bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2023–09–03
34 papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Spotlight on GOT2 in Cancer Metabolism.
  2. Ectopic expression of DOCK8 regulates lysosome-mediated pancreatic tumor cell invasion.
  3. ST6GAL1 sialyltransferase promotes acinar to ductal metaplasia and pancreatic cancer progression.
  4. Tumor-initiating cells establish a niche to overcome isolation stress.
  5. ATG2A-mediated bridge-like lipid transport regulates lipid droplet accumulation.
  6. Acid-base homeostasis orchestrated by NHE1 defines pancreatic stellate cell phenotype in pancreatic cancer.
  7. Adipocytes reprogram cancer cell metabolism by diverting glucose towards glycerol-3-phosphate thereby promoting metastasis.
  8. Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype.
  9. Intravital measurements of solid stresses in tumours reveal length-scale and microenvironmentally dependent force transmission.
  10. Identifying radiomics signatures in body composition imaging for the prediction of outcome following pancreatic cancer resection.
  11. Fibroblasts - the cellular choreographers of wound healing.
  12. Decoding the obesity-cancer connection: lessons from preclinical models of pancreatic adenocarcinoma.
  13. Multiplexed transcriptomic profiling of the fate of human CAR T cells in vivo via genetic barcoding with shielded small nucleotides.
  14. Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging.
  15. The exercise IL-6 enigma in cancer.
  16. Unanswered questions about the causes of obesity.
  17. Flow cytometric analysis of phosphatidylcholine metabolism using organelle-selective click labeling.
  18. An endoplasmic reticulum stress-related signature could robustly predict prognosis and closely associate with response to immunotherapy in pancreatic ductal adenocarcinoma.
  19. Preserved respiratory chain capacity and physiology in mice with profoundly reduced levels of mitochondrial respirasomes.
  20. Nimotuzumab Plus Gemcitabine for K-Ras Wild-Type Locally Advanced or Metastatic Pancreatic Cancer.
  21. Identification of an alternative triglyceride biosynthesis pathway.
  22. BRAFΔβ3-αC in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability.
  23. Lipids and the Hallmarks of Ageing: From Pathology to Interventions.
  24. Cell cycle-linked vacuolar pH dynamics regulate amino acid homeostasis and cell growth.
  25. A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization.
  26. Pancreatic panniculitis as the first presentation of pancreatic ductal adenocarcinoma.
  27. p16High senescence restricts cellular plasticity during somatic cell reprogramming.
  28. Co-chaperone BAG3 enters autophagic pathway via its interaction with microtubule associated protein 1 light chain 3 beta.
  29. Cascade Catalytic Nanoparticles Selectively Alkalize Cancerous Lysosomes to Suppress Cancer Progression And Metastasis.
  30. Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis.
  31. Adipose-Tumor Crosstalk contributes to CXCL5 Mediated Immune Evasion in PDAC.
  32. Proteomic changes induced by longevity-promoting interventions in mice.
  33. Formate promotes invasion and metastasis in reliance on lipid metabolism.
  34. Transformer-based biomarker prediction from colorectal cancer histology: A large-scale multicentric study.
  1. Onco Targets Ther. 2023 ;16 695-702
    Spotlight on GOT2 in Cancer Metabolism.
    Samuel A Kerk, Javier Garcia-Bermudez, Kivanc Birsoy, Mara H Sherman, Yatrik M Shah, Costas A Lyssiotis.
      GOT2 is at the nexus of several critical metabolic pathways in homeostatic cellular and dysregulated cancer metabolism. Despite this, recent work has emphasized the remarkable plasticity of cancer cells to employ compensatory pathways when GOT2 is inhibited. Here, we review the metabolic roles of GOT2, highlighting findings in both normal and cancer cells. We emphasize how cancer cells repurpose cell intrinsic metabolism and their flexibility when GOT2 is inhibited. We close by using this framework to discuss key considerations for future investigations into cancer metabolism.
    Keywords:  mitochondria; nucleotides; pancreatic cancer; redox; transaminase; tumor microenvironment
    DOI:  https://doi.org/10.2147/OTT.S382161
  2. Cell Rep. 2023 Aug 30. pii: S2211-1247(23)01053-7. [Epub ahead of print]42(9): 113042
    Ectopic expression of DOCK8 regulates lysosome-mediated pancreatic tumor cell invasion.
    Omar L Gutierrez-Ruiz, Katherine M Johnson, Eugene W Krueger, Roseanne E Nooren, Nicole Cruz-Reyes, Carrie Jo Heppelmann, Tara L Hogenson, Martin E Fernandez-Zapico, Mark A McNiven, Gina L Razidlo.
      Amplified lysosome activity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) orchestrated by oncogenic KRAS that mediates tumor growth and metastasis, though the mechanisms underlying this phenomenon remain unclear. Using comparative proteomics, we found that oncogenic KRAS significantly enriches levels of the guanine nucleotide exchange factor (GEF) dedicator of cytokinesis 8 (DOCK8) on lysosomes. Surprisingly, DOCK8 is aberrantly expressed in a subset of PDAC, where it promotes cell invasion in vitro and in vivo. DOCK8 associates with lysosomes and regulates lysosomal morphology and motility, with loss of DOCK8 leading to increased lysosome size. DOCK8 promotes actin polymerization at the surface of lysosomes while also increasing the proteolytic activity of the lysosomal protease cathepsin B. Critically, depletion of DOCK8 significantly reduces cathepsin-dependent extracellular matrix degradation and impairs the invasive capacity of PDAC cells. These findings implicate ectopic expression of DOCK8 as a key driver of KRAS-driven lysosomal regulation and invasion in pancreatic cancer cells.
    Keywords:  CP: Cancer; DOCK8; Invasion; cathepsin B; lysosome; matrix degradation; metastasis; pancreatic cancer
    DOI:  https://doi.org/10.1016/j.celrep.2023.113042
  3. JCI Insight. 2023 Aug 29. pii: e161563. [Epub ahead of print]
    ST6GAL1 sialyltransferase promotes acinar to ductal metaplasia and pancreatic cancer progression.
    Nikita Bhalerao, Asmi Chakraborty, Michael P Marciel, Jihye Hwang, Colleen M Britain, Austin D Silva, Isam E Eltoum, Robert B Jones, Katie L Alexander, Lesley E Smythies, Phillip D Smith, David K Crossman, Michael R Crowley, Boyoung Shin, Laurie E Harrington, Zhaoqi Yan, Maigen M Bethea, Chad S Hunter, Christopher A Klug, Donald J Buchsbaum, Susan L Bellis.
      The role of aberrant glycosylation in pancreatic ductal adenocarcinoma (PDAC) remains an under-investigated area of research. In this study, we determined that the ST6GAL1 sialyltransferase, which adds α2,6-linked sialic acids to N-glycosylated proteins, is upregulated in patients with early-stage PDAC, and further increased in advanced disease. A tumor-promoting function for ST6GAL1 was elucidated using tumor xenograft experiments with human PDAC cells. Additionally, we developed a genetically-engineered mouse (GEM) with transgenic expression of ST6GAL1 in the pancreas, and found that mice with dual expression of ST6GAL1 and oncogenic KRASG12D have greatly accelerated PDAC progression compared with mice expressing KRASG12D alone. As ST6GAL1 imparts progenitor-like characteristics, we interrogated ST6GAL1's role in acinar to ductal metaplasia (ADM), a process that fosters neoplasia by reprogramming acinar cells into ductal, progenitor-like cells. We confirmed ST6GAL1 promotes ADM using multiple models including the 266-6 cell line, GEM-derived organoids and tissues, and an in vivo model of inflammation-induced ADM. EGFR is a key driver of ADM and is known to be activated by ST6GAL1-mediated sialylation. Importantly, EGFR activation was dramatically increased in acinar cells and organoids from mice with transgenic ST6GAL1 expression. These collective results highlight a glycosylation-dependent mechanism involved in early stages of pancreatic neoplasia.
