bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2020–07–05
forty-one papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. CD81 Controls Beige Fat Progenitor Cell Growth and Energy Balance via FAK Signaling.
  2. Reduced mitochondrial resilience enables non-canonical induction of apoptosis after TNF receptor signaling in virus-infected hepatocytes.
  3. Metabolic Communication and Healthy Aging: Where Should We Focus Our Energy?
  4. Dietary glutamine supplementation suppresses epigenetically-activated oncogenic pathways to inhibit melanoma tumour growth.
  5. Hyperglycemia enhances pancreatic cancer progression accompanied by elevations in phosphorylated STAT3 and MYC levels.
  6. Subtypes of pancreatic stellate cells and distant metastasis of pancreatic ductal adenocarcinoma.
  7. Implementing cell-free DNA of pancreatic cancer patient-derived organoids for personalized oncology.
  8. Leukemia cell of origin influences apoptotic priming and sensitivity to LSD1 inhibition.
  9. Niche-Selective Inhibition of Pathogenic Th17 Cells by Targeting Metabolic Redundancy.
  10. CXCR4 in tumor epithelial cells mediates desmoplastic reaction in pancreatic ductal adenocarcinoma.
  11. Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes.
  12. Progressively De-Differentiated Pancreatic Cancer Cells Shift from Glycolysis to Oxidative Metabolism and Gain a Quiescent Stem State.
  13. An essential role for cardiolipin in the stability and function of the mitochondrial calcium uniporter.
  14. The Lysosome at the Intersection of Cellular Growth and Destruction.
  15. AMPK is activated during lysosomal damage via a galectin-ubiquitin signal transduction system.
  16. Persistent telomere cohesion protects aged cells from premature senescence.
  17. Conserved Ark1-related kinases function in a TORC2 signaling network.
  18. Exercise rejuvenates quiescent skeletal muscle stem cells in old mice through restoration of Cyclin D1.
  19. Endocytic regulation of cellular ion homeostasis controls lysosome biogenesis.
  20. Interaction mapping of endoplasmic reticulum ubiquitin ligases identifies modulators of innate immune signalling.
  21. The transcription factors aryl hydrocarbon receptor and MYC cooperate in the regulation of cellular metabolism.
  22. The type of KRAS mutation drives PI3Kα/γ signalling dependency: Implication for the choice of targeted therapy in pancreatic adenocarcinoma patients.
  23. Mitochondrial Substrate Utilization Regulates Cardiomyocyte Cell Cycle Progression.
  24. Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate.
  25. A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.
  26. An engineered chimeric toxin that cleaves activated mutant and wild-type RAS inhibits tumor growth.
  27. The plasticity of DNA replication forks in response to clinically relevant genotoxic stress.
  28. Pressure-enabled delivery of gemcitabine in an orthotopic pancreatic cancer mouse model.
  29. Origin and Function of Stress-Induced IL-6 in Murine Models.
  30. An Insulin-Sensitive Circular RNA that Regulates Lifespan in Drosophila.
  31. Telomere Stress Potentiates STING-Dependent Anti-tumor Immunity.
  32. Targeting Cellular Senescence in Cancer and Aging: Roles of p53 and its Isoforms.
  33. Branched actin networks are assembled on microtubules by adenomatous polyposis coli for targeted membrane protrusion.
  34. Turning Cold into Hot: Firing up the Tumor Microenvironment.
  35. Reprogramming of profibrotic macrophages for treatment of bleomycin-induced pulmonary fibrosis.
  36. Systematic quantitative analysis of ribosome inventory during nutrient stress.
  37. Mathematical Model of Muscle Wasting in Cancer Cachexia.
  38. Lymph node fibroblastic reticular cells deposit fibrosis-associated collagen following organ transplantation.
  39. Cell-by-Cell Deconstruction of Stem Cell Niches.
  40. JNK-mediated disruption of bile acid homeostasis promotes intrahepatic cholangiocarcinoma.
  41. Selective autophagy inhibition through disruption of the PIK3C3-containing complex I.
  1. Cell. 2020 Jun 26. pii: S0092-8674(20)30753-4. [Epub ahead of print]
    CD81 Controls Beige Fat Progenitor Cell Growth and Energy Balance via FAK Signaling.
    Yasuo Oguri, Kosaku Shinoda, Hyeonwoo Kim, Diana L Alba, W Reid Bolus, Qiang Wang, Zachary Brown, Rachana N Pradhan, Kazuki Tajima, Takeshi Yoneshiro, Kenji Ikeda, Yong Chen, Rachel T Cheang, Kazuyuki Tsujino, Caroline R Kim, Vanille Juliette Greiner, Ritwik Datta, Christopher D Yang, Kamran Atabai, Michael T McManus, Suneil K Koliwad, Bruce M Spiegelman, Shingo Kajimura.
      Adipose tissues dynamically remodel their cellular composition in response to external cues by stimulating beige adipocyte biogenesis; however, the developmental origin and pathways regulating this process remain insufficiently understood owing to adipose tissue heterogeneity. Here, we employed single-cell RNA-seq and identified a unique subset of adipocyte progenitor cells (APCs) that possessed the cell-intrinsic plasticity to give rise to beige fat. This beige APC population is proliferative and marked by cell-surface proteins, including PDGFRα, Sca1, and CD81. Notably, CD81 is not only a beige APC marker but also required for de novo beige fat biogenesis following cold exposure. CD81 forms a complex with αV/β1 and αV/β5 integrins and mediates the activation of integrin-FAK signaling in response to irisin. Importantly, CD81 loss causes diet-induced obesity, insulin resistance, and adipose tissue inflammation. These results suggest that CD81 functions as a key sensor of external inputs and controls beige APC proliferation and whole-body energy homeostasis.
    Keywords:  adipocyte progenitors; adipogenesis; beige fat; brown fat; diabetes; metabolic adaptation; metabolic disease; metabolism; obesity; tissue remodeling
    DOI:  https://doi.org/10.1016/j.cell.2020.06.021
  2. J Hepatol. 2020 Jun 26. pii: S0168-8278(20)30398-6. [Epub ahead of print]
    Reduced mitochondrial resilience enables non-canonical induction of apoptosis after TNF receptor signaling in virus-infected hepatocytes.
    Sandra Lampl, Marianne K Janas, Sainitin Donakonda, Marcus Brugger, Kerstin Lohr, Annika Schneider, Katrin Manske, Laura E Sperl, Jennifer Wettmarshausen, Constanze Müller, Melanie Laschinger, Daniel Hartmann, Norber Hüser, Fabiana Perrochi, Philippe Schmitt-Kopplin, Franz Hagn, Lars Zender, Veit Hornung, Christoph Borner, Andreas Pichlmair, Hamid Kashkar, Martin Klingenspor, Marco Prinz, Sabrina Schreiner, Marcus Conrad, Philipp J Jost, Hans Zischka, Katja Steiger, Martin Krönke, Dietmar Zehn, Ulrike Protzer, Mathias Heikenwälder, Percy A Knolle, Dirk Wohlleber.
       BACKGROUND & AIMS: Selective elimination of virus-infected hepatocytes occurs through virus-specific CD8 T-cells recognizing peptide-loaded MHC molecules. Here, we report that virus-infected hepatocytes are also selectively eliminated through a cell-autonomous mechanism.
    METHODS: We generated recombinant adenoviruses and genetically modified mouse models to identify the molecular mechanisms determining TNF-induced hepatocyte apoptosis in vivo and used in vivo bioluminescence imaging, immunohistochemistry, immunoblot analysis, RNAseq/proteome /phosphoproteome analyses, bioinformatic analyses, mitochondrial function tests.
    RESULTS: We found that TNF precisely eliminated only virus-infected hepatocytes independent from local inflammation and activation of immune sensory receptors. TNF receptor I was equally relevant for NFkB activation in healthy and infected hepatocytes, but selectively mediated apoptosis in infected hepatocytes. Caspase 8 activation downstream of TNF receptor signaling was dispensable for apoptosis in virus-infected hepatocytes, indicating a so far unknown non-canonical cell-intrinsic pathway promoting apoptosis in hepatocytes. We identified a unique state of mitochondrial vulnerability in virus-infected hepatocytes as cause for this non-canonical induction of apoptosis through TNF. Mitochondria from virus-infected hepatocytes showed normal biophysical and bioenergetic functions, but were characterized by reduced resilience towards calcium challenge. In the presence of unchanged TNF induced signaling, ROS-mediated calcium release from the ER caused mitochondrial permeability transition and apoptosis, which identified a link between extrinsic death receptor signaling and cell-intrinsic mitochondrial-mediated caspase activation.
    CONCLUSION: Our findings reveal a novel concept in immune surveillance by identifying a cell-autonomous cell defense mechanism to selectively eliminate virus-infected hepatocytes by mitochondrial permeability transition.
    Keywords:  TNF; anti-viral immunity; hepatocyte apoptosis; mitochondrial function; mitochondrial permeability transition
    DOI:  https://doi.org/10.1016/j.jhep.2020.06.026
  3. Dev Cell. 2020 Jun 26. pii: S1534-5807(20)30461-5. [Epub ahead of print]
    Metabolic Communication and Healthy Aging: Where Should We Focus Our Energy?
