bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2021–04–25
57 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs.
  2. The adverse metabolic effects of branched-chain amino acids are mediated by isoleucine and valine.
  3. Targeting cell-cycle machinery in cancer.
  4. Macropinocytosis: the big drinker behind cancer cell self-consumption.
  5. Contextual cues from cancer cells govern cancer-associated fibroblast heterogeneity.
  6. A comprehensive characterization of the cell-free transcriptome reveals tissue- and subtype-specific biomarkers for cancer detection.
  7. EPHA2-dependent outcompetition of KRASG12D mutant cells by wild-type neighbors in the adult pancreas.
  8. SPATA33 functions as a mitophagy receptor in mammalian germline.
  9. The Metabolic Landscape of RAS-Driven Cancers from biology to therapy.
  10. A cross-sectional study of functional and metabolic changes during aging through the lifespan in male mice.
  11. Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome.
  12. KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix.
  13. Suppression of pancreatic ductal adenocarcinoma growth and metastasis by fibrillar collagens produced selectively by tumor cells.
  14. XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.
  15. DDX11 loss causes replication stress and pharmacologically exploitable DNA repair defects.
  16. The emerging relationship between metabolism and DNA repair.
  17. GEO data mining and TCGA analysis reveal altered branched chain amino acid metabolism in pancreatic cancer patients.
  18. MCOLN1/TRPML1 finely controls oncogenic autophagy in cancer by mediating zinc influx.
  19. Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy.
  20. The bone microenvironment invigorates metastatic seeds for further dissemination.
  21. Regulation of Golgi turnover by CALCOCO1-mediated selective autophagy.
  22. Lipid metabolism and lipid signals in aging and longevity.
  23. Mucins reprogram stemness, metabolism and promote chemoresistance during cancer progression.
  24. Global Phosphoproteomics reveal CDK suppression as a vulnerability to KRAS addiction in Pancreatic Cancer.
  25. Autophagy promotes mitochondrial respiration by providing serine for one-carbon-metabolism.
  26. Potassium ions promote hexokinase-II dependent glycolysis.
  27. Enhanced substrate stress relaxation promotes filopodia-mediated cell migration.
  28. Downregulation of 5-hydroxymethylcytosine is an early event in pancreatic tumorigenesis.
  29. Mitochondrial NADP(H) generation is essential for proline biosynthesis.
  30. Organelle-Selective Labeling of Choline-Containing Phospholipids (CPLs) and Real-Time Imaging in Living Cells.
  31. Reciprocal regulation of cellular mechanics and metabolism.
  32. Pancreatic Cancer-Associated Pain Management.
  33. An integrative analysis of the age-associated multi-omic landscape across cancers.
  34. Four-Tier Pathologic Tumor Regression Grading System Predicts the Clinical Outcome in Patients Who Undergo Surgical Resection for Locally Advanced Pancreatic Cancer after Neoadjuvant Chemotherapy.
  35. Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.
  36. Proteomics of protein trafficking by in vivo tissue-specific labeling.
  37. The BioCyc Metabolic Network Explorer.
  38. Immune cell shuttle for precise delivery of nanotherapeutics for heart disease and cancer.
  39. Cells under pressure.
  40. Optogenetic-based Localization of Talin to the Plasma Membrane Promotes Activation of β3 Integrins.
  41. Hepatic transcriptional responses to fasting and feeding.
  42. Nicotinamide mononucleotide increases muscle insulin sensitivity in prediabetic women.
  43. MitopatHs: a new logically-framed tool for visualizing multiple mitochondrial pathways.
  44. Genetically increasing flux through β-oxidation in skeletal muscle increases mitochondrial reductive stress and glucose intolerance.
  45. Stroma Involvement in Pancreatic Ductal Adenocarcinoma: An Overview Focusing on Extracellular Matrix Proteins.
  46. Nuclear mechanosensing drives chromatin remodelling in persistently activated fibroblasts.
  47. Expanding cell-to-cell interactions.
  48. Desmoplastic Crosstalk in Pancreatic Ductal Adenocarcinoma Is Reflected by Different Responses of Panc-1, MIAPaCa-2, PaTu-8902, and CAPAN-2 Cell Lines to Cancer-associated/Normal Fibroblasts.
  49. Elusive cancer cells dissected using developmental-biology toolkit.
  50. Perivenous stellate cells are the main source of myofibroblasts and cancer-associated-fibroblasts formed after chronic liver injuries.
  51. Hypothalamic bile acid-TGR5 signaling protects from obesity.
  52. Predictors of early recurrence following neoadjuvant chemotherapy and surgical resection for localized pancreatic adenocarcinoma.
  53. Healing without scarring.
  54. Blood biomarkers for differential diagnosis and early detection of pancreatic cancer.
  55. Cancer-Mediated Muscle Cachexia: Etiology and Clinical Management.
  56. NAD+ Repletion Reverses Heart Failure with Preserved Ejection Fraction.
  57. Lack of transgenerational effects of ionizing radiation exposure from the Chernobyl accident.
  1. Proc Natl Acad Sci U S A. 2021 Apr 27. pii: e2018229118. [Epub ahead of print]118(17):
    Systems level profiling of chemotherapy-induced stress resolution in cancer cells reveals druggable trade-offs.
    Paula Saavedra-García, Monica Roman-Trufero, Hibah A Al-Sadah, Kevin Blighe, Elena López-Jiménez, Marilena Christoforou, Lucy Penfold, Daria Capece, Xiaobei Xiong, Yirun Miao, Katarzyna Parzych, Valentina S Caputo, Alexandros P Siskos, Vesela Encheva, Zijing Liu, Denise Thiel, Martin F Kaiser, Paolo Piazza, Aristeidis Chaidos, Anastasios Karadimitris, Guido Franzoso, Ambrosius P Snijders, Hector C Keun, Diego A Oyarzún, Mauricio Barahona, Holger W Auner.
      Cancer cells can survive chemotherapy-induced stress, but how they recover from it is not known. Using a temporal multiomics approach, we delineate the global mechanisms of proteotoxic stress resolution in multiple myeloma cells recovering from proteasome inhibition. Our observations define layered and protracted programs for stress resolution that encompass extensive changes across the transcriptome, proteome, and metabolome. Cellular recovery from proteasome inhibition involved protracted and dynamic changes of glucose and lipid metabolism and suppression of mitochondrial function. We demonstrate that recovering cells are more vulnerable to specific insults than acutely stressed cells and identify the general control nonderepressable 2 (GCN2)-driven cellular response to amino acid scarcity as a key recovery-associated vulnerability. Using a transcriptome analysis pipeline, we further show that GCN2 is also a stress-independent bona fide target in transcriptional signature-defined subsets of solid cancers that share molecular characteristics. Thus, identifying cellular trade-offs tied to the resolution of chemotherapy-induced stress in tumor cells may reveal new therapeutic targets and routes for cancer therapy optimization.
    Keywords:  GCN2; metabolism; myeloma; proteasome; proteostasis
    DOI:  https://doi.org/10.1073/pnas.2018229118
  2. Cell Metab. 2021 Apr 16. pii: S1550-4131(21)00166-2. [Epub ahead of print]
    The adverse metabolic effects of branched-chain amino acids are mediated by isoleucine and valine.
    Deyang Yu, Nicole E Richardson, Cara L Green, Alexandra B Spicer, Michaela E Murphy, Victoria Flores, Cholsoon Jang, Ildiko Kasza, Maria Nikodemova, Matthew H Wakai, Jay L Tomasiewicz, Shany E Yang, Blake R Miller, Heidi H Pak, Jacqueline A Brinkman, Jennifer M Rojas, William J Quinn, Eunhae P Cheng, Elizabeth N Konon, Lexington R Haider, Megan Finke, Michelle Sonsalla, Caroline M Alexander, Joshua D Rabinowitz, Joseph A Baur, Kristen C Malecki, Dudley W Lamming.
      Low-protein diets promote metabolic health in rodents and humans, and the benefits of low-protein diets are recapitulated by specifically reducing dietary levels of the three branched-chain amino acids (BCAAs), leucine, isoleucine, and valine. Here, we demonstrate that each BCAA has distinct metabolic effects. A low isoleucine diet reprograms liver and adipose metabolism, increasing hepatic insulin sensitivity and ketogenesis and increasing energy expenditure, activating the FGF21-UCP1 axis. Reducing valine induces similar but more modest metabolic effects, whereas these effects are absent with low leucine. Reducing isoleucine or valine rapidly restores metabolic health to diet-induced obese mice. Finally, we demonstrate that variation in dietary isoleucine levels helps explain body mass index differences in humans. Our results reveal isoleucine as a key regulator of metabolic health and the adverse metabolic response to dietary BCAAs and suggest reducing dietary isoleucine as a new approach to treating and preventing obesity and diabetes.
    Keywords:  FGF21; GCN2; body mass index; branched-chain amino acids; diabetes; insulin resistance; isoleucine; mTORC1; obesity; valine
    DOI:  https://doi.org/10.1016/j.cmet.2021.03.025
  3. Cancer Cell. 2021 Apr 16. pii: S1535-6108(21)00168-9. [Epub ahead of print]
    Targeting cell-cycle machinery in cancer.
    Jan M Suski, Marcin Braun, Vladislav Strmiska, Piotr Sicinski.
      Abnormal activity of the core cell-cycle machinery is seen in essentially all tumor types and represents a driving force of tumorigenesis. Recent studies revealed that cell-cycle proteins regulate a wide range of cellular functions, in addition to promoting cell division. With the clinical success of CDK4/6 inhibitors, it is becoming increasingly clear that targeting individual cell-cycle components may represent an effective anti-cancer strategy. Here, we discuss the potential of inhibiting different cell-cycle proteins for cancer therapy.
    DOI:  https://doi.org/10.1016/j.ccell.2021.03.010
  4. Autophagy. 2021 Apr 20.
    Macropinocytosis: the big drinker behind cancer cell self-consumption.
    Hua Su, Fei Yang, Beicheng Sun, Michael Karin.
      Poorly vascularized tumors embedded within a thick desmoplastic stroma, like pancreatic ductal adenocarcinoma (PDAC), are nutritionally stressed. Such tumors are also hypoxic and rely on a number of adaptive responses, including macroautophagy/autophagy and macropinocytosis (MP), to support their bioenergetic needs. Whereas autophagy enables starved cells to recycle intracellular macromolecules via lysosomal degradation and use the liberated amino acids (AA) to fuel their metabolism, MP allows cells to take up extracellular proteins via fluid-phase endocytosis and use them as an energy source. However, how any MP-enabled organism, including the prototypical cancer cell, coordinately regulates and balances autophagy and MP is not fully understood. We recently found that inhibition of autophagy results in upregulation of MP, which enables cancer cells to overcome autophagy deficiency and continue to support their bioenergetic demands. The NFE2L2/NRF2-driven induction of MP-related genes (MRGs) is responsible for the upregulation of MP in autophagy inhibited, hypoxic, and oxidatively stressed-exposed cancer cells. Concurrent autophagy and MP blockade effectively cuts off the cancer cell's nutrient and supplies, leading to rapid tumor regression. These findings suggest MP to be an important target in cancer treatment and that shutting off the energy spigot is a promising therapeutic strategy.
