bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2020‒08‒30
sixty-seven papers selected by
Kıvanç Görgülü
Technical University of Munich
  1. Beyond the cell factory: Homeostatic regulation of and by the UPRER.
  2. Lumenal Galectin-9-Lamp2 interaction regulates lysosome and autophagy to prevent pathogenesis in the intestine and pancreas.
  3. Epigenetic silencing of the ubiquitin ligase subunit FBXL7 impairs c-SRC degradation and promotes epithelial-to-mesenchymal transition and metastasis.
  4. CRISPR-engineered human brown-like adipocytes prevent diet-induced obesity and ameliorate metabolic syndrome in mice.
  5. Structure and Reconstitution of a MCU-EMRE Mitochondrial Ca2+ Uniporter Complex.
  6. A Specialized Niche in the Pancreatic Microenvironment Promotes Endocrine Differentiation.
  7. α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer.
  8. Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy.
  9. Defining the ATPome reveals cross-optimization of metabolic pathways.
  10. Metabolic excretion associated with nutrient-growth dysregulation promotes the rapid evolution of an overt metabolic defect.
  11. Fructose stimulated de novo lipogenesis is promoted by inflammation.
  12. Use of ratiometrically designed nanocarrier targeting CDK4/6 and autophagy pathways for effective pancreatic cancer treatment.
  13. Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling.
  14. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.
  15. Visualization of human T lymphocyte-mediated eradication of cancer cells in vivo.
  16. Senolytics prevent mt-DNA-induced inflammation and promote the survival of aged organs following transplantation.
  17. Puromycin reactivity does not accurately localize translation at the subcellular level.
  18. Cell-cell adhesion and 3D matrix confinement determine jamming transitions in breast cancer invasion.
  19. Rabgap1 promotes recycling of active β1 integrins to support effective cell migration.
  20. Glis1 facilitates induction of pluripotency via an epigenome-metabolome-epigenome signalling cascade.
  21. Hyperpolarized [1-13C]pyruvate-to-[1-13C]lactate conversion is rate-limited by monocarboxylate transporter-1 in the plasma membrane.
  22. Interplay of the nuclear envelope with chromatin in physiology and pathology.
  23. Sex differences in oncogenic mutational processes.
  24. The Autophagy-RNA Interplay: Degradation and Beyond.
  25. Impact of weight loss and partial weight regain on immune cell and inflammatory markers in adipose tissue in male mice.
  26. InVivo Cancer-Based Functional Genomics.
  27. A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress.
  28. KMT5c modulates adipocyte thermogenesis by regulating Trp53 expression.
  29. Antibody to CD137 activated by extracellular adenosine triphosphate is tumor selective and broadly effective in vivo without systemic immune activation.
  30. β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus.
  31. Immune checkpoint protein VSIG4 as a biomarker of aging in murine adipose tissue.
  32. Cell identity and nucleo-mitochondrial genetic context modulate OXPHOS performance and determine somatic heteroplasmy dynamics.
  33. De novo design of an intercellular signaling toolbox for multi-channel cell-cell communication and biological computation.
  34. Cellular Mechanisms of Conscious Processing.
  35. Lactate modulation of immune responses in inflammatory versus tumour microenvironments.
  36. Zena Werb (1945-2020).
  37. Tumor associated neutrophils promote the metastasis of pancreatic ductal adenocarcinoma.
  38. Autophagy Assays for Biological Discovery and Therapeutic Development.
  39. PARP1 inhibitors trigger innate immunity via PARP1 trapping-induced DNA damage response.
  40. Multivalent Proteins Rapidly and Reversibly Phase-Separate upon Osmotic Cell Volume Change.
  41. Expanding and validating the biomarkers for mitochondrial diseases.
  42. Caveolin-1-mediated sphingolipid oncometabolism underlies a metabolic vulnerability of prostate cancer.
  43. Systemic Inflammatory Biomarkers, Especially Fibrinogen to Albumin Ratio, Predict Prognosis in Patients with Pancreatic Cancer.
  44. Mitochondrial control of cellular protein homeostasis.
  45. Ageing compromises mouse thymus function and remodels epithelial cell differentiation.
  46. ATG16L1 autophagy pathway regulates BAX protein levels and programmed cell death.
  47. Quantitative Data Analysis in Single-Molecule Localization Microscopy.
  48. Fasting-mimicking diet plus chemotherapy in breast cancer treatment.
  49. Caveolin-1 scaffolding domain peptide regulates glucose metabolism in lung fibrosis.
  50. Metabolic rewiring in the promotion of cancer metastasis: mechanisms and therapeutic implications.
  51. Closed mitosis requires local disassembly of the nuclear envelope.
  52. How cholesterol stiffens unsaturated lipid membranes.
  53. 4-Hydroxyacetophenone modulates the actomyosin cytoskeleton to reduce metastasis.
  54. Serum- and glucocorticoid- inducible kinase 2, SGK2, is a novel autophagy regulator and modulates platinum drugs response in cancer cells.
  55. Effects of extracellular matrix viscoelasticity on cellular behaviour.
  56. Regular exercise and branched-chain amino acids prevent ischemic acute kidney injury-related muscle wasting in mice.
  57. Predicting distant metastasis and chemotherapy benefit in locally advanced rectal cancer.
  58. Keratins are asymmetrically inherited fate determinants in the mammalian embryo.
  59. Heterotypic cell-cell communication regulates glandular stem cell multipotency.
  60. The Role of Interleukin-6 and Inflammatory Cytokines in Pancreatic Cancer-Associated Depression.
  61. Early precursor T cells establish and propagate T cell exhaustion in chronic infection.
  62. Wnt activation as a therapeutic strategy in medulloblastoma.
  63. Mitochondrial-induced epigenetic modifications: from biology to clinical translation.
  64. The Roles of Autophagy and Senescence in the Tumor Cell Response to Radiation.
  65. Emerging preclinical evidence does not support broad use of hydroxychloroquine in COVID-19 patients.
  66. Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å.
  67. Whole-transcriptome Analysis of Fully Viable Energy Efficient Glycolytic-null Cancer Cells Established by Double Genetic Knockout of Lactate Dehydrogenase A/B or Glucose-6-Phosphate Isomerase.
  1. Sci Adv. 2020 Jul;6(29): eabb9614
    Beyond the cell factory: Homeostatic regulation of and by the UPRER.
    Melissa G Metcalf, Ryo Higuchi-Sanabria, Gilberto Garcia, C Kimberly Tsui, Andrew Dillin.
      The endoplasmic reticulum (ER) is commonly referred to as the factory of the cell, as it is responsible for a large amount of protein and lipid synthesis. As a membrane-bound organelle, the ER has a distinct environment that is ideal for its functions in synthesizing these primary cellular components. Many different quality control machineries exist to maintain ER stability under the stresses associated with synthesizing, folding, and modifying complex proteins and lipids. The best understood of these mechanisms is the unfolded protein response of the ER (UPRER), in which transmembrane proteins serve as sensors, which trigger a coordinated transcriptional response of genes dedicated for mitigating the stress. As the name suggests, the UPRER is most well described as a functional response to protein misfolding stress. Here, we focus on recent findings and emerging themes in additional roles of the UPRER outside of protein homeostasis, including lipid homeostasis, autophagy, apoptosis, and immunity.
    DOI:  https://doi.org/10.1126/sciadv.abb9614
  2. Nat Commun. 2020 Aug 27. 11(1): 4286
    Lumenal Galectin-9-Lamp2 interaction regulates lysosome and autophagy to prevent pathogenesis in the intestine and pancreas.
    Janaki N Sudhakar, Hsueh-Han Lu, Hung-Yu Chiang, Ching-Shu Suen, Ming-Jing Hwang, Sung-Yu Wu, Chia-Ning Shen, Yao-Ming Chang, Fu-An Li, Fu-Tong Liu, Jr-Wen Shui.
      Intracellular galectins are carbohydrate-binding proteins capable of sensing and repairing damaged lysosomes. As in the physiological conditions glycosylated moieties are mostly in the lysosomal lumen but not cytosol, it is unclear whether galectins reside in lysosomes, bind to glycosylated proteins, and regulate lysosome functions. Here, we show in gut epithelial cells, galectin-9 is enriched in lysosomes and predominantly binds to lysosome-associated membrane protein 2 (Lamp2) in a Asn(N)-glycan dependent manner. At the steady state, galectin-9 binding to glycosylated Asn175 of Lamp2 is essential for functionality of lysosomes and autophagy. Loss of N-glycan-binding capability of galectin-9 causes its complete depletion from lysosomes and defective autophagy, leading to increased endoplasmic reticulum (ER) stress preferentially in autophagy-active Paneth cells and acinar cells. Unresolved ER stress consequently causes cell degeneration or apoptosis that associates with colitis and pancreatic disorders in mice. Therefore, lysosomal galectins maintain homeostatic function of lysosomes to prevent organ pathogenesis.
    DOI:  https://doi.org/10.1038/s41467-020-18102-7
  3. Nat Cell Biol. 2020 Aug 24.
    Epigenetic silencing of the ubiquitin ligase subunit FBXL7 impairs c-SRC degradation and promotes epithelial-to-mesenchymal transition and metastasis.
    Loredana Moro, Daniele Simoneschi, Emma Kurz, Arnaldo A Arbini, Shaowen Jang, Nicoletta Guaragnella, Sergio Giannattasio, Wei Wang, Yu-An Chen, Geoffrey Pires, Andrew Dang, Elizabeth Hernandez, Payal Kapur, Ankita Mishra, Aristotelis Tsirigos, George Miller, Jer-Tsong Hsieh, Michele Pagano.
      Epigenetic plasticity is a pivotal factor that drives metastasis. Here, we show that the promoter of the gene that encodes the ubiquitin ligase subunit FBXL7 is hypermethylated in advanced prostate and pancreatic cancers, correlating with decreased FBXL7 mRNA and protein levels. Low FBXL7 mRNA levels are predictive of poor survival in patients with pancreatic and prostatic cancers. FBXL7 mediates the ubiquitylation and proteasomal degradation of active c-SRC after its phosphorylation at Ser 104. The DNA-demethylating agent decitabine recovers FBXL7 expression and limits epithelial-to-mesenchymal transition and cell invasion in a c-SRC-dependent manner. In vivo, FBXL7-depleted cancer cells form tumours with a high metastatic burden. Silencing of c-SRC or treatment with the c-SRC inhibitor dasatinib together with FBXL7 depletion prevents metastases. Furthermore, decitabine reduces metastases derived from prostate and pancreatic cancer cells in a FBXL7-dependent manner. Collectively, this research implicates FBXL7 as a metastasis-suppressor gene and suggests therapeutic strategies to counteract metastatic dissemination of pancreatic and prostatic cancer cells.
    DOI:  https://doi.org/10.1038/s41556-020-0560-6
  4. Sci Transl Med. 2020 Aug 26. pii: eaaz8664. [Epub ahead of print]12(558):
    CRISPR-engineered human brown-like adipocytes prevent diet-induced obesity and ameliorate metabolic syndrome in mice.
    Chih-Hao Wang, Morten Lundh, Accalia Fu, Rókus Kriszt, Tian Lian Huang, Matthew D Lynes, Luiz O Leiria, Farnaz Shamsi, Justin Darcy, Bennett P Greenwood, Niven R Narain, Vladimir Tolstikov, Kyle L Smith, Brice Emanuelli, Young-Tae Chang, Susan Hagen, Nika N Danial, Michael A Kiebish, Yu-Hua Tseng.
      Brown and brown-like beige/brite adipocytes dissipate energy and have been proposed as therapeutic targets to combat metabolic disorders. However, the therapeutic effects of cell-based therapy in humans remain unclear. Here, we created human brown-like (HUMBLE) cells by engineering human white preadipocytes using CRISPR-Cas9-SAM-gRNA to activate endogenous uncoupling protein 1 expression. Obese mice that received HUMBLE cell transplants showed a sustained improvement in glucose tolerance and insulin sensitivity, as well as increased energy expenditure. Mechanistically, increased arginine/nitric oxide (NO) metabolism in HUMBLE adipocytes promoted the production of NO that was carried by S-nitrosothiols and nitrite in red blood cells to activate endogenous brown fat and improved glucose homeostasis in recipient animals. Together, these data demonstrate the utility of using CRISPR-Cas9 technology to engineer human white adipocytes to display brown fat-like phenotypes and may open up cell-based therapeutic opportunities to combat obesity and diabetes.
    DOI:  https://doi.org/10.1126/scitranslmed.aaz8664
  5. J Mol Biol. 2020 Aug 22. pii: S0022-2836(20)30507-6. [Epub ahead of print]
    Structure and Reconstitution of a MCU-EMRE Mitochondrial Ca2+ Uniporter Complex.
    Chongyuan Wang, Rozbeh Baradaran, Stephen Barstow Long.
      The proteins MCU and EMRE form the minimal functional unit of the mitochondrial calcium uniporter complex in metazoans, a highly selective and tightly controlled Ca2+ channel of the inner mitochondrial membrane that regulates cellular metabolism. Here we present functional reconstitution of an MCU-EMRE complex from the red flour beetle, Tribolium castaneum, and a cryo-EM structure of the complex at 3.5 Å resolution. Using a novel assay, we demonstrate robust Ca2+ uptake into proteoliposomes containing the purified complex. Uptake is dependent on EMRE and also on the mitochondrial lipid cardiolipin. The structure reveals a tetrameric channel with a single ion pore. EMRE is located at the periphery of the transmembrane domain and associates primarily with the first transmembrane helix of MCU. Coiled coil and juxtamembrane domains within the matrix portion of the complex adopt markedly different conformations than in a structure of a human MCU-EMRE complex, suggesting that the structures represent different conformations of these functionally similar metazoan channels.
    Keywords:  Calcium channel; Flux assay; Ion channel; Membrane protein; Reconstitution
    DOI:  https://doi.org/10.1016/j.jmb.2020.08.013
  6. Dev Cell. 2020 Aug 20. pii: S1534-5807(20)30627-4. [Epub ahead of print]
    A Specialized Niche in the Pancreatic Microenvironment Promotes Endocrine Differentiation.