    Hannah J Smith, Arpit Sharma, William B Mair.
      Aging is associated with a loss of metabolic homeostasis and plasticity, which is causally linked to multiple age-onset pathologies. The majority of the interventions-genetic, dietary, and pharmacological-that have been found to slow aging and protect against age-related disease in various organisms do so by targeting central metabolic pathways. However, targeting metabolic pathways chronically and ubiquitously makes it difficult to define the downstream effects responsible for lifespan extension and often results in negative effects on growth and health, limiting therapeutic potential. Insight into how metabolic signals are relayed between tissues, cells, and organelles opens up new avenues to target metabolic regulators locally rather than globally for healthy aging. In this review, we discuss the pro-longevity effects of targeting metabolic pathways in specific tissues and how these interventions communicate with distal cells to modulate aging. These studies may be crucial in designing interventions that promote longevity without negative health consequences.
    Keywords:  AMPK; NAD+; aging; extracellular vesicles; insulin signaling; mTOR; metabolism; microRNA; sirtuins; tissue-specificity
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.011
  4. Nat Commun. 2020 Jul 03. 11(1): 3326
    Dietary glutamine supplementation suppresses epigenetically-activated oncogenic pathways to inhibit melanoma tumour growth.
    Mari B Ishak Gabra, Ying Yang, Haiqing Li, Parijat Senapati, Eric A Hanse, Xazmin H Lowman, Thai Q Tran, Lishi Zhang, Linda T Doan, Xiangdong Xu, Dustin E Schones, David A Fruman, Mei Kong.
      Tumour cells adapt to nutrient deprivation in vivo, yet strategies targeting the nutrient poor microenvironment remain unexplored. In melanoma, tumour cells often experience low glutamine levels, which promote cell dedifferentiation. Here, we show that dietary glutamine supplementation significantly inhibits melanoma tumour growth, prolongs survival in a transgenic melanoma mouse model, and increases sensitivity to a BRAF inhibitor. Metabolomic analysis reveals that dietary uptake of glutamine effectively increases the concentration of glutamine in tumours and its downstream metabolite, αKG, without increasing biosynthetic intermediates necessary for cell proliferation. Mechanistically, we find that glutamine supplementation uniformly alters the transcriptome in tumours. Our data further demonstrate that increase in intra-tumoural αKG concentration drives hypomethylation of H3K4me3, thereby suppressing epigenetically-activated oncogenic pathways in melanoma. Therefore, our findings provide evidence that glutamine supplementation can serve as a potential dietary intervention to block melanoma tumour growth and sensitize tumours to targeted therapy via epigenetic reprogramming.
    DOI:  https://doi.org/10.1038/s41467-020-17181-w
  5. PLoS One. 2020 ;15(7): e0235573
    Hyperglycemia enhances pancreatic cancer progression accompanied by elevations in phosphorylated STAT3 and MYC levels.
    Katsuhiko Sato, Hayato Hikita, Yuta Myojin, Kenji Fukumoto, Kazuhiro Murai, Sadatsugu Sakane, Takeshi Tamura, Takuo Yamai, Yasutoshi Nozaki, Teppei Yoshioka, Takahiro Kodama, Minoru Shigekawa, Ryotaro Sakamori, Tomohide Tatsumi, Tetsuo Takehara.
      Diabetes mellitus is a well-known risk factor for pancreatic cancer. We focused on hyperglycemia, a main feature of diabetes mellitus, and uncovered its effect on precancerous pancreatic intraepithelial neoplasia (PanIN) progression. In vivo induction of hyperglycemia with 100 mg/kg streptozotocin in KrasLSL G12D Pdx1Cre (KP) mice promoted the PanIN formation and progression. Preconditioning with a high- or low-glucose medium for 28 days showed that a high-glucose environment increased cell viability and sphere formation in PANC-1, a Kras-mutant human pancreatic ductal adenocarcinoma cell line, and mPKC1, a Kras-mutant murine pancreatic cancer cell line. In contrast, no changes were observed in BxPC3, a Kras-wild-type human pancreatic cancer cell line. Orthotopic injection of mPKC1 into the pancreatic tails of BL6/J mice showed that cells maintained in high-glucose medium grew into larger tumors than did those maintained in low-glucose medium. Hyperglycemia strengthened the STAT3 phosphorylation, which was accompanied by elevated MYC expression in Kras-mutant cells. Immunohistochemistry showed stronger phosphorylated STAT3 (pSTAT3) and MYC staining in PanINs from diabetic KP mice than in those from euglycemic counterparts. STAT3 inhibition with 1 μM STAT3 inhibitor STATTIC in Kras-mutant pancreatic cell lines blocked the cell viability- and sphere formation-enhancing effects of the hyperglycemic environment and reversed the elevated pSTAT3 and MYC expression. MYC knockdown did not affect cell viability but did reduce sphere formation. No decrease in pSTAT3 expression was observed upon siMYC treatment. In conclusion, hyperglycemia, on a Kras-mutant background, aggravates the PanIN progression, which is accompanied by elevated pSTAT3 and MYC expression.
    DOI:  https://doi.org/10.1371/journal.pone.0235573
  6. Ann Transl Med. 2020 Jun;8(11): 671
    Subtypes of pancreatic stellate cells and distant metastasis of pancreatic ductal adenocarcinoma.
    Yuhui Fan, Marina Lesina, Hana Algül.
      
    DOI:  https://doi.org/10.21037/atm.2020.03.136
  7. JCI Insight. 2020 Jul 02. pii: 137809. [Epub ahead of print]
    Implementing cell-free DNA of pancreatic cancer patient-derived organoids for personalized oncology.
    Zahra Dantes, Hsi-Yu Yen, Nicole Pfarr, Christof Winter, Katja Steiger, Alexander Muckenhuber, Alexander Hennig, Sebastian Lange, Thomas Engleitner, Rupert Öllinger, Roman Maresch, Felix Orben, Irina Heid, Georgios A Kaissis, Kuangyu Shi, Geoffrey J Topping, Fabian Stögbauer, Matthias Wirth, Katja Peschke, Aristeidis Papargyriou, Massoud Rezaee-Oghazi, Karin Feldmann, Arlett P G Schäfer, Raphela Ranjan, Clara Lubeseder-Martellato, Daniel E Stange, Thilo Welsch, Marc E Martignoni, Güralp Onur Ceyhan, Helmut Friess, Alexander Herner, Lucia Liotta, Matthias Treiber, Guido von Figura, Mohamed Abdelhafez, Peter Klare, Christoph Schlag, Hana Algül, Jens T Siveke, Rickmer F Braren, Gregor Weirich, Wilko Weichert, Dieter Saur, Roland Rad, Roland Schmid, Günter Schneider, Maximilian Reichert.
      One of the major challenges in using pancreatic cancer patient-derived organoids (PDOs) in precision oncology is the time from biopsy to functional characterization. This is particularly true for biopsy specimen with limited tumor cell yield, typical characteristics of biopsies from endoscopic ultrasound-guided fine needle aspirations (EUS-FNAs).Here, we tested conditioned media of individual PDOs for cell-free tumor DNA (cfDNA) to detect driver mutations already early on during the expansion process in order to accelerate the genetic characterization of PDOs as well as subsequent functional testing. Importantly, genetic alterations detected in the PDO supernatant, collected as early as 72h after biopsy, recapitulate the mutational profile of the primary tumor indicating suitability of this approach to subject PDOs to drug testing in a reduced timeframe. In addition, we demonstrate that this workflow is practicable even in patients of whom the amount of tumor material was not sufficient for molecular characterization by established means.Our findings demonstrate that generating PDOs from very limited biopsy material permits molecular profiling and drug testing. With our approach this can be achieved in a rapid and feasible fashion with broad implications in clinical practice.
    Keywords:  Gastroenterology; Oncology; Translation
    DOI:  https://doi.org/10.1172/jci.insight.137809
  8. Cancer Discov. 2020 Jun 30. pii: CD-19-1469. [Epub ahead of print]
    Leukemia cell of origin influences apoptotic priming and sensitivity to LSD1 inhibition.
    Sheng F Cai, S Haihua Chu, Aaron D Goldberg, Salma Parvin, Richard P Koche, Jacob L Glass, Eytan M Stein, Martin S Tallman, Filiz Sen, Christopher A Famulare, Monica Cusan, Chun-Hao Huang, Chun-Wei Chen, Lihua Zou, Keith B Cordner, Nicole L DelGaudio, Vidushi Durani, Mitali Kini, Madison Rex, Helen S Tian, Johannes Zuber, Timour Baslan, Scott W Lowe, Hugh Y Rienhoff, Anthony Letai, Ross L Levine, Scott A Armstrong.
