bims-cagime Biomed News
on Cancer, aging and metabolism
Issue of 2024–11–24
forty-five papers selected by
Kıvanç Görgülü, Technical University of Munich
  1. Cancer cachexia: multilevel metabolic dysfunction.
  2. Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study.
  3. ImmunoCellCycle-ID - a high-precision immunofluorescence-based method for cell cycle identification.
  4. An alternative route for β-hydroxybutyrate metabolism supports fatty acid synthesis in cancer cells.
  5. A multi-subunit autophagic capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer.
  6. Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms.
  7. Dietary control of peripheral adipose storage capacity through membrane lipid remodelling.
  8. Systemic and transcriptional response to intermittent fasting and fasting-mimicking diet in mice.
  9. Cellular senescence: mechanisms and relevance to cancer and aging.
  10. Chromatin compaction during confined cell migration induces and reshapes nuclear condensates.
  11. Gliocidin is a nicotinamide-mimetic prodrug that targets glioblastoma.
  12. Midkine at the Crossroads of Aging and Cancer.
  13. mxfda: a comprehensive toolkit for functional data analysis of single-cell spatial data.
  14. Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays.
  15. Real-Time Analysis of Lipid Droplet Morpho-Chemical Dynamics in Living Human Hepatocytes via Phase-Guided Raman Sampling.
  16. OSGIN1 promotes ferroptosis resistance by directly enhancing GCLM activity.
  17. Multimodal single cell-resolved spatial proteomics reveal pancreatic tumor heterogeneity.
  18. DFCP1 is a Regulator of Starvation-driven ATGL-mediated Lipid Droplet Lipolysis.
  19. Skeletal muscle is independently associated with grade 3-4 toxicity in advanced stage pancreatic ductal adenocarcinoma patients receiving chemotherapy.
  20. DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation.
  21. Nutrient control of growth and metabolism through mTORC1 regulation of mRNA splicing.
  22. Pancreatic CAF-derived Autotaxin (ATX) drives autocrine CTGF expression to modulate pro-tumorigenic signaling.
  23. NFκB and JNK pathways mediate metabolic adaptation upon ESCRT-I deficiency.
  24. Incretin-responsive human pancreatic adipose tissue organoids: A functional model for fatty pancreas research.
  25. An allosteric inhibitor of RhoGAP class-IX myosins suppresses the metastatic features of cancer cells.
  26. Probe set selection for targeted spatial transcriptomics.
  27. An expanded view of cell competition.
  28. Mg2+-driven selection of natural phosphatidic acids in primitive membranes.
  29. Automated workflow for the cell cycle analysis of (non-)adherent cells using a machine learning approach.
  30. Single-cell RNA-seq analysis of cancer-endothelial cell interactions in primary tumor and peritoneal metastasis from a single patient with colorectal cancer.
  31. Sensing, feeling and sentience in unicellular organisms and living cells.
  32. Impaired branched chain amino acid (BCAA) catabolism during adipocyte differentiation decreases glycolytic flux.
  33. Repurposing large-format microarrays for scalable spatial transcriptomics.
  34. PhosX: data-driven kinase activity inference from phosphoproteomics experiments.
  35. Evidence of persistent hyperphagia following a dietary weight-loss intervention in mice.
  36. Transmembrane coupling accelerates the growth of liquid-like protein condensates.
  37. The value of PET/CT radiomics for predicting survival outcomes in patients with pancreatic ductal adenocarcinoma.
  38. Directed evolution of the multicopper oxidase laccase for cell surface proximity labeling and electron microscopy.
  39. Increased translation driven by non-canonical EZH2 creates a synthetic vulnerability in enzalutamide-resistant prostate cancer.
  40. Real-time imaging reveals a role for macrophage protrusive motility in melanoma invasion.
  41. Whole-brain spatial transcriptional analysis at cellular resolution.
  42. A cell atlas foundation model for scalable search of similar human cells.
  43. Adipose tissue retains an epigenetic memory of obesity after weight loss.
  44. TNFR2 blockade promotes antitumoral immune response in PDAC by targeting activated Treg and reducing T cell exhaustion.
  45. PKN2 is a dependency of the mesenchymal-like cancer cell state.
  1. Nat Metab. 2024 Nov 22.
    Cancer cachexia: multilevel metabolic dysfunction.
    Mauricio Berriel Diaz, Maria Rohm, Stephan Herzig.
      Cancer cachexia is a complex metabolic disorder marked by unintentional body weight loss or 'wasting' of body mass, driven by multiple aetiological factors operating at various levels. It is associated with many malignancies and significantly contributes to cancer-related morbidity and mortality. With emerging recognition of cancer as a systemic disease, there is increasing awareness that understanding and treatment of cancer cachexia may represent a crucial cornerstone for improved management of cancer. Here, we describe the metabolic changes contributing to body wasting in cachexia and explain how the entangled action of both tumour-derived and host-amplified processes induces these metabolic changes. We discuss energy homeostasis and possible ways that the presence of a tumour interferes with or hijacks physiological energy conservation pathways. In that context, we highlight the role played by metabolic cross-talk mechanisms in cachexia pathogenesis. Lastly, we elaborate on the challenges and opportunities in the treatment of this devastating paraneoplastic phenomenon that arise from the complex and multifaceted metabolic cross-talk mechanisms and provide a status on current and emerging therapeutic approaches.
    DOI:  https://doi.org/10.1038/s42255-024-01167-9
  2. EMBO J. 2024 Nov 18.
    Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study.
    Johanna Tüshaus, Stephan Eckert, Marius Schliemann, Yuxiang Zhou, Pauline Pfeiffer, Christiane Halves, Federico Fusco, Johannes Weigel, Lisa Hönikl, Vicki Butenschön, Rumyana Todorova, Hilka Rauert-Wunderlich, Matthew The, Andreas Rosenwald, Volker Heinemann, Julian Holch, Katja Steiger, Claire Delbridge, Bernhard Meyer, Wilko Weichert, Carolin Mogler, Peer-Hendrik Kuhn, Bernhard Kuster.
      Proteome profiling of formalin-fixed paraffin-embedded (FFPE) specimens has gained traction for the analysis of cancer tissue for the discovery of molecular biomarkers. However, reports so far focused on single cancer entities, comprised relatively few cases and did not assess the long-term performance of experimental workflows. In this study, we analyze 1220 tumors from six cancer entities processed over the course of three years. Key findings include the need for a new normalization method ensuring equal and reproducible sample loading for LC-MS/MS analysis across cohorts, showing that tumors can, on average, be profiled to a depth of >4000 proteins and discovering that current software fails to process such large ion mobility-based online fractionated datasets. We report the first comprehensive pan-cancer proteome expression resource for FFPE material comprising 11,000 proteins which is of immediate utility to the scientific community, and can be explored via a web resource. It enables a range of analyses including quantitative comparisons of proteins between patients and cohorts, the discovery of protein fingerprints representing the tissue of origin or proteins enriched in certain cancer entities.
    Keywords:  Clinical Proteomics; Mass Spectrometry; Pan-cancer; Public Pan-cancer FFPE Resource; TIC Normalization
    DOI:  https://doi.org/10.1038/s44318-024-00289-w
  3. J Cell Sci. 2024 Nov 15. pii: jcs263414. [Epub ahead of print]137(22):
    ImmunoCellCycle-ID - a high-precision immunofluorescence-based method for cell cycle identification.
    Yu-Lin Chen, Yu-Chia Chen, Aussie Suzuki.
      The cell cycle is a fundamental process essential for cell proliferation, differentiation and development. It consists of four major phases: G1, S, G2 and M. These phases collectively drive the reproductive cycle and are meticulously regulated by various proteins that play crucial roles in both the prevention and progression of cancer. Traditional methods for studying these functions, such as flow cytometry, require a substantial number of cells to ensure accuracy. In this study, we have developed a user-friendly immunofluorescence-based method for identifying cell cycle stages, providing single-cell resolution and precise identification of G1, early/mid S, late S, early/mid G2, late G2, and each sub-stage of the M phase using fluorescence microscopy called ImmunoCellCycle-ID. This method provides high-precision cell cycle identification and can serve as an alternative to, or in combination with, traditional flow cytometry to dissect detailed sub-stages of the cell cycle in a variety of cell lines.
    Keywords:  Cell cycle; Imaging; Immunofluorescence-based cell cycle identification; Microscopy
    DOI:  https://doi.org/10.1242/jcs.263414
  4. bioRxiv. 2024 Nov 03. pii: 2024.10.31.621317. [Epub ahead of print]
    An alternative route for β-hydroxybutyrate metabolism supports fatty acid synthesis in cancer cells.
    Faith C Kaluba, Thomas J Rogers, Yu-Jin Jeong, Althea Waldhart, Kelly H Sokol, Cameron J Lee, Samuel R Daniels, Joseph Longo, Amy Johnson, Ryan D Sheldon, Russell G Jones, Evan C Lien.
      Cancer cells are exposed to diverse metabolites in the tumor microenvironment that are used to support the synthesis of nucleotides, amino acids, and lipids needed for rapid cell proliferation 1-3 . Recent work has shown that ketone bodies such as β-hydroxybutyrate (β-OHB), which are elevated in circulation under fasting conditions or low glycemic diets, can serve as an alternative fuel that is metabolized in the mitochondria to provide acetyl-CoA for the tricarboxylic acid (TCA) cycle in some tumors 4-7 . Here, we discover a non-canonical route for β-OHB metabolism, in which β-OHB can bypass the TCA cycle to generate cytosolic acetyl-CoA for de novo fatty acid synthesis in cancer cells. We show that β-OHB-derived acetoacetate in the mitochondria can be shunted into the cytosol, where acetoacetyl-CoA synthetase (AACS) and thiolase convert it into acetyl-CoA for fatty acid synthesis. This alternative metabolic routing of β-OHB allows it to avoid oxidation in the mitochondria and net contribute to anabolic biosynthetic processes. In cancer cells, β-OHB is used for fatty acid synthesis to support cell proliferation under lipid-limited conditions in vitro and contributes to tumor growth under lipid-limited conditions induced by a calorie-restricted diet in vivo . Together, these data demonstrate that β-OHB is preferentially used for fatty acid synthesis in cancer cells to support tumor growth.
