bims-cagime 2024-10-27 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2024‒10‒27
35 papers selected by
Kıvanç Görgülü, Technical University of Munich

Recruitment of autophagy initiator TAX1BP1 advances aggrephagy from cargo collection to sequestration.
Generation of Murine Cancer Cell Lines.
Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
Stromal reprogramming overcomes resistance to RAS-MAPK inhibition to improve pancreas cancer responses to cytotoxic and immune therapy.
Dietary pro-oxidant therapy by a vitamin K precursor targets PI 3-kinase VPS34 function.
Leveraging the tug-of-war with genomic retroelements to enhance immunotherapy of pancreatic cancer.
Cyclophilin D plays a critical role in the survival of senescent cells.
Suppression of dystroglycan function accompanies pancreatic acinar-to-ductal metaplasia and favours dysplasia development.
Selenocysteine tRNA methylation promotes oxidative stress resistance in melanoma metastasis.
Protocol for whole-slide image analysis of human multiplexed tumor tissues using QuPath and R.
Protocol using ex vivo mouse brain slice culture mimicking in vivo conditions to study tumor growth and cell motility of glioblastoma cells.
Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy.
The role of the dynamic epigenetic landscape in senescence: orchestrating SASP expression.
Multiplex Genomic Tagging of Mammalian ATG8s to Study Autophagy.
PhysiMeSS - a new physiCell addon for extracellular matrix modelling.
The preoperative prediction of lymph node metastasis of resectable pancreatic ductal adenocarcinoma using dual-layer spectral computed tomography.
A two-front nutrient supply environment fuels small intestinal physiology through differential regulation of nutrient absorption and host defense.
Glutamine sensing licenses cholesterol synthesis.
Using Spectral Flow Cytometry to Characterize Anti-Tumor Immunity in Orthotopic and Subcutaneous Mouse Models of Cancer.
Mitochondrial mechanotransduction through MIEF1 coordinates the nuclear response to forces.
Programmable Lipid Bilayer Tension-Control Apparatus for Quantitative Mechanobiology.
Lipid Compositions of Liquid-Ordered and Liquid-Disordered Phases in Ternary Membranes of Sphingomyelin, Cholesterol, and Dioleoylphosphatidylcholine Determined by 2H NMR: Stearoyl-Sphingomyelin Compared with Its Palmitoyl Counterpart.
New model to predict survival in advanced pancreatic ductal adenocarcinoma patients by measuring GGT and LDH levels and monocyte count.
Nuclear proteasomes as a backup for autophagy: interconnected proteostasis pathways.
Cancer cachexia.
Differential stiffness between brain vasculature and parenchyma promotes metastatic infiltration through vessel co-option.
Mitochondrial fatty acid oxidation drives senescence.
The double-edged sword of eliminating senescent cells.
metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels.
Genetically predicted gut bacteria, circulating bacteria-associated metabolites and pancreatic ductal adenocarcinoma: a Mendelian randomisation study.
Transgelin 2 guards T cell lipid metabolism and antitumour function.
NFAT5 governs cellular plasticity-driven resistance to KRAS-targeted therapy in pancreatic cancer.
Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq.
Intercellular fluid dynamics in tissue morphogenesis.
Emerging strategies to investigate the biology of early cancer.

EMBO J. 2024 Oct 24.

Recruitment of autophagy initiator TAX1BP1 advances aggrephagy from cargo collection to sequestration.

Bernd Bauer, Jonas Idinger, Martina Schuschnig, Luca Ferrari, Sascha Martens.

  Autophagy mediates the degradation of harmful material within lysosomes. In aggrephagy, the pathway mediating the degradation of aggregated, ubiquitinated proteins, this cargo material is collected in larger condensates prior to its sequestration by autophagosomes. In this process, the autophagic cargo receptors SQSTM1/p62 and NBR1 drive cargo condensation, while TAX1BP1, which binds to NBR1, recruits the autophagy machinery to facilitate autophagosome biogenesis at the condensates. The mechanistic basis for the TAX1BP1-mediated switch from cargo collection to its sequestration is unclear. Here we show that TAX1BP1 is not a constitutive component of the condensates. Its recruitment correlates with the induction of autophagosome biogenesis. TAX1BP1 is sufficient to recruit the TBK1 kinase via the SINTBAD adapter. We define the NBR1-TAX1BP1-binding site, which is adjacent to the GABARAP/LC3 interaction site, and demonstrate that the recruitment of TAX1BP1 to cargo mimetics can be enhanced by an increased ubiquitin load. Our study suggests that autophagosome biogenesis is initiated once sufficient cargo is collected in the condensates.

Keywords:  Aggrephagy p62; NBR1; Quality Control; Selective Autophagy; TAX1BP1

DOI:  https://doi.org/10.1038/s44318-024-00280-5
Curr Protoc. 2024 Oct;4(10): e70037

Generation of Murine Cancer Cell Lines.

Cheryl Zhang, Anthony Lin, Xiang Chen, Yi-Chieh Nancy Du.

  Cancer cell lines are important tools to investigate the biology of cancer and test hypotheses to improve cancer treatments. A major challenge in establishing epithelial cancer cell lines is the removal of cancer-associated fibroblasts (CAFs). CAFs are abundant within the tumor microenvironment. CAFs generally proliferate faster than epithelial cancer cells in culture. CAFs can be mistakenly identified as cancer cells, especially when cancer cells display spindle-shaped morphology. Among all cancer types, pancreatic ductal adenocarcinoma (PDAC) is characterized by an abundant desmoplastic stroma. Here, we describe protocols for establishing epithelial cancer cell lines from mouse models of PDAC and verifying that they are not CAFs. The approach is cost-effective and can be used for other types of cancer. If needed, CAF cell lines can also be established and preserved using this protocol. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Isolation of cells from tumors Basic Protocol 2: Isolation and cryopreservation of cancer cell clones Basic Protocol 3: Assessment of the identity of cancer cell lines and CAFs by western blotting.

Keywords:  cell culture; cell line; epithelial cancer cells; fibroblast; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1002/cpz1.70037
Cell Chem Biol. 2024 Oct 14. pii: S2451-9456(24)00404-5. [Epub ahead of print]

Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.

Kelly H Sokol, Cameron J Lee, Thomas J Rogers, Althea Waldhart, Abigail E Ellis, Sahithi Madireddy, Samuel R Daniels, Rachel Rae J House, Xinyu Ye, Mary Olesnavich, Amy Johnson, Benjamin R Furness, Ryan D Sheldon, Evan C Lien.

  Ferroptosis is a form of cell death caused by lipid peroxidation that is emerging as a target for cancer therapy, highlighting the need to identify factors that govern ferroptosis susceptibility. Lipid peroxidation occurs primarily on phospholipids containing polyunsaturated fatty acids (PUFAs). Here, we show that even though extracellular lipid limitation reduces cellular PUFA levels, lipid-starved cancer cells are paradoxically more sensitive to ferroptosis. Using mass spectrometry-based lipidomics with stable isotope fatty acid labeling, we show that lipid limitation induces a fatty acid trafficking pathway in which PUFAs are liberated from triglycerides to synthesize highly unsaturated PUFAs such as arachidonic and adrenic acid. These PUFAs then accumulate in phospholipids, including ether phospholipids, to promote ferroptosis sensitivity. Therefore, PUFA levels within cancer cells do not necessarily correlate with ferroptosis susceptibility. Rather, how cancer cells respond to extracellular lipid levels by trafficking PUFAs into proper phospholipid pools contributes to their sensitivity to ferroptosis.