      The cell of origin of oncogenic transformation is a determinant of therapeutic sensitivity, but the mechanisms governing cell-of-origin-driven differences in therapeutic response have not been delineated. Leukemias initiating in hematopoietic stem cells (HSC) are less sensitive to chemotherapy and highly express the transcription factor Evi1 compared to leukemias derived from myeloid progenitors. Here, we compared leukemias initiated in either HSCs or myeloid progenitors to reveal a novel function for Evi1 in modulating p53 protein abundance and activity. HSC-derived leukemias exhibit decreased apoptotic priming, attenuated p53 transcriptional output, and resistance to lysine-specific demethylase 1 inhibitors in addition to classical genotoxic stresses. p53 loss-of-function in Evi1-low progenitor-derived leukemias induces resistance to LSD1 inhibition, and Evi1-high leukemias are sensitized to LSD1 inhibition by venetoclax. Our findings demonstrate a role for EVI1 in p53 wild-type cancers in reducing p53 function and provide a strategy to circumvent drug resistance in chemoresistant EVI1-high AML.
    DOI:  https://doi.org/10.1158/2159-8290.CD-19-1469
  9. Cell. 2020 Jun 24. pii: S0092-8674(20)30745-5. [Epub ahead of print]
    Niche-Selective Inhibition of Pathogenic Th17 Cells by Targeting Metabolic Redundancy.
    Lin Wu, Kate E R Hollinshead, Yuhan Hao, Christy Au, Lina Kroehling, Charles Ng, Woan-Yu Lin, Dayi Li, Hernandez Moura Silva, Jong Shin, Juan J Lafaille, Richard Possemato, Michael E Pacold, Thales Papagiannakopoulos, Alec C Kimmelman, Rahul Satija, Dan R Littman.
      Targeting glycolysis has been considered therapeutically intractable owing to its essential housekeeping role. However, the context-dependent requirement for individual glycolytic steps has not been fully explored. We show that CRISPR-mediated targeting of glycolysis in T cells in mice results in global loss of Th17 cells, whereas deficiency of the glycolytic enzyme glucose phosphate isomerase (Gpi1) selectively eliminates inflammatory encephalitogenic and colitogenic Th17 cells, without substantially affecting homeostatic microbiota-specific Th17 cells. In homeostatic Th17 cells, partial blockade of glycolysis upon Gpi1 inactivation was compensated by pentose phosphate pathway flux and increased mitochondrial respiration. In contrast, inflammatory Th17 cells experience a hypoxic microenvironment known to limit mitochondrial respiration, which is incompatible with loss of Gpi1. Our study suggests that inhibiting glycolysis by targeting Gpi1 could be an effective therapeutic strategy with minimum toxicity for Th17-mediated autoimmune diseases, and, more generally, that metabolic redundancies can be exploited for selective targeting of disease processes.
    Keywords:  CRISPR; EAE; OXPHOS; autoimmunity; colitis; glycolysis; hypoxia; inflammation; metabolic plasticity; segmented filamentous bacteria
    DOI:  https://doi.org/10.1016/j.cell.2020.06.014
  10. Cancer Res. 2020 Jun 30. pii: canres.2745.2019. [Epub ahead of print]
    CXCR4 in tumor epithelial cells mediates desmoplastic reaction in pancreatic ductal adenocarcinoma.
    Toshihiro Morita, Yuzo Kodama, Masahiro Shiokawa, Katsutoshi Kuriyama, Saiko Marui, Takeshi Kuwada, Yuko Sogabe, Tomoaki Matsumori, Nobuyuki Kakiuchi, Teruko Tomono, Atsushi Mima, Tatsuki Ueda, Motoyuki Tsuda, Yuki Yamauchi, Yoshihiro Nishikawa, Yojiro Sakuma, Yuji Ota, Takahisa Maruno, Norimitsu Uza, Takashi Nagasawa, Tsutomu Chiba, Hiroshi Seno.
      Pancreatic ductal adenocarcinoma (PDAC) features abundant stromal cells with an excessive extracellular matrix (ECM), termed the desmoplastic reaction. CXCR4 is a cytokine receptor for stromal cell-derived factor-1 (CXCL12) expressed in PDAC, but its roles in PDAC and the characteristic desmoplastic reaction remain unclear. Here we generated a mouse model of PDAC with conditional knockout of Cxcr4 (KPC-Cxcr4-KO) by crossing Cxcr4 flox mice with Pdx1-Cre;KrasLSL-G12D/+;Trp53LSL-R172H/+ (KPC-Cxcr4-WT) mice to assess the development of pancreatic intraepithelial neoplasia (PanIN) and pancreatic cancers. Tumor cell characteristics of those two types were analyzed in vitro. In addition, CXCR4 expression in human pancreatic cancer specimens was evaluated by immunohistochemical staining. In KPC-Cxcr4-KO mice, the number and pathological grade of PanIN lesions were reduced, but the frequency of pancreatic cancers did not differ from that in KPC-Cxcr4-WT mice. The pancreatic tumor phenotype in KPC-Cxcr4-KO mice was significantly larger and undifferentiated, characterized by abundant vimentin-expressing cancer cells, significantly fewer fibroblasts, and markedly less deposition of ECM. In vitro, KPC-Cxcr4-KO tumor cells exhibited higher proliferative and migratory activity than KPC-Cxcr4-WT tumor cells. Myofibroblasts induced invasion activity in KPC-Cxcr4-WT tumor cells, showing an epithelial-mesenchymal interaction, whereas KPC-Cxcr4-KO tumor cells were unaffected by myofibroblasts, suggesting their unique nature. In human pancreatic cancer, undifferentiated carcinoma did not express CXCR4 and exhibited histological and immunohistochemical features similar to those in KPC-Cxcr4-KO mice. In summary, the CXCL12/CXCR4 axis may play an important role in the desmoplastic reaction in PDAC, and loss of CXCR4 induces phenotype changes in undifferentiated carcinoma without a desmoplastic reaction.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-19-2745
  11. Nat Commun. 2020 Jul 03. 11(1): 3306
    Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes.
    Keisuke Mochida, Akinori Yamasaki, Kazuaki Matoba, Hiromi Kirisako, Nobuo N Noda, Hitoshi Nakatogawa.
      The endoplasmic reticulum (ER) is selectively degraded by autophagy (ER-phagy) through proteins called ER-phagy receptors. In Saccharomyces cerevisiae, Atg40 acts as an ER-phagy receptor to sequester ER fragments into autophagosomes by binding Atg8 on forming autophagosomal membranes. During ER-phagy, parts of the ER are morphologically rearranged, fragmented, and loaded into autophagosomes, but the mechanism remains poorly understood. Here we find that Atg40 molecules assemble in the ER membrane concurrently with autophagosome formation via multivalent interaction with Atg8. Atg8-mediated super-assembly of Atg40 generates highly-curved ER regions, depending on its reticulon-like domain, and supports packing of these regions into autophagosomes. Moreover, tight binding of Atg40 to Atg8 is achieved by a short helix C-terminal to the Atg8-family interacting motif, and this feature is also observed for mammalian ER-phagy receptors. Thus, this study significantly advances our understanding of the mechanisms of ER-phagy and also provides insights into organelle fragmentation in selective autophagy of other organelles.
    DOI:  https://doi.org/10.1038/s41467-020-17163-y
  12. Cells. 2020 Jun 28. pii: E1572. [Epub ahead of print]9(7):
    Progressively De-Differentiated Pancreatic Cancer Cells Shift from Glycolysis to Oxidative Metabolism and Gain a Quiescent Stem State.
    Giulia Ambrosini, Elisa Dalla Pozza, Giuseppina Fanelli, Claudia Di Carlo, Andrea Vettori, Giuseppe Cannino, Chiara Cavallini, Cristian Andres Carmona-Carmona, Jessica Brandi, Sara Rinalducci, Maria Teresa Scupoli, Andrea Rasola, Daniela Cecconi, Marta Palmieri, Ilaria Dando.
      Pancreatic ductal adenocarcinoma (PDAC) is typically characterized by high chemoresistance and metastatic spread, features mainly attributable to cancer stem cells (CSCs). It is of central interest the characterization of CSCs and, in particular, the study of their metabolic features in order to selectively identify their peculiarities for an efficient therapeutic approach. In this study, CSCs have been obtained by culturing different PDAC cell lines with a specific growth medium. Cells were characterized for the typical stem/mesenchymal properties at short-, medium-, and long-term culture. Metabolomics, proteomics, analysis of oxygen consumption rate in live cells, and the effect of the inhibition of lactate transporter on cell proliferation have been performed to delineate the metabolism of CSCs. We show that gradually de-differentiated pancreatic cancer cells progressively increase the expression of both stem and epithelial-to-mesenchymal transition markers, shift their metabolism from a glycolytic to an oxidative one, and lastly gain a quiescent state. These quiescent stem cells are characterized by high chemo-resistance, clonogenic ability, and metastatic potential. Re-differentiation reverts these features, re-activating their proliferative capacity and glycolytic metabolism, which generally correlates with high aggressiveness. These observations add an important piece of knowledge to the comprehension of the biology of CSCs, whose metabolic plasticity could be exploited for the generation of promising and selective therapeutic approaches for PDAC patients.
    Keywords:  cancer metabolism; cancer stem cells; metabolic plasticity; pancreatic ductal adenocarcinoma; quiescence
    DOI:  https://doi.org/10.3390/cells9071572
  13. Proc Natl Acad Sci U S A. 2020 Jun 29. pii: 202000640. [Epub ahead of print]
    An essential role for cardiolipin in the stability and function of the mitochondrial calcium uniporter.