    DOI:  https://doi.org/10.1101/2024.10.31.621317
  5. bioRxiv. 2024 Oct 29. pii: 2024.10.27.620516. [Epub ahead of print]
    A multi-subunit autophagic capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer.
    Marine Berquez, Alexander L Li, Matthew A Luy, Anthony C Venida, Thomas O'Loughlin, Gilles Rademaker, Abhilash Barpanda, Jingjie Hu, Julian Yano, Arun Wiita, Luke A Gilbert, Peter M Bruno, Rushika M Perera.
      Pancreatic ductal adenocarcinoma (PDA) evades immune detection partly via autophagic capture and lysosomal degradation of major histocompatibility complex class I (MHC-I). Why MHC-I is susceptible to capture via autophagy remains unclear. By synchronizing exit of proteins from the endoplasmic reticulum (ER), we show that PDAC cells display prolonged retention of MHC-I in the ER and fail to efficiently route it to the plasma membrane. A capture-complex composed of NBR1 and the ER-phagy receptor TEX264 facilitates targeting of MHC-I for autophagic degradation, and suppression of either receptor is sufficient to increase total levels and re-route MHC-I to the plasma membrane. Binding of MHC-I to the capture complex is linked to antigen presentation efficiency, as inhibiting antigen loading via knockdown of TAP1 or beta 2-Microglobulin led to increased binding between MHC-I and the TEX264-NBR1 capture complex. Conversely, expression of ER directed high affinity antigenic peptides led to increased MHC-I at the cell surface and reduced lysosomal degradation. A genome-wide CRISPRi screen identified NFXL1, as an ER-resident E3 ligase that binds to MHC-I and mediates its autophagic capture. High levels of NFXL1 are negatively correlated with MHC-I protein expression and predicts poor patient prognosis. These data highlight an ER resident capture complex tasked with sequestration and degradation of non-conformational MHC-I in PDAC cells, and targeting this complex has the potential to increase PDAC immunogenicity.
    DOI:  https://doi.org/10.1101/2024.10.27.620516
  6. Immunity. 2024 Nov 20. pii: S1074-7613(24)00494-1. [Epub ahead of print]
    Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms.
    Siyu Sun, Eunae You, Jungeui Hong, David Hoyos, Isabella S Del Priore, Kaloyan M Tsanov, Om Mattagajasingh, Andrea Di Gioacchino, Sajid A Marhon, Jonathan Chacon-Barahona, Hao Li, Hua Jiang, Samira Hozeifi, Omar Rosas-Bringas, Katherine H Xu, Yuhui Song, Evan R Lang, Alexandra S Rojas, Linda T Nieman, Bidish K Patel, Rajmohan Murali, Pharto Chanda, Ali Karacay, Nicolas Vabret, Daniel D De Carvalho, Daniel Zenklusen, John LaCava, Scott W Lowe, David T Ting, Christine A Iacobuzio-Donahue, Alexander Solovyov, Benjamin D Greenbaum.
      To thrive, cancer cells must navigate acute inflammatory signaling accompanying oncogenic transformation, such as via overexpression of repeat elements. We examined the relationship between immunostimulatory repeat expression, tumor evolution, and the tumor-immune microenvironment. Integration of multimodal data from a cohort of pancreatic ductal adenocarcinoma (PDAC) patients revealed expression of specific Alu repeats predicted to form double-stranded RNAs (dsRNAs) and trigger retinoic-acid-inducible gene I (RIG-I)-like-receptor (RLR)-associated type-I interferon (IFN) signaling. Such Alu-derived dsRNAs also anti-correlated with pro-tumorigenic macrophage infiltration in late stage tumors. We defined two complementary pathways whereby PDAC may adapt to such anti-tumorigenic signaling. In mutant TP53 tumors, ORF1p from long interspersed nuclear element (LINE)-1 preferentially binds Alus and decreases their expression, whereas adenosine deaminases acting on RNA 1 (ADAR1) editing primarily reduces dsRNA formation in wild-type TP53 tumors. Depletion of either LINE-1 ORF1p or ADAR1 reduced tumor growth in vitro. The fact that tumors utilize multiple pathways to mitigate immunostimulatory repeats implies the stress from their expression is a fundamental phenomenon to which PDAC, and likely other tumors, adapt.
    Keywords:  ADAR1; Tp53; cancer evolution; cancer immunity; inverted Alus; retrotransposons; tumor-immune microenvironment
    DOI:  https://doi.org/10.1016/j.immuni.2024.10.015
  7. bioRxiv. 2024 Oct 29. pii: 2024.10.25.620374. [Epub ahead of print]
    Dietary control of peripheral adipose storage capacity through membrane lipid remodelling.
    Marcus J Tol, Yuta Shimanaka, Alexander H Bedard, Jennifer Sapia, Liujuan Cui, Mariana Colaço-Gaspar, Peter Hofer, Alessandra Ferrari, Kevin Qian, John P Kennelly, Stephen D Lee, Yajing Gao, Xu Xiao, Jie Gao, Julia J Mack, Thomas A Weston, Calvin Pan, Aldons J Lusis, Kevin J Williams, Baolong Su, Daniel P Pike, Alex Reed, Natalia Milosevich, Benjamin F Cravatt, Makoto Arita, Stephen G Young, David A Ford, Rudolf Zechner, Stefano Vanni, Peter Tontonoz.
      Complex genetic and dietary cues contribute to the development of obesity, but how these are integrated on a molecular level is incompletely understood. Here, we show that PPARγ supports hypertrophic expansion of adipose tissue via transcriptional control of LPCAT3, a membrane-bound O-acyltransferase that enriches diet-derived omega-6 ( n -6) polyunsaturated fatty acids (PUFAs) in the phospholipidome. In high-fat diet-fed mice, lowering membrane n -6 PUFA levels by adipocyte-specific Lpcat3 knockout ( Lpcat3 AKO ) or by dietary lipid manipulation leads to dysfunctional triglyceride (TG) storage, ectopic fat deposition and insulin resistance. Aberrant lipolysis of stored TGs in Lpcat3 AKO adipose tissues instigates a non-canonical adaptive response that engages a futile lipid cycle to increase energy expenditure and limit further body weight gain. Mechanistically, we find that adipocyte LPCAT3 activity promotes TG storage by selectively enriching n -6 arachidonoyl-phosphatidylethanolamine at the ER-lipid droplet interface, which in turn favours the budding of large droplets that exhibit greater resistance to ATGL-dependent hydrolysis. Thus, our study highlights the PPARγ-LPCAT3 pathway as a molecular link between dietary n -6 PUFA intake, adipose expandability and systemic energy balance.
    DOI:  https://doi.org/10.1101/2024.10.25.620374
  8. BMC Biol. 2024 Nov 20. 22(1): 268
    Systemic and transcriptional response to intermittent fasting and fasting-mimicking diet in mice.
    Helene Michenthaler, Kalina Duszka, Isabel Reinisch, Markus Galhuber, Elisabeth Moyschewitz, Sarah Stryeck, Tobias Madl, Andreas Prokesch, Jelena Krstic.
       BACKGROUND: Dietary restriction (DR) has multiple beneficial effects on health and longevity and can also improve the efficacy of certain therapies. Diets used to instigate DR are diverse and the corresponding response is not uniformly measured. We compared the systemic and liver-specific transcriptional response to intermittent fasting (IF) and commercially available fasting-mimicking diet (FMD) after short- and long-term use in C57BL/6 J mice.
    RESULTS: We show that neither DR regimen causes observable adverse effects in mice. The weight loss was limited to 20% and was quickly compensated during refeeding days. The slightly higher weight loss upon FMD versus IF correlated with stronger fasting response assessed by lower glucose levels and higher ketone body, free fatty acids and especially FGF21 concentrations in blood. RNA sequencing demonstrated similar transcriptional programs in the liver after both regimens, with PPARα signalling as top enriched pathway, while on individual gene level FMD more potently increased gluconeogenesis-related, and PPARα and p53 target gene expression compared to IF. Repeated IF induced similar transcriptional responses as acute IF. However, repeated cycles of FMD resulted in blunted expression of genes involved in ketogenesis and fatty acid oxidation.
    CONCLUSIONS: Short-term FMD causes more pronounced changes in blood parameters and slightly higher weight loss than IF, while both activate similar pathways (particularly PPARα signalling) in the liver. On individual gene level FMD induces a stronger transcriptional response, whereas cyclic application blunts transcriptional upregulation of fatty acid oxidation and ketogenesis only in FMD. Hence, our comparative characterization of IF and FMD protocols renders both as effective DR regimens and serves as resource in the fasting research field.
    Keywords:  Fasting-mimicking diet; Gene expression; Intermittent fasting; Metabolites; Mice; RNAseq; Systemic response; Transcription
    DOI:  https://doi.org/10.1186/s12915-024-02061-2
  9. J Biochem. 2024 Nov 16. pii: mvae079. [Epub ahead of print]
    Cellular senescence: mechanisms and relevance to cancer and aging.
    Shota Yamauchi, Akiko Takahashi.
      Cellular senescence is an irreversible cell cycle arrest induced by stresses such as telomere shortening and oncogene activation. It acts as a tumor suppressor mechanism that prevents the proliferation of potentially tumorigenic cells. Paradoxically, senescent stromal cells that arise in the tumor microenvironment have been shown to promote tumor progression. In addition, senescent cells that accumulate in vivo over time are thought to contribute to aging and age-related diseases. These deleterious effects of senescent cells involve the secretion of bioactive molecules such as inflammatory cytokines and chemokines, a phenomenon known as the senescence-associated secretory phenotype (SASP). While the role of cellular senescence in vivo is becoming increasingly clear, the intracellular signaling pathways that induce the expression of senescent phenotypes are not fully understood. In this review, we outline senescence-associated signaling pathways and their relevance to cancer and aging.
    Keywords:  SASP; aging; cancer; cellular senescence; stress signaling
    DOI:  https://doi.org/10.1093/jb/mvae079
  10. Nat Commun. 2024 Nov 18. 15(1): 9964
    Chromatin compaction during confined cell migration induces and reshapes nuclear condensates.