Keywords:  cancer; ferroptosis; lipid metabolism; phospholipids; polyunsaturated fatty acids; triglycerides

DOI:  https://doi.org/10.1016/j.chembiol.2024.09.008
Sci Transl Med. 2024 Oct 23. 16(770): eado2402

Stromal reprogramming overcomes resistance to RAS-MAPK inhibition to improve pancreas cancer responses to cytotoxic and immune therapy.

Xiuting Liu, John M Baer, Meredith L Stone, Brett L Knolhoff, Graham D Hogg, Madeleine C Turner, Yu-Lan Kao, Alyssa G Weinstein, Faiz Ahmad, Jie Chen, Andrew D Schmidt, Jeffrey A Klomp, Heather Coho, Kayjana S Coho, Silvia Coma, Jonathan A Pachter, Kirsten L Bryant, Liang-I Kang, Kian-Huat Lim, Gregory L Beatty, David G DeNardo.

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy that is often resistant to therapy. An immune suppressive tumor microenvironment (TME) and oncogenic mutations in KRAS have both been implicated as drivers of resistance to therapy. Mitogen-activated protein kinase (MAPK) inhibition has not yet shown clinical efficacy, likely because of rapid acquisition of tumor-intrinsic resistance. However, the unique PDAC TME may also be a driver of resistance. We found that long-term focal adhesion kinase (FAK) inhibitor treatment led to hyperactivation of the RAS/MAPK pathway in PDAC cells in mouse models and tissues from patients with PDAC. Concomitant inhibition of both FAK (with VS-4718) and rapidly accelerated fibrosarcoma and MAPK kinase (RAF-MEK) (with avutometinib) induced tumor growth inhibition and increased survival across multiple PDAC mouse models. In the TME, cancer-associated fibroblasts (CAFs) impaired the down-regulation of MYC by RAF-MEK inhibition in PDAC cells, resulting in resistance. By contrast, FAK inhibition reprogramed CAFs to suppress the production of FGF1, which can drive resistance to RAF-MEK inhibition. The addition of chemotherapy to combined FAK and RAF-MEK inhibition led to tumor regression, a decrease in liver metastasis, and improved survival in KRAS-driven PDAC mouse models. Combination of FAK and RAF-MEK inhibition alone improved antitumor immunity and priming of T cell responses in response to chemotherapy. These findings provided the rationale for an ongoing clinical trial evaluating the efficacy of avutometinib and defactinib in combination with gemcitabine and nab-paclitaxel in patients with PDAC and may suggest further paths for combined stromal and tumor-targeting therapies.

DOI: https://doi.org/10.1126/scitranslmed.ado2402
Science. 2024 Oct 25. 386(6720): eadk9167

Dietary pro-oxidant therapy by a vitamin K precursor targets PI 3-kinase VPS34 function.

Manojit M Swamynathan, Shan Kuang, Kaitlin E Watrud, Mary R Doherty, Charlotte Gineste, Grinu Mathew, Grace Q Gong, Hilary Cox, Eileen Cheng, David Reiss, Jude Kendall, Diya Ghosh, Colleen R Reczek, Xiang Zhao, Tali Herzka, Saulė Špokaitė, Antoine N Dessus, Seung Tea Kim, Olaf Klingbeil, Juan Liu, Dawid G Nowak, Habeeb Alsudani, Tse-Luen Wee, Youngkyu Park, Francesca Minicozzi, Keith Rivera, Ana S Almeida, Kenneth Chang, Ram P Chakrabarty, John E Wilkinson, Phyllis A Gimotty, Sarah D Diermeier, Mikala Egeblad, Christopher R Vakoc, Jason W Locasale, Navdeep S Chandel, Tobias Janowitz, James B Hicks, Michael Wigler, Darryl J Pappin, Roger L Williams, Paolo Cifani, David A Tuveson, Jocelyn Laporte, Lloyd C Trotman.

Men taking antioxidant vitamin E supplements have increased prostate cancer (PC) risk. However, whether pro-oxidants protect from PC remained unclear. In this work, we show that a pro-oxidant vitamin K precursor [menadione sodium bisulfite (MSB)] suppresses PC progression in mice, killing cells through an oxidative cell death: MSB antagonizes the essential class III phosphatidylinositol (PI) 3-kinase VPS34-the regulator of endosome identity and sorting-through oxidation of key cysteines, pointing to a redox checkpoint in sorting. Testing MSB in a myotubular myopathy model that is driven by loss of MTM1-the phosphatase antagonist of VPS34-we show that dietary MSB improved muscle histology and function and extended life span. These findings enhance our understanding of pro-oxidant selectivity and show how definition of the pathways they impinge on can give rise to unexpected therapeutic opportunities.

DOI: https://doi.org/10.1126/science.adk9167
Gut. 2024 Oct 22. pii: gutjnl-2024-333702. [Epub ahead of print]

Leveraging the tug-of-war with genomic retroelements to enhance immunotherapy of pancreatic cancer.

Elisa Espinet, Gioacchino Natoli.



Keywords:  IMMUNOTHERAPY; PANCREATIC CANCER

DOI:  https://doi.org/10.1136/gutjnl-2024-333702
EMBO J. 2024 Oct 24.

Cyclophilin D plays a critical role in the survival of senescent cells.

Margherita Protasoni, Vanessa López-Polo, Camille Stephan-Otto Attolini, Julian Brandariz, Nicolas Herranz, Joaquin Mateo, Sergio Ruiz, Oscar Fernandez-Capetillo, Marta Kovatcheva, Manuel Serrano.

  Senescent cells play a causative role in many diseases, and their elimination is a promising therapeutic strategy. Here, through a genome-wide CRISPR/Cas9 screen, we identify the gene PPIF, encoding the mitochondrial protein cyclophilin D (CypD), as a novel senolytic target. Cyclophilin D promotes the transient opening of the mitochondrial permeability transition pore (mPTP), which serves as a failsafe mechanism for calcium efflux. We show that senescent cells exhibit a high frequency of transient CypD/mPTP opening events, known as 'flickering'. Inhibition of CypD using genetic or pharmacologic tools, including cyclosporin A, leads to the toxic accumulation of mitochondrial Ca2+ and the death of senescent cells. Genetic or pharmacological inhibition of NCLX, another mitochondrial calcium efflux channel, also leads to senolysis, while inhibition of the main Ca2+ influx channel, MCU, prevents senolysis induced by CypD inhibition. We conclude that senescent cells are highly vulnerable to elevated mitochondrial Ca2+ ions, and that transient CypD/mPTP opening is a critical adaptation mechanism for the survival of senescent cells.

