bims-cagime 2025-02-02 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–02–02
thirty-two papers selected by
Kıvanç Görgülü, Technical University of Munich

GPR55 in the tumor microenvironment of pancreatic cancer controls tumorigenesis.
Rings of death: How NINJ1 executes plasma membrane rupture.
Clearing the path for whole-mount labeling and quantification of neuron- and vessel-density in adipose tissue.
Extracellular vesicles from pancreatic cancer and its tumour microenvironment promote increased Schwann cell migration.
AGER-dependent macropinocytosis drives resistance to KRAS-G12D-targeted therapy in advanced pancreatic cancer.
The spatial landscape of cancer hallmarks reveals patterns of tumor ecological dynamics and drug sensitivity.
Ferroptosis triggers mitochondrial fragmentation via Drp1 activation.
Probing and imaging phospholipid dynamics in live cells.
Breaking up clusters of circulating tumour cells to halt cancer spread.
Altered lipid homeostasis and autophagy precipitate diffuse alveolar hemorrhage in murine lupus.
Tumor Metabolism as a Factor Affecting Diversity in Cancer Cachexia.
Glucocorticoid receptor suppresses GATA6-mediated RNA polymerase II pause release to modulate classical subtype identity in pancreatic cancer.
Ketogenesis supports hepatic polyunsaturated fatty acid homeostasis via fatty acid elongation.
Plasma membrane-associated ARAF condensates fuel RAS-related cancer drug resistance.
Curvature Memory in Electrically Stimulated Lipid Membranes.
Genetically predicted causal link between the plasma lipidome and pancreatic diseases: a bidirectional Mendelian randomization study.
Autophagic flux-lipid droplet biogenesis cascade sustains mitochondrial fitness in colorectal cancer cells adapted to acidosis.
Rhythm is essential: Unraveling the relation between the circadian clock and cancer.
Cold induces brain region-selective cell activity-dependent lipid metabolism.
Targeting pancreatic cancer glutamine dependency confers vulnerability to GPX4-dependent ferroptosis.
Cell adhesion and spreading on fluid membranes through microtubules-dependent mechanotransduction.
Autophagic flux measurement: Cargo degradation versus generation of degradation products.
ImmuNet: a segmentation-free machine learning pipeline for immune landscape phenotyping in tumors by multiplex imaging.
Progesterone induces meiosis through two obligate co-receptors with PLA2 activity.
Brown adipose tissue is associated with reduced weight loss and risk of cancer cachexia: A retrospective cohort study.
Mechanisms of RCD-1 pore formation and membrane bending.
Cuproplasia and cuproptosis, two sides of the coin.
Cell after 50.
Atomic force microscopy combined with microfluidics for label-free sorting and automated nanomechanics of circulating tumor cells in liquid biopsy.
SLC25A38 is required for mitochondrial pyridoxal 5'-phosphate (PLP) accumulation.
Alteration of Lipid Metabolism in Hypoxic Cancer Cells.
Cell Labeling with 15-YNE Is Useful for Tracking Protein Palmitoylation and Metabolic Lipid Flux in the Same Sample.

Front Immunol. 2024 ;15 1513547

GPR55 in the tumor microenvironment of pancreatic cancer controls tumorigenesis.

Dušica Ristić, Thomas Bärnthaler, Eva Gruden, Melanie Kienzl, Laura Danner, Karolina Herceg, Arailym Sarsembayeva, Julia Kargl, Rudolf Schicho.