    Jessica Z Zhao, Jing Xia, Clifford P Brangwynne.
      Cell migration through small constrictions during cancer metastasis requires significant deformation of the nucleus, with associated mechanical stress on the nuclear lamina and chromatin. However, how mechanical deformation impacts various subnuclear structures, including protein and nucleic acid-rich biomolecular condensates, is largely unknown. Here, we find that cell migration through confined spaces gives rise to mechanical deformations of the chromatin network, which cause embedded nuclear condensates, including nucleoli and nuclear speckles, to deform and coalesce. Chromatin deformations exhibit differential behavior in the advancing vs. trailing region of the nucleus, with the trailing half being more permissive for de novo condensate formation. We show that this results from increased chromatin heterogeneity, which gives rise to a shift in the binodal phase boundary. Taken together, our findings show how chromatin deformation impacts condensate assembly and properties, which can potentially contribute to cellular mechanosensing.
    DOI:  https://doi.org/10.1038/s41467-024-54120-5
  11. Nature. 2024 Nov 20.
    Gliocidin is a nicotinamide-mimetic prodrug that targets glioblastoma.
    Yu-Jung Chen, Swathi V Iyer, David Chun-Cheng Hsieh, Buren Li, Harold K Elias, Tao Wang, Jing Li, Mungunsarnai Ganbold, Michelle C Lien, Yu-Chun Peng, Xuanhua P Xie, Chenura D Jayewickreme, Marcel R M van den Brink, Sean F Brady, S Kyun Lim, Luis F Parada.
      Glioblastoma is incurable and in urgent need of improved therapeutics1. Here we identify a small compound, gliocidin, that kills glioblastoma cells while sparing non-tumour replicative cells. Gliocidin activity targets a de novo purine synthesis vulnerability in glioblastoma through indirect inhibition of inosine monophosphate dehydrogenase 2 (IMPDH2). IMPDH2 blockade reduces intracellular guanine nucleotide levels, causing nucleotide imbalance, replication stress and tumour cell death2. Gliocidin is a prodrug that is anabolized into its tumoricidal metabolite, gliocidin-adenine dinucleotide (GAD), by the enzyme nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) of the NAD+ salvage pathway. The cryo-electron microscopy structure of GAD together with IMPDH2 demonstrates its entry, deformation and blockade of the NAD+ pocket3. In vivo, gliocidin penetrates the blood-brain barrier and extends the survival of mice with orthotopic glioblastoma. The DNA alkylating agent temozolomide induces Nmnat1 expression, causing synergistic tumour cell killing and additional survival benefit in orthotopic patient-derived xenograft models. This study brings gliocidin to light as a prodrug with the potential to improve the survival of patients with glioblastoma.
    DOI:  https://doi.org/10.1038/s41586-024-08224-z
  12. Cancer Res. 2024 Nov 21.
    Midkine at the Crossroads of Aging and Cancer.
    Huiru Bai, Shang Cai.
      Aging in mammals, including humans, is marked by a multitude of molecular, cellular, and systemic changes that increase the risk of various diseases, including cancer. While the link between aging and increased cancer incidence is well documented, the precise biological mechanisms driving tumor initiation remain less clear. In a recent issue of Cancer Cell, Yan and colleagues have identified Midkine, a heparin-binding growth factor, as an age-related biomarker mediating both ageing related phenotypes and cancer development. Further exploration of these molecular dynamics, alongside the development of targeted drugs, holds great promise for reducing aging-related cancer incidence.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-4381
  13. Bioinform Adv. 2024 ;4(1): vbae155
    mxfda: a comprehensive toolkit for functional data analysis of single-cell spatial data.
    Julia Wrobel, Alex C Soupir, Mitchell T Hayes, Lauren C Peres, Thao Vu, Andrew Leroux, Brooke L Fridley.
       Summary: Technologies that produce spatial single-cell (SC) data have revolutionized the study of tissue microstructures and promise to advance personalized treatment of cancer by revealing new insights about the tumor microenvironment. Functional data analysis (FDA) is an ideal analytic framework for connecting cell spatial relationships to patient outcomes, but can be challenging to implement. To address this need, we present mxfda, an R package for end-to-end analysis of SC spatial data using FDA. mxfda implements a suite of methods to facilitate spatial analysis of SC imaging data using FDA techniques.
    Availability and implementation: The mxfda R package is freely available at https://cran.r-project.org/package=mxfda and has detailed documentation, including four vignettes, available at http://juliawrobel.com/mxfda/.
    DOI:  https://doi.org/10.1093/bioadv/vbae155
  14. STAR Protoc. 2024 Nov 19. pii: S2666-1667(24)00622-1. [Epub ahead of print]5(4): 103457
    Protocol for using Multiomics2Targets to identify targets and driver kinases for cancer cohorts profiled with multi-omics assays.
    Giacomo B Marino, Eden Z Deng, Daniel J B Clarke, Ido Diamant, Adam C Resnick, Weiping Ma, Pei Wang, Avi Ma'ayan.
      The availability of multi-omics data applied to profile cancer cohorts is rapidly increasing. Here, we present a protocol for Multiomics2Targets, a computational pipeline that can identify driver cell signaling pathways, protein kinases, and cell-surface targets for immunotherapy. We describe steps for preparing the data, uploading files, and tuning parameters. We then detail procedures for running the workflow, visualizing the results, and exporting and sharing reports containing the analysis. For complete details on the use and execution of this protocol, please refer to Deng et al.1.
    Keywords:  bioinformatics; cancer; computer sciences; systems biology
    DOI:  https://doi.org/10.1016/j.xpro.2024.103457
  15. Anal Chem. 2024 Nov 20.
    Real-Time Analysis of Lipid Droplet Morpho-Chemical Dynamics in Living Human Hepatocytes via Phase-Guided Raman Sampling.
    Hao Zhang, Jingde Fang, Kaiqin Chu, Zachary J Smith.
      Lipid droplets (LDs) are highly dynamic organelles, undertaking many important functions such as maintaining lipid metabolism and cellular homeostasis. Traditional methods to analyze LD dynamics focus on morphological changes, while chemical dynamics cannot be easily probed with traditional analytical chemistry techniques. To overcome this challenge, we show here how our phase-guided Raman sampling method, where high-resolution phase microscopy images direct a Raman sampling beam, can perform label-free, multimodal characterization of LD dynamics in living cells at both the single-cell and single-LD levels with submicron accuracy and high temporal resolution. We demonstrate the study of the morphological-compositional dynamics of human hepatocellular carcinoma cells (PLC cells) under different environmental conditions and with and without fatty acid supplementation, providing insight into LD heterogeneity and heterogeneity of response. Finally, we introduce a measurement method for the dynamics of cell-average LD composition, which can quickly and accurately characterize the lipid dynamics at the single-cell level with <30 s temporal resolution. The results here show the promise of the phase-guided Raman sampling method for dynamic morpho-chemical profiling of organelle populations.
    DOI:  https://doi.org/10.1021/acs.analchem.4c03633
  16. Biochem Biophys Res Commun. 2024 Nov 17. pii: S0006-291X(24)01551-1. [Epub ahead of print]740 151015
    OSGIN1 promotes ferroptosis resistance by directly enhancing GCLM activity.
    Yuanyuan Jia, Xinyue Zhang, Yiqing Cai, Hanghui Yu, Guohua Cao, Enyong Dai, Rui Kang, Daolin Tang, Nanjun Hu, Leng Han.
      Oxidative stress induced growth inhibitor 1 (OSGIN1) is a tumor protein p53 (TP53)-target gene involved in the oxidative stress response and promotes apoptosis. Here, we present the first evidence that OSGIN1 functions conversely by inhibiting ferroptosis, a distinct form of oxidative cell death driven by excessive lipid peroxidation. OSGIN1 expression is upregulated by pharmacological ferroptosis inducers in an NFE2 like BZIP transcription factor 2 (NFE2L2)-dependent manner, rather than through the TP53 pathway, in human pancreatic ductal adenocarcinoma (PDAC) cells. Genetic depletion of OSGIN1 or NFE2L2 similarly promotes ferroptosis, while re-expression of OSGIN1 rescues ferroptosis resistance in NFE2L2-knockout cells, both in vitro and in animal models. Mechanistically, immunoprecipitation combined with mass spectrometry revealed that OSGIN1 interacts with glutamate-cysteine ligase modifier subunit (GCLM), enhancing glutathione production and thereby mitigating oxidative stress. Additionally, OSGIN1 expression shows a positive correlation with NFE2L2 expression in pancreatic tumors, which is linked to poorer prognosis in PDAC patients. Collectively, these findings establish a novel defense mechanism that regulates ferroptosis and may influence tumor suppression in PDAC.
    Keywords:  Ferroptosis; GCLM; Glutathione; OSGIN1; Oxidative stress
    DOI:  https://doi.org/10.1016/j.bbrc.2024.151015
  17. Nat Commun. 2024 Nov 21. 15(1): 10100
    Multimodal single cell-resolved spatial proteomics reveal pancreatic tumor heterogeneity.
    Yanfen Xu, Xi Wang, Yuan Li, Yiheng Mao, Yiran Su, Yize Mao, Yun Yang, Weina Gao, Changying Fu, Wendong Chen, Xueting Ye, Fuchao Liang, Panzhu Bai, Ying Sun, Shengping Li, Ruilian Xu, Ruijun Tian.
      Despite the advances in antibody-guided cell typing and mass spectrometry-based proteomics, their integration is hindered by challenges for processing rare cells in the heterogeneous tissue context. Here, we introduce Spatial and Cell-type Proteomics (SCPro), which combines multiplexed imaging and flow cytometry with ion exchange-based protein aggregation capture technology to characterize spatial proteome heterogeneity with single-cell resolution. The SCPro is employed to explore the pancreatic tumor microenvironment and reveals the spatial alternations of over 5000 proteins by automatically dissecting up to 100 single cells guided by multi-color imaging of centimeter-scale formalin-fixed, paraffin-embedded tissue slide. To enhance cell-type resolution, we characterize the proteome of 14 different cell types by sorting up to 1000 cells from the same tumor, which allows us to deconvolute the spatial distribution of immune cell subtypes and leads to the discovery of subtypes of regulatory T cells. Together, the SCPro provides a multimodal spatial proteomics approach for profiling tissue proteome heterogeneity.