    Keywords:  Cancer; Glycobiology; Oncogenes; Oncology
    DOI:  https://doi.org/10.1172/jci.insight.161563
  4. Trends Cell Biol. 2023 Aug 26. pii: S0962-8924(23)00165-4. [Epub ahead of print]
    Tumor-initiating cells establish a niche to overcome isolation stress.
    Chengsheng Wu, Sara M Weis, David A Cheresh.
      While the tumor microenvironment is a critical contributor to cancer progression, early steps of tumor initiation and metastasis also rely on the ability of individual tumor cells to survive and thrive at locations where tumor stroma or immune infiltration has yet to be established. In this opinion article, we use the term 'isolation stress' to broadly describe the challenges that individual tumor cells must overcome during the initiation and expansion of the primary tumor beyond permissive boundaries and metastatic spread into distant sites, including a lack of cell-cell contact, adhesion to protumor extracellular matrix proteins, and access to nutrients, oxygen, and soluble factors that support growth. In particular, we highlight the ability of solitary tumor cells to autonomously generate a specialized fibronectin-enriched extracellular matrix to create their own pericellular niche that supports tumor initiation. Cancer cells that can creatively evade the effects of isolation stress not only become more broadly stress tolerant, they also tend to show enhanced stemness, drug resistance, tumor initiation, and metastasis.
    Keywords:  fibronectin; integrins; isolation stress; tumor-initiating niche
    DOI:  https://doi.org/10.1016/j.tcb.2023.08.001
  5. bioRxiv. 2023 Aug 14. pii: 2023.08.14.553257. [Epub ahead of print]
    ATG2A-mediated bridge-like lipid transport regulates lipid droplet accumulation.
    Justin L Korfhage, Neng Wan, Helin Elhan, Lisa Kauffman, Mia Pineda, Devin M Fuller, Abdou Rachid Thiam, Karin M Reinisch, Thomas J Melia.
      ATG2 proteins facilitate bulk lipid transport between membranes. ATG2 is an essential autophagy protein, but ATG2 also localizes to lipid droplets (LDs), and genetic depletion of ATG2 increases LD numbers while impairing fatty acid transport from LDs to mitochondria. How ATG2 supports LD homeostasis and whether lipid transport regulates this homeostasis remains unknown. Here we demonstrate that ATG2 is preferentially recruited to phospholipid monolayers such as those surrounding LDs rather than to phospholipid bilayers. In vitro , ATG2 can drive phospholipid transport from artificial LDs with rates that correlate with the binding affinities, such that phospholipids are moved much more efficiently when one of the ATG2-interacting structures is an artificial LD. ATG2 is thought to exhibit 'bridge-like" lipid transport, with lipids flowing across the protein between membranes. We mutated key amino acids within the bridge to form a transport-dead ATG2 mutant (TD-ATG2A) which we show specifically blocks bridge-like, but not shuttle-like, lipid transport in vitro . TD-ATG2A still localizes to LDs, but is unable to rescue LD accumulation in ATG2 knockout cells. Thus, ATG2 has a natural affinity for, and an enhanced activity upon LD surfaces and uses bridge-like lipid transport to support LD dynamics in cells.
    DOI:  https://doi.org/10.1101/2023.08.14.553257
  6. JCI Insight. 2023 Aug 29. pii: e170928. [Epub ahead of print]
    Acid-base homeostasis orchestrated by NHE1 defines pancreatic stellate cell phenotype in pancreatic cancer.
    Zoltán Pethő, Karolina Najder, Stephanie Beel, Benedikt Fels, Ilka Neumann, Sandra Schimmelpfennig, Sarah Sargin, Maria Wolters, Klavs Grantins, Eva Wardelmann, Miso Mitkovski, Andrea Oeckinghaus, Albrecht Schwab.
      Pancreatic ductal adenocarcinoma (PDAC) progresses in an organ with a unique pH landscape, where the stroma acidifies after each meal. We hypothesized that disrupting this pH landscape during PDAC progression triggers pancreatic stellate cells (PSCs) and cancer-associated fibroblasts (CAFs) to induce PDAC fibrosis. We revealed that alkaline environmental pH is sufficient to induce PSC differentiation to a myofibroblastic phenotype. We then mechanistically dissected this finding focusing on the involvement of the Na+/H+ exchanger NHE1. Perturbing cellular pH homeostasis by inhibiting NHE1 with cariporide partially alters the myofibroblastic PSC phenotype. To show the relevance of this finding in vivo, we targeted NHE1 in murine PDAC (KPfC). Indeed, tumor fibrosis decreases when mice receive the NHE1-inhibitor cariporide in addition to gemcitabine treatment. Moreover, the tumor immune infiltrate shifts from granulocyte-rich to more lymphocytic. Taken together, our study provides mechanistic evidence on how the pancreatic pH landscape shapes pancreatic cancer through tuning PSC differentiation.
    Keywords:  Epithelial transport of ions and water; Fibrosis; Homeostasis; Metabolism; Oncology
    DOI:  https://doi.org/10.1172/jci.insight.170928
  7. Nat Metab. 2023 Aug 31.
    Adipocytes reprogram cancer cell metabolism by diverting glucose towards glycerol-3-phosphate thereby promoting metastasis.
    Abir Mukherjee, Divya Bezwada, Francesco Greco, Malu Zandbergen, Tong Shen, Chun-Yi Chiang, Medine Tasdemir, Johannes Fahrmann, Dmitry Grapov, Michael R La Frano, Hieu S Vu, Brandon Faubert, John W Newman, Liam A McDonnell, Luigi Nezi, Oliver Fiehn, Ralph J DeBerardinis, Ernst Lengyel.
      In the tumor microenvironment, adipocytes function as an alternate fuel source for cancer cells. However, whether adipocytes influence macromolecular biosynthesis in cancer cells is unknown. Here we systematically characterized the bidirectional interaction between primary human adipocytes and ovarian cancer (OvCa) cells using multi-platform metabolomics, imaging mass spectrometry, isotope tracing and gene expression analysis. We report that, in OvCa cells co-cultured with adipocytes and in metastatic tumors, a part of the glucose from glycolysis is utilized for the biosynthesis of glycerol-3-phosphate (G3P). Normoxic HIF1α protein regulates the altered flow of glucose-derived carbons in cancer cells, resulting in increased glycerophospholipids and triacylglycerol synthesis. The knockdown of HIF1α or G3P acyltransferase 3 (a regulatory enzyme of glycerophospholipid synthesis) reduced metastasis in xenograft models of OvCa. In summary, we show that, in an adipose-rich tumor microenvironment, cancer cells generate G3P as a precursor for critical membrane and signaling components, thereby promoting metastasis. Targeting biosynthetic processes specific to adipose-rich tumor microenvironments might be an effective strategy against metastasis.
    DOI:  https://doi.org/10.1038/s42255-023-00879-8
  8. Nat Commun. 2023 Aug 26. 14(1): 5226
    Coordinated single-cell tumor microenvironment dynamics reinforce pancreatic cancer subtype.
