bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2024–05–05
forty-nine papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Multiplexed Imaging Mass Cytometry Analysis Characterizes the Vascular Niche in Pancreatic Cancer.
  2. Systematic analysis of proteome turnover in an organoid model of pancreatic cancer by dSILO.
  3. Cycling back to folate metabolism in cancer.
  4. Macrophage-fibroblast JAK/STAT dependent crosstalk promotes liver metastatic outgrowth in pancreatic cancer.
  5. Mitochondria and Cancer.
  6. Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1.
  7. Senescence defines a distinct subset of myofibroblasts that orchestrates immunosuppression in pancreatic cancer.
  8. Mesoscale Metabolic Channeling Revealed by Multimodal Microscopy.
  9. Drivers of Morphogenesis: Curvature Sensor Self-Assembly at the Membrane.
  10. Spatially resolved analysis of microenvironmental gradient impact on cancer cell phenotypes.
  11. Inhibition of mammalian mtDNA transcription acts paradoxically to reverse diet-induced hepatosteatosis and obesity.
  12. PRMT1 promotes epigenetic reprogramming associated with acquired chemoresistance in pancreatic cancer.
  13. Smooth muscle cell-derived Cxcl12 directs macrophage accrual and sympathetic innervation to control thermogenic adipose tissue.
  14. Senescence Defines a Distinct Subset of Myofibroblasts That Orchestrates Immunosuppression in Pancreatic Cancer.
  15. Failure to Undergo Resection Following Neoadjuvant Therapy for Resectable Pancreatic Cancer: A Secondary Analysis of SWOG S1505.
  16. A pipeline for senolytics.
  17. Cryo-EM images of phase separated lipid bilayer vesicles analyzed with a machine learning approach.
  18. Unprocessed genomic uracil as a source of DNA replication stress in cancer cells.
  19. Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation.
  20. The mitochondrial multi-omic response to exercise training across rat tissues.
  21. Nude blebs expose cells to phagocytes.
  22. Aryl hydrocarbon receptor knockout accelerates PanIN formation and fibro-inflammation in a mutant Kras-driven pancreatic cancer model.
  23. Ferroptosis Biology.
  24. REDISCOVER guidelines for borderline-resectable and locally advanced pancreatic cancer: management algorithm, unanswered questions, and future perspectives.
  25. Senescent CAFs mediate immunosuppression and drive breast cancer progression.
  26. Immunometabolism of CD8+ T cell differentiation in cancer.
  27. Acinar to β-like cell conversion through inhibition of focal adhesion kinase.
  28. The Population-level Prevalence of Exocrine Pancreas Insufficiency and the Subsequent Risk of Pancreatic Cancer.
  29. Nucleocytoplasmic transport rates are regulated by cellular processes that modulate GTP availability.
  30. Iron retardation in lysosome protects senescent cells from ferroptosis.
  31. Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications.
  32. CDK4/6 activity is required during G2 arrest to prevent stress-induced endoreplication.
  33. A Versatile Microfluidic Platform for Extravasation Studies Based on DNA Origami - Cell Interactions.
  34. Acetate reprogrammes tumour metabolism and promotes PD-L1 expression and immune evasion by upregulating c-Myc.
  35. Mechanochemical dynamics of collective cells and hierarchical topological defects in multicellular lumens.
  36. Analysis of urinary potassium isotopes and association with pancreatic health: healthy, diabetic and cancerous states.
  37. Dietary dicarboxylic acids provide a non-storable alternative fat source that protects mice against obesity.
  38. cancercelllines.org-a novel resource for genomic variants in cancer cell lines.
  39. Career trajectories of MD-PhD physician scientists: The loss of women investigators.
  40. Build and operation of a custom 3D, multicolor, single-molecule localization microscope.
  41. A pipeline for evaluation of machine learning/AI models to quantify PD-L1 immunohistochemistry.
  42. In Situ Engineering Cancer Mask to Immobilize Tumor Cells and Block Metastasis.
  43. CX-4945 (Silmitasertib) Induces Cell Death by Impairing Lysosomal Utilization in KRAS Mutant Cholangiocarcinoma Cell Lines.
  44. Cholesterol Changes Interfacial Water Alignment in Model Cell Membranes.
  45. Fluorescence lifetime imaging microscopy of flexible and rigid dyes probes the biophysical properties of synthetic and biological membranes.
  46. The 1+Million Genomes Minimal Dataset for Cancer.
  47. 3D genomic mapping reveals multifocality of human pancreatic precancers.
  48. The epidermal circadian clock integrates and subverts brain signals to guarantee skin homeostasis.
  49. Dietary intake and glutamine-serine metabolism control pathologic vascular stiffness.
  1. Cancer Res. 2024 May 02.
    Multiplexed Imaging Mass Cytometry Analysis Characterizes the Vascular Niche in Pancreatic Cancer.
    Jonathan Sussman, Nathalia Y Kim, Samantha B Kemp, Daniel Traum, Takeshi Katsuda, Benjamin M Kahn, Jason Xu, Il-Kyu Kim, Cody Eskandarian, Devora Delman, Gregory L Beatty, Klaus H Kaestner, Amber L Simpson, Ben Z Stanger.
      Oncogenesis and progression of pancreatic ductal adenocarcinoma (PDAC) is driven by complex interactions between the neoplastic component and the tumor microenvironment (TME), which includes immune, stromal, and parenchymal cells. In particular, most PDACs are characterized by a hypovascular and hypoxic environment that alters tumor cell behavior and limits the efficacy of chemotherapy and immunotherapy. Characterization of the spatial features of the vascular niche could advance our understanding of inter- and intra-tumoral heterogeneity in PDAC. Here, we investigated the vascular microenvironment of PDAC by applying imaging mass cytometry using a 26-antibody panel on 35 regions of interest (ROIs) across 9 patients, capturing over 140,000 single cells. The approach distinguished major cell types, including multiple populations of lymphoid and myeloid cells, endocrine cells, ductal cells, stromal cells, and endothelial cells. Evaluation of cellular neighborhoods identified 10 distinct spatial domains, including multiple immune and tumor-enriched environments as well as the vascular niche. Focused analysis revealed differential interactions between immune populations and the vasculature and identified distinct spatial domains wherein tumor cell proliferation occurs. Importantly, the vascular niche was closely associated with a population of CD44-expressing macrophages enriched for a pro-angiogenic gene signature. Together, this study provides insights into the spatial heterogeneity of PDAC and suggests a role for CD44-expressing macrophages in shaping the vascular niche.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-23-2352
  2. Cell Rep Methods. 2024 Apr 24. pii: S2667-2375(24)00091-2. [Epub ahead of print] 100760
    Systematic analysis of proteome turnover in an organoid model of pancreatic cancer by dSILO.
    Alison B Ross, Darvesh Gorhe, Jenny Kim Kim, Stefanie Hodapp, Lela DeVine, Karina M Chan, Iok In Christine Chio, Marko Jovanovic, Marina Ayres Pereira.
      The role of protein turnover in pancreatic ductal adenocarcinoma (PDA) metastasis has not been previously investigated. We introduce dynamic stable-isotope labeling of organoids (dSILO): a dynamic SILAC derivative that combines a pulse of isotopically labeled amino acids with isobaric tandem mass-tag (TMT) labeling to measure proteome-wide protein turnover rates in organoids. We applied it to a PDA model and discovered that metastatic organoids exhibit an accelerated global proteome turnover compared to primary tumor organoids. Globally, most turnover changes are not reflected at the level of protein abundance. Interestingly, the group of proteins that show the highest turnover increase in metastatic PDA compared to tumor is involved in mitochondrial respiration. This indicates that metastatic PDA may adopt alternative respiratory chain functionality that is controlled by the rate at which proteins are turned over. Collectively, our analysis of proteome turnover in PDA organoids offers insights into the mechanisms underlying PDA metastasis.
    Keywords:  CP: Biotechnology; CP: Cancer biology; PDA; SILAC; dSILO; metastases; protein half-life; protein turnover; respirasome
    DOI:  https://doi.org/10.1016/j.crmeth.2024.100760
  3. Nat Cancer. 2024 May 02.
    Cycling back to folate metabolism in cancer.
    Younghwan Lee, Karen H Vousden, Marc Hennequart.
      Metabolic changes contribute to cancer initiation and progression through effects on cancer cells, the tumor microenvironment and whole-body metabolism. Alterations in serine metabolism and the control of one-carbon cycles have emerged as critical for the development of many tumor types. In this Review, we focus on the mitochondrial folate cycle. We discuss recent evidence that, in addition to supporting nucleotide synthesis, mitochondrial folate metabolism also contributes to metastasis through support of antioxidant defense, mitochondrial protein synthesis and the overflow of excess formate. These observations offer potential therapeutic opportunities, including the modulation of formate metabolism through dietary interventions and the use of circulating folate cycle metabolites as biomarkers for cancer detection.
    DOI:  https://doi.org/10.1038/s43018-024-00739-8
  4. Nat Commun. 2024 Apr 27. 15(1): 3593
    Macrophage-fibroblast JAK/STAT dependent crosstalk promotes liver metastatic outgrowth in pancreatic cancer.
    Meirion Raymant, Yuliana Astuti, Laura Alvaro-Espinosa, Daniel Green, Valeria Quaranta, Gaia Bellomo, Mark Glenn, Vatshala Chandran-Gorner, Daniel H Palmer, Christopher Halloran, Paula Ghaneh, Neil C Henderson, Jennifer P Morton, Manuel Valiente, Ainhoa Mielgo, Michael C Schmid.
      Pancreatic ductal adenocarcinoma (PDAC) is a highly metastatic disease for which better therapies are urgently needed. Fibroblasts and macrophages are heterogeneous cell populations able to enhance metastasis, but the role of a macrophage-fibroblast crosstalk in regulating their pro-metastatic functions remains poorly understood. Here we deconvolve how macrophages regulate metastasis-associated fibroblast (MAF) heterogeneity in the liver. We identify three functionally distinct MAF populations, among which the generation of pro-metastatic and immunoregulatory myofibroblastic-MAFs (myMAFs) critically depends on macrophages. Mechanistically, myMAFs are induced through a STAT3-dependent mechanism driven by macrophage-derived progranulin and cancer cell-secreted leukaemia inhibitory factor (LIF). In a reciprocal manner, myMAF secreted osteopontin promotes an immunosuppressive macrophage phenotype resulting in the inhibition of cytotoxic T cell functions. Pharmacological blockade of STAT3 or myMAF-specific genetic depletion of STAT3 restores an anti-tumour immune response and reduces metastases. Our findings provide molecular insights into the complex macrophage-fibroblast interactions in tumours and reveal potential targets to inhibit PDAC liver metastasis.
