA) but not from cell death induced by a topoisomerase inhibitor. Thapsigargin-treated SEC24A knockout cells showed a ∼2.5-fold increase in autophagic flux and ∼10-fold reduction in apoptosis compared to wild-type cells. Taken together, our findings indicate that SEC24A plays a previously unrecognized role in regulating association and calcium flux between the ER and mitochondria, thereby impacting processes dependent on mitochondrial calcium levels, including autophagy and apoptosis.
    Keywords:  Apoptosis; Autophagy; Calcium; ER stress; Mitochondrial-associated membranes; SEC24A; SERCA; Thapsigargin
    DOI:  https://doi.org/10.1242/jcs.249276
  30. Nat Metab. 2021 Feb;3(2): 274-286
    Gut microbiome pattern reflects healthy ageing and predicts survival in humans.
    Tomasz Wilmanski, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C Earls, Anat Zimmer, Gustavo Glusman, Max Robinson, James T Yurkovich, Deborah M Kado, Jane A Cauley, Joseph Zmuda, Nancy E Lane, Andrew T Magis, Jennifer C Lovejoy, Leroy Hood, Sean M Gibbons, Eric S Orwoll, Nathan D Price.
      The gut microbiome has important effects on human health, yet its importance in human ageing remains unclear. In the present study, we demonstrate that, starting in mid-to-late adulthood, gut microbiomes become increasingly unique to individuals with age. We leverage three independent cohorts comprising over 9,000 individuals and find that compositional uniqueness is strongly associated with microbially produced amino acid derivatives circulating in the bloodstream. In older age (over ~80 years), healthy individuals show continued microbial drift towards a unique compositional state, whereas this drift is absent in less healthy individuals. The identified microbiome pattern of healthy ageing is characterized by a depletion of core genera found across most humans, primarily Bacteroides. Retaining a high Bacteroides dominance into older age, or having a low gut microbiome uniqueness measure, predicts decreased survival in a 4-year follow-up. Our analysis identifies increasing compositional uniqueness of the gut microbiome as a component of healthy ageing, which is characterized by distinct microbial metabolic outputs in the blood.
    DOI:  https://doi.org/10.1038/s42255-021-00348-0
  31. Mol Biol Cell. 2021 Feb 24. mbcE20080533
    Fibronectin fibril alignment is established upon initiation of extracellular matrix assembly.
    Carly M Garrison, Jean E Schwarzbauer.
      The physical structure of the extracellular matrix (ECM) is tissue-specific and fundamental to normal tissue function. Proper alignment of ECM fibers is essential for the function of a variety of tissues. While matrix assembly in general has been intensively investigated, little is known about the mechanisms required for formation of aligned ECM fibrils. We investigated the initiation of fibronectin (FN) matrix assembly using fibroblasts that assemble parallel ECM fibrils and found that matrix assembly sites, where FN fibrillogenesis is initiated, were oriented in parallel at the cell poles. We show that these polarized matrix assembly sites progress into fibrillar adhesions and ultimately into aligned FN fibrils. Cells that assemble an unaligned, meshwork matrix formed matrix assembly sites around the cell periphery but the distribution of matrix assembly sites in these cells could be modulated through micropatterning or mechanical stretch. While an elongated cell shape corresponds with a polarized matrix assembly site distribution, these two features are not absolutely linked since we discovered that transforming growth factor beta (TGF-β1) enhances matrix assembly site polarity and assembly of aligned fibrils independently of cell elongation. We conclude the ultimate orientation of FN fibrils is determined by the alignment and distribution of matrix assembly sites which form during the initial stages of cell-FN interactions.
    DOI:  https://doi.org/10.1091/mbc.E20-08-0533
  32. Mol Cell. 2021 Feb 10. pii: S1097-2765(21)00058-7. [Epub ahead of print]
    DNA hypomethylating agents increase activation and cytolytic activity of CD8+ T cells.
    Helen Loo Yau, Emma Bell, Ilias Ettayebi, Felipe Campos de Almeida, Giselle M Boukhaled, Shu Yi Shen, David Allard, Beatriz Morancho, Sajid A Marhon, Charles A Ishak, Isabela M Gonzaga, Tiago da Silva Medina, Rajat Singhania, Ankur Chakravarthy, Raymond Chen, Parinaz Mehdipour, Sandra Pommey, Christian Klein, Gustavo P Amarante-Mendes, David Roulois, Joaquín Arribas, John Stagg, David G Brooks, Daniel D De Carvalho.
      We demonstrate that DNA hypomethylating agent (HMA) treatment can directly modulate the anti-tumor response and effector function of CD8+ T cells. In vivo HMA treatment promotes CD8+ T cell tumor infiltration and suppresses tumor growth via CD8+ T cell-dependent activity. Ex vivo, HMAs enhance primary human CD8+ T cell activation markers, effector cytokine production, and anti-tumor cytolytic activity. Epigenomic and transcriptomic profiling shows that HMAs vastly regulate T cell activation-related transcriptional networks, culminating with over-activation of NFATc1 short isoforms. Mechanistically, demethylation of an intragenic CpG island immediately downstream to the 3' UTR of the short isoform was associated with antisense transcription and alternative polyadenylation of NFATc1 short isoforms. High-dimensional single-cell mass cytometry analyses reveal a selective effect of HMAs on a subset of human CD8+ T cell subpopulations, increasing both the number and abundance of a granzyme Bhigh, perforinhigh effector subpopulation. Overall, our findings support the use of HMAs as a therapeutic strategy to boost anti-tumor immune response.
    Keywords:  CD8+ T cells; DNA methylation; NFATc1; cytolytic activity; decitabine; epigenetic therapy; granzyme B; killing potential
    DOI:  https://doi.org/10.1016/j.molcel.2021.01.038
  33. Cell. 2021 Feb 25. pii: S0092-8674(21)00169-0. [Epub ahead of print]
    In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer.
    Zeyu Chen, Eri Arai, Omar Khan, Zhen Zhang, Shin Foong Ngiow, Yuan He, Hua Huang, Sasikanth Manne, Zhendong Cao, Amy E Baxter, Zhangying Cai, Elizabeth Freilich, Mohammed A Ali, Josephine R Giles, Jennifer E Wu, Allison R Greenplate, Mohamed A Hakeem, Qingzhou Chen, Makoto Kurachi, Kito Nzingha, Viktoriya Ekshyyan, Divij Mathew, Zhuoyu Wen, Nancy A Speck, Alexis Battle, Shelley L Berger, E John Wherry, Junwei Shi.
      Improving effector activity of antigen-specific T cells is a major goal in cancer immunotherapy. Despite the identification of several effector T cell (TEFF)-driving transcription factors (TFs), the transcriptional coordination of TEFF biology remains poorly understood. We developed an in vivo T cell CRISPR screening platform and identified a key mechanism restraining TEFF biology through the ETS family TF, Fli1. Genetic deletion of Fli1 enhanced TEFF responses without compromising memory or exhaustion precursors. Fli1 restrained TEFF lineage differentiation by binding to cis-regulatory elements of effector-associated genes. Loss of Fli1 increased chromatin accessibility at ETS:RUNX motifs, allowing more efficient Runx3-driven TEFF biology. CD8+ T cells lacking Fli1 provided substantially better protection against multiple infections and tumors. These data indicate that Fli1 safeguards the developing CD8+ T cell transcriptional landscape from excessive ETS:RUNX-driven TEFF cell differentiation. Moreover, genetic deletion of Fli1 improves TEFF differentiation and protective immunity in infections and cancer.
    Keywords:  CD8; CRISPR; Fli1; cancer; chronic infection; effector CD8 T cell; exhausted CD8 T cell; exhaustion; immunotherapy; protective immunity
    DOI:  https://doi.org/10.1016/j.cell.2021.02.019
  34. Clin Cancer Res. 2021 Feb 22. pii: clincanres.CCR-20-3872-A.2020. [Epub ahead of print]
    Cell-type Specific Adaptive Signaling Responses to KRASG12C inhibition.
    Eric B Haura, Hitendra S Solanki, Eric A Welsh, Bin Fang, Victoria Izumi, Lancia N F Darville, Brandon Stone, Ryan Franzese, Sandip Chavan, Fumi Kinose, Denis Imbody, John M Koomen, Uwe Rix.
      PURPOSE: Covalent inhibitors of KRASG12C specifically target tumors driven by this form of mutant KRAS, yet early studies show that bypass signaling drives adaptive resistance. While several combination strategies have been shown to improve efficacy of KRASG12C inhibitors, underlying mechanisms and predictive strategies for patient enrichment are less clear.EXPERIMENTAL DESIGN: We performed mass spectrometry based phosphoproteomics analysis in KRASG12C cell lines after short term treatment with ARS-1620. To understand signaling diversity and cell-type specific markers, we compared proteome and phosphoproteomes of KRASG12C cells. Gene expression patterns of KRASG12C cell lines and lung tumor tissues were examined.
    RESULTS: Our analysis suggests cell-type specific perturbation to ERBB2/3 signaling compensate for repressed ERK and AKT signaling following ARS-1620 treatment in epithelial cell type, and this subtype was also more responsive to co-inhibition of SHP2 and SOS1. Conversely, both high basal and feedback activation of FGFR or AXL signaling was identified in mesenchymal cells. Inhibition of FGFR signaling suppress feedback activation of ERK and mTOR, while AXL inhibition suppress PI3K pathway. In both cell lines and human lung cancer tissues with KRASG12C we observed high basal ERBB2/3 associated with epithelial gene signatures while higher basal FGFR1 and AXL was observed in cells/tumors with mesenchymal gene signatures.
    CONCLUSIONS: Our phosphoproteomic study identified cell-type adaptive responses to KRASG12C inhibitors. Markers and targets associated with ERBB2/3 signaling in epithelial subtype and FGFR1/AXL signaling in mesenchymal subtype should be considered in patient enrichment schemes with KRASG12C inhibitors.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-20-3872
  35. Cancer Res. 2021 Feb 26. pii: canres.1750.2020. [Epub ahead of print]
    The Common Germline TP53-R337H Mutation is Hypomorphic and Confers Incomplete Penetrance and Late Tumor Onset in a Mouse Model.
    John R Jeffers, Emilia M Pinto, Jerold E Rehg, Michael R Clay, Jinling Wang, Geoffrey Neale, Richard J Heath, Guillermina Lozano, Enzo Lalli, Bonald C Figueiredo, Alberto S Pappo, Carlos Rodriguez-Galindo, Wenan Chen, Stanley Pounds, Raul C Ribeiro, Gerard P Zambetti.