    Ki Oh, Yun Jae Yoo, Luke A Torre-Healy, Manisha Rao, Danielle Fassler, Pei Wang, Michael Caponegro, Mei Gao, Joseph Kim, Aaron Sasson, Georgios Georgakis, Scott Powers, Richard A Moffitt.
      Bulk analyses of pancreatic ductal adenocarcinoma (PDAC) samples are complicated by the tumor microenvironment (TME), i.e. signals from fibroblasts, endocrine, exocrine, and immune cells. Despite this, we and others have established tumor and stroma subtypes with prognostic significance. However, understanding of underlying signals driving distinct immune and stromal landscapes is still incomplete. Here we integrate 92 single cell RNA-seq samples from seven independent studies to build a reproducible PDAC atlas with a focus on tumor-TME interdependence. Patients with activated stroma are synonymous with higher myofibroblastic and immunogenic fibroblasts, and furthermore show increased M2-like macrophages and regulatory T-cells. Contrastingly, patients with 'normal' stroma show M1-like recruitment, elevated effector and exhausted T-cells. To aid interoperability of future studies, we provide a pretrained cell type classifier and an atlas of subtype-based signaling factors that we also validate in mouse data. Ultimately, this work leverages the heterogeneity among single-cell studies to create a comprehensive view of the orchestra of signaling interactions governing PDAC.
    DOI:  https://doi.org/10.1038/s41467-023-40895-6
  9. Nat Biomed Eng. 2023 Aug 28.
    Intravital measurements of solid stresses in tumours reveal length-scale and microenvironmentally dependent force transmission.
    Sue Zhang, Gabrielle Grifno, Rachel Passaro, Kathryn Regan, Siyi Zheng, Muhamed Hadzipasic, Rohin Banerji, Logan O'Connor, Vinson Chu, Sung Yeon Kim, Jiarui Yang, Linzheng Shi, Kavon Karrobi, Darren Roblyer, Mark W Grinstaff, Hadi T Nia.
      In cancer, solid stresses impede the delivery of therapeutics to tumours and the trafficking and tumour infiltration of immune cells. Understanding such consequences and the origin of solid stresses requires their probing in vivo at the cellular scale. Here we report a method for performing volumetric and longitudinal measurements of solid stresses in vivo, and findings from its applicability to tumours. We used multimodal intravital microscopy of fluorescently labelled polyacrylamide beads injected in breast tumours in mice as well as mathematical modelling to compare solid stresses at the single-cell and tissue scales, in primary and metastatic tumours, in vitro and in mice, and in live mice and post-mortem tissue. We found that solid-stress transmission is scale dependent, with tumour cells experiencing lower stresses than their embedding tissue, and that tumour cells in lung metastases experience substantially higher solid stresses than those in the primary tumours. The dependence of solid stresses on length scale and the microenvironment may inform the development of therapeutics that sensitize cancer cells to such mechanical forces.
    DOI:  https://doi.org/10.1038/s41551-023-01080-8
  10. Front Oncol. 2023 ;13 1062937
    Identifying radiomics signatures in body composition imaging for the prediction of outcome following pancreatic cancer resection.
    Gregory van der Kroft, Leonard Wee, Sander S Rensen, Ralph Brecheisen, David P J van Dijk, Roman Eickhoff, Anjali A Roeth, Florian T Ulmer, Andre Dekker, Ulf P Neumann, Steven W M Olde Damink.
       Background: Computerized radiological image analysis (radiomics) enables the investigation of image-derived phenotypes by extracting large numbers of quantitative features. We hypothesized that radiomics features may contain prognostic information that enhances conventional body composition analysis. We aimed to investigate whether body composition-associated radiomics features hold additional value over conventional body composition analysis and clinical patient characteristics used to predict survival of pancreatic ductal adenocarcinoma (PDAC) patients.
    Methods: Computed tomography images of 304 patients undergoing elective pancreatic cancer resection were analysed. 2D radiomics features were extracted from skeletal muscle and subcutaneous and visceral adipose tissue (SAT and VAT) compartments from a single slice at the third lumbar vertebra. The study population was randomly split (80:20) into training and holdout subsets. Feature ranking with Least Absolute Shrinkage Selection Operator (LASSO) followed by multivariable stepwise Cox regression in 1000 bootstrapped re-samples of the training data was performed and tested on the holdout data. The fitted regression predictors were used as "scores" for a clinical (C-Score), body composition (B-Score), and radiomics (R-Score) model. To stratify patients into the highest 25% and lowest 25% risk of mortality compared to the middle 50%, the Harrell Concordance Index was used.
    Results: Based on LASSO and stepwise cox regression for overall survival, ASA ≥3 and age were the most important clinical variables and constituted the C-score, and VAT-index (VATI) was the most important body composition variable and constituted the B-score. Three radiomics features (SATI_original_shape2D_Perimeter, VATI_original_glszm_SmallAreaEmphasis, and VATI_original_firstorder_Maximum) emerged as the most frequent set of features and yielded an R-Score. Of the mean concordance indices of C-, B-, and R-scores, R-score performed best (0.61, 95% CI 0.56-0.65, p<0.001), followed by the C-score (0.59, 95% CI 0.55-0.63, p<0.001) and B-score (0.55, 95% CI 0.50-0.60, p=0.03). Kaplan-Meier projection revealed that C-, B, and R-scores showed a clear split in the survival curves in the training set, although none remained significant in the holdout set.
    Conclusion: It is feasible to implement a data-driven radiomics approach to body composition imaging. Radiomics features provided improved predictive performance compared to conventional body composition variables for the prediction of overall survival of PDAC patients undergoing primary resection.
    Keywords:  PDAC; body composition; pancreatic cancer; radiomics; survival; wasting disorders
    DOI:  https://doi.org/10.3389/fonc.2023.1062937
  11. Front Immunol. 2023 ;14 1233800
    Fibroblasts - the cellular choreographers of wound healing.
    Samuel Knoedler, Sonja Broichhausen, Ruiji Guo, Ruoxuan Dai, Leonard Knoedler, Martin Kauke-Navarro, Fortunay Diatta, Bohdan Pomahac, Hans-Guenther Machens, Dongsheng Jiang, Yuval Rinkevich.
      Injuries to our skin trigger a cascade of spatially- and temporally-synchronized healing processes. During such endogenous wound repair, the role of fibroblasts is multifaceted, ranging from the activation and recruitment of innate immune cells through the synthesis and deposition of scar tissue to the conveyor belt-like transport of fascial connective tissue into wounds. A comprehensive understanding of fibroblast diversity and versatility in the healing machinery may help to decipher wound pathologies whilst laying the foundation for novel treatment modalities. In this review, we portray the diversity of fibroblasts and delineate their unique wound healing functions. In addition, we discuss future directions through a clinical-translational lens.
    Keywords:  fascia; fibroblast; fibroblast diversity; skin injury; skin regeneration; wound healing; wound repair
    DOI:  https://doi.org/10.3389/fimmu.2023.1233800
  12. Life Sci Alliance. 2023 Nov;pii: e202302228. [Epub ahead of print]6(11):
    Decoding the obesity-cancer connection: lessons from preclinical models of pancreatic adenocarcinoma.
    Christian F Ruiz, Cathy Garcia, Jeremy B Jacox, Lauren Lawres, Mandar D Muzumdar.