    Keywords:  NRF2; PDAC; autophagy; cancer; macropinocytosis; metabolism
    DOI:  https://doi.org/10.1080/15548627.2021.1919969
  5. Cell Rep. 2021 Apr 20. pii: S2211-1247(21)00323-5. [Epub ahead of print]35(3): 109009
    Contextual cues from cancer cells govern cancer-associated fibroblast heterogeneity.
    Neus Bota-Rabassedas, Priyam Banerjee, Yichi Niu, Wenjian Cao, Jiayi Luo, Yuanxin Xi, Xiaochao Tan, Kuanwei Sheng, Young-Ho Ahn, Sieun Lee, Edwin Roger Parra, Jaime Rodriguez-Canales, Jacob Albritton, Michael Weiger, Xin Liu, Hou-Fu Guo, Jiang Yu, B Leticia Rodriguez, Joshua J A Firestone, Barbara Mino, Chad J Creighton, Luisa M Solis, Pamela Villalobos, Maria Gabriela Raso, Daniel W Sazer, Don L Gibbons, William K Russell, Gregory D Longmore, Ignacio I Wistuba, Jing Wang, Harold A Chapman, Jordan S Miller, Chenghang Zong, Jonathan M Kurie.
      Cancer cells function as primary architects of the tumor microenvironment. However, the molecular features of cancer cells that govern stromal cell phenotypes remain unclear. Here, we show that cancer-associated fibroblast (CAF) heterogeneity is driven by lung adenocarcinoma (LUAD) cells at either end of the epithelial-to-mesenchymal transition (EMT) spectrum. LUAD cells that have high expression of the EMT-activating transcription factor ZEB1 reprogram CAFs through a ZEB1-dependent secretory program and direct CAFs to the tips of invasive projections through a ZEB1-driven CAF repulsion process. The EMT, in turn, sensitizes LUAD cells to pro-metastatic signals from CAFs. Thus, CAFs respond to contextual cues from LUAD cells to promote metastasis.
    Keywords:  EMT; cancer-associated fibroblast; invasion; lung cancer; metastasis; microRNA; secretion; single-cell RNA sequencing; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.celrep.2021.109009
  6. Nat Commun. 2021 Apr 21. 12(1): 2357
    A comprehensive characterization of the cell-free transcriptome reveals tissue- and subtype-specific biomarkers for cancer detection.
    Matthew H Larson, Wenying Pan, Hyunsung John Kim, Ruth E Mauntz, Sarah M Stuart, Monica Pimentel, Yiqi Zhou, Per Knudsgaard, Vasiliki Demas, Alexander M Aravanis, Arash Jamshidi.
      Cell-free RNA (cfRNA) is a promising analyte for cancer detection. However, a comprehensive assessment of cfRNA in individuals with and without cancer has not been conducted. We perform the first transcriptome-wide characterization of cfRNA in cancer (stage III breast [n = 46], lung [n = 30]) and non-cancer (n = 89) participants from the Circulating Cell-free Genome Atlas (NCT02889978). Of 57,820 annotated genes, 39,564 (68%) are not detected in cfRNA from non-cancer individuals. Within these low-noise regions, we identify tissue- and cancer-specific genes, defined as "dark channel biomarker" (DCB) genes, that are recurrently detected in individuals with cancer. DCB levels in plasma correlate with tumor shedding rate and RNA expression in matched tissue, suggesting that DCBs with high expression in tumor tissue could enhance cancer detection in patients with low levels of circulating tumor DNA. Overall, cfRNA provides a unique opportunity to detect cancer, predict the tumor tissue of origin, and determine the cancer subtype.
    DOI:  https://doi.org/10.1038/s41467-021-22444-1
  7. Curr Biol. 2021 Apr 19. pii: S0960-9822(21)00467-X. [Epub ahead of print]
    EPHA2-dependent outcompetition of KRASG12D mutant cells by wild-type neighbors in the adult pancreas.
    William Hill, Andreas Zaragkoulias, Beatriz Salvador-Barbero, Geraint J Parfitt, Markella Alatsatianos, Ana Padilha, Sean Porazinski, Thomas E Woolley, Jennifer P Morton, Owen J Sansom, Catherine Hogan.
      As we age, our tissues are repeatedly challenged by mutational insult, yet cancer occurrence is a relatively rare event. Cells carrying cancer-causing genetic mutations compete with normal neighbors for space and survival in tissues. However, the mechanisms underlying mutant-normal competition in adult tissues and the relevance of this process to cancer remain incompletely understood. Here, we investigate how the adult pancreas maintains tissue health in vivo following sporadic expression of oncogenic Kras (KrasG12D), the key driver mutation in human pancreatic cancer. We find that when present in tissues in low numbers, KrasG12D mutant cells are outcompeted and cleared from exocrine and endocrine compartments in vivo. Using quantitative 3D tissue imaging, we show that before being cleared, KrasG12D cells lose cell volume, pack into round clusters, and E-cadherin-based cell-cell adhesions decrease at boundaries with normal neighbors. We identify EphA2 receptor as an essential signal in the clearance of KrasG12D cells from exocrine and endocrine tissues in vivo. In the absence of functional EphA2, KrasG12D cells do not alter cell volume or shape, E-cadherin-based cell-cell adhesions increase and KrasG12D cells are retained in tissues. The retention of KRasG12D cells leads to the early appearance of premalignant pancreatic intraepithelial neoplasia (PanINs) in tissues. Our data show that adult pancreas tissues remodel to clear KrasG12D cells and maintain tissue health. This study provides evidence to support a conserved functional role of EphA2 in Ras-driven cell competition in epithelial tissues and suggests that EphA2 is a novel tumor suppressor in pancreatic cancer.
    Keywords:  E-cadherin; EphA2; PanINs; cell competition; early tumorigenesis; epithelial tissue; homeostasis; oncogenic KRAS; pancreas; pancreatic cancer
    DOI:  https://doi.org/10.1016/j.cub.2021.03.094
  8. Autophagy. 2021 Apr 05. 1-3
    SPATA33 functions as a mitophagy receptor in mammalian germline.
    Xu Xu, Ying Zhang, Hanhua Cheng, Rongjia Zhou.
      Mitophagy is an essential mechanism in maintaining cellular homeostasis, in which damaged and superfluous mitochondria are selectively degraded by the autophagy-lysosome pathway. Our recent study revealed that SPATA33 functions as a novel receptor for mitophagy in the priming of mitochondria for degradation in male germline cells. SPATA33 directly mediates the interaction of the outer mitochondrial membrane protein VDAC2 with the autophagy machinery component ATG16L1 during mitophagy. Upon starvation induction, SPATA33 can promote mitophagy as an autophagy receptor. Thus, SPATA33 confers cargo selectivity during mitophagy in germline cells. These findings provide new insights into selective autophagy and mitochondrial homeostasis.
    Keywords:  Autophagy; SPATA33; mammals; mitochondria; spermatogenesis
    DOI:  https://doi.org/10.1080/15548627.2021.1909836
  9. Nat Cancer. 2021 Mar;2(3): 271-283
    The Metabolic Landscape of RAS-Driven Cancers from biology to therapy.
    Suman Mukhopadhyay, Matthew G Vander Heiden, Frank McCormick.
      Our understanding of how the RAS protein family, and in particular mutant KRAS promote metabolic dysregulation in cancer cells has advanced significantly over the last decade. In this Review, we discuss the metabolic reprogramming mediated by oncogenic RAS in cancer, and elucidating the underlying mechanisms could translate to novel therapeutic opportunities to target metabolic vulnerabilities in RAS-driven cancers.
    Keywords:  KRAS; autophagy; cancer therapeutics; chemoresistance; ferroptosis; glutaminolysis; glycolysis; macropinocytosis; metabolism
    DOI:  https://doi.org/10.1038/s43018-021-00184-x
  10. Elife. 2021 Apr 20. pii: e62952. [Epub ahead of print]10
    A cross-sectional study of functional and metabolic changes during aging through the lifespan in male mice.
    Michael A Petr, Irene Alfaras, Melissa Krawcyzk, Woei-Nan Bair, Sarah J Mitchell, Christopher H Morrell, Stephanie A Studenski, Nathan L Price, Kenneth W Fishbein, Richard G Spencer, Morten Scheibye-Knudsen, Edward G Lakatta, Luigi Ferrucci, Miguel A Aon, Michel Bernier, Rafael de Cabo.
      Aging is associated with distinct phenotypical, physiological, and functional changes, leading to disease and death. The progression of aging-related traits varies widely among individuals, influenced by their environment, lifestyle, and genetics. In this study, we conducted physiologic and functional tests cross-sectionally throughout the entire lifespan of male C57BL/6N mice. In parallel, metabolomics analyses in serum, brain, liver, heart, and skeletal muscle were also performed to identify signatures associated with frailty and age-dependent functional decline. Our findings indicate that declines in gait speed as a function of age and frailty are associated with a dramatic increase in the energetic cost of physical activity and decreases in working capacity. Aging and functional decline prompt organs to rewire their metabolism and substrate selection and towards redox-related pathways, mainly in liver and heart. Collectively, the data provide a framework to further understand and characterize processes of aging at the individual organism and organ levels.
    Keywords:  computational biology; mouse; systems biology
    DOI:  https://doi.org/10.7554/eLife.62952
  11. Cell. 2021 Apr 14. pii: S0092-8674(21)00379-2. [Epub ahead of print]
    Chaperone-mediated autophagy prevents collapse of the neuronal metastable proteome.
    Mathieu Bourdenx, Adrián Martín-Segura, Aurora Scrivo, Jose A Rodriguez-Navarro, Susmita Kaushik, Inmaculada Tasset, Antonio Diaz, Nadia J Storm, Qisheng Xin, Yves R Juste, Erica Stevenson, Enrique Luengo, Cristina C Clement, Se Joon Choi, Nevan J Krogan, Eugene V Mosharov, Laura Santambrogio, Fiona Grueninger, Ludovic Collin, Danielle L Swaney, David Sulzer, Evripidis Gavathiotis, Ana Maria Cuervo.
      Components of the proteostasis network malfunction in aging, and reduced protein quality control in neurons has been proposed to promote neurodegeneration. Here, we investigate the role of chaperone-mediated autophagy (CMA), a selective autophagy shown to degrade neurodegeneration-related proteins, in neuronal proteostasis. Using mouse models with systemic and neuronal-specific CMA blockage, we demonstrate that loss of neuronal CMA leads to altered neuronal function, selective changes in the neuronal metastable proteome, and proteotoxicity, all reminiscent of brain aging. Imposing CMA loss on a mouse model of Alzheimer's disease (AD) has synergistic negative effects on the proteome at risk of aggregation, thus increasing neuronal disease vulnerability and accelerating disease progression. Conversely, chemical enhancement of CMA ameliorates pathology in two different AD experimental mouse models. We conclude that functional CMA is essential for neuronal proteostasis through the maintenance of a subset of the proteome with a higher risk of misfolding than the general proteome.
    Keywords:  Alzheimer’s disease; aging; chaperones; chemical activators of autophagy; lysosomes; neurodegeneration; protein aggregation; proteotoxicity; supersaturated proteome; tau
    DOI:  https://doi.org/10.1016/j.cell.2021.03.048
  12. Mol Oncol. 2021 Apr 04.
    KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix.