Keywords:  Cellular Senescence; Cyclophilin D; Mitochondria; Senolytic Therapy; mPTP Flickering

DOI:  https://doi.org/10.1038/s44318-024-00259-2
J Pathol. 2024 Oct 22.

Suppression of dystroglycan function accompanies pancreatic acinar-to-ductal metaplasia and favours dysplasia development.

Ge Huang, Luke Ternes, Christian Lanciault, Kevin MacPherson-Hawthorne, Young Hwan Chang, Rosalie C Sears, John L Muschler.

  The basement membrane (BM) is among the predominant microenvironmental factors of normal epithelia and of precancerous epithelial lesions. Evidence suggests that the BM functions not only as a barrier to tumour invasion but also as an active tumour-suppressing signalling substrate during premalignancy. However, the molecular foundations of such mechanisms have not been elucidated. Here we explore potential tumour-suppressing functions of the BM during precancer evolution, focusing on the expression and function of the extracellular matrix receptor dystroglycan in the pancreas and pancreatic disease. We show that the dystroglycan protein is highly expressed in the acinar compartment of the normal pancreas but lower in the ductal compartment. Moreover, there is a strong suppression of dystroglycan protein expression with acinar-to-ductal metaplasia in chronic pancreatitis and in all stages of pancreatic precancer and cancer evolution, from acinar-to-ductal metaplasia to dysplasia to adenocarcinoma. The conditional knockout of dystroglycan in the murine pancreas produced little evidence of developmental or functional deficiency. However, conditional deletion of dystroglycan expression in the context of oncogenic Kras expression led to a clear acceleration of pancreatic disease evolution, including accelerated dysplasia development and decreased survival. These data establish dystroglycan as a suppressor of pancreatic dysplasia development and one that is muted in chronic pancreatitis and at the earliest stages of oncogene-induced transformation. We conclude that dystroglycan is an important mediator of the tumour-suppressing functions of the BM during precancer evolution and that reduced dystroglycan function increases cancer risk, highlighting the dynamics of cell-BM interactions as important determinants of early cancer progression. © 2024 The Pathological Society of Great Britain and Ireland.

Keywords:  basement membrane; dysplasia; extracellular matrix; precancer

DOI:  https://doi.org/10.1002/path.6356
Nat Cancer. 2024 Oct 22.

Selenocysteine tRNA methylation promotes oxidative stress resistance in melanoma metastasis.

Leona A Nease, Kellsey P Church, Ines Delclaux, Shino Murakami, Maider Astorkia, Marwa Zerhouni, Graciela Cascio, Riley O Hughes, Kelsey N Aguirre, Paul Zumbo, Lukas E Dow, Samie Jaffrey, Doron Betel, Elena Piskounova.

Selenocysteine-containing proteins play a central role in redox homeostasis. Their translation is a highly regulated process and is dependent on two tRNASec isodecoders differing by a single 2'-O-ribose methylation called Um34. Here we characterized FTSJ1 as the Um34 methyltransferase and show that its activity is required for efficient selenocysteine insertion at the UGA stop codon during translation. Specifically, loss of Um34 leads to ribosomal stalling and decreased UGA recoding. FTSJ1-deficient cells are more sensitive to oxidative stress and show decreased metastatic colonization in xenograft models of melanoma metastasis. We found that FTSJ1 mediates efficient translation of selenoproteins essential for the cellular antioxidant response. Our findings uncover a role for tRNASec Um34 modification in oxidative stress resistance and highlight FTSJ1 as a potential therapeutic target specific for metastatic disease.

DOI: https://doi.org/10.1038/s43018-024-00844-8
STAR Protoc. 2024 Oct 24. pii: S2666-1667(24)00435-0. [Epub ahead of print]5(4): 103270

Protocol for whole-slide image analysis of human multiplexed tumor tissues using QuPath and R.

Amelie Franken, Michel Bila, Diether Lambrechts.

  The spatial organization of cells within tissues aids in understanding physiological and pathological processes, as well as elucidating the mechanisms of action underlying treatments. We present a protocol for analyzing image-based spatial proteomics data. To illustrate, we focus on whole-slide images of human multiplexed tumor tissues acquired using the PhenoCycler-Fusion 2.0 platform from Akoya Biosciences. We describe steps for cell segmentation, cell phenotyping, intercellular distance calculation, and data visualization. For complete details on the use and execution of this protocol, please refer to Franken et al.1.

Keywords:  Bioinformatics; Cancer; Immunology; Proteomics; Single Cell

DOI:  https://doi.org/10.1016/j.xpro.2024.103270
STAR Protoc. 2024 Oct 18. pii: S2666-1667(24)00566-5. [Epub ahead of print]5(4): 103401

Protocol using ex vivo mouse brain slice culture mimicking in vivo conditions to study tumor growth and cell motility of glioblastoma cells.

Laura Neises, Catherine Delbrouck, Anne Schuster, Mahsa Rezaipour, Kim Eiden, Anais Oudin, Carina Fabian, Simone P Niclou, Anna Golebiewska, Johannes Meiser.

  Herein, we present an ex vivo approach to study glioblastoma (GBM) cell motility in viable mouse brain slice cultures, closely mimicking in vivo features. We detail the preparation and culturing of mouse brain slices followed by tumor cell injection, allowing for the analysis of different aspects of the cellular migration and invasion process. Our assay facilitates testing diverse perturbations including genetic modifications and treatments in a physiological context. Thus, the protocol provides a compromise between in vitro assays and in vivo models. For complete details on the use and execution of this protocol, please refer to Delbrouck et al.1 and Schuster et al.2.

Keywords:  cancer; cell culture; tissue engineering

DOI:  https://doi.org/10.1016/j.xpro.2024.103401
Proc Natl Acad Sci U S A. 2024 Oct 29. 121(44): e2408071121

Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy.

Sergio Alejandro Poveda-Cuevas, Kateryna Lohachova, Borna Markusic, Ivan Dikic, Gerhard Hummer, Ramachandra M Bhaskara.

  Intrinsically disordered regions (IDRs) play a pivotal role in organellar remodeling. They transduce signals across membranes, scaffold signaling complexes, and mediate vesicular traffic. Their functions are regulated by constraining conformational ensembles through specific intra- and intermolecular interactions, physical tethering, and posttranslational modifications. The endoplasmic reticulum (ER)-phagy receptor FAM134B/RETREG1, known for its reticulon homology domain (RHD), includes a substantial C-terminal IDR housing the LC3 interacting motif. Beyond engaging the autophagic machinery, the function of the FAM134B-IDR is unclear. Here, we investigate the characteristics of the FAM134B-IDR by extensive modeling and molecular dynamics simulations. We present detailed structural models for the IDR, mapping its conformational landscape in solution and membrane-anchored configurations. Our analysis reveals that depending on the membrane anchor, the IDRs collapse onto the membrane and induce positive membrane curvature to varying degrees. The charge patterns underlying this Janus-like behavior are conserved across other ER-phagy receptors. We found that IDRs alone are sufficient to sense curvature. When combined with RHDs, they intensify membrane remodeling and drive efficient protein clustering, leading to faster budding, thereby amplifying RHD remodeling functions. Our simulations provide a perspective on IDRs of FAM134B, their Janus-like membrane interactions, and the resulting modulatory functions during large-scale ER remodeling.