      The TP53-R337H founder mutation exists at a high frequency throughout southern Brazil and represents one of the most common germline TP53 mutations reported to date. It was identified in pediatric adrenocortical tumors in families with a low incidence of cancer. The R337H mutation has since been found in association with early-onset breast cancers and Li-Fraumeni syndrome (LFS). To study this variability in tumor susceptibility, we generated a knockin mutant p53 mouse model (R334H). Endogenous murine p53-R334H protein was naturally expressed at high levels in multiple tissues and was functionally compromised in a tissue- and stress-specific manner. Mutant p53-R334H mice developed tumors with long latency and incomplete penetrance, consistent with many human carriers being at a low but elevated risk for cancer. These findings suggest the involvement of additional cooperating genetic alterations when TP53-R337H occurs in the context of LFS, which has important implications for genetic counseling and long-term clinical follow up.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1750
  36. Cell Death Dis. 2021 Feb 24. 12(2): 204
    p53 induces ARTS to promote mitochondrial apoptosis.
    Qian Hao, Jiaxiang Chen, Junming Liao, Yingdan Huang, Yu Gan, Sarit Larisch, Shelya X Zeng, Hua Lu, Xiang Zhou.
      Apoptosis related protein in TGF-β signaling pathway (ARTS) was originally discovered in cells undergoing apoptosis in response to TGF-β, but ARTS also acts downstream of many other apoptotic stimuli. ARTS induces apoptosis by antagonizing the anti-apoptotic proteins XIAP and Bcl-2. Here we identified the pro-apoptotic Sept4/ARTS gene as a p53-responsive target gene. Ectopic p53 and a variety of p53-inducing agents increased both mRNA and protein levels of ARTS, whereas ablation of p53 reduced ARTS expression in response to multiple stress conditions. Also, γ-irradiation induced p53-dependent ARTS expression in mice. Consistently, p53 binds to the responsive DNA element on the ARTS promoter and transcriptionally activated the promoter-driven expression of a luciferase reporter gene. Interestingly, ARTS binds to and sequesters p53 at mitochondria, enhancing the interaction of the latter with Bcl-XL. Ectopic ARTS markedly augments DNA damage stress- or Nutlin-3-triggered apoptosis, while ablation of ARTS preferentially impairs p53-induced apoptosis. Altogether, these findings demonstrate that ARTS collaborates with p53 in mitochondria-engaged apoptosis.
    DOI:  https://doi.org/10.1038/s41419-021-03463-8
  37. Cell Metab. 2021 Feb 17. pii: S1550-4131(21)00057-7. [Epub ahead of print]
    Asparagine couples mitochondrial respiration to ATF4 activity and tumor growth.
    Abigail S Krall, Peter J Mullen, Felicia Surjono, Milica Momcilovic, Ernst W Schmid, Christopher J Halbrook, Apisadaporn Thambundit, Steven D Mittelman, Costas A Lyssiotis, David B Shackelford, Simon R V Knott, Heather R Christofk.
      Mitochondrial respiration is critical for cell proliferation. In addition to producing ATP, respiration generates biosynthetic precursors, such as aspartate, an essential substrate for nucleotide synthesis. Here, we show that in addition to depleting intracellular aspartate, electron transport chain (ETC) inhibition depletes aspartate-derived asparagine, increases ATF4 levels, and impairs mTOR complex I (mTORC1) activity. Exogenous asparagine restores proliferation, ATF4 and mTORC1 activities, and mTORC1-dependent nucleotide synthesis in the context of ETC inhibition, suggesting that asparagine communicates active respiration to ATF4 and mTORC1. Finally, we show that combination of the ETC inhibitor metformin, which limits tumor asparagine synthesis, and either asparaginase or dietary asparagine restriction, which limit tumor asparagine consumption, effectively impairs tumor growth in multiple mouse models of cancer. Because environmental asparagine is sufficient to restore tumor growth in the context of respiration impairment, our findings suggest that asparagine synthesis is a fundamental purpose of tumor mitochondrial respiration, which can be harnessed for therapeutic benefit to cancer patients.
    Keywords:  asparaginase; asparagine; cancer metabolism; cancer treatment; dietary restriction; metformin; respiration
    DOI:  https://doi.org/10.1016/j.cmet.2021.02.001
  38. Nature. 2021 Feb;590(7847): 649-654
    Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
    Diana Mahdessian, Anthony J Cesnik, Christian Gnann, Frida Danielsson, Lovisa Stenström, Muhammad Arif, Cheng Zhang, Trang Le, Fredric Johansson, Rutger Shutten, Anna Bäckström, Ulrika Axelsson, Peter Thul, Nathan H Cho, Oana Carja, Mathias Uhlén, Adil Mardinoglu, Charlotte Stadler, Cecilia Lindskog, Burcu Ayoglu, Manuel D Leonetti, Fredrik Pontén, Devin P Sullivan, Emma Lundberg.
      The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.
    DOI:  https://doi.org/10.1038/s41586-021-03232-9
  39. J Biol Chem. 2021 Feb 19. pii: S0021-9258(21)00218-0. [Epub ahead of print] 100445
    Protein kinase C fusion proteins are paradoxically loss-of-function in cancer.
    An-Angela N Van, Maya T Kunkel, Timothy R Baffi, Gema Lordén, Corina E Antal, Sourav Banerjee, Alexandra C Newton.
      Within the AGC kinase superfamily, gene fusions resulting from chromosomal rearrangements have been most frequently described for protein kinase C (PKC), with gene fragments encoding either the C-terminal catalytic domain or the N-terminal regulatory moiety fused to other genes. Kinase fusions that eliminate regulatory domains are typically gain-of-function and often oncogenic. However, several quality control pathways prevent accumulation of aberrant PKC, suggesting that PKC fusions may paradoxically be loss-of-function. To explore this topic, we used biochemical, cellular, and genome editing approaches to investigate the function of fusions that retain the portion of the gene encoding either the catalytic domain or regulatory domain of PKC. Overexpression studies revealed that PKC catalytic domain fusions were constitutively active but vulnerable to degradation. Genome editing of endogenous genes to generate a cancer-associated PKC fusion resulted in cells with detectable levels of fusion transcript but no detectable protein. Hence, PKC catalytic domain fusions are paradoxically loss-of-function as a result of their instability, preventing appreciable accumulation of protein in cells. Overexpression of a PKC regulatory domain fusion suppressed both basal and agonist-induced endogenous PKC activity, acting in a dominant-negative manner by competing for diacylglycerol. For both catalytic and regulatory domain fusions, the PKC component of the fusion proteins mediated the effects of the full-length fusions on the parameters examined, suggesting that the partner protein is dispensable in these contexts. Taken together, our findings reveal that PKC gene fusions are distinct from oncogenic fusions and present a mechanism by which loss of PKC function occurs in cancer.
    Keywords:  autoinhibition; cancer; catalytic domain; constitutively active; dominant negative; gene fusions; loss-of-function; protein degradation; protein kinase C (PKC); regulatory domain
    DOI:  https://doi.org/10.1016/j.jbc.2021.100445
  40. Cancer Res. 2021 Feb 25. pii: canres.2929.2020. [Epub ahead of print]
    Targeting eIF4A Dependent Translation of KRAS Signaling Molecules.
    Kamini Singh, Jianan Lin, Nicolas Lecomte, Prathibha Mohan, Askan Gokce, Viraj R Sanghvi, Man Jiang, Olivera Grbovic-Huezo, Antonija Burčul, Stefan G Stark, Paul B Romesser, Qing Chang, Jerry P Melchor, Rachel K Beyer, Mark Duggan, Yoshiyuki Fukase, Guangli Yang, Ouathek Ouerfelli, Agnes Viale, Elisa de Stanchina, Andrew W Stamford, Peter T Meinke, Gunnar Rätsch, Steven D Leach, Zhengqing Ouyang, Hans-Guido Wendel.
      Pancreatic adenocarcinoma (PDAC) epitomizes a deadly cancer driven by abnormal KRAS signalling. Here we show that the eIF4A RNA helicase is required for translation of key KRAS signaling molecules and that pharmacological inhibition of eIF4A has single-agent activity against murine and human PDAC models at safe dose levels. EIF4A was uniquely required for the translation of mRNAs with long and highly structured 5'UTRs including those with multiple G-quadruplex (GQ) elements. Computational analyses identified these features in mRNAs encoding KRAS and key downstream molecules. Transcriptome-scale ribosome footprinting accurately identified eIF4A-dependent mRNAs in PDAC including critical KRAS signaling molecules such as PI3K, RALA, RAC2, MET, MYC, and YAP1. These findings contrast with a recent study that relied on an older method, polysome fractionation, and implicated redox-related genes as eIF4A clients. Together, our findings highlight the power of ribosome footprinting in conjunction with deep RNA sequencing in accurately decoding translational control mechanisms and define the therapeutic mechanism of eIF4A inhibitors in PDAC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-2929
  41. Nat Metab. 2021 Feb;3(2): 196-210
    Murine neonatal ketogenesis preserves mitochondrial energetics by preventing protein hyperacetylation.
    Yuichiro Arima, Yoshiko Nakagawa, Toru Takeo, Toshifumi Ishida, Toshihiro Yamada, Shinjiro Hino, Mitsuyoshi Nakao, Sanshiro Hanada, Terumasa Umemoto, Toshio Suda, Tetsushi Sakuma, Takashi Yamamoto, Takehisa Watanabe, Katsuya Nagaoka, Yasuhito Tanaka, Yumiko K Kawamura, Kazuo Tonami, Hiroki Kurihara, Yoshifumi Sato, Kazuya Yamagata, Taishi Nakamura, Satoshi Araki, Eiichiro Yamamoto, Yasuhiro Izumiya, Kenji Sakamoto, Koichi Kaikita, Kenichi Matsushita, Koichi Nishiyama, Naomi Nakagata, Kenichi Tsujita.
      Ketone bodies are generated in the liver and allow for the maintenance of systemic caloric and energy homeostasis during fasting and caloric restriction. It has previously been demonstrated that neonatal ketogenesis is activated independently of starvation. However, the role of ketogenesis during the perinatal period remains unclear. Here, we show that neonatal ketogenesis plays a protective role in mitochondrial function. We generated a mouse model of insufficient ketogenesis by disrupting the rate-limiting hydroxymethylglutaryl-CoA synthase 2 enzyme gene (Hmgcs2). Hmgcs2 knockout (KO) neonates develop microvesicular steatosis within a few days of birth. Electron microscopic analysis and metabolite profiling indicate a restricted energy production capacity and accumulation of acetyl-CoA in Hmgcs2 KO mice. Furthermore, acetylome analysis of Hmgcs2 KO cells revealed enhanced acetylation of mitochondrial proteins. These findings suggest that neonatal ketogenesis protects the energy-producing capacity of mitochondria by preventing the hyperacetylation of mitochondrial proteins.
    DOI:  https://doi.org/10.1038/s42255-021-00342-6
  42. Front Oncol. 2020 ;10 619727
    Pro-Tumoral Functions of Autophagy Receptors in the Modulation of Cancer Progression.
    Cristóbal Cerda-Troncoso, Manuel Varas-Godoy, Patricia V Burgos.