    Sagnika Ghosh, Writoban Basu Ball, Travis R Madaris, Subramanya Srikantan, Muniswamy Madesh, Vamsi K Mootha, Vishal M Gohil.
      Calcium uptake by the mitochondrial calcium uniporter coordinates cytosolic signaling events with mitochondrial bioenergetics. During the past decade all protein components of the mitochondrial calcium uniporter have been identified, including MCU, the pore-forming subunit. However, the specific lipid requirements, if any, for the function and formation of this channel complex are currently not known. Here we utilize yeast, which lacks the mitochondrial calcium uniporter, as a model system to address this problem. We use heterologous expression to functionally reconstitute human uniporter machinery both in wild-type yeast as well as in mutants defective in the biosynthesis of phosphatidylethanolamine, phosphatidylcholine, or cardiolipin (CL). We uncover a specific requirement of CL for in vivo reconstituted MCU stability and activity. The CL requirement of MCU is evolutionarily conserved with loss of CL triggering rapid turnover of MCU homologs and impaired calcium transport. Furthermore, we observe reduced abundance and activity of endogenous MCU in mammalian cellular models of Barth syndrome, which is characterized by a partial loss of CL. MCU abundance is also decreased in the cardiac tissue of Barth syndrome patients. Our work raises the hypothesis that impaired mitochondrial calcium transport contributes to the pathogenesis of Barth syndrome, and more generally, showcases the utility of yeast phospholipid mutants in dissecting the phospholipid requirements of ion channel complexes.
    Keywords:  Barth syndrome; EMRE; cardiolipin; mitochondrial calcium uniporter (MCU); uniplex
    DOI:  https://doi.org/10.1073/pnas.2000640117
  14. Dev Cell. 2020 Jun 30. pii: S1534-5807(20)30460-3. [Epub ahead of print]
    The Lysosome at the Intersection of Cellular Growth and Destruction.
    Hijai R Shin, Roberto Zoncu.
      The lysosome is an essential catabolic organelle that consumes cellular biomass to regenerate basic building blocks that can fuel anabolic reactions. This simple view has evolved more recently to integrate novel functions of the lysosome as a key signaling center, which can steer the metabolic trajectory of cells in response to changes in nutrients, growth factors, and stress. Master protein kinases and transcription factors mediate the growth-promoting and catabolic activities of the lysosome and undergo a complex interplay that enables cellular adaptation to ever-changing metabolic conditions. Understanding how this coordination occurs will shed light on the fundamental logic of how the lysosome functions to control growth in the context of development, tissue homeostasis, and cancer.
    Keywords:  TFEB; anabolism; autophagy; catabolism; lysosome; mTORC1; nutrient sensing
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.010
  15. Autophagy. 2020 Jun 28.
    AMPK is activated during lysosomal damage via a galectin-ubiquitin signal transduction system.
    Jingyue Jia, Bhawana Bissa, Lukas Brecht, Lee Allers, Seong Won Choi, Yuexi Gu, Mark Zbinden, Mark R Burge, Graham Timmins, Kenneth Hallows, Christian Behrends, Vojo Deretic.
      Lysosomal damage activates AMPK, a regulator of macroautophagy/autophagy and metabolism, and elicits a strong ubiquitination response. Here we show that the cytosolic lectin LGALS9 detects lysosomal membrane breach by binding to lumenal glycoepitopes, and directs both the ubiquitination response and AMPK activation. Proteomic analyses have revealed increased LGALS9 association with lysosomes, and concomitant changes in LGALS9 interactions with its newly identified partners that control ubiquitination-deubiquitination processes. An LGALS9-inetractor, deubiquitinase USP9X, dissociates from damaged lysosomes upon recognition of lumenal glycans by LGALS9. USP9X's departure from lysosomes promotes K63 ubiquitination and stimulation of MAP3K7/TAK1, an upstream kinase and activator of AMPK hitherto orphaned for a precise physiological function. Ubiquitin-activated MAP3K7/TAK1 controls AMPK specifically during lysosomal injury, caused by a spectrum of membrane-damaging or -permeabilizing agents, including silica crystals, the intracellular pathogen Mycobacterium tuberculosis, TNFSF10/TRAIL signaling, and the anti-diabetes drugs metformin. The LGALS9-ubiquitin system activating AMPK represents a novel signal transduction system contributing to various physiological outputs that are under the control of AMPK, including autophagy, MTOR, lysosomal maintenance and biogenesis, immunity, defense against microbes, and metabolic reprograming.
    Keywords:   Mycobacterium tuberculosis ; AMPK; TAK1; TRAIL; USP9X; autophagy; diabetes; lysosome; metabolism; metformin
    DOI:  https://doi.org/10.1080/15548627.2020.1788890
  16. Nat Commun. 2020 Jul 03. 11(1): 3321
    Persistent telomere cohesion protects aged cells from premature senescence.
    Kameron Azarm, Amit Bhardwaj, Eugenie Kim, Susan Smith.
      Human telomeres are bound by the telomere repeat binding proteins TRF1 and TRF2. Telomere shortening in human cells leads to a DNA damage response that signals replicative senescence. While insufficient loading of TRF2 at shortened telomeres contributes to the DNA damage response in senescence, the contribution of TRF1 to senescence induction has not been determined. Here we show that counter to TRF2 deficiency-mediated induction of DNA damage, TRF1 deficiency serves a protective role to limit induction of DNA damage induced by subtelomere recombination. Shortened telomeres recruit insufficient TRF1 and as a consequence inadequate tankyrase 1 to resolve sister telomere cohesion. Our findings suggest that the persistent cohesion protects short telomeres from inappropriate recombination. Ultimately, in the final division, telomeres are no longer able to maintain cohesion and subtelomere copying ensues. Thus, the gradual loss of TRF1 and concomitant persistent cohesion that occurs with telomere shortening ensures a measured approach to replicative senescence.
    DOI:  https://doi.org/10.1038/s41467-020-17133-4
  17. Mol Biol Cell. 2020 Jul 02. mbcE19120685
    Conserved Ark1-related kinases function in a TORC2 signaling network.
    Maria Alcaide-Gavilán, Rafael Lucena, Selene Banuelos, Douglas R Kellogg.
      In all orders of life, cell cycle progression in proliferating cells is dependent upon cell growth, and the extent of growth required for cell cycle progression is proportional to growth rate. Thus, cells growing rapidly in rich nutrients are substantially larger than slow growing cells. In budding yeast, a conserved signaling network surrounding Tor complex 2 (TORC2) controls growth rate and cell size in response to nutrient availability. Here, a search for new components of the TORC2 network identified a pair of redundant kinase paralogs called Ark1 and Prk1. Previous studies found that Ark/Prk play roles in endocytosis. Here, we show that Ark/Prk are embedded in the TORC2 network, where they appear to influence TORC2 signaling independently of their roles in endocytosis. We also show that reduced endocytosis leads to increased cell size, which suggests that cell size homeostasis requires coordinated control of plasma membrane growth and endocytosis. The discovery that Ark/Prk are embedded in the TORC2 network suggests a model in which TORC2-dependent signals control both plasma membrane growth and endocytosis, which would ensure that the rates of each process are matched to each other and to the availability of nutrients so that cells achieve and maintain an appropriate size.
    DOI:  https://doi.org/10.1091/mbc.E19-12-0685
  18. Nat Metab. 2020 Apr;2(4): 307-317
    Exercise rejuvenates quiescent skeletal muscle stem cells in old mice through restoration of Cyclin D1.
    Jamie O Brett, Marina Arjona, Mika Ikeda, Marco Quarta, Antoine de Morrée, Ingrid M Egner, Luiz A Perandini, Heather D Ishak, Armon Goshayeshi, Daniel I Benjamin, Pieter Both, Cristina Rodríguez-Mateo, Michael J Betley, Tony Wyss-Coray, Thomas A Rando.
      Aging impairs tissue repair. This is pronounced in skeletal muscle, whose regeneration by muscle stem cells (MuSCs) is robust in young adult animals but inefficient in older organisms. Despite this functional decline, old MuSCs are amenable to rejuvenation through strategies that improve the systemic milieu, such as heterochronic parabiosis. One such strategy, exercise, has long been appreciated for its benefits on healthspan, but its effects on aged stem cell function in the context of tissue regeneration are incompletely understood. Here we show that exercise in the form of voluntary wheel running accelerates muscle repair in old animals and improves old MuSC function. Through transcriptional profiling and genetic studies, we discovered that the restoration of old MuSC activation ability hinges on restoration of Cyclin D1, whose expression declines with age in MuSCs. Pharmacologic studies revealed that Cyclin D1 maintains MuSC activation capacity by repressing TGFβ signaling. Taken together, these studies demonstrate that voluntary exercise is a practicable intervention for old MuSC rejuvenation. Furthermore, this work highlights the distinct role of Cyclin D1 in stem cell quiescence.
    DOI:  https://doi.org/10.1038/s42255-020-0190-0
  19. Nat Cell Biol. 2020 Jun 29.
    Endocytic regulation of cellular ion homeostasis controls lysosome biogenesis.
    Tania López-Hernández, Dmytro Puchkov, Eberhard Krause, Tanja Maritzen, Volker Haucke.