Keywords:  ER remodeling; IDRs; conformational entropy; curvature induction; structural ensemble

DOI:  https://doi.org/10.1073/pnas.2408071121
NPJ Aging. 2024 Oct 24. 10(1): 48

The role of the dynamic epigenetic landscape in senescence: orchestrating SASP expression.

Nirmalya Dasgupta, Rouven Arnold, Anais Equey, Armin Gandhi, Peter D Adams.

Senescence and epigenetic alterations stand out as two well-characterized hallmarks of aging. When cells become senescent, they cease proliferation and release inflammatory molecules collectively termed the Senescence-Associated Secretory Phenotype (SASP). Senescence and SASP are implicated in numerous age-related diseases. Senescent cell nuclei undergo epigenetic reprogramming, which intricately regulates SASP expression. This review outlines the current understanding of how senescent cells undergo epigenetic changes and how these alterations govern SASP expression.

DOI: https://doi.org/10.1038/s41514-024-00172-2
J Biol Chem. 2024 Oct 19. pii: S0021-9258(24)02410-4. [Epub ahead of print] 107908

Multiplex Genomic Tagging of Mammalian ATG8s to Study Autophagy.

Korina Goldin-Azulay, Milana Fraiberg, Olena Trofimyuk, Yishai Levin, Nina Reuven, Ekaterina Kopitman, Zvulun Elazar.

  Atg8 proteins play a crucial role in autophagy. There is a single Atg8 isoform in yeast, while mammals have up to seven homologs categorized into LC3s and GABARAPs. The GABARAP subfamily consists of GABARAP, GABARAPL1, and GABARAPL2/GATE16, implicated in various stages along the pathway. However, the intricacies among GABARAP proteins are complex and require a more precise delineation. Here, we introduce a new cellular platform to study autophagy using CRISPR/Cas9-mediated tagging of endogenous genes of the GABARAP subfamily with different fluorescent proteins. This platform allows robust examination of autophagy by flow cytometry of cell populations and monitoring of GABARAP homologs at single-cell resolution using fluorescence microscopy. Strikingly, the simultaneous labeling of the different endogenous GABARAPs allows the identification and isolation of autophagosomes differentially marked by these proteins. Using this system, we found that the different GABARAPs are associated with different autophagosomes. We argue that this new cellular platform will be crucial in studying the unique roles of individual GABARAP proteins in autophagy and other putative cellular processes.

Keywords:  CRISPR/Cas; autophagy; degradation; gene knockout; proteomics; starvation

DOI:  https://doi.org/10.1016/j.jbc.2024.107908
GigaByte. 2024 ;2024 gigabyte136

PhysiMeSS - a new physiCell addon for extracellular matrix modelling.

Vincent Noël, Marco Ruscone, Robyn Shuttleworth, Cicely K Macnamara.

The extracellular matrix, composed of macromolecules like collagen fibres, provides structural support to cells and acts as a barrier that metastatic cells degrade to spread beyond the primary tumour. While agent-based frameworks, such as PhysiCell, can simulate the spatial dynamics of tumour evolution, they only implement cells as circles (2D) or spheres (3D). To model the extracellular matrix as a network of fibres, we require a new type of agent represented by line segments (2D) or cylinders (3D). Here, we present PhysiMeSS, an addon of PhysiCell, introducing a new agent type to describe fibres and their physical interactions with cells and other fibres. PhysiMeSS implementation is available at https://github.com/PhysiMeSS/PhysiMeSS and in the official PhysiCell repository. We provide examples describing the possibilities of this framework. This tool may help tackle important biological questions, such as diseases linked to dysregulation of the extracellular matrix or the processes leading to cancer metastasis.

DOI: https://doi.org/10.46471/gigabyte.136
Eur Radiol. 2024 Oct 24.

The preoperative prediction of lymph node metastasis of resectable pancreatic ductal adenocarcinoma using dual-layer spectral computed tomography.

Yi Chen, Tiansong Xie, Lei Chen, Zehua Zhang, Yu Wang, Zhengrong Zhou, Wei Liu.

  OBJECTIVES: To investigate the value of dual-layer spectral computed tomography (DLCT) parameters derived from primary tumors in predicting lymph node metastasis (LNM) of resectable pancreatic ductal adenocarcinoma (PDAC).MATERIALS AND METHODS: In this retrospective study, patients with resectable PDAC who underwent DLCT within 2-week intervals before surgery were enrolled and randomly divided into training and validation sets at a 7:3 ratio. The patients' clinical data, CT morphological features, and DLCT parameters were analyzed. Univariate and multivariate logistic analyses were used to identify the predictors and construct a predictive model, and receiver operator characteristic (ROC) curves were programmed to evaluate the predictive efficacy.
RESULTS: We enrolled 107 patients (44 patients with LNM and 63 patients without LNM). Among all variables, iodine concentration in the venous phase, extracellular volume, and tumor size were identified as independent predictors of LNM. The nomogram model, incorporating the two DLCT parameters and the morphological feature, achieved an area under the curve (AUC) of 0.877 (95% confidence interval [CI]: 0.803-0.952) and 0.842 (95% CI: 0.707-0.977) for predicting LNM in the training and validation sets, respectively. Furthermore, the AUC of the nomogram model was greater than that of morphological features of lymph nodes in the training (AUC = 0.877 vs. 0.570) and validation (AUC = 0.842 vs. 0.583) sets.
CONCLUSIONS: DLCT has the potential to predict LNM in patients with resectable PDAC and show a better predictive value than morphological features of lymph nodes.
KEY POINTS: Question Morphological features of lymph nodes are of limited value in detecting metastatic lymph nodes in pancreatic ductal adenocarcinoma (PDAC). Findings Dual-layer spectral computed tomography (DLCT) parameters and morphological features derived from PDAC lesions show good preoperatively predictive efficacy for lymph node metastasis. Clinical relevance The proposed DLCT-based nomogram model may serve as an effective and convenient tool for preoperatively predicting lymph node metastasis of resectable PDAC.

Keywords:  Dual-layer spectral CT; Lymph node metastasis; Nomogram; Pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1007/s00330-024-11143-2
Cell. 2024 Oct 19. pii: S0092-8674(24)00903-6. [Epub ahead of print]

A two-front nutrient supply environment fuels small intestinal physiology through differential regulation of nutrient absorption and host defense.

Jian Zhang, Ruonan Tian, Jia Liu, Jie Yuan, Siwen Zhang, Zhexu Chi, Weiwei Yu, Qianzhou Yu, Zhen Wang, Sheng Chen, Mobai Li, Dehang Yang, Tianyi Hu, Qiqi Deng, Xiaoyang Lu, Yidong Yang, Rongbin Zhou, Xue Zhang, Wanlu Liu, Di Wang.