      Cancer progression involves a variety of pro-tumorigenic biological processes including cell proliferation, migration, invasion, and survival. A cellular pathway implicated in these pro-tumorigenic processes is autophagy, a catabolic route used for recycling of cytoplasmic components to generate macromolecular building blocks and energy, under stress conditions, to remove damaged cellular constituents to adapt to changing nutrient conditions and to maintain cellular homeostasis. During autophagy, cells form a double-membrane sequestering a compartment termed the phagophore, which matures into an autophagosome. Following fusion with the lysosome, the cargo is degraded inside the autolysosomes and the resulting macromolecules released back into the cytosol for reuse. Cancer cells use this recycling system during cancer progression, however the key autophagy players involved in this disease is unclear. Accumulative evidences show that autophagy receptors, crucial players for selective autophagy, are overexpressed during cancer progression, yet the mechanisms whereby pro-tumorigenic biological processes are modulated by these receptors remains unknown. In this review, we summarized the most important findings related with the pro-tumorigenic role of autophagy receptors p62/SQSTM1, NBR1, NDP52, and OPTN in cancer progression. In addition, we showed the most relevant cargos degraded by these receptors that have been shown to function as critical regulators of pro-tumorigenic processes. Finally, we discussed the role of autophagy receptors in the context of the cellular pathways implicated in this disease, such as growth factors signaling, oxidative stress response and apoptosis. In summary, we highlight that autophagy receptors should be considered important players of cancer progression, which could offer a niche for the development of novel diagnosis and cancer treatment strategies.
    Keywords:  aggressiveness; autophagy; autophagy receptors; cancer progression; metastasis
    DOI:  https://doi.org/10.3389/fonc.2020.619727
  43. Biochem Soc Trans. 2021 Feb 22. pii: BST20190008. [Epub ahead of print]
    One-carbon metabolism in cancer cells: a critical review based on a core model of central metabolism.
    Jean-Pierre Mazat.
      One-carbon metabolism (1C-metabolism), also called folate metabolism because the carbon group is attached to folate-derived tetrahydrofolate, is crucial in metabolism. It is at the heart of several essential syntheses, particularly those of purine and thymidylate. After a short reminder of the organization of 1C-metabolism, I list its salient features as reported in the literature. Then, using flux balance analysis, a core model of central metabolism and the flux constraints for an 'average cancer cell metabolism', I explore the fundamentals underlying 1C-metabolism and its relationships with the rest of metabolism. Some unreported properties of 1C-metabolism emerge, such as its potential roles in mitochondrial NADH exchange with cytosolic NADPH, participation in NADH recycling, and optimization of cell proliferation.
    Keywords:  average cancer cell; cancer cells’ metabolism; flux balance analysis; metabolic model; one-carbon metabolism
    DOI:  https://doi.org/10.1042/BST20190008
  44. Oxid Med Cell Longev. 2021 ;2021 8832541
    Autophagy Paradox of Cancer: Role, Regulation, and Duality.
    Amit Kumar Verma, Prahalad Singh Bharti, Sahar Rafat, Deepti Bhatt, Yamini Goyal, Kamlesh Kumar Pandey, Sanjeev Ranjan, Saleh A Almatroodi, Mohammed A Alsahli, Arshad Husain Rahmani, Ahmad Almatroudi, Kapil Dev.
      Autophagy, a catabolic process, degrades damaged and defective cellular materials through lysosomes, thus working as a recycling mechanism of the cell. It is an evolutionarily conserved and highly regulated process that plays an important role in maintaining cellular homeostasis. Autophagy is constitutively active at the basal level; however, it gets enhanced to meet cellular needs in various stress conditions. The process involves various autophagy-related genes that ultimately lead to the degradation of targeted cytosolic substrates. Many factors modulate both upstream and downstream autophagy pathways like nutritional status, energy level, growth factors, hypoxic conditions, and localization of p53. Any problem in executing autophagy can lead to various pathological conditions including neurodegeneration, aging, and cancer. In cancer, autophagy plays a contradictory role; it inhibits the formation of tumors, whereas, during advanced stages, autophagy promotes tumor progression. Besides, autophagy protects the tumor from various therapies by providing recycled nutrition and energy to the tumor cells. Autophagy is stimulated by tumor suppressor proteins, whereas it gets inhibited by oncogenes. Due to its dynamic and dual role in the pathogenesis of cancer, autophagy provides promising opportunities in developing novel and effective cancer therapies along with managing chemoresistant cancers. In this article, we summarize different strategies that can modulate autophagy in cancer to overcome the major obstacle, i.e., resistance developed in cancer to anticancer therapies.
    DOI:  https://doi.org/10.1155/2021/8832541
  45. Autophagy. 2021 Feb 25. 1-3
    Neuronal autophagy controls the axonal endoplasmic reticulum to regulate neurotransmission in healthy neurons.
    Marijn Kuijpers, Volker Haucke.
      Neurons are long-lived cells that communicate via release of neurotransmitter at specialized contacts termed synapses. The maintenance of neuronal health and the regulation of synaptic function requires the efficient removal of damaged or dispensable proteins and organelles from synapses. How macroautophagy/autophagy contributes to neuronal and synaptic protein turnover, and what its main physiological substrates are in healthy neurons is largely unknown. We have now shown that loss of neuronal autophagy facilitates presynaptic neurotransmission by controlling the axonal endoplasmic reticulum and, thereby, axonal and synaptic calcium homeostasis.
    Keywords:  Autophagy; SV protein; calcium; endoplasmic reticulum; er-phagy; neurotransmission; reticulophagy; ryanodine receptor; synapse
    DOI:  https://doi.org/10.1080/15548627.2021.1893569
  46. Oncotarget. 2021 Feb 02. 12(3): 145-159
    High mRNA expression of LY6 gene family is associated with overall survival outcome in pancreatic ductal adenocarcinoma.
    Eric Russ, Krithika Bhuvaneshwar, Guisong Wang, Benjamin Jin, Michele M Gage, Subha Madhavan, Yuriy Gusev, Geeta Upadhyay.
      Pancreatic cancer ranks one of the worst in overall survival outcome with a 5 year survival rate being less than 10%. Pancreatic cancer faces unique challenges in its diagnosis and treatment, such as the lack of clinically validated biomarkers and the immensely immunosuppressive tumor microenvironment. Recently, the LY6 gene family has received increasing attention for its multi-faceted roles in cancer development, stem cell maintenance, immunomodulation, and association with more aggressive and hard-to-treat cancers. A detailed study of mRNA expression of LY6 gene family and its association with overall survival (OS) outcome in pancreatic cancers is lacking. We used publicly available clinical datasets to analyze the mRNA expression of a set of LY6 genes and its effect on OS outcome in the context of the tumor microenvironment and immunomodulation. We used web-based tools Kaplan-Meier Plotter, cBioPortal, Oncomine and R-programming to analyze copy number alterations, mRNA expression and its association with OS outcome in pancreatic cancer. These analyses demonstrated that high expression of LY6 genes is associated with OS and disease free survival (DFS) outcome. High expression of LY6 genes and their association with OS outcome is dependent on the composition of tumor microenvironment. Considering that LY6 proteins are anchored to the outer cell membrane or secreted, making them readily accessible, these findings highlight the potential of LY6 family members in the future of pancreatic cancer diagnosis and treatment.
    Keywords:  LY6 genes; immune cells; pancreatic cancer; survival outcome
    DOI:  https://doi.org/10.18632/oncotarget.27880
  47. Dig Dis Sci. 2021 Feb 25.
    Incidence and Risk of Pancreatic Cancer in Patients with a New Diagnosis of Chronic Pancreatitis.
    Satish Munigala, Divya S Subramaniam, Dipti P Subramaniam, Thomas E Burroughs, Darwin L Conwell, Sunil G Sheth.
      BACKGROUND: Chronic pancreatitis (CP) is a risk factor for pancreatic ductal adenocarcinoma (PDAC); nevertheless, the true incidence of PDAC in CP patients in the United States remains unclear.AIMS: We evaluated the risk of developing PDAC two or more years after a new diagnosis of CP.
    METHODS: Retrospective study of veterans from September 1999 to October 2015. A three-year washout period was applied to exclude patients with preexisting CP and PDAC. PDAC risk was evaluated in patients with new-diagnosis CP and compared with controls without CP using Cox-proportional hazards model. CP, PDAC, and other covariates were extracted using ICD-9 codes.
    RESULTS: After exclusions, we identified 7,883,893 patients [new-diagnosis CP - 21,765 (0.28%)]. PDAC was diagnosed in 226 (1.04%) patients in the CP group and 15,858 (0.20%) patients in the control group (p < 0.001). CP patients had a significantly higher PDAC risk compared to controls > 2 years [adjusted hazard ratio (HR) 4.28, 95% confidence interval (CI) 3.74-4.89, p < 0.001], 5 years (adjusted HR 3.32, 95% CI 2.75-4.00, p < 0.001) and 10 years of follow-up (adjusted HR 3.14, 95% CI 1.99-4.93, p < 0.001), respectively. By multivariable analysis, age (odds ratio 1.02, 95% CI 1.00-1.03, p = 0.03), current smoker (odds ratio 1.67, 95% CI 1.02-2.74, p = 0.042), current smoker + alcoholic (odds ratio 2.29, 95% CI 1.41-3.52, p < 0.001), and diabetes (odds ratio 1.51, 95% CI 1.14-1.99, p = 0.004) were the independent risk factors for PDAC.
    CONCLUSION: Our data show that after controlling for etiology of CP and other cofactors, the risk of PDAC increased in CP patients after two years of follow-up, and risk was consistent and sustained beyond 5 years and 10 years of follow-up.
    Keywords:  Chronic pancreatitis; Inflammation; Pancreatic cancer risk; Pancreatic carcinogenesis
    DOI:  https://doi.org/10.1007/s10620-021-06886-7
  48. Dev Cell. 2021 Feb 24. pii: S1534-5807(21)00116-7. [Epub ahead of print]
    FoxA-dependent demethylation of DNA initiates epigenetic memory of cellular identity.
    Yitzhak Reizel, Ashleigh Morgan, Long Gao, Jonathan Schug, Sarmistha Mukherjee, Meilín Fernández García, Greg Donahue, Joseph A Baur, Kenneth S Zaret, Klaus H Kaestner.
      Tissue-specific DNA methylation patterns are created by transcription factors that recruit methylation and demethylation enzymes to cis-regulatory elements. To date, it is not known whether transcription factors are needed to continuously maintain methylation profiles in development and mature tissues or whether they only establish these marks during organ development. We queried the role of the pioneer factor FoxA in generating hypomethylated DNA at liver enhancers. We discovered a set of FoxA-binding sites that undergo regional, FoxA-dependent demethylation during organ development. Conditional ablation of FoxA genes in the adult liver demonstrated that continued FoxA presence was not required to maintain the hypomethylated state, even when massive cell proliferation was induced. This study provides strong evidence for the stable, epigenetic nature of tissue-specific DNA methylation patterns directed by lineage-determining transcription factors during organ development.
    Keywords:  DNA methylation; FoxA; enhancer activity; liver; tissue differentiation
    DOI:  https://doi.org/10.1016/j.devcel.2021.02.005
  49. Cell Physiol Biochem. 2021 Feb 22. 55(S1): 71-88
    Cell Volume Regulation in Immune Cell Function, Activation and Survival.