    DOI:  https://doi.org/10.1038/s41467-024-47949-3
  5. Cold Spring Harb Perspect Med. 2024 May 01. pii: a041534. [Epub ahead of print]
    Mitochondria and Cancer.
    Timothy C Kenny, Kıvanç Birsoy.
      Mitochondria are semiautonomous organelles with diverse metabolic and cellular functions including anabolism and energy production through oxidative phosphorylation. Following the pioneering observations of Otto Warburg nearly a century ago, an immense body of work has examined the role of mitochondria in cancer pathogenesis and progression. Here, we summarize the current state of the field, which has coalesced around the position that functional mitochondria are required for cancer cell proliferation. In this review, we discuss how mitochondria influence tumorigenesis by impacting anabolism, intracellular signaling, and the tumor microenvironment. Consistent with their critical functions in tumor formation, mitochondria have become an attractive target for cancer therapy. We provide a comprehensive update on the numerous therapeutic modalities targeting the mitochondria of cancer cells making their way through clinical trials.
    DOI:  https://doi.org/10.1101/cshperspect.a041534
  6. Nature. 2024 May 01.
    Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1.
    Yeeun Son, Timothy C Kenny, Artem Khan, Kıvanç Birsoy, Richard K Hite.
      Phosphatidylcholine and phosphatidylethanolamine, the two most abundant phospholipids in mammalian cells, are synthesized de novo by the Kennedy pathway from choline and ethanolamine, respectively1-6. Despite the essential roles of these lipids, the mechanisms that enable the cellular uptake of choline and ethanolamine remain unknown. Here we show that the protein encoded by FLVCR1, whose mutation leads to the neurodegenerative syndrome posterior column ataxia and retinitis pigmentosa7-9, transports extracellular choline and ethanolamine into cells for phosphorylation by downstream kinases to initiate the Kennedy pathway. Structures of FLVCR1 in the presence of choline and ethanolamine reveal that both metabolites bind to a common binding site comprising aromatic and polar residues. Despite binding to a common site, FLVCR1 interacts in different ways with the larger quaternary amine of choline in and with the primary amine of ethanolamine. Structure-guided mutagenesis identified residues that are crucial for the transport of ethanolamine, but dispensable for choline transport, enabling functional separation of the entry points into the two branches of the Kennedy pathway. Altogether, these studies reveal how FLVCR1 is a high-affinity metabolite transporter that serves as the common origin for phospholipid biosynthesis by two branches of the Kennedy pathway.
    DOI:  https://doi.org/10.1038/s41586-024-07374-4
  7. Cancer Discov. 2024 Apr 29.
    Senescence defines a distinct subset of myofibroblasts that orchestrates immunosuppression in pancreatic cancer.
    Jad I Belle, Devashish Sen, John M Baer, Xiuting Liu, Varintra E Lander, Jiayu Ye, Blake E Sells, Brett L Knolhoff, Ahmad Faiz, Liang-I Kang, Guhan Qian, Ryan C Fields, Li Ding, Hyun Kim, Paolo P Provenzano, Sheila A Stewart, David G DeNardo.
      PDAC therapeutic resistance is largely attributed to a unique tumor microenvironment embedded with an abundance of cancer associated fibroblasts (CAFs). Distinct CAF populations were recently identified, but the phenotypic drivers and specific impact of CAF heterogeneity remain unclear. In this study, we identify a subpopulation of senescent myofibroblastic CAFs (SenCAFs) in mouse and human PDAC. These SenCAFs are a phenotypically distinct subset of myofibroblastic CAFs that localize near tumor ducts and accumulate with PDAC progression. To assess the impact of endogenous SenCAFs in PDAC, we employed a LSL-KRASG12D;p53flox;p48-CRE;INK-ATTAC (KPPC-IA) mouse model of spontaneous PDAC with inducible senescent cell depletion. Depletion of senescent stromal cells in genetic and pharmacologic PDAC models relieved immune suppression by macrophages, delayed tumor progression and increased responsiveness to chemotherapy. Collectively, our findings demonstrate that SenCAFs promote PDAC progression and immune cell dysfunction.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-0428
  8. Res Sq. 2024 Apr 17. pii: rs.3.rs-4096781. [Epub ahead of print]
    Mesoscale Metabolic Channeling Revealed by Multimodal Microscopy.
    Rafael Arrojo E Drigo, Aliyah Habashy, Christopher Acree, Keun-Young Kim, Thomas Deerinck, Emilee Patterson, Louise Lantier, Owen McGuinness, Mark Ellisman.
      Metabolic homeostasis within cells and tissues requires engagement of catabolic and anabolic pathways consuming nutrients needed to generate energy to drive these and other subcellular processes. However, the current understanding of cell homeostasis and metabolism, including how cells utilize nutrients, comes largely from tissue and cell models analyzed after fractionation. These bulk strategies do not reveal the spatial characteristics of cell metabolism at the single cell level, and how these aspects relate to the location of cells and organelles within the complexity of the tissue they reside within. Here we pioneer the use of high-resolution electron and stable isotope microscopy (MIMS-EM) to quantitatively map the fate of nutrient-derived 13 C atoms at subcellular scale. When combined with machine-learning image segmentation, our approach allows us to establish the cellular and organellar spatial pattern of glucose 13 C flux in hepatocytes in situ . We applied network analysis algorithms to chart the landscape of organelle-organelle contact networks and identified subpopulations of mitochondria and lipid droplets that have distinct organelle interactions and 13 C enrichment levels. In addition, we revealed a new relationship between the initiation of glycogenesis and proximity of lipid droplets. Our results establish MIMS-EM as a new tool for tracking and quantifying nutrient metabolism at the subcellular scale, and to identify the spatial channeling of nutrient-derived atoms in the context of organelle-organelle interactions in situ .
    DOI:  https://doi.org/10.21203/rs.3.rs-4096781/v1
  9. Cold Spring Harb Perspect Biol. 2024 May 02. pii: a041528. [Epub ahead of print]
    Drivers of Morphogenesis: Curvature Sensor Self-Assembly at the Membrane.
    Brandy N Curtis, Amy S Gladfelter.
      This review examines the relationships between membrane chemistry, curvature-sensing proteins, and cellular morphogenesis. Curvature-sensing proteins are often orders of magnitude smaller than the membrane curvatures they localize to. How are nanometer-scale proteins used to sense micrometer-scale membrane features? Here, we trace the journey of curvature-sensing proteins as they engage with lipid membranes through a combination of electrostatic and hydrophobic interactions. We discuss how curvature sensing hinges on membrane features like lipid charge, packing, and the directionality of membrane curvature. Once bound to the membrane, many curvature sensors undergo self-assembly (i.e., they oligomerize or form higher-order assemblies that are key for initiating and regulating cell shape transformations). Central to these discussions are the micrometer-scale curvature-sensing proteins' septins. By discussing recent literature surrounding septin membrane association, assembly, and their many functions in morphogenesis with support from other well-studied curvature sensors, we aim to synthesize possible mechanisms underlining cell shape sensing.
    DOI:  https://doi.org/10.1101/cshperspect.a041528
  10. Sci Adv. 2024 May 03. 10(18): eadn3448
    Spatially resolved analysis of microenvironmental gradient impact on cancer cell phenotypes.
    Jamie Auxillos, Roxane Crouigneau, Yan-Fang Li, Yifan Dai, Arnaud Stigliani, Isabella Tavernaro, Ute Resch-Genger, Albin Sandelin, Rodolphe Marie, Stine F Pedersen.
      Despite the physiological and pathophysiological significance of microenvironmental gradients, e.g., for diseases such as cancer, tools for generating such gradients and analyzing their impact are lacking. Here, we present an integrated microfluidic-based workflow that mimics extracellular pH gradients characteristic of solid tumors while enabling high-resolution live imaging of, e.g., cell motility and chemotaxis, and preserving the capacity to capture the spatial transcriptome. Our microfluidic device generates a pH gradient that can be rapidly controlled to mimic spatiotemporal microenvironmental changes over cancer cells embedded in a 3D matrix. The device can be reopened allowing immunofluorescence analysis of selected phenotypes, as well as the transfer of cells and matrix to a Visium slide for spatially resolved analysis of transcriptional changes across the pH gradient. This workflow is easily adaptable to other gradients and multiple cell types and can therefore prove invaluable for integrated analysis of roles of microenvironmental gradients in biology.
    DOI:  https://doi.org/10.1126/sciadv.adn3448
  11. Nat Metab. 2024 Apr 30.
    Inhibition of mammalian mtDNA transcription acts paradoxically to reverse diet-induced hepatosteatosis and obesity.
    Shan Jiang, Taolin Yuan, Florian A Rosenberger, Arnaud Mourier, Nathalia R V Dragano, Laura S Kremer, Diana Rubalcava-Gracia, Fynn M Hansen, Melissa Borg, Mara Mennuni, Roberta Filograna, David Alsina, Jelena Misic, Camilla Koolmeister, Polyxeni Papadea, Martin Hrabe de Angelis, Lipeng Ren, Olov Andersson, Anke Unger, Tim Bergbrede, Raffaella Di Lucrezia, Rolf Wibom, Juleen R Zierath, Anna Krook, Patrick Giavalisco, Matthias Mann, Nils-Göran Larsson.
      The oxidative phosphorylation system1 in mammalian mitochondria plays a key role in transducing energy from ingested nutrients2. Mitochondrial metabolism is dynamic and can be reprogrammed to support both catabolic and anabolic reactions, depending on physiological demands or disease states. Rewiring of mitochondrial metabolism is intricately linked to metabolic diseases and promotes tumour growth3-5. Here, we demonstrate that oral treatment with an inhibitor of mitochondrial transcription (IMT)6 shifts whole-animal metabolism towards fatty acid oxidation, which, in turn, leads to rapid normalization of body weight, reversal of hepatosteatosis and restoration of normal glucose tolerance in male mice on a high-fat diet. Paradoxically, the IMT treatment causes a severe reduction of oxidative phosphorylation capacity concomitant with marked upregulation of fatty acid oxidation in the liver, as determined by proteomics and metabolomics analyses. The IMT treatment leads to a marked reduction of complex I, the main dehydrogenase feeding electrons into the ubiquinone (Q) pool, whereas the levels of electron transfer flavoprotein dehydrogenase and other dehydrogenases connected to the Q pool are increased. This rewiring of metabolism caused by reduced mtDNA expression in the liver provides a principle for drug treatment of obesity and obesity-related pathology.