    Jin K Kim, Michael R Marco, Seo-Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M Barriga, Lukas E Dow, Kevin O'Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova-Todorova, Philip B Paty, Jinru Shia, Christina Leslie, J Joshua Smith, Scott Lowe, Raphael Pelossof, Francisco Sanchez-Vega, Julio Garcia-Aguilar.
      Somatic mutations in the KRAS oncogene are associated with poor outcomes in locally advanced rectal cancer but the underlying biologic mechanisms are not fully understood. We profiled mRNA in 76 locally advanced rectal adenocarcinomas from patients that were enrolled in a prospective clinical trial and investigated differences in gene expression between KRAS-mutant (KRAS-mt) and KRAS-wild-type (KRAS-wt) patients. We found that KRAS-mt tumors display lower expression of genes related to the tumor stroma and remodeling of the extracellular matrix. We validated our findings using samples from The Cancer Genome Atlas (TCGA) data and also by performing immunohistochemistry (IHC) and immunofluorescence (IF) in orthogonal cohorts. Using in vitro and in vivo models, we show that oncogenic KRAS signaling within the epithelial cancer cells modulates the activity of the surrounding fibroblasts in the tumor microenvironment.
    Keywords:  KRAS; cancer-associated-fibroblast; extracellular matrix; rectal cancer; tumor response; tumor stroma
    DOI:  https://doi.org/10.1002/1878-0261.12960
  13. Nat Commun. 2021 Apr 20. 12(1): 2328
    Suppression of pancreatic ductal adenocarcinoma growth and metastasis by fibrillar collagens produced selectively by tumor cells.
    Chenxi Tian, Ying Huang, Karl R Clauser, Steffen Rickelt, Allison N Lau, Steven A Carr, Matthew G Vander Heiden, Richard O Hynes.
      Pancreatic ductal adenocarcinoma (PDAC) has a collagen-rich dense extracellular matrix (ECM) that promotes malignancy of cancer cells and presents a barrier for drug delivery. Data analysis of our published mass spectrometry (MS)-based studies on enriched ECM from samples of progressive PDAC stages reveal that the C-terminal prodomains of fibrillar collagens are partially uncleaved in PDAC ECM, suggesting reduced procollagen C-proteinase activity. We further show that the enzyme responsible for procollagen C-proteinase activity, bone morphogenetic protein1 (BMP1), selectively suppresses tumor growth and metastasis in cells expressing high levels of COL1A1. Although BMP1, as a secreted proteinase, promotes fibrillar collagen deposition from both cancer cells and stromal cells, only cancer-cell-derived procollagen cleavage and deposition suppresses tumor malignancy. These studies reveal a role for cancer-cell-derived fibrillar collagen in selectively restraining tumor growth and suggest stratification of patients based on their tumor epithelial collagen I expression when considering treatments related to perturbation of fibrillar collagens.
    DOI:  https://doi.org/10.1038/s41467-021-22490-9
  14. Sci Adv. 2021 Apr;pii: eabg4755. [Epub ahead of print]7(17):
    XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment.
    Youjin Lee, Derek Bogdanoff, Yutong Wang, George C Hartoularos, Jonathan M Woo, Cody T Mowery, Hunter M Nisonoff, David S Lee, Yang Sun, James Lee, Sadaf Mehdizadeh, Joshua Cantlon, Eric Shifrut, David N Ngyuen, Theodore L Roth, Yun S Song, Alexander Marson, Eric D Chow, Chun Jimmie Ye.
      Single-cell RNA sequencing (scRNA-seq) of tissues has revealed remarkable heterogeneity of cell types and states but does not provide information on the spatial organization of cells. To better understand how individual cells function within an anatomical space, we developed XYZeq, a workflow that encodes spatial metadata into scRNA-seq libraries. We used XYZeq to profile mouse tumor models to capture spatially barcoded transcriptomes from tens of thousands of cells. Analyses of these data revealed the spatial distribution of distinct cell types and a cell migration-associated transcriptomic program in tumor-associated mesenchymal stem cells (MSCs). Furthermore, we identify localized expression of tumor suppressor genes by MSCs that vary with proximity to the tumor core. We demonstrate that XYZeq can be used to map the transcriptome and spatial localization of individual cells in situ to reveal how cell composition and cell states can be affected by location within complex pathological tissue.
    DOI:  https://doi.org/10.1126/sciadv.abg4755
  15. Proc Natl Acad Sci U S A. 2021 Apr 27. pii: e2024258118. [Epub ahead of print]118(17):
    DDX11 loss causes replication stress and pharmacologically exploitable DNA repair defects.
    Nanda Kumar Jegadesan, Dana Branzei.
      DDX11 encodes an iron-sulfur cluster DNA helicase required for development, mutated, and overexpressed in cancers. Here, we show that loss of DDX11 causes replication stress and sensitizes cancer cells to DNA damaging agents, including poly ADP ribose polymerase (PARP) inhibitors and platinum drugs. We find that DDX11 helicase activity prevents chemotherapy drug hypersensitivity and accumulation of DNA damage. Mechanistically, DDX11 acts downstream of 53BP1 to mediate homology-directed repair and RAD51 focus formation in manners nonredundant with BRCA1 and BRCA2. As a result, DDX11 down-regulation aggravates the chemotherapeutic sensitivity of BRCA1/2-mutated cancers and resensitizes chemotherapy drug-resistant BRCA1/2-mutated cancer cells that regained homologous recombination proficiency. The results further indicate that DDX11 facilitates recombination repair by assisting double strand break resection and the loading of both RPA and RAD51 on single-stranded DNA substrates. We propose DDX11 as a potential target in cancers by creating pharmacologically exploitable DNA repair vulnerabilities.
    Keywords:  BRCA1/2; DDX11; chemotherapy; homologous recombination; replication stress
    DOI:  https://doi.org/10.1073/pnas.2024258118
  16. Cell Cycle. 2021 Apr 20. 1-17
    The emerging relationship between metabolism and DNA repair.
    Danilo Cucchi, Amy Gibson, Sarah A Martin.
      The DNA damage response (DDR) consists of multiple specialized pathways that recognize different insults sustained by DNA and repairs them where possible to avoid the accumulation of mutations. While loss of activity of genes in the DDR has been extensively associated with cancer predisposition and progression, in recent years it has become evident that there is a relationship between the DDR and cellular metabolism. The activity of the metabolic pathways can influence the DDR by regulating the availability of substrates required for the repair process and the function of its players. Additionally, proteins of the DDR can regulate the metabolic flux through the major pathways such as glycolysis, tricarboxylic acid cycle (TCA) and pentose phosphate pathway (PPP) and the production of reactive oxygen species (ROS). This newly discovered connection bears great importance in the biology of cancer and represents a new therapeutic opportunity. Here we describe the nature of the relationship between DDR and metabolism and its potential application in the treatment of cancer. Keywords: DNA repair, metabolism, mitochondria.
    Keywords:  DNA repair; metabolism; mitochondria
    DOI:  https://doi.org/10.1080/15384101.2021.1912889
  17. Aging (Albany NY). 2021 Apr 21. 13
    GEO data mining and TCGA analysis reveal altered branched chain amino acid metabolism in pancreatic cancer patients.
    Jun-Yi Li, Fei Sun, Chun-Liang Yang, Hai-Feng Zhou, Min Gao, Qi Zhang, Hui Chen, Peng Zhou, Jun Xiao, Heng Fan.
      Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive tumor of the digestive system which has a less than 1% 5-year survival rate. The pathogenesis of PDAC development is incompletely understood. Genetic predisposition, disease history of chronic pancreatitis and diabetes elevate the risk of PDAC while environmental and dietary factors including smoking, alcohol abuse, high fat/protein intake as well as air pollution exacerbate PDAC progression. BCAAs, consisting of leucine, isoleucine and valine are essential amino acids that are obtained from food and play versatile roles in carcinogenesis. Recent studies have demonstrated that BCAA metabolism affects PDAC development but the results are controversial. To explore the possible engagement of BCAA metabolism in PDAC, we took advantage of the GEO and TCGA database and discovered that BCAA uptake is closely related to PDAC development while BCAA catabolism is down-regulated in PDAC tissue. Besides, NOTCH and MYC are differentially involved in BCAA metabolism in tumor and muscle, and enhanced lipid synthesis is independent of BCAA catabolism. Altogether, we highlight BCAA uptake as a promising target for PDAC treatment.
    Keywords:  BCAA uptake; branched chain amino acids; data mining; pancreatic ductal adenocarcinoma
    DOI:  https://doi.org/10.18632/aging.202892
  18. Autophagy. 2021 Apr 23. 1-22
    MCOLN1/TRPML1 finely controls oncogenic autophagy in cancer by mediating zinc influx.
    Jiansong Qi, Yanhong Xing, Yucheng Liu, Meng-Meng Wang, Xiangqing Wei, Zhongheng Sui, Lin Ding, Yang Zhang, Chen Lu, Yuan-Hui Fei, Nan Liu, Rong Chen, Mengmei Wu, Lijuan Wang, Zhenyu Zhong, Ting Wang, Yifan Liu, Yuqing Wang, Jiamei Liu, Haoxing Xu, Feng Guo, Wuyang Wang.
      Macroautophagy/autophagy is elevated to ensure the high demand for nutrients for the growth of cancer cells. Here we demonstrated that MCOLN1/TRPML1 is a pharmaceutical target of oncogenic autophagy in cancers such as pancreatic cancer, breast cancer, gastric cancer, malignant melanoma, and glioma. First, we showed that activating MCOLN1, by increasing expression of the channel or using the MCOLN1 agonists, ML-SA5 or MK6-83, arrests autophagic flux by perturbing fusion between autophagosomes and lysosomes. Second, we demonstrated that MCOLN1 regulates autophagy by mediating the release of zinc from the lysosome to the cytosol. Third, we uncovered that zinc influx through MCOLN1 blocks the interaction between STX17 (syntaxin 17) in the autophagosome and VAMP8 in the lysosome and thereby disrupting the fusion process that is determined by the two SNARE proteins. Furthermore, we demonstrated that zinc influx originating from the extracellular fluid arrests autophagy by the same mechanism as lysosomal zinc, confirming the fundamental function of zinc as a participant in membrane trafficking. Last, we revealed that activating MCOLN1 with the agonists, ML-SA5 or MK6-83, triggers cell death of a number of cancer cells by evoking autophagic arrest and subsequent apoptotic response and cell cycle arrest, with little or no effect observed on normal cells. Consistent with the in vitro results, administration of ML-SA5 in Patu 8988 t xenograft mice profoundly suppresses tumor growth and improves survival. These results establish that a lysosomal cation channel, MCOLN1, finely controls oncogenic autophagy in cancer by mediating zinc influx into the cytosol.
    Keywords:  Autophagic arrest; MCOLN1; autophagosome-lysosome fusion; cancer; zinc influx
    DOI:  https://doi.org/10.1080/15548627.2021.1917132
  19. Sci Adv. 2021 Apr;pii: eabg4922. [Epub ahead of print]7(17):
    Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy.
