bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2023–10–01
27 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Stromal-derived NRG1 enables oncogenic KRAS bypass in pancreas cancer.
  2. Hourglass, a rapid analysis framework for heterogeneous bioimaging data, identifies sex disparity in IL-6/STAT3-associated immune phenotypes in pancreatic cancer.
  3. Abstract Proceedings of 7th Cancer Cachexia Conference, 28-30 September 2023, Edinburgh.
  4. Trogocytosis of cancer-associated fibroblasts promotes pancreatic cancer growth and immune suppression via phospholipid scramblase anoctamin 6 (ANO6).
  5. BET inhibition rescues ciliogenesis and ameliorates pancreatitis-driven phenotypic changes in mice with Par3 loss.
  6. Endothelial Notch1 signaling in white adipose tissue promotes cancer cachexia.
  7. Inhibiting Stromal Class I HDACs Curbs Pancreatic Cancer Progression.
  8. Global lipid remodelling by hypoxia aggravates migratory potential in pancreatic cancer while maintaining plasma membrane homeostasis.
  9. TIMP1 is an early biomarker for detection and prognosis of lung cancer.
  10. Proteome census upon nutrient stress reveals Golgiphagy membrane receptors.
  11. Arterial Resection for Pancreatic Cancer: Feasibility and Current Standing in a High-Volume Center.
  12. The role of lipid scramblases in regulating lipid distributions at cellular membranes.
  13. Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens.
  14. Prime editing GEMMs to model cancer mutations.
  15. HAVOC: Small-scale histomic mapping of cancer biodiversity across large tissue distances using deep neural networks.
  16. Oncogenic KRAS drives lipo-fibrogenesis to promote angiogenesis and colon cancer progression.
  17. Concept of lipid droplet biogenesis.
  18. Efficacy of staging laparoscopy for resectable pancreatic cancer on imaging and the therapeutic effect of systemic chemotherapy for positive peritoneal cytology.
  19. Lipid peroxidation drives liquid-liquid phase separation and disrupts raft protein partitioning in biological membranes.
  20. Direct regulation of FNIP1 and FNIP2 by MEF2 sustains MTORC1 activation and tumor progression in pancreatic cancer.
  21. A brown fat-enriched adipokine, ASRA, is a leptin receptor antagonist that stimulates appetite.
  22. Spatial and temporal mapping of breast cancer lung metastases identify TREM2 macrophages as regulators of the metastatic boundary.
  23. A mechanosensing mechanism controls plasma membrane shape homeostasis at the nanoscale.
  24. Single-cell epigenome analysis identifies molecular events controlling direct conversion of human fibroblasts to pancreatic ductal-like cells.
  25. Studying stochastic systems biology of the cell with single-cell genomics data.
  26. Inhibition of fatty acid oxidation enables heart regeneration in adult mice.
  27. An integrated analysis identifies six molecular subtypes of pancreatic ductal adenocarcinoma revealing cellular and molecular landscape.
  1. Genes Dev. 2023 Sep 29.
    Stromal-derived NRG1 enables oncogenic KRAS bypass in pancreas cancer.
    Jincheng Han, Jiaqian Xu, Yonghong Liu, Shaoheng Liang, Kyle A LaBella, Deepavali Chakravarti, Denise J Spring, Yan Xia, Ronald A DePinho.
      Activating KRAS mutations (KRAS*) in pancreatic ductal adenocarcinoma (PDAC) drive anabolic metabolism and support tumor maintenance. KRAS* inhibitors show initial antitumor activity followed by recurrence due to cancer cell-intrinsic and immune-mediated paracrine mechanisms. Here, we explored the potential role of cancer-associated fibroblasts (CAFs) in enabling KRAS* bypass and identified CAF-derived NRG1 activation of cancer cell ERBB2 and ERBB3 receptor tyrosine kinases as a mechanism by which KRAS*-independent growth is supported. Genetic extinction or pharmacological inhibition of KRAS* resulted in up-regulation of ERBB2 and ERBB3 expression in human and murine models, which prompted cancer cell utilization of CAF-derived NRG1 as a survival factor. Genetic depletion or pharmacological inhibition of ERBB2/3 or NRG1 abolished KRAS* bypass and synergized with KRASG12D inhibitors in combination treatments in mouse and human PDAC models. Thus, we found that CAFs can contribute to KRAS* inhibitor therapy resistance via paracrine mechanisms, providing an actionable therapeutic strategy to improve the effectiveness of KRAS* inhibitors in PDAC patients.
    Keywords:  ERBB3; NRG1; cancer-associated fibroblasts; oncogenic KRAS bypass; pancreas cancer; receptor tyrosine kinase; tumor microenvironment
    DOI:  https://doi.org/10.1101/gad.351037.123
  2. J Pathol. 2023 Sep 28.
    Hourglass, a rapid analysis framework for heterogeneous bioimaging data, identifies sex disparity in IL-6/STAT3-associated immune phenotypes in pancreatic cancer.
    Kazeera Aliar, Henry R Waterhouse, Foram Vyas, Niklas Krebs, Bowen Zhang, Emily Poulton, Nathan Chan, Ricardo Gonzalez, Gun Ho Jang, Peter Bronsert, Sandra E Fischer, Steven Gallinger, Barbara T Grünwald, Rama Khokha.
      Integration and mining of bioimaging data remains a challenge and lags behind the rapidly expanding digital pathology field. We introduce Hourglass, an open-access analytical framework that streamlines biology-driven visualization, interrogation, and statistical assessment of multiparametric datasets. Cognizant of tissue and clinical heterogeneity, Hourglass systematically organizes observations across spatial and global levels and within patient subgroups. Applied to an extensive bioimaging dataset, Hourglass promptly consolidated a breadth of known interleukin-6 (IL-6) functions via its downstream effector STAT3 and uncovered a so-far unknown sexual dimorphism in the IL-6/STAT3-linked intratumoral T-cell response in human pancreatic cancer. As an R package and cross-platform application, Hourglass facilitates knowledge extraction from multi-layered bioimaging datasets for users with or without computational proficiency and provides unique and widely accessible analytical means to harness insights hidden within heterogeneous tissues at the sample and patient level. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
    Keywords:  bioimaging analysis; data visualization; digital pathology; interleukin-6; pancreatic cancer; tissue microarray
    DOI:  https://doi.org/10.1002/path.6199
  3. J Cachexia Sarcopenia Muscle. 2023 09;14 Suppl 1 3-59
    Abstract Proceedings of 7th Cancer Cachexia Conference, 28-30 September 2023, Edinburgh.