    DOI:  https://doi.org/10.1038/s42255-024-01038-3
  12. Cell Rep. 2024 Apr 30. pii: S2211-1247(24)00504-7. [Epub ahead of print]43(5): 114176
    PRMT1 promotes epigenetic reprogramming associated with acquired chemoresistance in pancreatic cancer.
    Chan D K Nguyen, Benjamín A Colón-Emeric, Shigekazu Murakami, Mia N Y Shujath, Chunling Yi.
      Pancreatic ductal adenocarcinoma (PDAC) carries a dismal prognosis due to therapeutic resistance. We show that PDAC cells undergo global epigenetic reprogramming to acquire chemoresistance, a process that is driven at least in part by protein arginine methyltransferase 1 (PRMT1). Genetic or pharmacological PRMT1 inhibition impairs adaptive epigenetic reprogramming and delays acquired resistance to gemcitabine and other common chemo drugs. Mechanistically, gemcitabine treatment induces translocation of PRMT1 into the nucleus, where its enzymatic activity limits the assembly of chromatin-bound MAFF/BACH1 transcriptional complexes. Cut&Tag chromatin profiling of H3K27Ac, MAFF, and BACH1 suggests a pivotal role for MAFF/BACH1 in global epigenetic response to gemcitabine, which is confirmed by genetically silencing MAFF. PRMT1 and MAFF/BACH1 signature genes identified by Cut&Tag analysis distinguish gemcitabine-resistant from gemcitabine-sensitive patient-derived xenografts of PDAC, supporting the PRMT1-MAFF/BACH1 epigenetic regulatory axis as a potential therapeutic avenue for improving the efficacy and durability of chemotherapies in patients of PDAC.
    Keywords:  BACH1; CP: Cancer; MAFF; PRMT1; chemoresistance; epigenetic reprogramming; pancreatic cancer
    DOI:  https://doi.org/10.1016/j.celrep.2024.114176
  13. Cell Rep. 2024 Apr 27. pii: S2211-1247(24)00497-2. [Epub ahead of print]43(5): 114169
    Smooth muscle cell-derived Cxcl12 directs macrophage accrual and sympathetic innervation to control thermogenic adipose tissue.
    Derek Lee, Abigail M Benvie, Benjamin M Steiner, Nikolai J Kolba, Josie G Ford, Sean M McCabe, Yuwei Jiang, Daniel C Berry.
      Sympathetic innervation of brown adipose tissue (BAT) controls mammalian adaptative thermogenesis. However, the cellular and molecular underpinnings contributing to BAT innervation remain poorly defined. Here, we show that smooth muscle cells (SMCs) support BAT growth, lipid utilization, and thermogenic plasticity. Moreover, we find that BAT SMCs express and control the bioavailability of Cxcl12. SMC deletion of Cxcl12 fosters brown adipocyte lipid accumulation, reduces energy expenditure, and increases susceptibility to diet-induced metabolic dysfunction. Mechanistically, we find that Cxcl12 stimulates CD301+ macrophage recruitment and supports sympathetic neuronal maintenance. Administering recombinant Cxcl12 to obese mice or leptin-deficient (Ob/Ob) mice is sufficient to boost macrophage presence and drive sympathetic innervation to restore BAT morphology and thermogenic responses. Altogether, our data reveal an SMC chemokine-dependent pathway linking immunological infiltration and sympathetic innervation as a rheostat for BAT maintenance and thermogenesis.
    Keywords:  CP: Immunology; CP: Metabolism; Cxcl2; brown adipocytes; macrophage; smooth muscle cells; sympathetic innervation; thermogenesis
    DOI:  https://doi.org/10.1016/j.celrep.2024.114169
  14. Cancer Discov. 2024 Apr 29. OF1-OF32
    Senescence Defines a Distinct Subset of Myofibroblasts That Orchestrates Immunosuppression in Pancreatic Cancer.
    Jad I Belle, Devashish Sen, John M Baer, Xiuting Liu, Varintra E Lander, Jiayu Ye, Blake E Sells, Brett L Knolhoff, Ahmad Faiz, Liang-I Kang, Guhan Qian, Ryan C Fields, Li Ding, Hyun Kim, Paolo P Provenzano, Sheila A Stewart, David G DeNardo.
      Pancreatic ductal adenocarcinoma (PDAC) therapeutic resistance is largely attributed to a unique tumor microenvironment embedded with an abundance of cancer-associated fibroblasts (CAF). Distinct CAF populations were recently identified, but the phenotypic drivers and specific impact of CAF heterogeneity remain unclear. In this study, we identify a subpopulation of senescent myofibroblastic CAFs (SenCAF) in mouse and human PDAC. These SenCAFs are a phenotypically distinct subset of myofibroblastic CAFs that localize near tumor ducts and accumulate with PDAC progression. To assess the impact of endogenous SenCAFs in PDAC, we used an LSL-KRASG12D;p53flox;p48-CRE;INK-ATTAC (KPPC-IA) mouse model of spontaneous PDAC with inducible senescent cell depletion. Depletion of senescent stromal cells in genetic and pharmacologic PDAC models relieved immune suppression by macrophages, delayed tumor progression, and increased responsiveness to chemotherapy. Collectively, our findings demonstrate that SenCAFs promote PDAC progression and immune cell dysfunction.
    SIGNIFICANCE: CAF heterogeneity in PDAC remains poorly understood. In this study, we identify a novel subpopulation of senescent CAFs that promotes PDAC progression and immunosuppression. Targeting CAF senescence in combination therapies could increase tumor vulnerability to chemo- or immunotherapy. See related article by Ye et al.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-0428
  15. J Natl Compr Canc Netw. 2024 Apr 29. 1-6
    Failure to Undergo Resection Following Neoadjuvant Therapy for Resectable Pancreatic Cancer: A Secondary Analysis of SWOG S1505.
    Jordan M Cloyd, Sarah Colby, Katherine A Guthrie, Andy M Lowy, E Gabrielle Chiorean, Phillip Philip, Davendra Sohal, Syed Ahmad.
       BACKGROUND: Neoadjuvant therapy (NT) is increasingly used for patients with pancreatic ductal adenocarcinoma (PDAC), and yet reasons for not undergoing subsequent pancreatectomy are poorly understood. Given the importance of completing multimodality therapy, we investigated factors associated with failure to undergo surgical resection following NT for PDAC.
    METHODS: SWOG S1505 was a multicenter phase II randomized trial of preoperative mFOLFIRINOX or gemcitabine/nab-paclitaxel prior to planned pancreatectomy for patients with potentially resectable PDAC. Associations between clinical, demographic, and hospital-level characteristics and receipt of surgical resection were estimated via multiple logistic regression. Differences in overall survival from 18 weeks postrandomization (scheduled time of surgery) according to resection status were assessed via Cox regression models.
    RESULTS: Among 102 eligible patients, 73 (71.6%) underwent successful pancreatectomy, whereas 29 (28.4%) did not, primarily because of progression (n=11; 10.8%) or toxicity during NT (n=9; 8.8%). Weight loss during NT (odds ratio [OR], 0.34; 95% CI, 0.11-0.93) and the hospital's city size (small: OR, 0.24 [95% CI, 0.07-0.80] and large: OR, 0.28 [95% CI, 0.10-0.79] compared with midsize) were significantly associated with a lower probability of surgical resection in adjusted models, whereas age, sex, race, body mass index, performance status, insurance type, geographic region, treatment arm, tumor location, chemotherapy delays/modifications, and hospital characteristics were not. Surgical resection following NT was associated with improved overall survival (median, 23.8 vs 10.8 months; P<.01) even after adjusting for grade 3-5 adverse events during NT, performance status, and body mass index (hazard ratio, 0.55; 95% CI, 0.32-0.95).
    CONCLUSIONS: Failure to undergo resection following NT was relatively common among patients with potentially resectable PDAC and associated with worse survival. Although few predictive factors were identified in this secondary analysis of the SWOG S1505 randomized trial, further research must focus on risk factors for severe toxicities during NT that preclude surgical resection so that patient-centered interventions can be delivered or alternate treatment sequencing can be recommended.
    Keywords:  FOLFIRINOX; pancreatic ductal adenocarcinoma, preoperative therapy, pancreatic surgery; randomized controlled trial
    DOI:  https://doi.org/10.6004/jnccn.2023.7099
  16. J Clin Invest. 2024 May 01. pii: e180558. [Epub ahead of print]134(9):
    A pipeline for senolytics.
    Sundeep Khosla.
      There is intense interest in identifying compounds that selectively kill senescent cells, termed senolytics, for ameliorating age-related comorbidities. However, screening for senolytic compounds currently relies on primary cells or cell lines where senescence is induced in vitro. Given the complexity of senescent cells across tissues and diseases, this approach may not target the senescent cells that develop under specific conditions in vivo. In this issue of the JCI, Lee et al. describe a pipeline for high-throughput drug screening of senolytic compounds where senescence was induced in vivo and identify the HSP90 inhibitor XL888 as a candidate senolytic to treat idiopathic pulmonary fibrosis.
    DOI:  https://doi.org/10.1172/JCI180558
  17. Biophys J. 2024 Apr 30. pii: S0006-3495(24)00291-1. [Epub ahead of print]
    Cryo-EM images of phase separated lipid bilayer vesicles analyzed with a machine learning approach.
    Karan D Sharma, Milka Doktorova, M Neal Waxham, Frederick A Heberle.
      Lateral lipid heterogeneity (i.e., raft formation) in biomembranes plays a functional role in living cells. Three-component mixtures of low- and high-melting lipids plus cholesterol offer a simplified experimental model for raft domains in which a liquid-disordered (Ld) phase coexists with a liquid-ordered (Lo) phase. Using such models, we recently showed that cryogenic electron microscopy (cryo-EM) can detect phase separation in lipid vesicles based on differences in bilayer thickness. However, the considerable noise within cryo-EM data poses a significant challenge for accurately determining the membrane phase state at high spatial resolution. To this end, we have developed an image processing pipeline that utilizes machine learning (ML) to predict the bilayer phase in projection images of lipid vesicles. Importantly, the ML method exploits differences in both the thickness and molecular density of Lo compared to Ld, which leads to improved phase identification. To assess accuracy, we used artificial images of phase-separated lipid vesicles generated from all-atom molecular dynamics simulations of Lo and Ld phases. Synthetic ground truth datasets mimicking a series of compositions along a tieline of Ld+Lo coexistence were created and then analyzed with various ML models. For all tieline compositions, we find that the ML approach can correctly identify the bilayer phase with > 90% accuracy, thus providing a means to isolate the intensity profiles of coexisting Ld and Lo phases, as well as accurately determine domain size distributions, number of domains, and phase area fractions. The method described here provides a framework for characterizing nanoscopic lateral heterogeneities in membranes and paves the way for a more detailed understanding of raft properties in biological contexts.