    Chunmei Chang, Xiaoshan Shi, Liv E Jensen, Adam L Yokom, Dorotea Fracchiolla, Sascha Martens, James H Hurley.
      Selective autophagy of damaged mitochondria, protein aggregates, and other cargoes is essential for health. Cargo initiates phagophore biogenesis, which entails the conjugation of LC3 to phosphatidylethanolamine. Current models suggest that clustered ubiquitin chains on a cargo trigger a cascade from autophagic cargo receptors through the core complexes ULK1 and class III phosphatidylinositol 3-kinase complex I, WIPI2, and the ATG7, ATG3, and ATG12ATG5-ATG16L1 machinery of LC3 lipidation. This was tested using giant unilamellar vesicles (GUVs), GST-Ub4 as a model cargo, the cargo receptors NDP52, TAX1BP1, and OPTN, and the autophagy core complexes. All three cargo receptors potently stimulated LC3 lipidation on GUVs. NDP52- and TAX1BP1-induced LC3 lipidation required all components, but not ULK1 kinase activity. However, OPTN bypassed the ULK1 requirement. Thus, cargo-dependent stimulation of LC3 lipidation is common to multiple autophagic cargo receptors, yet the details of core complex engagement vary between the different receptors.
    DOI:  https://doi.org/10.1126/sciadv.abg4922
  20. Cell. 2021 Apr 10. pii: S0092-8674(21)00296-8. [Epub ahead of print]
    The bone microenvironment invigorates metastatic seeds for further dissemination.
    Weijie Zhang, Igor L Bado, Jingyuan Hu, Ying-Wooi Wan, Ling Wu, Hai Wang, Yang Gao, Hyun-Hwan Jeong, Zhan Xu, Xiaoxin Hao, Bree M Lege, Rami Al-Ouran, Lucian Li, Jiasong Li, Liqun Yu, Swarnima Singh, Hin Ching Lo, Muchun Niu, Jun Liu, Weiyu Jiang, Yi Li, Stephen T C Wong, Chonghui Cheng, Zhandong Liu, Xiang H-F Zhang.
      Metastasis has been considered as the terminal step of tumor progression. However, recent genomic studies suggest that many metastases are initiated by further spread of other metastases. Nevertheless, the corresponding pre-clinical models are lacking, and underlying mechanisms are elusive. Using several approaches, including parabiosis and an evolving barcode system, we demonstrated that the bone microenvironment facilitates breast and prostate cancer cells to further metastasize and establish multi-organ secondary metastases. We uncovered that this metastasis-promoting effect is driven by epigenetic reprogramming that confers stem cell-like properties on cancer cells disseminated from bone lesions. Furthermore, we discovered that enhanced EZH2 activity mediates the increased stemness and metastasis capacity. The same findings also apply to single cell-derived populations, indicating mechanisms distinct from clonal selection. Taken together, our work revealed an unappreciated role of the bone microenvironment in metastasis evolution and elucidated an epigenomic reprogramming process driving terminal-stage, multi-organ metastases.
    Keywords:  EZH2; bone metastasis; circulating tumor cells; disseminated tumor cells; epigenomic reprograming; evolving barcodes; organ tropism; plasticity; secondary metastasis; stemness
    DOI:  https://doi.org/10.1016/j.cell.2021.03.011
  21. J Cell Biol. 2021 Jun 07. pii: e202006128. [Epub ahead of print]220(6):
    Regulation of Golgi turnover by CALCOCO1-mediated selective autophagy.
    Thaddaeus Mutugi Nthiga, Birendra Kumar Shrestha, Jack-Ansgar Bruun, Kenneth Bowitz Larsen, Trond Lamark, Terje Johansen.
      The Golgi complex is essential for the processing, sorting, and trafficking of newly synthesized proteins and lipids. Golgi turnover is regulated to meet different cellular physiological demands. The role of autophagy in the turnover of Golgi, however, has not been clarified. Here we show that CALCOCO1 binds the Golgi-resident palmitoyltransferase ZDHHC17 to facilitate Golgi degradation by autophagy during starvation. Depletion of CALCOCO1 in cells causes expansion of the Golgi and accumulation of its structural and membrane proteins. ZDHHC17 itself is degraded by autophagy together with other Golgi membrane proteins such as TMEM165. Taken together, our data suggest a model in which CALCOCO1 mediates selective Golgiphagy to control Golgi size and morphology in eukaryotic cells via its interaction with ZDHHC17.
    DOI:  https://doi.org/10.1083/jcb.202006128
  22. Dev Cell. 2021 Apr 16. pii: S1534-5807(21)00309-9. [Epub ahead of print]
    Lipid metabolism and lipid signals in aging and longevity.
    Ayse Sena Mutlu, Jonathon Duffy, Meng C Wang.
      Lipids play crucial roles in regulating aging and longevity. In the past few decades, a series of genetic pathways have been discovered to regulate lifespan in model organisms. Interestingly, many of these regulatory pathways are linked to lipid metabolism and lipid signaling. Lipid metabolic enzymes undergo significant changes during aging and are regulated by different longevity pathways. Lipids also actively modulate lifespan and health span as signaling molecules. In this review, we summarize recent insights into the roles of lipid metabolism and lipid signaling in aging and discuss lipid-related interventions in promoting longevity.
    Keywords:  aging; lipid metabolism; lipid signals; longevity
    DOI:  https://doi.org/10.1016/j.devcel.2021.03.034
  23. Cancer Metastasis Rev. 2021 Apr 04.
    Mucins reprogram stemness, metabolism and promote chemoresistance during cancer progression.
    Saravanakumar Marimuthu, Sanchita Rauth, Koelina Ganguly, Chunmeng Zhang, Imayavaramban Lakshmanan, Surinder K Batra, Moorthy P Ponnusamy.
      Mucins are high-molecular-weight glycoproteins dysregulated in aggressive cancers. The role of mucins in disease progression, tumor proliferation, and chemotherapy resistance has been studied extensively. This article provides a comprehensive review of mucin's function as a physical barrier and the implication of mucin overexpression in impeded drug delivery to solid tumors. Mucins regulate the epithelial to mesenchymal transition (EMT) of cancer cells via several canonical and non-canonical oncogenic signaling pathways. Furthermore, mucins play an extensive role in enriching and maintaining the cancer stem cell (CSC) population, thereby sustaining the self-renewing and chemoresistant cellular pool in the bulk tumor. It has recently been demonstrated that mucins regulate the metabolic reprogramming during oncogenesis and cancer progression, which account for tumor cell survival, proliferation, and drug-resistance. This review article focuses on delineating mucin's role in oncogenic signaling and aberrant regulation of gene expressions, culminating in CSC maintenance, metabolic rewiring, and development of chemoresistance, tumor progression, and metastasis.
    Keywords:  Cancer stem cell; Chemoresistance; Epithelial to mesenchymal transition; Metabolic reprogramming; Metastasis; Mucins
    DOI:  https://doi.org/10.1007/s10555-021-09959-1
  24. Clin Cancer Res. 2021 Apr 20. pii: clincanres.4781.2020. [Epub ahead of print]
    Global Phosphoproteomics reveal CDK suppression as a vulnerability to KRAS addiction in Pancreatic Cancer.
    Aslamuzzaman Kazi, Liwei Chen, Shengyan Xiang, Rajanikanth Vangipurapu, Hua Yang, Francisca Beato, Bin Fang, Terence M Williams, Kazim Husain, Patrick W Underwood, Jason B Fleming, Mokenge P Malafa, Eric A Welsh, John M Koomen, Jose G Trevino, Said M Sebti.
       PURPOSE: Among human cancers that harbor mutant (mt) KRas, some, but not all, are dependent on mt KRas. However, little is known about what drives KRas dependency.
    EXPERIMENTAL DESIGN: Global phosphoproteomics, screening of a chemical library of FDA drugs and genome-wide CRISPR/Cas9 viability database analysis were used to identify vulnerabilities of KRAS dependency.
    RESULTS: Global phosphoproteomics revealed that KRas dependency is driven by a cyclin dependent kinase (CDK) network. CRISPR/Cas9 viability database analysis revealed that, in mt KRas-driven pancreatic cancer cells, knocking out the cell cycle regulators CDK1 or CDK2 or the transcriptional regulators CDK7 or CDK9 was as effective as knocking out KRas. Furthermore, screening of a library of FDA drugs identified AT7519, a CDK 1, 2, 7, and 9 inhibitor, as a potent inducer of apoptosis in mt KRas-dependent, but not in mt KRas-independent, human cancer cells. In vivo AT7519 inhibited the phosphorylation of CDK1, 2, 7 and 9 substrates and suppressed growth of xenografts from 5 pancreatic cancer patients. AT7519 also abrogated mt KRas and mt p53 primary and metastatic pancreatic cancer in 3D organoids from 2 patients, 3D co-cultures from 8 patients, and mouse 3D organoids from PanIN, primary and metastatic tumors.
    CONCLUSION: A link between CDK hyperactivation and mt KRas dependency was uncovered and pharmacologically-exploited to abrogate mt KRas-driven pancreatic cancer in highly relevant models, warranting clinical investigations of AT7519 in pancreatic cancer patients.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-20-4781
  25. Autophagy. 2021 Apr 18. 1-4
    Autophagy promotes mitochondrial respiration by providing serine for one-carbon-metabolism.
    Rajesh Kumar, Andreas S Reichert.
      Whether macroautophagy/autophagy is physiologically relevant to regulate mitochondrial function for a rapid and dynamic adaptation of yeast cells to respiratory growth was not fully understood until recently. May et al. (2020. Nat Commun) report that bulk autophagy provides serine as a one-carbon (1C) metabolite that controls respiratory growth onset by initiating mitochondrial initiator tRNAMet modification and mitochondrial translation linking autophagy mechanistically to mitochondrial function. We discuss the mechanistic interplay between autophagy, one-carbon-metabolism, and mitochondrial function and the possible implications in neurodegeneration, aging, and carcinogenesis.
    Keywords:  Autophagy; mitochondrial respiration; mitochondrial translation; one-carbon metabolism; respiratory growth
    DOI:  https://doi.org/10.1080/15548627.2021.1909408
  26. iScience. 2021 Apr 23. 24(4): 102346
    Potassium ions promote hexokinase-II dependent glycolysis.
    Helmut Bischof, Sandra Burgstaller, Anna Springer, Lucas Matt, Thomas Rauter, Olaf A Bachkönig, Tony Schmidt, Klaus Groschner, Rainer Schindl, Tobias Madl, Nikolaus Plesnila, Robert Lukowski, Wolfgang F Graier, Roland Malli.
      High expression levels of mitochondria-associated hexokinase-II (HKII) represent a hallmark of metabolically highly active cells such as fast proliferating cancer cells. Typically, the enzyme provides a crucial metabolic switch towards aerobic glycolysis. By imaging metabolic activities on the single-cell level with genetically encoded fluorescent biosensors, we here demonstrate that HKII activity requires intracellular K+. The K+ dependency of glycolysis in cells expressing HKII was confirmed in cell populations using extracellular flux analysis and nuclear magnetic resonance-based metabolomics. Reductions of intracellular K+ by gramicidin acutely disrupted HKII-dependent glycolysis and triggered energy stress pathways, while K+ re-addition promptly restored glycolysis-dependent adenosine-5'-triphosphate generation. Moreover, expression and activation of KV1.3, a voltage-gated K+ channel, lowered cellular K+ content and the glycolytic activity of HEK293 cells. Our findings unveil K+ as an essential cofactor of HKII and provide a mechanistic link between activities of distinct K+ channels and cell metabolism.