      Obesity is a metabolic state of energy excess and a risk factor for over a dozen cancer types. Because of the rising worldwide prevalence of obesity, decoding the mechanisms by which obesity promotes tumor initiation and early progression is a societal imperative and could broadly impact human health. Here, we review results from preclinical models that link obesity to cancer, using pancreatic adenocarcinoma as a paradigmatic example. We discuss how obesity drives cancer development by reprogramming the pretumor or tumor cell and its micro- and macro-environments. Specifically, we describe evidence for (1) altered cellular metabolism, (2) hormone dysregulation, (3) inflammation, and (4) microbial dysbiosis in obesity-driven pancreatic tumorigenesis, denoting variables that confound interpretation of these studies, and highlight remaining gaps in knowledge. Recent advances in preclinical modeling and emerging unbiased analytic approaches will aid in further unraveling the complex link between obesity and cancer, informing novel strategies for prevention, interception, and therapy in pancreatic adenocarcinoma and other obesity-associated cancers.
    DOI:  https://doi.org/10.26508/lsa.202302228
  13. Nat Biomed Eng. 2023 Aug 31.
    Multiplexed transcriptomic profiling of the fate of human CAR T cells in vivo via genetic barcoding with shielded small nucleotides.
    Xiaoyin Lu, Shane M Lofgren, Yuehui Zhao, Pawel K Mazur.
      The design of chimeric antigen receptor (CAR) T cells would benefit from knowledge of the fate of the cells in vivo. This requires the permanent labelling of CAR T cell products and their pooling in the same microenvironment. Here, we report a cell-barcoding method for the multiplexed longitudinal profiling of cells in vivo using single-cell RNA sequencing (scRNA-seq). The method, which we named shielded-small-nucleotide-based scRNA-seq (SSN-seq), is compatible with both 3' and 5' single-cell profiling, and enables the recording of cell identity, from cell infusion to isolation, by leveraging the ubiquitous Pol III U6 promoters to robustly express small-RNA barcodes modified with direct-capture sequences. By using SSN-seq to track the dynamics of the states of CAR T cells in a tumour-rechallenge mouse model of leukaemia, we found that a combination of cytokines and small-molecule inhibitors that are used in the ex vivo manufacturing of CAR T cells promotes the in vivo expansion of persistent populations of CD4+ memory T cells. By facilitating the probing of cell-state dynamics in vivo, SSN-seq may aid the development of adoptive cell therapies.
    DOI:  https://doi.org/10.1038/s41551-023-01085-3
  14. Nat Methods. 2023 Aug 31.
    Multielement Z-tag imaging by X-ray fluorescence microscopy for next-generation multiplex imaging.
    Merrick Strotton, Tsuyoshi Hosogane, Marco di Michiel, Holger Moch, Zsuzsanna Varga, Bernd Bodenmiller.
      Rapid, highly multiplexed, nondestructive imaging that spans the molecular to the supra-cellular scale would be a powerful tool for tissue analysis. However, the physical constraints of established imaging methods limit the simultaneous improvement of these parameters. Whole-organism to atomic-level imaging is possible with tissue-penetrant, picometer-wavelength X-rays. To enable highly multiplexed X-ray imaging, we developed multielement Z-tag X-ray fluorescence (MEZ-XRF) that can operate at kHz speeds when combined with signal amplification by exchange reaction (SABER)-amplified Z-tag reagents. We demonstrated parallel imaging of 20 Z-tag or SABER Z-tag reagents at subcellular resolution in cell lines and multiple human tissues. We benchmarked MEZ-XRF against imaging mass cytometry and demonstrated the nondestructive multiscale repeat imaging capabilities of MEZ-XRF with rapid tissue overview scans, followed by slower, more sensitive imaging of low-abundance markers such as immune checkpoint proteins. The unique multiscale, nondestructive nature of MEZ-XRF, combined with SABER Z-tags for high sensitivity or enhanced speed, enables highly multiplexed bioimaging across biological scales.
    DOI:  https://doi.org/10.1038/s41592-023-01977-x
  15. Trends Endocrinol Metab. 2023 Aug 24. pii: S1043-2760(23)00154-6. [Epub ahead of print]
    The exercise IL-6 enigma in cancer.
    Samuel T Orange, Jack Leslie, Mark Ross, Derek A Mann, Henning Wackerhage.
      Interleukin (IL)-6 elicits both anticancer and procancer effects depending on the context, which we have termed the 'exercise IL-6 enigma'. IL-6 is released from skeletal muscles during exercise to regulate short-term energy availability. Exercise-induced IL-6 provokes biological effects that may protect against cancer by improving insulin sensitivity, stimulating the production of anti-inflammatory cytokines, mobilising immune cells, and reducing DNA damage in early malignant cells. By contrast, IL-6 continuously produced by leukocytes in inflammatory sites drives tumorigenesis by promoting chronic inflammation and activating tumour-promoting signalling pathways. How can a molecule have such opposing effects on cancer? Here, we review the roles of IL-6 in chronic inflammation, tumorigenesis, and exercise-associated cancer prevention and define the factors that underpin the exercise IL-6 enigma.
    Keywords:  cancer; exercise; inflammation; interleukin-6; muscle
    DOI:  https://doi.org/10.1016/j.tem.2023.08.001
  16. Science. 2023 Sep;381(6661): 944-946
    Unanswered questions about the causes of obesity.
    John R Speakman, Thorkild I A Sørensen, Kevin D Hall, David B Allison.
      Obesity is now a global pandemic, but there is little consensus about the causes.
    DOI:  https://doi.org/10.1126/science.adg2718
  17. STAR Protoc. 2023 Aug 26. pii: S2666-1667(23)00492-6. [Epub ahead of print]4(3): 102525
    Flow cytometric analysis of phosphatidylcholine metabolism using organelle-selective click labeling.
    Masaki Tsuchiya, Nobuhiko Tachibana, Itaru Hamachi.
      Here, we present a protocol to analyze phosphatidylcholine (PC) metabolism in mammalian cells using organelle-selective click labeling coupled with flow cytometry (O-ClickFC). We describe steps for the metabolic incorporation of azide-choline into PC. We then detail fluorescent labeling of the azide-modified PC with organelle-targeting clickable dyes in the ER-Golgi, plasma membrane, and mitochondria, and by flow cytometry. This protocol is optimized for flow cytometric quantification of the labeled PC at the organelle level within single live cells. For complete details on the use and execution of this protocol, please refer to Tsuchiya et al. (2023).1.
    Keywords:  Chemistry; Flow Cytometry/Mass Cytometry; Metabolism; Molecular/Chemical Probes
    DOI:  https://doi.org/10.1016/j.xpro.2023.102525
  18. J Cancer Res Clin Oncol. 2023 Aug 31.
    An endoplasmic reticulum stress-related signature could robustly predict prognosis and closely associate with response to immunotherapy in pancreatic ductal adenocarcinoma.
    Shuguang Liu, Qianying Hu, Zishan Xie, Shaojing Chen, Yixuan Li, Nali Quan, Kaimeng Huang, Riqing Li, Lishan Fang.
       PURPOSE: Pancreatic ductal adenocarcinoma (PDAC) is one of the most malignant tumors. Endoplasmic reticulum stress (ERS) plays an essential role in PDAC progression. Here, we aim to identify the ERS-related genes in PDAC and build reliable risk models for diagnosis, prognosis and immunotherapy response of PDAC patients as well as investigate the potential mechanism.