    DOI:  https://doi.org/10.1038/s41467-024-54438-0
  18. J Lipid Res. 2024 Nov 18. pii: S0022-2275(24)00205-0. [Epub ahead of print] 100700
    DFCP1 is a Regulator of Starvation-driven ATGL-mediated Lipid Droplet Lipolysis.
    V A Ismail, M N Harvey, Zak Baker, J Castillo-Badillo, T Naismith, D J Pagliarini, D J Kast.
      Lipid droplets (LDs) are transient lipid storage organelles that can be readily tapped to resupply cells with energy or lipid building blocks, and therefore play a central role in cellular metabolism. Double FYVE Domain Containing Protein 1 (DFCP1/ZFYV1) has emerged as a key regulator of LD metabolism, where the nucleotide-dependent accumulation of DFCP1 on LDs influences their size, number, and dynamics. Here we show that DFCP1 regulates lipid metabolism by directly modulating the activity of Adipose Triglyceride Lipase (ATGL/PNPLA2), the rate-limiting lipase driving the catabolism of LDs. We show through pharmacological inhibition of key enzymes associated with LD metabolism that DFCP1 specifically regulates lipolysis and, to a lesser extent, lipophagy. Consistent with this observation, DFCP1 interacts with and recruits ATGL to LDs in starved cells, irrespective of other known regulatory factors of ATGL. We further establish that this interaction prevents dynamic disassociation of ATGL from LDs and thereby impedes the rate of LD lipolysis. Collectively, our findings indicate that DFCP1 is a nutrient-sensitive regulator of LD catabolism.
    Keywords:  ABHD5; ATGL; CGI-58; DFCP1; FRAP; PLPL2; ZFYVE1; diglycerides; fatty acids; lipid droplets; triglycerides
    DOI:  https://doi.org/10.1016/j.jlr.2024.100700
  19. Clin Nutr ESPEN. 2024 Nov 20. pii: S2405-4577(24)01513-4. [Epub ahead of print]
    Skeletal muscle is independently associated with grade 3-4 toxicity in advanced stage pancreatic ductal adenocarcinoma patients receiving chemotherapy.
    Merel R Aberle, Mariëlle M E Coolsen, Gilles Wenmaekers, Leroy Volmer, Ralph Brecheisen, David van Dijk, Leonard Wee, Ronald M Van Dam, Judith de Vos-Geelen, Sander S Rensen, Steven W M Olde Damink.
       BACKGROUND: Patients with advanced-stage pancreatic ductal adenocarcinoma (PDAC) are regularly treated with FOLFIRINOX, a chemotherapy regimen based on 5-fluorouracil, irinotecan and oxaliplatin, which is associated with high toxicity. Dosing of FOLFIRINOX is based on body surface area, risking under- or overdosing caused by altered pharmacokinetics due to interindividual differences in body composition. This study aimed to investigate the relationship between body composition and treatment toxicity in advanced stage PDAC patients treated with FOLFIRINOX.
    METHODS: Data from patients treated at the Maastricht University Medical Centre+ between 2012-2020 were collected retrospectively (n=65). Skeletal muscle-, visceral adipose tissue, subcutaneous adipose tissue-, (SM-Index, VAT-Index, SAT-Index resp.) and Skeletal Muscle Radiation Attenuation (SM-RA) were calculated after segmentation of computed tomography (CT) images at the third lumbar level using a validated deep learning method. Lean body mass (LBM) was estimated using SM-Index. Toxicities were scored and grade 3-4 adverse events were considered dose-limiting toxicities (DLTs).
    RESULTS: Sixty-seven DLTs were reported during the median follow-up of 51.4 (95%CI 39.2 - 63.7) weeks. Patients who experienced at least one DLT had significantly higher dose intensity per LBM for all separate cytotoxics of FOLFIRINOX. Independent prognostic factors for the number of DLTs per cycle were: sarcopenia (β=0.292; 95%CI 0.013 - 0.065; p=0.013), SM-Index change (% per 30 days, β=-0.045; 95%CI -0.079 - -0.011; p=0.011), VAT-Index change (% per 30 days, β=-0.006; 95%CI -0.012 - 0.000; p=0.040) between diagnosis and the first follow-up CT scan, and cumulative relative dose intensity >80% (β=-0.315; 95% CI -0.543 - -0.087; p=0.008).
    CONCLUSION: Sarcopenia and early muscle and fat wasting during FOLFIRINOX treatment were associated with treatment-related toxicity, warranting exploration of body composition guided personalized dosing of chemotherapeutics to limit DLTs.
    Keywords:  Personalized medicine; chemotherapy; pancreatic cancer; systemic therapy; toxicity
    DOI:  https://doi.org/10.1016/j.clnesp.2024.11.004
  20. bioRxiv. 2024 Oct 29. pii: 2024.10.26.620414. [Epub ahead of print]
    DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation.
    Emily K W Lo, Adrian Idrizi, Rakel Tryggvadottir, Weiqiang Zhou, Wenpin Hou, Hongkai Ji, Patrick Cahan, Andrew P Feinberg.
      A critical area of recent cancer research is the emergence of transition states between normal and cancer that exhibit increased cell plasticity which underlies tumor cell heterogeneity. Pancreatic ductal adenocarcinoma (PDAC) can arise from the combination of a transition state termed acinar-to-ductal metaplasia (ADM) and a gain-of-function mutation in the proto-oncogene KRAS . During ADM, digestive enzyme-producing acinar cells acquire a transient ductal epithelium-like phenotype while maintaining their geographical acinar organization. One route of ADM initiation is the overexpression of the Krüppel-like factor 4 gene ( KLF4 ) in the absence of oncogenic driver mutations. Here, we asked to what extent cells acquire and retain an epigenetic memory of the ADM transition state in the absence of oncogene mutation. We identified differential DNA methylation at Kras-downstream PI3K and Rho / Rac / Cdc42 GTPase pathway genes during ADM, as well as a corresponding gene expression increase in these pathways. Importantly, differential methylation persisted after gene expression returned to normal. Caerulein exposure, which induces widespread digestive system changes in addition to ADM, showed similar changes in DNA methylation in ADM cells. Regions of differential methylation were enriched for motifs of KLF and AP-1 family transcription factors, as were those of human pancreatic intraepithelial neoplasia (PanIN) samples, demonstrating the relevance of this epigenetic transition state memory in human carcinogenesis. Finally, single-cell spatial transcriptomics revealed that these ADM transition cells were enriched for PI3K pathway and AP1 family members, linking epigenetic memory to cancer cell plasticity even in the absence of oncogene mutation.
    DOI:  https://doi.org/10.1101/2024.10.26.620414
  21. Mol Cell. 2024 Nov 15. pii: S1097-2765(24)00877-3. [Epub ahead of print]
    Nutrient control of growth and metabolism through mTORC1 regulation of mRNA splicing.
    Takafumi Ogawa, Meltem Isik, Ziyun Wu, Kiran Kurmi, Jin Meng, Sungyun Cho, Gina Lee, L Paulette Fernandez-Cardenas, Masaki Mizunuma, John Blenis, Marcia C Haigis, T Keith Blackwell.
      Cellular growth and organismal development are remarkably complex processes that require the nutrient-responsive kinase mechanistic target of rapamycin complex 1 (mTORC1). Anticipating that important mTORC1 functions remained to be identified, we employed genetic and bioinformatic screening in C. elegans to uncover mechanisms of mTORC1 action. Here, we show that during larval growth, nutrients induce an extensive reprogramming of gene expression and alternative mRNA splicing by acting through mTORC1. mTORC1 regulates mRNA splicing and the production of protein-coding mRNA isoforms largely independently of its target p70 S6 kinase (S6K) by increasing the activity of the serine/arginine-rich (SR) protein RSP-6 (SRSF3/7) and other splicing factors. mTORC1-mediated mRNA splicing regulation is critical for growth; mediates nutrient control of mechanisms that include energy, nucleotide, amino acid, and other metabolic pathways; and may be conserved in humans. Although mTORC1 inhibition delays aging, mTORC1-induced mRNA splicing promotes longevity, suggesting that when mTORC1 is inhibited, enhancement of this splicing might provide additional anti-aging benefits.
    Keywords:  C. elegans; SR proteins; development; gene expression; growth; human cell growth; longevity; mRNA splicing; mTORC1; metabolism; nutrient response
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.037
  22. Mol Cancer Ther. 2024 Nov 21.
    Pancreatic CAF-derived Autotaxin (ATX) drives autocrine CTGF expression to modulate pro-tumorigenic signaling.
    Fanny Volat, Ragini Medhi, Lauren Z Maggs, Marcel A Deken, Alice Price, Lauren Andrews, Jonathan Clark, Diane Taylor, Alan Carruthers, Ewan Taylor-Smith, Natalia Pacheco, Simon A Rudge, Amy Fraser, Andrea F Lopez-Clavijo, Bebiana C Sousa, Zoë Johnson, Giusy Di Conza, Lars van der Veen, Pritom Shah, Hilary Sandig, Hayley J Sharpe, Stuart Farrow.