    Keywords:  Biochemical Mechanism; Biochemistry; Molecular Physiology
    DOI:  https://doi.org/10.1016/j.isci.2021.102346
  27. Nat Mater. 2021 Apr 19.
    Enhanced substrate stress relaxation promotes filopodia-mediated cell migration.
    Kolade Adebowale, Ze Gong, Jay C Hou, Katrina M Wisdom, Damien Garbett, Hong-Pyo Lee, Sungmin Nam, Tobias Meyer, David J Odde, Vivek B Shenoy, Ovijit Chaudhuri.
      Cell migration on two-dimensional substrates is typically characterized by lamellipodia at the leading edge, mature focal adhesions and spread morphologies. These observations result from adherent cell migration studies on stiff, elastic substrates, because most cells do not migrate on soft, elastic substrates. However, many biological tissues are soft and viscoelastic, exhibiting stress relaxation over time in response to a deformation. Here, we have systematically investigated the impact of substrate stress relaxation on cell migration on soft substrates. We observed that cells migrate minimally on substrates with an elastic modulus of 2 kPa that are elastic or exhibit slow stress relaxation, but migrate robustly on 2-kPa substrates that exhibit fast stress relaxation. Strikingly, migrating cells were not spread out and did not extend lamellipodial protrusions, but were instead rounded, with filopodia protrusions extending at the leading edge, and exhibited small nascent adhesions. Computational models of cell migration based on a motor-clutch framework predict the observed impact of substrate stress relaxation on cell migration and filopodia dynamics. Our findings establish substrate stress relaxation as a key requirement for robust cell migration on soft substrates and uncover a mode of two-dimensional cell migration marked by round morphologies, filopodia protrusions and weak adhesions.
    DOI:  https://doi.org/10.1038/s41563-021-00981-w
  28. J Pathol. 2021 Apr 19.
    Downregulation of 5-hydroxymethylcytosine is an early event in pancreatic tumorigenesis.
    Kohei Fujikura, Zainab I Alruwaii, Michael C Haffner, Maria A Trujillo, Nicholas J Roberts, Seung-Mo Hong, Anne Macgregor-Das, Michael G Goggins, Sujayita Roy, Alan K Meeker, Ding Ding, Michael Wright, Jin He, Ralph H Hruban, Laura D Wood.
      Epigenetic alterations are increasingly recognized as important contributors to the development and progression of pancreatic ductal adenocarcinoma (PDAC). 5-hydroxymethylcytosine (5hmC) is an epigenetic DNA mark generated through the ten-eleven translocation (TET) enzyme-mediated pathway and is closely linked to gene activation. However, the timing of alterations in epigenetic regulation in the progression of pancreatic neoplasia is not well understood. In this study, we hypothesized that aberrant expression of ten-eleven translocation methylcytosine dioxygenase 1 (TET1) and subsequent global 5hmC alteration are linked to early tumorigenesis in the pancreas. Therefore, we evaluated alterations of 5hmC and TET1 levels using immunohistochemistry in pancreatic neoplasms (n = 380) and normal ducts (n = 118). The study cohort included representation of the full spectrum of precancerous lesions from low- and high-grade pancreatic intraepithelial neoplasia (PanINs, n = 95), intraductal papillary mucinous neoplasms (IPMNs, all subtypes, n = 129), intraductal oncocytic papillary neoplasms (IOPNs, n = 12), and mucinous cystic neoplasms (MCNs, n = 144). 5hmC and TET1 were significantly downregulated in all types of precancerous lesions and associated invasive PDACs compared with normal ductal epithelium (all P < 0.001), and expression of 5hmC positively correlated with expression of TET1. Importantly, downregulation of both 5hmC and TET1 was observed in most low-grade precancerous lesions. There were no clear associations between 5hmC levels and clinicopathological factors, thereby suggesting a common epigenetic abnormality across precancerous lesions. We conclude that downregulation of 5hmC and TET1 is an early event in pancreatic tumorigenesis. This article is protected by copyright. All rights reserved.
    Keywords:  5-hydroxymethylcytosine; IOPN; IPMN; MCN; PanIN; TET1; epigenetics; immunohistochemistry; pancreatic precancerous lesion
    DOI:  https://doi.org/10.1002/path.5682
  29. Science. 2021 Apr 22. pii: eabd5491. [Epub ahead of print]
    Mitochondrial NADP(H) generation is essential for proline biosynthesis.
    Jiajun Zhu, Simon Schwörer, Mirela Berisa, Yeon Ju Kyung, Keun Woo Ryu, Junmei Yi, Xuejun Jiang, Justin R Cross, Craig B Thompson.
      The coenzyme nicotinamide adenine dinucleotide phosphate (NADP+) and its reduced form (NADPH) regulate reductive metabolism in a subcellularly compartmentalized manner. Mitochondrial NADP(H) production depends on the phosphorylation of NAD(H) by NAD kinase 2 (NADK2). Deletion of NADK2 in human cell lines did not alter mitochondrial folate pathway activity, tricarboxylic acid cycle activity, or mitochondrial oxidative stress, but led to impaired cell proliferation in minimal medium. This growth defect was rescued by proline supplementation. NADK2-mediated mitochondrial NADP(H) generation was required for the reduction of glutamate and hence proline biosynthesis. Furthermore, mitochondrial NADP(H) availability determined the production of collagen proteins by cells of mesenchymal lineage. Thus, a primary function of the mitochondrial NADP(H) pool is to support proline biosynthesis for use in cytosolic protein synthesis.
    DOI:  https://doi.org/10.1126/science.abd5491
  30. Curr Protoc. 2021 Apr;1(4): e105
    Organelle-Selective Labeling of Choline-Containing Phospholipids (CPLs) and Real-Time Imaging in Living Cells.
    Masaki Tsuchiya, Tomonori Tamura, Itaru Hamachi.
      Choline-containing phospholipids (CPLs), including phosphatidylcholine (PC) and sphingomyelin (SM), are the major components of mammalian cell membranes and play critical roles during a variety of cellular processes. However, intracellular dynamics of CPLs is poorly understood due to a lack of methods to trace CPL trafficking at organelle resolution. Here, we describe protocols that make it possible to fluorescently label CPLs at the targeted organelles and to monitor their movement within living cells using confocal microscopy. © 2021 Wiley Periodicals LLC. Basic Protocol 1: ER-Golgi-selective labeling of azide-tagged CPLs for confocal imaging Basic Protocol 2: Mitochondria-selective labeling of azide-tagged CPLs for confocal imaging.
    Keywords:  choline-containing phospholipids; click chemistry; live-cell imaging; organelle-selective labeling
    DOI:  https://doi.org/10.1002/cpz1.105
  31. Nat Metab. 2021 Apr;3(4): 456-468
    Reciprocal regulation of cellular mechanics and metabolism.
    Tom M J Evers, Liam J Holt, Simon Alberti, Alireza Mashaghi.
      Metabolism and mechanics are intrinsically intertwined. External forces, sensed through the cytoskeleton or distortion of the cell and organelles, induce metabolic changes in the cell. The resulting changes in metabolism, in turn, feed back to regulate every level of cell biology, including the mechanical properties of cells and tissues. Here we examine the links between metabolism and mechanics, highlighting signalling pathways involved in the regulation and response to cellular mechanosensing. We consider how forces and metabolism regulate one another through nanoscale molecular sensors, micrometre-scale cytoskeletal networks, organelles and dynamic biomolecular condensates. Understanding this cross-talk will create diagnostic and therapeutic opportunities for metabolic disorders such as cancer, cardiovascular pathologies and obesity.
    DOI:  https://doi.org/10.1038/s42255-021-00384-w
  32. Oncologist. 2021 Apr 22.
    Pancreatic Cancer-Associated Pain Management.
    Precision Promise Consortium
      Pain is highly prevalent in patients with pancreatic cancer and contributes to the morbidity of the disease. Pain may be due to pancreatic enzyme insufficiency, obstruction, and/or a direct mass effect on nerves in the celiac plexus. Proper supportive care to decrease pain is an important aspect of the overall management of these patients. There are limited data specific to the management of pain caused by pancreatic cancer. Here we review the literature and offer recommendations regarding multiple modalities available to treat pain in these patients. The dissemination and adoption of these best supportive care practices can improve quantity and quality of life for patients with pancreatic cancer. IMPLICATIONS FOR PRACTICE: Pain management is important to improve the quality of life and survival of a patient with cancer. The pathophysiology of pain in pancreatic cancer is complex and multifactorial. Despite tumor response to chemotherapy, a sizeable percentage of patients are at risk for ongoing cancer-related pain and its comorbid consequences. Accordingly, the management of pain in patients with pancreatic cancer can be challenging and often requires a multifaceted approach.
    Keywords:  Pain management; Palliative care; Pancreatic neoplasms
    DOI:  https://doi.org/10.1002/onco.13796
  33. Nat Commun. 2021 Apr 20. 12(1): 2345
    An integrative analysis of the age-associated multi-omic landscape across cancers.
    Kasit Chatsirisupachai, Tom Lesluyes, Luminita Paraoan, Peter Van Loo, João Pedro de Magalhães.
      Age is the most important risk factor for cancer, as cancer incidence and mortality increase with age. However, how molecular alterations in tumours differ among patients of different age remains largely unexplored. Here, using data from The Cancer Genome Atlas, we comprehensively characterise genomic, transcriptomic and epigenetic alterations in relation to patients' age across cancer types. We show that tumours from older patients present an overall increase in genomic instability, somatic copy-number alterations (SCNAs) and somatic mutations. Age-associated SCNAs and mutations are identified in several cancer-driver genes across different cancer types. The largest age-related genomic differences are found in gliomas and endometrial cancer. We identify age-related global transcriptomic changes and demonstrate that these genes are in part regulated by age-associated DNA methylation changes. This study provides a comprehensive, multi-omics view of age-associated alterations in cancer and underscores age as an important factor to consider in cancer research and clinical practice.
    DOI:  https://doi.org/10.1038/s41467-021-22560-y
  34. Gut Liver. 2021 Apr 23.
    Four-Tier Pathologic Tumor Regression Grading System Predicts the Clinical Outcome in Patients Who Undergo Surgical Resection for Locally Advanced Pancreatic Cancer after Neoadjuvant Chemotherapy.
    Soomin Ahn, Jong-Chan Lee, Jaihwan Kim, Young Hoon Kim, Yoo-Seok Yoon, Ho-Seong Han, Haeryoung Kim, Jin-Hyeok Hwang.
       Background/Aims: Neoadjuvant chemotherapy is increasingly utilized in patients with borderline or locally advanced pancreatic cancer (LAPC). However, the pathologic evaluation of tumor regression is not routinely performed or well established. We aimed to evaluate the prognostic value of three tumor regression grading systems frequently used in LAPC and to determine the correlation between pathologic and clinical response.