   Background: The G protein-coupled receptor 55 (GPR55) is part of an expanded endocannabinoid system (ECS), and plays a pro-tumorigenic role in different cancer models, including pancreatic cancer. Next to cancer cells, various cells of the immune tumor microenvironment (TME) express receptors of the ECS that critically determine tumor growth. The role of GPR55 in cancer cells has been widely described, but its role in the immune TME is not well understood.
Methods: We intended to uncover the role of GPR55 in tumor immunity in a model of pancreatic ductal adenocarcinoma (PDAC). To this end, a KPCY tumor cell line or a GPR55-overexpressing KPCY cell line (KPCY55) from murine PDAC were subcutaneously injected into wildtype (WT) and GPR55 knockout (KO) mice, and immune cell populations were evaluated by flow cytometry.
Results: Deficiency of GPR55 in the TME led to reduced tumor weight and volume, and altered the immune cell composition of tumors, favoring an anti-tumorigenic environment by increasing the number of CD3+ T cells, particularly CD8+ T cells, and the expression of PDL1 on macrophages. RNA-seq pathway analysis revealed higher T cell activity in KPCY55 tumors of GPR55 KO vs. WT mice. In addition, tumors from GPR55 KO mice displayed increased levels of T cell chemokines Cxcl9 and Cxcl10. Migration of T cells from GPR55 KO mice towards CXCL9 was increased in comparison to T cells from WT mice, suggesting that a CXCR3/CXCL9 axis was involved in T cell influx into tumors of GPR55 KO mice. Notably, anti-PD-1 immunotherapy increased tumor burden in WT mice, while this effect was absent in the GPR55 KO mice.
Conclusion: Our study indicates that GPR55 in TME cells may drive tumor growth by suppressing T cell functions, such as migration, in a model of PDAC, making it an interesting target for immunotherapies.

Keywords:  CXCR3/CXCL9 axis; GPR55; KPCY model; anti-PD-1 antibody; checkpoint inhibitors; pancreatic cancer; tumor microenvironment

DOI:  https://doi.org/10.3389/fimmu.2024.1513547
Cell. 2025 Jan 23. pii: S0092-8674(24)01473-9. [Epub ahead of print]188(2): 277-279

Rings of death: How NINJ1 executes plasma membrane rupture.

Zhonghua Liu, Tsan Sam Xiao.

Plasma membrane rupture during lytic cell death was previously believed to occur through passive osmosis that burst open the membrane. Recent publications, including one in this issue of Cell, suggest that plasma membrane rupture is an active process mediated by ninjurin-1 (NINJ1) oligomers that dissolve membranes and/or assemble large pores.

DOI: https://doi.org/10.1016/j.cell.2024.12.030
J Cell Sci. 2025 Jan 29. pii: jcs.263438. [Epub ahead of print]

Clearing the path for whole-mount labeling and quantification of neuron- and vessel-density in adipose tissue.

Thomas Rauchenwald, Pia Benedikt-Kühnast, Sandra Eder, Gernot F Grabner, Sebastian Forstreiter, Michaela Lang, Roko Sango, Tobias Eisenberg, Thomas Rattei, Arvand Haschemi, Heimo Wolinski, Martina Schweiger.

  White adipose tissue (WAT) comprises a plethora of cell types beyond adipocytes forming a regulatory network that ensures systemic energy homeostasis. Intertissue communication is facilitated by metabolites and signaling molecules that are spread by vasculature and nerves. Previous works indicated that WAT responds to environmental cues by adapting the abundance of these "communication routes", however, high intra-tissue heterogeneity questions the informative value of bulk or single cell analyses and underscores the necessity of whole-mount imaging. The applicability of whole-mount WAT-imaging is currently limited by two factors: I) Methanol-based tissue clearing protocols restrict the usable antibody portfolio to methanol resistant antibodies and II) The vast amounts of data resulting from 3D imaging of whole-tissue samples require high computational expertise and advanced equipment. Here, we present a protocol for whole-mount WAT clearing, overcoming the constraints of antibody-methanol sensitivity. Additionally, we introduce TiNeQuant (Tissue Network Quantifier) a Fiji tool for automated 3D quantification of neuron- or vascular network density, freely available at https://github.com/SchweigerLab/TiNeQuant. Given TiNeQuants versatility beyond WAT, it simplifies future efforts studying neuronal or vascular alterations in numerous pathologies.

Keywords:  Adipose tissue clearing; Image processing; Network density; Quantitative microscopy; Spatial analysis; Whole-mount imaging

DOI:  https://doi.org/10.1242/jcs.263438
Br J Cancer. 2025 Jan 25.

Extracellular vesicles from pancreatic cancer and its tumour microenvironment promote increased Schwann cell migration.