      Autotaxin (ATX), encoded by ENPP2, is a clinical target in pancreatic ductal adenocarcinoma (PDAC). ATX catalyzes the production of lysophosphatidic acid (LPA), an important regulator within the tumor microenvironment (TME), yet the pro-tumorigenic action of the ATX/LPA axis in PDAC remains unclear. Here, by interrogating patient samples and cell line datasets, we show that the PDAC TME, rather than cancer cells, is responsible for the majority of ENPP2 expression, and highlight a key role for cancer associated fibroblast (CAF)-derived ATX in autocrine and paracrine pro-tumorigenic signaling. Using the clinical-stage ATX inhibitor, IOA-289, we identified connective tissue growth factor (CTGF) as a downstream mediator of ATX signaling in the PDAC CAF-derived cell line, 0082T. Genetic ablation or pharmacological inhibition of ATX in 0082T CAFs reduced CTGF secretion via modulation of LPA/LPA receptor (LPAR) signaling. Despite the loss of ATX function, extracellular levels of LPA were paradoxically increased, indicating a role for ATX beyond its enzymatic activity and suggesting a role for its LPA chaperone function in the LPA/LPAR signaling in CAFs. As CAFs are the main source for CTGF in the PDAC TME, these findings suggest a role for ATX in promoting pro-tumorigenic microenvironment via modulation of CAF secretion, not only via its LPA-producing activity but also via its LPA chaperone function, providing a potential mechanism for the anti-tumor effects of ATX inhibition.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-23-0522
  23. Cell Mol Life Sci. 2024 Nov 19. 81(1): 458
    NFκB and JNK pathways mediate metabolic adaptation upon ESCRT-I deficiency.
    Jaroslaw Cendrowski, Marta Wrobel, Michal Mazur, Bartosz Jary, Ranjana Maurya, Surui Wang, Michal Korostynski, Anna Dziewulska, Maria Rohm, Patryk Kuropka, Natalia Pudelko-Malik, Piotr Mlynarz, Agnieszka Dobrzyn, Anja Zeigerer, Marta Miaczynska.
      Endosomal Sorting Complexes Required for Transport (ESCRTs) are crucial for delivering membrane receptors or intracellular organelles for lysosomal degradation which provides the cell with lysosome-derived nutrients. Yet, how ESCRT dysfunction affects cell metabolism remained elusive. To address this, we analyzed transcriptomes of cells lacking TSG101 or VPS28 proteins, components of ESCRT-I subcomplex. ESCRT-I deficiency reduced the expression of genes encoding enzymes involved in oxidation of fatty acids and amino acids, such as branched-chain amino acids, and increased the expression of genes encoding glycolytic enzymes. The changes in metabolic gene expression were associated with Warburg effect-like metabolic reprogramming that included intracellular accumulation of lipids, increased glucose/glutamine consumption and lactate production. Moreover, depletion of ESCRT-I components led to expansion of the ER and accumulation of small mitochondria, most of which retained proper potential and performed ATP-linked respiration. Mechanistically, the observed transcriptional reprogramming towards glycolysis in the absence of ESCRT-I occurred due to activation of the canonical NFκB and JNK signaling pathways and at least in part by perturbed lysosomal degradation. We propose that by activating the stress signaling pathways ESCRT-I deficiency leads to preferential usage of extracellular nutrients, like glucose and glutamine, for energy production instead of lysosome-derived nutrients, such as fatty acids and branched-chain amino acids.
    Keywords:  ESCRT; JNK; NFκB; fatty acid oxidation; glycolysis; mitochondria
    DOI:  https://doi.org/10.1007/s00018-024-05490-y
  24. Mol Metab. 2024 Nov 14. pii: S2212-8778(24)00198-4. [Epub ahead of print] 102067
    Incretin-responsive human pancreatic adipose tissue organoids: A functional model for fatty pancreas research.
    E Lorza-Gil, O Strauss, E Ziegler, K Kansy, M-T Katschke, G Rahimi, D Neuscheler, L Sandforth, A Sandforth, G Sancar, B Kaufmann, D Hartmann, S Singer, A L Mihaljevic, R Jumpertz-von Schwartzenberg, J Sbierski-Kind, T D Müller, A L Birkenfeld, F Gerst.
      Infiltration of adipocytes into the pancreatic parenchyma has been linked to impaired insulin secretion in individuals with increased genetic risk of T2D and prediabetic conditions. However, the study of this ectopic fat depot has been limited by the lack of suitable in vitro models. Here, we developed a novel 3D model of functionally mature human pancreatic adipose tissue organoids by aggregating human pancreatic adipose tissue-derived stromal vascular fraction (SVF) cells into organoids and differentiating them over 19 days. These organoids carry biological properties of the in situ pancreatic fat, presenting levels of adipogenic markers comparable to native pancreatic adipocytes and improved lipolytic and anti-lipolytic response compared to conventional 2D cultures. The organoids harbour a small population of immune cells, mimicking in vivo adipose environment. Furthermore, they express GIPR, allowing investigation of incretin effects in pancreatic fat. In accordance, GIP and the dual GLP1R/GIPR agonist tirzepatide stimulate lipolysis but had distinct effects on the expression of proinflammatory cytokines. This novel adipose organoid model is a valuable tool to study the metabolic impact of incretin signalling in pancreatic adipose tissue, revealing potential therapeutic targets of incretins beyond islets. The donor-specific metabolic memory of these organoids enables examination of the pancreatic fat-islet crosstalk in a donor-related metabolic context.
    Keywords:  Adipogenesis; Incretins; Inflammation; Organoids; Pancreatic adipose tissue
    DOI:  https://doi.org/10.1016/j.molmet.2024.102067
  25. Nat Commun. 2024 Nov 16. 15(1): 9947
    An allosteric inhibitor of RhoGAP class-IX myosins suppresses the metastatic features of cancer cells.
    Despoina Kyriazi, Lea Voth, Almke Bader, Wiebke Ewert, Juliane Gerlach, Kerstin Elfrink, Peter Franz, Mariana I Tsap, Bastian Schirmer, Julia Damiano-Guercio, Falk K Hartmann, Masina Plenge, Azam Salari, Dennis Schöttelndreier, Katharina Strienke, Nadine Bresch, Claudio Salinas, Herwig O Gutzeit, Nora Schaumann, Kais Hussein, Heike Bähre, Inga Brüsch, Peter Claus, Detlef Neumann, Manuel H Taft, Halyna R Shcherbata, Anaclet Ngezahayo, Martin Bähler, Mahdi Amiri, Hans-Joachim Knölker, Matthias Preller, Georgios Tsiavaliaris.
      Aberrant Ras homologous (Rho) GTPase signalling is a major driver of cancer metastasis, and GTPase-activating proteins (GAPs), the negative regulators of RhoGTPases, are considered promising targets for suppressing metastasis, yet drug discovery efforts have remained elusive. Here, we report the identification and characterization of adhibin, a synthetic allosteric inhibitor of RhoGAP class-IX myosins that abrogates ATPase and motor function, suppressing RhoGTPase-mediated modes of cancer cell metastasis. In human and murine adenocarcinoma and melanoma cell models, including three-dimensional spheroid cultures, we reveal anti-migratory and anti-adhesive properties of adhibin that originate from local disturbances in RhoA/ROCK-regulated signalling, affecting actin-dynamics and actomyosin-based cell-contractility. Adhibin blocks membrane protrusion formation, disturbs remodelling of cell-matrix adhesions, affects contractile ring formation, and disrupts epithelial junction stability; processes severely impairing single/collective cell migration and cytokinesis. Combined with the non-toxic, non-pathological signatures of adhibin validated in organoids, mouse and Drosophila models, this mechanism of action provides the basis for developing anti-metastatic cancer therapies.
    DOI:  https://doi.org/10.1038/s41467-024-54181-6
  26. Nat Methods. 2024 Nov 18.
    Probe set selection for targeted spatial transcriptomics.
    Louis B Kuemmerle, Malte D Luecken, Alexandra B Firsova, Lisa Barros de Andrade E Sousa, Lena Straßer, Ilhem Isra Mekki, Francesco Campi, Lukas Heumos, Maiia Shulman, Valentina Beliaeva, Soroor Hediyeh-Zadeh, Anna C Schaar, Krishnaa T Mahbubani, Alexandros Sountoulidis, Tamás Balassa, Ferenc Kovacs, Peter Horvath, Marie Piraud, Ali Ertürk, Christos Samakovlis, Fabian J Theis.
      Targeted spatial transcriptomic methods capture the topology of cell types and states in tissues at single-cell and subcellular resolution by measuring the expression of a predefined set of genes. The selection of an optimal set of probed genes is crucial for capturing the spatial signals present in a tissue. This requires selecting the most informative, yet minimal, set of genes to profile (gene set selection) for which it is possible to build probes (probe design). However, current selections often rely on marker genes, precluding them from detecting continuous spatial signals or new states. We present Spapros, an end-to-end probe set selection pipeline that optimizes both gene set specificity for cell type identification and within-cell type expression variation to resolve spatially distinct populations while considering prior knowledge as well as probe design and expression constraints. We evaluated Spapros and show that it outperforms other selection approaches in both cell type recovery and recovering expression variation beyond cell types. Furthermore, we used Spapros to design a single-cell resolution in situ hybridization on tissues (SCRINSHOT) experiment of adult lung tissue to demonstrate how probes selected with Spapros identify cell types of interest and detect spatial variation even within cell types.
    DOI:  https://doi.org/10.1038/s41592-024-02496-z
  27. Development. 2024 Nov 15. pii: dev204212. [Epub ahead of print]151(22):
    An expanded view of cell competition.
    Ameya Khandekar, Stephanie J Ellis.
      Cell competition arises in heterogeneous tissues when neighbouring cells sense their relative fitness and undergo selection. It has been a challenge to define contexts in which cell competition is a physiologically relevant phenomenon and to understand the cellular features that underlie fitness and fitness sensing. Drawing on examples across a range of contexts and length scales, we illuminate molecular and cellular features that could underlie fitness in diverse tissue types and processes to promote and reinforce long-term maintenance of tissue function. We propose that by broadening the scope of how fitness is defined and the circumstances in which cell competition can occur, the field can unlock the potential of cell competition as a lens through which heterogeneity and its role in the fundamental principles of complex tissue organisation can be understood.
    Keywords:  Cell competition; Cell selection; Cellular fitness sensing; Complex tissue organization; Heterogeneity; Tissue robustness
    DOI:  https://doi.org/10.1242/dev.204212
  28. Chem Sci. 2024 Oct 29.
    Mg2+-driven selection of natural phosphatidic acids in primitive membranes.
    Krishnakavya Thaipurayil Madanan, Yuhan Li, Valeria J Boide-Trujillo, David A Russell, Claudia Bonfio.