    Methods: We included a total of 38 patients with LAPC who were treated with neoadjuvant chemotherapy and subsequent resection. Pathologic tumor regression was graded based on the College of American Pathologists (CAP), Evans, and MD Anderson grading systems.
    Results: One out of 38 patients (2.6%) achieved a pathologic complete response. Unlike other grading systems (Evans, p=0.063; MD Anderson, p=0.110), the CAP grading system was a significant prognostic factor for overall survival (p=0.043). Pathologic N stage (p=0.023), margin status (p=0.044), and radiologic response (p=0.016) correlated with overall survival. In the multivariate analysis, CAP 3 was an independent predictor of shorter overall survival (p=0.026). The CAP grading system correlated with the radiologic response (p=0.007) but not the carbohydrate antigen 19-9 level (p=0.333).
    Conclusions: The four-tier CAP pathologic tumor regression grading system predicted the clinical outcome in LAPC patients who underwent resection after neoadjuvant chemotherapy. Therefore, a more comprehensive pathologic evaluation is warranted in these patients.
    Keywords:  Neoadjuvant therapy; Pancreatic neoplasms; Tumor regression grading
    DOI:  https://doi.org/10.5009/gnl20312
  35. Mol Cell. 2021 Apr 09. pii: S1097-2765(21)00263-X. [Epub ahead of print]
    Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.
    Eva Kummer, Katharina Noel Schubert, Tanja Schoenhut, Alain Scaiola, Nenad Ban.
      The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.
    Keywords:  ICT1; cryo-EM; mitochondria; mtEFG2; mtRF1a; mtRRF; recycling; ribosome; termination; translation
    DOI:  https://doi.org/10.1016/j.molcel.2021.03.042
  36. Nat Commun. 2021 Apr 22. 12(1): 2382
    Proteomics of protein trafficking by in vivo tissue-specific labeling.
    Ilia A Droujinine, Amanda S Meyer, Dan Wang, Namrata D Udeshi, Yanhui Hu, David Rocco, Jill A McMahon, Rui Yang, JinJin Guo, Luye Mu, Dominique K Carey, Tanya Svinkina, Rebecca Zeng, Tess Branon, Areya Tabatabai, Justin A Bosch, John M Asara, Alice Y Ting, Steven A Carr, Andrew P McMahon, Norbert Perrimon.
      Conventional approaches to identify secreted factors that regulate homeostasis are limited in their abilities to identify the tissues/cells of origin and destination. We established a platform to identify secreted protein trafficking between organs using an engineered biotin ligase (BirA*G3) that biotinylates, promiscuously, proteins in a subcellular compartment of one tissue. Subsequently, biotinylated proteins are affinity-enriched and identified from distal organs using quantitative mass spectrometry. Applying this approach in Drosophila, we identify 51 muscle-secreted proteins from heads and 269 fat body-secreted proteins from legs/muscles, including CG2145 (human ortholog ENDOU) that binds directly to muscles and promotes activity. In addition, in mice, we identify 291 serum proteins secreted from conditional BirA*G3 embryo stem cell-derived teratomas, including low-abundance proteins with hormonal properties. Our findings indicate that the communication network of secreted proteins is vast. This approach has broad potential across different model systems to identify cell-specific secretomes and mediators of interorgan communication in health or disease.
    DOI:  https://doi.org/10.1038/s41467-021-22599-x
  37. BMC Bioinformatics. 2021 Apr 21. 22(1): 208
    The BioCyc Metabolic Network Explorer.
    Suzanne Paley, Peter D Karp.
       BACKGROUND: The Metabolic Network Explorer is a new addition to the BioCyc.org website and the Pathway Tools software suite that supports the interactive exploration of metabolic networks. Any metabolic network visualization tool must by necessity show only a subset of all possible metabolite connections, or the results will be visually overwhelming. Existing tools, even those that purport to show an organism's full metabolic network, limit the set of displayed connections based on predefined pathways or other preselected criteria. We sought instead to provide a tool that would give the user dynamic control over which connections to follow.
    RESULTS: The Metabolic Network Explorer is an easy-to-use, web-based software tool that allows the user to specify a starting metabolite of interest and interactively explore its immediate metabolic neighborhood in either or both directions to any desired depth, letting the user select from the full set of connected reactions. Although, as for other tools, only a small portion of the metabolic network is visible at a time, that portion is selected by the user, based on the full reaction complement, and it is easy to switch among alternate paths of interest. The display is intuitive, customizable, and provides copious links to more detailed information pages.
    CONCLUSIONS: The Metabolic Network Explorer fills a gap in the set of metabolic network visualization tools and complements other modes of exploration. Its primary strengths are its ease of use, diagrams that are intuitive to biologists, and its integration with the broader corpus of data provided by a BioCyc Pathway/Genome Database.
    DOI:  https://doi.org/10.1186/s12859-021-04132-5
  38. Sci Adv. 2021 Apr;pii: eabf2400. [Epub ahead of print]7(17):
    Immune cell shuttle for precise delivery of nanotherapeutics for heart disease and cancer.
    San-Shan Huang, Keng-Jung Lee, Hung-Chih Chen, Ray Putra Prajnamitra, Chia-Hsin Hsu, Cheng-Bang Jian, Xu-En Yu, Di-Yen Chueh, Chiung Wen Kuo, Tsai-Chen Chiang, Oi Kuan Choong, Shao-Chan Huang, Chaw Yee Beh, Li-Lun Chen, James J Lai, Peilin Chen, Timothy J Kamp, Yu-Wen Tien, Hsien-Ming Lee, Patrick Ching-Ho Hsieh.
      The delivery of therapeutics through the circulatory system is one of the least arduous and less invasive interventions; however, this approach is hampered by low vascular density or permeability. In this study, by exploiting the ability of monocytes to actively penetrate into diseased sites, we designed aptamer-based lipid nanovectors that actively bind onto the surface of monocytes and are released upon reaching the diseased sites. Our method was thoroughly assessed through treating two of the top causes of death in the world, cardiac ischemia-reperfusion injury and pancreatic ductal adenocarcinoma with or without liver metastasis, and showed a significant increase in survival and healing with no toxicity to the liver and kidneys in either case, indicating the success and ubiquity of our platform. We believe that this system provides a new therapeutic method, which can potentially be adapted to treat a myriad of diseases that involve monocyte recruitment in their pathophysiology.
    DOI:  https://doi.org/10.1126/sciadv.abf2400
  39. Elife. 2021 Apr 23. pii: e68643. [Epub ahead of print]10
    Cells under pressure.
    Dhiraj Indana, Ovijit Chaudhuri.
      A new method for applying solid stress to aggregates of cells is shedding light on the impact of mechanical forces on cancer cells.
    Keywords:  cancer; compression; extracellular matrix; mechanical stress; mouse; multicellular aggregates; physics of living systems; tumor
    DOI:  https://doi.org/10.7554/eLife.68643
  40. J Biol Chem. 2021 Apr 15. pii: S0021-9258(21)00464-6. [Epub ahead of print] 100675
    Optogenetic-based Localization of Talin to the Plasma Membrane Promotes Activation of β3 Integrins.
    Zhongji Liao, Alexandre R Gingras, Frederic Lagarrigue, Mark H Ginsberg, Sanford J Shattil.
      Interaction of talin with the cytoplasmic tails of integrin β triggers integrin activation, leading to an increase of integrin affinity/avidity for extracellular ligands. In talin knockout mice, loss of talin interaction with platelet integrin αIIbβ3 causes a severe hemostatic defect, and loss of talin interaction with endothelial cell integrin αVβ3 affects angiogenesis. In normal cells, talin is auto-inhibited and localized in the cytoplasm. Here we employed an optogenetic platform to assess whether recruitment of full-length talin to the plasma membrane was sufficient to induce integrin activation. A dimerization module (CRY2 fused to the N-terminus of talin; CIBN-CAAX) responsive to 450 nm (blue) light was inserted into CHO cells and endothelial cells also expressing αIIbβ3 or αVβ3, respectively. Thus, exposure of the cells to blue light caused a rapid and reversible recruitment of CRY2-talin to the CIBN-CAAX-decorated plasma membrane. This resulted in β3 integrin activation in both cell types, as well as increasing migration of the endothelial cells. However, membrane recruitment of talin was not sufficient for integrin activation, as membrane-associated Rap1-GTP was also required. Moreover, talin mutations that interfered with its direct binding to Rap1 abrogated β3 integrin activation. Altogether, these results define a role for the plasma membrane recruitment of talin in β3 integrin activation, and they suggest a nuanced sequence of events thereafter involving Rap1-GTP.
    Keywords:  endothelial cell; integrin; optogenetics; platelet; talin
    DOI:  https://doi.org/10.1016/j.jbc.2021.100675
  41. Genes Dev. 2021 Apr 22.
    Hepatic transcriptional responses to fasting and feeding.
    Lara Bideyan, Rohith Nagari, Peter Tontonoz.
      Mammals undergo regular cycles of fasting and feeding that engage dynamic transcriptional responses in metabolic tissues. Here we review advances in our understanding of the gene regulatory networks that contribute to hepatic responses to fasting and feeding. The advent of sequencing and -omics techniques have begun to facilitate a holistic understanding of the transcriptional landscape and its plasticity. We highlight transcription factors, their cofactors, and the pathways that they impact. We also discuss physiological factors that impinge on these responses, including circadian rhythms and sex differences. Finally, we review how dietary modifications modulate hepatic gene expression programs.
    Keywords:  liver; metabolism; transcription
    DOI:  https://doi.org/10.1101/gad.348340.121
  42. Science. 2021 Apr 22. pii: eabe9985. [Epub ahead of print]
    Nicotinamide mononucleotide increases muscle insulin sensitivity in prediabetic women.
    Mihoko Yoshino, Jun Yoshino, Brandon D Kayser, Gary Patti, Michael P Franczyk, Kathryn F Mills, Miriam Sindelar, Terri Pietka, Bruce W Patterson, Shin-Ichiro Imai, Samuel Klein.
      In rodents, obesity and aging impair nicotinamide adenine dinucleotide (NAD+) biosynthesis, which contributes to metabolic dysfunction. Nicotinamide mononucleotide (NMN) availability is a rate-limiting factor in mammalian NAD+ biosynthesis. We conducted a 10-week, randomized, placebo-controlled, double-blind trial to evaluate the effect of NMN supplementation on metabolic function in postmenopausal women with prediabetes who were overweight or obese. Insulin-stimulated glucose disposal, assessed by using the hyperinsulinemic-euglycemic clamp, and skeletal muscle insulin signaling (phosphorylation of AKT and mTOR) increased after NMN supplementation, but did not change after placebo treatment. NMN supplementation up-regulated the expression of platelet-derived growth factor receptor β and other genes related to muscle remodeling. These results demonstrate NMN increases muscle insulin sensitivity, insulin signaling and remodeling in women with prediabetes who are overweight or obese (ClinicalTrial.gov NCT03151239).
    DOI:  https://doi.org/10.1126/science.abe9985
  43. iScience. 2021 Apr 23. 24(4): 102324
    MitopatHs: a new logically-framed tool for visualizing multiple mitochondrial pathways.