Fang Cheng Wong, Sebastian R Merker, Lisa Bauer, Yi Han, Van Manh Hung Le, Carina Wenzel, Lukas Böthig, Max Heiduk, Pascal Drobisch, Venkatesh Sadananda Rao, Farzaneh Malekian, Ana Mansourkiaei, Christian Sperling, Heike Polster, Mathieu Pecqueux, Rouzanna Istvanffy, Linhan Ye, Bo Kong, Daniela E Aust, Gustavo Baretton, Lena Seifert, Adrian M Seifert, Jürgen Weitz, Ihsan Ekin Demir, Christoph Kahlert.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) exhibits a high frequency of neural invasion (NI). Schwann cells (SCs) have been shown to be reprogrammed to facilitate cancer cell migration and invasion into nerves. Since extracellular vesicles (EVs) affect the tumour microenvironment and promote metastasis, the present study analysed the involvement of EVs from pancreatic cancer cells and their microenvironment in altering SC phenotype as part of the early events in the process of NI.
METHODS: EVs were isolated from human/murine PDAC cells, pancreatic stellate cells (PSCs), human tissues and plasma to perform a novel 3D migration assay, qRT-PCR and western blot. Kaplan-Meier and Cox regression analyses were employed to evaluate the clinical potential of plasma EV-derived candidate from 165 PDAC patients.
RESULTS: The EVs from PDAC cells, PSCs derived from human tumour tissues, other cell types in the tumour microenvironment from tumour tissues and circulating plasma act as drivers of a pro-migratory phenotype of SCs by inducing dedifferentiation in SCs. Notably, p75NTR expression was upregulated in the plasma-derived EVs from patients with NI (Pn1) relative to those without NI (Pn0). High expression of plasma-derived EV p75NTR correlated with reduced overall survival and was identified as an independent prognostic factor.
CONCLUSIONS: These findings suggest that EV-mediated SC migration underlies the interactions contributing to PDAC-associated NI with implications for improved outcome and therapeutic strategy.

DOI: https://doi.org/10.1038/s41416-024-02915-0
Sci Transl Med. 2025 Jan 29. 17(783): eadp4986

AGER-dependent macropinocytosis drives resistance to KRAS-G12D-targeted therapy in advanced pancreatic cancer.

Changfeng Li, Yuanda Liu, Chang Liu, Fangquan Chen, Yangchun Xie, Herbert J Zeh, Chunhua Yu, Jiao Liu, Daolin Tang, Rui Kang.

Pancreatic ductal adenocarcinoma (PDAC) driven by the KRAS-G12D mutation presents a formidable health challenge because of limited treatment options. MRTX1133 is a highly selective and first-in-class KRAS-G12D inhibitor under clinical development. Here, we report that the advanced glycosylation end product-specific receptor (AGER) plays a key role in mediating MRTX1133 resistance in PDAC cells. The up-regulation of AGER within cancer cells instigates macropinocytosis, facilitating the internalization of serum albumin and subsequent amino acid generation. These amino acids are then used to synthesize the antioxidant glutathione, leading to resistance to MRTX1133 treatment due to the inhibition of apoptosis. The underlying molecular mechanism involves AGER's interaction with diaphanous-related formin 1 (DIAPH1), a formin protein responsible for driving Rac family small GTPase 1 (RAC1)-dependent macropinosome formation. The effectiveness and safety of combining MRTX1133 with pharmacological inhibitors of the AGER-DIAPH1 complex (using RAGE299) or macropinocytosis (using EIPA) were confirmed in patient-derived xenografts, orthotopic models, and genetically engineered mouse PDAC models. This combination therapy also induces high-mobility group box 1 (HMGB1) release, resulting in a subsequent antitumor CD8+ T cell response in immunocompetent mice. Collectively, the study findings underscore the potential to enhance the efficacy of KRAS-G12D blockade therapy by targeting AGER-dependent macropinocytosis.

DOI: https://doi.org/10.1126/scitranslmed.adp4986
Cell Rep. 2025 Jan 24. pii: S2211-1247(24)01580-8. [Epub ahead of print]44(2): 115229

The spatial landscape of cancer hallmarks reveals patterns of tumor ecological dynamics and drug sensitivity.

DUTRENEO Study Investigators

  Tumors are complex ecosystems of interacting cell types. The concept of cancer hallmarks distills this complexity into underlying principles that govern tumor growth. Here, we explore the spatial distribution of cancer hallmarks across 63 primary untreated tumors from 10 cancer types using spatial transcriptomics. We show that hallmark activity is spatially organized, with the cancer compartment contributing to the activity of seven out of 13 hallmarks, while the tumor microenvironment (TME) contributes to the activity of the rest. Additionally, we discover that genomic distance between tumor subclones correlates with differences in hallmark activity, even leading to clone-hallmark specialization. Finally, we demonstrate interdependent relationships between hallmarks at the junctions of TME and cancer compartments and how they relate to sensitivity to different neoadjuvant treatments in 33 bladder cancer patients from the DUTRENEO trial. In conclusion, our findings may improve our understanding of tumor ecology and help identify new drug biomarkers.