      Lysosomes serve as cellular degradation and signalling centres that coordinate metabolism in response to intracellular cues and extracellular signals. Lysosomal capacity is adapted to cellular needs by transcription factors, such as TFEB and TFE3, which activate the expression of lysosomal and autophagy genes. Nuclear translocation and activation of TFEB are induced by a variety of conditions such as starvation, lysosome stress and lysosomal storage disorders. How these various cues are integrated remains incompletely understood. Here, we describe a pathway initiated at the plasma membrane that controls lysosome biogenesis via the endocytic regulation of intracellular ion homeostasis. This pathway is based on the exo-endocytosis of NHE7, a Na+/H+ exchanger mutated in X-linked intellectual disability, and serves to control intracellular ion homeostasis and thereby Ca2+/calcineurin-mediated activation of TFEB and downstream lysosome biogenesis in response to osmotic stress to promote the turnover of toxic proteins and cell survival.
    DOI:  https://doi.org/10.1038/s41556-020-0535-7
  20. Elife. 2020 Jul 02. pii: e57306. [Epub ahead of print]9
    Interaction mapping of endoplasmic reticulum ubiquitin ligases identifies modulators of innate immune signalling.
    Emma J Fenech, Federica Lari, Philip D Charles, Roman Fischer, Marie Laétitia-Thézénas, Katrin Bagola, Adrienne W Paton, James C Paton, Mads Gyrd-Hansen, Benedikt M Kessler, John C Christianson.
      Ubiquitin ligases (E3s) embedded in the endoplasmic reticulum (ER) membrane regulate essential cellular activities including protein quality control, calcium flux, and sterol homeostasis. At least 25 different, transmembrane domain (TMD)-containing E3s are predicted to be ER-localised, but for most their organisation and cellular roles remain poorly defined. Using a comparative proteomic workflow, we mapped over 450 protein-protein interactions for 21 stably expressed, full-length E3s. Bioinformatic analysis linked ER-E3s and their interactors to multiple homeostatic, regulatory, and metabolic pathways. Among these were four membrane-embedded interactors of RNF26, a polytopic E3 whose abundance is auto-regulated by ubiquitin-proteasome dependent degradation. RNF26 co-assembles with TMEM43, ENDOD1, TMEM33 and TMED1 to form a complex capable of modulating innate immune signalling through the cGAS-STING pathway. This RNF26 complex represents a new modulatory axis of STING and innate immune signalling at the ER membrane. Collectively, these data reveal the broad scope of regulation and differential functionalities mediated by ER-E3s for both membrane-tethered and cytoplasmic processes.
    Keywords:  RNF26; STING; cell biology; endoplasmic reticulum; immunology; inflammation; innate immune response; none; ubiquitin ligase
    DOI:  https://doi.org/10.7554/eLife.57306
  21. J Biol Chem. 2020 Jul 01. pii: jbc.AC120.014189. [Epub ahead of print]
    The transcription factors aryl hydrocarbon receptor and MYC cooperate in the regulation of cellular metabolism.
    M Carmen Lafita-Navarro, Lizbeth Perez-Castro, Lauren G Zacharias, Spencer Barnes, Ralph J DeBerardinis, Maralice Conacci-Sorrell.
      The transcription factor aryl hydrocarbon receptor (AHR) drives the expression of genes involved in detoxification pathways in cells exposed to pollutants and other small molecules. Moreover, AHR supports transcriptional programs that promote ribosome biogenesis and protein synthesis in cells stimulated to proliferate by the oncoprotein MYC. Thus, AHR is necessary for the proliferation of MYC-overexpressing cells. To define metabolic pathways in which AHR cooperates with MYC in supporting cell growth, here we used LC-MS-based metabolomics to examine the metabolome of MYC-expressing cells uponAHR knockdown. We found that AHR knockdown reduced lactate, S-lactoyl-glutathione,N-acetyl-L-alanine, 2-hydroxyglutarate, and uridine-5-monophosphate (UMP) levels. Using our previously obtained RNA-seq data, we found that AHR mediates the expression of the UMP-generating enzymes dihydroorotate dehydrogenase (quinone) (DHODH) and uridine monophosphate synthetase (UMPS), as well as lactate dehydrogenase A (LDHA), establishing a mechanism by which AHR regulates lactate and UMP production in MYC-overexpressing cells. AHR knockdown in glioblastoma cells also reduced the expression of LDHA (and lactate), DHODH,and UMPS, but did not affect UMP levels, likely due to compensatory mechanisms in these cells. Our results indicate that AHR contributes to the regulation of metabolic pathways necessary for the proliferation of transformed cells.
    Keywords:  Myc (c-Myc); aryl hydrocarbon receptor (AhR) (AHR); cancer; gene regulation; glioblastoma; glycolysis; metabolism; metabolomics; oncogene; pyrimidine
    DOI:  https://doi.org/10.1074/jbc.AC120.014189
  22. Clin Res Hepatol Gastroenterol. 2020 Jun 24. pii: S2210-7401(20)30166-2. [Epub ahead of print]
    The type of KRAS mutation drives PI3Kα/γ signalling dependency: Implication for the choice of targeted therapy in pancreatic adenocarcinoma patients.
    Coralie Cayron, Julie Guillermet-Guibert.
      Pancreatic ductal adenocarcinoma PDAC is a complex disease with an important diversity of genetic alterations found between patients. KRAS mutation is considered as a major oncogenic driver in this cancer (around 90% of the patients), but there exists different KRAS mutation types. The type of KRAS mutation was recently shown to be of importance to detect signalling vulnerabilities in a subset of PDAC patients. We comment on these innovative results and discuss their importance when designing clinical trials with PI3K targeted therapies in this cancer.
    Keywords:  KRAS mutation; Macropinocytosis; PDAC; PI3K; Pancreatic adenocarcinoma; Pancreatic cancer
    DOI:  https://doi.org/10.1016/j.clinre.2020.05.021
  23. Nat Metab. 2020 Feb;2(2): 167-178
    Mitochondrial Substrate Utilization Regulates Cardiomyocyte Cell Cycle Progression.
    Alisson C Cardoso, Nicholas T Lam, Jainy J Savla, Yuji Nakada, Ana Helena M Pereira, Abdallah Elnwasany, Ivan Menendez-Montes, Emily L Ensley, Ursa Bezan Petric, Gaurav Sharma, A Dean Sherry, Craig R Malloy, Chalermchai Khemtong, Michael T Kinter, Wilson Lek Wen Tan, Chukwuemeka George Anene-Nzelu, Roger Sik-Yin Foo, Ngoc Uyen Nhi Nguyen, Shujuan Li, Mahmoud Salama Ahmed, Waleed M Elhelaly, Salim Abdisalaam, Aroumougame Asaithamby, Chao Xing, Mohammed Kanchwala, Goncalo Vale, Kaitlyn M Eckert, Matthew A Mitsche, Jeffrey G McDonald, Joseph A Hill, Linzhang Huang, Philip W Shaul, Luke I Szweda, Hesham A Sadek.
      The neonatal mammalian heart is capable of regeneration for a brief window of time after birth. However, this regenerative capacity is lost within the first week of life, which coincides with a postnatal shift from anaerobic glycolysis to mitochondrial oxidative phosphorylation, particularly towards fatty-acid utilization. Despite the energy advantage of fatty-acid beta-oxidation, cardiac mitochondria produce elevated rates of reactive oxygen species when utilizing fatty acids, which is thought to play a role in cardiomyocyte cell-cycle arrest through induction of DNA damage and activation of DNA-damage response (DDR) pathway. Here we show that inhibiting fatty-acid utilization promotes cardiomyocyte proliferation in the postnatatal heart. First, neonatal mice fed fatty-acid deficient milk showed prolongation of the postnatal cardiomyocyte proliferative window, however cell cycle arrest eventually ensued. Next, we generated a tamoxifen-inducible cardiomyocyte-specific, pyruvate dehydrogenase kinase 4 (PDK4) knockout mouse model to selectively enhance oxidation of glycolytically derived pyruvate in cardiomyocytes. Conditional PDK4 deletion resulted in an increase in pyruvate dehydrogenase activity and consequently an increase in glucose relative to fatty-acid oxidation. Loss of PDK4 also resulted in decreased cardiomyocyte size, decreased DNA damage and expression of DDR markers and an increase in cardiomyocyte proliferation. Following myocardial infarction, inducible deletion of PDK4 improved left ventricular function and decreased remodelling. Collectively, inhibition of fatty-acid utilization in cardiomyocytes promotes proliferation, and may be a viable target for cardiac regenerative therapies.
  24. Cell. 2020 Jun 23. pii: S0092-8674(20)30693-0. [Epub ahead of print]
    Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate.
    Colin Chih-Chien Wu, Amy Peterson, Boris Zinshteyn, Sergi Regot, Rachel Green.