    Keywords:  bilayer structure; lipid raft; liquid-disordered; liquid-ordered; nanodomains
    DOI:  https://doi.org/10.1016/j.bpj.2024.04.029
  18. Mol Cell. 2024 Apr 22. pii: S1097-2765(24)00282-X. [Epub ahead of print]
    Unprocessed genomic uracil as a source of DNA replication stress in cancer cells.
    Sneha Saxena, Christopher S Nabel, Turner W Seay, Parasvi S Patel, Ajinkya S Kawale, Caroline R Crosby, Helene Tigro, Eugene Oh, Matthew G Vander Heiden, Aaron N Hata, Zucai Suo, Lee Zou.
      Alterations of bases in DNA constitute a major source of genomic instability. It is believed that base alterations trigger base excision repair (BER), generating DNA repair intermediates interfering with DNA replication. Here, we show that genomic uracil, a common type of base alteration, induces DNA replication stress (RS) without being processed by BER. In the absence of uracil DNA glycosylase (UNG), genomic uracil accumulates to high levels, DNA replication forks slow down, and PrimPol-mediated repriming is enhanced, generating single-stranded gaps in nascent DNA. ATR inhibition in UNG-deficient cells blocks the repair of uracil-induced gaps, increasing replication fork collapse and cell death. Notably, a subset of cancer cells upregulates UNG2 to suppress genomic uracil and limit RS, and these cancer cells are hypersensitive to co-treatment with ATR inhibitors and drugs increasing genomic uracil. These results reveal unprocessed genomic uracil as an unexpected source of RS and a targetable vulnerability of cancer cells.
    Keywords:  ATR; BER; PrimPol; UNG; cancer therapy; gaps; lung cancer; permetrexed; replication fork; replication stress; ssDNA gaps; synthetic lethality; uracil
    DOI:  https://doi.org/10.1016/j.molcel.2024.04.004
  19. Nat Cell Biol. 2024 Apr 30.
    Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation.
    Tianchi Xin, Sara Gallini, Haoyang Wei, David G Gonzalez, Catherine Matte-Martone, Hiroki Machida, Hironobu Fujiwara, H Amalia Pasolli, Kathleen C Suozzi, Lauren E Gonzalez, Sergi Regot, Valentina Greco.
      Tissue regeneration and maintenance rely on coordinated stem cell behaviours. This orchestration can be impaired by oncogenic mutations leading to cancer. However, it is largely unclear how oncogenes perturb stem cells' orchestration to disrupt tissue. Here we used intravital imaging to investigate the mechanisms by which oncogenic Kras mutation causes tissue disruption in the hair follicle. Through longitudinally tracking hair follicles in live mice, we found that KrasG12D, a mutation that can lead to squamous cell carcinoma, induces epithelial tissue deformation in a spatiotemporally specific manner, linked with abnormal cell division and migration. Using a reporter mouse capture real-time ERK signal dynamics at the single-cell level, we discovered that KrasG12D, but not a closely related mutation HrasG12V, converts ERK signal in stem cells from pulsatile to sustained. Finally, we demonstrated that interrupting sustained ERK signal reverts KrasG12D-induced tissue deformation through modulating specific features of cell migration and division.
    DOI:  https://doi.org/10.1038/s41556-024-01413-y
  20. Cell Metab. 2024 Apr 15. pii: S1550-4131(23)00472-2. [Epub ahead of print]
    The mitochondrial multi-omic response to exercise training across rat tissues.
    MoTrPAC Study Group
      Mitochondria have diverse functions critical to whole-body metabolic homeostasis. Endurance training alters mitochondrial activity, but systematic characterization of these adaptations is lacking. Here, the Molecular Transducers of Physical Activity Consortium mapped the temporal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats trained for 1, 2, 4, or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart, and skeletal muscle. The colon showed non-linear response dynamics, whereas mitochondrial pathways were downregulated in brown adipose and adrenal tissues. Protein acetylation increased in the liver, with a shift in lipid metabolism, whereas oxidative proteins increased in striated muscles. Exercise-upregulated networks were downregulated in human diabetes and cirrhosis. Knockdown of the central network protein 17-beta-hydroxysteroid dehydrogenase 10 (HSD17B10) elevated oxygen consumption, indicative of metabolic stress. We provide a multi-omic, multi-tissue, temporal atlas of the mitochondrial response to exercise training and identify candidates linked to mitochondrial dysfunction.
    Keywords:  HSD17B10; acetylome; aerobic; exercise; metabolism; metabolomics; mitochondria; multi-omics; proteomics; transcriptomics
    DOI:  https://doi.org/10.1016/j.cmet.2023.12.021
  21. Sci Signal. 2024 Apr 30. 17(834): eadq0353
    Nude blebs expose cells to phagocytes.
    Annalisa M VanHook.
      Displacement of the glycocalyx by membrane blebbing enables macrophages to recognize apoptotic cells.
    DOI:  https://doi.org/10.1126/scisignal.adq0353
  22. Pancreas. 2024 May 01.
    Aryl hydrocarbon receptor knockout accelerates PanIN formation and fibro-inflammation in a mutant Kras-driven pancreatic cancer model.
    Morgan T Walcheck, Patrick B Schwartz, Noah D Carrillo, Kristina A Matkowsky, Manabu Nukaya, Christopher A Bradfield, Sean M Ronnekleiv-Kelly.
       OBJECTIVES: The pathogenesis of pancreas cancer (PDAC) remains poorly understood, hindering efforts to develop a more effective therapy for PDAC. Recent discoveries show the aryl hydrocarbon receptor (AHR) plays a crucial role in the development of several cancers, and can be targeted for therapeutic effect. However, its involvement in the pathogenesis of PDAC remains unclear. To address this gap, we evaluated the role of AHR in the development of PDAC pre-cancerous lesions in vivo.
    METHODS: We created a global AHR-null, mutant Kras-driven PDAC mouse model (A-/-KC) and evaluated the changes in PDAC precursor lesion formation (Pan-IN 1, 2, and 3) and associated fibro-inflammation between KC and A-/-KC at 5 months of age. We then examined the changes in the immune microenvironment followed by single-cell RNA-sequencing analysis to evaluate concomitant transcriptomic changes.
    RESULTS: We identified a significant increase in PanIN-1 lesion formation and PanIN-1 associated fibro-inflammatory infiltrate in A-/-KC vs KC mice. This was associated with significant changes in the adaptive immune system, particularly a decrease in the CD4+/CD8+ T-cell ratio, as well as a decrease in the T-regulatory/Th17 T-cell ratio suggesting unregulated inflammation.
    CONCLUSION: These findings show the loss of AHR results in heightened Kras-induced PanIN formation, through modulation of immune cells within the pancreatic tumor microenvironment.
    DOI:  https://doi.org/10.1097/MPA.0000000000002357
  23. Nephrol Dial Transplant. 2024 Apr 29. pii: gfae097. [Epub ahead of print]
    Ferroptosis Biology.
    Tobias Seibt, Adam Wahida, Konrad Hoeft, Stephan Kemmner, Andreas Linkermann, Eikan Mishima, Marcus Conrad.
      Ferroptosis is a regulated cell death modality triggered by iron-dependent lipid peroxidation. Ferroptosis plays a causal role in the pathophysiology of various diseases, making it a promising therapeutic target. Unlike all other cell death modalities dependent on distinct signaling cues, ferroptosis occurs when cellular antioxidative defense mechanisms fail to suppress the oxidative destruction of cellular membranes, eventually leading to cell membrane rupture. Physiologically, only two such surveillance systems are known to efficiently prevent the lipid peroxidation chain reaction by reducing (phospho)lipid hydroperoxides to their corresponding alcohols or by reducing radicals in phospholipid bilayers, thus maintaining the integrity of lipid membranes. Mechanistically, these two systems are linked to the reducing capacity of glutathione peroxidase 4 (GPX4) by consuming glutathione (GSH) on the one and ferroptosis suppressor protein 1 (FSP1, formerly AIFM2) on the other hand. Notably, the importance of ferroptosis suppression in physiological contexts has been linked to a particular vulnerability of renal tissue. In fact, early work has shown that mice genetically lacking Gpx4 rapidly succumb to acute renal failure with pathohistological features of acute tubular necrosis. Promising research attempting to implicate ferroptosis in various renal disease entities, particularly those with proximal tubular involvement, has generated a wealth of knowledge with widespread potential for clinical translation. Here, we provide a brief overview of the involvement of ferroptosis in nephrology. Our goal is to introduce this expanding field for clinically versed nephrologists in the hope of spurring future efforts to prevent ferroptosis in the pathophysiological processes of the kidney.
    Keywords:  GPX4; acute kidney injury; ferroptosis; iron metabolism; lipid peroxidation
    DOI:  https://doi.org/10.1093/ndt/gfae097
  24. Updates Surg. 2024 Apr 29.
    REDISCOVER guidelines for borderline-resectable and locally advanced pancreatic cancer: management algorithm, unanswered questions, and future perspectives.
    REDISCOVER guidelines group
      The REDISCOVER guidelines present 34 recommendations for the selection and perioperative care of borderline-resectable (BR-PDAC) and locally advanced ductal adenocarcinoma of the pancreas (LA-PDAC). These guidelines represent a significant shift from previous approaches, prioritizing tumor biology over anatomical features as the primary indication for resection. Condensed herein, they provide a practical management algorithm for clinical practice. However, the guidelines also highlight the need to redefine LA-PDAC to align with modern treatment strategies and to solve some contradictions within the current definition, such as grouping "difficult" and "impossible" to resect tumors together. Furthermore, the REDISCOVER guidelines highlight several areas requiring urgent research. These include the resection of the superior mesenteric artery, the management strategies for patients with LA-PDAC who are fit for surgery but unable to receive multi-agent neoadjuvant chemotherapy, the approach to patients with LA-PDAC who are fit for surgery but demonstrate high serum Ca 19.9 levels even after neoadjuvant treatment, and the optimal timing and number of chemotherapy cycles prior to surgery. Additionally, the role of primary chemoradiotherapy versus chemotherapy alone in LA-PDAC, the timing of surgical resection post-neoadjuvant/primary chemoradiotherapy, the efficacy of ablation therapies, and the management of oligometastasis in patients with LA-PDAC warrant investigation. Given the limited evidence for many issues, refining existing management strategies is imperative. The establishment of the REDISCOVER registry ( https://rediscover.unipi.it/ ) offers promise of a unified research platform to advance understanding and improve the management of BR-PDAC and LA-PDAC.