    Matt Como, Bhavesh Reddy Koppala, Md Nabiul Hasan, Vanessa L Han, Ishika Arora, Dandan Sun.
      The regulation of cell volume is an essential cellular process in nearly every living organism. The importance of volume regulation in immune cells cannot be understated, as it ensures proper cellular function and effective immune response. These cells utilize ion channels and transporters to maintain volume homeostasis through rapid ion transport across the cell membrane. Immune cells express mechanisms controlling regulatory volume decrease (RVD), regulatory volume increase (RVI), proliferative RVD, and apoptotic volume decrease (AVD). In this review, we summarize recent studies examining the importance of several ion channels, particularly potassium and chloride channels in regulating ion transport during osmotic stress, and in immune cell function, activation, proliferation, and death. We also review the key mechanisms functioning in immune cell proliferation and apoptosis. They serve a crucial role in maintaining adequate ionic concentrations, mediating immune cell activation, and generating proliferative pathways. These regulatory mechanisms play key roles in the function and survival of immune cells, as impaired volume regulation contributes to the pathophysiology of various disorders. A complete understanding of immune cell volume regulatory mechanisms may be a starting point for the development of therapeutic agents targeting these ion channels to treat inflammatory diseases.
    Keywords:  Apoptotic volume decrease; Cell volume; Immune cells; Regulatory volume decrease; Regulatory volume increase
    DOI:  https://doi.org/10.33594/000000331
  50. Aging (Albany NY). 2021 Feb 24. 13
    Aging and rejuvenation - a modular epigenome model.
    Priscila Chiavellini, Martina Canatelli-Mallat, Marianne Lehmann, Maria D Gallardo, Claudia B Herenu, Jose L Cordeiro, James Clement, Rodolfo G Goya.
      The view of aging has evolved in parallel with the advances in biomedical sciences. Long considered as an irreversible process where interventions were only aimed at slowing down its progression, breakthrough discoveries like animal cloning and cell reprogramming have deeply changed our understanding of postnatal development, giving rise to the emerging view that the epigenome is the driver of aging. The idea was significantly strengthened by the converging discovery that DNA methylation (DNAm) at specific CpG sites could be used as a highly accurate biomarker of age defined by an algorithm known as the Horvath clock. It was at this point where epigenetic rejuvenation came into play as a strategy to reveal to what extent biological age can be set back by making the clock tick backwards. Initial evidence suggests that when the clock is forced to tick backwards in vivo, it is only able to drag the phenotype to a partially rejuvenated condition. In order to explain the results, a bimodular epigenome is proposed, where module A represents the DNAm clock component and module B the remainder of the epigenome. Epigenetic rejuvenation seems to hold the key to arresting or even reversing organismal aging.
    Keywords:  DNA methylation; aging; cell reprogramming; epigenetic clock; rejuvenation
    DOI:  https://doi.org/10.18632/aging.202712
  51. Aging (Albany NY). 2021 Feb 11. 13(3): 3313-3341
    Ageing transcriptome meta-analysis reveals similarities and differences between key mammalian tissues.
    Daniel Palmer, Fabio Fabris, Aoife Doherty, Alex A Freitas, João Pedro de Magalhães.
      By combining transcriptomic data with other data sources, inferences can be made about functional changes during ageing. Thus, we conducted a meta-analysis on 127 publicly available microarray and RNA-Seq datasets from mice, rats and humans, identifying a transcriptomic signature of ageing across species and tissues. Analyses on subsets of these datasets produced transcriptomic signatures of ageing for brain, heart and muscle. We then applied enrichment analysis and machine learning to functionally describe these signatures, revealing overexpression of immune and stress response genes and underexpression of metabolic and developmental genes. Further analyses revealed little overlap between genes differentially expressed with age in different tissues, despite ageing differentially expressed genes typically being widely expressed across tissues. Additionally we show that the ageing gene expression signatures (particularly the overexpressed signatures) of the whole meta-analysis, brain and muscle tend to include genes that are central in protein-protein interaction networks. We also show that genes underexpressed with age in the brain are highly central in a co-expression network, suggesting that underexpression of these genes may have broad phenotypic consequences. In sum, we show numerous functional similarities between the ageing transcriptomes of these important tissues, along with unique network properties of genes differentially expressed with age in both a protein-protein interaction and co-expression networks.
    Keywords:  Artificial Intelligence; functional genomics; machine learning; microarray; mitochondria
    DOI:  https://doi.org/10.18632/aging.202648
  52. Proc Natl Acad Sci U S A. 2021 Mar 02. pii: e2021795118. [Epub ahead of print]118(9):
    Depletion of H3K36me2 recapitulates epigenomic and phenotypic changes induced by the H3.3K36M oncohistone mutation.
    Kartik N Rajagopalan, Xiao Chen, Daniel N Weinberg, Haifen Chen, Jacek Majewski, C David Allis, Chao Lu.
      Hotspot histone H3 mutations have emerged as drivers of oncogenesis in cancers of multiple lineages. Specifically, H3 lysine 36 to methionine (H3K36M) mutations are recurrently identified in chondroblastomas, undifferentiated sarcomas, and head and neck cancers. While the mutation reduces global levels of both H3K36 dimethylation (H3K36me2) and trimethylation (H3K36me3) by dominantly inhibiting their respective specific methyltransferases, the relative contribution of these methylation states to the chromatin and phenotypic changes associated with H3K36M remains unclear. Here, we specifically deplete H3K36me2 or H3K36me3 in mesenchymal cells, using CRISPR-Cas9 to separately knock out the corresponding methyltransferases NSD1/2 or SETD2. By profiling and comparing the epigenomic and transcriptomic landscapes of these cells with cells expressing the H3.3K36M oncohistone, we find that the loss of H3K36me2 could largely recapitulate H3.3K36M's effect on redistribution of H3K27 trimethylation (H3K27me3) and gene expression. Consistently, knockout of Nsd1/2, but not Setd2, phenocopies the differentiation blockade and hypersensitivity to the DNA-hypomethylating agent induced by H3K36M. Together, our results support a functional divergence between H3K36me2 and H3K36me3 and their nonredundant roles in H3K36M-driven oncogenesis.
    Keywords:  H3K36 methylation; NSD; cancer; chromatin and epigenomics; oncohistone
    DOI:  https://doi.org/10.1073/pnas.2021795118
  53. J Pathol. 2021 Feb 26.
    The foggy world(s) of p63 isoform regulation in normal cells and cancer.
    Zuzana Pokorná, Jan Vysloužil, Václav Hrabal, Bořivoj Vojtěšek, Philip J Coates.
      The p53-family member, p63, exists as two major protein variants (TAp63 and ΔNp63) with distinct expression patterns and functional properties. Whilst downstream target genes of p63 have been studied intensively, how p63 variants are themselves controlled has been relatively neglected. Here, we review advances in understanding ΔNp63 and TAp63 regulation, highlighting their distinct pathways. TAp63 has roles in senescence and metabolism, and in germ cell genome maintenance, where it is activated post-transcriptionally by phosphorylation cascades after DNA damage. The function and regulation of TAp63 in mesenchymal and haematopoietic cells is less clear but may involve epigenetic control through DNA methylation. ΔNp63 functions to maintain stem/progenitor cells in various epithelia and is overexpressed in squamous and certain other cancers. ΔNp63 is transcriptionally regulated through multiple enhancers in concert with chromatin modifying proteins. Many signalling pathways including growth factors, morphogens, inflammation and the extracellular matrix influence ΔNp63 levels, with inconsistent results reported. There is also evidence for reciprocal regulation, including ΔNp63 activating its own transcription. ΔNp63 is downregulated during cell differentiation through transcriptional regulation, while post-transcriptional events cause proteasomal degradation. Throughout the review, we identify knowledge gaps and highlight discordances, providing potential explanations including cell-context and cell-matrix interactions. Identifying individual p63 variants has roles in differential diagnosis and prognosis, and understanding their regulation suggests clinically approved agents for targeting p63 that may be useful combination therapies for selected cancer patients. This article is protected by copyright. All rights reserved.
    Keywords:  HDAC inhibitors; chromatin modification; gene enhancers; p63; squamous cell cancer; stem cells
    DOI:  https://doi.org/10.1002/path.5656
  54. EMBO J. 2021 Feb 22. e106065
    5-Fluorouracil efficacy requires anti-tumor immunity triggered by cancer-cell-intrinsic STING.
    Jingru Tian, Dingyao Zhang, Vadim Kurbatov, Qinrong Wang, Yadong Wang, Dorthy Fang, Lizhen Wu, Marcus Bosenberg, Mandar D Muzumdar, Sajid Khan, Qianjin Lu, Qin Yan, Jun Lu.
      5-Fluorouracil (5-FU) is a widely used chemotherapeutic drug, but the mechanisms underlying 5-FU efficacy in immunocompetent hosts in vivo remain largely elusive. Through modeling 5-FU response of murine colon and melanoma tumors, we report that effective reduction of tumor burden by 5-FU is dependent on anti-tumor immunity triggered by the activation of cancer-cell-intrinsic STING. While the loss of STING does not induce 5-FU resistance in vitro, effective 5-FU responsiveness in vivo requires cancer-cell-intrinsic cGAS, STING, and subsequent type I interferon (IFN) production, as well as IFN-sensing by bone-marrow-derived cells. In the absence of cancer-cell-intrinsic STING, a much higher dose of 5-FU is needed to reduce tumor burden. 5-FU treatment leads to increased intratumoral T cells, and T-cell depletion significantly reduces the efficacy of 5-FU in vivo. In human colorectal specimens, higher STING expression is associated with better survival and responsiveness to chemotherapy. Our results support a model in which 5-FU triggers cancer-cell-initiated anti-tumor immunity to reduce tumor burden, and our findings could be harnessed to improve therapeutic effectiveness and toxicity for colon and other cancers.
    Keywords:  5-FU resistance; Dacarbazine; Ifnb; Mb21d1; Tmem173
    DOI:  https://doi.org/10.15252/embj.2020106065
  55. J Hepatol. 2021 Feb 22. pii: S0168-8278(21)00112-4. [Epub ahead of print]
    TARGETING CELL-INTRINSIC METABOLISM FOR ANTI-FIBROGENIC THERAPY.
    Helene Gilgenkrantz, Ariane Mallat, Richard Moreau, Sophie Lotersztajn.
      In recent years, major advances have been made regarding our understanding on the mechanisms underlying fibrosis progression and regression, and on how coordinated dialog between parenchymal and non-parenchymal cells impacts on the fibrogenic process. Recent studies have highlighted that metabolic reprogramming of parenchymal cells, immune cells (immunometabolism) and hepatic stellate cells is required to support their energy and anabolic demands for acquisition and/or changes in their phenotype and effector functions. In this review, we summarize the current knowledge on how targeting cell-intrinsic metabolic modifications of the main fibrogenic cell actors may impact on fibrosis progression and discuss the anti-fibrogenic potential of metabolically-targeted interventions.