      Problems arising during translation of mRNAs lead to ribosome stalling and collisions that trigger a series of quality control events. However, the global cellular response to ribosome collisions has not been explored. Here, we uncover a function for ribosome collisions in signal transduction. Using translation elongation inhibitors and general cellular stress conditions, including amino acid starvation and UV irradiation, we show that ribosome collisions activate the stress-activated protein kinase (SAPK) and GCN2-mediated stress response pathways. We show that the MAPKKK ZAK functions as the sentinel for ribosome collisions and is required for immediate early activation of both SAPK (p38/JNK) and GCN2 signaling pathways. Selective ribosome profiling and biochemistry demonstrate that although ZAK generally associates with elongating ribosomes on polysomal mRNAs, it specifically auto-phosphorylates on the minimal unit of colliding ribosomes, the disome. Together, these results provide molecular insights into how perturbation of translational homeostasis regulates cell fate.
    Keywords:  SAPK; UV radiation; ZAK; amino acid starvation; integrated stress response; ribosome collisions
    DOI:  https://doi.org/10.1016/j.cell.2020.06.006
  25. Genes Dev. 2020 Jul 02.
    A role for alternative splicing in circadian control of exocytosis and glucose homeostasis.
    Biliana Marcheva, Mark Perelis, Benjamin J Weidemann, Akihiko Taguchi, Haopeng Lin, Chiaki Omura, Yumiko Kobayashi, Marsha V Newman, Eugene J Wyatt, Elizabeth M McNally, Jocelyn E Manning Fox, Heekyung Hong, Archana Shankar, Emily C Wheeler, Kathryn Moynihan Ramsey, Patrick E MacDonald, Gene W Yeo, Joseph Bass.
      The circadian clock is encoded by a negative transcriptional feedback loop that coordinates physiology and behavior through molecular programs that remain incompletely understood. Here, we reveal rhythmic genome-wide alternative splicing (AS) of pre-mRNAs encoding regulators of peptidergic secretion within pancreatic β cells that are perturbed in Clock -/- and Bmal1 -/- β-cell lines. We show that the RNA-binding protein THRAP3 (thyroid hormone receptor-associated protein 3) regulates circadian clock-dependent AS by binding to exons at coding sequences flanking exons that are more frequently skipped in clock mutant β cells, including transcripts encoding Cask (calcium/calmodulin-dependent serine protein kinase) and Madd (MAP kinase-activating death domain). Depletion of THRAP3 restores expression of the long isoforms of Cask and Madd, and mimicking exon skipping in these transcripts through antisense oligonucleotide delivery in wild-type islets reduces glucose-stimulated insulin secretion. Finally, we identify shared networks of alternatively spliced exocytic genes from islets of rodent models of diet-induced obesity that significantly overlap with clock mutants. Our results establish a role for pre-mRNA alternative splicing in β-cell function across the sleep/wake cycle.
    Keywords:  CASK; MADD; RNA sequencing; SNAP25; THRAP3; alternative splicing; circadian clock; exocytosis; insulin secretion; transcriptomics
    DOI:  https://doi.org/10.1101/gad.338178.120
  26. Proc Natl Acad Sci U S A. 2020 Jul 02. pii: 202000312. [Epub ahead of print]
    An engineered chimeric toxin that cleaves activated mutant and wild-type RAS inhibits tumor growth.
    Vania Vidimar, Greg L Beilhartz, Minyoung Park, Marco Biancucci, Matthew B Kieffer, David R Gius, Roman A Melnyk, Karla J F Satchell.
      Despite nearly four decades of effort, broad inhibition of oncogenic RAS using small-molecule approaches has proven to be a major challenge. Here we describe the development of a pan-RAS biologic inhibitor composed of the RAS-RAP1-specific endopeptidase fused to the protein delivery machinery of diphtheria toxin. We show that this engineered chimeric toxin irreversibly cleaves and inactivates intracellular RAS at low picomolar concentrations terminating downstream signaling in receptor-bearing cells. Furthermore, we demonstrate in vivo target engagement and reduction of tumor burden in three mouse xenograft models driven by either wild-type or mutant RAS Intracellular delivery of a potent anti-RAS biologic through a receptor-mediated mechanism represents a promising approach to developing RAS therapeutics against a broad array of cancers.
    Keywords:  RAS; RRSP; cancer; recombinant toxins; xenograft
    DOI:  https://doi.org/10.1073/pnas.2000312117
  27. Nat Rev Mol Cell Biol. 2020 Jul 01.
    The plasticity of DNA replication forks in response to clinically relevant genotoxic stress.
    Matteo Berti, David Cortez, Massimo Lopes.
      Complete and accurate DNA replication requires the progression of replication forks through DNA damage, actively transcribed regions, structured DNA and compact chromatin. Recent studies have revealed a remarkable plasticity of the replication process in dealing with these obstacles, which includes modulation of replication origin firing, of the architecture of replication forks, and of the functional organization of the replication machinery in response to replication stress. However, these specialized mechanisms also expose cells to potentially dangerous transactions while replicating DNA. In this Review, we discuss how replication forks are actively stalled, remodelled, processed, protected and restarted in response to specific types of stress. We also discuss adaptations of the replication machinery and the role of chromatin modifications during these transactions. Finally, we discuss interesting recent data on the relevance of replication fork plasticity to human health, covering its role in tumorigenesis, its crosstalk with innate immunity responses and its potential as an effective cancer therapy target.
    DOI:  https://doi.org/10.1038/s41580-020-0257-5
  28. Surgery. 2020 Jun 30. pii: S0039-6060(20)30273-7. [Epub ahead of print]
    Pressure-enabled delivery of gemcitabine in an orthotopic pancreatic cancer mouse model.
    Jayanth S Shankara Narayanan, Diego A Vicente, Partha Ray, Louis F Chai, Suna Erdem, Matthew J Carr, Benedict A Capacio, Bryan F Cox, David B Jaroch, Steven C Katz, Rebekah R White.
       BACKGROUND: We describe the use of pancreatic retrograde venous infusion in an orthotopic murine model of pancreatic ductal adenocarcinoma and hypothesize that pancreatic retrograde venous infusion delivery of gemcitabine will increase concentrations of gemcitabine in the tumor and the subsequent tumor response to treatment.
    METHODS: Murine pancreatic ductal adenocarcinoma (KPC4580P) was transplanted onto the pancreatic tail of C57BL/6J mice. Groups (n = 15) of mice were assigned to sham laparotomy and 100 mg/kg intraperitoneal infusion of gemcitabine (systemic gemcitabine), pancreatic venous isolation with pancreatic retrograde venous infusion of 100 mg/kg gemcitabine, or pancreatic retrograde venous infusion with saline infusion. Tumor pressures were recorded during pancreatic retrograde venous infusion. Mice were killed at 1 hour or 7 days after infusion.
    RESULTS: Baseline tumor pressures were 45 ± 8 mm Hg, and pancreatic retrograde venous infusion increased tumor pressures by 29 ± 6 mm Hg (P < .01). Pancreatic retrograde venous infusion gemcitabine mice had greater tumor gemcitabine concentrations compared with systemic gemcitabine (127 vs 19 ng/mg; P < .01) and lesser tumor volumes compared with both systemic gem and pancreatic retrograde venous infusion with saline (274 vs 857 vs 629 mm3; P < .01).
    CONCLUSION: Pancreatic retrograde venous infusion increased tumor pressures greater than baseline, improved gemcitabine delivery, and increased the treatment response. These findings suggest that pressurized, regional delivery overcomes the increased pressure barrier in pancreatic ductal adenocarcinoma. Additional preclinical studies with cytotoxic and immunotherapeutic agents and clinical trials using pressure-enabled drug delivery with pancreatic retrograde venous infusion devices are underway.
    DOI:  https://doi.org/10.1016/j.surg.2020.04.059
  29. Cell. 2020 Jun 27. pii: S0092-8674(20)30687-5. [Epub ahead of print]
    Origin and Function of Stress-Induced IL-6 in Murine Models.
    Hua Qing, Reina Desrouleaux, Kavita Israni-Winger, Yann S Mineur, Nia Fogelman, Cuiling Zhang, Saleh Rashed, Noah W Palm, Rajita Sinha, Marina R Picciotto, Rachel J Perry, Andrew Wang.
      Acute psychological stress has long been known to decrease host fitness to inflammation in a wide variety of diseases, but how this occurs is incompletely understood. Using mouse models, we show that interleukin-6 (IL-6) is the dominant cytokine inducible upon acute stress alone. Stress-inducible IL-6 is produced from brown adipocytes in a beta-3-adrenergic-receptor-dependent fashion. During stress, endocrine IL-6 is the required instructive signal for mediating hyperglycemia through hepatic gluconeogenesis, which is necessary for anticipating and fueling "fight or flight" responses. This adaptation comes at the cost of enhancing mortality to a subsequent inflammatory challenge. These findings provide a mechanistic understanding of the ontogeny and adaptive purpose of IL-6 as a bona fide stress hormone coordinating systemic immunometabolic reprogramming. This brain-brown fat-liver axis might provide new insights into brown adipose tissue as a stress-responsive endocrine organ and mechanistic insight into targeting this axis in the treatment of inflammatory and neuropsychiatric diseases.
    Keywords:  IL-6; acute stress; beta-adrenergic receptors; brown adipose tissue; gluconeogenesis; immunometabolism; inflammation; neuroendocrine-immune axis; neuroimmunology; tolerance
    DOI:  https://doi.org/10.1016/j.cell.2020.05.054
  30. Mol Cell. 2020 Jun 19. pii: S1097-2765(20)30396-8. [Epub ahead of print]
    An Insulin-Sensitive Circular RNA that Regulates Lifespan in Drosophila.