    METHODS: We obtained PDAC cohorts with transcriptional profiles and clinical data from the ArrayExpress, The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Univariate Cox regression, LASSO regression and multivariate Cox regression analyses were used to construct an ERS-related prognostic signature. The CIBERSORT and ssGSEA algorithms were applied to explore the correlation between the prognostic signature and immune cell infiltration and immune-related pathways. The GDSC database and TIDE algorithm were used to predict responses to chemotherapy and immunotherapy, identifying potential drugs for treating patients with PDAC.
    RESULTS: We established and validated an ERS-related prognostic signature comprising eight genes (HMOX1, TGFB1, JSRP1, GAPDH, CAV1, CHRNE, CD74 and ERN2). Patients with higher risk scores displayed worse outcomes than those with lower risk scores. PDAC patients in low-risk groups might benefit from immunotherapy. Dasatinib and lapatinib might have potential therapeutic implications in high-risk PDAC patients.
    CONCLUSION: We established and validated an ERS-related prognostic signature comprising eight genes to predict the overall survival outcome of PDAC patients, which closely correlating with the response to immunotherapy and sensitivity to anti-tumor drugs, as well as could be beneficial for formulating clinical strategies and administering individualized treatments.
    Keywords:  Endoplasmic reticulum stress; Immunotherapy response; Overall survival; Pancreatic ductal adenocarcinoma; Prognosis
    DOI:  https://doi.org/10.1007/s00432-023-05312-x
  19. Cell Metab. 2023 Aug 22. pii: S1550-4131(23)00289-9. [Epub ahead of print]
    Preserved respiratory chain capacity and physiology in mice with profoundly reduced levels of mitochondrial respirasomes.
    Dusanka Milenkovic, Jelena Misic, Johannes F Hevler, Thibaut Molinié, Injae Chung, Ilian Atanassov, Xinping Li, Roberta Filograna, Andrea Mesaros, Arnaud Mourier, Albert J R Heck, Judy Hirst, Nils-Göran Larsson.
      The mammalian respiratory chain complexes I, III2, and IV (CI, CIII2, and CIV) are critical for cellular bioenergetics and form a stable assembly, the respirasome (CI-CIII2-CIV), that is biochemically and structurally well documented. The role of the respirasome in bioenergetics and the regulation of metabolism is subject to intense debate and is difficult to study because the individual respiratory chain complexes coexist together with high levels of respirasomes. To critically investigate the in vivo role of the respirasome, we generated homozygous knockin mice that have normal levels of respiratory chain complexes but profoundly decreased levels of respirasomes. Surprisingly, the mutant mice are healthy, with preserved respiratory chain capacity and normal exercise performance. Our findings show that high levels of respirasomes are dispensable for maintaining bioenergetics and physiology in mice but raise questions about their alternate functions, such as those relating to the regulation of protein stability and prevention of age-associated protein aggregation.
    Keywords:  OXPHOS; mitochondria; mitochondrial respirasomes; supercomplexes
    DOI:  https://doi.org/10.1016/j.cmet.2023.07.015
  20. J Clin Oncol. 2023 Aug 30. JCO2202630
    Nimotuzumab Plus Gemcitabine for K-Ras Wild-Type Locally Advanced or Metastatic Pancreatic Cancer.
    Shukui Qin, Jin Li, Yuxian Bai, Zishu Wang, Zhendong Chen, Ruihua Xu, Jianming Xu, Hongmei Zhang, Jia Chen, Ying Yuan, Tianshu Liu, Lin Yang, Haijun Zhong, Donghui Chen, Lin Shen, Chunyi Hao, Deliang Fu, Ying Cheng, Jianwei Yang, Qiong Wang, Baoli Qin, Hongming Pan, Jun Zhang, Xianhong Bai, Qingshan Zheng.
       PURPOSE: In a phase IIb trial of nimotuzumab plus gemcitabine, substantial clinical benefits were observed in patients with locally advanced or metastatic pancreatic cancer (PC). Therefore, we conducted a phase III clinical study to verify the efficacy and safety of this combination regimen in patients with K-Ras wild-type tumors (ClinicalTrials.gov identifier: NCT02395016).
    PATIENTS AND METHODS: Eligible patients were randomly assigned to receive nimotuzumab (400 mg once per week) or placebo followed by gemcitabine (1,000 mg/m2 on days 1, 8, and 15, once every 4 weeks) until disease progression or unacceptable toxicity. The primary end point was overall survival (OS) and the secondary end points were progression-free survival (PFS), response rates, and safety.
    RESULTS: A total of 480 patients were screened; 92 patients were enrolled and 82 patients with K-Ras wild-type tumors were eligible. In the full analysis set, the median OS was 10.9 versus 8.5 months, while the restricted mean survival time (RMST) was 18.05 versus 11.14 months for the investigational versus control arm (ratio of control v investigation = 0.62 [0.40-0.97]; P = .036). Median PFS was 4.2 versus 3.6 months in the investigational versus control arm (log-rank P = .04; hazard ratio, 0.60 [0.37-0.99]) and the restricted mean PFS time was 8.08 versus 4.76 months (RMST ratio, 0.58 [0.38-0.90]; P = .036). Both OS and PFS were longer in the nimotuzumab group than in the placebo group. The objective response rates and disease control rates were 7% versus 10% and 68% versus 63% for the investigational and control groups, respectively. The incidence of adverse events were comparable between the two groups.
    CONCLUSION: In patients with locally advanced or metastatic K-Ras wild-type PC, nimotuzumab plus gemcitabine significantly improved OS and PFS with a good safety profile.
    DOI:  https://doi.org/10.1200/JCO.22.02630
  21. Nature. 2023 Aug 30.
    Identification of an alternative triglyceride biosynthesis pathway.
    Gian-Luca McLelland, Marta Lopez-Osias, Cristy R C Verzijl, Brecht D Ellenbroek, Rafaela A Oliveira, Nicolaas J Boon, Marleen Dekker, Lisa G van den Hengel, Rahmen Ali, Hans Janssen, Ji-Ying Song, Paul Krimpenfort, Tim van Zutphen, Johan W Jonker, Thijn R Brummelkamp.
      Triacylglycerols (TAGs) are the main source of stored energy in the body, providing an important substrate pool for mitochondrial beta-oxidation. Imbalances in the amount of TAGs are associated with obesity, cardiac disease and various other pathologies1,2. In humans, TAGs are synthesized from excess, coenzyme A-conjugated fatty acids by diacylglycerol O-acyltransferases (DGAT1 and DGAT2)3. In other organisms, this activity is complemented by additional enzymes4, but whether such alternative pathways exist in humans remains unknown. Here we disrupt the DGAT pathway in haploid human cells and use iterative genetics to reveal an unrelated TAG-synthesizing system composed of a protein we called DIESL (also known as TMEM68, an acyltransferase of previously unknown function) and its regulator TMX1. Mechanistically, TMX1 binds to and controls DIESL at the endoplasmic reticulum, and loss of TMX1 leads to the unconstrained formation of DIESL-dependent lipid droplets. DIESL is an autonomous TAG synthase, and expression of human DIESL in Escherichia coli endows this organism with the ability to synthesize TAG. Although both DIESL and the DGATs function as diacylglycerol acyltransferases, they contribute to the cellular TAG pool under specific conditions. Functionally, DIESL synthesizes TAG at the expense of membrane phospholipids and maintains mitochondrial function during periods of extracellular lipid starvation. In mice, DIESL deficiency impedes rapid postnatal growth and affects energy homeostasis during changes in nutrient availability. We have therefore identified an alternative TAG biosynthetic pathway driven by DIESL under potent control by TMX1.