      
    DOI:  https://doi.org/10.1002/jcsm.13325
  4. bioRxiv. 2023 Sep 17. pii: 2023.09.15.557802. [Epub ahead of print]
    Trogocytosis of cancer-associated fibroblasts promotes pancreatic cancer growth and immune suppression via phospholipid scramblase anoctamin 6 (ANO6).
    Charline Ogier, Akino Mercy Charles Solomon, Zhen Lu, Ludmila Recoules, Alena Klochkova, Linara Gabitova-Cornell, Battuya Bayarmagnai, Diana Restifo, Aizhan Surumbayeva, Débora B Vendramini-Costa, Alexander Y Deneka, Ralph Francescone, Anna C Lilly, Alyssa Sipman, Jaye C Gardiner, Tiffany Luong, Janusz Franco-Barraza, Nina Ibeme, Kathy Q Cai, Margret B Einarson, Emmanuelle Nicolas, Andrei Efimov, Emily Megill, Nathaniel W Snyder, Corinne Bousquet, Jerome Cros, Yunyun Zhou, Erica A Golemis, Bojana Gligorijevic, Jonathan Soboloff, Serge Y Fuchs, Edna Cukierman, Igor Astsaturov.
      In pancreatic ductal adenocarcinoma (PDAC), the fibroblastic stroma constitutes most of the tumor mass and is remarkably devoid of functional blood vessels. This raises an unresolved question of how PDAC cells obtain essential metabolites and water-insoluble lipids. We have found a critical role for cancer-associated fibroblasts (CAFs) in obtaining and transferring lipids from blood-borne particles to PDAC cells via trogocytosis of CAF plasma membranes. We have also determined that CAF-expressed phospholipid scramblase anoctamin 6 (ANO6) is an essential CAF trogocytosis regulator required to promote PDAC cell survival. During trogocytosis, cancer cells and CAFs form synapse-like plasma membranes contacts that induce cytosolic calcium influx in CAFs via Orai channels. This influx activates ANO6 and results in phosphatidylserine exposure on CAF plasma membrane initiating trogocytosis and transfer of membrane lipids, including cholesterol, to PDAC cells. Importantly, ANO6-dependent trogocytosis also supports the immunosuppressive function of pancreatic CAFs towards cytotoxic T cells by promoting transfer of excessive amounts of cholesterol. Further, blockade of ANO6 antagonizes tumor growth via disruption of delivery of exogenous cholesterol to cancer cells and reverses immune suppression suggesting a potential new strategy for PDAC therapy.
    DOI:  https://doi.org/10.1101/2023.09.15.557802
  5. bioRxiv. 2023 Sep 17. pii: 2023.09.14.557654. [Epub ahead of print]
    BET inhibition rescues ciliogenesis and ameliorates pancreatitis-driven phenotypic changes in mice with Par3 loss.
    Mario A Shields, Anastasia E Metropulos, Christina Spaulding, Tomonori Hirose, Shigeo Ohno, Thao N D Pham, Hidayatullah G Munshi.
      The apical-basal polarity of pancreatic acinar cells is essential for maintaining tissue architecture. However, the mechanisms by which polarity proteins regulate acinar pancreas tissue homeostasis are poorly understood. Here, we evaluate the role of Par3 in acinar pancreas injury and homeostasis. While Par3 loss in the mouse pancreas disrupts tight junctions, Par3 loss is dispensable for pancreatogenesis. However, with aging, Par3 loss results in low-grade inflammation, acinar degeneration, and pancreatic lipomatosis. Par3 loss also exacerbates pancreatitis-induced acinar cell loss, resulting in pronounced pancreatic lipomatosis and failure to regenerate. Moreover, Par3 loss in mice harboring mutant Kras causes extensive pancreatic intraepithelial neoplastic (PanIN) lesions and large pancreatic cysts. We also show that Par3 loss restricts injury-induced primary ciliogenesis. Significantly, targeting BET proteins enhances primary ciliogenesis during pancreatitis-induced injury and, in mice with Par3 loss, limits pancreatitis-induced acinar loss and facilitates acinar cell regeneration. Combined, this study demonstrates how Par3 restrains pancreatitis- and Kras-induced changes in the pancreas and identifies a potential role for BET inhibitors to attenuate pancreas injury and facilitate pancreas tissue regeneration.
    DOI:  https://doi.org/10.1101/2023.09.14.557654
  6. Nat Cancer. 2023 Sep 25.
    Endothelial Notch1 signaling in white adipose tissue promotes cancer cachexia.
    Jacqueline Taylor, Leonie Uhl, Iris Moll, Sana Safatul Hasan, Lena Wiedmann, Jakob Morgenstern, Benedetto Daniele Giaimo, Tobias Friedrich, Elisenda Alsina-Sanchis, Francesca De Angelis Rigotti, Ronja Mülfarth, Sarah Kaltenbach, Darius Schenk, Felix Nickel, Thomas Fleming, David Sprinzak, Carolin Mogler, Thomas Korff, Adrian T Billeter, Beat P Müller-Stich, Mauricio Berriel Diaz, Tilman Borggrefe, Stephan Herzig, Maria Rohm, Juan Rodriguez-Vita, Andreas Fischer.
      Cachexia is a major cause of morbidity and mortality in individuals with cancer and is characterized by weight loss due to adipose and muscle tissue wasting. Hallmarks of white adipose tissue (WAT) remodeling, which often precedes weight loss, are impaired lipid storage, inflammation and eventually fibrosis. Tissue wasting occurs in response to tumor-secreted factors. Considering that the continuous endothelium in WAT is the first line of contact with circulating factors, we postulated whether the endothelium itself may orchestrate tissue remodeling. Here, we show using human and mouse cancer models that during precachexia, tumors overactivate Notch1 signaling in distant WAT endothelium. Sustained endothelial Notch1 signaling induces a WAT wasting phenotype in male mice through excessive retinoic acid production. Pharmacological blockade of retinoic acid signaling was sufficient to inhibit WAT wasting in a mouse cancer cachexia model. This demonstrates that cancer manipulates the endothelium at distant sites to mediate WAT wasting by altering angiocrine signals.