    Saverio Marchi, Marco Zanella, Paolo Pinton, Silvia Crafa, Giovanni Boniolo.
      Mitochondria are key organelles inside the cell that house a wide range of molecular pathways involved in energy metabolism, ions homeostasis, and cell death. Several databases characterize the different mitochondrial aspects and thus support basic and clinical research. Here we present MitopatHs, a web-based data set that allows navigating among the biochemical signaling pathways (PatHs) of human (H) mitochondria (Mito). MitopatHs is designed to visualize and comprehend virtually all types of pathways in two complementary ways: a logical view, where the sequence of biochemical reactions is presented as logical deductions, and an intuitive graphical visualization, which enables the examination and the analysis of each step of the pathway. MitopatHs is a manually curated, open access and collaborative tool, whose goal is to enable the visualization and comprehension of complicated molecular routes in an easy and fast way.
    Keywords:  Cell Biology; Molecular Network; Software
    DOI:  https://doi.org/10.1016/j.isci.2021.102324
  44. Am J Physiol Endocrinol Metab. 2021 Apr 05.
    Genetically increasing flux through β-oxidation in skeletal muscle increases mitochondrial reductive stress and glucose intolerance.
    Cody D Smith, Chein-Te Lin, Shawna L McMillin, Luke A Weyrauch, Cameron Alan Schmidt, Cheryl A Smith, Irwin J Kurland, Carol A Witczak, P Darrell Neufer.
      Elevated mitochondrial H2O2 emission and an oxidative shift in cytosolic redox environment have been linked to high fat diet-induced insulin resistance in skeletal muscle. To test specifically whether increased flux through mitochondrial fatty acid oxidation, in the absence of elevated energy demand, directly alters mitochondrial function and redox state in muscle, two genetic models characterized by increased muscle β-oxidation flux were studied. In mice overexpressing peroxisome proliferator activated receptor-α in muscle (MCK-PPARα), lipid supported mitochondrial respiration, membrane potential (ΔΨm) and H2O2 production rate (JH2O2) were increased, which coincided with a more oxidized cytosolic redox environment, reduced muscle glucose uptake, and whole-body glucose intolerance despite an increased rate of energy expenditure. Similar results were observed in lipin-1 deficient, fatty-liver dystrophic mice, another model characterized by increased β-oxidation flux and glucose intolerance. Crossing MCAT (mitochondrial-targeted catalase) with MCK-PPARα mice normalized JH2O2 production, redox environment and glucose tolerance, but surprisingly both basal and absolute insulin-stimulated rates of glucose uptake in muscle remained depressed. Also surprising, when placed on a high fat diet MCK-PPARα mice were characterized by much lower whole body, fat and lean mass as well as improved glucose tolerance relative to wild-type mice, providing additional evidence that overexpression of PPARα in muscle imposes more extensive metabolic stress than experienced by wild-type mice on a high fat diet. Overall, the findings suggest that driving an increase in skeletal muscle fatty acid oxidation in the absence of metabolic demand imposes mitochondrial reductive stress and elicits multiple counterbalance metabolic responses in attempt to restore bioenergetic homeostasis.
    Keywords:  fat oxidation; glucose tolerance; insulin resistance; mitochondria; skeletal muscle
    DOI:  https://doi.org/10.1152/ajpendo.00010.2021
  45. Front Immunol. 2021 ;12 612271
    Stroma Involvement in Pancreatic Ductal Adenocarcinoma: An Overview Focusing on Extracellular Matrix Proteins.
    Sophie Liot, Jonathan Balas, Alexandre Aubert, Laura Prigent, Perrine Mercier-Gouy, Bernard Verrier, Philippe Bertolino, Ana Hennino, Ulrich Valcourt, Elise Lambert.
      Pancreatic cancer is the seventh leading cause of cancer-related deaths worldwide and is predicted to become second in 2030 in industrialized countries if no therapeutic progress is made. Among the different types of pancreatic cancers, Pancreatic Ductal Adenocarcinoma (PDAC) is by far the most represented one with an occurrence of more than 90%. This specific cancer is a devastating malignancy with an extremely poor prognosis, as shown by the 5-years survival rate of 2-9%, ranking firmly last amongst all cancer sites in terms of prognostic outcomes for patients. Pancreatic tumors progress with few specific symptoms and are thus at an advanced stage at diagnosis in most patients. This malignancy is characterized by an extremely dense stroma deposition around lesions, accompanied by tissue hypovascularization and a profound immune suppression. Altogether, these combined features make access to cancer cells almost impossible for conventional chemotherapeutics and new immunotherapeutic agents, thus contributing to the fatal outcomes of the disease. Initially ignored, the Tumor MicroEnvironment (TME) is now the subject of intensive research related to PDAC treatment and could contain new therapeutic targets. In this review, we will summarize the current state of knowledge in the field by focusing on TME composition to understand how this specific compartment could influence tumor progression and resistance to therapies. Attention will be paid to Tenascin-C, a matrix glycoprotein commonly upregulated during cancer that participates to PDAC progression and thus contributes to poor prognosis.
    Keywords:  extracellular matrix; pancreatic ductal adenocarcinoma; stroma; tenascin; tumor microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2021.612271
  46. Nat Biomed Eng. 2021 Apr 19.
    Nuclear mechanosensing drives chromatin remodelling in persistently activated fibroblasts.
    Cierra J Walker, Claudia Crocini, Daniel Ramirez, Anouk R Killaars, Joseph C Grim, Brian A Aguado, Kyle Clark, Mary A Allen, Robin D Dowell, Leslie A Leinwand, Kristi S Anseth.
      Fibrotic disease is caused by the continuous deposition of extracellular matrix by persistently activated fibroblasts (also known as myofibroblasts), even after the resolution of the injury. Using fibroblasts from porcine aortic valves cultured on hydrogels that can be softened via exposure to ultraviolet light, here we show that increased extracellular stiffness activates the fibroblasts, and that cumulative tension on the nuclear membrane and increases in the activity of histone deacetylases transform transiently activated fibroblasts into myofibroblasts displaying condensed chromatin with genome-wide alterations. The condensed structure of the myofibroblasts is associated with cytoskeletal stability, as indicated by the inhibition of chromatin condensation and myofibroblast persistence after detachment of the nucleus from the cytoskeleton via the displacement of endogenous nesprins from the nuclear envelope. We also show that the chromatin structure of myofibroblasts from patients with aortic valve stenosis is more condensed than that of myofibroblasts from healthy donors. Our findings suggest that nuclear mechanosensing drives distinct chromatin signatures in persistently activated fibroblasts.
    DOI:  https://doi.org/10.1038/s41551-021-00709-w
  47. Science. 2021 Apr 23. 372(6540): 342-343
    Expanding cell-to-cell interactions.
    Aymeric Silvin, Florent Ginhoux.
      
    DOI:  https://doi.org/10.1126/science.abh2810
  48. Cancer Genomics Proteomics. 2021 May-Jun;18(3):18(3): 221-243
    Desmoplastic Crosstalk in Pancreatic Ductal Adenocarcinoma Is Reflected by Different Responses of Panc-1, MIAPaCa-2, PaTu-8902, and CAPAN-2 Cell Lines to Cancer-associated/Normal Fibroblasts.
    Štepán Novák, Michal Kolář, Arpád Szabó, Zdena Vernerová, Lukáš Lacina, Hynek Strnad, Jana Šáchová, Miluše Hradilová, Jan Havránek, Michal Španko, Matúš Čoma, Lukáš Urban, Miriam Kaňuchová, Nikola Melegová, Robert Gürlich, Josef Dvořák, Karel Smetana, Peter Gál, Pavol Szabo.
       BACKGROUND/AIM: Pancreatic ductal adenocarcinoma (PDAC) still represents one of the most aggressive cancers. Understanding of the epithelial-mesenchymal crosstalk as a crucial part of the tumor microenvironment should pave the way for therapies to improve patient survival rates. Well-established cell lines present a useful and reproducible model to study PDAC biology. However, the tumor-stromal interactions between cancer cells and cancer-associated fibroblasts (CAFs) are still poorly understood.
    MATERIALS AND METHODS: We studied interactions between four PDAC cell lines (Panc-1, CAPAN-2, MIAPaCa-2, and PaTu-8902) and conditioned media derived from primary cultures of normal fibroblasts/PDAC-derived CAFs (PANFs).
    RESULTS: When the tested PDAC cell lines were stimulated by PANF-derived conditioned media, the most aggressive behavior was acquired by the Panc-1 cell line (increased number and size of colonies, remaining expression of vimentin and keratin 8 as well as increase of epithelial-to-mesenchymal polarization markers), whereas PaTu-8902 cells were rather inhibited. Of note, administration of the conditioned media to MIAPaCa-2 cells resulted in an inverse effect on the size and number of colonies, whereas CAPAN-2 cells were rather stimulated. To explain the heterogeneous pattern of the observed PDAC crosstalk at the in vitro level, we further compared the phenotype of primary cultures of cells derived from ascitic fluid with that of the tested PDAC cell lines, analyzed tumor samples of PDAC patients, and performed gene expression profiling of PANFs. Immuno-cyto/histo-chemical analysis found specific phenotype differences within the group of examined patients and tested PDAC cell lines, whereas the genomic approach in PANFs found the key molecules (IL6, IL8, MFGE8 and periostin) that may contribute to the cancer aggressive behavior.
    CONCLUSION: The desmoplastic patient-specific regulation of cancer cells by CAFs (also demonstrated by the heterogeneous response of PDAC cell lines to fibroblasts) precludes simple targeting and development of an effective treatment strategy and rather requires establishment of an individualized tumor-specific treatment protocol.
    Keywords:  Epithelial–mesenchymal interaction; cancer stem cell; pancreas; tumor micro - environment; tumor stroma
    DOI:  https://doi.org/10.21873/cgp.20254
  49. Nature. 2021 Apr;592(7855): 647-649
    Elusive cancer cells dissected using developmental-biology toolkit.
    Jyoti Madhusoodanan.
      
    Keywords:  Biological techniques; Cancer; Molecular biology; Stem cells
    DOI:  https://doi.org/10.1038/d41586-021-01029-4
  50. Hepatology. 2021 Apr 05.
    Perivenous stellate cells are the main source of myofibroblasts and cancer-associated-fibroblasts formed after chronic liver injuries.
    Shan-Shan Wang, Xinyu Thomas Tang, Minghui Lin, Jia Yuan, Yi Jacky Peng, Xiujuan Yin, GuoGuo Shang, Gaoxiang Ge, Zhenggang Ren, Bo O Zhou.
      Studies of the identity and pathophysiology of fibrogenic hepatic stellate cells (HSCs) have been hampered by a lack of genetic tools that permit specific and inducible fate-mapping of these cells in vivo. Here, by single cell RNA sequencing of non-parenchymal cells from mouse liver, we identified Tcf21 as a unique marker that restricted its expression to quiescent HSCs. Tracing Tcf21+ cells by Tcf21-CreER targeted ~10% of all HSCs, most of which located at periportal and pericentral zones. These HSCs were quiescent under steady state, but became activated upon injuries, generating 62-67% of all myofibroblasts in fibrotic livers and ~85% of all cancer-associated-fibroblasts (CAFs) in liver tumors. Conditional deletion of Tgfbr2 by Tcf21-CreER blocked HSC activation, compromised liver fibrosis, and inhibited liver tumor progression. In conclusion, Tcf21-CreER-targeted perivenous stellate cells are the main source of myofibroblasts and CAFs in chronically injured livers. TGF-β signaling links HSC activation to liver fibrosis and tumorigenesis.