Keywords:  CP: cancer; cancer hallmarks; drug sensitivity; ecosystem; intratumoral heterogeneity; spatial transcriptomics; tumor microenvironment

DOI:  https://doi.org/10.1016/j.celrep.2024.115229
Cell Death Dis. 2025 Jan 25. 16(1): 40

Ferroptosis triggers mitochondrial fragmentation via Drp1 activation.

Lohans Pedrera, Laura Prieto Clemente, Alina Dahlhaus, Sara Lotfipour Nasudivar, Sofya Tishina, Daniel Olmo González, Jenny Stroh, Fatma Isil Yapici, Randhwaj Pratap Singh, Nils Grotehans, Thomas Langer, Ana J García-Sáez, Silvia von Karstedt.

Constitutive mitochondrial dynamics ensure quality control and metabolic fitness of cells, and their dysregulation has been implicated in various human diseases. The large GTPase Dynamin-related protein 1 (Drp1) is intimately involved in mediating constitutive mitochondrial fission and has been implicated in mitochondrial cell death pathways. During ferroptosis, a recently identified type of regulated necrosis driven by excessive lipid peroxidation, mitochondrial fragmentation has been observed. Yet, how this is regulated and whether it is involved in ferroptotic cell death has remained unexplored. Here, we provide evidence that Drp1 is activated upon experimental induction of ferroptosis and promotes cell death execution and mitochondrial fragmentation. Using time-lapse microscopy, we found that ferroptosis induced mitochondrial fragmentation and loss of mitochondrial membrane potential, but not mitochondrial outer membrane permeabilization. Importantly, Drp1 accelerated ferroptotic cell death kinetics. Notably, this function was mediated by the regulation of mitochondrial dynamics, as overexpression of Mitofusin 2 phenocopied the effect of Drp1 deficiency in delaying ferroptosis cell death kinetics. Mechanistically, we found that Drp1 is phosphorylated and activated after induction of ferroptosis and that it translocates to mitochondria. Further activation at mitochondria through the phosphatase PGAM5 promoted ferroptotic cell death. Remarkably, Drp1 depletion delayed mitochondrial and plasma membrane lipid peroxidation. These data provide evidence for a functional role of Drp1 activation and mitochondrial fragmentation in the acceleration of ferroptotic cell death, with important implications for targeting mitochondrial dynamics in diseases associated with ferroptosis.

DOI: https://doi.org/10.1038/s41419-024-07312-2
Life Metab. 2024 Aug;3(4): loae014

Probing and imaging phospholipid dynamics in live cells.

Zhongsheng Wu, Yongtao Du, Tom Kirchhausen, Kangmin He.

  Distinct phospholipid species display specific distribution patterns across cellular membranes, which are important for their structural and signaling roles and for preserving the integrity and functionality of the plasma membrane and organelles. Recent advancements in lipid biosensor technology and imaging modalities now allow for direct observation of phospholipid distribution, trafficking, and dynamics in living cells. These innovations have markedly advanced our understanding of phospholipid function and regulation at both cellular and subcellular levels. Herein, we summarize the latest developments in phospholipid biosensor design and application, emphasizing the contribution of cutting-edge imaging techniques to elucidating phospholipid dynamics and distribution with unparalleled spatiotemporal precision.

Keywords:  biosensor; lipid-binding domain; live-cell imaging; phospholipid

DOI:  https://doi.org/10.1093/lifemeta/loae014
Nature. 2025 Jan 28.

Breaking up clusters of circulating tumour cells to halt cancer spread.

Daniel J Smit, Klaus Pantel.



Keywords:  Cancer; Medical research

DOI:  https://doi.org/10.1038/d41586-025-00251-8
Autophagy Rep. 2024 ;pii: 2379193. [Epub ahead of print]3(1):

Altered lipid homeostasis and autophagy precipitate diffuse alveolar hemorrhage in murine lupus.

Shuhong Han, Haoyang Zhuang, Yanpeng Diao, Mark Segal, Tanzia Islam Tithi, Weizhou Zhang, Westley H Reeves.