    DOI:  https://doi.org/10.1038/s43018-023-00622-y
  7. bioRxiv. 2023 Sep 14. pii: 2023.09.12.557260. [Epub ahead of print]
    Inhibiting Stromal Class I HDACs Curbs Pancreatic Cancer Progression.
    Gaoyang Liang, Tae Gyu Oh, Nasun Hah, Hervé Tiriac, Yu Shi, Morgan L Truitt, Corina E Antal, Annette R Atkins, Yuwenbin Li, Cory Fraser, Serina Ng, Antonio F M Pinto, Dylan C Nelson, Gabriela Estepa, Senada Bashi, Ester Banayo, Yang Dai, Christopher Liddle, Ruth T Yu, Tony Hunter, Dannielle D Engle, Haiyong Han, Daniel D Von Hoff, Michael Downes, Ronald M Evans.
      Oncogenic lesions in pancreatic ductal adenocarcinoma (PDAC) hijack the epigenetic machinery in stromal components to establish a desmoplastic and therapeutic resistant tumor microenvironment (TME). Here we identify Class I histone deacetylases (HDACs) as key epigenetic factors facilitating the induction of pro-desmoplastic and pro-tumorigenic transcriptional programs in pancreatic stromal fibroblasts. Mechanistically, HDAC-mediated changes in chromatin architecture enable the activation of pro-desmoplastic programs directed by serum response factor (SRF) and forkhead box M1 (FOXM1). HDACs also coordinate fibroblast pro-inflammatory programs inducing leukemia inhibitory factor (LIF) expression, supporting paracrine pro-tumorigenic crosstalk. HDAC depletion in cancer-associated fibroblasts (CAFs) and treatment with the HDAC inhibitor entinostat (Ent) in PDAC mouse models reduce stromal activation and curb tumor progression. Notably, HDAC inhibition (HDACi) enriches a lipogenic fibroblast subpopulation, a potential precursor for myofibroblasts in the PDAC stroma. Overall, our study reveals the stromal targeting potential of HDACi, highlighting the utility of this epigenetic modulating approach in PDAC therapeutics.
    DOI:  https://doi.org/10.1101/2023.09.12.557260
  8. Biochim Biophys Acta Mol Cell Biol Lipids. 2023 Sep 23. pii: S1388-1981(23)00122-1. [Epub ahead of print] 159398
    Global lipid remodelling by hypoxia aggravates migratory potential in pancreatic cancer while maintaining plasma membrane homeostasis.
    Prema Kumari Agarwala, Shuai Nie, Gavin E Reid, Shobhna Kapoor.
      Hypoxia plays an important role in pancreatic cancer progression. It drives various metabolic reprogramming in cells including that of lipids, which in turn, can modify the structure and function of cell membranes. Homeostatic adaptation of membranes is well-recognized, but how and if it is regulated in hypoxic pancreatic cancer and its relation to aggressive phenotype and metastasis remains elusive. Here we show hypoxia-induced extensive global lipid remodelling spanning changes in lipid classes, unsaturation levels, glyceryl backbone and acyl chain lengths. No major modulation of plasma membrane biophysical properties revealed a decoupling of lipidome modulation from membrane properties under hypoxia. This was supported by observing minor changes in the lipidome of plasma membranes under hypoxia. Further, hypoxia increased migration and invasion underpinned by reduced actin volume, cell cortical stiffness and facile tether dynamics. In conclusion, we demonstrate buffering of the lipidome alterations leading to a homeostatic membrane response. These findings will help to understand the hypoxic regulation of pancreatic membrane homeostasis and identify tangible theranostic avenues.
    Keywords:  Cell membranes; Hypoxia; Lipidomics; Membrane biophysics; Pancreatic cancer
    DOI:  https://doi.org/10.1016/j.bbalip.2023.159398
  9. Clin Transl Med. 2023 Oct;13(10): e1391
    TIMP1 is an early biomarker for detection and prognosis of lung cancer.
    Ezequiel Dantas, Anirudh Murthy, Tanvir Ahmed, Mujmmail Ahmed, Shakti Ramsamooj, Maurice A Hurd, Tiffany Lam, Murtaza Malbari, Christopher Agrusa, Olivier Elemento, Chen Zhang, Darryl J Pappin, Timothy E McGraw, Brendon M Stiles, Nasser K Altorki, Marcus D Goncalves.
       BACKGROUND: Lung cancer remains the major cause of cancer-related deaths worldwide. Early stages of lung cancer are characterized by long asymptomatic periods that are ineffectively identified with the current screening programs. This deficiency represents a lost opportunity to improve the overall survival of patients. Serum biomarkers are among the most effective strategies for cancer screening and follow up.
    METHODS: Using bead-based multiplexing assays we screened plasma and tumours of the KrasG12D/+; Lkb1f/f (KL) mouse model of lung cancer for cytokines that could be used as biomarkers. We identified tissue inhibitor of metalloproteinase 1 (TIMP1) as an early biomarker and validated this finding in the plasma of lung cancer patients. We used immunohistochemistry (IHC), previously published single-cell RNA-seq and bulk RNA-seq data to assess the source and expression of TIMP1in the tumour. The prognostic value of TIMP1 was assessed using publicly available human proteomic and transcriptomic databases.
    RESULTS: We found that TIMP1 is a tumour-secreted protein with high sensitivity and specificity for aggressive cancer, even at early stages in mice. We showed that TIMP1 levels in the tumour and serum correlate with tumour burden and worse survival in mice. We validated this finding using clinical samples from our institution and publicly available human proteomic and transcriptomic databases. These data support the finding that high tumour expression of TIMP1 correlates with an unfavorable prognosis in lung cancer patients.
    CONCLUSION: TIMP1 is a suitable biomarker for lung cancer detection.