  The small intestine contains a two-front nutrient supply environment created by luminal dietary and microbial metabolites (enteral side) and systemic metabolites from the host (serosal side). Yet, it is unknown how each side contributes differentially to the small intestinal physiology. Here, we generated a comprehensive, high-resolution map of the small intestinal two-front nutrient supply environment. Using in vivo tracing of macronutrients and spatial metabolomics, we visualized the spatiotemporal dynamics and cell-type tropism in nutrient absorption and the region-specific metabolic heterogeneity within the villi. Specifically, glutamine from the enteral side fuels goblet cells to support mucus production, and the serosal side loosens the epithelial barrier by calibrating fungal metabolites. Disorganized feeding patterns, akin to the human lifestyle of skipping breakfast, increase the risk of metabolic diseases by inducing epithelial memory of lipid absorption. This study improves our understanding of how the small intestine is spatiotemporally regulated by its unique nutritional environment.

Keywords:  adaptation; breakfast skipping; in vivo metabolite tracing; metabolic heterogeneity; multi-omics; the small intestine; two-front nutrient supply; zonated function of enterocyte

DOI:  https://doi.org/10.1016/j.cell.2024.08.012
EMBO J. 2024 Oct 21.

Glutamine sensing licenses cholesterol synthesis.

Bruna Martins Garcia, Philipp Melchinger, Tania Medeiros, Sebastian Hendrix, Kavan Prabhu, Mauro Corrado, Jenina Kingma, Andrej Gorbatenko, Soni Deshwal, Matteo Veronese, Luca Scorrano, Erika Pearce, Patrick Giavalisco, Noam Zelcer, Lena Pernas.

  The mevalonate pathway produces essential lipid metabolites such as cholesterol. Although this pathway is negatively regulated by metabolic intermediates, little is known of the metabolites that positively regulate its activity. We found that the amino acid glutamine is required to activate the mevalonate pathway. Glutamine starvation inhibited cholesterol synthesis and blocked transcription of the mevalonate pathway-even in the presence of glutamine derivatives such as ammonia and α-ketoglutarate. We pinpointed this glutamine-dependent effect to a loss in the ER-to-Golgi trafficking of SCAP that licenses the activation of SREBP2, the major transcriptional regulator of cholesterol synthesis. Both enforced Golgi-to-ER retro-translocation and the expression of a nuclear SREBP2 rescued mevalonate pathway activity during glutamine starvation. In a cell model of impaired mitochondrial respiration in which glutamine uptake is enhanced, SREBP2 activation and cellular cholesterol were increased. Thus, the mevalonate pathway senses and is activated by glutamine at a previously uncharacterized step, and the modulation of glutamine synthesis may be a strategy to regulate cholesterol levels in pathophysiological conditions.

Keywords:  Cholesterol; HMGCR; MFN2; Nutrient Sensing; SREBP2

DOI:  https://doi.org/10.1038/s44318-024-00269-0
Curr Protoc. 2024 Oct;4(10): e70032

Using Spectral Flow Cytometry to Characterize Anti-Tumor Immunity in Orthotopic and Subcutaneous Mouse Models of Cancer.

Giampiero Valenzano, Shannon N Russell, Simei Go, Eric O'Neill, Keaton I Jones.

  Mouse models remain at the forefront of immuno-oncology research, providing invaluable insights into the complex interactions between the immune system and developing tumors. While several flow cytometry panels have been developed to study cancer immunity in mice, most are limited in their capacity to address the complexity of anti-cancer immune responses. For example, many of the panels developed to date focus on a restricted number of leukocyte populations (T cells or antigen-presenting cells), failing to include the multitude of other subsets that participate in anti-cancer immunity. In addition, these panels were developed using blood or splenic leukocytes. While the immune composition of the blood or spleen can provide information on systemic immune responses to cancer, it is in the tumor microenvironment (TME) that local immunity takes place. Therefore, we optimized this spectral flow cytometry panel to identify the chief cell types that take part in cancer immunity using immune cells from cancer tissue. We used pancreatic tumors implanted both orthotopically and subcutaneously to demonstrate the panel's flexibility and suitability in diverse mouse models. The panel was also validated in peripheral immune districts (the blood, spleen, and liver of tumor-bearing mice) to allow comparisons between local and systemic anti-tumor immunity. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Tumor induction-Orthotopic Alternate Protocol: Tumor induction-Subcutaneous Basic Protocol 2: Preparation of single-cell suspensions from the tumor, spleen, liver, and blood of tumor-bearing mice Basic Protocol 3: Staining single-cell suspensions from the tumor, spleen, liver, and blood of tumor-bearing mice.

Keywords:  cancer; immuno‐oncology; mouse models; spectral flow cytometry; tumor microenvironment

DOI:  https://doi.org/10.1002/cpz1.70032
Nat Cell Biol. 2024 Oct 21.

Mitochondrial mechanotransduction through MIEF1 coordinates the nuclear response to forces.

Patrizia Romani, Giada Benedetti, Martina Cusan, Mattia Arboit, Carmine Cirillo, Xi Wu, Georgia Rouni, Vassiliki Kostourou, Mariaceleste Aragona, Costanza Giampietro, Paolo Grumati, Graziano Martello, Sirio Dupont.

Tissue-scale architecture and mechanical properties instruct cell behaviour under physiological and diseased conditions, but our understanding of the underlying mechanisms remains fragmentary. Here we show that extracellular matrix stiffness, spatial confinements and applied forces, including stretching of mouse skin, regulate mitochondrial dynamics. Actomyosin tension promotes the phosphorylation of mitochondrial elongation factor 1 (MIEF1), limiting the recruitment of dynamin-related protein 1 (DRP1) at mitochondria, as well as peri-mitochondrial F-actin formation and mitochondrial fission. Strikingly, mitochondrial fission is also a general mechanotransduction mechanism. Indeed, we found that DRP1- and MIEF1/2-dependent fission is required and sufficient to regulate three transcription factors of broad relevance-YAP/TAZ, SREBP1/2 and NRF2-to control cell proliferation, lipogenesis, antioxidant metabolism, chemotherapy resistance and adipocyte differentiation in response to mechanical cues. This extends to the mouse liver, where DRP1 regulates hepatocyte proliferation and identity-hallmark YAP-dependent phenotypes. We propose that mitochondria fulfil a unifying signalling function by which the mechanical tissue microenvironment coordinates complementary cell functions.

DOI: https://doi.org/10.1038/s41556-024-01527-3
ACS Nano. 2024 Oct 22.

Programmable Lipid Bilayer Tension-Control Apparatus for Quantitative Mechanobiology.

Yuka Matsuki, Masayuki Iwamoto, Takahisa Maki, Masako Takashima, Toshiyuki Yoshida, Shigetoshi Oiki.