    Keywords:  Borderline resectable pancreatic cancer; Locally advanced pancreatic cancer; Pancreatic cancer; Pancreatic ductal adenocarcinoma; REDISCOVER guidelines; REDISCOVER registry
    DOI:  https://doi.org/10.1007/s13304-024-01860-0
  25. Cancer Discov. 2024 Apr 29.
    Senescent CAFs mediate immunosuppression and drive breast cancer progression.
    Jiayu Ye, John M Baer, Douglas V Faget, Vasilios A Morikis, Qihao Ren, Anupama Melam, Ana Paula Delgado, Xianmin Luo, Satarupa Mullick Bagchi, Jad I Belle, Edward Campos, Michael Friedman, Deborah J Veis, Erik S Knudsen, Agnieszka K Witkiewicz, Scott Powers, Gregory D Longmore, David G DeNardo, Sheila A Stewart.
      The tumor microenvironment (TME) profoundly influences tumorigenesis, with gene expression in the breast TME capable of predicting clinical outcomes. The TME is complex and includes distinct cancer-associated fibroblast (CAF) subtypes whose contribution to tumorigenesis remains unclear. Here, we identify a subset of myofibroblast cancer associated fibroblasts (myCAF) that are senescent (senCAF) in mouse and human breast tumors. Utilizing the MMTV-PyMT;INK-ATTAC (INK) mouse model, we found that senCAF-secreted extracellular matrix specifically limits natural killer (NK) cell cytotoxicity to promote tumor growth. Genetic or pharmacologic senCAF elimination unleashes NK cell killing, restricting tumor growth. Finally, we show that senCAFs are present in Her2+, ER+, and triple negative breast cancer and in ductal carcinoma in situ (DCIS) where they predict tumor recurrence. Together, these findings demonstrate that senCAFs are potently tumor promoting and raise the possibility that targeting them by senolytic therapy could restrain breast cancer development.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-0426
  26. Trends Cancer. 2024 Apr 30. pii: S2405-8033(24)00059-1. [Epub ahead of print]
    Immunometabolism of CD8+ T cell differentiation in cancer.
    Hao Shi, Sidi Chen, Hongbo Chi.
      CD8+ cytotoxic T lymphocytes (CTLs) are central mediators of tumor immunity and immunotherapies. Upon tumor antigen recognition, CTLs differentiate from naive/memory-like toward terminally exhausted populations with more limited function against tumors. Such differentiation is regulated by both immune signals, including T cell receptors (TCRs), co-stimulation, and cytokines, and metabolism-associated processes. These immune signals shape the metabolic landscape via signaling, transcriptional and post-transcriptional mechanisms, while metabolic processes in turn exert spatiotemporal effects to modulate the strength and duration of immune signaling. Here, we review the bidirectional regulation between immune signals and metabolic processes, including nutrient uptake and intracellular metabolic pathways, in shaping CTL differentiation and exhaustion. We also discuss the mechanisms underlying how specific nutrient sources and metabolite-mediated signaling events orchestrate CTL biology. Understanding how metabolic programs and their interplay with immune signals instruct CTL differentiation and exhaustion is crucial to uncover tumor-immune interactions and design novel immunotherapies.
    Keywords:  T cell differentiation; TCR; antitumor function; cytokines; exhaustion; mitochondrial fitness
    DOI:  https://doi.org/10.1016/j.trecan.2024.03.010
  27. Nat Commun. 2024 May 03. 15(1): 3740
    Acinar to β-like cell conversion through inhibition of focal adhesion kinase.
    Shakti Dahiya, Mohamed Saleh, Uylissa A Rodriguez, Dhivyaa Rajasundaram, Jorge R Arbujas, Arian Hajihassani, Kaiyuan Yang, Anuradha Sehrawat, Ranjeet Kalsi, Shiho Yoshida, Krishna Prasadan, Heiko Lickert, Jing Hu, Jon D Piganelli, George K Gittes, Farzad Esni.
      Insufficient functional β-cell mass causes diabetes; however, an effective cell replacement therapy for curing diabetes is currently not available. Reprogramming of acinar cells toward functional insulin-producing cells would offer an abundant and autologous source of insulin-producing cells. Our lineage tracing studies along with transcriptomic characterization demonstrate that treatment of adult mice with a small molecule that specifically inhibits kinase activity of focal adhesion kinase results in trans-differentiation of a subset of peri-islet acinar cells into insulin producing β-like cells. The acinar-derived insulin-producing cells infiltrate the pre-existing endocrine islets, partially restore β-cell mass, and significantly improve glucose homeostasis in diabetic mice. These findings provide evidence that inhibition of the kinase activity of focal adhesion kinase can convert acinar cells into insulin-producing cells and could offer a promising strategy for treating diabetes.
    DOI:  https://doi.org/10.1038/s41467-024-47972-4
  28. Pancreas. 2024 May 01.
    The Population-level Prevalence of Exocrine Pancreas Insufficiency and the Subsequent Risk of Pancreatic Cancer.
    Oyedotun Babajide, Aakash Desai, Chinelo Eruchalu, Mary Sedarous, Deborah Adekunle, Michael Youssef, Muftah Mahmud, Philip N Okafor.
       OBJECTIVES: To study the prevalence of exocrine pancreas insufficiency (EPI) at a population level and the subsequent risk of pancreatic ductal adenocarcinoma (PDAC).
    METHODS: Using TriNetX (a database of over 79 million US residents), we included patients ≥18 years with EPI (identified via ICD-10 codes) and continuous follow-up from 2016-2022. Patients with prior pancreas resection and PDAC before an EPI diagnosis were excluded. The primary outcome was EPI prevalence. Secondary outcomes included imaging utilization, PDAC risk and, pancreas enzyme replacement therapy (PERT) utilization. We performed 1:1 propensity score matching of patients with EPI vs. patients without an EPI diagnosis. Adjusted odds ratio (aOR) and hazard ratios (aHR) with 95% confidence intervals were reported.
    RESULTS: The population prevalence of EPI was 0.8% (n = 24,080) with a mean age of 55.6 years at diagnosis. After propensity score matching, PDAC risk among patients with EPI was twice as high compared to patients without EPI (AHR 1.97, 95% confidence interval [CI] 1.66-2.36). This risk persisted even after excluding patients with a history of acute or chronic pancreatitis (aOR: 4.25, 95% CI 2.99-6.04). Only 58% (n = 13, 390) of patients with EPI received PERT with a mean treatment duration of 921 days. No difference was observed in PDAC risk between patients with EPI treated with PERT vs. those that did not receive PERT (AHR 1.10, 95% CI 0.95-1.26, p = 0.17).
    CONCLUSIONS: Despite a low prevalence, patients with EPI may have a higher risk of PDAC and many of these patients with EPI were not on PERT. PERT did not appear to impact incident PDAC risk after an EPI diagnosis.
    DOI:  https://doi.org/10.1097/MPA.0000000000002359
  29. J Cell Biol. 2024 Jul 01. pii: e202308152. [Epub ahead of print]223(7):
    Nucleocytoplasmic transport rates are regulated by cellular processes that modulate GTP availability.
    Kelsey L Scott, Charles T Halfmann, Allison D Hoefakker, Purboja Purkayastha, Ting Ching Wang, Tanmay P Lele, Kyle J Roux.
      Nucleocytoplasmic transport (NCT), the facilitated diffusion of cargo molecules between the nucleus and cytoplasm through nuclear pore complexes (NPCs), enables numerous fundamental eukaryotic cellular processes. Ran GTPase uses cellular energy in the direct form of GTP to create a gradient across the nuclear envelope (NE) that drives the majority of NCT. We report here that changes in GTP availability resulting from altered cellular physiology modulate the rate of NCT, as monitored using synthetic and natural cargo, and the dynamics of Ran itself. Cell migration, cell spreading, and/or modulation of the cytoskeleton or its connection to the nucleus alter GTP availability and thus rates of NCT, regulating RNA export and protein synthesis. These findings support a model in which changes in cellular physiology that alter GTP availability can regulate the rate of NCT, impacting fundamental cellular processes that extensively utilize NCT.
    DOI:  https://doi.org/10.1083/jcb.202308152
  30. Aging (Albany NY). 2024 Apr 26. 16
    Iron retardation in lysosome protects senescent cells from ferroptosis.
    Yujing Feng, Huaiqing Wei, Meng Lyu, Zhiyuan Yu, Jia Chen, Xinxing Lyu, Fengfeng Zhuang.
      Ferroptosis, an iron-triggered modality of cellular death, has been reported to closely relate to human aging progression and aging-related diseases. However, the involvement of ferroptosis in the development and maintenance of senescent cells still remains elusive. Here, we established a doxorubicin-induced senescent HSkM cell model and found that both iron accumulation and lipid peroxidation increase in senescent cells. Moreover, such iron overload in senescent cells has changed the expression panel of the ferroptosis-response proteins. Interestingly, the iron accumulation and lipid peroxidation does not trigger ferroptosis-induced cell death. Oppositely, senescent cells manifest resistance to the ferroptosis inducers, compared to the proliferating cells. To further investigate the mechanism of ferroptosis-resistance for senescent cells, we traced the iron flux in cell and found iron arrested in lysosome. Moreover, disruption of lysosome functions by chloroquine and LLOMe dramatically triggered the senescent cell death. Besides, the ferroitinophagy-related proteins FTH1/FTL and NCOA4 knockdown also increases the senescent cell death. Thus, we speculated that iron retardation in lysosome of senescent cells is the key mechanism for ferroptosis resistance. And the lysosome is a promising target for senolytic drugs to selectively clear senescent cells and alleviate the aging related diseases.
    Keywords:  ferritinophagy; ferroptosis; iron accumulation; lysosome; senescent cells
    DOI:  https://doi.org/10.18632/aging.205777
  31. Mol Cancer. 2024 May 03. 23(1): 87
    Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications.
    Joo Kyung Park, Hyoung-Oh Jeong, Hyemin Kim, Jin Ho Choi, Eun Mi Lee, Seunghoon Kim, Jinho Jang, David Whee-Young Choi, Se-Hoon Lee, Kyoung Mee Kim, Kee-Taek Jang, Kwang Hyuck Lee, Kyu Taek Lee, Min Woo Lee, Jong Kyun Lee, Semin Lee.