    DOI:  https://doi.org/10.1038/s41586-023-06497-4
  22. Sci Adv. 2023 Sep;9(35): eade7486
    BRAFΔβ3-αC in-frame deletion mutants differ in their dimerization propensity, HSP90 dependence, and druggability.
    Manuel Lauinger, Daniel Christen, Rhena F U Klar, Carole Roubaty, Christoph E Heilig, Michael Stumpe, Jennifer J Knox, Nikolina Radulovich, Laura Tamblyn, Irene Y Xie, Peter Horak, Andrea Forschner, Michael Bitzer, Uwe A Wittel, Melanie Boerries, Claudia R Ball, Christoph Heining, Hanno Glimm, Martina Fröhlich, Daniel Hübschmann, Steven Gallinger, Ralph Fritsch, Stefan Fröhling, Grainne M O'Kane, Jörn Dengjel, Tilman Brummer.
      In-frame BRAF exon 12 deletions are increasingly identified in various tumor types. The resultant BRAFΔβ3-αC oncoproteins usually lack five amino acids in the β3-αC helix linker and sometimes contain de novo insertions. The dimerization status of BRAFΔβ3-αC oncoproteins, their precise pathomechanism, and their direct druggability by RAF inhibitors (RAFi) has been under debate. Here, we functionally characterize BRAFΔLNVTAP>F and two novel mutants, BRAFdelinsFS and BRAFΔLNVT>F, and compare them with other BRAFΔβ3-αC oncoproteins. We show that BRAFΔβ3-αC oncoproteins not only form stable homodimers and large multiprotein complexes but also require dimerization. Nevertheless, details matter as aromatic amino acids at the deletion junction of some BRAFΔβ3-αC oncoproteins, e.g., BRAFΔLNVTAP>F, increase their stability and dimerization propensity while conferring resistance to monomer-favoring RAFi such as dabrafenib or HSP 90/CDC37 inhibition. In contrast, dimer-favoring inhibitors such as naporafenib inhibit all BRAFΔβ3-αC mutants in cell lines and patient-derived organoids, suggesting that tumors driven by such oncoproteins are vulnerable to these compounds.
    DOI:  https://doi.org/10.1126/sciadv.ade7486
  23. Mech Ageing Dev. 2023 Aug 29. pii: S0047-6374(23)00084-2. [Epub ahead of print] 111858
    Lipids and the Hallmarks of Ageing: From Pathology to Interventions.
    Rohit Sharma, Bhawna Diwan.
      Lipids are critical structural and functional architects of cellular homeostasis. Change in systemic lipid profile is a clinical indicator of underlying metabolic pathologies, and emerging evidence is now defining novel roles of lipids in modulating organismal ageing. Characteristic alterations in lipid metabolism correlate with age, and impaired systemic lipid profile can also accelerate the development of ageing phenotype. The present work provides a comprehensive review of the extent of lipids as regulators of the modern hallmarks of ageing viz., cellular senescence, chronic inflammation, gut dysbiosis, telomere attrition, genome instability, proteostasis and autophagy, epigenetic alterations, and stem cells dysfunctions. Current evidence on the modulation of each of these hallmarks has been discussed with emphasis on inherent age-dependent deficiencies in lipid metabolism as well as exogenous lipid changes. There appears to be sufficient evidence to consider impaired lipid metabolism as key driver of the ageing process although much of knowledge is yet fragmented. Considering dietary lipids, the type and quantity of lipids in the diet is a significant, but often overlooked determinant that governs the effects of lipids on ageing. Further research using integrative approaches amidst the known aging hallmarks is highly desirable for understanding the therapeutics of lipids associated with ageing.
    Keywords:  Ageing; Cellular senescence; Diet; Hallmarks; Inflammation; Lipidome; Lipids
    DOI:  https://doi.org/10.1016/j.mad.2023.111858
  24. Nat Metab. 2023 Aug 28.
    Cell cycle-linked vacuolar pH dynamics regulate amino acid homeostasis and cell growth.
    Voytek Okreglak, Rachel Ling, Maria Ingaramo, Nathaniel H Thayer, Alfred Millett-Sikking, Daniel E Gottschling.
      Amino acid homeostasis is critical for many cellular processes. It is well established that amino acids are compartmentalized using pH gradients generated between organelles and the cytoplasm; however, the dynamics of this partitioning has not been explored. Here we develop a highly sensitive pH reporter and find that the major amino acid storage compartment in Saccharomyces cerevisiae, the lysosome-like vacuole, alkalinizes before cell division and re-acidifies as cells divide. The vacuolar pH dynamics require the uptake of extracellular amino acids and activity of TORC1, the v-ATPase and the cycling of the vacuolar specific lipid phosphatidylinositol 3,5-bisphosphate, which is regulated by the cyclin-dependent kinase Pho85 (CDK5 in mammals). Vacuolar pH regulation enables amino acid sequestration and mobilization from the organelle, which is important for mitochondrial function, ribosome homeostasis and cell size control. Collectively, our data provide a new paradigm for the use of dynamic pH-dependent amino acid compartmentalization during cell growth/division.
    DOI:  https://doi.org/10.1038/s42255-023-00872-1
  25. Cold Spring Harb Perspect Biol. 2023 Aug 29. pii: a041394. [Epub ahead of print]
    A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization.
    Satyajit Mayor, Abrar Bhat, Akihiro Kusumi.
      The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for a better understanding of the physical nature, organization, and composition of cell membranes. This has been made possible by visualizing membrane heterogeneities and their dynamics and appreciating the asymmetrical arrangement of lipids in living cell membranes. Despite these advances, mechanisms underlying the local spatiotemporal organization of membrane components remain unclear. This review surveys various models of membrane organization, culminating in a new model that incorporates nonequilibrium processes and forces exerted by interactions with extramembrane elements such as the actin cytoskeleton. The proposed model provides a comprehensive understanding of membrane organization, taking into account the dynamic nature of the cell membrane and its interactions with its immediate environment.
    DOI:  https://doi.org/10.1101/cshperspect.a041394
  26. Hepatobiliary Pancreat Dis Int. 2023 Aug 22. pii: S1499-3872(23)00135-2. [Epub ahead of print]
    Pancreatic panniculitis as the first presentation of pancreatic ductal adenocarcinoma.
    Wei-Fang Zhu, Shan Fang, Jian-Jun Qiao.
      
    DOI:  https://doi.org/10.1016/j.hbpd.2023.08.016
  27. Nat Cell Biol. 2023 Aug 31.
    p16High senescence restricts cellular plasticity during somatic cell reprogramming.
    Bogdan B Grigorash, Dominic van Essen, Guixian Liang, Laurent Grosse, Alexander Emelyanov, Zhixin Kang, Alexey Korablev, Benoît Kanzler, Clement Molina, Elsa Lopez, Oleg N Demidov, Carmen Garrido, Feng Liu, Simona Saccani, Dmitry V Bulavin.