  Abnormal autophagy regulation is implicated in lupus and other autoimmune diseases. We investigated autophagy in the murine pristane-induced lupus model. Pristane causes monocyte/macrophage-mediated endoplasmic reticulum (ER) stress in lung endothelial cells and diffuse alveolar hemorrhage (DAH) indistinguishable from DAH in lupus patients. Enlarged macrophages with abundant lipid droplets containing neutral lipid and exhibiting increased autophagosome staining were observed in the lung and peritoneal macrophages after pristane treatment. Cellular overload of neutral lipid can lead to selective autophagy (lipophagy) of lipid droplets and transport to lysosomes. The autophagy inducer rapamycin decreased neutral lipid staining but aggravated DAH, while an autophagy inhibitor (3-methyladenine) blocked the onset of DAH. Pristane-induced autophagy in macrophages was confirmed by acridine orange assay and LC3 western blot. Pristane also enlarged lysosomal volume and enhanced cathepsin S, D, and K expression while decreasing lysosomal acid lipase activity. If the capacity to degrade neutral lipid into free cholesterol and fatty acids is overwhelmed, lysosomes enlarge and can release cathepsins into the cytoplasm promoting cell death. Increasing lysosomal cholesterol content by blocking the Niemann-Pick C disease protein NPC1 protects against lysosome-dependent cell death. Treatment with NPC1 inhibitors U18666A or cepharanthine, which stabilize lysosomes, normalized lysosomal volume, reversed ER stress, and prevented DAH in pristane-treated mice. We conclude that pristane disrupts lipid homeostasis, promoting autophagy, lysosomal dysfunction, ER stress, and cell death leading to DAH. NPC1 inhibition reverses these abnormalities, preventing DAH. The findings shed light on the role of autophagy and lysosomal dysfunction in the pathogenesis of lupus.

Keywords:  Cholesterol; Endoplasmic reticulum stress; Lipid droplets; Lung; Lysosomes; Macrophages; Niemann-Pick C disease; Pristane; Rapamycin; Systemic lupus erythematosus

DOI:  https://doi.org/10.1080/27694127.2024.2379193
Am J Physiol Cell Physiol. 2025 Jan 27.

Tumor Metabolism as a Factor Affecting Diversity in Cancer Cachexia.

Oliver F Bathe.

  Cancer cachexia is a multifaceted metabolic syndrome characterized by muscle wasting, fat redistribution, and metabolic dysregulation, commonly associated with advanced cancer but sometimes also evident in early-stage disease. More subtle body composition changes have also been reported in association with cancer, including sarcopenia, myosteatosis, and increased fat radiodensity. Emerging evidence reveals that body composition changes including sarcopenia, myosteatosis, and increased fat radiodensity, arise from distinct biological mechanisms and significantly impact survival outcomes. Importantly, these features often occur independently, with their combined presence exacerbating poor prognoses. Tumor plays a pivotal role in driving these host changes, either by acting as a metabolic parasite or by releasing mediators that disrupt normal tissue function. This review explores the diversity of tumor metabolism. It highlights the potential for tumor-specific metabolic phenotypes to influence systemic effects, including fat redistribution and sarcopenia. Addressing this tumorhost metabolic interplay requires personalized approaches that disrupt tumor metabolism while preserving host health. Promising strategies include targeted pharmacologic interventions and anti-cachexia agents like GDF-15 inhibitors. Nutritional modifications such as ketogenic diets and omega-3 fatty acid supplementation also merit further investigation. In addition to preserving muscle, these therapies will need to be evaluated for their capability to improve survival and quality of life. This review underscores the need for further research into tumor-driven metabolic effects on the host and the development of integrative treatment strategies to address the interconnected challenges of cancer progression and cachexia.

Keywords:  cachexia; cancer; host response; metabolism; tumor microenvironment

DOI:  https://doi.org/10.1152/ajpcell.00677.2024
Gut. 2025 Jan 30. pii: gutjnl-2024-334374. [Epub ahead of print]

Glucocorticoid receptor suppresses GATA6-mediated RNA polymerase II pause release to modulate classical subtype identity in pancreatic cancer.