       BACKGROUND: Intratumoral heterogeneity (ITH) and tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) play important roles in tumor evolution and patient outcomes. However, the precise characterization of diverse cell populations and their crosstalk associated with PDAC progression and metastasis is still challenging.
    METHODS: We performed single-cell RNA sequencing (scRNA-seq) of treatment-naïve primary PDAC samples with and without paired liver metastasis samples to understand the interplay between ITH and TME in the PDAC evolution and its clinical associations.
    RESULTS: scRNA-seq analysis revealed that even a small proportion (22%) of basal-like malignant ductal cells could lead to poor chemotherapy response and patient survival and that epithelial-mesenchymal transition programs were largely subtype-specific. The clonal homogeneity significantly increased with more prevalent and pronounced copy number gains of oncogenes, such as KRAS and ETV1, and losses of tumor suppressor genes, such as SMAD2 and MAP2K4, along PDAC progression and metastasis. Moreover, diverse immune cell populations, including naïve SELLhi regulatory T cells (Tregs) and activated TIGIThi Tregs, contributed to shaping immunosuppressive TMEs of PDAC through cellular interactions with malignant ductal cells in PDAC evolution. Importantly, the proportion of basal-like ductal cells negatively correlated with that of immunoreactive cell populations, such as cytotoxic T cells, but positively correlated with that of immunosuppressive cell populations, such as Tregs.
    CONCLUSION: We uncover that the proportion of basal-like subtype is a key determinant for chemotherapy response and patient outcome, and that PDAC clonally evolves with subtype-specific dosage changes of cancer-associated genes by forming immunosuppressive microenvironments in its progression and metastasis.
    Keywords:  Intratumoral heterogeneity; Liver metastasis; Pancreatic ductal adenocarcinoma; Single-cell RNA-sequencing; Tumor microenvironment
    DOI:  https://doi.org/10.1186/s12943-024-02003-0
  32. Science. 2024 May 03. 384(6695): eadi2421
    CDK4/6 activity is required during G2 arrest to prevent stress-induced endoreplication.
    Connor McKenney, Yovel Lendner, Adler Guerrero Zuniga, Niladri Sinha, Benjamin Veresko, Timothy J Aikin, Sergi Regot.
      Cell cycle events are coordinated by cyclin-dependent kinases (CDKs) to ensure robust cell division. CDK4/6 and CDK2 regulate the growth 1 (G1) to synthesis (S) phase transition of the cell cycle by responding to mitogen signaling, promoting E2F transcription and inhibition of the anaphase-promoting complex. We found that this mechanism was still required in G2-arrested cells to prevent cell cycle exit after the S phase. This mechanism revealed a role for CDK4/6 in maintaining the G2 state, challenging the notion that the cell cycle is irreversible and that cells do not require mitogens after passing the restriction point. Exit from G2 occurred during ribotoxic stress and was actively mediated by stress-activated protein kinases. Upon relief of stress, a significant fraction of cells underwent a second round of DNA replication that led to whole-genome doubling.
    DOI:  https://doi.org/10.1126/science.adi2421
  33. Angew Chem Int Ed Engl. 2024 Apr 30. e202318805
    A Versatile Microfluidic Platform for Extravasation Studies Based on DNA Origami - Cell Interactions.
    Miguel García-Chamé, Parvesh Wadhwani, Juliana Pfeifer, Ute Schepers, Christof Niemeyer, Carmen M Domínguez.
      The adhesion of circulating tumor cells (CTCs) to the endothelial lumen and their extravasation to surrounding tissues are crucial in the seeding of metastases and remain the most complex events of the metastatic cascade to study. Integrins expressed on CTCs are major regulators of the extravasation process. This knowledge is primarily derived from animal models and biomimetic systems based on artificial endothelial layers, but these methods have ethical or technical limitations. We present a versatile microfluidic device to study cancer cell extravasation that mimics the endothelial barrier by using a porous membrane functionalized with DNA origami nanostructures (DONs) that display nanoscale patterns of adhesion peptides to circulating cancer cells. The device simulates physiological flow conditions and allows direct visualization of cell transmigration through microchannel pores using 3D confocal imaging. Using this system, we studied integrin-specific adhesion in the absence of other adhesive events. Specifically, we show that the transmigration ability of the metastatic cancer cell line MDA-MB-231 is influenced by the type, distance, and density of adhesion peptides present on the DONs. Furthermore, studies with mixed ligand systems indicate that integrins binding to RGD (arginine-glycine-aspartic acid) and IDS (isoleucine-aspartic acid-serine) did not synergistically enhance the extravasation process of MDA-MB-231 cells.
    Keywords:  Cancer; DNA structures; extravasation; integrins; microfluidics
    DOI:  https://doi.org/10.1002/anie.202318805
  34. Nat Metab. 2024 May 03.
    Acetate reprogrammes tumour metabolism and promotes PD-L1 expression and immune evasion by upregulating c-Myc.
    Juhong Wang, Yannan Yang, Fei Shao, Ying Meng, Dong Guo, Jie He, Zhimin Lu.
      Acetate, a precursor of acetyl-CoA, is instrumental in energy production, lipid synthesis and protein acetylation. However, whether acetate reprogrammes tumour metabolism and plays a role in tumour immune evasion remains unclear. Here, we show that acetate is the most abundant short-chain fatty acid in human non-small cell lung cancer tissues, with increased tumour-enriched acetate uptake. Acetate-derived acetyl-CoA induces c-Myc acetylation, which is mediated by the moonlighting function of the metabolic enzyme dihydrolipoamide S-acetyltransferase. Acetylated c-Myc increases its stability and subsequent transcription of the genes encoding programmed death-ligand 1, glycolytic enzymes, monocarboxylate transporter 1 and cell cycle accelerators. Dietary acetate supplementation promotes tumour growth and inhibits CD8+ T cell infiltration, whereas disruption of acetate uptake inhibits immune evasion, which increases the efficacy of anti-PD-1-based therapy. These findings highlight a critical role of acetate promoting tumour growth beyond its metabolic role as a carbon source by reprogramming tumour metabolism and immune evasion, and underscore the potential of controlling acetate metabolism to curb tumour growth and improve the response to immune checkpoint blockade therapy.
    DOI:  https://doi.org/10.1038/s42255-024-01037-4
  35. Sci Adv. 2024 May 03. 10(18): eadn0172
    Mechanochemical dynamics of collective cells and hierarchical topological defects in multicellular lumens.
    Pengyu Yu, Yue Li, Wei Fang, Xi-Qiao Feng, Bo Li.
      Collective cell dynamics is essential for tissue morphogenesis and various biological functions. However, it remains incompletely understood how mechanical forces and chemical signaling are integrated to direct collective cell behaviors underlying tissue morphogenesis. Here, we propose a three-dimensional (3D) mechanochemical theory accounting for biochemical reaction-diffusion and cellular mechanotransduction to investigate the dynamics of multicellular lumens. We show that the interplay between biochemical signaling and mechanics can trigger either pitchfork or Hopf bifurcation to induce diverse static mechanochemical patterns or generate oscillations with multiple modes both involving marked mechanical deformations in lumens. We uncover the crucial role of mechanochemical feedback in emerging morphodynamics and identify the evolution and morphogenetic functions of hierarchical topological defects including cell-level hexatic defects and tissue-level orientational defects. Our theory captures the common mechanochemical traits of collective dynamics observed in experiments and could provide a mechanistic context for understanding morphological symmetry breaking in 3D lumen-like tissues.
    DOI:  https://doi.org/10.1126/sciadv.adn0172
  36. Front Endocrinol (Lausanne). 2024 ;15 1332895
    Analysis of urinary potassium isotopes and association with pancreatic health: healthy, diabetic and cancerous states.
    Kathrin Schilling, Heng Chen, Ronald A Glabonjat, Silvana Debernardi, Oleg Blyuss, Ana Navas-Acien, Alex N Halliday, Tatjana Crnogorac-Jurcevic.
       Background: More than 700 million people worldwide suffer from diseases of the pancreas, such as diabetes, pancreatitis and pancreatic cancer. Often dysregulation of potassium (K+) channels, co-transporters and pumps can promote development and progression of many types of these diseases. The role of K+ transport system in pancreatic cell homeostasis and disease development remains largely unexplored. Potassium isotope analysis (δ41K), however, might have the potential to detect minute changes in metabolic processes relevant for pancreatic diseases.
    Methods: We assessed urinary K isotope composition in a case-control study by measuring K concentrations and δ41K in spot urines collected from patients diagnosed with pancreatic cancer (n=18), other pancreas-related diseases (n=14) and compared those data to healthy controls (n=16).
    Results: Our results show that urinary K+ levels for patients with diseased pancreas (benign and pancreatic cancer) are significantly lower than the healthy controls. For δ41K, the values tend to be higher for individuals with pancreatic cancer (mean δ41K = -0.58 ± 0.33‰) than for healthy individuals (mean δ41K = -0.78 ± 0.19‰) but the difference is not significant (p=0.08). For diabetics, urinary K+ levels are significantly lower (p=0.03) and δ41K is significantly higher (p=0.009) than for the healthy controls. These results suggest that urinary K+ levels and K isotopes can help identify K disturbances related to diabetes, an associated factors of all-cause mortality for diabetics.
    Conclusion: Although the K isotope results should be considered exploratory and hypothesis-generating and future studies should focus on larger sample size and δ41K analysis of other K-disrupting diseases (e.g., chronic kidney disease), our data hold great promise for K isotopes as disease marker.
    Keywords:  cancer; diabetes; dysregulation; pancreas; potassium isotopes; urine
    DOI:  https://doi.org/10.3389/fendo.2024.1332895
  37. J Clin Invest. 2024 Apr 30. pii: e174186. [Epub ahead of print]
    Dietary dicarboxylic acids provide a non-storable alternative fat source that protects mice against obesity.
    Eric S Goetzman, Bob B Zhang, Yuxun Zhang, Sivakama S Bharathi, Joanna Bons, Jacob Rose, Samah Shah, Keaton J Solo, Alexandra V Schmidt, Adam C Richert, Steven J Mullett, Stacy L Gelhaus, Krithika S Rao, Sruti S Shiva, Katherine E Pfister, Anne Silva Barbosa, Sunder Sims-Lucas, Steven F Dobrowolski, Birgit Schilling.