    Keywords:  TIMP1; biomarkers; lung cancer; prognosis
    DOI:  https://doi.org/10.1002/ctm2.1391
  10. Nature. 2023 Sep 27.
    Proteome census upon nutrient stress reveals Golgiphagy membrane receptors.
    Kelsey L Hickey, Sharan Swarup, Ian R Smith, Julia C Paoli, Enya Miguel Whelan, Joao A Paulo, J Wade Harper.
      During nutrient stress, macroautophagy degrades cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodeling the proteome1,2. While machinery responsible for initiation of macroautophagy is well characterized3,4, our understanding of the extent to which individual proteins, protein complexes and organelles are selected for autophagic degradation, and the underlying targeting mechanisms is limited. Here, we use orthogonal proteomic strategies to provide a spatial proteome census of autophagic cargo during nutrient stress in mammalian cells. We find that macroautophagy has selectivity for recycling membrane-bound organelles (principally Golgi and ER). Through autophagic cargo prioritization, we identify a complex of membrane-embedded proteins, YIPF3 and YIPF4, as receptors for Golgiphagy. During nutrient stress, YIPF3 and YIPF4 interact with ATG8s via LIR motifs and are mobilized into autophagosomes that traffic to lysosomes in a process that requires the canonical autophagic machinery. Cells lacking YIPF3 or YIPF4 are selectively defective in elimination of a specific cohort of Golgi membrane proteins during nutrient stress. Moreover, YIPF3/4 play an analogous role in Golgi remodeling during programmed conversion of stem cells to the neuronal lineage in vitro. Collectively, this study reveals prioritization of membrane protein cargo during nutrient stress-dependent proteome remodeling and identifies an unanticipated Golgi remodeling pathway requiring membrane-embedded receptors.
    DOI:  https://doi.org/10.1038/s41586-023-06657-6
  11. Ann Surg Open. 2023 Sep;4(3): e302
    Arterial Resection for Pancreatic Cancer: Feasibility and Current Standing in a High-Volume Center.
    Lei Ren, Carsten Jäger, Stephan Schorn, Ilaria Pergolini, Rüdiger Göß, Okan Safak, Maximilian Kießler, Marc E Martignoni, Alexander R Novotny, Helmut Friess, Güralp O Ceyhan, Ihsan Ekin Demir.
       Background: Arterial resection (AR) during pancreatectomy for curative R0 resection of pancreatic ductal adenocarcinoma (PDAC) remains a controversial procedure with high morbidity.
    Objective: To investigate the feasibility and oncological outcomes of pancreatectomy combined with AR at a high-volume center for pancreatic surgery.
    Methods: We retrospectively analyzed our experience in PDAC patients, who underwent pancreatic resection with AR and/or venous resection (VR) between 2007 and 2021.
    Results: In total 259 PDAC patients with borderline resectable (n = 138) or locally advanced (n = 121) PDAC underwent vascular resection during tumor resection. From these, 23 patients had AR (n = 4 due to intraoperative injury, n = 19 due to suspected arterial infiltration). However, 12 out of 23 patients (52.2%) underwent simultaneous VR including 1 case with intraoperative arterial injury. In comparison, 11 patients (47.8%) underwent AR only including 3 intraoperative arterial injury patients. Although the operation time and bleeding rate of patients with AR were respectively longer and higher than in VR, no significant difference was detected in postoperative complications between VR and AR (P = 0.11). The final histopathological findings of PDAC patients were similar, including M stage, regional lymph node metastases, and R0 margin resection. The mortality of the entire cohort was 6.2% (16/259), with a tendency to increase mortality in the AR cohort, yet without statistical significance (VR: 5% vs AR: 21.1%; P = 0.05). Although 19 (82.6%) patients had PDAC in the final histopathology, only 6 were confirmed to have infiltrated arteria. The microscopic distribution of PDAC in these infiltrated arterial walls on hematoxylin-eosin staining was classified into 3 patterns. Strikingly, the perivascular nerves frequently exhibited perineural invasion.
    Conclusions: AR can be performed in high-volume centers for pancreatic surgery with an acceptable morbidity, which is comparable to that of VR. However, the likelihood of arterial infiltration seems to be rather overestimated, and as such, AR might be avoidable or replaced by less invasive techniques such as divestment during PDAC surgery.
    Keywords:  R0 resection; arterial resection; pancreatic cancer; venous resection
    DOI:  https://doi.org/10.1097/AS9.0000000000000302
  12. Biochem Soc Trans. 2023 Sep 28. pii: BST20221455. [Epub ahead of print]
    The role of lipid scramblases in regulating lipid distributions at cellular membranes.
    Yicheng Wang, Taroh Kinoshita.
      Glycerophospholipids, sphingolipids and cholesterol assemble into lipid bilayers that form the scaffold of cellular membranes, in which proteins are embedded. Membrane composition and membrane protein profiles differ between plasma and intracellular membranes and between the two leaflets of a membrane. Lipid distributions between two leaflets are mediated by lipid translocases, including flippases and scramblases. Flippases use ATP to catalyze the inward movement of specific lipids between leaflets. In contrast, bidirectional flip-flop movements of lipids across the membrane are mediated by scramblases in an ATP-independent manner. Scramblases have been implicated in disrupting the lipid asymmetry of the plasma membrane, protein glycosylation, autophagosome biogenesis, lipoprotein secretion, lipid droplet formation and communications between organelles. Although scramblases in plasma membranes were identified over 10 years ago, most progress about scramblases localized in intracellular membranes has been made in the last few years. Herein, we review the role of scramblases in regulating lipid distributions in cellular membranes, focusing primarily on intracellular membrane-localized scramblases.
    Keywords:  flippase; glycolipids; lipid transfer; phospholipids; post translational modification; scramblase
    DOI:  https://doi.org/10.1042/BST20221455
  13. JCI Insight. 2023 Sep 26. pii: e172449. [Epub ahead of print]
    Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens.
    Min Yao, Jonathan Preall, Johannes Yeh, Darryl J Pappin, Paolo Cifani, Yixin Zhao, Sophia Shen, Philip Moresco, Brian He, Hardik Patel, Amber N Habowski, Daniel A King, Kara L Raphael, Arvind Rishi, Divyesh V Sejpal, Matthew Weiss, David Tuveson, Douglas T Fearon.
      Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA sequencing (scRNA-Seq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from seven primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. Ig sequencing identified plasma cell (PC) clones expressing isotype-switched and hyper-mutated Igs, suggesting the occurrence of T cell-dependent B cell responses. We assessed the reactivity of 41 recombinant antibodies that represented the products of 235 PCs and 12 B cells toward multiple cell lines and PDAC tissues, and observed frequent staining of intracellular self-antigens. Three of these antigens were identified: the filamentous actin (F-actin), the nucleic protein, RUVBL2, and the mitochondrial protein, HSPD1. Antibody titers to F-actin and HSPD1 were significantly elevated in the plasma of PDAC patients (n=59) compared to healthy donors (n=61). Thus, PCs in PDAC produce auto-antibodies reacting with intracellular self-antigens, which may result from promotion of pre-existing, autoreactive B cell responses. These observations indicate that the chronic inflammatory microenvironment of PDAC can support the adaptive immune response.
    Keywords:  Adaptive immunity; Antigen; Cancer; Immunology; Oncology
    DOI:  https://doi.org/10.1172/jci.insight.172449
  14. Nat Rev Cancer. 2023 Sep 28.
    Prime editing GEMMs to model cancer mutations.
    Nicolas Mathey-Andrews.
      
    DOI:  https://doi.org/10.1038/s41568-023-00627-w
  15. Sci Adv. 2023 Sep 29. 9(39): eadg1894
    HAVOC: Small-scale histomic mapping of cancer biodiversity across large tissue distances using deep neural networks.
    Anglin Dent, Kevin Faust, K H Brian Lam, Narges Alhangari, Alberto J Leon, Queenie Tsang, Zaid Saeed Kamil, Andrew Gao, Prodipto Pal, Stephanie Lheureux, Amit Oza, Phedias Diamandis.
      Intratumoral heterogeneity can wreak havoc on current precision medicine strategies because of challenges in sufficient sampling of geographically separated areas of biodiversity distributed across centimeter-scale tumor distances. To address this gap, we developed a deep learning pipeline that leverages histomorphologic fingerprints of tissue to create "Histomic Atlases of Variation Of Cancers" (HAVOC). Using a number of objective molecular readouts, we demonstrate that HAVOC can define regional cancer boundaries with distinct biology. Using larger tumor specimens, we show that HAVOC can map biodiversity even across multiple tissue sections. By guiding profiling of 19 partitions across six high-grade gliomas, HAVOC revealed that distinct differentiation states can often coexist and be regionally distributed within these tumors. Last, to highlight generalizability, we benchmark HAVOC on additional tumor types. Together, we establish HAVOC as a versatile tool to generate small-scale maps of tissue heterogeneity and guide regional deployment of molecular resources to relevant biodiverse niches.
    DOI:  https://doi.org/10.1126/sciadv.adg1894
  16. Cancer Discov. 2023 Sep 28.
    Oncogenic KRAS drives lipo-fibrogenesis to promote angiogenesis and colon cancer progression.
    Wen-Hao Hsu, Kyle A LaBella, Yiyun Lin, Ping Xu, Rumi Lee, Cheng-En Hsieh, Lei Yang, Ashley Zhou, Jonathan M Blecher, Chang-Jiun Wu, Kangyu Lin, Xiaoying Shang, Shan Jiang, Denise J Spring, Yan Xia, Peiwen Chen, John Paul Shen, Scott Kopetz, Ronald A DePinho.
      Oncogenic KRAS (KRAS*) contributes to many cancer hallmarks. In colorectal cancer (CRC), KRAS* suppresses anti-tumor immunity to promote tumor invasion and metastasis. Here, we uncovered that KRAS* transforms the phenotype of carcinoma-associated fibroblasts (CAFs) into lipid-laden CAFs, promoting angiogenesis and tumor progression. Mechanistically, KRAS* activates the transcription factor CP2 (TFCP2) which upregulates the expression of the pro-adipogenic factors BMP4 and WNT5B, triggering the transformation of CAFs into lipid-rich CAFs. These lipid-rich CAFs, in turn, produce vascular endothelial growth factor A (VEGFA) to spur angiogenesis. In KRAS*-driven CRC mouse models, genetic or pharmacological neutralization of TFCP2 reduced lipid-rich CAFs, lessened tumor angiogenesis, and improved overall survival. Correspondingly, in human CRC, lipid-rich CAF and TFCP2 signatures correlate with worse prognosis. This work unveils a new role for KRAS* in transforming CAFs, driving tumor angiogenesis and disease progression, providing an actionable therapeutic intervention for KRAS*-driven CRC.
    DOI:  https://doi.org/10.1158/2159-8290.CD-22-1467
  17. Eur J Cell Biol. 2023 Sep 19. pii: S0171-9335(23)00077-8. [Epub ahead of print]102(4): 151362
    Concept of lipid droplet biogenesis.
    R Mankamna Kumari, Amit Khatri, Ritika Chaudhary, Vineet Choudhary.
      Lipid droplets (LD) are functionally conserved fat storage organelles found in all cell types. LDs have a unique structure comprising of a hydrophobic core of neutral lipids (fat), triacylglycerol (TAG) and cholesterol esters (CE) surrounded by a phospholipid monolayer. LD surface is decorated by a multitude of proteins and enzymes rendering this compartment functional. Accumulating evidence suggests that LDs originate from discrete ER-subdomains, demarcated by the lipodystrophy protein seipin, however, the mechanisms of which are not well understood. LD biogenesis factors together with biophysical properties of the ER membrane orchestrate spatiotemporal regulation of LD nucleation and growth at specific ER subdomains in response to metabolic cues. Defects in LD formation manifests in several human pathologies, including obesity, lipodystrophy, ectopic fat accumulation, and insulin resistance. Here, we review recent advances in understanding the molecular events during initial stages of eukaryotic LD assembly and discuss the critical role of factors that ensure fidelity of this process.