    Corinna Cozzitorto, Laura Mueller, Silvia Ruzittu, Nancy Mah, David Willnow, Jean-Francois Darrigrand, Heather Wilson, Daniel Khosravinia, Amir-Ala Mahmoud, Maurizio Risolino, Licia Selleri, Francesca M Spagnoli.
      The interplay between pancreatic epithelium and the surrounding microenvironment is pivotal for pancreas formation and differentiation as well as adult organ homeostasis. The mesenchyme is the main component of the embryonic pancreatic microenvironment, yet its cellular identity is broadly defined, and whether it comprises functionally distinct cell subsets is not known. Using genetic lineage tracing, transcriptome, and functional studies, we identified mesenchymal populations with different roles during pancreatic development. Moreover, we showed that Pbx transcription factors act within the mouse pancreatic mesenchyme to define a pro-endocrine specialized niche. Pbx directs differentiation of endocrine progenitors into insulin- and glucagon-positive cells through non-cell-autonomous regulation of ECM-integrin interactions and soluble molecules. Next, we measured functional conservation between mouse and human pancreatic mesenchyme by testing identified mesenchymal factors in an iPSC-based differentiation model. Our findings provide insights into how lineage-specific crosstalk between epithelium and neighboring mesenchymal cells underpin the generation of different pancreatic cell types.
    Keywords:  ECM-Integrin; PBX; SLIT; endocrine differentiation; iPSC; lineage tracing; pancreas; pancreatic mesenchyme
    DOI:  https://doi.org/10.1016/j.devcel.2020.08.003
  7. Nat Cancer. 2020 Mar;1(3): 345-358
    α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer.
    Thai Q Tran, Eric A Hanse, Amber N Habowski, Haiqing Li, Mari B Ishak Gabra, Ying Yang, Xazmin H Lowman, Amelia M Ooi, Shu Y Liao, Robert A Edwards, Marian L Waterman, Mei Kong.
      Genetic-driven deregulation of the Wnt pathway is crucial but not sufficient for colorectal cancer (CRC) tumourigenesis. Here, we show that environmental glutamine restriction further augments Wnt signaling in APC mutant intestinal organoids to promote stemness and leads to adenocarcinoma formation in vivo via decreasing intracellular alpha-ketoglutarate (aKG) levels. aKG supplementation is sufficient to rescue low-glutamine induced stemness and Wnt hyperactivation. Mechanistically, we found that aKG promotes hypomethylation of DNA and histone H3K4me3, leading to an upregulation of differentiation-associated genes and downregulation of Wnt target genes, respectively. Using CRC patient-derived organoids and several in vivo CRC tumour models, we show that aKG supplementation suppresses Wnt signaling and promotes cellular differentiation, thereby significantly restricting tumour growth and extending survival. Together, our results reveal how metabolic microenvironment impacts Wnt signaling and identify aKG as a potent antineoplastic metabolite for potential differentiation therapy for CRC patients.
    Keywords:  Wnt signaling; cancer metabolism; colon cancer; epigenetics; glutamine
    DOI:  https://doi.org/10.1038/s43018-020-0035-5
  8. Nat Cell Biol. 2020 Aug 24.
    Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy.
    Yang Gao, Naoe Taira Nihira, Xia Bu, Chen Chu, Jinfang Zhang, Aleksandra Kolodziejczyk, Yizeng Fan, Ngai Ting Chan, Leina Ma, Jing Liu, Dong Wang, Xiaoming Dai, Huadong Liu, Masaya Ono, Akira Nakanishi, Hiroyuki Inuzuka, Brian J North, Yu-Han Huang, Samanta Sharma, Yan Geng, Wei Xu, X Shirley Liu, Lei Li, Yoshio Miki, Piotr Sicinski, Gordon J Freeman, Wenyi Wei.
      Immunotherapies that target programmed cell death protein 1 (PD-1) and its ligand PD-L1 as well as cytotoxic T-lymphocyte-associated protein 4 (CTLA4) have shown impressive clinical outcomes for multiple tumours. However, only a subset of patients achieves durable responses, suggesting that the mechanisms of the immune checkpoint pathways are not completely understood. Here, we report that PD-L1 translocates from the plasma membrane into the nucleus through interactions with components of the endocytosis and nucleocytoplasmic transport pathways, regulated by p300-mediated acetylation and HDAC2-dependent deacetylation of PD-L1. Moreover, PD-L1 deficiency leads to compromised expression of multiple immune-response-related genes. Genetically or pharmacologically modulating PD-L1 acetylation blocks its nuclear translocation, reprograms the expression of immune-response-related genes and, as a consequence, enhances the anti-tumour response to PD-1 blockade. Thus, our results reveal an acetylation-dependent regulation of PD-L1 nuclear localization that governs immune-response gene expression, and thereby advocate targeting PD-L1 translocation to enhance the efficacy of PD-1/PD-L1 blockade.
    DOI:  https://doi.org/10.1038/s41556-020-0562-4
  9. Nat Commun. 2020 Aug 28. 11(1): 4319
    Defining the ATPome reveals cross-optimization of metabolic pathways.
    Neal K Bennett, Mai K Nguyen, Maxwell A Darch, Hiroki J Nakaoka, Derek Cousineau, Johanna Ten Hoeve, Thomas G Graeber, Markus Schuelke, Emin Maltepe, Martin Kampmann, Bryce A Mendelsohn, Jean L Nakamura, Ken Nakamura.
      Disrupted energy metabolism drives cell dysfunction and disease, but approaches to increase or preserve ATP are lacking. To generate a comprehensive metabolic map of genes and pathways that regulate cellular ATP-the ATPome-we conducted a genome-wide CRISPR interference/activation screen integrated with an ATP biosensor. We show that ATP level is modulated by distinct mechanisms that promote energy production or inhibit consumption. In our system HK2 is the greatest ATP consumer, indicating energy failure may not be a general deficiency in producing ATP, but rather failure to recoup the ATP cost of glycolysis and diversion of glucose metabolites to the pentose phosphate pathway. We identify systems-level reciprocal inhibition between the HIF1 pathway and mitochondria; glycolysis-promoting enzymes inhibit respiration even when there is no glycolytic ATP production, and vice versa. Consequently, suppressing alternative metabolism modes paradoxically increases energy levels under substrate restriction. This work reveals mechanisms of metabolic control, and identifies therapeutic targets to correct energy failure.
    DOI:  https://doi.org/10.1038/s41467-020-18084-6
  10. PLoS Biol. 2020 Aug 24. 18(8): e3000757
    Metabolic excretion associated with nutrient-growth dysregulation promotes the rapid evolution of an overt metabolic defect.
    Robin Green, Sonal, Lin Wang, Samuel F M Hart, Wenyun Lu, David Skelding, Justin C Burton, Hanbing Mi, Aric Capel, Hung Alex Chen, Aaron Lin, Arvind R Subramaniam, Joshua D Rabinowitz, Wenying Shou.
      In eukaryotes, conserved mechanisms ensure that cell growth is coordinated with nutrient availability. Overactive growth during nutrient limitation ("nutrient-growth dysregulation") can lead to rapid cell death. Here, we demonstrate that cells can adapt to nutrient-growth dysregulation by evolving major metabolic defects. Specifically, when yeast lysine-auxotrophic mutant lys- encountered lysine limitation, an evolutionarily novel stress, cells suffered nutrient-growth dysregulation. A subpopulation repeatedly evolved to lose the ability to synthesize organosulfurs (lys-orgS-). Organosulfurs, mainly reduced glutathione (GSH) and GSH conjugates, were released by lys- cells during lysine limitation when growth was dysregulated, but not during glucose limitation when growth was regulated. Limiting organosulfurs conferred a frequency-dependent fitness advantage to lys-orgS- by eliciting a proper slow growth program, including autophagy. Thus, nutrient-growth dysregulation is associated with rapid organosulfur release, which enables the selection of organosulfur auxotrophy to better tune cell growth to the metabolic environment. We speculate that evolutionarily novel stresses can trigger atypical release of certain metabolites, setting the stage for the evolution of new ecological interactions.
    DOI:  https://doi.org/10.1371/journal.pbio.3000757
  11. Nat Metab. 2020 Aug 24.
    Fructose stimulated de novo lipogenesis is promoted by inflammation.
    Jelena Todoric, Giuseppe Di Caro, Saskia Reibe, Darren C Henstridge, Courtney R Green, Alison Vrbanac, Fatih Ceteci, Claire Conche, Reginald McNulty, Shabnam Shalapour, Koji Taniguchi, Peter J Meikle, Jeramie D Watrous, Rafael Moranchel, Mahan Najhawan, Mohit Jain, Xiao Liu, Tatiana Kisseleva, Maria T Diaz-Meco, Jorge Moscat, Rob Knight, Florian R Greten, Lester F Lau, Christian M Metallo, Mark A Febbraio, Michael Karin.
      Benign hepatosteatosis, affected by lipid uptake, de novo lipogenesis and fatty acid (FA) oxidation, progresses to non-alcoholic steatohepatitis (NASH) on stress and inflammation. A key macronutrient proposed to increase hepatosteatosis and NASH risk is fructose. Excessive intake of fructose causes intestinal-barrier deterioration and endotoxaemia. However, how fructose triggers these alterations and their roles in hepatosteatosis and NASH pathogenesis remain unknown. Here we show, using mice, that microbiota-derived Toll-like receptor (TLR) agonists promote hepatosteatosis without affecting fructose-1-phosphate (F1P) and cytosolic acetyl-CoA. Activation of mucosal-regenerative gp130 signalling, administration of the YAP-induced matricellular protein CCN1 or expression of the antimicrobial peptide Reg3b (beta) peptide counteract fructose-induced barrier deterioration, which depends on endoplasmic-reticulum stress and subsequent endotoxaemia. Endotoxin engages TLR4 to trigger TNF production by liver macrophages, thereby inducing lipogenic enzymes that convert F1P and acetyl-CoA to FA in both mouse and human hepatocytes.
    DOI:  https://doi.org/10.1038/s42255-020-0261-2
  12. Nat Commun. 2020 Aug 25. 11(1): 4249
    Use of ratiometrically designed nanocarrier targeting CDK4/6 and autophagy pathways for effective pancreatic cancer treatment.
    Ying Ji, Xiangsheng Liu, Juan Li, Xiaodong Xie, Max Huang, Jinhong Jiang, Yu-Pei Liao, Timothy Donahue, Huan Meng.
      Aberrant cell cycle machinery and loss of the CDKN2A tumor suppressor locus make CDK4/6 a potential target in pancreatic ductal adenocarcinoma (PDAC). However, a vast majority of PDAC cases do not harbor a durable response to monotherapy of CDK4/6 inhibitor. Utilizing remote loading to co-encapsulate CDK4/6 inhibitor palbociclib (PAL) and an autophagy inhibitor hydroxychloroquine (HCQ), we demonstrate a ratiometrically designed mesoporous silica nanoformulation with synergistic efficacy in subcutaneous and orthotopic PDAC mouse models. The synergism is attributed to the effective intratumoral buildup of PAL/HCQ, which otherwise exhibit distinctly different circulatory and biodistribution profile. PAL/HCQ co-delivery nanoparticles lead to the most effective shrinkage of PDAC compared to various controls, including free drug mixture. Immunohistochemistry reveals that PAL/HCQ co-delivery nanoparticles trigger anti-apoptotic pathway after repetitive intravenous administrations in mice. When combined with a Bcl inhibitor, the performance of co-delivery nanoparticles is further improved, leading to a long-lasting anti-PDAC effect in vivo.
    DOI:  https://doi.org/10.1038/s41467-020-17996-7
  13. Cell. 2020 Aug 20. pii: S0092-8674(20)30991-0. [Epub ahead of print]
    Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling.
    Jason Z Zhang, Tsan-Wen Lu, Lucas M Stolerman, Brian Tenner, Jessica R Yang, Jin-Fan Zhang, Martin Falcke, Padmini Rangamani, Susan S Taylor, Sohum Mehta, Jin Zhang.
      The fidelity of intracellular signaling hinges on the organization of dynamic activity architectures. Spatial compartmentation was first proposed over 30 years ago to explain how diverse G protein-coupled receptors achieve specificity despite converging on a ubiquitous messenger, cyclic adenosine monophosphate (cAMP). However, the mechanisms responsible for spatially constraining this diffusible messenger remain elusive. Here, we reveal that the type I regulatory subunit of cAMP-dependent protein kinase (PKA), RIα, undergoes liquid-liquid phase separation (LLPS) as a function of cAMP signaling to form biomolecular condensates enriched in cAMP and PKA activity, critical for effective cAMP compartmentation. We further show that a PKA fusion oncoprotein associated with an atypical liver cancer potently blocks RIα LLPS and induces aberrant cAMP signaling. Loss of RIα LLPS in normal cells increases cell proliferation and induces cell transformation. Our work reveals LLPS as a principal organizer of signaling compartments and highlights the pathological consequences of dysregulating this activity architecture.
    Keywords:  DnaJB1-PKA; FLC; FRET; biosensor; fibrolamellar carcinoma; live cell imaging; membraneless organelle; signal transduction; split GFP
    DOI:  https://doi.org/10.1016/j.cell.2020.07.043
  14. Cell. 2020 Aug 18. pii: S0092-8674(20)30938-7. [Epub ahead of print]
    Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.
    Sarah E Johnstone, Alejandro Reyes, Yifeng Qi, Carmen Adriaens, Esmat Hegazi, Karin Pelka, Jonathan H Chen, Luli S Zou, Yotam Drier, Vivian Hecht, Noam Shoresh, Martin K Selig, Caleb A Lareau, Sowmya Iyer, Son C Nguyen, Eric F Joyce, Nir Hacohen, Rafael A Irizarry, Bin Zhang, Martin J Aryee, Bradley E Bernstein.