    Keywords:  Fibrosis; autophagy; glucose metabolism; hepatic stellate cells; hepatocytes; immunometabolism; innate-like lymphoid cells; lipid metabolism; macrophages; nuclear receptors
    DOI:  https://doi.org/10.1016/j.jhep.2021.02.012
  56. Front Physiol. 2020 ;11 570170
    Exercise Training as Therapeutic Approach in Cancer Cachexia: A Review of Potential Anti-inflammatory Effect on Muscle Wasting.
    Luana G Leal, Magno A Lopes, Sidney B Peres, Miguel L Batista.
      Cachexia is a multifactorial inflammatory syndrome with high prevalence in cancer patients. It is characterized by a metabolic chaos culminating in drastic reduction in body weight, mainly due to skeletal muscle and fat depletion. Currently, there is not a standard intervention for cachexia, but it is believed that a dynamic approach should be applied early in the course of the disease to maintain or slow the loss of physical function. The present review sought to explain the different clinical and experimental applications of different models of exercise and their contribution to a better prognosis of the disease. Here the advances in knowledge about the application of physical training in experimental models are elucidated, tests that contribute substantially to elucidate the cellular and biochemical mechanisms of exercise in different ways, as well as clinical trials that present not only the impacts of exercise in front cachexia but also the challenges of its application in clinical practice.
    Keywords:  aerobic; muscle atrophy; muscle wasting; neoplasms; resistance; systemic inflammation; therapeutic exercise; tumor
    DOI:  https://doi.org/10.3389/fphys.2020.570170
  57. Trends Cancer. 2021 Feb 19. pii: S2405-8033(21)00022-4. [Epub ahead of print]
    Drivers of Gene Expression Dysregulation in Pancreatic Cancer.
    Swati Venkat, Abdulrahman A Alahmari, Michael E Feigin.
      Pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease with a poor prognosis. The functional consequences of common genetic aberrations and their roles in treatment strategies have been extensively reviewed. In addition to these genomic aberrations, consideration of non-genetic drivers of altered oncogene expression is essential to account for the diversity in PDAC phenotypes. In this review we seek to assess our current understanding of mechanisms of gene expression dysregulation. We focus on four drivers of gene expression dysregulation, including mutations, transcription factors, epigenetic regulators, and RNA stability/isoform regulation, in the context of PDAC pathogenesis. Recent studies provide much-needed insight into the role of gene expression dysregulation in dissecting tumor heterogeneity and stratifying patients for the development of personalized treatment strategies.
    Keywords:  RNA regulation; epigenetics; gene expression; mutations; pancreatic ductal adenocarcinoma (PDAC); transcription factors
    DOI:  https://doi.org/10.1016/j.trecan.2021.01.008
  58. Oncogenesis. 2021 Feb 26. 10(2): 19
    MYB oncoproteins: emerging players and potential therapeutic targets in human cancer.
    Ylenia Cicirò, Arturo Sala.
      MYB transcription factors are highly conserved from plants to vertebrates, indicating that their functions embrace fundamental mechanisms in the biology of cells and organisms. In humans, the MYB gene family is composed of three members: MYB, MYBL1 and MYBL2, encoding the transcription factors MYB, MYBL1, and MYBL2 (also known as c-MYB, A-MYB, and B-MYB), respectively. A truncated version of MYB, the prototype member of the MYB family, was originally identified as the product of the retroviral oncogene v-myb, which causes leukaemia in birds. This led to the hypothesis that aberrant activation of vertebrate MYB could also cause cancer. Despite more than three decades have elapsed since the isolation of v-myb, only recently investigators were able to detect MYB genes rearrangements and mutations, smoking gun evidence of the involvement of MYB family members in human cancer. In this review, we will highlight studies linking the activity of MYB family members to human malignancies and experimental therapeutic interventions tailored for MYB-expressing cancers.
    DOI:  https://doi.org/10.1038/s41389-021-00309-y
  59. Nat Commun. 2021 02 24. 12(1): 1270
    Sialic acids in pancreatic cancer cells drive tumour-associated macrophage differentiation via the Siglec receptors Siglec-7 and Siglec-9.
    Ernesto Rodriguez, Kelly Boelaars, Kari Brown, R J Eveline Li, Laura Kruijssen, Sven C M Bruijns, Thomas van Ee, Sjoerd T T Schetters, Matheus H W Crommentuijn, Joost C van der Horst, Nicole C T van Grieken, Sandra J van Vliet, Geert Kazemier, Elisa Giovannetti, Juan J Garcia-Vallejo, Yvette van Kooyk.
      Changes in glycosylation during tumour progression are a key hallmark of cancer. One of the glycan moieties generally overexpressed in cancer are sialic acids, which can induce immunomodulatory properties via binding to Siglec receptors. We here show that Pancreatic Ductal Adenocarcinoma (PDAC) tumour cells present an increased sialylation that can be recognized by Siglec-7 and Siglec-9 on myeloid cells. We identified the expression of the α2,3 sialyltransferases ST3GAL1 and ST3GAL4 as main contributor to the synthesis of ligands for Siglec-7 and Siglec-9 in tumour cells. Analysing the myeloid composition in PDAC, using single cell and bulk transcriptomics data, we identified monocyte-derived macrophages as contributors to the poor clinical outcome. Tumour-derived sialic acids dictate monocyte to macrophage differentiation via signalling through Siglec-7 and Siglec-9. Moreover, triggering of Siglec-9 in macrophages reduce inflammatory programmes, while increasing PD-L1 and IL-10 expression, illustrating that sialic acids modulate different myeloid cells. This work highlights a critical role for sialylated glycans in controlling immune suppression and provides new potential targets for cancer immunotherapy in PDAC.
    DOI:  https://doi.org/10.1038/s41467-021-21550-4
  60. Oncogene. 2021 Feb 24.
    H2A.Z overexpression suppresses senescence and chemosensitivity in pancreatic ductal adenocarcinoma.
    P A Ávila-López, G Guerrero, H N Nuñez-Martínez, C A Peralta-Alvarez, G Hernández-Montes, L G Álvarez-Hilario, R Herrera-Goepfert, J Albores-Saavedra, N Villegas-Sepúlveda, L Cedillo-Barrón, A E Montes-Gómez, M Vargas, M Schnoor, F Recillas-Targa, R Hernández-Rivas.
      Pancreatic ductal adenocarcinoma (PDAC) is one of the most intractable and devastating malignant tumors. Epigenetic modifications such as DNA methylation and histone modification regulate tumor initiation and progression. However, the contribution of histone variants in PDAC is unknown. Here, we demonstrated that the histone variant H2A.Z is highly expressed in PDAC cell lines and PDAC patients and that its overexpression correlates with poor prognosis. Moreover, all three H2A.Z isoforms (H2A.Z.1, H2A.Z.2.1, and H2A.Z.2.2) are highly expressed in PDAC cell lines and PDAC patients. Knockdown of these H2A.Z isoforms in PDAC cell lines induces a senescent phenotype, cell cycle arrest in phase G2/M, increased expression of cyclin-dependent kinase inhibitor CDKN2A/p16, SA-β-galactosidase activity and interleukin 8 production. Transcriptome analysis of H2A.Z-depleted PDAC cells showed altered gene expression in fatty acid biosynthesis pathways and those that regulate cell cycle and DNA damage repair. Importantly, depletion of H2A.Z isoforms reduces the tumor size in a mouse xenograft model in vivo and sensitizes PDAC cells to gemcitabine. Overexpression of H2A.Z.1 and H2A.Z.2.1 more than H2A.Z.2.2 partially restores the oncogenic phenotype. Therefore, our data suggest that overexpression of H2A.Z isoforms enables cells to overcome the oncoprotective barrier associated with senescence, favoring PDAC tumor grow and chemoresistance. These results make H2A.Z a potential candidate as a diagnostic biomarker and therapeutic target for PDAC.
    DOI:  https://doi.org/10.1038/s41388-021-01664-1
  61. Free Radic Biol Med. 2021 Feb 23. pii: S0891-5849(21)00110-6. [Epub ahead of print]
    PINK1/PARK2 Dependent Mitophagy Effectively Suppresses NLRP3 Inflammasome to Alleviate Acute Pancreatitis.
    Jie Zhang, Weiguo Huang, Qikuan He, Tuo Deng, Boda Wu, Feifei Huang, Jiayang Bi, Yuepeng Jin, Hongwei Sun, Qiyu Zhang, Keqing Shi.
      BACKGROUND: Acute pancreatitis (AP) is a clinically common acute inflammatory disease in digestive system, leading to systemic inflammatory response syndrome (SIRS) and severe acute pancreatitis (SAP). It was reported that PINK1/PARK2 dependent mitophagy played an important role in various inflammatory diseases. However, its role in AP has not been elucidated. Herein, we explore the effect of mitophagy in the pathogenesis of AP.METHODS: Firstly, we established cerulein-induced AP group and arginine-induced SAP group based on wild, PINK1-/- and PARK2-/- mice. Pancreatic samples were harvested for further investing the mitochondrial dynamics, mitophagy alterations, NLRP3 inflammatory pathway etc. Furthermore, peripheral blood mononuclear cells from SAP patients were collected to examine the expression of mitophagy-related indicators. Additionally, the interrelationship between mitophagy and NLRP3 inflammasome was also explored in AP.
    RESULTS: It was confirmed that mitochondria were damaged in both AP and SAP models. The expressions of PINK1, PARK2 and mitochondrial autophagosomes were elevated in wild AP group, which were decreased in SAP group over time. Similarly, the expressions of PINK1 and PAKR2 in peripheral blood mononuclear cells were significantly lower in SAP patients. Besides, in PINK1-/- and PARK2-/- mice AP groups, more pronounced inflammatory infiltration, increased apoptotic and necrotic levels and upregulated NLRP3 inflammasome pathway were detected. After injection with MCC950, NLRP3 inflammasome production was notably reduced in PINK1-/-and PARK2-/-mice, which effectively alleviated the pancreatic damage and inflammatory cell infiltration.
    CONCLUSION: Our study suggested that mitochondrial dysfunction activates PINK1/PARK2-mediated mitophagy in AP, while mitophagy was impaired in SAP. PINK1-/- and PARK2-/- mice were more sensitive to onset of SAP and the deficiency of mitophagy could lead to the formation of NLRP3 inflammasome.
    Keywords:  Acute pancreatitis; Inflammasome; Mitophagy; PARK2; PINK1
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2021.02.019
  62. Elife. 2021 Feb 26. pii: e60916. [Epub ahead of print]10
    DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for Alagille syndrome.
    Simona Hankeova, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, Jakub Laznovsky, Feven Dawit, Josef Jaros, Vítězslav Bryja, Urban Lendahl, Ewa Ellis, Antal Nemeth, Björn Fischler, Edouard Hannezo, Jozef Kaiser, Emma Rachel Andersson.
      Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.
    Keywords:  Alagille syndrome; MicroCT; cholangiopathy; human; mouse; physics of living systems; regenerative medicine; resin; stem cells; vasculature
    DOI:  https://doi.org/10.7554/eLife.60916
  63. Mol Cell. 2021 Feb 17. pii: S1097-2765(21)00087-3. [Epub ahead of print]
    PAF remodels the DREAM complex to bypass cell quiescence and promote lung tumorigenesis.