    Keywords:  Endoplasmic reticulum; Fat storage; Lipid droplet; Lipid storage disorders; Lipodystrophy; Membrane trafficking; Metabolic syndrome; Organelle biogenesis; Seipin; TAG
    DOI:  https://doi.org/10.1016/j.ejcb.2023.151362
  18. J Hepatobiliary Pancreat Sci. 2023 Sep 26.
    Efficacy of staging laparoscopy for resectable pancreatic cancer on imaging and the therapeutic effect of systemic chemotherapy for positive peritoneal cytology.
    Mina Fukasawa, Toru Watanabe, Haruyoshi Tanaka, Ayaka Itoh, Nana Kimura, Kazuto Shibuya, Isaku Yoshioka, Kenta Murotani, Kenichi Hirabayashi, Tsutomu Fujii.
       BACKGROUND: The frequency and prognosis of positive peritoneal washing cytology (CY1) in resectable pancreatic ductal adenocarcinoma (R-PDAC) remains unclear. The objective of this study was to identify the clinical implications of CY1 in R-PDAC and staging laparoscopy (SL).
    METHODS: We retrospectively analyzed 115 consecutive patients with R-PDAC who underwent SL between 2018 and 2022. Patients with negative cytology (CY0) received radical surgery after neoadjuvant chemotherapy, while CY1 patients received systemic chemotherapy and were continuously evaluated for cytology.
    RESULTS: Of the 115 patients, 84 had no distant metastatic factors, 22 had only CY1, and nine had distant metastasis. Multivariate logistic regression revealed that larger tumor size was an independent predictor of the presence of any distant metastatic factor (OR: 6.30, p = .002). Patients with CY1 showed a significantly better prognosis than patients with distant metastasis (MST: 24.6 vs. 18.9 months, p = .040). A total of 11 CY1 patients were successfully converted to CY-negative, and seven underwent conversion surgery. There was no significant difference in overall survival between patients with CY0 and those converted to CY-negative.
    CONCLUSION: SL is effective even for R-PDAC. The prognosis of CY1 patients converted to CY-negative is expected to be similar to that of CY0 patients.
    Keywords:  conversion surgery; pancreatic ductal adenocarcinoma; peritoneal washing cytology; resectable; staging laparoscopy
    DOI:  https://doi.org/10.1002/jhbp.1356
  19. bioRxiv. 2023 Sep 14. pii: 2023.09.12.557355. [Epub ahead of print]
    Lipid peroxidation drives liquid-liquid phase separation and disrupts raft protein partitioning in biological membranes.
    Muthuraj Balakrishnan, Anne K Kenworthy.
      The peroxidation of membrane lipids by free radicals contributes to aging, numerous diseases, and ferroptosis, an iron-dependent form of cell death. Peroxidation changes the structure, conformation and physicochemical properties of lipids, leading to major membrane alterations including bilayer thinning, altered fluidity, and increased permeability. Whether and how lipid peroxidation impacts the lateral organization of proteins and lipids in biological membranes, however, remains poorly understood. Here, we employ cell-derived giant plasma membrane vesicles (GPMVs) as a model to investigate the impact of lipid peroxidation on ordered membrane domains, often termed membrane rafts. We show that lipid peroxidation induced by the Fenton reaction dramatically enhances phase separation propensity of GPMVs into co-existing liquid ordered (raft) and liquid disordered (non-raft) domains and increases the relative abundance of the disordered, non-raft phase. Peroxidation also leads to preferential accumulation of peroxidized lipids and 4-hydroxynonenal (4-HNE) adducts in the disordered phase, decreased lipid packing in both raft and non-raft domains, and translocation of multiple classes of proteins out of rafts. These findings indicate that peroxidation of plasma membrane lipids disturbs many aspects of membrane rafts, including their stability, abundance, packing, and protein and lipid composition. We propose that these disruptions contribute to the pathological consequences of lipid peroxidation during aging and disease, and thus serve as potential targets for therapeutic intervention.
    DOI:  https://doi.org/10.1101/2023.09.12.557355
  20. Autophagy. 2023 Sep 29. 1-20
    Direct regulation of FNIP1 and FNIP2 by MEF2 sustains MTORC1 activation and tumor progression in pancreatic cancer.
    Li Xia, Tiejian Nie, Fangfang Lu, Lu Huang, Xiaolong Shi, Dongni Ren, Jianjun Lu, Xiaobin Li, Tuo Xu, Bozhou Cui, Qing Wang, Guodong Gao, Qian Yang.
      MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) orchestrates diverse environmental signals to facilitate cell growth and is frequently activated in cancer. Translocation of MTORC1 from the cytosol to the lysosomal surface by the RRAG GTPases is the key step in MTORC1 activation. Here, we demonstrated that transcription factors MEF2A and MEF2D synergistically regulated MTORC1 activation via modulating its cyto-lysosome shutting. Mechanically, MEF2A and MEF2D controlled the transcription of FNIP1 and FNIP2, the components of the FLCN-FNIP1 or FNIP2 complex that acts as a RRAGC-RRAGD GTPase-activating element to promote the recruitment of MTORC1 to lysosome and its activation. Furthermore, we determined that the pro-oncogenic protein kinase SRC/c-Src directly phosphorylated MEF2D at three conserved tyrosine residues. The tyrosine phosphorylation enhanced MEF2D transcriptional activity and was indispensable for MTORC1 activation. Finally, both the protein and tyrosine phosphorylation levels of MEF2D are elevated in human pancreatic cancers, positively correlating with MTORC1 activity. Depletion of both MEF2A and MEF2D or expressing the unphosphorylatable MEF2D mutant suppressed tumor cell growth. Thus, our study revealed a transcriptional regulatory mechanism of MTORC1 that promoted cell anabolism and proliferation and uncovered its critical role in pancreatic cancer progression.Abbreviation: ACTB: actin beta; ChIP: chromatin immunoprecipitation; EGF: epidermal growth factor; EIF4EBP1: eukaryotic translation initiation factor 4E binding protein 1; FLCN: folliculin; FNIP1: folliculin interacting protein 1; FNIP2: folliculin interacting protein 2; GAP: GTPase activator protein; GEF: guanine nucleotide exchange factors; GTPase: guanosine triphosphatase; LAMP2: lysosomal associated membrane protein 2; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MEF2: myocyte enhancer factor 2; MEF2A: myocyte enhancer factor 2A; MEF2D: myocyte enhancer factor 2D; MEF2D-3YF: Y131F, Y333F, Y337F mutant; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; NR4A1: nuclear receptor subfamily 4 group A member 1; RPTOR: regulatory associated protein of MTOR complex 1; RHEB: Ras homolog, mTORC1 binding; RPS6KB1: ribosomal protein S6 kinase B1; RRAG: Ras related GTP binding; RT-qPCR: real time-quantitative PCR; SRC: SRC proto-oncogene, non-receptor tyrosine kinase; TMEM192: transmembrane protein 192; WT: wild-type.