      Widespread changes to DNA methylation and chromatin are well documented in cancer, but the fate of higher-order chromosomal structure remains obscure. Here we integrated topological maps for colon tumors and normal colons with epigenetic, transcriptional, and imaging data to characterize alterations to chromatin loops, topologically associated domains, and large-scale compartments. We found that spatial partitioning of the open and closed genome compartments is profoundly compromised in tumors. This reorganization is accompanied by compartment-specific hypomethylation and chromatin changes. Additionally, we identify a compartment at the interface between the canonical A and B compartments that is reorganized in tumors. Remarkably, similar shifts were evident in non-malignant cells that have accumulated excess divisions. Our analyses suggest that these topological changes repress stemness and invasion programs while inducing anti-tumor immunity genes and may therefore restrain malignant progression. Our findings call into question the conventional view that tumor-associated epigenomic alterations are primarily oncogenic.
    Keywords:  DNA methylation; chromatin; colon cancer; compartment; epigenetics; genome topology; nuclear architecture
    DOI:  https://doi.org/10.1016/j.cell.2020.07.030
  15. Proc Natl Acad Sci U S A. 2020 Aug 28. pii: 202009092. [Epub ahead of print]
    Visualization of human T lymphocyte-mediated eradication of cancer cells in vivo.
    Xingkang He, Xin Yin, Jing Wu, Stina L Wickström, Yanhong Duo, Qiqiao Du, Shuhang Qin, Shuzhong Yao, Xu Jing, Kayoko Hosaka, Jieyu Wu, Lasse D Jensen, Andreas Lundqvist, Alexander I Salter, Lars Bräutigam, Wei Tao, Yuguo Chen, Rolf Kiessling, Yihai Cao.
      Lymphocyte-based immunotherapy has emerged as a breakthrough in cancer therapy for both hematologic and solid malignancies. In a subpopulation of cancer patients, this powerful therapeutic modality converts malignancy to clinically manageable disease. However, the T cell- and chimeric antigen receptor T (CAR-T) cell-mediated antimetastatic activity, especially their impacts on microscopic metastatic lesions, has not yet been investigated. Here we report a living zebrafish model that allows us to visualize the metastatic cancer cell killing effect by tumor- infiltrating lymphocytes (TILs) and CAR-T cells in vivo at the single-cell level. In a freshly isolated primary human melanoma, specific TILs effectively eliminated metastatic cancer cells in the living body. This potent metastasis-eradicating effect was validated using a human lymphoma model with CAR-T cells. Furthermore, cancer-associated fibroblasts protected metastatic cancer cells from T cell-mediated killing. Our data provide an in vivo platform to validate antimetastatic effects by human T cell-mediated immunotherapy. This unique technology may serve as a precision medicine platform for assessing anticancer effects of cellular immunotherapy in vivo before administration to human cancer patients.
    Keywords:  cancer; cancer therapy; lymphocyte; metastasis; zebrafish
    DOI:  https://doi.org/10.1073/pnas.2009092117
  16. Nat Commun. 2020 Aug 27. 11(1): 4289
    Senolytics prevent mt-DNA-induced inflammation and promote the survival of aged organs following transplantation.
    Jasper Iske, Midas Seyda, Timm Heinbokel, Ryoichi Maenosono, Koichiro Minami, Yeqi Nian, Markus Quante, Christine S Falk, Haruhito Azuma, Friederike Martin, João F Passos, Claus U Niemann, Tamara Tchkonia, James L Kirkland, Abdallah Elkhal, Stefan G Tullius.
      Older organs represent an untapped potential to close the gap between demand and supply in organ transplantation but are associated with age-specific responses to injury and increased immunogenicity, thereby aggravating transplant outcomes. Here we show that cell-free mitochondrial DNA (cf-mt-DNA) released by senescent cells accumulates with aging and augments immunogenicity. Ischemia reperfusion injury induces a systemic increase of cf-mt-DNA that promotes dendritic cell-mediated, age-specific inflammatory responses. Comparable events are observed clinically, with the levels of cf-mt-DNA elevated in older deceased organ donors, and with the isolated cf-mt-DNA capable of activating human dendritic cells. In experimental models, treatment of old donor animals with senolytics clear senescent cells and diminish cf-mt-DNA release, thereby dampening age-specific immune responses and prolonging the survival of old cardiac allografts comparable to young donor organs. Collectively, we identify accumulating cf-mt-DNA as a key factor in inflamm-aging and present senolytics as a potential approach to improve transplant outcomes and availability.
    DOI:  https://doi.org/10.1038/s41467-020-18039-x
  17. Elife. 2020 Aug 26. pii: e60303. [Epub ahead of print]9
    Puromycin reactivity does not accurately localize translation at the subcellular level.
    Syed Usman Enam, Boris Zinshteyn, Daniel H Goldman, Madeline Cassani, Nathan M Livingston, Geraldine Seydoux, Rachel Green.
      Puromycin is a tyrosyl-tRNA mimic that blocks translation by labeling and releasing elongating polypeptide chains from translating ribosomes. Puromycin has been used in molecular biology research for decades as a translation inhibitor. The development of puromycin antibodies and derivatized puromycin analogs has enabled the quantification of active translation in bulk and single-cell assays. More recently, in vivo puromycylation assays have become popular tools for localizing translating ribosomes in cells. These assays often use elongation inhibitors to purportedly inhibit the release of puromycin-labeled nascent peptides from ribosomes. Using in vitro and in vivo experiments in various eukaryotic systems, we demonstrate that, even in the presence of elongation inhibitors, puromycylated peptides are released and diffuse away from ribosomes. Puromycylation assays reveal subcellular sites, such as nuclei, where puromycylated peptides accumulate post-release and which do not necessarily coincide with sites of active translation. Our findings urge caution when interpreting puromycylation assays in vivo.
    Keywords:  C. elegans; biochemistry; cell biology; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.60303
  18. Nat Cell Biol. 2020 Aug 24.
    Cell-cell adhesion and 3D matrix confinement determine jamming transitions in breast cancer invasion.
    Olga Ilina, Pavlo G Gritsenko, Simon Syga, Jürgen Lippoldt, Caterina A M La Porta, Oleksandr Chepizhko, Steffen Grosser, Manon Vullings, Gert-Jan Bakker, Jörn Starruß, Peter Bult, Stefano Zapperi, Josef A Käs, Andreas Deutsch, Peter Friedl.
      Plasticity of cancer invasion and metastasis depends on the ability of cancer cells to switch between collective and single-cell dissemination, controlled by cadherin-mediated cell-cell junctions. In clinical samples, E-cadherin-expressing and -deficient tumours both invade collectively and metastasize equally, implicating additional mechanisms controlling cell-cell cooperation and individualization. Here, using spatially defined organotypic culture, intravital microscopy of mammary tumours in mice and in silico modelling, we identify cell density regulation by three-dimensional tissue boundaries to physically control collective movement irrespective of the composition and stability of cell-cell junctions. Deregulation of adherens junctions by downregulation of E-cadherin and p120-catenin resulted in a transition from coordinated to uncoordinated collective movement along extracellular boundaries, whereas single-cell escape depended on locally free tissue space. These results indicate that cadherins and extracellular matrix confinement cooperate to determine unjamming transitions and stepwise epithelial fluidization towards, ultimately, cell individualization.
    DOI:  https://doi.org/10.1038/s41556-020-0552-6
  19. J Cell Sci. 2020 Aug 25. pii: jcs.243683. [Epub ahead of print]
    Rabgap1 promotes recycling of active β1 integrins to support effective cell migration.
    Anna V Samarelli, Tilman Ziegler, Alexander Meves, Reinhard Fässler, Ralph T Böttcher.
      Integrin function depends on the continuous internalization of integrins and their subsequent endosomal recycling to the plasma membrane to drive adhesion dynamics, cell migration and invasion. Here we assign a pivotal role of Rabgap1 (GapCenA) for the recycling of endocytosed active β1 integrins to the plasma membrane. Rabgap1 binds with its PTB domain to the membrane-proximal NPxY motif in the cytoplasmic domain of β1 integrin subunit on endosomes. Silencing Rabgap1 in mouse fibroblasts leads to the intracellular accumulation of active β1 integrins, alters focal adhesions formation and decreases cell migration and cancer cell invasion. Functionally, Rabgap1 facilitates active β1 integrin recycling to the plasma membrane through attenuation of Rab11 activity. Together our results identify Rabgap1 as important factor for conformation-specific integrin trafficking and define its role for β1 integrin-mediated cell migration in mouse fibroblast and in breast cancer cells.
    Keywords:  Active β1 integrins; Cancer cell invasion; Cell migration; Integrin recycling; Rabgap1
    DOI:  https://doi.org/10.1242/jcs.243683
  20. Nat Metab. 2020 Aug 24.
    Glis1 facilitates induction of pluripotency via an epigenome-metabolome-epigenome signalling cascade.
    Linpeng Li, Keshi Chen, Tianyu Wang, Yi Wu, Guangsuo Xing, Mengqi Chen, Zhihong Hao, Cheng Zhang, Jinye Zhang, Bochao Ma, Zihuang Liu, Hao Yuan, Zijian Liu, Qi Long, Yanshuang Zhou, Juntao Qi, Danyun Zhao, Mi Gao, Duanqing Pei, Jinfu Nie, Dan Ye, Guangjin Pan, Xingguo Liu.
      Somatic cell reprogramming provides insight into basic principles of cell fate determination, which remain poorly understood. Here we show that the transcription factor Glis1 induces multi-level epigenetic and metabolic remodelling in stem cells that facilitates the induction of pluripotency. We find that Glis1 enables reprogramming of senescent cells into pluripotent cells and improves genome stability. During early phases of reprogramming, Glis1 directly binds to and opens chromatin at glycolytic genes, whereas it closes chromatin at somatic genes to upregulate glycolysis. Subsequently, higher glycolytic flux enhances cellular acetyl-CoA and lactate levels, thereby enhancing acetylation (H3K27Ac) and lactylation (H3K18la) at so-called 'second-wave' and pluripotency gene loci, opening them up to facilitate cellular reprogramming. Our work highlights Glis1 as a powerful reprogramming factor, and reveals an epigenome-metabolome-epigenome signalling cascade that involves the glycolysis-driven coordination of histone acetylation and lactylation in the context of cell fate determination.
    DOI:  https://doi.org/10.1038/s42255-020-0267-9
  21. Proc Natl Acad Sci U S A. 2020 Aug 24. pii: 202003537. [Epub ahead of print]
    Hyperpolarized [1-13C]pyruvate-to-[1-13C]lactate conversion is rate-limited by monocarboxylate transporter-1 in the plasma membrane.
    Yi Rao, Seth Gammon, Niki M Zacharias, Tracy Liu, Travis Salzillo, Yuanxin Xi, Jing Wang, Pratip Bhattacharya, David Piwnica-Worms.
      Hyperpolarized [1-13C]pyruvate magnetic resonance spectroscopic imaging (MRSI) is a noninvasive metabolic-imaging modality that probes carbon flux in tissues and infers the state of metabolic reprograming in tumors. Prevailing models attribute elevated hyperpolarized [1-13C]pyruvate-to-[1-13C]lactate conversion rates in aggressive tumors to enhanced glycolytic flux and lactate dehydrogenase A (LDHA) activity (Warburg effect). By contrast, we find by cross-sectional analysis using genetic and pharmacological tools in mechanistic studies applied to well-defined genetically engineered cell lines and tumors that initial hyperpolarized [1-13C]pyruvate-to-[1-13C]lactate conversion rates as well as global conversion were highly dependent on and critically rate-limited by the transmembrane influx of [1-13C]pyruvate mediated predominately by monocarboxylate transporter-1 (MCT1). Specifically, in a cell-encapsulated alginate bead model, induced short hairpin (shRNA) knockdown or overexpression of MCT1 quantitatively inhibited or enhanced, respectively, unidirectional pyruvate influxes and [1-13C]pyruvate-to-[1-13C]lactate conversion rates, independent of glycolysis or LDHA activity. Similarly, in tumor models in vivo, hyperpolarized [1-13C]pyruvate-to-[1-13C]lactate conversion was highly dependent on and critically rate-limited by the induced transmembrane influx of [1-13C]pyruvate mediated by MCT1. Thus, hyperpolarized [1-13C]pyruvate MRSI measures primarily MCT1-mediated [1-13C]pyruvate transmembrane influx in vivo, not glycolytic flux or LDHA activity, driving a reinterpretation of this maturing new technology during clinical translation. Indeed, Kaplan-Meier survival analysis for patients with pancreatic, renal, lung, and cervical cancers showed that high-level expression of MCT1 correlated with poor overall survival, and only in selected tumors, coincident with LDHA expression. Thus, hyperpolarized [1-13C]pyruvate MRSI provides a noninvasive functional assessment primarily of MCT1 as a clinical biomarker in relevant patient populations.
    Keywords:  MCT1; [1-13C]pyruvate; hyperpolarized NMR; imaging biomarker; monocarboxylate transporters
    DOI:  https://doi.org/10.1073/pnas.2003537117
  22. Nucleus. 2020 Dec;11(1): 205-218
    Interplay of the nuclear envelope with chromatin in physiology and pathology.
    Romina Burla, Mattia La Torre, Klizia Maccaroni, Fiammetta Verni, Simona Giunta, Isabella Saggio.
      The nuclear envelope compartmentalizes chromatin in eukaryotic cells. The main nuclear envelope components are lamins that associate with a panoply of factors, including the LEM domain proteins. The nuclear envelope of mammalian cells opens up during cell division. It is reassembled and associated with chromatin at the end of mitosis when telomeres tether to the nuclear periphery. Lamins, LEM domain proteins, and DNA binding factors, as BAF, contribute to the reorganization of chromatin. In this context, an emerging role is that of the ESCRT complex, a machinery operating in multiple membrane assembly pathways, including nuclear envelope reformation. Research in this area is unraveling how, mechanistically, ESCRTs link to nuclear envelope associated factors as LEM domain proteins. Importantly, ESCRTs work also during interphase for repairing nuclear envelope ruptures. Altogether the advances in this field are giving new clues for the interpretation of diseases implicating nuclear envelope fragility, as laminopathies and cancer.ABBREVIATIONS: na, not analyzed; ko, knockout; kd, knockdown; NE, nuclear envelope; LEM, LAP2-emerin-MAN1 (LEM)-domain containing proteins; LINC, linker of nucleoskeleton and cytoskeleton complexes; Cyt, cytoplasm; Chr, chromatin; MB, midbody; End, endosomes; Tel, telomeres; INM, inner nuclear membrane; NP, nucleoplasm; NPC, Nuclear Pore Complex; ER, Endoplasmic Reticulum; SPB, spindle pole body.