Thomas L Ekstrom, Raya M Rosok, Amro M Abdelrahman, Christina Parassiadis, Meghana Manjunath, Marianna Y Dittrich, Xin Wang, Ana P Kutschat, Akshay Kanakan, Ashish Rajput, Nadine Schacherer, Teodora Lukic, Danielle M Carlson, Julia Thiel, Waltraut Kopp, Philipp Stroebel, Volker Ellenrieder, Jochen Gaedcke, Meng Dong, Zeynab Najafova, Mark J Truty, Elisabeth Hessmann, Steven A Johnsen.

   BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer with a 5-year survival rate of 12%. It has two major molecular subtypes: classical and basal, regulated by the master transcription factors (MTFs) GATA6 and ΔNp63, respectively.
OBJECTIVE: This study sought to uncover the transcriptional regulatory mechanisms controlling PDAC subtype identity.
DESIGN: We integrated primary tumour single-cell RNA-seq, patient-derived xenograft RNA-seq and multispectral imaging to identify MTF-dependent, subtype-specific markers. We created subtype-specific fluorescent reporter systems and conducted drug screenings to find actionable targets. We analysed chromatin accessibility (ATAC-seq), genome-wide occupancy (ChIP-seq) for epigenetic status (H3K27ac), MTFs (GATA6, ΔNp63), RNA polymerase II (Pol II), H3K4me3-anchored chromatin topology (HiChIP) and nascent RNA capture sequencing (PRO-seq). Additionally, we used nuclease-dead Cas9 (dCas9) to manipulate transcriptional regulatory mechanisms.
RESULTS: Our approach identified glucocorticoid receptor (GR) agonists as agents that suppress the classical transcriptional programme by interacting with GATA6. GATA6 regulates classical-specific transcription through promoter-proximal pause release. Depletion of GATA6 increased Pol II occupancy at GATA6-bound enhancers and transcriptional start sites, stabilising enhancer-promoter interactions. Artificially inducing pausing at GATA6-bound enhancers with dCas9 abrogated target gene expression and induced pausing at both the enhancer and target gene promoter. Conversely, in basal PDAC ΔNp63 promotes Pol II recruitment and stabilises enhancer-promoter interactions.
CONCLUSION: This study provides new insights into the transcriptional control and role of GR agonists in controlling PDAC molecular subtype identity.

Keywords:  GENE REGULATION; MOLECULAR BIOLOGY; PANCREATIC CANCER; RNA EXPRESSION

DOI:  https://doi.org/10.1136/gutjnl-2024-334374
Sci Adv. 2025 Jan 31. 11(5): eads0535

Ketogenesis supports hepatic polyunsaturated fatty acid homeostasis via fatty acid elongation.

Eric D Queathem, Zahra Moazzami, David B Stagg, Alisa B Nelson, Kyle Fulghum, Abdirahman Hayir, Alisha Seay, Jacob R Gillingham, D André d'Avignon, Xianlin Han, Hai-Bin Ruan, Peter A Crawford, Patrycja Puchalska.

Ketogenesis is a dynamic metabolic conduit supporting hepatic fat oxidation particularly when carbohydrates are in short supply. Ketone bodies may be recycled into anabolic substrates, but a physiological role for this process has not been identified. Here, we use mass spectrometry-based 13C-isotope tracing and shotgun lipidomics to establish a link between hepatic ketogenesis and lipid anabolism. Unexpectedly, mouse liver and primary hepatocytes consumed ketone bodies to support fatty acid biosynthesis via both de novo lipogenesis (DNL) and polyunsaturated fatty acid (PUFA) elongation. While an acetoacetate intermediate was not absolutely required for ketone bodies to source DNL, PUFA elongation required activation of acetoacetate by cytosolic acetoacetyl-coenzyme A synthetase (AACS). Moreover, AACS deficiency diminished free and esterified PUFAs in hepatocytes, while ketogenic insufficiency depleted PUFAs and increased liver triacylglycerols. These findings suggest that hepatic ketogenesis influences PUFA metabolism, representing a molecular mechanism through which ketone bodies could influence systemic physiology and chronic diseases.

DOI: https://doi.org/10.1126/sciadv.ads0535
Nat Chem Biol. 2025 Jan 27.

Plasma membrane-associated ARAF condensates fuel RAS-related cancer drug resistance.

Wen Li, Xiaoxian Shi, Caiwei Tan, Zhaodi Jiang, Mingyi Li, Zhiheng Ji, Jing Zhou, Mengxin Luo, Zuyan Fan, Zhifan Ding, Yue Fang, Jun Sun, Junjun Ding, Huasong Lu, Weirui Ma, Wei Xie, Wenjing Su.