    Keywords:  Autophagy; cell metabolism; oncogenesis; protein kinase; transcription factor
    DOI:  https://doi.org/10.1080/15548627.2023.2259735
  21. bioRxiv. 2023 Sep 12. pii: 2023.09.12.557454. [Epub ahead of print]
    A brown fat-enriched adipokine, ASRA, is a leptin receptor antagonist that stimulates appetite.
    Lei Huang, Pengpeng Liu, Yong Du, Dongning Pan, Alexandra Lee, Scot A Wolfe, Yong-Xu Wang.
      The endocrine control of food intake remains incompletely understood, and whether the leptin receptor-mediated anorexigenic pathway in the hypothalamus is negatively regulated by a humoral factor is unknown. Here we identify an appetite-stimulating factor - ASRA - that acts as a leptin receptor antagonist. ASRA encodes an 8 kD protein that is abundantly and selectively expressed in adipose tissue and to a lesser extent, in liver, and is upregulated during fasting and cold. ASRA protein associates with autophagosomes and its secretion is induced by energy deficiency. Overexpression of ASRA in mice attenuates leptin receptor signaling leading to elevated blood glucose and development of severe hyperphagic obesity, whereas either adipose- or liver-specific ASRA knockout mice display increased leptin sensitivity, improved glucose homeostasis, reduced food intake, and resistance to high fat diet-induced obesity. Furthermore, ASRA is indispensable for cold-evoked feeding response. Recombinant ASRA (rASRA) protein binds to leptin receptor and suppresses leptin receptor signaling in cultured cells. In vivo, rASRA promotes food intake and increases blood glucose in a leptin receptor signaling-dependent manner. Our studies collectively show that ASRA, acting as a peripheral signal of energy deficit, stimulates appetite and regulates glucose metabolism by antagonizing leptin receptor signaling, thus revealing a previously unknown endocrine mechanism that has important implications for our understanding of leptin resistance.
    DOI:  https://doi.org/10.1101/2023.09.12.557454
  22. Cancer Discov. 2023 Sep 27.
    Spatial and temporal mapping of breast cancer lung metastases identify TREM2 macrophages as regulators of the metastatic boundary.
    Ido Yofe, Tamar Shami, Noam Cohen, Tomer Landsberger, Fadi Sheban, Liat Stoler-Barak, Adam Yalin, Truong San Phan, Baoguo Li, Lea Monteran, Ye'ela Scharff, Amir Giladi, Miriam Elbaz, Eyal David, Anna Gurevich-Shapiro, Chamutal Gur, Ziv Shulman, Neta Erez, Ido Amit.
      Cancer mortality primarily stems from metastatic recurrence, emphasizing the urgent need for developing effective metastasis targeted immunotherapies. To better understand the cellular and molecular events shaping metastatic niches, we used a spontaneous breast cancer lung metastasis model to create a single-cell atlas spanning different metastatic stages and regions. We found that pre-metastatic lungs are infiltrated by inflammatory neutrophils and monocytes, followed by accumulation of suppressive macrophages with the emergence of metastases. Spatial profiling revealed that metastasis-associated immune cells were present in the metastasis core, with the exception of TREM2+ regulatory macrophages uniquely enriched at the metastatic invasive margin, consistent across both murine models and human patient samples. These regulatory macrophages (Mreg) contribute to the formation of an immune-suppressive niche, cloaking tumor cells from immune surveillance. Our study provides a compendium of immune cell dynamics across metastatic stages and niches, informing the development of metastasis-targeting immunotherapies.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-0299
  23. Elife. 2023 Sep 25. pii: e72316. [Epub ahead of print]12
    A mechanosensing mechanism controls plasma membrane shape homeostasis at the nanoscale.
    Xarxa Quiroga, Nikhil Walani, Andrea Disanza, Albert Chavero, Alexandra Mittens, Francesc Tebar, Xavier Trepat, Robert G Parton, María Isabel Geli, Giorgio Scita, Marino Arroyo, Anabel-Lise Le Roux, Pere Roca-Cusachs.
      As cells migrate and experience forces from their surroundings, they constantly undergo mechanical deformations which reshape their plasma membrane (PM). To maintain homeostasis, cells need to detect and restore such changes, not only in terms of overall PM area and tension as previously described, but also in terms of local, nano-scale topography. Here we describe a novel phenomenon, by which cells sense and restore mechanically induced PM nano-scale deformations. We show that cell stretch and subsequent compression reshape the PM in a way that generates local membrane evaginations in the 100 nm scale. These evaginations are recognized by I-BAR proteins, which triggers a burst of actin polymerization mediated by Rac1 and Arp2/3. The actin polymerization burst subsequently re-flattens the evagination, completing the mechanochemical feedback loop. Our results demonstrate a new mechanosensing mechanism for PM shape homeostasis, with potential applicability in different physiological scenarios.
    Keywords:  cell biology; human; mouse; physics of living systems
    DOI:  https://doi.org/10.7554/eLife.72316
  24. Dev Cell. 2023 Sep 25. pii: S1534-5807(23)00438-0. [Epub ahead of print]58(18): 1701-1715.e8
    Single-cell epigenome analysis identifies molecular events controlling direct conversion of human fibroblasts to pancreatic ductal-like cells.
    Liangru Fei, Kaiyang Zhang, Nikita Poddar, Sampsa Hautaniemi, Biswajyoti Sahu.