  The biological membrane is not just a platform for information processing but also a field of mechanics. The lipid bilayer that constitutes the membrane is an elastic body, generating stress upon deformation, while the membrane protein embedded therein deforms the bilayer through structural changes. Among membrane-protein interplays, various channel species act as tension-current converters for signal transduction, serving as elementary processes in mechanobiology. However, in situ studies in chaotically complex cell membranes are challenging, and characterizing the tension dependency of mechanosensitive channels remains semiquantitative owing to technical limitations. Here, we developed a programmable membrane tension-control apparatus on a lipid bilayer system. This synthetic membrane system [contact bubble bilayer (CBB)] uses pressure to drive bilayer tension changes via the Young-Laplace principle, whereas absolute bilayer tension is monitored in real-time through image analysis of the bubble geometry via the Young principle. Consequently, the mechanical nature of the system permits the implementation of closed-loop feedback control of bilayer tension (tension-clamp CBB), maintaining a constant tension for minutes and allowing stepwise tension changes within a hundred milliseconds in the tension range of 0.8 to 15 mN·m-1. We verified the system performance by examining the single-channel behavior of tension-dependent KcsA and TREK-1 potassium channels under scheduled tension time courses prescribed via visual interfaces. The result revealed steady-state activity and dynamic responses to the step tension changes, which are essential to the biophysical characterization of the channels. The apparatus explores a frontier for quantitative mechanobiology studies and promotes the development of a tension-operating experimental robot.

Keywords:  TREK-1 channels; contact bubble bilayer; feedback control; flicker gating; imaging; lipid bilayer; membrane tension

DOI:  https://doi.org/10.1021/acsnano.4c09017
Langmuir. 2024 Oct 21.

Lipid Compositions of Liquid-Ordered and Liquid-Disordered Phases in Ternary Membranes of Sphingomyelin, Cholesterol, and Dioleoylphosphatidylcholine Determined by 2H NMR: Stearoyl-Sphingomyelin Compared with Its Palmitoyl Counterpart.

Shinya Hanashima, Ayana Yamanaka, Yuki Ibata, Tomokazu Yasuda, Yuichi Umegawa, Michio Murata.

Sphingomyelin (SM) and cholesterol are the major lipids in the signaling platforms of cell membranes, known as lipid rafts. In particular, SM with a stearoyl chain (C18-SM) is abundant in specific tissues such as the brain, the most cholesterol-rich organ, whereas the distribution of palmitoyl (C16)-SM is ubiquitous. Here, we reveal the differences between palmitoyl- and stearoyl-SM in lipid-lipid interactions based on the tie lines obtained from the 2H solid-state NMR spectra of bilayer systems composed of SM/dioleoylphosphatidylcholine/cholesterol 33:33:33 and 40:40:20. Lipid probes carrying position-selective deuterations, 10',10'-d2-SM, 24-d1-cholesterol, and 6″,6″-d2-dioleoyl-phosphatidylcholine, were incorporated into the membranes. 2H NMR peaks from these probes in the membranes directly provide the lipid compositions of the liquid-ordered (Lo) and liquid-disordered (Ld) regions. Without using bulky fluorescent groups, these probes allow us to obtain the end points of the tie lines in a ternary phase diagram based on the lever rule. Consequently, the tie lines of the stearoyl-SM membranes were steeper than those of the palmitoyl-SM membranes, indicating that cholesterol content was higher in the Lo domains of stearoyl-SM, regardless of the total concentration of unsaturated phospholipids. When comparing the content of unsaturated lipids in the Lo domain, the stearoyl-SM membranes had a higher content than palmitoyl-SM membranes. These results revealed that stearoyl-SM is suitable for stabilizing biologically functional microdomains in cholesterol-rich organs, whereas palmitoyl-SM may be better suited for stabilizing domains in tissue membranes with normal cholesterol content. The small but significant differences in the lipid interactions between stearoyl-SM and palmitoyl-SM may be related to the spatiotemporal formation of functional domains in biological environments.

DOI: https://doi.org/10.1021/acs.langmuir.4c03104
Front Oncol. 2024 ;14 1411096

New model to predict survival in advanced pancreatic ductal adenocarcinoma patients by measuring GGT and LDH levels and monocyte count.

Rocío Del Campo-Pedrosa, Alfonso Martín-Carnicero, Ana González-Marcos, Alfredo Martínez.

  Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer with a poor survival outcome. Predicting patient survival allows physicians to tailor treatments to specific individuals. Thus, a simple and cost-effective prognosis model is sorely needed.Methods: This retrospective study assesses the prognostic value of blood biomarkers in advanced and metastatic PDAC patients (n=96) from Spain. Cut-off points for hematological parameters were calculated and correlated with overall survival (OS) using Kaplan-Meier, log-rank test, robust Cox proportional hazards and logistic regressions.
Results: In univariate analysis, individuals with low levels of GGT, LDH, ALP, leukocyte-, neutrophil- and monocyte counts showed significantly longer survival than patients with higher levels. In multivariate analysis, lower levels of GGT (HR (95%CI), 2.734 (1.223-6.111); p=0.014), LDH (HR (95%CI), 1.876 (1.035-3.400); p=0.038) and monocyte count (HR (95%CI), 1.657 (1.095-2.506); p = 0.017) remained significantly beneficial. In consequence, we propose a prognostic model based on logistic regression (AUC=0.741) of these three biomarkers as a pioneer tool to estimate OS in PDAC.
Conclusion: This study has demonstrated that the joint use of GGT (<92.00), LDH (<220.00) and monocyte count (<800) are independent positive prognostic factors in PDAC that can predict one-year survival in a novel prognostic logistic model.

Keywords:  advanced and metastatic pancreatic cancer; gamma glutamyl transferase (GGT); lactate dehydrogenase (LDH); overall survival; pancreatic ductal adenocarcinoma (PDAC); prognosis model; prognostic biomarkers

DOI:  https://doi.org/10.3389/fonc.2024.1411096
Autophagy. 2024 Oct 20. 1-2

Nuclear proteasomes as a backup for autophagy: interconnected proteostasis pathways.

Meiyan Jin, Daniel J Klionsky.

  Protein homeostasis (proteostasis) refers to the balance of the cellular protein environment, tightly regulated by pathways governing protein synthesis, folding, trafficking, and degradation. Growing evidence supports the interconnection of these pathways to ensure the robustness of the proteo-stasis network. A recent study by Park et al. showed that, in macroautophagy/autophagy-deficient cells, the loss of proteasome or nuclear pore components causes synthetic lethality, as cytoplasmic proteins that accumulate under impaired autophagy are transported to the nucleus and degraded by nuclear proteasomes. The authors illustrated the mechanistic basis for why cells with conditions such as Huntington disease, where both autophagy and cytoplasm-to-nuclear shuttling are compromised, are more vulnerable to proteostasis perturbation.Abbreviation: UPR: unfolded protein response; UPS: ubiquitin-proteasome system.

Keywords:  Autophagy; nuclear pore complex; nuclear proteasome; proteasome; proteostasis

DOI:  https://doi.org/10.1080/15548627.2024.2416261
BMJ. 2024 Oct 23. 387 e080040

Cancer cachexia.