    Keywords:  Hepatic stellate cells; Liver fibrosis; Liver tumor; Tcf21
    DOI:  https://doi.org/10.1002/hep.31848
  51. Cell Metab. 2021 Apr 19. pii: S1550-4131(21)00175-3. [Epub ahead of print]
    Hypothalamic bile acid-TGR5 signaling protects from obesity.
    Ashley Castellanos-Jankiewicz, Omar Guzmán-Quevedo, Valérie S Fénelon, Philippe Zizzari, Carmelo Quarta, Luigi Bellocchio, Anne Tailleux, Julie Charton, Daniela Fernandois, Marcus Henricsson, Catherine Piveteau, Vincent Simon, Camille Allard, Sandrine Quemener, Valentine Guinot, Nathalie Hennuyer, Alessia Perino, Alexia Duveau, Marlène Maitre, Thierry Leste-Lasserre, Samantha Clark, Nathalie Dupuy, Astrid Cannich, Delphine Gonzales, Benoit Deprez, Gilles Mithieux, David Dombrowicz, Fredrik Bäckhed, Vincent Prevot, Giovanni Marsicano, Bart Staels, Kristina Schoonjans, Daniela Cota.
      Bile acids (BAs) improve metabolism and exert anti-obesity effects through the activation of the Takeda G protein-coupled receptor 5 (TGR5) in peripheral tissues. TGR5 is also found in the brain hypothalamus, but whether hypothalamic BA signaling is implicated in body weight control and obesity pathophysiology remains unknown. Here we show that hypothalamic BA content is reduced in diet-induced obese mice. Central administration of BAs or a specific TGR5 agonist in these animals decreases body weight and fat mass by activating the sympathetic nervous system, thereby promoting negative energy balance. Conversely, genetic downregulation of hypothalamic TGR5 expression in the mediobasal hypothalamus favors the development of obesity and worsens established obesity by blunting sympathetic activity. Lastly, hypothalamic TGR5 signaling is required for the anti-obesity action of dietary BA supplementation. Together, these findings identify hypothalamic TGR5 signaling as a key mediator of a top-down neural mechanism that counteracts diet-induced obesity.
    Keywords:  GPBAR1; TGR5; bile acids; body weight; diet; energy expenditure; food intake; hypothalamus; obesity; sympathetic nervous system
    DOI:  https://doi.org/10.1016/j.cmet.2021.04.009
  52. J Surg Oncol. 2021 Apr 24.
    Predictors of early recurrence following neoadjuvant chemotherapy and surgical resection for localized pancreatic adenocarcinoma.
    Sowmya Narayanan, Samer AlMasri, Mazen Zenati, Ibrahim Nassour, Asmita Chopra, Caroline Rieser, Katelyn Smith, Vivianne Oyefusi, Tracy Daum, Nathan Bahary, David Bartlett, Kenneth Lee, Amer Zureikat, Alessandro Paniccia.
       BACKGROUND AND OBJECTIVES: Neoadjuvant chemotherapy (NAT) for pancreatic adenocarcinoma (PDAC) is increasingly being utilized. However, a significant number of patients will experience early recurrence, possibly negating the benefit of surgery. We aimed to identify factors implicated in early disease recurrence.
    METHODS: A retrospective review of pancreaticoduodenectomies performed between 2005 and 2017 at our institution for PDAC following NAT was performed. A 6-month cut-off was used to stratify patients into early/late recurrence groups. Multivariate analysis was performed to identify predictors of recurrence.
    RESULTS: Of 273 patients, 64 (23%) developed early recurrence or died within 90 days of surgery. The median time to recurrence was 4 months (95% confidence interval [CI]: 2.2-4.3) in the early group versus 16 months (95% CI: 13.7-19.9) in the late group. The former had higher baseline and post-NAT Ca19-9 levels than the latter (472 vs. 153 IU/ml, p = 0.001 and 71 vs. 39 IU/ml, p = 0.005, respectively). A higher positive lymph node ratio significantly increased the risk of early recurrence (hazard ratio [HR]: 15.9, p < 0.001) while adjuvant chemotherapy was protective (HR: 0.4, p < 0.001).
    CONCLUSION: Our findings acknowledge the limitations of clinically measured factors used to ascertain response to NAT and underline the need for individualized molecular markers that take into consideration the specific tumor biology.
    Keywords:  early recurrence; neoadjuvant chemotherapy; pancreatic cancer; pancreaticoduodenectomy
    DOI:  https://doi.org/10.1002/jso.26510
  53. Science. 2021 Apr 23. 372(6540): 346-347
    Healing without scarring.
    Piotr Konieczny, Shruti Naik.
      
    DOI:  https://doi.org/10.1126/science.abi5770
  54. Cancer Treat Rev. 2021 Mar 24. pii: S0305-7372(21)00041-4. [Epub ahead of print]96 102193
    Blood biomarkers for differential diagnosis and early detection of pancreatic cancer.
    Fawaz N Al-Shaheri, Mohamed S S Alhamdani, Andrea S Bauer, Nathalia Giese, Markus W Büchler, Thilo Hackert, Jörg D Hoheisel.
      Pancreatic cancer is currently the most lethal tumor entity and case numbers are rising. It will soon be the second most frequent cause of cancer-related death in the Western world. Mortality is close to incidence and patient survival after diagnosis stands at about five months. Blood-based diagnostics could be one crucial factor for improving this dismal situation and is at a stage that could make this possible. Here, we are reviewing the current state of affairs with its problems and promises, looking at various molecule types. Reported results are evaluated in the overall context. Also, we are proposing steps toward clinical utility that should advance the development toward clinical application by improving biomarker quality but also by defining distinct clinical objectives and the respective diagnostic accuracies required to achieve them. Many of the discussed points and conclusions are highly relevant to other solid tumors, too.
    Keywords:  Blood-based biomarkers; Circulating tumor DNA (ctDNA); Circulating tumor cells; Differential diagnosis; Early detection; Liquid biopsy; Pancreatic cancer; Proteins; microRNAs
    DOI:  https://doi.org/10.1016/j.ctrv.2021.102193
  55. Trends Endocrinol Metab. 2021 Apr 19. pii: S1043-2760(21)00068-0. [Epub ahead of print]
    Cancer-Mediated Muscle Cachexia: Etiology and Clinical Management.
    Thomas Siff, Parash Parajuli, Mohammed S Razzaque, Azeddine Atfi.
      Muscle cachexia has a major detrimental impact on cancer patients, being responsible for 30% of all cancer deaths. It is characterized by a debilitating loss in muscle mass and function, which ultimately deteriorates patients' quality of life and dampens therapeutic treatment efficacy. Muscle cachexia stems from widespread alterations in whole-body metabolism as well as immunity and neuroendocrine functions and these global defects often culminate in aberrant signaling within skeletal muscle, causing muscle protein breakdown and attendant muscle atrophy. This review summarizes recent landmark discoveries that significantly enhance our understanding of the molecular etiology of cancer-driven muscle cachexia and further discuss emerging therapeutic approaches seeking to simultaneously target those newly discovered mechanisms to efficiently curb this lethal syndrome.
    Keywords:  inflammatory cytokines; muscle cachexia; muscle protein breakdown; muscle wasting; therapeutics targeting cachexia
    DOI:  https://doi.org/10.1016/j.tem.2021.03.007
  56. Circ Res. 2021 Apr 22.
    NAD+ Repletion Reverses Heart Failure with Preserved Ejection Fraction.
    Dan Tong, Gabriele G Schiattarella, Nan Jiang, Francisco Altamirano, Pamela A Szweda, Abdallah Elnwasany, Dong I Lee, Heesoo Yoo, David A Kass, Luke I Szweda, Sergio Lavandero, Eric Verdin, Thomas G Gillette, Joseph A Hill.
      Rationale: Heart failure with preserved ejection fraction (HFpEF) is a mortal clinical syndrome without effective therapies. We recently demonstrated in mice that a combination of metabolic and hypertensive stress recapitulates key features of human HFpEF.Objective: Using this novel preclinical HFpEF model, we set out to define and manipulate metabolic dysregulations occurring in HFpEF myocardium. Methods and Results: We observed impairment in mitochondrial fatty acid oxidation associated with hyperacetylation of key enzymes in the pathway. Down-regulation of sirtuin 3 and deficiency of NAD+ secondary to an impaired NAD+ salvage pathway contribute to this mitochondrial protein hyperacetylation. Impaired expression of genes involved in NAD+ biosynthesis was confirmed in cardiac tissue from HFpEF patients. Supplementing HFpEF mice with nicotinamide riboside or a direct activator of NAD+ biosynthesis led to improvement in mitochondrial function and amelioration of the HFpEF phenotype. Conclusions: Collectively, these studies demonstrate that HFpEF is associated with myocardial mitochondrial dysfunction and unveil NAD+ repletion as a promising therapeutic approach in the syndrome.
    DOI:  https://doi.org/10.1161/CIRCRESAHA.120.317046
  57. Science. 2021 Apr 22. pii: eabg2365. [Epub ahead of print]
    Lack of transgenerational effects of ionizing radiation exposure from the Chernobyl accident.
    Meredith Yeager, Mitchell J Machiela, Prachi Kothiyal, Michael Dean, Clara Bodelon, Shalabh Suman, Mingyi Wang, Lisa Mirabello, Chase W Nelson, Weiyin Zhou, Cameron Palmer, Bari Ballew, Leandro M Colli, Neal D Freedman, Casey Dagnall, Amy Hutchinson, Vibha Vij, Yosi Maruvka, Maureen Hatch, Iryna Illienko, Yuri Belayev, Nori Nakamura, Vadim Chumak, Elena Bakhanova, David Belyi, Victor Kryuchkov, Ivan Golovanov, Natalia Gudzenko, Elizabeth K Cahoon, Paul Albert, Vladimir Drozdovitch, Mark P Little, Kiyohiko Mabuchi, Chip Stewart, Gad Getz, Dimitry Bazyka, Amy Berrington de Gonzalez, Stephen J Chanock.
      Effects of radiation exposure from the Chernobyl nuclear accident remain a topic of interest. We investigated whether children born to parents employed as cleanup workers or exposed to occupational and environmental ionizing radiation post-accident were born with more germline de novo mutations (DNMs). Whole-genome sequencing of 130 children (born 1987-2002) and their parents did not reveal an increase in the rates, distributions, or types of DNMs versus previous studies. We find no elevation in total DNMs regardless of cumulative preconception gonadal paternal (mean = 365 mGy, range = 0-4,080 mGy) or maternal (mean = 19 mGy, range = 0-550 mGy) exposure to ionizing radiation and conclude over this exposure range, evidence is lacking for a substantial effect on germline DNMs in humans, suggesting minimal impact on health of subsequent generations.
    DOI:  https://doi.org/10.1126/science.abg2365
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