      Despite advances in four-factor (4F)-induced reprogramming (4FR) in vitro and in vivo, how 4FR interconnects with senescence remains largely under investigated. Here, using genetic and chemical approaches to manipulate senescent cells, we show that removal of p16High cells resulted in the 4FR of somatic cells into totipotent-like stem cells. These cells expressed markers of both pluripotency and the two-cell embryonic state, readily formed implantation-competent blastoids and, following morula aggregation, contributed to embryonic and extraembryonic lineages. We identified senescence-dependent regulation of nicotinamide N-methyltransferase as a key mechanism controlling the S-adenosyl-L-methionine levels during 4FR that was required for expression of the two-cell genes and acquisition of an extraembryonic potential. Importantly, a partial 4F epigenetic reprogramming in old mice was able to reverse several markers of liver aging only in conjunction with the depletion of p16High cells. Our results show that the presence of p16High senescent cells limits cell plasticity, whereas their depletion can promote a totipotent-like state and histopathological tissue rejuvenation during 4F reprogramming.
    DOI:  https://doi.org/10.1038/s41556-023-01214-9
  28. Traffic. 2023 Sep 01.
    Co-chaperone BAG3 enters autophagic pathway via its interaction with microtubule associated protein 1 light chain 3 beta.
    Hagen Körschgen, Marius Baeken, Daniel Schmitt, Heike Nagel, Christian Behl.
      The co-chaperone BAG3 is a hub for a variety of cellular pathways via its multiple domains and its interaction with chaperones of the HSP70 family or small HSPs. During aging and under cellular stress conditions in particular, BAG3, together with molecular chaperones, ensures the sequestration of aggregated or aggregation-prone ubiquitinated proteins to the autophagic-lysosomal system via ubiquitin receptors. Accumulating evidence for BAG3-mediated selective autophagy independent of cargo ubiquitination led to analyses predicting a direct interaction of BAG3 with LC3 proteins. Phylogenetically, BAG3 comprises several highly conserved potential LIRs, LC3-interacting regions, which might allow for the direct targeting of BAG3 including its cargo to autophagosomes and drive their autophagic degradation. Based on pull-down experiments, peptide arrays and proximity ligation assays, our results provide evidence of an interaction of BAG3 with LC3B. In addition, we could demonstrate that disabling all predicted LIRs abolished the inducibility of a colocalization of BAG3 with LC3B-positive structures and resulted in a substantial decrease of BAG3 levels within purified native autophagic vesicles compared with wild-type BAG3. These results suggest an autophagic targeting of BAG3 via interaction with LC3B. Therefore, we conclude that, in addition to being a key co-chaperone to HSP70, BAG3 may also act as a cargo receptor for client proteins, which would significantly extend the role of BAG3 in selective macroautophagy and protein quality control.
    Keywords:  BAG3; BAG3-mediated autophagy; Bcl2-associated athanogene 3; LC3; LIR
    DOI:  https://doi.org/10.1111/tra.12916
  29. Adv Mater. 2023 Aug 29. e2305394
    Cascade Catalytic Nanoparticles Selectively Alkalize Cancerous Lysosomes to Suppress Cancer Progression And Metastasis.
    Limin Pan, Haibao Peng, Bowon Lee, Jiaxu Zhao, Xiulian Shen, Ximei Yan, Yipeng Hua, Jeonghyun Kim, Dokyoon Kim, Mouhong Lin, Shengjian Zhang, Xiaohui Li, Xueying Yi, Feibai Yao, Zhiyong Qin, Jiulin Du, Yudan Chi, Jwa-Min Nam, Taeghwan Hyeon, Jianan Liu.
      Lysosomes are critical in modulating the progression and metastasis for various cancers. There is currently an unmet need for lysosomal alkalizers that can selectively and safely alter the pH and inhibit the function of cancer lysosomes. Here we report an effective, selective, and safe lysosomal alkalizer that can inhibit autophagy and suppress tumors in mice. Our lysosomal alkalizer consists of an Fex Oy core that generates hydroxyl radicals (•OH) in the presence of excessive H+ and H2 O2 inside cancer lysosomes and CeO2-z satellites that capture and convert •OH into hydroxide ions (OH- ). Alkalized lysosomes, which display impaired enzyme activity and autophagy, lead to cancer cell apoptosis. We show that our alkalizer effectively inhibited both local and systemic tumor growth and metastasis in mice. Our work demonstrates that the intrinsic properties of nanoparticles can be harnessed to build effective lysosomal alkalizers that are both selective and safe. This article is protected by copyright. All rights reserved.
    Keywords:  autophagy; lysosome alkalization; metastasis; nanoparticles; tumor therapy
    DOI:  https://doi.org/10.1002/adma.202305394
  30. J Clin Invest. 2023 Aug 29. pii: e163591. [Epub ahead of print]
    Epithelial TNF controls cell differentiation and CFTR activity to maintain intestinal mucin homeostasis.
    Efren A Reyes, David Castillo-Azofeifa, Jérémie Rispal, Tomas Wald, Rachel K Zwick, Brisa Palikuqi, Angela Mujukian, Shervin Rabizadeh, Alexander R Gupta, James M Gardner, Dario Boffelli, Zev J Gartner, Ophir D Klein.
      The gastrointestinal tract relies on the production, maturation, and transit of mucin to protect against pathogens and to lubricate the epithelial lining. Although the molecular and cellular mechanisms that regulate mucin production and movement are beginning to be understood, the upstream epithelial signals that contribute to mucin regulation remain unclear. Here, we report that the inflammatory cytokine tumor necrosis factor (TNF), generated by the epithelium, contributes to mucin homeostasis by regulating both cell differentiation and cystic fibrosis transmembrane conductance regulator (CFTR) activity. We used genetic mouse models and non-inflamed samples from Inflammatory Bowel Disease (IBD) patients undergoing anti-TNF therapy to assess the effect of in vivo perturbation of TNF. We found that inhibition of epithelial TNF promotes the differentiation of secretory progenitor cells into mucus-producing goblet cells. Furthermore, TNF treatment and CFTR inhibition in intestinal organoids demonstrated that TNF promotes ion transport and luminal flow via CFTR. The absence of TNF led to slower gut transit times, which we propose results from increased mucus accumulation coupled with decreased luminal fluid pumping. These findings point to a TNF-CFTR signaling axis in the adult intestine and identify epithelial-derived TNF as an upstream regulator of mucin homeostasis.
    Keywords:  Cytokines; Epithelial transport of ions and water; Gastroenterology; Molecular genetics
    DOI:  https://doi.org/10.1172/JCI163591
  31. bioRxiv. 2023 Aug 16. pii: 2023.08.15.553432. [Epub ahead of print]
    Adipose-Tumor Crosstalk contributes to CXCL5 Mediated Immune Evasion in PDAC.
    R McKinnon Walsh, Joseph Ambrose, Jarrid L Jack, Austin E Eades, Bailey Bye, Mariana T Ruckert, Appolinaire A Olou, Fanuel Messaggio, Prabhakar Chalise, Dong Pei, Michael N VanSaun.
       Background: CXCR1/2 inhibitors are being implemented with immunotherapies in PDAC clinical trials. Cytokines responsible for stimulating these receptors include CXCL ligands, typically secreted by activated immune cells, fibroblasts, and even adipocytes. Obesity has been linked to poor patient outcome and altered anti-tumor immunity. Adipose-derived cytokines and chemokines have been implicated as potential drivers of tumor cell immune evasion, suggesting a possibility of susceptibility to targeting specifically in the context of obesity.
    Methods: RNA-sequencing of human PDAC cell lines was used to assess differential influences on the cancer cell transcriptome after treatment with conditioned media from peri-pancreatic adipose tissue of lean and obese PDAC patients. The adipose-induced secretome of PDAC cells was then assessed by cytokine arrays and ELISAs. Lentiviral transduction and CRISPR-Cas9 was used to knock out CXCL5 from a murine PDAC cell line for orthotopic tumor studies in diet-induced obese, syngeneic mice. Flow cytometry was used to define the immune profiles of tumors. Anti-PD-1 immune checkpoint blockade therapy was administered to alleviate T cell exhaustion and invoke an immune response, while the mice were monitored at endpoint for differences in tumor size.