    Keywords:  Chromatin; ESCRT; cancer; genome rearrangements; midbody; nuclear envelope; telomeres
    DOI:  https://doi.org/10.1080/19491034.2020.1806661
  23. Nat Commun. 2020 Aug 28. 11(1): 4330
    Sex differences in oncogenic mutational processes.
    Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, , Paul C Boutros, .
      Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
    DOI:  https://doi.org/10.1038/s41467-020-17359-2
  24. Trends Biochem Sci. 2020 Aug 19. pii: S0968-0004(20)30192-4. [Epub ahead of print]
    The Autophagy-RNA Interplay: Degradation and Beyond.
    Marie H Abildgaard, Sólveig H Brynjólfsdóttir, Lisa B Frankel.
      Autophagy is a highly conserved degradation pathway that ensures nutrient recycling and removal of unwanted substrates. This process has a fundamental role in stress adaptation and maintenance of cellular homeostasis. Here, we discuss emerging aspects of the autophagy-RNA interplay, including autophagy-mediated degradation of RNA, RNA-binding proteins (RBPs), and ribonucleoprotein (RNP) complexes. Beyond degradation, we review new roles for autophagy players in the secretion and intracellular transport of RNA and related complexes. We discuss the physiological importance of these events for RNA homeostasis and gene expression programs, as well as their implications for disease, including cancer and neurodegeneration. Lastly, we examine how post-transcriptional regulation of autophagy, through specialized processing and selective translation of key transcripts, challenges and updates our current view of autophagy complexity.
    Keywords:  RNA homeostasis; RNA-binding proteins; autophagy; degradation; post-transcriptional regulation; translation
    DOI:  https://doi.org/10.1016/j.tibs.2020.07.007
  25. J Appl Physiol (1985). 2020 Aug 27.
    Impact of weight loss and partial weight regain on immune cell and inflammatory markers in adipose tissue in male mice.
    Alexander T Sougiannis, Brandon N VanderVeen, Taryn L Cranford, Reilly T Enos, Kandy T Velazquez, Sierra McDonald, Jackie E Bader, Ioulia Chatzistamou, Daping Fan, E Angela Murphy.
      Weight fluctuations are common among individuals with obesity and are associated with increased morbidity. We examined adipose tissue immune and inflammatory markers in mice following weight loss and partial weight regain. Male C57BL/6 mice were randomized into four groups (n=8-10/group): low-fat diet for 32 weeks (LFD), high-fat diet for 32 weeks (HFD), LFD for 28 weeks then changed to a HFD for 4 weeks (LFD->H), HFD for 21 weeks then changed to LFD for 7 weeks and then changed to HFD for 4 weeks (HFD->L->H). LFD->H and HFD->L->H mice did not differ in body weight, fat mass, or fat percentage; however, these parameters were greater than in LFD (p<0.05), but lower than HFD (p<0.05). HFD->L->H had smaller adipocytes compared to HFD and LFD->H (p<0.05), but not LFD. Expression of CD11c and CD8a genes were elevated in epididymal fat of HFD->L->H compared to LFD->H and LFD (p<0.05). However, CD11c was lower in HFD->L->H compared to HFD (p<0.05) but there was no difference in CD8a between these groups. TNFα and IFNγ expression were increased in HFD->L->H compared to LFD and LFD->H (p<0.05); although HFD->L->H had lower expression of these cytokines compared to HFD (P<0.05). IL-1β was greater in HFD->L->H compared to LFD (p<0.05) but was not different from LFD->H or HFD. MCP1 was lower (p<0.05) in HFD->L->H compared to LFD->H. These data reinforce the importance of maintaining a body weight in the range that is recommended for optimal health to reduce immune and inflammatory perturbations associated with obesity.
    Keywords:  adipose tissue inflammation; immune markers; obesogenic programming; weight fluctuations
    DOI:  https://doi.org/10.1152/japplphysiol.00356.2020
  26. Trends Cancer. 2020 Aug 19. pii: S2405-8033(20)30212-0. [Epub ahead of print]
    InVivo Cancer-Based Functional Genomics.
    Chennan Li, Andrea L Kasinski.
      Pinpointing the underlying mechanisms that drive tumorigenesis in human patients is a prerequisite for identifying suitable therapeutic targets for precision medicine. In contrast to cell culture systems, mouse models are highly favored for evaluating tumor progression and therapeutic response in a more realistic in vivo context. The past decade has witnessed a dramatic increase in the number of functional genomic studies using diverse mouse models, including in vivo clustered regularly interspaced short palindromic repeats (CRISPR) and RNA interference (RNAi) screens, and these have provided a wealth of knowledge addressing multiple essential questions in translational cancer research. We compare the multiple mouse systems and genomic tools that are commonly used for in vivo screens to illustrate their strengths and limitations. Crucial components of screen design and data analysis are also discussed.
    Keywords:  CRISPR; RNAi; genomic screen; mouse model
    DOI:  https://doi.org/10.1016/j.trecan.2020.07.004
  27. Elife. 2020 Aug 27. pii: e58396. [Epub ahead of print]9
    A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress.
    Madlen Stephani, Lorenzo Picchianti, Alexander Gajic, Rebecca Beveridge, Emilio Skarwan, Victor Sanchez de Medina Hernandez, Azadeh Mohseni, Marion Clavel, Yonglun Zeng, Christin Naumann, Mateusz Matuszkiewicz, Eleonora Turco, Christian Loefke, Baiying Li, Gerhard Dürnberger, Michael Schutzbier, Hsiao Tieh Chen, Alibek Abdrakhmanov, Adriana Savova, Khong-Sam Chia, Armin Djamei, Irene Schaffner, Steffen Abel, Liwen Jiang, Karl Mechtler, Fumiyo Ikeda, Sascha Martens, Tim Clausen, Yasin Dagdas.
      Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the ER. Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control in the ER.
    Keywords:  A. thaliana; cell biology; human; plant biology; viruses
    DOI:  https://doi.org/10.7554/eLife.58396
  28. Proc Natl Acad Sci U S A. 2020 Aug 24. pii: 201922548. [Epub ahead of print]
    KMT5c modulates adipocyte thermogenesis by regulating Trp53 expression.
    Qingwen Zhao, Zhe Zhang, Weiqiong Rong, Weiwei Jin, Linyu Yan, Wenfang Jin, Yingjiang Xu, Xuan Cui, Qi-Qun Tang, Dongning Pan.
      Brown and beige adipocytes harbor the thermogenic capacity to adapt to environmental thermal or nutritional changes. Histone methylation is an essential epigenetic modification involved in the modulation of nonshivering thermogenesis in adipocytes. Here, we describe a molecular network leading by KMT5c, a H4K20 methyltransferase, that regulates adipocyte thermogenesis and systemic energy expenditure. The expression of Kmt5c is dramatically induced by a β3-adrenergic signaling cascade in both brown and beige fat cells. Depleting Kmt5c in adipocytes in vivo leads to a decreased expression of thermogenic genes in both brown and subcutaneous (s.c.) fat tissues. These mice are prone to high-fat-diet-induced obesity and develop glucose intolerance. Enhanced transformation related protein 53 (Trp53) expression in Kmt5c knockout (KO) mice, that is due to the decreased repressive mark H4K20me3 on its proximal promoter, is responsible for the metabolic phenotypes. Together, these findings reveal the physiological role for KMT5c-mediated H4K20 methylation in the maintenance and activation of the thermogenic program in adipocytes.
    Keywords:  H4K20me3; KMT5c; adaptive thermogenesis; beige adipocyte; brown adipocyte
    DOI:  https://doi.org/10.1073/pnas.1922548117
  29. Cancer Discov. 2020 Aug 25. pii: CD-20-0328. [Epub ahead of print]
    Antibody to CD137 activated by extracellular adenosine triphosphate is tumor selective and broadly effective in vivo without systemic immune activation.
    Mika Kamata-Sakurai, Yoshinori Narita, Yuji Hori, Takayuki Nemoto, Ryo Uchikawa, Masaki Honda, Naoka Hironiwa, Kenji Taniguchi, Meiri Shida-Kawazoe, Shoichi Metsugi, Taro Miyazaki, Naoko A Wada, Yuki Ohte, Shun Shimizu, Hirofumi Mikami, Tatsuhiko Tachibana, Natsuki Ono, Kenji Adachi, Tetsushi Sakiyama, Tomochika Matsushita, Shojiro Kadono, Shun-Ichiro Komatsu, Akihisa Sakamoto, Sayuri Horikawa, Ayano Hirako, Koki Hamada, Sotaro Naoi, Nasa Savory, Yasuko Satoh, Motohiko Sato, Yuki Noguchi, Junko Shinozuka, Haruka Kuroi, Ami Ito, Tetsuya Wakabayashi, Masaki Kamimura, Fumihisa Isomura, Yasushi Tomii, Noriaki Sawada, Atsuhiko Kato, Otoya Ueda, Yoshito Nakanishi, Mika Endo, Kou-Ichi Jishage, Yoshiki Kawabe, Takehisa Kitazawa, Tomoyuki Igawa.
      Agonistic antibodies targeting CD137 have been clinically unsuccessful due to systemic toxicity. Since conferring tumor selectivity through tumor-associated antigen limits its clinical use to cancers that highly express such antigen, we exploited extracellular adenosine triphosphate (exATP), which is a hallmark of the tumor microenvironment and highly elevated in solid tumors, as a broadly tumor selective switch. We generated a novel anti-CD137 switch antibody, STA551, which exerts agonistic activity only in the presence of exATP. STA551 demonstrated potent and broad anti-tumor efficacy against all mouse and human tumors tested and a wide therapeutic window without systemic immune activation in mice. STA551 was well tolerated even at 150 mg/kg/week in cynomolgus monkeys. These results provide a strong rationale for the clinical testing of STA551 against a broad variety of cancers regardless of antigen expression, and for the further application of this novel platform to other targets in cancer therapy.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-0328
  30. Sci Adv. 2020 Jul;6(29): eaba1593
    β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus.
    Meng Zhang, Yiwei Lai, Vladislav Krupalnik, Pengcheng Guo, Xiangpeng Guo, Jianguo Zhou, Yan Xu, Zhijun Yu, Longqi Liu, Ao Jiang, Wenjuan Li, Mazid Md Abdul, Gang Ma, Na Li, Xiuling Fu, Yuan Lv, Mengling Jiang, Muqddas Tariq, Shahzina Kanwal, Hao Liu, Xueting Xu, Hui Zhang, Yinghua Huang, Lulu Wang, Shuhan Chen, Isaac A Babarinde, Zhiwei Luo, Dongye Wang, Tiantian Zhou, Carl Ward, Minghui He, David P Ibañez, Yunpan Li, Jiajian Zhou, Jie Yuan, Yayan Feng, Karthik Arumugam, Umberto Di Vicino, Xichen Bao, Guangming Wu, Axel Schambach, Huating Wang, Hao Sun, Fei Gao, Baoming Qin, Andrew P Hutchins, Bradley W Doble, Christine Hartmann, Maria Pia Cosma, Yan Qin, Guo-Liang Xu, Runsheng Chen, Giacomo Volpe, Liang Chen, Jacob H Hanna, Miguel A Esteban.
      Mouse embryonic stem cells cultured with MEK (mitogen-activated protein kinase kinase) and GSK3 (glycogen synthase kinase 3) inhibitors (2i) more closely resemble the inner cell mass of preimplantation blastocysts than those cultured with SL [serum/leukemia inhibitory factor (LIF)]. The transcriptional mechanisms governing this pluripotent ground state are unresolved. Release of promoter-proximal paused RNA polymerase II (Pol2) is a multistep process necessary for pluripotency and cell cycle gene transcription in SL. We show that β-catenin, stabilized by GSK3 inhibition in medium with 2i, supplies transcriptional coregulators at pluripotency loci. This selectively strengthens pluripotency loci and renders them addicted to transcription initiation for productive gene body elongation in detriment to Pol2 pause release. By contrast, cell cycle genes are not bound by β-catenin, and proliferation/self-renewal remains tightly controlled by Pol2 pause release under 2i conditions. Our findings explain how pluripotency is reinforced in the ground state and also provide a general model for transcriptional resilience/adaptation upon network perturbation in other contexts.
    DOI:  https://doi.org/10.1126/sciadv.aba1593
  31. Aging Cell. 2020 Aug 28. e13219
    Immune checkpoint protein VSIG4 as a biomarker of aging in murine adipose tissue.
    Brandon M Hall, Anatoli S Gleiberman, Evguenia Strom, Peter A Krasnov, David Frescas, Slavoljub Vujcic, Olga V Leontieva, Marina P Antoch, Valeria Kogan, Igor E Koman, Yi Zhu, Tamara Tchkonia, James L Kirkland, Olga B Chernova, Andrei V Gudkov.