Michael S Yule, Leo R Brown, Rachel Waller, Stephen J Wigmore.

DOI: https://doi.org/10.1136/bmj-2024-080040
Nat Cell Biol. 2024 Oct 24.

Differential stiffness between brain vasculature and parenchyma promotes metastatic infiltration through vessel co-option.

Marina Uroz, Amy E Stoddard, Bryan P Sutherland, Olivia Courbot, Roger Oria, Linqing Li, Cara R Ravasio, Mai T Ngo, Jinling Yang, Juliann B Tefft, Jeroen Eyckmans, Xue Han, Alberto Elosegui-Artola, Valerie M Weaver, Christopher S Chen.

In brain metastasis, cancer cells remain in close contact with the existing vasculature and can use vessels as migratory paths-a process known as vessel co-option. However, the mechanisms regulating this form of migration are poorly understood. Here we use ex vivo brain slices and an organotypic in vitro model for vessel co-option to show that cancer cell invasion along brain vasculature is driven by the difference in stiffness between vessels and the brain parenchyma. Imaging analysis indicated that cells move along the basal surface of vessels by adhering to the basement membrane extracellular matrix. We further show that vessel co-option is enhanced by both the stiffness of brain vasculature, which reinforces focal adhesions through a talin-dependent mechanism, and the softness of the surrounding environment that permits cellular movement. Our work reveals a mechanosensing mechanism that guides cell migration in response to the tissue's intrinsic mechanical heterogeneity, with implications in cancer invasion and metastasis.

DOI: https://doi.org/10.1038/s41556-024-01532-6
Sci Adv. 2024 Oct 25. 10(43): eado5887

Mitochondrial fatty acid oxidation drives senescence.

Shota Yamauchi, Yuki Sugiura, Junji Yamaguchi, Xiangyu Zhou, Satoshi Takenaka, Takeru Odawara, Shunsuke Fukaya, Takao Fujisawa, Isao Naguro, Yasuo Uchiyama, Akiko Takahashi, Hidenori Ichijo.

Cellular senescence is a stress-induced irreversible cell cycle arrest involved in tumor suppression and aging. Many stresses, such as telomere shortening and oncogene activation, induce senescence by damaging nuclear DNA. However, the mechanisms linking DNA damage to senescence remain unclear. Here, we show that DNA damage response (DDR) signaling to mitochondria triggers senescence. A genome-wide small interfering RNA screen implicated the outer mitochondrial transmembrane protein BNIP3 in senescence induction. We found that BNIP3 is phosphorylated by the DDR kinase ataxia telangiectasia mutated (ATM) and contributes to an increase in the number of mitochondrial cristae. Stable isotope labeling metabolomics indicated that the increase in cristae enhances fatty acid oxidation (FAO) to acetyl-coenzyme A (acetyl-CoA). This promotes histone acetylation and expression of the cyclin-dependent kinase inhibitor p16INK4a. Notably, pharmacological activation of FAO alone induced senescence both in vitro and in vivo. Thus, mitochondrial energy metabolism plays a critical role in senescence induction and is a potential intervention target to control senescence.

DOI: https://doi.org/10.1126/sciadv.ado5887
Nat Rev Mol Cell Biol. 2024 Oct 24.

The double-edged sword of eliminating senescent cells.

Eric Gilson.

DOI: https://doi.org/10.1038/s41580-024-00798-w
Nucleic Acids Res. 2024 Oct 21. pii: gkae916. [Epub ahead of print]

metsDB: a knowledgebase of cancer metastasis at bulk, single-cell and spatial levels.

Sijia Wu, Jiajin Zhang, Yanfei Wang, Xinyu Qin, Zhaocan Zhang, Zhennan Lu, Pora Kim, Xiaobo Zhou, Liyu Huang.

Cancer metastasis, the process by which tumour cells migrate and colonize distant organs from a primary site, is responsible for the majority of cancer-related deaths. Understanding the cellular and molecular mechanisms underlying this complex process is essential for developing effective metastasis prevention and therapy strategies. To this end, we systematically analysed 1786 bulk tissue samples from 13 cancer types, 988 463 single cells from 17 cancer types, and 40 252 spots from 45 spatial slides across 10 cancer types. The results of these analyses are compiled in the metsDB database, accessible at https://relab.xidian.edu.cn/metsDB/. This database provides insights into alterations in cell constitutions, cell relationships, biological pathways, molecular biomarkers, and drug responses during cancer metastasis at bulk, single-cell, and spatial levels. Users can perform cell or gene searches to obtain multi-view and multi-scale metastasis-related data. This comprehensive resource is invaluable for understanding the metastasis process and for designing molecular therapies.

DOI: https://doi.org/10.1093/nar/gkae916
Sci Rep. 2024 Oct 24. 14(1): 25144

Genetically predicted gut bacteria, circulating bacteria-associated metabolites and pancreatic ductal adenocarcinoma: a Mendelian randomisation study.

Neil Daniel, Riccardo Farinella, Anastasia Chrysovalantou Chatziioannou, Mazda Jenab, Ana-Lucia Mayén, Cosmeri Rizzato, Flavia Belluomini, Federico Canzian, Arianna Tavanti, Pekka Keski-Rahkonen, David J Hughes, Daniele Campa.

  Pancreatic ductal adenocarcinoma (PDAC) has high mortality and rising incidence rates. Recent data indicate that the gut microbiome and associated metabolites may play a role in the development of PDAC. To complement and inform observational studies, we investigated associations of genetically predicted abundances of individual gut bacteria and genetically predicted circulating concentrations of microbiome-associated metabolites with PDAC using Mendelian randomisation (MR). Gut microbiome-associated metabolites were identified through a comprehensive search of Pubmed, Exposome Explorer and Human Metabolome Database. Single Nucleotide Polymorphisms (SNPs) associated by Genome-Wide Association Studies (GWAS) with circulating levels of 109 of these metabolites were collated from Pubmed and the GWAS catalogue. SNPs for 119 taxonomically defined gut genera were selected from a meta-analysis performed by the MiBioGen consortium. Two-sample MR was conducted using GWAS summary statistics from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4), including a total of 8,769 cases and 7,055 controls. Inverse variance-weighted MR analyses were performed along with sensitivity analyses to assess potential violations of MR assumptions. Nominally significant associations were noted for genetically predicted circulating concentrations of mannitol (odds ratio per standard deviation [ORSD] = 0.97; 95% confidence interval [CI]: 0.95-0.99, p = 0.006), methionine (ORSD= 0.97; 95%CI: 0.94-1.00, p = 0.031), stearic acid (ORSD= 0.93; 95%CI: 0.87-0.99, p = 0.027), carnitine = (ORSD=1.01; 95% CI: 1.00-1.03, p = 0.027), hippuric acid (ORSD= 1.02; 95%CI: 1.00-1.04, p = 0.038) and 3-methylhistidine (ORSD= 1.05; 95%CI: 1.01-1.10, p = 0.02). Two gut microbiome genera were associated with reduced PDAC risk; Clostridium sensu stricto 1 (OR: 0.88; 95%CI: 0.78-0.99, p = 0.027) and Romboutsia (OR: 0.87; 95%CI: 0.80-0.96, p = 0.004). These results, though based only on genetically predicted gut microbiome characteristics and circulating bacteria-related metabolite concentrations, provide evidence for causal associations with pancreatic carcinogenesis.