    Moon Jong Kim, Christopher Cervantes, Youn-Sang Jung, Xiaoshan Zhang, Jie Zhang, Sung Ho Lee, Sohee Jun, Larisa Litovchick, Wenqi Wang, Junjie Chen, Bingliang Fang, Jae-Il Park.
      The DREAM complex orchestrates cell quiescence and the cell cycle. However, how the DREAM complex is deregulated in cancer remains elusive. Here, we report that PAF (PCLAF/KIAA0101) drives cell quiescence exit to promote lung tumorigenesis by remodeling the DREAM complex. PAF is highly expressed in lung adenocarcinoma (LUAD) and is associated with poor prognosis. Importantly, Paf knockout markedly suppressed LUAD development in mouse models. PAF depletion induced LUAD cell quiescence and growth arrest. PAF is required for the global expression of cell-cycle genes controlled by the repressive DREAM complex. Mechanistically, PAF inhibits DREAM complex formation by binding to RBBP4, a core DREAM subunit, leading to transactivation of DREAM target genes. Furthermore, pharmacological mimicking of PAF-depleted transcriptomes inhibited LUAD tumor growth. Our results unveil how the PAF-remodeled DREAM complex bypasses cell quiescence to promote lung tumorigenesis and suggest that the PAF-DREAM axis may be a therapeutic vulnerability in lung cancer.
    Keywords:  Cell Cycle; DREAM complex; KIAA0101; KRAS; PAF; PCLAF; PCNA; RBBP4; cell quiescence; lung cancer
    DOI:  https://doi.org/10.1016/j.molcel.2021.02.001
  64. Nature. 2021 Feb;590(7847): 528
    Collaborations with artists go beyond communicating the science.
      
    Keywords:  Arts; Careers; Communication; Lab life
    DOI:  https://doi.org/10.1038/d41586-021-00469-2
  65. J Natl Cancer Inst. 2021 Feb 22. pii: djab015. [Epub ahead of print]
    Underreporting of symptomatic adverse events in phase I clinical trials.
    Zachary W Veitch, Daniel Shepshelovich, Christina Gallagher, Lisa Wang, Albiruni R Abdul Razak, Anna Spreafico, Philippe L Bedard, Lillian L Siu, Lori Minasian, Aaron R Hansen.
      BACKGROUND: Clinician reporting of symptomatic adverse events (AEs) in phase I trials utilizes the Common Terminology Criteria for Adverse Events (CTCAE). The utility of the patient-reported outcomes (PRO) version of the CTCAE (PRO-CTCAE) in this setting is unknown. This prospective, observational study compared patient- and clinician-reported symptomatic-AEs in phase I patients.METHODS: Phase I study eligible patients at Princess Margaret were surveyed with the PRO-CTCAE full item library (78 symptomatic-AEs) at baseline (BL), mid-cycle 1 (C1) and mid-cycle 2 (C2). Patient and trial characteristics, best response, and survival data were collected. Presence/absence of patient- (PRO-CTCAE) or clinician-reported (CTCAEv4) symptomatic-AEs were compared (kappa) at defined timepoints and overall (BL+C1+C2).
    RESULTS: Of 292 patients approached from 05/2017-01/2019, 265 (90.8%) were consented, with 243 (91.7%) evaluable and 552 PRO-CTCAE surveys (completion rate = 98.7%) included in analyses. Evaluation of overall patient-reported symptomatic-AEs identified 50 PRO-CTCAE and 11 CTCAE items with ≥10% reporting frequency. 19 CTCAE items were reported at ≤ 1% despite matched PRO-CTCAE items with reporting ≥10%. Underreported categories included sexual health, bodily emissions, and cognition. Clinician- relative to patient-reporting frequency (ratio) demonstrated 9 symptomatic-AEs with a ≥ 50-fold lower clinician reporting rate. Overall patient-clinician agreement for individual symptomatic-AEs ranged from poor (kappa = 0.00-0.19) to moderate (kappa = 0.40-0.59) with discordance driven by lack of clinician reporting. Dyspnea (kappa = 0.54) and peripheral neuropathy (kappa = 0.63) at BL, and limb edema (kappa = 0.55) at C2 demonstrated highest patient-clinician agreement.
    CONCLUSION: Poor to moderate patient-clinician agreement for symptomatic-AEs suggests clinician underreporting in phase I trials. Analyses of severity and interference PRO categories are ongoing.
    Keywords:  Clinical trials; PRO-CTCAE; Patient-reported Outcomes; Phase I
    DOI:  https://doi.org/10.1093/jnci/djab015
  66. Biochem J. 2021 Feb 26. 478(4): 765-776
    Whole-body metabolic fate of branched-chain amino acids.
    Megan C Blair, Michael D Neinast, Zoltan Arany.
      Oxidation of branched-chain amino acids (BCAAs) is tightly regulated in mammals. We review here the distribution and regulation of whole-body BCAA oxidation. Phosphorylation and dephosphorylation of the rate-limiting enzyme, branched-chain α-ketoacid dehydrogenase complex directly regulates BCAA oxidation, and various other indirect mechanisms of regulation also exist. Most tissues throughout the body are capable of BCAA oxidation, and the flux of oxidative BCAA disposal in each tissue is influenced by three key factors: 1. tissue-specific preference for BCAA oxidation relative to other fuels, 2. the overall oxidative activity of mitochondria within a tissue, and 3. total tissue mass. Perturbations in BCAA oxidation have been implicated in many disease contexts, underscoring the importance of BCAA homeostasis in overall health.
    Keywords:  branched chain amino acids; isoleucine; leucine; organismal metabolism; valine
    DOI:  https://doi.org/10.1042/BCJ20200686
  67. Elife. 2021 Feb 22. pii: e60220. [Epub ahead of print]10
    Identifying molecular features that are associated with biological function of intrinsically disordered protein regions.
    Taraneh Zarin, Bob Strome, Gang Peng, Iva Pritišanac, Julie Deborah Forman-Kay, Alan M Moses.
      In previous work, we showed that intrinsically disordered regions (IDRs) of proteins contain sequence-distributed molecular features that are conserved over evolution, despite little sequence similarity that can be detected in alignments (Zarin et al. 2019). Here, we aim to use these molecular features to predict specific biological functions for individual IDRs and identify the molecular features within them that are associated with these functions. We find that the predictable functions are diverse. Examining the associated molecular features, we note some that are consistent with previous reports, and identify others that were previously unknown. We experimentally confirm that elevated isoelectric point and hydrophobicity, features that are positively associated with mitochondrial localization, are necessary for mitochondrial targeting function. Remarkably, increasing isoelectric point in a synthetic IDR restores weak mitochondrial targeting. We believe feature analysis represents a new systematic approach to understand how biological functions of IDRs are specified by their protein sequences.
    Keywords:  S. cerevisiae; cell biology; computational biology; systems biology
    DOI:  https://doi.org/10.7554/eLife.60220
  68. Nat Genet. 2021 Feb 25.
    ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis.
    Jeffrey M Granja, M Ryan Corces, Sarah E Pierce, S Tansu Bagdatli, Hani Choudhry, Howard Y Chang, William J Greenleaf.
      The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/ ) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.
    DOI:  https://doi.org/10.1038/s41588-021-00790-6
  69. Semin Oncol. 2021 Feb 11. pii: S0093-7754(21)00005-1. [Epub ahead of print]
    Pancreatic ductal adenocarcinoma in the era of precision medicine.
    Binbin Zheng-Lin, Eileen M O'Reilly.
      The paradigm for treatment of PDAC is shifting from a "one size fits all" of cytotoxic therapy to a precision medicine approach based on specific predictive biomarkers for a subset of patients. As the genomic landscape of pancreatic carcinogenesis has become increasingly defined, several oncogenic alterations have emerged as actionable targets and their use has been validated in novel approaches such as targeting mutated germline DNA damage response genes (BRCA) and mismatch deficiency (dMMR/MSI-H) or blockade of rare somatic oncogenic fusions. Chemotherapy selection based on transcriptomic subtypes and developing stroma- and immune-modulating strategies have yielded encouraging results and may open therapeutic refinement to a broader PDAC population. Notwithstanding, a series of negative late-stage trials over the last year continue to underscore the inherent challenges in the treatment of PDAC. Multifactorial therapy resistance warrants further exploration in PDAC "omics" and tumor-stroma-immune cells crosstalk. Herein, we discuss precision medicine approaches applied to the treatment of PDAC, its current state and future perspective.
    Keywords:  BRCA; KRAS; germline; pancreatic ductal adenocarcinoma; precision medicine; somatic; targeted therapy
    DOI:  https://doi.org/10.1053/j.seminoncol.2021.01.005
  70. JAMA. 2021 Feb 23. 325(8): 713
    Common Weight Loss Surgeries' Benefits Sustained at Year 7.
    Anita Slomski.
      
    DOI:  https://doi.org/10.1001/jama.2021.1257
  71. F1000Res. 2021 ;10 3
    Energy-dependent protein folding: modeling how a protein folding machine may work.
    Harutyun Sahakyan, Karen Nazaryan, Arcady Mushegian, Irina Sorokina.
      Background: Proteins fold robustly and reproducibly in vivo, but many cannot fold in vitro in isolation from cellular components. Despite the remarkable progress that has been achieved by the artificial intelligence approaches in predicting the protein native conformations, the pathways that lead to such conformations, either in vitro or in vivo, remain largely unknown. The slow progress in recapitulating protein folding pathways in silico may be an indication of the fundamental deficiencies in our understanding of folding as it occurs in nature. Here we consider the possibility that protein folding in living cells may not be driven solely by the decrease in Gibbs free energy and propose that protein folding in vivo should be modeled as an active energy-dependent process. The mechanism of action of such a protein folding machine might include direct manipulation of the peptide backbone. Methods: To show the feasibility of a protein folding machine, we conducted molecular dynamics simulations that were augmented by the application of mechanical force to rotate the C-terminal amino acid while simultaneously limiting the N-terminal amino acid movements. Results: Remarkably, the addition of this simple manipulation of peptide backbones to the standard molecular dynamics simulation indeed facilitated the formation of native structures in five diverse alpha-helical peptides. Steric clashes that arise in the peptides due to the forced directional rotation resulted in the behavior of the peptide backbone no longer resembling a freely jointed chain. Conclusions: These simulations show the feasibility of a protein folding machine operating under the conditions when the movements of the polypeptide backbone are restricted by applying external forces and constraints. Further investigation is needed to see whether such an effect may play a role during co-translational protein folding in vivo and how it can be utilized to facilitate folding of proteins in artificial environments.
    Keywords:  Protein folding; chaperone; co-translational protein folding; computer modeling; energy-dependent protein folding; molecular dynamics; nascent peptide rotation; peptide backbone manipulation; protein folding machine; ribosome function
    DOI:  https://doi.org/10.12688/f1000research.28175.1
  72. Cell Death Dis. 2021 Feb 26. 12(2): 215
    The crosstalk between HIFs and mitochondrial dysfunctions in cancer development.