      Biological membranes are composed exclusively of phospholipids comprising glycerol-1-phosphate or glycerol-3-phosphate. By contrast, primitive membranes would have likely been composed of heterogeneous mixtures of phospholipids, including non-natural analogues comprising glycerol-2-phosphate, as delivered by prebiotic synthesis. Thus, it is not clear how the selection of natural phospholipids could have come about. Here we show how differences in supramolecular properties, but not molecular properties, could have driven the selection of natural phosphatidic acids in primitive membranes. First, we demonstrate that at the molecular level it is unlikely that any prebiotic synthesis or hydrolysis pathway would have enabled the selection of natural phosphatidic acids. Second, we report that at the supramolecular level, natural phospholipids display a greater tendency to self-assemble in more packed and rigid membranes than non-natural analogues of the same chain length. Finally, taking advantage of these differences, we highlight that Mg2+, but not Na+, K+, Ca2+ or Zn2+, drives the selective precipitation of non-natural phosphatidic acids from heterogeneous mixtures obtained by prebiotic synthesis, leaving membranes proportionally enriched in natural phosphatidic acids. Our findings delineate a plausible pathway by which the transition towards biological membranes could have occurred under conditions compatible with prebiotic metal-driven processes, such as non-enzymatic RNA polymerization.
    DOI:  https://doi.org/10.1039/d4sc05362a
  29. Elife. 2024 Nov 22. pii: RP94689. [Epub ahead of print]13
    Automated workflow for the cell cycle analysis of (non-)adherent cells using a machine learning approach.
    Kourosh Hayatigolkhatmi, Chiara Soriani, Emanuel Soda, Elena Ceccacci, Oualid El Menna, Sebastiano Peri, Ivan Negrelli, Giacomo Bertolini, Gian Martino Franchi, Roberta Carbone, Saverio Minucci, Simona Rodighiero.
      Understanding the cell cycle at the single-cell level is crucial for cellular biology and cancer research. While current methods using fluorescent markers have improved the study of adherent cells, non-adherent cells remain challenging. In this study, we addressed this gap by combining a specialized surface to enhance cell attachment, the FUCCI(CA)2 sensor, an automated image analysis pipeline, and a custom machine learning algorithm. This approach enabled precise measurement of cell cycle phase durations in non-adherent cells. This method was validated in acute myeloid leukemia cell lines NB4 and Kasumi-1, which have unique cell cycle characteristics, and we tested the impact of cell cycle-modulating drugs on NB4 cells. Our cell cycle analysis system, which is also compatible with adherent cells, is fully automated and freely available, providing detailed insights from hundreds of cells under various conditions. This report presents a valuable tool for advancing cancer research and drug development by enabling comprehensive, automated cell cycle analysis in both adherent and non-adherent cells.
    Keywords:  AML; cancer biology; cell biology; cell cycle; cell tracking; human; live-cell imaging; machine learning; non-adherent cells
    DOI:  https://doi.org/10.7554/eLife.94689
  30. BJC Rep. 2024 Nov 18. 2(1): 88
    Single-cell RNA-seq analysis of cancer-endothelial cell interactions in primary tumor and peritoneal metastasis from a single patient with colorectal cancer.
    Yuri Sakimoto, Kohei Kumegawa, Shimpei Matsui, Tomohiro Yamaguchi, Toshiki Mukai, Koji Okabayashi, Seiichi Mori, Yuko Kitagawa, Takashi Akiyoshi, Reo Maruyama.
       BACKGROUND: Peritoneal metastasis, a major complication of colorectal cancer (CRC), often leads to poor quality of life and unfavorable outcomes. Despite numerous studies characterizing its biological features in CRC, intratumor heterogeneity and interactions between cancer cells and tumor microenvironment cells remain poorly understood.
    METHODS: To explore these aspects, we performed single-cell transcriptome analysis of matched primary tumor and peritoneal metastasis samples from a treatment-naïve patient.
    RESULTS: Our analysis revealed enrichment of "tip" endothelial cells in the primary tumor, driving angiogenic sprouting, whereas these cells were absent in peritoneal metastases. Moreover, cancer cells in peritoneal metastasis displayed a distinct expression signature associated with epithelial-mesenchymal transition and tumor invasiveness. Analysis of cell-cell communication between endothelial and tumor cells revealed decreased VEGF signaling and increased CXCL-ACKR1 interactions in peritoneal metastasis.
    CONCLUSIONS: Although limited by its N-of-1 design and requiring further validation, our study provides preliminary observations suggesting that alterations in cancer-endothelial cell interactions could reduce dependence on VEGF signaling and influence immune cell infiltration in CRC peritoneal metastasis.
    DOI:  https://doi.org/10.1038/s44276-024-00112-3
  31. Biosystems. 2024 Nov 17. pii: S0303-2647(24)00259-4. [Epub ahead of print]247 105374
    Sensing, feeling and sentience in unicellular organisms and living cells.
    F Baluška, W B Miller, P Slijepcevic, A S Reber.
      Cells represent the basic units of life, not only as structural building blocks, but also as cognitive agents endowed with subjective cellular feelings, sentience (consciousness), and cognitive infocomputatioal competence. Living cells act as 'Kantian Wholes': All of its parts exist for and by means of the whole system, allowing cells to use sentient agency for solving existential problems and evolve as living self-organizing units. Cell sentience is based on its excitable plasma membrane generating bioelectromagnetic fields that link to a whole-cell sensory architecture. This cellular sensory apparatus, termed its senome, represents the totality of cellular self-referential information obtained by cells via their sensory systems, including the subjective cellular inside and the cell's self-referential appraisal of its external environment. The plasma membrane was 'invented' by the very first cells and has been uninterruptedly inherited by cells for billions of years through successive cell divisions.
    Keywords:  Agency; Cells; Consciousness; Feelings; Kantian wholes; Senome; Sentience; Subjectivity
    DOI:  https://doi.org/10.1016/j.biosystems.2024.105374
  32. J Biol Chem. 2024 Nov 15. pii: S0021-9258(24)02506-7. [Epub ahead of print] 108004
    Impaired branched chain amino acid (BCAA) catabolism during adipocyte differentiation decreases glycolytic flux.
    Courtney R Green, Lynn M Alaeddine, Karl A Wessendorf-Rodriguez, Rory Turner, Merve Elmastas, Justin D Hover, Anne N Murphy, Mikael Ryden, Niklas Mejhert, Christian M Metallo, Martina Wallace.
      Dysregulated branched chain amino acid (BCAA) metabolism has emerged as a key metabolic feature associated with the obese insulin resistant state, and adipose BCAA catabolism is decreased in this context. BCAA catabolism is upregulated early in adipogenesis, but the impact of suppressing this pathway on the broader metabolic functions of the resultant adipocyte remains unclear. Here, we use CRISPR/Cas9 to decrease BCKDHA in 3T3-L1 and human pre-adipocytes, and ACAD8 in 3T3-L1 pre-adipocytes to induce a deficiency in BCAA catabolism through differentiation. We characterize the transcriptional and metabolic phenotype of 3T1-L1 cells using RNAseq and 13C metabolic flux analysis within a network spanning glycolysis, tricarboxylic acid (TCA) metabolism, BCAA catabolism, and fatty acid synthesis. While lipid droplet accumulation is maintained in Bckdha-deficient adipocytes, they display a more fibroblast-like transcriptional signature. In contrast, Acad8 deficiency minimally impacts gene expression. Decreased glycolytic flux emerges as the most distinct metabolic feature of 3T3-L1 Bckdha-deficient cells, accompanied by a ∼40% decrease in lactate secretion, yet pyruvate oxidation and utilization for de novo lipogenesis are increased to compensate for loss of BCAA carbon. Deletion of BCKDHA in human adipocyte progenitors also led to a decrease in glucose uptake and lactate secretion, however these cells did not upregulate pyruvate utilisation and lipid droplet accumulation and expression of adipocyte differentiation markers was decreased in BCKDH knockout cells. Overall our data suggest that human adipocyte differentiation may be more sensitive to the impact of decreased BCKDH activity than 3T3-L1 cells, and that both metabolic and regulatory cross-talk exists between BCAA catabolism and glycolysis in adipocytes. Suppression of BCAA catabolism associated with metabolic syndrome may result in a metabolically compromised adipocyte.
    Keywords:  adipogenesis; adipose; branched chain amino acids; glycolysis; metabolic flux
    DOI:  https://doi.org/10.1016/j.jbc.2024.108004
  33. Nat Methods. 2024 Nov 19.
    Repurposing large-format microarrays for scalable spatial transcriptomics.
    Denis Cipurko, Tatsuki Ueda, Linghan Mei, Nicolas Chevrier.
      Spatiomolecular analyses are key to study tissue functions and malfunctions. However, we lack profiling tools for spatial transcriptomics that are easy to adopt, low cost and scalable in terms of sample size and number. Here, we describe a method, Array-seq, to repurpose classical oligonucleotide microarrays for spatial transcriptomics profiling. We generate Array-seq slides from microarrays carrying custom-design probes that contain common sequences flanking unique barcodes at known coordinates. Then we perform a simple, two-step reaction that produces mRNA capture probes across all spots on the microarray. We demonstrate that Array-seq yields spatial transcriptomes with high detection sensitivity and localization specificity using histological sections from mouse tissues as test systems. Moreover, we show that the large surface area of Array-seq slides yields spatial transcriptomes (i) at high throughput by profiling multi-organ sections, (ii) in three dimensions by processing serial sections from one sample, and (iii) across whole human organs. Thus, by combining classical DNA microarrays and next-generation sequencing, we have created a simple and flexible platform for spatiomolecular studies of small-to-large specimens at scale.
    DOI:  https://doi.org/10.1038/s41592-024-02501-5
  34. Bioinformatics. 2024 Nov 19. pii: btae697. [Epub ahead of print]
    PhosX: data-driven kinase activity inference from phosphoproteomics experiments.
    Alessandro Lussana, Sophia Müller-Dott, Julio Saez-Rodriguez, Evangelia Petsalaki.