      Dicarboxylic fatty acids are generated in the liver and kidney in a minor pathway called fatty acid ω-oxidation. The effects of consuming dicarboxylic fatty acids as an alternative source of dietary fat have not been explored. Here, we fed dodecanedioic acid, a 12-carbon dicarboxylic (DC12), to mice at 20% of daily caloric intake for nine weeks. DC12 increased metabolic rate, reduced body fat, reduced liver fat, and improved glucose tolerance. We observed DC12-specific breakdown products in liver, kidney, muscle, heart, and brain, indicating that oral DC12 escaped first-pass liver metabolism and was utilized by many tissues. In tissues expressing the "a" isoform of acyl-CoA oxidase-1 (ACOX1), a key peroxisomal fatty acid oxidation enzyme, DC12 was chain shortened to the TCA cycle intermediate succinyl-CoA. In tissues with low peroxisomal fatty acid oxidation capacity, DC12 was oxidized by mitochondria. In vitro, DC12 was catabolized even by adipose tissue and was not stored intracellularly. We conclude that DC12 and other dicarboxylic acids may be useful for combatting obesity and for treating metabolic disorders.
    Keywords:  Fatty acid oxidation; Metabolism; Mitochondria; Obesity
    DOI:  https://doi.org/10.1172/JCI174186
  38. Database (Oxford). 2024 Apr 30. pii: baae030. [Epub ahead of print]2024
    cancercelllines.org-a novel resource for genomic variants in cancer cell lines.
    Rahel Paloots, Michael Baudis.
      Cancer cell lines are an important component in biological and medical research, enabling studies of cellular mechanisms as well as the development and testing of pharmaceuticals. Genomic alterations in cancer cell lines are widely studied as models for oncogenetic events and are represented in a wide range of primary resources. We have created a comprehensive, curated knowledge resource-cancercelllines.org-with the aim to enable easy access to genomic profiling data in cancer cell lines, curated from a variety of resources and integrating both copy number and single nucleotide variants data. We have gathered over 5600 copy number profiles as well as single nucleotide variant annotations for 16 000 cell lines and provide these data with mappings to the GRCh38 reference genome. Both genomic variations and associated curated metadata can be queried through the GA4GH Beacon v2 Application Programming Interface (API) and a graphical user interface with extensive data retrieval enabled using GA4GH data schemas under a permissive licensing scheme. Database URL: https://cancercelllines.org.
    DOI:  https://doi.org/10.1093/database/baae030
  39. Cancer Cell. 2024 Apr 25. pii: S1535-6108(24)00130-2. [Epub ahead of print]
    Career trajectories of MD-PhD physician scientists: The loss of women investigators.
    Richard A Steinman, Lisa M Gandy, Hanfei Qi, Elana J Fertig, Amanda L Blackford, Jennifer R Grandis.
      Advances in biomedical research require a robust physician scientist workforce. Despite being equally successful at securing early career awards from the NIH as men, women MD-PhD physician scientists are less likely to serve as principal investigators on mid- and later careers awards. Here, Steinman et al. discuss the causes of gender disparities in academic medicine, the implications of losing highly trained women physician scientists, and the institutional and systemic changes needed to sustain this pool of talented investigators.
    DOI:  https://doi.org/10.1016/j.ccell.2024.04.006
  40. Nat Protoc. 2024 May 03.
    Build and operation of a custom 3D, multicolor, single-molecule localization microscope.
    Rory M Power, Aline Tschanz, Timo Zimmermann, Jonas Ries.
      Single-molecule localization microscopy (SMLM) enables imaging scientists to visualize biological structures with unprecedented resolution. Particularly powerful implementations of SMLM are capable of three-dimensional, multicolor and high-throughput imaging and can yield key biological insights. However, widespread access to these technologies is limited, primarily by the cost of commercial options and complexity of de novo development of custom systems. Here we provide a comprehensive guide for interested researchers who wish to establish a high-end, custom-built SMLM setup in their laboratories. We detail the initial configuration and subsequent assembly of the SMLM, including the instructions for the alignment of all the optical pathways, the software and hardware integration, and the operation of the instrument. We describe the validation steps, including the preparation and imaging of test and biological samples with structures of well-defined geometries, and assist the user in troubleshooting and benchmarking the system's performance. Additionally, we provide a walkthrough of the reconstruction of a super-resolved dataset from acquired raw images using the Super-resolution Microscopy Analysis Platform. Depending on the instrument configuration, the cost of the components is in the range US$95,000-180,000, similar to other open-source advanced SMLMs, and substantially lower than the cost of a commercial instrument. A builder with some experience of optical systems is expected to require 4-8 months from the start of the system construction to attain high-quality three-dimensional and multicolor biological images.
    DOI:  https://doi.org/10.1038/s41596-024-00989-x
  41. Lab Invest. 2024 Apr 25. pii: S0023-6837(24)01748-3. [Epub ahead of print] 102070
    A pipeline for evaluation of machine learning/AI models to quantify PD-L1 immunohistochemistry.
    Beatrice S Knudsen, Alok Jadhav, Lindsey J Perry, Jeppe Thagaard, Georgios Deftereos, Jian Ying, Ben J Brintz, Wei Zhang.
      Immunohistochemistry (IHC) is used to guide treatment decisions in multiple cancer types. For treatment with checkpoint inhibitors, PD-L1 IHC is used as a companion diagnostic. However, the scoring of PD-L1 is complicated by its expression in cancer and immune cells. Separation of cancer and non-cancer regions is needed to calculate tumor proportion scores (TPS) of PD-L1, which is based on the percentage of PD-L1 positive cancer cells. Evaluation of PD-L1 expression requires highly experienced pathologists and is often challenging and time consuming. Here we used a multi-institutional cohort of 77 lung cancer cases stained centrally with the PD-L1 22C3 clone. We developed a four-step pipeline for measuring TPS that includes the co-registration of H&E, PD-L1 and negative control (NC) digital slides for exclusion of necrosis, segmentation of cancer regions and quantification of PD-L1+ cells. As cancer segmentation is a challenging step for TPS generation, we trained DeepLab V3 in the Visiopharm software package to outline cancer regions in PD-L1 and negative control (NC) images and evaluated the model performance by mean intersection over union (mIoU) against manual outlines. Only 14 cases were required to accomplish an mIoU of 0.82 for cancer segmentation in hematoxylin stained NC cases. For PD-L1 stained slides, a model trained on PD-L1 tiles augmented by registered NC tiles achieved an mIoU of 0.79. In segmented cancer regions from whole slide images, the digital TPS achieved an accuracy of 75% against the manual TPS scores from the pathology report. Major reasons for algorithmic inaccuracies include the inclusion of immune cells in cancer outlines and poor nuclear segmentation of cancer cells. Our transparent and stepwise approach and performance metrics can be applied to any IHC assay to provide pathologists with important insights when to apply and how to evaluate commercial automated IHC scoring systems.
    Keywords:  Cancer segmentation; Digital Pathology; PD-L1; TPS
    DOI:  https://doi.org/10.1016/j.labinv.2024.102070
  42. Adv Healthc Mater. 2024 Apr 27. e2400742
    In Situ Engineering Cancer Mask to Immobilize Tumor Cells and Block Metastasis.
    Xiaoke Zhang, Cheng Li, Dan Zhu, Hui Mao, Xiqun Jiang.
      This work reports a new concept of cancer mask in situ to alter the specific biological functions of cancer cells. Metastatic cancer cells are highly invasive in part due to the presence of the glycan matrix in the cell membrane. Using a rational designed bio-orthogonal reaction, the cancer cell surface is reconstructed in situ by incorporating endogenous polysialic acids in the glycan matrix on the cell membrane to form a mesh-like network, called cancer mask. The network of the glycan matrix can not only immobilize cancer cells but also effectively block the stimulation of metastasis promoters to tumor cells and inhibit the formation of epithelial to mesenchymal transition (EMT), causing metastatic cancer cells incarceration. The results demonstrate a new strategy to control and even eliminate the cancer metastasis that is a major cause of treatment failure and poor patient outcome.
    Keywords:  glycan matrix; metabolic glycoengineering; polysialic acid network; tumor metastasis
    DOI:  https://doi.org/10.1002/adhm.202400742
  43. Anticancer Res. 2024 May;44(5): 1939-1946
    CX-4945 (Silmitasertib) Induces Cell Death by Impairing Lysosomal Utilization in KRAS Mutant Cholangiocarcinoma Cell Lines.
    DA Sol Lee, Min Woo Han, Yonghyun Kang, Chorong Kim, Seonmin Lee, Kyu-Pyo Kim, Changhoon Yoo.
       BACKGROUND/AIM: Macropinocytosis is a non-selective form of endocytosis that facilitates the uptake of extracellular substances, such as nutrients and macromolecules, into the cells. In KRAS-driven cancers, including pancreatic ductal adenocarcinoma, macropinocytosis and subsequent lysosomal utilization are known to be enhanced to overcome metabolic stress. In this study, we investigated the role of Casein Kinase 2 (CK2) inhibition in macropinocytosis and subsequent metabolic processes in KRAS mutant cholangiocarcinoma (CCA) cell lines.
    MATERIALS AND METHODS: The bovine serum albumin (BSA) uptake indicating macropinocytosis was performed by flow cytometry using the HuCCT1 KRAS mutant CCA cell line. To validate macropinosome, the Rab7 and LAMP2 were labeled and analyzed via immunocytochemistry and western blot. The CX-4945 (Silmitasertib), CK2 inhibitor, was used to investigate the role of CK2 in macropinocytosis and subsequent lysosomal metabolism.
    RESULTS: The TFK-1, a KRAS wild-type CCA cell line, showed only apoptotic morphological changes. However, the HuCCT1 cell line showed macropinocytosis. Although CX-4945 induced morphological changes accompanied by the accumulation of intracellular vacuoles and cell death, the level of macropinocytosis did not change. These intracellular vacuoles were identified as late macropinosomes, representing Rab7+ vesicles before fusion with lysosomes. In addition, CX-4945 suppressed LAMP2 expression following the inhibition of the Akt-mTOR signaling pathway, which interrupts mature macropinosome and lysosomal metabolic utilization.
    CONCLUSION: Macropinocytosis is used as an energy source in the KRAS mutant CCA cell line HuCCT1. The inhibition of CK2 by CX-4945 leads to cell death in HuCCT1 cells through alteration of the lysosome-dependent metabolism.
    Keywords:  CK2 inhibitor; CX-4945; KRAS; cholangiocarcinoma; macropinocytosis
    DOI:  https://doi.org/10.21873/anticanres.16996
  44. J Am Chem Soc. 2024 Apr 30.
    Cholesterol Changes Interfacial Water Alignment in Model Cell Membranes.