      Adipose tissue is recognized as a major source of systemic inflammation with age, driving age-related tissue dysfunction and pathogenesis. Macrophages (Mφ) are central to these changes yet adipose tissue Mφ (ATMs) from aged mice remain poorly characterized. To identify biomarkers underlying changes in aged adipose tissue, we performed an unbiased RNA-seq analysis of ATMs from young (8-week-old) and healthy aged (80-week-old) mice. One of the genes identified, V-set immunoglobulin-domain-containing 4 (VSIG4/CRIg), encodes a Mφ-associated complement receptor and B7 family-related immune checkpoint protein. Here, we demonstrate that Vsig4 expression is highly upregulated with age in perigonadal white adipose tissue (gWAT) in two mouse strains (inbred C57BL/6J and outbred NIH Swiss) independent of gender. The accumulation of VSIG4 was mainly attributed to a fourfold increase in the proportion of VSIG4+ ATMs (13%-52%). In a longitudinal study, VSIG4 expression in gWAT showed a strong correlation with age within a cohort of male and female mice and correlated strongly with physiological frailty index (PFI, a multi-parameter assessment of health) in male mice. Our results indicate that VSIG4 is a novel biomarker of aged murine ATMs. VSIG4 expression was also found to be elevated in other aging tissues (e.g., thymus) and was strongly induced in tumor-adjacent stroma in cases of spontaneous and xenograft lung cancer models. VSIG4 expression was recently associated with cancer and several inflammatory diseases with diagnostic and prognostic potential in both mice and humans. Further investigation is required to determine whether VSIG4-positive Mφ contribute to immunosenescence and/or systemic age-related deficits.
    Keywords:  VSIG4; adipose tissue; aging; frailty index; immune checkpoint; inflammation; macrophage; mouse
    DOI:  https://doi.org/10.1111/acel.13219
  32. Sci Adv. 2020 Jul;6(31): eaba5345
    Cell identity and nucleo-mitochondrial genetic context modulate OXPHOS performance and determine somatic heteroplasmy dynamics.
    Ana Victoria Lechuga-Vieco, Ana Latorre-Pellicer, Iain G Johnston, Gennaro Prota, Uzi Gileadi, Raquel Justo-Méndez, Rebeca Acín-Pérez, Raquel Martínez-de-Mena, Jose María Fernández-Toro, Daniel Jimenez-Blasco, Alfonso Mora, Jose A Nicolás-Ávila, Demetrio J Santiago, Silvia G Priori, Juan Pedro Bolaños, Guadalupe Sabio, Luis Miguel Criado, Jesús Ruíz-Cabello, Vincenzo Cerundolo, Nick S Jones, José Antonio Enríquez.
      Heteroplasmy, multiple variants of mitochondrial DNA (mtDNA) in the same cytoplasm, may be naturally generated by mutations but is counteracted by a genetic mtDNA bottleneck during oocyte development. Engineered heteroplasmic mice with nonpathological mtDNA variants reveal a nonrandom tissue-specific mtDNA segregation pattern, with few tissues that do not show segregation. The driving force for this dynamic complex pattern has remained unexplained for decades, challenging our understanding of this fundamental biological problem and hindering clinical planning for inherited diseases. Here, we demonstrate that the nonrandom mtDNA segregation is an intracellular process based on organelle selection. This cell type-specific decision arises jointly from the impact of mtDNA haplotypes on the oxidative phosphorylation (OXPHOS) system and the cell metabolic requirements and is strongly sensitive to the nuclear context and to environmental cues.
    DOI:  https://doi.org/10.1126/sciadv.aba5345
  33. Nat Commun. 2020 Aug 24. 11(1): 4226
    De novo design of an intercellular signaling toolbox for multi-channel cell-cell communication and biological computation.
    Pei Du, Huiwei Zhao, Haoqian Zhang, Ruisha Wang, Jianyi Huang, Ye Tian, Xudong Luo, Xunxun Luo, Min Wang, Yanhui Xiang, Long Qian, Yihua Chen, Yong Tao, Chunbo Lou.
      Intercellular signaling is indispensable for single cells to form complex biological structures, such as biofilms, tissues and organs. The genetic tools available for engineering intercellular signaling, however, are quite limited. Here we exploit the chemical diversity of biological small molecules to de novo design a genetic toolbox for high-performance, multi-channel cell-cell communications and biological computations. By biosynthetic pathway design for signal molecules, rational engineering of sensing promoters and directed evolution of sensing transcription factors, we obtain six cell-cell signaling channels in bacteria with orthogonality far exceeding the conventional quorum sensing systems and successfully transfer some of them into yeast and human cells. For demonstration, they are applied in cell consortia to generate bacterial colony-patterns using up to four signaling channels simultaneously and to implement distributed bio-computation containing seven different strains as basic units. This intercellular signaling toolbox paves the way for engineering complex multicellularity including artificial ecosystems and smart tissues.
    DOI:  https://doi.org/10.1038/s41467-020-17993-w
  34. Trends Cogn Sci. 2020 Aug 24. pii: S1364-6613(20)30175-3. [Epub ahead of print]
    Cellular Mechanisms of Conscious Processing.
    Jaan Aru, Mototaka Suzuki, Matthew E Larkum.
      Recent breakthroughs in neurobiology indicate that the time is ripe to understand how cellular-level mechanisms are related to conscious experience. Here, we highlight the biophysical properties of pyramidal cells, which allow them to act as gates that control the evolution of global activation patterns. In conscious states, this cellular mechanism enables complex sustained dynamics within the thalamocortical system, whereas during unconscious states, such signal propagation is prohibited. We suggest that the hallmark of conscious processing is the flexible integration of bottom-up and top-down data streams at the cellular level. This cellular integration mechanism provides the foundation for Dendritic Information Theory, a novel neurobiological theory of consciousness.
    Keywords:  anesthesia; dendrites; dendritic integration theory; pyramidal cells
    DOI:  https://doi.org/10.1016/j.tics.2020.07.006
  35. Nat Rev Immunol. 2020 Aug 24.
    Lactate modulation of immune responses in inflammatory versus tumour microenvironments.
    Michelangelo Certo, Chin-Hsien Tsai, Valentina Pucino, Ping-Chih Ho, Claudio Mauro.
      The microenvironment in cancerous tissues is immunosuppressive and pro-tumorigenic, whereas the microenvironment of tissues affected by chronic inflammatory disease is pro-inflammatory and anti-resolution. Despite these opposing immunological states, the metabolic states in the tissue microenvironments of cancer and inflammatory diseases are similar: both are hypoxic, show elevated levels of lactate and other metabolic by-products and have low levels of nutrients. In this Review, we describe how the bioavailability of lactate differs in the microenvironments of tumours and inflammatory diseases compared with normal tissues, thus contributing to the establishment of specific immunological states in disease. A clear understanding of the metabolic signature of tumours and inflammatory diseases will enable therapeutic intervention aimed at resetting the bioavailability of metabolites and correcting the dysregulated immunological state, triggering beneficial cytotoxic, inflammatory responses in tumours and immunosuppressive responses in chronic inflammation.
    DOI:  https://doi.org/10.1038/s41577-020-0406-2
  36. Science. 2020 Aug 28. 369(6507): 1059
    Zena Werb (1945-2020).
    Nancy Boudreau, Mina Bissell.
      
    DOI:  https://doi.org/10.1126/science.abe0952
  37. Cancer Biol Ther. 2020 Aug 23. 1-9
    Tumor associated neutrophils promote the metastasis of pancreatic ductal adenocarcinoma.
    Tao Lianyuan, Li Gang, Tao Ming, Xiu Dianrong, Yuan Chunhui, Ma Zhaolai, Jiang Bin.
      The aim of this study was to investigate the role of tumor-associated neutrophils (TANs) in the metastasis of pancreatic ductal adenocarcinoma (PDAC), to explore the regulation of TANs, and to determine the mechanisms governing the metastasis of PDAC. The correlation between neutrophils and the patient's clinical pathological data was first evaluated. Then, the effects of neutrophils on the invasion of PDAC were analyzed using a combination of conditioned media, direct and indirect coculture of human peripheral blood neutrophils, and PDAC cell lines (Panc-1, MiaPaCa-2 and AsPC-1). The cytokines secreted by neutrophils were detected through ELISA. TAN density was significantly correlated with poor metastasis-free survival (P < .05). Through coculture, it was found that the effect of neutrophils on pancreatic cancer cells was dependent on concentration, and a high concentration of neutrophils showed a lethal effect, while a low concentration of neutrophils primarily promoted the migration ability of cancer cells. The results of the wound-healing assay, the Transwell invasion assay, and laser confocal microscopy confirmed the promoting effect and indicated that the effect of neutrophils toward cancer cells may function indirectly by releasing a series of cytokines. The results of ELISA show that this effect may be achieved through the secretion of a large amount of TNF-α and TGF-β1 by neutrophils. Our study indicated that neutrophils may increase the metastasis of PDAC by releasing a series of cell cytokines, such as TNF-α and TGF-β1.
    Keywords:  PDAC; TGF-Β1; TNF-ɑ; metastasis; neutrophils
    DOI:  https://doi.org/10.1080/15384047.2020.1807250
  38. Trends Biochem Sci. 2020 Aug 21. pii: S0968-0004(20)30191-2. [Epub ahead of print]
    Autophagy Assays for Biological Discovery and Therapeutic Development.
    Noboru Mizushima, Leon O Murphy.
      Autophagy is a lysosome-dependent intracellular degradation system required for various physiological processes and can be dysregulated in human disease. To understand its biological significance and underlying mechanisms, measuring autophagic activity (i.e., autophagic flux) is critical. However, navigating which assays to use, and when, is complicated and at times the results are often interpreted inappropriately. This review will summarize both advantages and disadvantages of currently available methods to monitor autophagy. In addition, we discuss how these assays should be used in high-throughput screens to identify autophagy-modulating drugs and genes and the general features needed for biomarkers to assess autophagy in humans.
    Keywords:  autophagic flux; autophagy biomarkers; high-throughput screens; selective autophagy
    DOI:  https://doi.org/10.1016/j.tibs.2020.07.006
  39. Elife. 2020 Aug 26. pii: e60637. [Epub ahead of print]9
    PARP1 inhibitors trigger innate immunity via PARP1 trapping-induced DNA damage response.
    Chiho Kim, Xu-Dong Wang, Yonghao Yu.
      It is being increasingly appreciated that the immunomodulatory functions of PARP inhibitors (PARPi) underlie their clinical activities in various BRCA-mutated tumors. PARPi possess both PARP1 inhibition and PARP1 trapping activities. The relative contribution of these two mechanisms toward PARPi-induced innate immune signaling, however, is poorly understood. We find that the presence of the PARP1 protein with uncompromised DNA-binding activities is required for PARPi-induced innate immune response. The activation of cGAS-STING signaling induced by various PARPi closely depends on their PARP1 trapping activities. Finally, we show that a small molecule PARP1 degrader blocks the enzymatic activity of PARP1 without eliciting PARP1 trapping or cGAS-STING activation. Our findings thus identify PARP1 trapping as a major contributor of the immunomodulatory functions of PARPi. Although PARPi-induced innate immunity is highly desirable in human malignancies, the ability of "non-trapping" PARP1 degraders to avoid the activation of innate immune response could be useful in non-oncological diseases.
    Keywords:  cancer biology; cell biology; human
    DOI:  https://doi.org/10.7554/eLife.60637
  40. Mol Cell. 2020 Aug 18. pii: S1097-2765(20)30547-5. [Epub ahead of print]
    Multivalent Proteins Rapidly and Reversibly Phase-Separate upon Osmotic Cell Volume Change.
    Ameya P Jalihal, Sethuramasundaram Pitchiaya, Lanbo Xiao, Pushpinder Bawa, Xia Jiang, Karan Bedi, Abhijit Parolia, Marcin Cieslik, Mats Ljungman, Arul M Chinnaiyan, Nils G Walter.
      Processing bodies (PBs) and stress granules (SGs) are prominent examples of subcellular, membraneless compartments that are observed under physiological and stress conditions, respectively. We observe that the trimeric PB protein DCP1A rapidly (within ∼10 s) phase-separates in mammalian cells during hyperosmotic stress and dissolves upon isosmotic rescue (over ∼100 s) with minimal effect on cell viability even after multiple cycles of osmotic perturbation. Strikingly, this rapid intracellular hyperosmotic phase separation (HOPS) correlates with the degree of cell volume compression, distinct from SG assembly, and is exhibited broadly by homo-multimeric (valency ≥ 2) proteins across several cell types. Notably, HOPS sequesters pre-mRNA cleavage factor components from actively transcribing genomic loci, providing a mechanism for hyperosmolarity-induced global impairment of transcription termination. Our data suggest that the multimeric proteome rapidly responds to changes in hydration and molecular crowding, revealing an unexpected mode of globally programmed phase separation and sequestration.
    Keywords:  cell volume; hydration; hyperosmotic stress; molecular crowding; phase separation; processing bodies; protein multivalency; self-interaction; stress granules; stress response
    DOI:  https://doi.org/10.1016/j.molcel.2020.08.004
  41. J Mol Med (Berl). 2020 Aug 26.
    Expanding and validating the biomarkers for mitochondrial diseases.
    Alessandra Maresca, Valentina Del Dotto, Martina Romagnoli, Chiara La Morgia, Lidia Di Vito, Mariantonietta Capristo, Maria Lucia Valentino, Valerio Carelli, .
      Mitochondrial diseases are highly heterogeneous metabolic disorders caused by genetic alterations in the mitochondrial DNA (mtDNA) or in the nuclear genome. In this study, we investigated a panel of blood biomarkers in a cohort of 123 mitochondrial patients, with prominent neurological and muscular manifestations. These biomarkers included creatine, fibroblast growth factor 21 (FGF21) and growth/differentiation factor 15 (GDF-15), and the novel cell free circulating-mtDNA (ccf-mtDNA). All biomarkers were significantly increased in the patient group. After stratification by the specific phenotypes, ccf-mtDNA was significantly increased in the Mitochondrial Encephalomyopathy Lactic Acidosis Stroke-like episodes syndrome (MELAS) group, and FGF21 and GDF-15 were significantly elevated in patients with MELAS and Myoclonic Epilepsy Ragged Red Fibers syndrome. On the contrary, in our cohort, creatine was not associated to a specific clinical phenotype. Longitudinal assessment in four MELAS patients showed increased levels of ccf-mtDNA in relation to acute events (stroke-like episodes/status epilepticus) or progression of neurodegeneration. Our results confirm the association of FGF21 and GDF-15 with mitochondrial translation defects due to tRNA mutations. Most notably, the novel ccf-mtDNA was strongly associated with MELAS and may be used for monitoring the disease course or to evaluate the efficacy of therapies, especially in the acute phase. KEY MESSAGES: • FGF21/GDF15 efficiently identifies mitochondrial diseases due to mutations in tRNA genes. • The novel ccf-mtDNA is associated with MELAS and increases during acute events. • Creatine only discriminates severe mitochondrial patients. • FGF21, GDF-15, and ccf-mtDNA are possibly useful for monitoring therapy efficacy.