      Cell fate can be reprogrammed by ectopic expression of lineage-specific transcription factors (TFs). However, the exact cell state transitions during transdifferentiation are still poorly understood. Here, we have generated pancreatic exocrine cells of ductal epithelial identity from human fibroblasts using a set of six TFs. We mapped the molecular determinants of lineage dynamics using a factor-indexing method based on single-nuclei multiome sequencing (FI-snMultiome-seq) that enables dissecting the role of each individual TF and pool of TFs in cell fate conversion. We show that transition from mesenchymal fibroblast identity to epithelial pancreatic exocrine fate involves two deterministic steps: an endodermal progenitor state defined by activation of HHEX with FOXA2 and SOX17 and a temporal GATA4 activation essential for the maintenance of pancreatic cell fate program. Collectively, our data suggest that transdifferentiation-although being considered a direct cell fate conversion method-occurs through transient progenitor states orchestrated by stepwise activation of distinct TFs.
    Keywords:  cell fate; direct reprogramming; epigenetics; exocrine pancreas; gene regulation; single-cell multiome sequencing; transcription factor
    DOI:  https://doi.org/10.1016/j.devcel.2023.08.023
  25. Cell Syst. 2023 Sep 22. pii: S2405-4712(23)00244-2. [Epub ahead of print]
    Studying stochastic systems biology of the cell with single-cell genomics data.
    Gennady Gorin, John J Vastola, Lior Pachter.
      Recent experimental developments in genome-wide RNA quantification hold considerable promise for systems biology. However, rigorously probing the biology of living cells requires a unified mathematical framework that accounts for single-molecule biological stochasticity in the context of technical variation associated with genomics assays. We review models for a variety of RNA transcription processes, as well as the encapsulation and library construction steps of microfluidics-based single-cell RNA sequencing, and present a framework to integrate these phenomena by the manipulation of generating functions. Finally, we use simulated scenarios and biological data to illustrate the implications and applications of the approach.
    Keywords:  Fokker-Planck equations; Markov chains; bioinformatics; chemical master equations; genomics; single-cell RNA sequencing; single-cell genomics; single-cell transcriptomics; stochastic differential equations; stochastic processes; transcriptomics
    DOI:  https://doi.org/10.1016/j.cels.2023.08.004
  26. Nature. 2023 Sep 27.
    Inhibition of fatty acid oxidation enables heart regeneration in adult mice.
    Xiang Li, Fan Wu, Stefan Günther, Mario Looso, Carsten Kuenne, Ting Zhang, Marion Wiesnet, Stephan Klatt, Sven Zukunft, Ingrid Fleming, Gernot Poschet, Astrid Wietelmann, Ann Atzberger, Michael Potente, Xuejun Yuan, Thomas Braun.
      Postnatal maturation of cardiomyocytes is characterized by a metabolic switch from glycolysis to fatty acid oxidation, chromatin reconfiguration and exit from the cell cycle, instating a barrier for adult heart regeneration1,2. Here, to explore whether metabolic reprogramming can overcome this barrier and enable heart regeneration, we abrogate fatty acid oxidation in cardiomyocytes by inactivation of Cpt1b. We find that disablement of fatty acid oxidation in cardiomyocytes improves resistance to hypoxia and stimulates cardiomyocyte proliferation, allowing heart regeneration after ischaemia-reperfusion injury. Metabolic studies reveal profound changes in energy metabolism and accumulation of α-ketoglutarate in Cpt1b-mutant cardiomyocytes, leading to activation of the α-ketoglutarate-dependent lysine demethylase KDM5 (ref. 3). Activated KDM5 demethylates broad H3K4me3 domains in genes that drive cardiomyocyte maturation, lowering their transcription levels and shifting cardiomyocytes into a less mature state, thereby promoting proliferation. We conclude that metabolic maturation shapes the epigenetic landscape of cardiomyocytes, creating a roadblock for further cell divisions. Reversal of this process allows repair of damaged hearts.
    DOI:  https://doi.org/10.1038/s41586-023-06585-5
  27. Carcinogenesis. 2023 Sep 25. pii: bgad068. [Epub ahead of print]
    An integrated analysis identifies six molecular subtypes of pancreatic ductal adenocarcinoma revealing cellular and molecular landscape.
    Lixing Li, Lu Shen, Hao Wu, Mo Li, Luan Chen, Qiang Zhou, Jingsong Ma, Cong Huai, Wei Zhou, Muyun Wei, Mingzhe Zhao, Xianglong Zhao, Huihui Du, Bixuan Jiang, Yidan Sun, Na Zhang, Shengying Qin, Tonghai Xing.
      Pancreatic ductal adenocarcinoma (PDA) has been found to have a high mortality rate. Despite continuous efforts, current histopathological classification is insufficient to guide individualized therapies of PDA. We first define the molecular subtypes of PDA (MSOP) based on a meta cohort of 845 samples from 11 PDA datasets. We then performed functional analyses involving immunity, fibrosis, and metabolism. We recognized six molecular subtypes with different survival statistics and molecular composition. The squamous basal-like (SBL) subtype had a poor prognosis and high infiltration of ENO1 + (Enolase 1)/ADM + (Adrenomedullin) cancer-associated fibroblasts (CAFs). The immune mesenchymal-like (IML) subtype and the normal mesenchymal-like (NML) subtype were characterized by genes associated with ECM (Extracellular matrix) activities and immune responses, having favorable prognoses. IML was featured by elevated exhausted immune signaling and inflammatory CAFs infiltration, whereas NML was featured with myofibroblastic CAFs infiltration. The exocrine-like (EL) subtype was high in exocrine signals, while the pure classical-like (PCL) subtype lacked immunocytes infiltration. The quiescent-like (QL) subtype had diminished metabolic signaling and high infiltration of NK cells. SBL, IML, and NML were enriched in innate anti-PD-1 resistance signatures. In sum, this MSOP depicts a vivid cell-to-molecular atlas of the tumor microenvironment of PDA and might facilitate to design a precise combination of therapies that target immunity, metabolism, and stroma.
    Keywords:  cancer-associated fibroblasts; molecular subtypes; pancreatic ductal adenocarcinoma; scRNA-seq; transcriptome analysis
    DOI:  https://doi.org/10.1093/carcin/bgad068
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