       SUMMARY: The inference of kinase activity from phosphoproteomics data can point to causal mechanisms driving signalling processes and potential drug targets. Identifying the kinases whose change in activity explains the observed phosphorylation profiles, however, remains challenging, and constrained by the manually curated knowledge of kinase-substrate associations. Recently, experimentally determined substrate sequence specificities of human kinases have become available, but robust methods to exploit this new data for kinase activity inference are still missing. We present PhosX, a method to estimate differential kinase activity from phosphoproteomics data that combines state-of-the art statistics in enrichment analysis with kinases' substrate sequence specificity information. Using a large phosphoproteomics dataset with known differentially regulated kinases we show that our method identifies upregulated and downregulated kinases by only relying on the input phosphopeptides' sequences and intensity changes. We find that PhosX outperforms the currently available approach for the same task, and performs better or similarly to state-of-the-art methods that rely on previously known kinase-substrate associations. We therefore recommend its use for data-driven kinase activity inference.
    AVAILABILITY AND IMPLEMENTATION: PhosX is implemented in Python, open-source under the Apache-2.0 licence, and distributed on the Python Package Index. The code is available on GitHub (https://github.com/alussana/phosx).
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btae697
  35. bioRxiv. 2024 Aug 19. pii: 2024.08.16.608348. [Epub ahead of print]
    Evidence of persistent hyperphagia following a dietary weight-loss intervention in mice.
    Frankie D Heyward, Evan D Rosen.
      This study sought to determine whether the drive to regain weight following weight loss was truly long-lived in mice. We generated a model of reduced dietary obesity (ReDO) whereby male mice with diet-induced obesity (DIO) mice were calorically restricted until weight matched to control mice, and then after a 24-hour food assessment period were pair-fed relative to control mice. We subsequently generated ReDO mice that, after CR, were pair-fed relative to control mice for 0, 8, or 28 days, or chronically. Body weight, food intake, and select metabolic parameters were measured, along with whole hypothalamic Pomc gene expression. ReDO mice in both experiments exhibited hyperphagia following CR, while a persistent form of hyperphagia was detected in ReDO_8d and ReDO_28d mice relative to control and chronically pair-fed mice. 4-week initial weight gain on a high-fat diet was predictive of the degree of weight regain across ReDO_8d and ReDO_28d mice. In summary, this study showcases the perdurance of weight loss-associated hyperphagia and introduces a prognostic tool for identifying mice that are prone towards weight regain, while setting the stage for future inquiries into the neurobiological basis of persistent hunger following weight loss owed to a dietary intervention in mice.
    DOI:  https://doi.org/10.1101/2024.08.16.608348
  36. bioRxiv. 2024 Nov 08. pii: 2024.11.07.622512. [Epub ahead of print]
    Transmembrane coupling accelerates the growth of liquid-like protein condensates.
    Yohan Lee, Feng Yuan, Jerry L Cabriales, Jeanne C Stachowiak.
      Timely and precise assembly of protein complexes on membrane surfaces is essential to the physiology of living cells. Recently, protein phase separation has been observed at cellular membranes, suggesting it may play a role in the assembly of protein complexes. Inspired by these findings, we observed that protein condensates on one side of a planar suspended membrane spontaneously colocalized with those on the opposite side. How might this phenomenon contribute to the assembly of stable transmembrane complexes? To address this question, we examined the diffusion and growth of protein condensates on both sides of membranes. Our results reveal that transmembrane coupling of protein condensates on opposite sides of the membrane slows down condensate diffusion while accelerating condensate growth. How can the rate of condensate growth increase simultaneously with a decrease in the rate of condensate diffusion? We provide insights into these seemingly contradictory observations by distinguishing between diffusion-limited and coupling-driven growth processes. While transmembrane coupling slows down diffusion, it also locally concentrates condensates within a confined area. This confinement increases the probability of condensate coalescence and thereby enhances the overall rate of growth for coupled condensates, substantially surpassing the growth rate for uncoupled condensates. These findings suggest that transmembrane coupling could play a role in the assembly of diverse membrane-bound structures by promoting the localization and growth of protein complexes on both membrane surfaces. This phenomenon could help to explain the efficient assembly of transmembrane structures in diverse cellular contexts.
    Significance: Protein assemblies that span biological membranes are critical to cellular physiology. In the past decade, liquid-like protein condensates, which are flexible, multivalent protein assemblies, have been discovered on diverse membrane surfaces. Recently, we observed that protein condensates on opposite sides of a membrane spontaneously colocalize to form coupled, transmembrane complexes. Interestingly, while transmembrane coupling slows down the diffusion of membrane-bound condensates, it substantially accelerates their growth by strongly localizing interactions between them. These findings suggest that transmembrane coupling of protein condensates may play a role in promoting the robust assembly of membrane-bound protein complexes in crowded, complex cellular environments.
    DOI:  https://doi.org/10.1101/2024.11.07.622512
  37. Sci Rep. 2024 Nov 22. 14(1): 28958
    The value of PET/CT radiomics for predicting survival outcomes in patients with pancreatic ductal adenocarcinoma.
    Yeon-Koo Kang, Seunggyun Ha, Ji Bong Jeong, So Won Oh.
      Pancreatic ductal adenocarcinoma (PDAC) is associated with poor prognosis even without distant metastases, necessitating in-depth characterization of primary tumors for survival prediction. We assessed the feasibility of using FDG-PET/CT radiomics to predict overall survival (OS) in PDAC. This retrospective study included PDAC patients without distant metastasis who underwent FDG-PET/CT for initial staging. Primary tumors were segmented from FDG-PET/CT images, extracting 222 radiomics features. A radiomics-based risk score (Rad-score) was developed using Cox proportional hazards regression with LASSO to predict OS. The prognostic performance of the Rad-score was compared with a clinical model (demographics, disease stage, laboratory results) using Harrell's concordance index (C-index) and bootstrapping. 140 patients were included, with a mortality rate was 72.9% during follow-up (total population, 19.5 ± 19.2 months; survivors, 34.4 ± 28.8 months). Eleven radiomics features were significant for survival prediction. The Rad-score predicted OS with a C-index of 0.681 [95% CI, 0.632-0.731]. A model integrating clinical parameters and Rad-score outperformed the clinical-only model in predicting OS (C-index 0.740 [0.715-0.816] vs. 0.673 [0.650-0.766]; C-index difference 0.067 [0.014-0.113]; P < 0.001). These findings suggest that incorporating FDG-PET/CT radiomics into preexisting prognotic stratification paradiagm may enhance survival prediction in PDAC, warranting large-scale studies to confirm its applicability in clinical practice.
    Keywords:  FDG-PET/CT; Pancreas cancer; Radiomics; Survival
    DOI:  https://doi.org/10.1038/s41598-024-77022-4
  38. bioRxiv. 2024 Oct 29. pii: 2024.10.29.620861. [Epub ahead of print]
    Directed evolution of the multicopper oxidase laccase for cell surface proximity labeling and electron microscopy.
    Song-Yi Lee, Heegwang Roh, David Gonzalez-Perez, Mason R Mackey, Keun-Young Kim, Daniel Hoces, Colleen N McLaughlin, Stephen R Adams, Khanh Nguyen, David J Luginbuhl, Liqun Luo, Namrata D Udeshi, Steven A Carr, Rogelio A Hernández-López, Mark H Ellisman, Miguel Alcalde, Alice Y Ting.
      Enzymes that oxidize aromatic substrates have shown utility in a range of cell-based technologies including live cell proximity labeling (PL) and electron microscopy (EM), but are associated with drawbacks such as the need for toxic H2O2. Here, we explore laccases as a novel enzyme class for PL and EM in mammalian cells. LaccID, generated via 11 rounds of directed evolution from an ancestral fungal laccase, catalyzes the one-electron oxidation of diverse aromatic substrates using O2 instead of toxic H2O2, and exhibits activity selective to the surface plasma membrane of both living and fixed cells. We show that LaccID can be used with mass spectrometry-based proteomics to map the changing surface composition of T cells that engage with tumor cells via antigen-specific T cell receptors. In addition, we use LaccID as a genetically-encodable tag for EM visualization of cell surface features in mammalian cell culture and in the fly brain. Our study paves the way for future cell-based applications of LaccID.
    DOI:  https://doi.org/10.1101/2024.10.29.620861
  39. Nat Commun. 2024 Nov 20. 15(1): 9755
    Increased translation driven by non-canonical EZH2 creates a synthetic vulnerability in enzalutamide-resistant prostate cancer.
    Shankha S Chatterjee, Juan F Linares, Tania Cid-Diaz, Angeles Duran, Mohd Imran K Khan, Marta Osrodek, Nicholas J Brady, Miguel Reina-Campos, Antonio Marzio, Varadha Balaji Venkadakrishnan, Martin K Bakht, Francesca Khani, Juan Miguel Mosquera, Brian D Robinson, Jenna Moyer, Olivier Elemento, Andrew C Hsieh, David W Goodrich, David S Rickman, Himisha Beltran, Jorge Moscat, Maria T Diaz-Meco.
      Overcoming resistance to therapy is a major challenge in castration-resistant prostate cancer (CRPC). Lineage plasticity towards a neuroendocrine phenotype enables CRPC to adapt and survive targeted therapies. However, the molecular mechanisms of epigenetic reprogramming during this process are still poorly understood. Here we show that the protein kinase PKCλ/ι-mediated phosphorylation of enhancer of zeste homolog 2 (EZH2) regulates its proteasomal degradation and maintains EZH2 as part of the canonical polycomb repressive complex (PRC2). Loss of PKCλ/ι promotes a switch during enzalutamide treatment to a non-canonical EZH2 cistrome that triggers the transcriptional activation of the translational machinery to induce a transforming growth factor β (TGFβ) resistance program. The increased reliance on protein synthesis creates a synthetic vulnerability in PKCλ/ι-deficient CRPC.
    DOI:  https://doi.org/10.1038/s41467-024-53874-2
  40. J Cell Biol. 2025 Feb 03. pii: e202403096. [Epub ahead of print]224(2):
    Real-time imaging reveals a role for macrophage protrusive motility in melanoma invasion.
    Gayathri Ramakrishnan, Veronika Miskolci, Miranda Hunter, Morgan A Giese, Daniela Münch, Yiran Hou, Kevin W Eliceiri, Michael R Lasarev, Richard M White, Anna Huttenlocher.