    Keywords:  Biomarkers; Cell free circulating-mtDNA; Creatine; FGF21; GDF-15; Mitochondrial diseases
    DOI:  https://doi.org/10.1007/s00109-020-01967-y
  42. Nat Commun. 2020 Aug 27. 11(1): 4279
    Caveolin-1-mediated sphingolipid oncometabolism underlies a metabolic vulnerability of prostate cancer.
    Jody Vykoukal, Johannes F Fahrmann, Justin R Gregg, Zhe Tang, Spyridon Basourakos, Ehsan Irajizad, Sanghee Park, Guang Yang, Chad J Creighton, Alia Fleury, Jeffrey Mayo, Adriana Paulucci-Holthauzen, Jennifer B Dennison, Eunice Murage, Christine B Peterson, John W Davis, Jeri Kim, Samir Hanash, Timothy C Thompson.
      Plasma and tumor caveolin-1 (Cav-1) are linked with disease progression in prostate cancer. Here we report that metabolomic profiling of longitudinal plasmas from a prospective cohort of 491 active surveillance (AS) participants indicates prominent elevations in plasma sphingolipids in AS progressors that, together with plasma Cav-1, yield a prognostic signature for disease progression. Mechanistic studies of the underlying tumor supportive onco-metabolism reveal coordinated activities through which Cav-1 enables rewiring of cancer cell lipid metabolism towards a program of 1) exogenous sphingolipid scavenging independent of cholesterol, 2) increased cancer cell catabolism of sphingomyelins to ceramide derivatives and 3) altered ceramide metabolism that results in increased glycosphingolipid synthesis and efflux of Cav-1-sphingolipid particles containing mitochondrial proteins and lipids. We also demonstrate, using a prostate cancer syngeneic RM-9 mouse model and established cell lines, that this Cav-1-sphingolipid program evidences a metabolic vulnerability that is targetable to induce lethal mitophagy as an anti-tumor therapy.
    DOI:  https://doi.org/10.1038/s41467-020-17645-z
  43. Cancer Res Treat. 2020 Aug 24.
    Systemic Inflammatory Biomarkers, Especially Fibrinogen to Albumin Ratio, Predict Prognosis in Patients with Pancreatic Cancer.
    Lin Fang, Fei-Hu Yan, Chao Liu, Jing Chen, Dan Wang, Chun-Hui Zhang, Chang-Jie Lou, Jie Lian, Yang Yao, Bo-Jun Wang, Rui-Yang Li, Shu-Ling Han, Yi-Bing Bai, Jia-Ni Yang, Zhi-Wei Li, Yan-Qiao Zhang.
      Purpose: Systemic inflammatory response is a critical factor that promotes the initiation and metastasis of malignancies including pancreatic cancer (PC). This study was designed to determine and compare the prognostic value of neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), and fibrinogen-to-albumin ratio (FAR) in resectable PC and locally advanced or metastatic PC.Materials and Methods: Three hundred fifty-three patients with resectable PC and 807 patients with locally advanced or metastatic PC were recruited in this study. These patients were classified into a training set (n=758) and a validation set (n=402). Kaplan-Meier survival plots and Cox proportional hazards regression models were used to analyze prognosis.
    Results: Overall survival (OS) was significantly better for patients with resectable PC with low preoperative PLR (p=0.048) and MLR (p=0.027). Low FAR, MLR, NLR (p<0.001) and PLR (p=0.003) were significantly associated with decreased risk of death for locally advanced or metastatic PC patients. FAR (hazard ratio [HR], 1.522; 95% confidential interval [CI], 1.261 to 1.837; p<0.001) and MLR (HR, 1.248; 95% CI, 1.017 to 1.532; p=0.034) were independent prognostic factors for locally advanced or metastatic PC.
    Conclusion: The prognostic roles of FAR, MLR, NLR, and PLR in resectable PC and locally advanced or metastatic PC were different. FAR showed the most prognostic power in locally advanced or metastatic PC. Low FAR was positively correlated with OS in locally advanced or metastatic PC, which could be used to predict the prognosis.
    Keywords:  Fibrinogen-to-albumin ratio; Pancreatic neoplasms; Prognosis; Survival; Systemic inflammatory markers
    DOI:  https://doi.org/10.4143/crt.2020.330
  44. Biochem J. 2020 Aug 28. 477(16): 3033-3054
    Mitochondrial control of cellular protein homeostasis.
    Karthik Mohanraj, Urszula Nowicka, Agnieszka Chacinska.
      Mitochondria are involved in several vital functions of the eukaryotic cell. The majority of mitochondrial proteins are coded by nuclear DNA. Constant import of proteins from the cytosol is a prerequisite for the efficient functioning of the organelle. The protein import into mitochondria is mediated by diverse import pathways and is continuously under watch by quality control systems. However, it is often challenged by both internal and external factors, such as oxidative stress or energy shortage. The impaired protein import and biogenesis leads to the accumulation of mitochondrial precursor proteins in the cytosol and activates several stress response pathways. These defense mechanisms engage a network of processes involving transcription, translation, and protein clearance to restore cellular protein homeostasis. In this review, we provide a comprehensive analysis of various factors and processes contributing to mitochondrial stress caused by protein biogenesis failure and summarize the recovery mechanisms employed by the cell.
    Keywords:  mitochondrial dysfunction; oxidative stress; protein import; protein misfolding; translation
    DOI:  https://doi.org/10.1042/BCJ20190654
  45. Elife. 2020 Aug 25. pii: e56221. [Epub ahead of print]9
    Ageing compromises mouse thymus function and remodels epithelial cell differentiation.
    Jeanette Baran-Gale, Michael D Morgan, Stefano Maio, Fatima Dhalla, Irene Calvo-Asensio, Mary E Deadman, Adam E Handel, Ashley Maynard, Steven Chen, Foad Green, Rene V Sit, Norma F Neff, Spyros Darmanis, Weilun Tan, Andy P May, John C Marioni, Chris P Ponting, Georg A Holländer.
      Ageing is characterised by cellular senescence, leading to imbalanced tissue maintenance, cell death and compromised organ function. This is first observed in the thymus, the primary lymphoid organ that generates and selects T cells. However, the molecular and cellular mechanisms underpinning these ageing processes remain unclear. Here, we show that mouse ageing leads to less efficient T cell selection, decreased self-antigen representation and increased T cell receptor repertoire diversity. Using a combination of single-cell RNA-seq and lineage-tracing, we find that progenitor cells are the principal targets of ageing, whereas the function of individual mature thymic epithelial cells is compromised only modestly. Specifically, an early-life precursor cell population, retained in the mouse cortex postnatally, is virtually extinguished at puberty. Concomitantly, a medullary precursor cell quiesces, thereby impairing maintenance of the medullary epithelium. Thus, ageing disrupts thymic progenitor differentiation and impairs the core immunological functions of the thymus.
    Keywords:  immunology; inflammation; mouse
    DOI:  https://doi.org/10.7554/eLife.56221
  46. J Biol Chem. 2020 Aug 26. pii: jbc.RA120.013999. [Epub ahead of print]
    ATG16L1 autophagy pathway regulates BAX protein levels and programmed cell death.
    Fenfen Chen, Dulguun Amgalan, Richard N Kitsis, Jeffrey E Pessin, Daorong Feng.
      Previously we reported that adipocyte SNAP23 (synaptosome-associated protein of 23 kDa) deficiency blocks the activation of macroautophagy leading to an increased abundance of BAX, a pro-death Bcl-2 family member, and activation and adipocyte cell death both in vitro and in vivo. Here, we found that knockdown of SNAP23 inhibited the association of the autophagosome regulators ATG16L1 and ATG9 compartments by nutrient depletion and reduced the formation of ATG16L1 membrane puncta. ATG16L1 knockdown inhibited autophagy flux and increased BAX protein levels by suppressing BAX degradation. The elevation in BAX protein had no effect on BAX activation or cell death in the nutrient-replete state. However, following nutrient depletion BAX was activated with a concomitant induction of cell death. Co-immunoprecipitation analyses demonstrated that SNAP23 and ATG16L1 proteins form a stable complex independent of nutrient condition, while in the nutrient-deplete state BAX binds to SNAP23 to form a ternary BAX/SNAP23/ATG16L1 protein complex. Taken together, these data support a model in which SNAP23 plays a crucial function as a scaffold for ATG16L1 necessary for the suppression of BAX activation and induction of the intrinsic cell death program.
    Keywords:  ATG16L1; ATG9; Bax; SNAP23; SNARE proteins; adipocyte; apoptosis; autophagy
    DOI:  https://doi.org/10.1074/jbc.RA120.013999
  47. Trends Cell Biol. 2020 Aug 20. pii: S0962-8924(20)30146-X. [Epub ahead of print]
    Quantitative Data Analysis in Single-Molecule Localization Microscopy.
    Yu-Le Wu, Aline Tschanz, Leonard Krupnik, Jonas Ries.
      Super-resolution microscopy, and specifically single-molecule localization microscopy (SMLM), is becoming a transformative technology for cell biology, as it allows the study of cellular structures with nanometer resolution. Here, we review a wide range of data analyses approaches for SMLM that extract quantitative information about the distribution, size, shape, spatial organization, and stoichiometry of macromolecular complexes to guide biological interpretation. We present a case study using the nuclear pore complex as an example that highlights the power of combining complementary approaches by identifying its symmetry, ringlike structure, and protein copy number. In face of recent technical and computational advances, this review serves as a guideline for selecting appropriate analysis tools and controls to exploit the potential of SMLM for a wide range of biological questions.
    Keywords:  coordinate-based data; nuclear pore complex; quantitative analysis; single-molecule localization microscopy; super-resolution microscopy
    DOI:  https://doi.org/10.1016/j.tcb.2020.07.005
  48. Nat Commun. 2020 Aug 26. 11(1): 4274
    Fasting-mimicking diet plus chemotherapy in breast cancer treatment.
    Claudio Vernieri, Francesca Ligorio, Emma Zattarin, Licia Rivoltini, Filippo de Braud.
      
    DOI:  https://doi.org/10.1038/s41467-020-18194-1
  49. JCI Insight. 2020 Aug 25. pii: 137969. [Epub ahead of print]
    Caveolin-1 scaffolding domain peptide regulates glucose metabolism in lung fibrosis.
    Venkadesaperumal Gopu, Liang Fan, Rashmi Shetty, M R Nagaraja, Sreerama Shetty.
      Increased metabolism distinguishes myofibroblasts or fibrotic lung fibroblasts (fLfs) from the normal lung fibroblasts (nLfs). The mechanism of metabolic activation in fLfs has not been fully elucidated. Further, the anti-fibrogenic effects of caveolin-1 scaffolding domain peptide CSP/CSP7 involve metabolic reprogramming in fLfs is unclear. We therefore analyzed lactate and succinate levels, and the expression of glycolytic enzymes, and hypoxia inducible factor-1alpha (HIF-1α). Lactate and succinate levels as well as the basal expression of glycolytic enzymes and HIF-1α αwere increased in fLfs. These changes were reversed following restoration of p53 or its transcriptional target microRNA-34a (miR-34a) expression in fLfs. Conversely, inhibition of basal p53 or miR-34a increased glucose metabolism, glycolytic enzymes and HIF-1α in nLfs. Treatment of fLfs or mice having bleomycin- or TGF-beta1-induced lung fibrosis with CSP/CSP7, reduced the expression of glycolytic enzymes and HIF-1α. Further, inhibition of p53 or miR-34a abrogated CSP/CSP7-mediated restoration of glycolytic flux in fLfs in vitro and in mice with pulmonary fibrosis and lacking p53 or miR-34a expression in fibroblasts in vivo. Our data indicate that dysregulation of glucose metabolism in fLfs is causally linked to loss of basal expression of p53 and miR-34a. Treatment with CSP/CSP7 constrains aberrant glucose metabolism through restoration of p53 and miR-34a.
    Keywords:  Fibrosis; Glucose metabolism; P53; Pulmonology
    DOI:  https://doi.org/10.1172/jci.insight.137969
  50. Oncogene. 2020 Aug 24.
    Metabolic rewiring in the promotion of cancer metastasis: mechanisms and therapeutic implications.
    Qinyao Wei, Yun Qian, Jun Yu, Chi Chun Wong.
      Tumor metastasis is the major cause of mortality from cancer. Metabolic rewiring and the metastatic cascade are highly intertwined, co-operating to promote multiple steps of cancer metastasis. Metabolites generated by cancer cells influence the metastatic cascade, encompassing epithelial-mesenchymal transition (EMT), survival of cancer cells in circulation, and metastatic colonization at distant sites. A variety of molecular mechanisms underlie the prometastatic effect of tumor-derived metabolites, such as epigenetic deregulation, induction of matrix metalloproteinases (MMPs), promotion of cancer stemness, and alleviation of oxidative stress. Conversely, metastatic signaling regulates expression and activity of rate-limiting metabolic enzymes to generate prometastatic metabolites thereby reinforcing the metastasis cascade. Understanding the complex interplay between metabolism and metastasis could unravel novel molecular targets, whose intervention could lead to improvements in the treatment of cancer. In this review, we summarized the recent discoveries involving metabolism and tumor metastasis, and emphasized the promising molecular targets, with an update on the development of small molecule or biologic inhibitors against these aberrant situations in cancer.
    DOI:  https://doi.org/10.1038/s41388-020-01432-7
  51. Nature. 2020 Aug 26.
    Closed mitosis requires local disassembly of the nuclear envelope.
    Gautam Dey, Siân Culley, Scott Curran, Uwe Schmidt, Ricardo Henriques, Wanda Kukulski, Buzz Baum.