    Carina Marianne Weigelt, Rohan Sehgal, Luke Stephen Tain, Jun Cheng, Jacqueline Eßer, André Pahl, Christoph Dieterich, Sebastian Grönke, Linda Partridge.
      Circular RNAs (circRNAs) are abundant and accumulate with age in neurons of diverse species. However, only few circRNAs have been functionally characterized, and their role during aging has not been addressed. Here, we use transcriptome profiling during aging and find that accumulation of circRNAs is slowed down in long-lived insulin mutant flies. Next, we characterize the in vivo function of a circRNA generated by the sulfateless gene (circSfl), which is consistently upregulated, particularly in the brain and muscle, of diverse long-lived insulin mutants. Strikingly, lifespan extension of insulin mutants is dependent on circSfl, and overexpression of circSfl alone is sufficient to extend the lifespan. Moreover, circSfl is translated into a protein that shares the N terminus and potentially some functions with the full-length Sfl protein encoded by the host gene. Our study demonstrates that insulin signaling affects global circRNA accumulation and reveals an important role of circSfl during aging in vivo.
    Keywords:  Drosophila; ageing; alternative splicing; backsplicing; circRNA; heparan sulfate; insulin; longevity; non-coding RNAs; sulfateless
    DOI:  https://doi.org/10.1016/j.molcel.2020.06.011
  31. Cancer Cell. 2020 Jun 10. pii: S1535-6108(20)30270-1. [Epub ahead of print]
    Telomere Stress Potentiates STING-Dependent Anti-tumor Immunity.
    Ilgen Mender, Anli Zhang, Zhenhua Ren, Chuanhui Han, Yafang Deng, Silvia Siteni, Huiyu Li, Jiankun Zhu, Aishwarya Vemula, Jerry W Shay, Yang-Xin Fu.
      Telomerase is an attractive target for anti-tumor therapy as it is almost universally expressed in cancer cells. Here, we show that treatment with a telomere-targeting drug, 6-thio-2'-deoxyguanosine (6-thio-dG), leads to tumor regression through innate and adaptive immune-dependent responses in syngeneic and humanized mouse models of telomerase-expressing cancers. 6-thio-dG treatment causes telomere-associated DNA damages that are sensed by dendritic cells (DCs) and activates the host cytosolic DNA sensing STING/interferon I pathway, resulting in enhanced cross-priming capacity of DCs and tumor-specific CD8+ T cell activation. Moreover, 6-thio-dG overcomes resistance to checkpoint blockade in advanced cancer models. Our results unveil how telomere stress increases innate sensing and adaptive anti-tumor immunity and provide strong rationales for combining telomere-targeting therapy with immunotherapy.
    Keywords:  6-thio-dG; DNA damage; PD-1/PD-L1; STING; anti-tumor immunity; checkpoint blockade; immunotherapy; innate sensing; telomerase; telomere-targeting therapy
    DOI:  https://doi.org/10.1016/j.ccell.2020.05.020
  32. Carcinogenesis. 2020 Jul 03. pii: bgaa071. [Epub ahead of print]
    Targeting Cellular Senescence in Cancer and Aging: Roles of p53 and its Isoforms.
    Jessica Beck, Casmir Turnquist, Izumi Horikawa, Curtis Harris.
      Cellular senescence and the associated secretory phenotype (SASP) promote disease in the aged population. Targeting senescent cells by means of removal, modulation of SASP, or through cellular reprogramming, represents a novel therapeutic avenue for treating cancer- and age-related diseases such as neurodegeneration, pulmonary fibrosis, and renal disease. Cellular senescence is partly regulated by the TP53 gene, a critical tumor suppressor gene which encodes 12 or more p53 protein isoforms. This review marks a significant milestone of 40 years of Carcinogenesis publication history and p53 research and 15 years of p53 isoform research. The p53 isoforms are produced through initiation at alternative transcriptional and translational start sites and alternative mRNA splicing. These truncated p53 isoform proteins are endogenously expressed in normal human cells and maintain important functional roles, including modulation of full-length p53 (FLp53)-mediated cellular senescence, apoptosis and DNA repair. In this review, we discuss the mechanisms and functions of cellular senescence and SASP in health and disease, the regulation of cellular senescence by p53 isoforms, and the therapeutic potential of targeting cellular senescence to treat cancer- and age-associated diseases.
    Keywords:  CAR T-Cell Immunotherapy; DNA Repair; Neurodegeneration; Progeria; Senescence-associated Secretory Phenotype (SASP)
    DOI:  https://doi.org/10.1093/carcin/bgaa071
  33. J Cell Biol. 2020 Sep 07. pii: e202003091. [Epub ahead of print]219(9):
    Branched actin networks are assembled on microtubules by adenomatous polyposis coli for targeted membrane protrusion.
    Nadia Efimova, Changsong Yang, Jonathan X Chia, Ning Li, Christopher J Lengner, Kristi L Neufeld, Tatyana M Svitkina.
      Cell migration is driven by pushing and pulling activities of the actin cytoskeleton, but migration directionality is largely controlled by microtubules. This function of microtubules is especially critical for neuron navigation. However, the underlying mechanisms are poorly understood. Here we show that branched actin filament networks, the main pushing machinery in cells, grow directly from microtubule tips toward the leading edge in growth cones of hippocampal neurons. Adenomatous polyposis coli (APC), a protein with both tumor suppressor and cytoskeletal functions, concentrates at the microtubule-branched network interface, whereas APC knockdown nearly eliminates branched actin in growth cones and prevents growth cone recovery after repellent-induced collapse. Conversely, encounters of dynamic APC-positive microtubule tips with the cell edge induce local actin-rich protrusions. Together, we reveal a novel mechanism of cell navigation involving APC-dependent assembly of branched actin networks on microtubule tips.
    DOI:  https://doi.org/10.1083/jcb.202003091
  34. Trends Cancer. 2020 Jul;pii: S2405-8033(20)30083-2. [Epub ahead of print]6(7): 605-618
    Turning Cold into Hot: Firing up the Tumor Microenvironment.
    Qianqian Duan, Hualing Zhang, Junnian Zheng, Lianjun Zhang.
      Cancers develop within complex tissue environments consisting of diverse innate and adaptive immune cells, along with stromal cells, vascular networks, and many other cellular and noncellular components. The high heterogeneity within the tumor microenvironment (TME) remains a key obstacle in understanding and treating cancer. Understanding the dynamic functional interplay within this intricate ecosystem will provide important insights into the design of effective combinatorial strategies against cancer. Here, we present recent technical advances to explore the complexity of the TME. Then, we discuss how innate immune sensing machinery, genetic alterations of oncogenic signaling, cellular metabolism, and epigenetic factors are involved in modulating the TME. Finally, we summarize the potential strategies to boost antitumor immunity by therapeutically exploiting the TME.
    Keywords:  epigenetic; immune checkpoint blockade; metabolism; single cell profiling; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.trecan.2020.02.022
  35. EMBO Mol Med. 2020 Jun 29. e12034
    Reprogramming of profibrotic macrophages for treatment of bleomycin-induced pulmonary fibrosis.
    Fenghua Zhang, Ehab A Ayaub, Bingbing Wang, Estela Puchulu-Campanella, Yen-Hsing Li, Suraj U Hettiarachchi, Spencer D Lindeman, Qian Luo, Sasmita Rout, Madduri Srinivasarao, Abigail Cox, Konstantin Tsoyi, Cheryl Nickerson-Nutter, Ivan O Rosas, Philip S Low.
      Fibrotic diseases cause organ failure that lead to ~45% of all deaths in the United States. Activated macrophages stimulate fibrosis by secreting cytokines that induce fibroblasts to synthesize collagen and extracellular matrix proteins. Although suppression of macrophage-derived cytokine production can halt progression of fibrosis, therapeutic agents that prevent release of these cytokines (e.g., TLR7 agonists) have proven too toxic to administer systemically. Based on the expression of folate receptor β solely on activated myeloid cells, we have created a folate-targeted TLR7 agonist (FA-TLR7-54) that selectively accumulates in profibrotic macrophages and suppresses fibrosis-inducing cytokine production. We demonstrate that FA-TLR7-54 reprograms M2-like fibrosis-inducing macrophages into fibrosis-suppressing macrophages, resulting in dramatic declines in profibrotic cytokine release, hydroxyproline biosynthesis, and collagen deposition, with concomitant increases in alveolar airspaces. Although nontargeted TLR7-54 is lethal at fibrosis-suppressing doses, FA-TLR7-54 halts fibrosis without evidence of toxicity. Taken together, FA-TLR7-54 is shown to constitute a novel and potent approach for treating fibrosis without causing dose-limiting systemic toxicities.
    Keywords:  bleomycin; folate receptor β; idiopathic pulmonary fibrosis; macrophages; toll-like receptor 7
    DOI:  https://doi.org/10.15252/emmm.202012034
  36. Nature. 2020 Jul 01.
    Systematic quantitative analysis of ribosome inventory during nutrient stress.
    Heeseon An, Alban Ordureau, Maria Körner, Joao A Paulo, J Wade Harper.