    Xingting Bao, Jinhua Zhang, Guomin Huang, Junfang Yan, Caipeng Xu, Zhihui Dou, Chao Sun, Hong Zhang.
      Mitochondria are essential cellular organelles that are involved in regulating cellular energy, metabolism, survival, and proliferation. To some extent, cancer is a genetic and metabolic disease that is closely associated with mitochondrial dysfunction. Hypoxia-inducible factors (HIFs), which are major molecules that respond to hypoxia, play important roles in cancer development by participating in multiple processes, such as metabolism, proliferation, and angiogenesis. The Warburg phenomenon reflects a pseudo-hypoxic state that activates HIF-1α. In addition, a product of the Warburg effect, lactate, also induces HIF-1α. However, Warburg proposed that aerobic glycolysis occurs due to a defect in mitochondria. Moreover, both HIFs and mitochondrial dysfunction can lead to complex reprogramming of energy metabolism, including reduced mitochondrial oxidative metabolism, increased glucose uptake, and enhanced anaerobic glycolysis. Thus, there may be a connection between HIFs and mitochondrial dysfunction. In this review, we systematically discuss the crosstalk between HIFs and mitochondrial dysfunctions in cancer development. Above all, the stability and activity of HIFs are closely influenced by mitochondrial dysfunction related to tricarboxylic acid cycle, electron transport chain components, mitochondrial respiration, and mitochondrial-related proteins. Furthermore, activation of HIFs can lead to mitochondrial dysfunction by affecting multiple mitochondrial functions, including mitochondrial oxidative capacity, biogenesis, apoptosis, fission, and autophagy. In general, the regulation of tumorigenesis and development by HIFs and mitochondrial dysfunction are part of an extensive and cooperative network.
    DOI:  https://doi.org/10.1038/s41419-021-03505-1
  73. Nat Rev Cancer. 2021 Feb 24.
    Clonal expansion in non-cancer tissues.
    Nobuyuki Kakiuchi, Seishi Ogawa.
      Cancer is a clonal disorder derived from a single ancestor cell and its progenies that are positively selected by acquisition of 'driver mutations'. However, the evolution of positively selected clones does not necessarily imply the presence of cancer. On the contrary, it has become clear that expansion of these clones in phenotypically normal or non-cancer tissues is commonly seen in association with ageing and/or in response to environmental insults and chronic inflammation. Recent studies have reported expansion of clones harbouring mutations in cancer driver genes in the blood, skin, oesophagus, bronchus, liver, endometrium and bladder, where the expansion could be so extensive that tissues undergo remodelling of an almost entire tissue. The presence of common cancer driver mutations in normal tissues suggests a strong link to cancer development, providing an opportunity to understand early carcinogenic processes. Nevertheless, some driver mutations are unique to normal tissues or have a mutation frequency that is much higher in normal tissue than in cancer, indicating that the respective clones may not necessarily be destined for evolution to cancer but even negatively selected for carcinogenesis depending on the mutated gene. Moreover, tissues that are remodelled by genetically altered clones might define functionalities of aged tissues or modified inflammatory processes. In this Review, we provide an overview of major findings on clonal expansion in phenotypically normal or non-cancer tissues and discuss their biological significance not only in cancer development but also in ageing and inflammatory diseases.
    DOI:  https://doi.org/10.1038/s41568-021-00335-3
  74. Cell Chem Biol. 2021 Feb 16. pii: S2451-9456(21)00052-0. [Epub ahead of print]
    Re-defining synthetic lethality by phenotypic profiling for precision oncology.
    Yevhen Akimov, Tero Aittokallio.
      High-throughput functional and genomic screening techniques provide systematic means for phenotypic discovery. Using synthetic lethality (SL) as a paradigm for anticancer drug and target discovery, we describe how these screening technologies may offer new possibilities to identify therapeutically relevant and selective SL interactions by addressing some of the challenges that have made robust discovery of SL candidates difficult. We further introduce an extended concept of SL interaction, in which a simultaneous perturbation of two or more cellular components reduces cell viability more than expected by their individual effects, which we feel is highly befitting for anticancer applications. We also highlight the potential benefits and challenges related to computational quantification of synergistic interactions and cancer selectivity. Finally, we explore how tumoral heterogeneity can be exploited to find phenotype-specific SL interactions for precision oncology using high-throughput functional screening and the exciting opportunities these methods provide for the identification of subclonal SL interactions.
    Keywords:  CRISPR screening; drug combinations; phenotypic screening; precision oncology; synergistic interactions; synthetic lethality
    DOI:  https://doi.org/10.1016/j.chembiol.2021.01.026
  75. FASEB Bioadv. 2021 Feb;3(2): 69-82
    Human-specific polymorphic pseudogenization of SIGLEC12 protects against advanced cancer progression.
    Shoib S Siddiqui, Michael Vaill, Raymond Do, Naazneen Khan, Andrea L Verhagen, Wu Zhang, Heinz-Josef Lenz, Teresa L Johnson-Pais, Robin J Leach, Gary Fraser, Charles Wang, Gen-Sheng Feng, Nissi Varki, Ajit Varki.
      Compared with our closest living evolutionary cousins, humans appear unusually prone to develop carcinomas (cancers arising from epithelia). The SIGLEC12 gene, which encodes the Siglec-XII protein expressed on epithelial cells, has several uniquely human features: a fixed homozygous missense mutation inactivating its natural ligand recognition property; a polymorphic frameshift mutation eliminating full-length protein expression in ~60%-70% of worldwide human populations; and, genomic features suggesting a negative selective sweep favoring the pseudogene state. Despite the loss of canonical sialic acid binding, Siglec-XII still recruits Shp2 and accelerates tumor growth in a mouse model. We hypothesized that dysfunctional Siglec-XII facilitates human carcinoma progression, correlating with known tumorigenic signatures of Shp2-dependent cancers. Immunohistochemistry was used to detect Siglec-XII expression on tissue microarrays. PC-3 prostate cancer cells were transfected with Siglec-XII and transcription of genes enriched with Siglec-XII was determined. Genomic SIGLEC12 status was determined for four different cancer cohorts. Finally, a dot blot analysis of human urinary epithelial cells was established to determine the Siglec-XII expressors versus non-expressors. Forced expression in a SIGLEC12 null carcinoma cell line enriched transcription of genes associated with cancer progression. While Siglec-XII was detected as expected in ~30%-40% of normal epithelia, ~80% of advanced carcinomas showed strong expression. Notably, >80% of late-stage colorectal cancers had a functional SIGLEC12 allele, correlating with overall increased mortality. Thus, advanced carcinomas are much more likely to occur in individuals whose genomes have an intact SIGLEC12 gene, likely because the encoded Siglec-XII protein recruits Shp2-related oncogenic pathways. The finding has prognostic, diagnostic, and therapeutic implications.
    Keywords:  SIGLEC12; advanced carcinoma; dot blot; immunohistochemistry; pseudogenization
    DOI:  https://doi.org/10.1096/fba.2020-00092
  76. Cell Calcium. 2021 Feb 13. pii: S0143-4160(21)00022-1. [Epub ahead of print]95 102368
    Ca2+ as the prime trigger of aerobic glycolysis in astrocytes.
    Anemari Horvat, Marko Muhič, Tina Smolič, Ena Begić, Robert Zorec, Marko Kreft, Nina Vardjan.
      Astroglial aerobic glycolysis, a process during which d-glucose is converted to l-lactate, a brain fuel and signal, is regulated by the plasmalemmal receptors, including adrenergic receptors (ARs) and purinergic receptors (PRs), modulating intracellular Ca2+ and cAMP signals. However, the extent to which the two signals regulate astroglial aerobic glycolysis is poorly understood. By using agonists to stimulate intracellular α1-/β-AR-mediated Ca2+/cAMP signals, β-AR-mediated cAMP and P2R-mediated Ca2+ signals and genetically encoded fluorescence resonance energy transfer-based glucose and lactate nanosensors in combination with real-time microscopy, we show that intracellular Ca2+, but not cAMP, initiates a robust increase in the concentration of intracellular free d-glucose ([glc]i) and l-lactate ([lac]i), both depending on extracellular d-glucose, suggesting Ca2+-triggered glucose uptake and aerobic glycolysis in astrocytes. When the glycogen shunt, a process of glycogen remodelling, was inhibited, the α1-/β-AR-mediated increases in [glc]i and [lac]i were reduced by ∼65 % and ∼30 %, respectively, indicating that at least ∼30 % of the utilization of d-glucose is linked to glycogen remodelling and aerobic glycolysis. Additional activation of β-AR/cAMP signals aided to α1-/β-AR-triggered [lac]i increase, whereas the [glc]i increase was unaltered. Taken together, an increase in intracellular Ca2+ is the prime mechanism of augmented aerobic glycolysis in astrocytes, while cAMP has only a moderate role. The results provide novel information on the signals regulating brain metabolism and open new avenues to explore whether astroglial Ca2+ signals are dysregulated and contribute to neuropathologies with impaired brain metabolism.
    Keywords:  Aerobic glycolysis; Astrocytes; Ca(2+)/cAMP signalling; d-Glucose; l-Lactate
    DOI:  https://doi.org/10.1016/j.ceca.2021.102368
  77. Science. 2021 Feb 25. pii: eabc1855. [Epub ahead of print]
    T cell circuits that sense antigen density with an ultrasensitive threshold.
    Rogelio A Hernandez-Lopez, Wei Yu, Katelyn A Cabral, Olivia A Creasey, Maria Del Pilar Lopez Pazmino, Yurie Tonai, Arsenia De Guzman, Anna Mäkelä, Kalle Saksela, Zev J Gartner, Wendell A Lim.
      Overexpressed tumor associated antigens (e.g., HER2 and epidermal growth factor receptor) are attractive targets for therapeutic T cells, but toxic "off-tumor" cross-reaction with normal tissues expressing low levels of target antigen can occur with Chimeric Antigen Receptor (CAR) T cells. Inspired by natural ultrasensitive response circuits, we engineered a two-step positive feedback circuit that allows T cells to discriminate targets based on a sigmoidal antigen density threshold. In this circuit, a low affinity synthetic Notch receptor for HER2 controls the expression of a high affinity CAR for HER2. Increasing HER2 density thus has cooperative effects on T cells-it both increases CAR expression and activation-leading to a sigmoidal response. T cells with this circuit show sharp discrimination between target cells expressing normal amounts of HER2 and cancer cells expressing 100-fold more HER2, both in vitro and in vivo.
    DOI:  https://doi.org/10.1126/science.abc1855
  78. Nat Metab. 2021 Feb 25.
    POMC neuronal heterogeneity in energy balance and beyond: an integrated view.
    Carmelo Quarta, Marc Claret, Lori M Zeltser, Kevin W Williams, Giles S H Yeo, Matthias H Tschöp, Sabrina Diano, Jens C Brüning, Daniela Cota.