      At the end of mitosis, eukaryotic cells must segregate the two copies of their replicated genome into two new nuclear compartments1. They do this either by first dismantling and later reassembling the nuclear envelope in an 'open mitosis' or by reshaping an intact nucleus and then dividing it into two in a 'closed mitosis'2,3. Mitosis has been studied in a wide variety of eukaryotes for more than a century4, but how the double membrane of the nuclear envelope is split into two at the end of a closed mitosis without compromising the impermeability of the nuclear compartment remains unknown5. Here, using the fission yeast Schizosaccharomyces pombe (a classical model for closed mitosis5), genetics, live-cell imaging and electron tomography, we show that nuclear fission is achieved via local disassembly of nuclear pores within the narrow bridge that links segregating daughter nuclei. In doing so, we identify the protein Les1, which is localized to the inner nuclear envelope and restricts the process of local nuclear envelope breakdown to the bridge midzone to prevent the leakage of material from daughter nuclei. The mechanism of local nuclear envelope breakdown in a closed mitosis therefore closely mirrors nuclear envelope breakdown in open mitosis3, revealing an unexpectedly high conservation of nuclear remodelling mechanisms across diverse eukaryotes.
    DOI:  https://doi.org/10.1038/s41586-020-2648-3
  52. Proc Natl Acad Sci U S A. 2020 Aug 25. pii: 202004807. [Epub ahead of print]
    How cholesterol stiffens unsaturated lipid membranes.
    Saptarshi Chakraborty, Milka Doktorova, Trivikram R Molugu, Frederick A Heberle, Haden L Scott, Boris Dzikovski, Michihiro Nagao, Laura-Roxana Stingaciu, Robert F Standaert, Francisco N Barrera, John Katsaras, George Khelashvili, Michael F Brown, Rana Ashkar.
      Cholesterol is an integral component of eukaryotic cell membranes and a key molecule in controlling membrane fluidity, organization, and other physicochemical parameters. It also plays a regulatory function in antibiotic drug resistance and the immune response of cells against viruses, by stabilizing the membrane against structural damage. While it is well understood that, structurally, cholesterol exhibits a densification effect on fluid lipid membranes, its effects on membrane bending rigidity are assumed to be nonuniversal; i.e., cholesterol stiffens saturated lipid membranes, but has no stiffening effect on membranes populated by unsaturated lipids, such as 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). This observation presents a clear challenge to structure-property relationships and to our understanding of cholesterol-mediated biological functions. Here, using a comprehensive approach-combining neutron spin-echo (NSE) spectroscopy, solid-state deuterium NMR (2H NMR) spectroscopy, and molecular dynamics (MD) simulations-we report that cholesterol locally increases the bending rigidity of DOPC membranes, similar to saturated membranes, by increasing the bilayer's packing density. All three techniques, inherently sensitive to mesoscale bending fluctuations, show up to a threefold increase in effective bending rigidity with increasing cholesterol content approaching a mole fraction of 50%. Our observations are in good agreement with the known effects of cholesterol on the area-compressibility modulus and membrane structure, reaffirming membrane structure-property relationships. The current findings point to a scale-dependent manifestation of membrane properties, highlighting the need to reassess cholesterol's role in controlling membrane bending rigidity over mesoscopic length and time scales of important biological functions, such as viral budding and lipid-protein interactions.
    Keywords:  area compressibility; deuterium NMR; membrane viscosity; molecular dynamics simulations; neutron spin echo
    DOI:  https://doi.org/10.1073/pnas.2004807117
  53. Proc Natl Acad Sci U S A. 2020 Aug 26. pii: 202014639. [Epub ahead of print]
    4-Hydroxyacetophenone modulates the actomyosin cytoskeleton to reduce metastasis.
    Darren S Bryan, Melinda Stack, Katarzyna Krysztofiak, Urszula Cichoń, Dustin G Thomas, Alexandra Surcel, Eric S Schiffhauer, Michael A Beckett, Nikolai N Khodarev, Lai Xue, Elizabeth C Poli, Alexander T Pearson, Mitchell C Posner, Douglas N Robinson, Ronald S Rock, Ralph R Weichselbaum.
      Metastases are the cause of the vast majority of cancer deaths. In the metastatic process, cells migrate to the vasculature, intravasate, extravasate, and establish metastatic colonies. This pattern of spread requires the cancer cells to change shape and to navigate tissue barriers. Approaches that block this mechanical program represent new therapeutic avenues. We show that 4-hydroxyacetophenone (4-HAP) inhibits colon cancer cell adhesion, invasion, and migration in vitro and reduces the metastatic burden in an in vivo model of colon cancer metastasis to the liver. Treatment with 4-HAP activates nonmuscle myosin-2C (NM2C) (MYH14) to alter actin organization, inhibiting the mechanical program of metastasis. We identify NM2C as a specific therapeutic target. Pharmacological control of myosin isoforms is a promising approach to address metastatic disease, one that may be readily combined with other therapeutic strategies.
    Keywords:  4-hydroxyacetophenone; colorectal cancer; ex vivo motility; metastasis; nonmuscle myosin 2C
    DOI:  https://doi.org/10.1073/pnas.2014639117
  54. Oncogene. 2020 Aug 27.
    Serum- and glucocorticoid- inducible kinase 2, SGK2, is a novel autophagy regulator and modulates platinum drugs response in cancer cells.
    Valentina Ranzuglia, Ilaria Lorenzon, Ilenia Pellarin, Maura Sonego, Alessandra Dall'Acqua, Sara D'Andrea, Sara Lovisa, Ilenia Segatto, Michela Coan, Jerry Polesel, Diego Serraino, Patrizia Sabatelli, Paola Spessotto, Barbara Belletti, Gustavo Baldassarre, Monica Schiappacassi.
      For many tumor types chemotherapy still represents the therapy of choice and many standard treatments are based on the use of platinum (PT) drugs. However, de novo or acquired resistance to platinum is frequent and leads to disease progression. In Epithelial Ovarian Cancer (EOC) patients, PT-resistant recurrences are very common and improving the response to treatment still represents an unmet clinical need. To identify new modulators of PT-sensitivity, we performed a loss-of-function screening targeting 680 genes potentially involved in the response of EOC cells to platinum. We found that SGK2 (Serum-and Glucocorticoid-inducible kinase 2) plays a key role in PT-response. We show here that EOC cells relay on the induction of autophagy to escape PT-induced death and that SGK2 inhibition increases PT sensitivity inducing a block in the autophagy cascade due to the impairment of lysosomal acidification. Mechanistically we demonstrate that SGK2 controls autophagy in a kinase-dependent manner by binding and inhibiting the V-ATPase proton pump. Accordingly, SGK2 phosphorylates the subunit V1H (ATP6V1H) of V-ATPase and silencing or chemical inhibition of SGK2, affects the normal autophagic flux and sensitizes EOC cells to platinum. Hence, we identified a new pathway that links autophagy to the survival of cancer cells under platinum treatment in which the druggable kinase SGK2 plays a central role. Our data suggest that blocking autophagy via SGK2 inhibition could represent a novel therapeutic strategy to improve patients' response to platinum.
    DOI:  https://doi.org/10.1038/s41388-020-01433-6
  55. Nature. 2020 Aug;584(7822): 535-546
    Effects of extracellular matrix viscoelasticity on cellular behaviour.
    Ovijit Chaudhuri, Justin Cooper-White, Paul A Janmey, David J Mooney, Vivek B Shenoy.
      Substantial research over the past two decades has established that extracellular matrix (ECM) elasticity, or stiffness, affects fundamental cellular processes, including spreading, growth, proliferation, migration, differentiation and organoid formation. Linearly elastic polyacrylamide hydrogels and polydimethylsiloxane (PDMS) elastomers coated with ECM proteins are widely used to assess the role of stiffness, and results from such experiments are often assumed to reproduce the effect of the mechanical environment experienced by cells in vivo. However, tissues and ECMs are not linearly elastic materials-they exhibit far more complex mechanical behaviours, including viscoelasticity (a time-dependent response to loading or deformation), as well as mechanical plasticity and nonlinear elasticity. Here we review the complex mechanical behaviours of tissues and ECMs, discuss the effect of ECM viscoelasticity on cells, and describe the potential use of viscoelastic biomaterials in regenerative medicine. Recent work has revealed that matrix viscoelasticity regulates these same fundamental cell processes, and can promote behaviours that are not observed with elastic hydrogels in both two- and three-dimensional culture microenvironments. These findings have provided insights into cell-matrix interactions and how these interactions differentially modulate mechano-sensitive molecular pathways in cells. Moreover, these results suggest design guidelines for the next generation of biomaterials, with the goal of matching tissue and ECM mechanics for in vitro tissue models and applications in regenerative medicine.
    DOI:  https://doi.org/10.1038/s41586-020-2612-2
  56. Physiol Rep. 2020 Aug;8(16): e14557
    Regular exercise and branched-chain amino acids prevent ischemic acute kidney injury-related muscle wasting in mice.
    Soichiro Nagata, Akihiko Kato, Shinsuke Isobe, Tomoyuki Fujikura, Naro Ohashi, Hiroaki Miyajima, Hideo Yasuda.
      Acute kidney injury (AKI) causes glucose and protein metabolism abnormalities that result in muscle wasting, thereby affecting the long-term prognosis of critical illness survivors. Here, we examined whether early intervention with treadmill exercise and branched-chain amino acids (BCAA) can prevent AKI-related muscle wasting and reduced physical performance in mice. Unilateral 15 min ischemia-reperfusion injury was induced in contralateral nephrectomized mice, and muscle histological and physiological changes were assessed and compared with those of pair-fed control mice, since AKI causes severe anorexia. Mice exercised for 30 min each day and received oral BCAA for 7 days after AKI insult. By day 7, ischemic AKI significantly decreased wet weight, myofiber cross-sectional area, and central mitochondrial volume density of the anterior tibialis muscle, and significantly reduced maximal exercise time. Regular exercise and BCAA prevented AKI-related muscle wasting and low physical performance by suppressing myostatin and atrogin-1 mRNA upregulation, and restoring reduced phosphorylated Akt and PGC-1α mRNA expression in the muscle. Ischemic AKI induces muscle wasting by accelerating muscle protein degradation and reducing protein synthesis; however, we found that regular exercise and BCAA prevented AKI-related muscle wasting without worsening kidney damage, suggesting that early rehabilitation with nutritional support could prevent AKI-related muscle wasting.
    Keywords:  acute kidney injury; branched-chain amino acid; exercise; muscle wasting
    DOI:  https://doi.org/10.14814/phy2.14557
  57. Nat Commun. 2020 Aug 27. 11(1): 4308
    Predicting distant metastasis and chemotherapy benefit in locally advanced rectal cancer.
    Zhenyu Liu, Xiaochun Meng, Hongmei Zhang, Zhenhui Li, Jiangang Liu, Kai Sun, Yankai Meng, Weixing Dai, Peiyi Xie, Yingying Ding, Meiyun Wang, Guoxiang Cai, Jie Tian.
      Distant metastasis (DM) is the main cause of treatment failure in locally advanced rectal cancer. Adjuvant chemotherapy is usually used for distant control. However, not all patients can benefit from adjuvant chemotherapy, and particularly, some patients may even get worse outcomes after the treatment. We develop and validate an MRI-based radiomic signature (RS) for prediction of DM within a multicenter dataset. The RS is proved to be an independent prognostic factor as it not only demonstrates good accuracy for discriminating patients into high and low risk of DM in all the four cohorts, but also outperforms clinical models. Within the stratified analysis, good chemotherapy efficacy is observed for patients with pN2 disease and low RS, whereas poor chemotherapy efficacy is detected in patients with pT1-2 or pN0 disease and high RS. The RS may help individualized treatment planning to select patients who may benefit from adjuvant chemotherapy for distant control.
    DOI:  https://doi.org/10.1038/s41467-020-18162-9
  58. Nature. 2020 Aug 26.
    Keratins are asymmetrically inherited fate determinants in the mammalian embryo.
    Hui Yi Grace Lim, Yanina D Alvarez, Maxime Gasnier, Yiming Wang, Piotr Tetlak, Stephanie Bissiere, Hongmei Wang, Maté Biro, Nicolas Plachta.
      To implant in the uterus, the mammalian embryo first specifies two cell lineages: the pluripotent inner cell mass that forms the fetus, and the outer trophectoderm layer that forms the placenta1. In many organisms, asymmetrically inherited fate determinants drive lineage specification2, but this is not thought to be the case during early mammalian development. Here we show that intermediate filaments assembled by keratins function as asymmetrically inherited fate determinants in the mammalian embryo. Unlike F-actin or microtubules, keratins are the first major components of the cytoskeleton that display prominent cell-to-cell variability, triggered by heterogeneities in the BAF chromatin-remodelling complex. Live-embryo imaging shows that keratins become asymmetrically inherited by outer daughter cells during cell division, where they stabilize the cortex to promote apical polarization and YAP-dependent expression of CDX2, thereby specifying the first trophectoderm cells of the embryo. Together, our data reveal a mechanism by which cell-to-cell heterogeneities that appear before the segregation of the trophectoderm and the inner cell mass influence lineage fate, via differential keratin regulation, and identify an early function for intermediate filaments in development.
    DOI:  https://doi.org/10.1038/s41586-020-2647-4
  59. Nature. 2020 Aug;584(7822): 608-613
    Heterotypic cell-cell communication regulates glandular stem cell multipotency.
    Alessia Centonze, Shuheng Lin, Elisavet Tika, Alejandro Sifrim, Marco Fioramonti, Milan Malfait, Yura Song, Aline Wuidart, Jens Van Herck, Anne Dannau, Gaelle Bouvencourt, Christine Dubois, Nina Dedoncker, Amar Sahay, Viviane de Maertelaer, Christian W Siebel, Alexandra Van Keymeulen, Thierry Voet, Cédric Blanpain.