RAF protein kinases are major RAS effectors that function by phosphorylating MEK. Although all three RAF isoforms share a conserved RAS binding domain and bind to GTP-loaded RAS, only ARAF uniquely enhances RAS activity. Here we uncovered the molecular basis of ARAF in regulating RAS activation. The disordered N-terminal sequence of ARAF drives self-assembly, forming ARAF-RAS condensates tethered to the plasma membrane. These structures concentrate active RAS locally, impeding NF1-mediated negative regulation of RAS, thereby fostering receptor tyrosine kinase (RTK)-triggered RAS activation. In RAS-mutant tumors, loss of the ARAF N terminus sensitizes tumor cells to pan-RAF inhibition. In hormone-sensitive cancers, increased ARAF condensates drive endocrine therapy resistance, whereas ARAF depletion reverses RTK-dependent resistance. Our findings delineate ARAF-RAS protein condensates as distinct subcellular structures sustaining RAS activity and facilitating oncogenic RAS signaling. Targeting ARAF-RAS condensation may offer a strategy to overcome drug resistance in both wild-type and mutant ARAF-mediated scenarios.

DOI: https://doi.org/10.1038/s41589-024-01826-8
Langmuir. 2025 Jan 27.

Curvature Memory in Electrically Stimulated Lipid Membranes.

Maxim O Lavrentovich, Jan-Michael Y Carrillo, Charles Patrick Collier, John Katsaras, Dima Bolmatov.

We demonstrate, using non-equilibrium molecular dynamics simulations, that lipid membrane capacitance varies with surface charge accumulation linked to membrane shape and curvature changes. Specifically, we show that lipid membranes exhibit a hysteretic response when exposed to oscillatory electric fields. The electromechanical coupling in these membranes leads to hysteretic buckling, in which the membrane can spontaneously buckle in one of two distinct directions along the electric field, even for the same ionic charge accumulation at the water-membrane interface. In this regard, these binary buckled membrane states suggest potential applications in neuromorphic computing. Their bistable nature, characterized by two distinct and stable configurations, could serve as a foundation for implementing memory storage systems and logic operations. Furthermore, we introduce a circuit model that captures these dynamic effects, offering insights into emergent memory effects in electrically stimulated lipid membranes. Finally, this work presents lipid bilayers as dynamic, adaptable elements and suggests a new platform for exploring energy storage, information processing, and memory encoding at the lipid membrane level.

DOI: https://doi.org/10.1021/acs.langmuir.4c03799
Front Nutr. 2024 ;11 1466509

Genetically predicted causal link between the plasma lipidome and pancreatic diseases: a bidirectional Mendelian randomization study.

Liaoyi Lin, Yingbao Huang, Songzan Qian, Lifang Chen, Houzhang Sun.

   Background: Recent studies have increasingly emphasized the strong correlation between the lipidome and the risk of pancreatic diseases. To determine causality, a Mendelian randomization (MR) analysis was performed to identify connections between the lipidome and pancreatic diseases.
Methods: Statistics from a genome-wide association study of the plasma lipidome, which included a diverse array of 179 lipid species, were obtained from the GeneRISK cohort study with 7,174 participants. Genetic associations with four types of pancreatitis and pancreatic cancer were sourced from the R11 release of the FinnGen consortium. Two pancreatitis datasets from UK Biobank were employed as the validation cohort. MR analysis was conducted to assess the relationship between the genetically predicted plasma lipidome and these pancreatic diseases. Inverse variance weighted was adopted as the main statistical method. Bayesian weighted MR was employed for further verification. The MR-Egger intercept test for pleiotropy and Cochrane's Q statistics test for heterogeneity were performed to ensure the robustness.
Results: MR analysis yielded significant evidence that 26, 25, 2, and 19 lipid species were correlated with diverse outcomes of pancreatitis, and 8 lipid species were correlated with pancreatic cancer. Notably, sterol ester (27:1/20:2) levels (OR: 0.84, 95% CI: 0.78-0.90, P = 5.79 × 10-7) were significantly associated with acute pancreatitis, and phosphatidylcholine (17:0_20:4) levels (OR: 0.89, 95% CI: 0.84-0.94, P = 1.78 × 10-4) and sterol ester (27:1/20:4) levels (OR: 0.90, 95% CI: 0.86-0.95, P = 2.71 × 10-4) levels were significantly associated with chronic pancreatitis after the Bonferroni-corrected test. As for validation, 14 and 9 lipid species were correlated with acute and chronic pancreatitis of UK Biobank. Some lipid classes showed significant effects both in the FinnGen consortium and UK Biobank datasets.
Conclusions: The findings of this study indicate a potential genetic predisposition linking the plasma lipidome to pancreatic diseases and good prospects for future pancreatic disease clinical trials.