      Hypothalamic AgRP and POMC neurons are conventionally viewed as the yin and yang of the body's energy status, since they act in an opposite manner to modulate appetite and systemic energy metabolism. However, although AgRP neurons' functions are comparatively well understood, a unifying theory of how POMC neuronal cells operate has remained elusive, probably due to their high level of heterogeneity, which suggests that their physiological roles might be more complex than initially thought. In this Perspective, we propose a conceptual framework that integrates POMC neuronal heterogeneity with appetite regulation, whole-body metabolic physiology and the development of obesity. We highlight emerging evidence indicating that POMC neurons respond to distinct combinations of interoceptive signals and food-related cues to fine-tune divergent metabolic pathways and behaviours necessary for survival. The new framework we propose reflects the high degree of developmental plasticity of this neuronal population and may enable progress towards understanding of both the aetiology and treatment of metabolic disorders.
    DOI:  https://doi.org/10.1038/s42255-021-00345-3
  79. J Vis Exp. 2021 Feb 03.
    Discovery of Metastatic Regulators using a Rapid and Quantitative Intravital Chick Chorioallantoic Membrane Model.
    Konstantin Stoletov, Lian Willetts, Perrin H Beatty, John D Lewis.
      Recent advances in cancer research has illustrated the highly complex nature of cancer metastasis. Multiple genes or genes networks have been found to be involved in differentially regulating cancer metastatic cascade genes and gene products dependent on the cancer type, tissue, and individual patient characteristics. These represent potentially important targets for genetic therapeutics and personalized medicine approaches. The development of rapid screening platforms is essential for the identification of these genetic targets. The chick chorioallantoic membrane (CAM) is a highly vascularized, collagen rich membrane located under the eggshell that allows for gas exchange in the developing embryo. Due to the location and vascularization of the CAM, we developed it as an intravital human cancer metastasis model that allows for robust human cancer cell xenografting and real-time imaging of cancer cell interactions with the collagen rich matrix and vasculature. Using this model, a quantitative screening platform was designed for the identification of novel drivers or suppressors of cancer metastasis. We transduced a pool of head and neck HEp3 cancer cells with a complete human genome shRNA gene library, then injected the cells, at low density, into the CAM vasculature. The cells proliferated and formed single-tumor cell colonies. Individual colonies that were unable to invade into the CAM tissue were visible as a compact colony phenotype and excised for identification of the transduced shRNA present in the cells. Images of individual colonies were evaluated for their invasiveness. Multiple rounds of selections were performed to decreases the rate of false positives. Individual, isolated cancer cell clones or newly engineered clones that express genes of interest were subjected to primary tumor formation assay or cancer cell vasculature co-option analysis. In summary we present a rapid screening platform that allows for anti-metastatic target identification and intravital analysis of a dynamic and complex cascade of events.
    DOI:  https://doi.org/10.3791/62077
  80. Genomics Proteomics Bioinformatics. 2021 Feb 18. pii: S1672-0229(21)00022-X. [Epub ahead of print]
    Computational Screening of Biological Phase-separating Proteins.
    Boyan Shen, Zhaoming Chen, Chunyu Yu, Taoyu Chen, Minglei Shi, Tingting Li.
      Phase separation is an important mechanism that mediates the compartmentalization of proteins in cells. Proteins that can undergo phase separation in cells share certain typical sequence features, like intrinsically disordered regions (IDRs) and multiple modular domains. Sequence-based analysis tools are commonly used in the screening of these proteins. However, current phase separation predictors are mostly designed for IDR-containing proteins, thus inevitably overlook the phase-separating proteins with relatively low IDR content. Features other than amino acid sequence could provide crucial information for identifying possible phase-separating proteins: protein-protein interaction (PPI) networks imply multivalent interactions that underlines phase separation process; post-translational modifications (PTMs) are crucial in the regulation of phase separation behavior; spherical structures appearing on immunofluorescence (IF) images indicate condensed droplets formed by phase-separating proteins, distinguishing these proteins from non-phase-separating proteins. Here, we summarized the sequence-based tools for predicting phase-separating proteins and highlighted the importance of incorporating PPIs, PTMs, and IF images into phase separation prediction in future studies.
    Keywords:  Immunofluorescence images; Phase separation; Prediction; Protein post-translational modifications; Protein–protein interaction
    DOI:  https://doi.org/10.1016/j.gpb.2020.11.003
  81. Nat Rev Neurol. 2021 Feb 23.
    Applying genomic and transcriptomic advances to mitochondrial medicine.
    William L Macken, Jana Vandrovcova, Michael G Hanna, Robert D S Pitceathly.
      Next-generation sequencing (NGS) has increased our understanding of the molecular basis of many primary mitochondrial diseases (PMDs). Despite this progress, many patients with suspected PMD remain without a genetic diagnosis, which restricts their access to in-depth genetic counselling, reproductive options and clinical trials, in addition to hampering efforts to understand the underlying disease mechanisms. Although they represent a considerable improvement over their predecessors, current methods for sequencing the mitochondrial and nuclear genomes have important limitations, and molecular diagnostic techniques are often manual and time consuming. However, recent advances in genomics and transcriptomics offer realistic solutions to these challenges. In this Review, we discuss the current genetic testing approach for PMDs and the opportunities that exist for increased use of whole-genome NGS of nuclear and mitochondrial DNA (mtDNA) in the clinical environment. We consider the possible role for long-read approaches in sequencing of mtDNA and in the identification of novel nuclear genomic causes of PMDs. We examine the expanding applications of RNA sequencing, including the detection of cryptic variants that affect splicing and gene expression and the interpretation of rare and novel mitochondrial transfer RNA variants.
    DOI:  https://doi.org/10.1038/s41582-021-00455-2
  82. Oxid Med Cell Longev. 2021 ;2021 8811935
    Autophagy in Acute Pancreatitis: Organelle Interaction and microRNA Regulation.
    Xiaohui Yuan, Jun Wu, Xin Guo, Wei Li, Chen Luo, Shuai Li, Bing Wang, Lijun Tang, Hongyu Sun.
      Acute pancreatitis (AP) is a common disorder with significant hospital admission and mortality. Due to the unclarified pathological mechanism, there is still no effective and specific treatment for AP. Recently, autophagy has been found to be closely related with occurrence and development of AP, which is crucial in determining its severity and outcomes. Emerging evidence indicates that autophagy can be regulated and influenced by microRNAs and organelles, including mitochondria, endoplasmic reticulum and lysosome, through various ways in AP. Of note, the complex interplays and close relationships among autophagy, microRNA and organelles in AP are vital for figuring out pathogenesis but not clear yet. Thus, this review summarizes the role of autophagy in the pathological mechanism of AP, especially the relationship between impaired autophagy and organelles, and discusses the regulatory mechanism of microRNA on autophagy, which could offer new insights into understanding the pathogenesis of AP and developing new potential therapeutic targets against AP.
    DOI:  https://doi.org/10.1155/2021/8811935
  83. Gland Surg. 2021 Jan;10(1): 279-289
    A nomogram of preoperative predictors for occult metastasis in patients with PDAC during laparoscopic exploration.
    Jiachen Ge, Lei Li, Zhaolai Ma, Bin Jiang, Chunhui Yuan, Hangyan Wang, Ying Peng, Dianrong Xiu.
      Background: Surgical resection is the only potentially curative treatment for pancreatic ductal adenocarcinoma (PDAC). However, most of patients lose the chance of surgery due to the unresectable disease at the time of diagnosis. Despite the improvement of radiological imaging, a portion of patients intended for radical resection were proven to be unresectable at surgical exploration due to occult metastasis.Methods: Patients who were aimed to undergo radical pancreatectomy for PDAC from 2010 to 2019 were reviewed retrospectively. All patients included underwent diagnostic laparoscopic exploration. Patients were divided into two groups depending on whether distant metastasis were encountered during exploration. Univariate and multivariate logistic regression analyses were used to identify risk factors for occult metastasis. A nomogram to predict occult metastasis of PDAC on exploration was developed and evaluated.
    Results: A total of 273 patients who underwent diagnostic laparoscopic exploration were included in this study. Nineteen (7.0%) patients were found with distant metastasis during exploration. Multivariate logistic regression analysis showed that ALT>40U/L, CA19-9, CA125 and regional nodes enlargement were independent predictors for occult metastasis. Incorporating these four factors, the nomogram achieved concordance index of 0.799, with a well-fitted calibration curve.
    Conclusions: Occult metastasis is not unusual during surgical exploration in patients with resectable or borderline resectable PDAC. The nomogram could achieve a personal prediction of unexpected distant metastasis on exploration. It may help to sift through patients with PDAC who would benefit from laparoscopic exploration.
    Keywords:  Pancreatic ductal adenocarcinoma (PDAC); laparoscopic exploration; nomogram; occult metastasis; risk factors
    DOI:  https://doi.org/10.21037/gs-20-605
  84. JCO Clin Cancer Inform. 2021 Feb;5 221-230
    OncoTree: A Cancer Classification System for Precision Oncology.
    Ritika Kundra, Hongxin Zhang, Robert Sheridan, Sahussapont Joseph Sirintrapun, Avery Wang, Angelica Ochoa, Manda Wilson, Benjamin Gross, Yichao Sun, Ramyasree Madupuri, Baby A Satravada, Dalicia Reales, Efsevia Vakiani, Hikmat A Al-Ahmadie, Ahmet Dogan, Maria Arcila, Ahmet Zehir, Steven Maron, Michael F Berger, Cristina Viaplana, Katherine Janeway, Matthew Ducar, Lynette Sholl, Snjezana Dogan, Philippe Bedard, Lea F Surrey, Iker Huerga Sanchez, Aijaz Syed, Anoop Balakrishnan Rema, Debyani Chakravarty, Sarah Suehnholz, Moriah Nissan, Gopakumar V Iyer, Rajmohan Murali, Nancy Bouvier, Robert A Soslow, David Hyman, Anas Younes, Andrew Intlekofer, James J Harding, Richard D Carvajal, Paul J Sabbatini, Ghassan K Abou-Alfa, Luc Morris, Yelena Y Janjigian, Meighan M Gallagher, Tara A Soumerai, Ingo K Mellinghoff, Abraham A Hakimi, Matthew Fury, Jason T Huse, Aditya Bagrodia, Meera Hameed, Stacy Thomas, Stuart Gardos, Ethan Cerami, Tali Mazor, Priti Kumari, Pichai Raman, Priyanka Shivdasani, Suzanne MacFarland, Scott Newman, Angela Waanders, Jianjiong Gao, David Solit, Nikolaus Schultz.
      PURPOSE: Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research.METHODS: To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface.
    RESULTS: OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics.
    CONCLUSION: OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.
    DOI:  https://doi.org/10.1200/CCI.20.00108
  85. Trends Cancer. 2021 Feb 23. pii: S2405-8033(21)00040-6. [Epub ahead of print]
    Integrating Quantitative Approaches in Cancer Research and Oncology.
      
    DOI:  https://doi.org/10.1016/j.trecan.2021.01.011
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