      Mammalian cells reorganize their proteomes in response to nutrient stress through translational suppression and degradative mechanisms using the proteasome and autophagy systems1,2. Ribosomes are central targets of this response, as they are responsible for translation and subject to lysosomal turnover during nutrient stress3-5. The abundance of ribosomal (r)-proteins (around 6% of the proteome; 107 copies per cell)6,7 and their high arginine and lysine content has led to the hypothesis that they are selectively used as a source of basic amino acids during nutrient stress through autophagy4,7. However, the relative contributions of translational and degradative mechanisms to the control of r-protein abundance during acute stress responses is poorly understood, as is the extent to which r-proteins are used to generate amino acids when specific building blocks are limited7. Here, we integrate quantitative global translatome and degradome proteomics8 with genetically encoded Ribo-Keima5 and Ribo-Halo reporters to interrogate r-protein homeostasis with and without active autophagy. In conditions of acute nutrient stress, cells strongly suppress the translation of r-proteins, but, notably, r-protein degradation occurs largely through non-autophagic pathways. Simultaneously, the decrease in r-protein abundance is compensated for by a reduced dilution of pre-existing ribosomes and a reduction in cell volume, thereby maintaining the density of ribosomes within single cells. Withdrawal of basic or hydrophobic amino acids induces translational repression without differential induction of ribophagy, indicating that ribophagy is not used to selectively produce basic amino acids during acute nutrient stress. We present a quantitative framework that describes the contributions of biosynthetic and degradative mechanisms to r-protein abundance and proteome remodelling in conditions of nutrient stress.
    DOI:  https://doi.org/10.1038/s41586-020-2446-y
  37. J Clin Med. 2020 Jun 28. pii: E2029. [Epub ahead of print]9(7):
    Mathematical Model of Muscle Wasting in Cancer Cachexia.
    Suzan Farhang-Sardroodi, Kathleen P Wilkie.
      Cancer cachexia is a debilitating condition characterized by an extreme loss of skeletal muscle mass, which negatively impacts patients' quality of life, reduces their ability to sustain anti-cancer therapies, and increases the risk of mortality. Recent discoveries have identified the myostatin/activin A/ActRIIB pathway as critical to muscle wasting by inducing satellite cell quiescence and increasing muscle-specific ubiquitin ligases responsible for atrophy. Remarkably, pharmacological blockade of the ActRIIB pathway has been shown to reverse muscle wasting and prolong the survival time of tumor-bearing animals. To explore the implications of this signaling pathway and potential therapeutic targets in cachexia, we construct a novel mathematical model of muscle tissue subjected to tumor-derived cachectic factors. The model formulation tracks the intercellular interactions between cancer cell, satellite cell, and muscle cell populations. The model is parameterized by fitting to colon-26 mouse model data, and the analysis provides insight into tissue growth in healthy, cancerous, and post-cachexia treatment conditions. Model predictions suggest that cachexia fundamentally alters muscle tissue health, as measured by the stem cell ratio, and this is only partially recovered by anti-cachexia treatment. Our mathematical findings suggest that after blocking the myostatin/activin A pathway, partial recovery of cancer-induced muscle loss requires the activation and proliferation of the satellite cell compartment with a functional differentiation program.
    Keywords:  cancer cachexia; dynamical systems; mathematical modeling; mathematical oncology; muscle wasting
    DOI:  https://doi.org/10.3390/jcm9072029
  38. J Clin Invest. 2020 Jun 29. pii: 136618. [Epub ahead of print]
    Lymph node fibroblastic reticular cells deposit fibrosis-associated collagen following organ transplantation.
    Xiaofei Li, Jing Zhao, Vivek Kasinath, Mayuko Uehara, Liwei Jiang, Naima Banouni, Martina M McGrath, Takaharu Ichimura, Paolo Fiorina, Dario R Lemos, Su Ryon Shin, Carl F Ware, Jonathan S Bromberg, Reza Abdi.
      Although the immune response within draining lymph nodes (DLNs) has been studied for decades, how their stromal compartment contributes to this process remains to be fully explored. Here, we show that donor mast cells were prominent activators of collagen I deposition by fibroblastic reticular cells (FRCs) in DLNs shortly following transplantation. Serial analysis of the DLN indicated that the LN stroma did not return to its baseline microarchitecture following organ rejection and that the DLN contained significant fibrosis following repetitive organ transplants. Using several FRC conditional-knockout mice, we show that induction of senescence in the FRCs of the DLN resulted in massive production of collagen I and a proinflammatory milieu within the DLN. Stimulation of herpes virus entry mediator (HVEM) on FRCs by its ligand LIGHT contributed chiefly to the induction of senescence in FRCs and overproduction of collagen I. Systemic administration of ex vivo-expanded FRCs to mice decreased DLN fibrosis and strengthened the effect of anti-CD40L in prolonging heart allograft survival. These data demonstrate that the transformation of FRCs into proinflammatory myofibroblasts is critically important for the maintenance of a proinflammatory milieu within a fibrotic DLN.
    Keywords:  Fibrosis; Immunology; Organ transplantation; Therapeutics
    DOI:  https://doi.org/10.1172/JCI136618
  39. Cell Stem Cell. 2020 Jul 02. pii: S1934-5909(20)30280-0. [Epub ahead of print]27(1): 19-34
    Cell-by-Cell Deconstruction of Stem Cell Niches.
    Anastasia N Tikhonova, Audrey Lasry, Rebecca Austin, Iannis Aifantis.
      Single-cell sequencing approaches offer exploration of tissue architecture at unprecedented resolution. These tools are especially powerful when deconvoluting highly specialized microenvironments, such as stem cell (SC) niches. Here, we review single-cell studies that map the cellular and transcriptional makeup of stem and progenitor niches and discuss how these high-resolution analyses fundamentally advance our understanding of how niche factors shape SC biology and activity. In-depth characterization of the blueprint of SC-niche crosstalk, as well as understanding how it becomes dysregulated, will undoubtedly inform the development of more efficient therapies for malignancies and other pathologies.
    DOI:  https://doi.org/10.1016/j.stem.2020.06.013
  40. Proc Natl Acad Sci U S A. 2020 Jun 29. pii: 202002672. [Epub ahead of print]
    JNK-mediated disruption of bile acid homeostasis promotes intrahepatic cholangiocarcinoma.
    Elisa Manieri, Cintia Folgueira, María Elena Rodríguez, Luis Leiva-Vega, Laura Esteban-Lafuente, Chaobo Chen, Francisco Javier Cubero, Tamera Barrett, Julie Cavanagh-Kyros, Davide Seruggia, Alejandro Rosell, Fátima Sanchez-Cabo, Manuel Jose Gómez, Maria J Monte, Jose J G Marin, Roger J Davis, Alfonso Mora, Guadalupe Sabio.
      Metabolic stress causes activation of the cJun NH2-terminal kinase (JNK) signal transduction pathway. It is established that one consequence of JNK activation is the development of insulin resistance and hepatic steatosis through inhibition of the transcription factor PPARα. Indeed, JNK1/2 deficiency in hepatocytes protects against the development of steatosis, suggesting that JNK inhibition represents a possible treatment for this disease. However, the long-term consequences of JNK inhibition have not been evaluated. Here we demonstrate that hepatic JNK controls bile acid production. We found that hepatic JNK deficiency alters cholesterol metabolism and bile acid synthesis, conjugation, and transport, resulting in cholestasis, increased cholangiocyte proliferation, and intrahepatic cholangiocarcinoma. Gene ablation studies confirmed that PPARα mediated these effects of JNK in hepatocytes. This analysis highlights potential consequences of long-term use of JNK inhibitors for the treatment of metabolic syndrome.
    Keywords:  JNK; PPARa; bile acid; cholangiocarcinoma
    DOI:  https://doi.org/10.1073/pnas.2002672117
  41. Autophagy. 2020 Jul 03. 1-3
    Selective autophagy inhibition through disruption of the PIK3C3-containing complex I.
    I Pavlinov, M Salkovski, L N Aldrich.
      The PIK3C3/VPS34-containing phosphatidylinositol 3-kinase (PtdIns3K) initiation complex (complex I) is necessary for macroautophagy/autophagy initiation and is comprised of PIK3R4/VPS15-PIK3C3/VPS34-BECN1-ATG14, while the endosomal trafficking complex (complex II) is necessary for vesicle trafficking and is comprised of PIK3R4/VPS15-PIK3C3/VPS34-BECN1-UVRAG. This composition difference was exploited to identify novel and specific autophagy inhibitors that disrupted the BECN1-ATG14 protein-protein interaction, without affecting vesicle trafficking. A cellular NanoBRET assay was implemented to identify these inhibitors, and one compound was able to successfully disrupt the BECN1-ATG14 interaction and inhibit autophagy, with limited impact on vesicle trafficking. These results reveal the first protein-protein interaction inhibitor targeting the autophagy initiation machinery and demonstrate the viability of targeting protein-protein interactions for the discovery of autophagy-specific modulators.
    Keywords:  ATG14; BECN1; PIK3C3; autophagy; inhibitor; protein-protein interaction
    DOI:  https://doi.org/10.1080/15548627.2020.1786268
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