      Macrophages are primary cells of the innate immune system that mediate tumor progression. However, the motile behavior of macrophages and interactions with tumor cells are not well understood. Here, we exploit the optical transparency of larval zebrafish and perform real-time imaging of macrophage-melanoma interactions. We found that macrophages are highly motile in the tumor microenvironment. Macrophages extend dynamic projections between tumor cells that precede invasive melanoma migration. Modulating macrophage motility with a dominant inhibitory mutation in Rac2 inhibits recruitment to the tumor and impairs tumor invasion. However, a hyperactivating mutation in Rac2 does not affect macrophage recruitment but limits macrophage projections into the melanoma mass and reduces invasive melanoma cell migration. Taken together, these findings reveal a role for Rac2-mediated macrophage protrusive motility in melanoma invasion.
    DOI:  https://doi.org/10.1083/jcb.202403096
  41. Science. 2024 Nov 22. 386(6724): 907-915
    Whole-brain spatial transcriptional analysis at cellular resolution.
    Shigeaki Kanatani, Judith C Kreutzmann, Yue Li, Zoe West, Lea Lydolph Larsen, Danai Vougesi Nikou, Ilse Eidhof, Abigail Walton, Songbai Zhang, Leslie Rubio Rodríguez-Kirby, Jacob Lercke Skytte, Casper Gravesen Salinas, Kimiharu Takamatsu, Xiaofei Li, Daisuke H Tanaka, Dagmara Kaczynska, Keishiro Fukumoto, Razieh Karamzadeh, Yujiao Xiang, Naofumi Uesaka, Tsutomu Tanabe, Mikael Adner, Johan Hartman, Ayako Miyakawa, Erik Sundström, Gonçalo Castelo-Branco, Urmas Roostalu, Jacob Hecksher-Sørensen, Per Uhlén.
      Recent advances in RNA analysis have deepened our understanding of cellular states in biological tissues. However, a substantial gap remains in integrating RNA expression data with spatial context across organs, primarily owing to the challenges associated with RNA detection within intact tissue volumes. Here, we developed Tris buffer-mediated retention of in situ hybridization chain reaction signal in cleared organs (TRISCO), an effective tissue-clearing method designed for whole-brain spatial three-dimensional (3D) RNA imaging. TRISCO resolved several crucial issues, including the preservation of RNA integrity, achieving uniform RNA labeling, and enhancing tissue transparency. We tested TRISCO using a broad range of cell-identity markers, noncoding and activity-dependent RNAs, within diverse organs of varying sizes and species. TRISCO thus emerges as a powerful tool for single-cell, whole-brain, 3D imaging that enables comprehensive transcriptional spatial analysis across the entire brain.
    DOI:  https://doi.org/10.1126/science.adn9947
  42. Nature. 2024 Nov 20.
    A cell atlas foundation model for scalable search of similar human cells.
    Graham Heimberg, Tony Kuo, Daryle J DePianto, Omar Salem, Tobias Heigl, Nathaniel Diamant, Gabriele Scalia, Tommaso Biancalani, Shannon J Turley, Jason R Rock, Héctor Corrada Bravo, Josh Kaminker, Jason A Vander Heiden, Aviv Regev.
      Single-cell RNA-seq (scRNA-seq) has profiled hundreds of millions of human cells across organs, diseases, development, and perturbations to date. Mining these growing atlases could reveal cell-disease associations, discover cell states in unexpected tissue contexts, and relate in vivo biology to in vitro models. These require a common measure of cell similarity across the body and an efficient way to search. Here, we develop SCimilarity, a metric learning framework to learn a unified and interpretable representation that enables rapid queries of tens of millions of cell profiles from diverse studies for cells that are transcriptionally similar to an input cell profile or state. We use SCimilarity to query a 23.4 million cell atlas of 412 scRNA-seq studies for macrophage and fibroblast profiles from interstitial lung disease1 and reveal similar cell profiles across other fibrotic diseases and tissues. The top scoring in vitro hit for the macrophage query was a 3D hydrogel system2, which we experimentally demonstrated reproduces this cell state. SCimilarity serves as a foundation model for single-cell profiles that enables researchers to query for similar cellular states across the human body, providing a powerful tool for generating biological insights from the Human Cell Atlas.
    DOI:  https://doi.org/10.1038/s41586-024-08411-y
  43. Nature. 2024 Nov 18.
    Adipose tissue retains an epigenetic memory of obesity after weight loss.
    Laura C Hinte, Daniel Castellano-Castillo, Adhideb Ghosh, Kate Melrose, Emanuel Gasser, Falko Noé, Lucas Massier, Hua Dong, Wenfei Sun, Anne Hoffmann, Christian Wolfrum, Mikael Rydén, Niklas Mejhert, Matthias Blüher, Ferdinand von Meyenn.
      Reducing body weight to improve metabolic health and related comorbidities is a primary goal in treating obesity1,2. However, maintaining weight loss is a considerable challenge, especially as the body seems to retain an obesogenic memory that defends against body weight changes3,4. Overcoming this barrier for long-term treatment success is difficult because the molecular mechanisms underpinning this phenomenon remain largely unknown. Here, by using single-nucleus RNA sequencing, we show that both human and mouse adipose tissues retain cellular transcriptional changes after appreciable weight loss. Furthermore, we find persistent obesity-induced alterations in the epigenome of mouse adipocytes that negatively affect their function and response to metabolic stimuli. Mice carrying this obesogenic memory show accelerated rebound weight gain, and the epigenetic memory can explain future transcriptional deregulation in adipocytes in response to further high-fat diet feeding. In summary, our findings indicate the existence of an obesogenic memory, largely on the basis of stable epigenetic changes, in mouse adipocytes and probably other cell types. These changes seem to prime cells for pathological responses in an obesogenic environment, contributing to the problematic 'yo-yo' effect often seen with dieting. Targeting these changes in the future could improve long-term weight management and health outcomes.
    DOI:  https://doi.org/10.1038/s41586-024-08165-7
  44. J Immunother Cancer. 2024 Nov 19. pii: e008898. [Epub ahead of print]12(11):
    TNFR2 blockade promotes antitumoral immune response in PDAC by targeting activated Treg and reducing T cell exhaustion.
    Anais Debesset, Caroline Pilon, Sylvain Meunier, Orianne Cuelenaere-Bonizec, Wilfrid Richer, Allan Thiolat, Claire Houppe, Matteo Ponzo, Jeanne Magnan, Jonathan Caron, Pamela Caudana, Jimena Tosello Boari, Sylvain Baulande, Nhu Han To, Benoit Laurent Salomon, Eliane Piaggio, Ilaria Cascone, José Laurent Cohen.
       BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers, highly resistant to standard chemotherapy and immunotherapy. Regulatory T cells (Tregs) expressing tumor necrosis factor α receptor 2 (TNFR2) contribute to immunosuppression in PDAC. Treg infiltration correlates with poor survival and tumor progression in patients with PDAC. We hypothesized that TNFR2 inhibition using a blocking monoclonal antibody (mAb) could shift the Treg-effector T cell balance in PDAC, thus enhancing antitumoral responses.
    METHOD: To support this hypothesis, we first described TNFR2 expression in a cohort of 24 patients with PDAC from publicly available single-cell analysis data. In orthotopic and immunocompetent mouse models of PDAC, we also described the immune environment of PDAC after immune cell sorting and single-cell analysis. The modifications of the immune environment before and after anti-TNFR2 mAb treatment were evaluated as well as the effect on tumor progression.
    RESULTS: Patients with PDAC exhibited elevated TNFR2 expression in Treg, myeloid cells and endothelial cells and lower level in tumor cells. By flow cytometry and single-cell RNA-seq analysis, we identified two Treg populations in orthotopic mouse models: Resting and activated Tregs. The anti-TNFR2 mAb selectively targeted activated tumor-infiltrating Tregs, reducing T cell exhaustion markers in CD8+ T cells. However, anti-TNFR2 treatment alone had limited efficacy in activating CD8+ T cells and only slightly reduced the tumor growth. The combination of the anti-TNFR2 mAb with agonistic anti-CD40 mAb promoted stronger T cell activation, tumor growth inhibition, and improved survival and immunological memory in PDAC-bearing mice.
    CONCLUSION: Our data suggest that combining a CD40 agonist with a TNFR2 antagonist represents a promising therapeutic strategy for patients with PDAC.
    Keywords:  Adenocarcinoma; Immune modulatory; T regulatory cell - Treg; Tumor infiltrating lymphocyte - TIL; Tumor microenvironment - TME
    DOI:  https://doi.org/10.1136/jitc-2024-008898
  45. Cancer Discov. 2024 Nov 19.
    PKN2 is a dependency of the mesenchymal-like cancer cell state.
    Shane T Killarney, Gabriel Mesa, Rachel Washart, Benjamin Mayro, Kerry Dillon, Suzanne E Wardell, Madeline Newlin, Min Lu, Areej Abu Rmaileh, Nicky Liu, Donald P McDonnell, Ann Marie Pendergast, Kris C Wood.
      Cancer cells exploit a mesenchymal-like transcriptional state (MLS) to survive drug treatments. Although the MLS is well characterized, few therapeutic vulnerabilities targeting this program have been identified. Here, we systematically identify the dependency network of mesenchymal-like cancers through an analysis of gene essentiality scores in ~800 cancer cell lines, nominating a poorly studied kinase, PKN2, as a top therapeutic target of the MLS. Co-essentiality relationships, biochemical experiments, and genomic analyses of patient tumors revealed that PKN2 promotes mesenchymal-like cancer growth through a PKN2-SAV1-TAZ signaling mechanism. Notably, pairing genetic PKN2 inhibition with clinically relevant targeted therapies against EGFR, KRAS, and BRAF oncogenes suppresses drug resistance by depleting mesenchymal-like drug-tolerant persister cells. These findings provide evidence that PKN2 is a core regulator of the Hippo tumor suppressor pathway and highlight the potential of PKN2 inhibition as a generalizable therapeutic strategy to overcome drug resistance driven by the MLS across cancer contexts.
    DOI:  https://doi.org/10.1158/2159-8290.CD-24-0928
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒24 at 22:59.