    Results: The chemokine CXCL5 was secreted in response to stimulation of PDAC cells with human adipose conditioned media (hAT-CM). PDAC CXCL5 secretion was induced by either IL-1β or TNF, but neutralization of both was required to limit secretion. Ablation of CXCL5 from tumors promoted an immune phenotype susceptible to PD-1 inhibitor therapy. While application of anti-PD-1 treatment to control tumors failed to alter tumor growth, knockout CXCL5 tumors were diminished.
    Conclusions: In summary, our findings show that known adipokines TNF and IL-1β can stimulate CXCL5 release from PDAC cells in vitro. In vivo , CXCL5 depletion alone is sufficient to promote T cell infiltration into tumors in an obese setting, but requires checkpoint blockade inhibition to alleviate tumor burden.
    DATA AVAILABILITY STATEMENT: Raw and processed RNAseq data will be further described in the GEO accession database ( awaiting approval from GEO for PRJ number ). Additional raw data is included in the supplemental material and available upon reasonable request.
    WHAT IS ALREADY KNOWN ON THIS TOPIC: Obesity is linked to a worsened patient outcome and immunogenic tumor profile in PDAC. CXCR1/2 inhibitors have begun to be implemented in combination with immune checkpoint blockade therapies to promote T cell infiltration under the premise of targeting the myeloid rich TME.
    WHAT THIS STUDY ADDS: Using in vitro/ex vivo cell and tissue culture-based assays with in vivo mouse models we have identified that adipose derived IL-1β and TNF can promote tumor secretion of CXCL5 which acts as a critical deterrent to CD8 T cell tumor infiltration, but loss of CXCL5 also leads to a more immune suppressive myeloid profile.
    HOW THIS STUDY MIGHT AFFECT RESEARCH PRACTICE OR POLICY: This study highlights a mechanism and emphasizes the efficacy of single CXCR1/2 ligand targeting that could be beneficial to overcoming tumor immune-evasion even in the obese PDAC patient population.
    DOI:  https://doi.org/10.1101/2023.08.15.553432
  32. Geroscience. 2023 Aug 31.
    Proteomic changes induced by longevity-promoting interventions in mice.
    Adam R Burns, Jack Wiedrick, Alicia Feryn, Michal Maes, Mukul K Midha, David H Baxter, Seamus R Morrone, Timothy J Prokop, Charu Kapil, Michael R Hoopmann, Ulrike Kusebauch, Eric W Deutsch, Noa Rappaport, Kengo Watanabe, Robert L Moritz, Richard A Miller, Jodi A Lapidus, Eric S Orwoll.
      Using mouse models and high-throughput proteomics, we conducted an in-depth analysis of the proteome changes induced in response to seven interventions known to increase mouse lifespan. This included two genetic mutations, a growth hormone receptor knockout (GHRKO mice) and a mutation in the Pit-1 locus (Snell dwarf mice), four drug treatments (rapamycin, acarbose, canagliflozin, and 17α-estradiol), and caloric restriction. Each of the interventions studied induced variable changes in the concentrations of proteins across liver, kidney, and gastrocnemius muscle tissue samples, with the strongest responses in the liver and limited concordance in protein responses across tissues. To the extent that these interventions promote longevity through common biological mechanisms, we anticipated that proteins associated with longevity could be identified by characterizing shared responses across all or multiple interventions. Many of the proteome alterations induced by each intervention were distinct, potentially implicating a variety of biological pathways as being related to lifespan extension. While we found no protein that was affected similarly by every intervention, we identified a set of proteins that responded to multiple interventions. These proteins were functionally diverse but tended to be involved in peroxisomal oxidation and metabolism of fatty acids. These results provide candidate proteins and biological mechanisms related to enhancing longevity that can inform research on therapeutic approaches to promote healthy aging.
    Keywords:  Longevity; Mass spectrometry; Mouse model; Proteomics
    DOI:  https://doi.org/10.1007/s11357-023-00917-z
  33. Cell Rep. 2023 Aug 30. pii: S2211-1247(23)01045-8. [Epub ahead of print]42(9): 113034
    Formate promotes invasion and metastasis in reliance on lipid metabolism.
    Catherine Delbrouck, Nicole Kiweler, Oleg Chen, Vitaly I Pozdeev, Lara Haase, Laura Neises, Anaïs Oudin, Aymeric Fouquier d'Hérouël, Ruolin Shen, Lisa Schlicker, Rashi Halder, Antoine Lesur, Anne Schuster, Nadja I Lorenz, Christian Jaeger, Maureen Feucherolles, Gilles Frache, Martyna Szpakowska, Andy Chevigne, Michael W Ronellenfitsch, Etienne Moussay, Marie Piraud, Alexander Skupin, Almut Schulze, Simone P Niclou, Elisabeth Letellier, Johannes Meiser.
      Metabolic rewiring is essential for cancer onset and progression. We previously showed that one-carbon metabolism-dependent formate production often exceeds the anabolic demand of cancer cells, resulting in formate overflow. Furthermore, we showed that increased extracellular formate concentrations promote the in vitro invasiveness of glioblastoma cells. Here, we substantiate these initial observations with ex vivo and in vivo experiments. We also show that exposure to exogeneous formate can prime cancer cells toward a pro-invasive phenotype leading to increased metastasis formation in vivo. Our results suggest that the increased local formate concentration within the tumor microenvironment can be one factor to promote metastases. Additionally, we describe a mechanistic interplay between formate-dependent increased invasiveness and adaptations of lipid metabolism and matrix metalloproteinase activity. Our findings consolidate the role of formate as pro-invasive metabolite and warrant further research to better understand the interplay between formate and lipid metabolism.
    Keywords:  CP: Cancer; CP: Metabolism; cancer metastasis; formate overflow; invasion; one-carbon metabolism
    DOI:  https://doi.org/10.1016/j.celrep.2023.113034
  34. Cancer Cell. 2023 Aug 23. pii: S1535-6108(23)00278-7. [Epub ahead of print]
    Transformer-based biomarker prediction from colorectal cancer histology: A large-scale multicentric study.
    TransSCOT consortium
      Deep learning (DL) can accelerate the prediction of prognostic biomarkers from routine pathology slides in colorectal cancer (CRC). However, current approaches rely on convolutional neural networks (CNNs) and have mostly been validated on small patient cohorts. Here, we develop a new transformer-based pipeline for end-to-end biomarker prediction from pathology slides by combining a pre-trained transformer encoder with a transformer network for patch aggregation. Our transformer-based approach substantially improves the performance, generalizability, data efficiency, and interpretability as compared with current state-of-the-art algorithms. After training and evaluating on a large multicenter cohort of over 13,000 patients from 16 colorectal cancer cohorts, we achieve a sensitivity of 0.99 with a negative predictive value of over 0.99 for prediction of microsatellite instability (MSI) on surgical resection specimens. We demonstrate that resection specimen-only training reaches clinical-grade performance on endoscopic biopsy tissue, solving a long-standing diagnostic problem.
    Keywords:  artificial intelligence; biomarker; colorectal cancer; deep learning; microsatellite instability; multiple instance learning; transformer
    DOI:  https://doi.org/10.1016/j.ccell.2023.08.002
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