    Hanna Orlikowska-Rzeznik, Jan Versluis, Huib J Bakker, Lukasz Piatkowski.
      The nanoscopic layer of water that directly hydrates biological membranes plays a critical role in maintaining the cell structure, regulating biochemical processes, and managing intermolecular interactions at the membrane interface. Therefore, comprehending the membrane structure, including its hydration, is essential for understanding the chemistry of life. While cholesterol is a fundamental lipid molecule in mammalian cells, influencing both the structure and dynamics of cell membranes, its impact on the structure of interfacial water has remained unknown. We used surface-specific vibrational sum-frequency generation spectroscopy to study the effect of cholesterol on the structure and hydration of monolayers of the lipids 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and egg sphingomyelin (SM). We found that for the unsaturated lipid DOPC, cholesterol intercalates in the membrane without significantly changing the orientation of the lipid tails and the orientation of the water molecules hydrating the headgroups of DOPC. In contrast, for the saturated lipids DPPC and SM, the addition of cholesterol leads to clearly enhanced packing and ordering of the hydrophobic tails. It is also observed that the orientation of the water hydrating the lipid headgroups is enhanced upon the addition of cholesterol. These results are important because the orientation of interfacial water molecules influences the cell membranes' dipole potential and the strength and specificity of interactions between cell membranes and peripheral proteins and other biomolecules. The lipid nature-dependent role of cholesterol in altering the arrangement of interfacial water molecules offers a fresh perspective on domain-selective cellular processes, such as protein binding.
    DOI:  https://doi.org/10.1021/jacs.4c00474
  45. Biophys J. 2024 May 02. pii: S0006-3495(24)00313-8. [Epub ahead of print]
    Fluorescence lifetime imaging microscopy of flexible and rigid dyes probes the biophysical properties of synthetic and biological membranes.
    Rafael B Lira, Laura S Dillingh, Jan-Jacob Schuringa, Gokhan Yahioglu, Klaus Suhling, Wouter H Roos.
      Sensing of the biophysical properties of membranes using molecular reporters has recently regained wide-spread attention. This was elicited by the development of new probes of exquisite optical properties and increased performance, combined with developments in fluorescence detection. Here, we report on fluorescence lifetime imaging (FLIM) of various rigid and flexible fluorescent dyes to probe the biophysical properties of synthetic and biological membranes at steady state as well as upon the action of external membrane-modifying agents. We tested the solvatochromic dyes Nile Red and NBD, the viscosity sensor Bodipy C12, the flipper dye FliptR as well as the dyes DiO, Bodipy C16, lissamine-rhodamine, Atto647 which are dyes with no previous reported environmental sensitivity. The performance of the fluorescent probes, many of which are commercially available, was benchmarked with the well-known environmental reporters, with Nile Red and Bodipy C12 being specific reporters of medium hydration and viscosity, respectively. We show that some widely used ordinary dyes with no previous report of sensing capabilities can exhibit competing performance compared to highly sensitive commercially available or custom-based solvatochromic, molecular rotors or flipper in a wide range of biophysics experiments. Compared to other methods, FLIM is a minimally invasive and non-destructive method with optical resolution. It enables biophysical mapping at steady state or assessment of the changes induced by membrane-active molecules at subcellular level in both synthetic and biological membranes when intensity measurements fail to do so. The results have important consequences for the specific choice of the sensor and take into consideration factors such as probe sensitivity, response to environmental changes, ease and speed of data analysis and the probe's intracellular distribution, as well as potential side effects induced by labelling and imaging.
    DOI:  https://doi.org/10.1016/j.bpj.2024.04.033
  46. Nat Genet. 2024 May 03.
    The 1+Million Genomes Minimal Dataset for Cancer.
    Michela Riba, Cinzia Sala, Aedin C Culhane, Åsmund Flobak, Attila Patocs, Kjetil Boye, Karla Plevova, Šárka Pospíšilová, Giorgia Gandolfi, Marco J Morelli, Gabriele Bucci, Anders Edsjö, Ulrik Lassen, Fátima Al-Shahrour, Nuria Lopez-Bigas, Randi Hovland, Edwin Cuppen, Alfonso Valencia, Helene A Poirel, Richard Rosenquist, Serena Scollen, Juan Arenas Marquez, Jeroen Belien, Arcangela De Nicolo, Ruggero De Maria, David Torrents, Giovanni Tonon.
      
    DOI:  https://doi.org/10.1038/s41588-024-01721-x
  47. Nature. 2024 May 01.
    3D genomic mapping reveals multifocality of human pancreatic precancers.
    Alicia M Braxton, Ashley L Kiemen, Mia P Grahn, André Forjaz, Jeeun Parksong, Jaanvi Mahesh Babu, Jiaying Lai, Lily Zheng, Noushin Niknafs, Liping Jiang, Haixia Cheng, Qianqian Song, Rebecca Reichel, Sarah Graham, Alexander I Damanakis, Catherine G Fischer, Stephanie Mou, Cameron Metz, Julie Granger, Xiao-Ding Liu, Niklas Bachmann, Yutong Zhu, YunZhou Liu, Cristina Almagro-Pérez, Ann Chenyu Jiang, Jeonghyun Yoo, Bridgette Kim, Scott Du, Eli Foster, Jocelyn Y Hsu, Paula Andreu Rivera, Linda C Chu, Fengze Liu, Elliot K Fishman, Alan Yuille, Nicholas J Roberts, Elizabeth D Thompson, Robert B Scharpf, Toby C Cornish, Yuchen Jiao, Rachel Karchin, Ralph H Hruban, Pei-Hsun Wu, Denis Wirtz, Laura D Wood.
      Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study1. Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution. To elucidate genetic relationships between and within PanINs, we developed a workflow in which 3D modelling guides multi-region microdissection and targeted and whole-exome sequencing. From these samples, we calculated a mean burden of 13 PanINs per cm3 and extrapolated that the normal intact adult pancreas harbours hundreds of PanINs, almost all with oncogenic KRAS hotspot mutations. We found that most PanINs originate as independent clones with distinct somatic mutation profiles. Some spatially continuous PanINs were found to contain multiple KRAS mutations; computational and in situ analyses demonstrated that different KRAS mutations localize to distinct cell subpopulations within these neoplasms, indicating their polyclonal origins. The extensive multifocality and genetic heterogeneity of PanINs raises important questions about mechanisms that drive precancer initiation and confer differential progression risk in the human pancreas. This detailed 3D genomic mapping of molecular alterations in human PanINs provides an empirical foundation for early detection and rational interception of pancreatic cancer.
    DOI:  https://doi.org/10.1038/s41586-024-07359-3
  48. Cell Stem Cell. 2024 Apr 27. pii: S1934-5909(24)00140-1. [Epub ahead of print]
    The epidermal circadian clock integrates and subverts brain signals to guarantee skin homeostasis.
    Thomas Mortimer, Valentina M Zinna, Muge Atalay, Carmelo Laudanna, Oleg Deryagin, Guillem Posas, Jacob G Smith, Elisa García-Lara, Mireia Vaca-Dempere, Leonardo Vinícius Monteiro de Assis, Isabel Heyde, Kevin B Koronowski, Paul Petrus, Carolina M Greco, Stephen Forrow, Henrik Oster, Paolo Sassone-Corsi, Patrick-Simon Welz, Pura Muñoz-Cánoves, Salvador Aznar Benitah.
      In mammals, the circadian clock network drives daily rhythms of tissue-specific homeostasis. To dissect daily inter-tissue communication, we constructed a mouse minimal clock network comprising only two nodes: the peripheral epidermal clock and the central brain clock. By transcriptomic and functional characterization of this isolated connection, we identified a gatekeeping function of the peripheral tissue clock with respect to systemic inputs. The epidermal clock concurrently integrates and subverts brain signals to ensure timely execution of epidermal daily physiology. Timely cell-cycle termination in the epidermal stem cell compartment depends upon incorporation of clock-driven signals originating from the brain. In contrast, the epidermal clock corrects or outcompetes potentially disruptive feeding-related signals to ensure the optimal timing of DNA replication. Together, we present an approach for cataloging the systemic dependencies of daily temporal organization in a tissue and identify an essential gate-keeping function of peripheral circadian clocks that guarantees tissue homeostasis.
    Keywords:  aging; circadian; homeostasis; peripheral clocks; stem cells; systemic communication
    DOI:  https://doi.org/10.1016/j.stem.2024.04.013
  49. Cell Metab. 2024 Apr 24. pii: S1550-4131(24)00130-X. [Epub ahead of print]
    Dietary intake and glutamine-serine metabolism control pathologic vascular stiffness.
    Nesrine S Rachedi, Ying Tang, Yi-Yin Tai, Jingsi Zhao, Caroline Chauvet, Julien Grynblat, Kouamé Kan Firmin Akoumia, Leonard Estephan, Stéphanie Torrino, Chaima Sbai, Amel Ait-Mouffok, Joseph D Latoche, Yassmin Al Aaraj, Frederic Brau, Sophie Abélanet, Stephan Clavel, Yingze Zhang, Christelle Guillermier, Naveen V G Kumar, Sina Tavakoli, Olaf Mercier, Michael G Risbano, Zhong-Ke Yao, Guangli Yang, Ouathek Ouerfelli, Jason S Lewis, David Montani, Marc Humbert, Matthew L Steinhauser, Carolyn J Anderson, William M Oldham, Frédéric Perros, Thomas Bertero, Stephen Y Chan.
      Perivascular collagen deposition by activated fibroblasts promotes vascular stiffening and drives cardiovascular diseases such as pulmonary hypertension (PH). Whether and how vascular fibroblasts rewire their metabolism to sustain collagen biosynthesis remains unknown. Here, we found that inflammation, hypoxia, and mechanical stress converge on activating the transcriptional coactivators YAP and TAZ (WWTR1) in pulmonary arterial adventitial fibroblasts (PAAFs). Consequently, YAP and TAZ drive glutamine and serine catabolism to sustain proline and glycine anabolism and promote collagen biosynthesis. Pharmacologic or dietary intervention on proline and glycine anabolic demand decreases vascular stiffening and improves cardiovascular function in PH rodent models. By identifying the limiting metabolic pathways for vascular collagen biosynthesis, our findings provide guidance for incorporating metabolic and dietary interventions for treating cardiopulmonary vascular disease.
    Keywords:  cardiovascular disease; collagen metabolism; fibrosis; glutamine metabolism; metabolism; nutrition; pulmonary hypertension; serine metabolism; vascular fibroblast
    DOI:  https://doi.org/10.1016/j.cmet.2024.04.010
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