      Glandular epithelia, including the mammary and prostate glands, are composed of basal cells (BCs) and luminal cells (LCs)1,2. Many glandular epithelia develop from multipotent basal stem cells (BSCs) that are replaced in adult life by distinct pools of unipotent stem cells1,3-8. However, adult unipotent BSCs can reactivate multipotency under regenerative conditions and upon oncogene expression3,9-13. This suggests that an active mechanism restricts BSC multipotency under normal physiological conditions, although the nature of this mechanism is unknown. Here we show that the ablation of LCs reactivates the multipotency of BSCs from multiple epithelia both in vivo in mice and in vitro in organoids. Bulk and single-cell RNA sequencing revealed that, after LC ablation, BSCs activate a hybrid basal and luminal cell differentiation program before giving rise to LCs-reminiscent of the genetic program that regulates multipotency during embryonic development7. By predicting ligand-receptor pairs from single-cell data14, we find that TNF-which is secreted by LCs-restricts BC multipotency under normal physiological conditions. By contrast, the Notch, Wnt and EGFR pathways were activated in BSCs and their progeny after LC ablation; blocking these pathways, or stimulating the TNF pathway, inhibited regeneration-induced BC multipotency. Our study demonstrates that heterotypic communication between LCs and BCs is essential to maintain lineage fidelity in glandular epithelial stem cells.
    DOI:  https://doi.org/10.1038/s41586-020-2632-y
  60. Cureus. 2020 Aug 23. 12(8): e9969
    The Role of Interleukin-6 and Inflammatory Cytokines in Pancreatic Cancer-Associated Depression.
    Maria Daniela Jarrin Jara, Avneesh S Gautam, Venkata Sri Ramani Peesapati, Mohammad Sadik, Safeera Khan.
      Pancreatic cancer is historically known for representing a challenge for both diagnosis and treatment. Despite the advances in medicine, science, and technology, it remains the third leading cause of cancer-related deaths in the United States. The association between pancreatic cancer and major depression preceding the diagnosis is well known; however, it is still poorly understood, being considered an obscure piece of the puzzle the disease represents. It has been characterized as a paraneoplastic syndrome caused by the dysregulation of inflammatory cytokines, especially interleukin-6 (IL-6). Despite many types of studies describing the association, researchers have been reluctant to recommend it as a screening tool or early marker of the disease, mainly because of the non-specific nature of depression and anxiety in the studied patients. In this literature review, we aim to better understand the relationship between pancreatic cancer and major depression and characterize the immunologic mechanism of action behind the association.
    Keywords:  depression; inflammatory cytokines; interleukin (il)-6; pancreatic cancer; paraneoplastic syndrome
    DOI:  https://doi.org/10.7759/cureus.9969
  61. Nat Immunol. 2020 Aug 24.
    Early precursor T cells establish and propagate T cell exhaustion in chronic infection.
    Daniel T Utzschneider, Sarah S Gabriel, David Chisanga, Renee Gloury, Patrick M Gubser, Ajithkumar Vasanthakumar, Wei Shi, Axel Kallies.
      CD8+ T cells responding to chronic infections or tumors acquire an 'exhausted' state associated with elevated expression of inhibitory receptors, including PD-1, and impaired cytokine production. Exhausted T cells are continuously replenished by T cells with precursor characteristics that self-renew and depend on the transcription factor TCF1; however, their developmental requirements are poorly understood. In the present study, we demonstrate that high antigen load promoted the differentiation of precursor T cells, which acquired hallmarks of exhaustion within days of infection, whereas early effector cells retained polyfunctional features. Early precursor T cells showed epigenetic imprinting characteristic of T cell receptor-dependent transcription factor binding and were restricted to the generation of cells displaying exhaustion characteristics. Transcription factors BACH2 and BATF were key regulators with opposing functions in the generation of early precursor T cells. Overall, we demonstrate that exhaustion manifests first in TCF1+ precursor T cells and is propagated subsequently to the pool of antigen-specific T cells.
    DOI:  https://doi.org/10.1038/s41590-020-0760-z
  62. Nat Commun. 2020 Aug 28. 11(1): 4323
    Wnt activation as a therapeutic strategy in medulloblastoma.
    Branavan Manoranjan, Chitra Venugopal, David Bakhshinyan, Ashley A Adile, Laura Richards, Michelle M Kameda-Smith, Owen Whitley, Anna Dvorkin-Gheva, Minomi Subapanditha, Neil Savage, Nazanin Tatari, Dillon McKenna, Blessing Bassey-Archibong, Neil Winegarden, Robin Hallett, John P Provias, Blake Yarascavitch, Olufemi Ajani, Adam Fleming, Gary D Bader, Trevor J Pugh, Bradley W Doble, Sheila K Singh.
      Medulloblastoma (MB) is defined by four molecular subgroups (Wnt, Shh, Group 3, Group 4) with Wnt MB having the most favorable prognosis. Since prior reports have illustrated the antitumorigenic role of Wnt activation in Shh MB, we aimed to assess the effects of activated canonical Wnt signaling in Group 3 and 4 MBs. By using primary patient-derived MB brain tumor-initiating cell (BTIC) lines, we characterize differences in the tumor-initiating capacity of Wnt, Group 3, and Group 4 MB. With single cell RNA-seq technology, we demonstrate the presence of rare Wnt-active cells in non-Wnt MBs, which functionally retain the impaired tumorigenic potential of Wnt MB. In treating MB xenografts with a Wnt agonist, we provide a rational therapeutic option in which the protective effects of Wnt-driven MBs may be augmented in Group 3 and 4 MB and thereby support emerging data for a context-dependent tumor suppressive role for Wnt/β-catenin signaling.
    DOI:  https://doi.org/10.1038/s41467-020-17953-4
  63. Curr Pharm Des. 2020 Aug 26.
    Mitochondrial-induced epigenetic modifications: from biology to clinical translation.
    Jahnavi Sharma, Roshani Kumari, Arpit Bhargava, Rajnarayan Tiwari, Pradyumna Kumar Mishra.
      Mitochondria are maternally inherited semi-autonomous organelles that play a central role in redox balance, energy metabolism, control of integrated stress responses, and cellular homeostasis. The molecular communication between mitochondria and the nucleus is intricate and bidirectional in nature. Though mitochondrial genome encodes for a number of key proteins involved in oxidative phosphorylation, several regulatory factors encoded by nuclear DNA are prominent contributors to mitochondrial biogenesis and function. The loss of synergy between this reciprocal control of anterograde (nuclear to mitochondrial) and retrograde (mitochondrial to nuclear) signaling, triggers epigenomic imbalance, and affects mitochondrial function and global gene expressions. Recent expansions of our knowledge on mitochondrial epigenomics have offered novel perspectives for the study of several non-communicable diseases including cancer. As mitochondria are considered beacons for pharmacological interventions, new frontiers in targeted delivery approaches could provide opportunities for effective disease management and cure through reversible epigenetic reprogramming. This review focuses on recent progress in the area of mitochondrial-nuclear cross-talk and epigenetic regulation of mitochondrial DNA methylation, mitochondrial micro RNAs, and post-translational modification of mitochondrial nucleoid-associated proteins that hold major opportunities for targeted drug delivery and clinical translation.
    Keywords:  Epigenomicsignatures; Mitochondrial medicine; Mitochondrial targeting; Mitochondrial-nuclear cross-talk; Translational research
    DOI:  https://doi.org/10.2174/1381612826666200826165735
  64. Radiat Res. 2020 Aug 01. 194(2): 103-115
    The Roles of Autophagy and Senescence in the Tumor Cell Response to Radiation.
    Nipa H Patel, Sahib S Sohal, Masoud H Manjili, J Chuck Harrell, David A Gewirtz.
      Radiation is a critical pillar in cancer therapeutics, exerting its anti-tumor DNA-damaging effects through various direct and indirect mechanisms. Radiation has served as an effective mode of treatment for a number of cancer types, providing both curative and palliative treatment; however, resistance to therapy persists as a fundamental limitation. While cancer cell death is the ideal outcome of any anti-tumor treatment, radiation induces several responses, including apoptotic cell death, mitotic catastrophe, autophagy and senescence, where autophagy and senescence may promote cell survival. In most cases, autophagy, a conventionally cytoprotective mechanism, is a "first" responder to damage incurred from chemotherapy and radiation treatment. The paradigm developed on the premise that autophagy is cytoprotective in nature has provided the rationale for current clinical trials designed with the goal of radiosensitizing cancer cells through the use of autophagy inhibitors; however, these have failed to produce consistent results. Delving further into pre-clinical studies, autophagy has actually been shown to take diverse, sometimes opposing, forms, such as acting in a cytotoxic or nonprotective fashion, which may be partially responsible for the inconsistency of clinical outcomes. Furthermore, autophagy can have both pro- and anti-tumorigenic effects, while also having an important immune modulatory function. Senescence often occurs in tandem with autophagy, which is also the case with radiation. Radiation-induced senescence is frequently followed by a phase of proliferative recovery in a subset of cells and has been proposed as a tumor dormancy model, which can contribute to resistance to therapy and possibly also disease recurrence. Senescence induction is often accompanied by a unique secretory phenotype that can either promote or suppress immune functions, depending on the expression profile of cytokines and chemokines. Novel therapeutics selectively cytotoxic to senescent cells (senolytics) may prove to prolong remission by delaying disease recurrence in patients. Accurate assessment of primary responses to radiation may provide potential targets that can be manipulated for therapeutic benefit to sensitize cancer cells to radiotherapy, while sparing normal tissue.
    DOI:  https://doi.org/10.1667/RADE-20-00009
  65. Nat Commun. 2020 08 26. 11(1): 4253
    Emerging preclinical evidence does not support broad use of hydroxychloroquine in COVID-19 patients.
    S G P Funnell, W E Dowling, C Muñoz-Fontela, P-S Gsell, D E Ingber, G A Hamilton, L Delang, J Rocha-Pereira, S Kaptein, K H Dallmeier, J Neyts, K Rosenke, E de Wit, H Feldmann, P Maisonnasse, R Le Grand, M B Frieman, C M Coleman.
      
    DOI:  https://doi.org/10.1038/s41467-020-17907-w
  66. Nat Commun. 2020 Aug 28. 11(1): 4331
    Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å.
    Jonathan A Flores, Bassam G Haddad, Kimberly A Dolan, Janette B Myers, Craig C Yoshioka, Jeremy Copperman, Daniel M Zuckerman, Steve L Reichow.
      Gap junctions establish direct pathways for cells to transfer metabolic and electrical messages. The local lipid environment is known to affect the structure, stability and intercellular channel activity of gap junctions; however, the molecular basis for these effects remains unknown. Here, we incorporate native connexin-46/50 (Cx46/50) intercellular channels into a dual lipid nanodisc system, mimicking a native cell-to-cell junction. Structural characterization by CryoEM reveals a lipid-induced stabilization to the channel, resulting in a 3D reconstruction at 1.9 Å resolution. Together with all-atom molecular dynamics simulations, it is shown that Cx46/50 in turn imparts long-range stabilization to the dynamic local lipid environment that is specific to the extracellular lipid leaflet. In addition, ~400 water molecules are resolved in the CryoEM map, localized throughout the intercellular permeation pathway and contributing to the channel architecture. These results illustrate how the aqueous-lipid environment is integrated with the architectural stability, structure and function of gap junction communication channels.
    DOI:  https://doi.org/10.1038/s41467-020-18120-5
  67. Cancer Genomics Proteomics. 2020 Sep-Oct;17(5):17(5): 469-497
    Whole-transcriptome Analysis of Fully Viable Energy Efficient Glycolytic-null Cancer Cells Established by Double Genetic Knockout of Lactate Dehydrogenase A/B or Glucose-6-Phosphate Isomerase.
    Elizabeth Mazzio, Ramesh Badisa, Nzinga Mack, Shamir Cassim, Masa Zdralevic, Jacques Pouyssegur, Karam F A Soliman.
      BACKGROUND/AIM: Nearly all mammalian tumors of diverse tissues are believed to be dependent on fermentative glycolysis, marked by elevated production of lactic acid and expression of glycolytic enzymes, most notably lactic acid dehydrogenase (LDH). Therefore, there has been significant interest in developing chemotherapy drugs that selectively target various isoforms of the LDH enzyme. However, considerable questions remain as to the consequences of biological ablation of LDH or upstream targeting of the glycolytic pathway.MATERIALS AND METHODS: In this study, we explore the biochemical and whole transcriptomic effects of CRISPR-Cas9 gene knockout (KO) of lactate dehydrogenases A and B [LDHA/B double KO (DKO)] and glucose-6-phosphate isomerase (GPI KO) in the human colon cancer cell line LS174T, using Affymetrix 2.1 ST arrays.
    RESULTS: The metabolic biochemical profiles corroborate that relative to wild type (WT), LDHA/B DKO produced no lactic acid, (GPI KO) produced minimal lactic acid and both KOs displayed higher mitochondrial respiration, and minimal use of glucose with no loss of cell viability. These findings show a high biochemical energy efficiency as measured by ATP in glycolysis-null cells. Next, transcriptomic analysis conducted on 48,226 mRNA transcripts reflect 273 differentially expressed genes (DEGS) in the GPI KO clone set, 193 DEGS in the LDHA/B DKO clone set with 47 DEGs common to both KO clones. Glycolytic-null cells reflect up-regulation in gene transcripts typically associated with nutrient deprivation / fasting and possible use of fats for energy: thioredoxin interacting protein (TXNIP), mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), PPARγ coactivator 1α (PGC-1α), and acetyl-CoA acyltransferase 2 (ACAA2). Other changes in non-ergometric transcripts in both KOs show losses in "stemness", WNT signaling pathway, chemo/radiation resistance, retinoic acid synthesis, drug detoxification, androgen/estrogen activation, and extracellular matrix reprogramming genes.
    CONCLUSION: These findings demonstrate that: 1) The "Warburg effect" is dispensable, 2) loss of the LDHAB gene is not only inconsequential to viability but fosters greater mitochondrial energy, and 3) drugs that target LDHA/B are likely to be ineffective without a plausible combination second drug target.
    Keywords:  Cancer; GPI; LDHA; LDHB; Warburg effect; genes; metabolism
    DOI:  https://doi.org/10.21873/cgp.20205
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