Keywords:  Bacteria-related metabolites; Gut microbiome; Mendelian randomisation; Pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1038/s41598-024-77431-5
Nature. 2024 Oct 23.

Transgelin 2 guards T cell lipid metabolism and antitumour function.

Sung-Min Hwang, Deepika Awasthi, Jieun Jeong, Tito A Sandoval, Chang-Suk Chae, Yusibeska Ramos, Chen Tan, Matías Marin Falco, Camilla Salvagno, Alexander Emmanuelli, Ian T McBain, Bikash Mishra, Lionel B Ivashkiv, Dmitriy Zamarin, Evelyn Cantillo, Eloise Chapman-Davis, Kevin Holcomb, Diana K Morales, Xiaoqing Yu, Paulo C Rodriguez, Jose R Conejo-Garcia, Martin Kaczocha, Anna Vähärautio, Minkyung Song, Juan R Cubillos-Ruiz.

Mounting effective immunity against pathogens and tumours relies on the successful metabolic programming of T cells by extracellular fatty acids1-3. Fatty-acid-binding protein 5 (FABP5) has a key role in this process by coordinating the efficient import and trafficking of lipids that fuel mitochondrial respiration to sustain the bioenergetic requirements of protective CD8+ T cells4,5. However, the mechanisms that govern this immunometabolic axis remain unexplored. Here we report that the cytoskeletal organizer transgelin 2 (TAGLN2) is necessary for optimal fatty acid uptake, mitochondrial respiration and anticancer function in CD8+ T cells. TAGLN2 interacts with FABP5 to facilitate its cell surface localization and function in activated CD8+ T cells. Analyses of ovarian cancer specimens revealed that endoplasmic reticulum (ER) stress responses induced by the tumour microenvironment repress TAGLN2 in infiltrating CD8+ T cells, thereby enforcing their dysfunctional state. Restoring TAGLN2 expression in ER-stressed CD8+ T cells increased their lipid uptake, mitochondrial respiration and cytotoxic capacity. Accordingly, chimeric antigen receptor T cells overexpressing TAGLN2 bypassed the detrimental effects of tumour-induced ER stress and demonstrated therapeutic efficacy in mice with metastatic ovarian cancer. Our study establishes the role of cytoskeletal TAGLN2 in T cell lipid metabolism and highlights the potential to enhance cellular immunotherapy in solid malignancies by preserving the TAGLN2-FABP5 axis.

DOI: https://doi.org/10.1038/s41586-024-08071-y
J Exp Med. 2024 Nov 04. pii: e20240766. [Epub ahead of print]221(11):

NFAT5 governs cellular plasticity-driven resistance to KRAS-targeted therapy in pancreatic cancer.

Daiyong Deng, Habeebunnisa Begum, Tong Liu, Jiangyan Zhang, Qiang Zhang, Ting-Yu Chu, Hong Li, Alexander Lemenze, Mainul Hoque, Patricia Soteropoulos, Pingping Hou.

Resistance to KRAS therapy in pancreatic ductal adenocarcinoma (PDAC) involves cellular plasticity, particularly the epithelial-to-mesenchymal transition (EMT), which poses challenges for effective targeting. Chronic pancreatitis, a known risk factor for PDAC, elevates TGFβ levels in the tumor microenvironment (TME), promoting resistance to KRAS therapy. Mechanistically, TGFβ induces the formation of a novel protein complex composed of SMAD3, SMAD4, and the nuclear factor NFAT5, triggering EMT and resistance by activating key mediators such as S100A4. Inhibiting NFAT5 attenuates pancreatitis-induced resistance to KRAS inhibition and extends mouse survival. Additionally, TGFβ stimulates PDAC cells to secrete CCL2, recruiting macrophages that contribute to KRAS bypass through paracrine S100A4. Our findings elucidate the role of TGFβ signaling in EMT-associated KRAS therapy resistance and identify NFAT5 as a druggable target. Targeting NFAT5 could disrupt this regulatory network, offering a potential avenue for preventing resistance in PDAC.

DOI: https://doi.org/10.1084/jem.20240766
Nat Methods. 2024 Oct 21.

Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq.

Jessica J Simon, Douglas M Fowler, Dustin J Maly.

Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein-protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability.

DOI: https://doi.org/10.1038/s41592-024-02456-7
Curr Biol. 2024 Oct 21. pii: S0960-9822(24)00738-3. [Epub ahead of print]34(20): R1031-R1044

Intercellular fluid dynamics in tissue morphogenesis.

Louise Dagher, Stéphanie Descroix, Jean-Léon Maître.

During embryonic development, cells shape our body, which is mostly made up of water. It is often forgotten that some of this water is found in intercellular fluid, which, for example, immerses the cells of developing embryos. Intercellular fluid contributes to the properties of tissues and influences cell behaviour, thereby participating in tissue morphogenesis. While our understanding of the role of cells in shaping tissues advances, the exploration of the contribution of intercellular fluid dynamics is just beginning. In this review, we delve into the intricate mechanisms employed by cells to control fluid movements both across and within sealed tissue compartments. These mechanisms encompass sealing by tight junctions and controlled leakage, osmotic pumping, hydraulic fracturing of cell adhesion, cell and tissue contractions, as well as beating cilia. We illustrate key concepts by drawing extensively from the early mouse embryo, which successively forms multiple lumens that play essential roles in its development. Finally, we detail experimental approaches and emerging techniques that allow for the quantitative characterization and the manipulation of intercellular fluids in vivo, as well as theoretical frameworks that are crucial for comprehending their dynamics.

DOI: https://doi.org/10.1016/j.cub.2024.05.061
Nat Rev Cancer. 2024 Oct 21.

Emerging strategies to investigate the biology of early cancer.

Ran Zhou, Xiwen Tang, Yuan Wang.

Early detection and intervention of cancer or precancerous lesions hold great promise to improve patient survival. However, the processes of cancer initiation and the normal-precancer-cancer progression within a non-cancerous tissue context remain poorly understood. This is, in part, due to the scarcity of early-stage clinical samples or suitable models to study early cancer. In this Review, we introduce clinical samples and model systems, such as autochthonous mice and organoid-derived or stem cell-derived models that allow longitudinal analysis of early cancer development. We also present the emerging techniques and computational tools that enhance our understanding of cancer initiation and early progression, including direct imaging, lineage tracing, single-cell and spatial multi-omics, and artificial intelligence models. Together, these models and techniques facilitate a more comprehensive understanding of the poorly characterized early malignant transformation cascade, holding great potential to unveil key drivers and early biomarkers for cancer development. Finally, we discuss how these new insights can potentially be translated into mechanism-based strategies for early cancer detection and prevention.

DOI: https://doi.org/10.1038/s41568-024-00754-y