Keywords:  Mendelian randomization; causal relation; lipids; pancreatic cancer; pancreatitis

DOI:  https://doi.org/10.3389/fnut.2024.1466509
Cell Death Discov. 2025 Jan 25. 11(1): 21

Autophagic flux-lipid droplet biogenesis cascade sustains mitochondrial fitness in colorectal cancer cells adapted to acidosis.

Xiaojie Liu, Xue Sun, Wenqing Mu, Yanan Li, Wenqing Bu, Tingting Yang, Jia Zhang, Rui Liu, Jiayu Ren, Jin Zhou, Peishan Li, Yufang Shi, Changshun Shao.

Cancer development is associated with adaptation to various stressful conditions, such as extracellular acidosis. The adverse tumor microenvironment also selects for increased malignancy. Mitochondria are integral in stress sensing to allow for tumor cells to adapt to stressful conditions. Here, we show that colorectal cancer cells adapted to acidic microenvironment (CRC-AA) are more reliant on oxidative phosphorylation than their parental cells, and the acetyl-CoA in CRC-AA cells are generated from fatty acids and glutamine, but not from glucose. Consistently, CRC-AA cells exhibit increased mitochondrial mass and fitness that depends on an upregulated autophagic flux-lipid droplet axis. Lipid droplets (LDs) function as a buffering system to store the fatty acids derived from autophagy and to protect mitochondria from lipotoxicity in CRC-AA cells. Blockade of LD biogenesis causes mitochondrial dysfunction that can be rescued by inhibiting carnitine palmitoyltransferase 1 α (CPT1α). High level of mitochondrial superoxide is essential for the AMPK activation, resistance to apoptosis, high autophagic flux and mitochondrial function in CRC-AA cells. Thus, our results demonstrate that the cascade of autophagic flux and LD formation plays an essential role in sustaining mitochondrial fitness to promote cancer cell survival under chronic acidosis. Our findings provide insight into the pro-survival metabolic plasticity in cancer cells under microenvironmental or therapeutic stress and imply that this pro-survival cascade may potentially be targeted in cancer therapy.

DOI: https://doi.org/10.1038/s41420-025-02301-6
Crit Rev Oncol Hematol. 2025 Jan 24. pii: S1040-8428(25)00020-4. [Epub ahead of print] 104632

Rhythm is essential: Unraveling the relation between the circadian clock and cancer.

Olajumoke Ogunlusi, Abantika Ghosh, Mrinmoy Sarkar, Kayla Carter, Harshini Davuluri, Mahul Chakraborty, Kristin Eckel-Mahan, Alex Keene, Jerome S Menet, Deborah Bell-Pedersen, Tapasree Roy Sarkar.

  Physiological processes such as the sleep-wake cycle, metabolism, hormone secretion, neurotransmitter release, sensory capabilities, and a variety of behaviors, including sleep, are controlled by a circadian rhythm adapted to 24-hour day-night periodicity. Disruption of circadian rhythm may lead to the risks of numerous diseases, including cancers. Several epidemiological and clinical data reveal a connection between the disruption of circadian rhythms and cancer. On the contrary, oncogenic processes may suppress the homeostatic balance imposed by the circadian clock. The integration of circadian biology into cancer research offers new options for making cancer treatment more effective, and the pharmacological modulation of core clock genes is a new approach in cancer therapy. This review highlights the role of the circadian clock in tumorigenesis, how clock disruption alters the tumor microenvironment, and discusses how pharmacological modulation of circadian clock genes can lead to new therapeutic options.

Keywords:  Circadian disruption; Circadian rhythm; chronotherapy; circulatory tumor cells; clock genes; tumor; tumor metabolism; tumor microenvironment

DOI:  https://doi.org/10.1016/j.critrevonc.2025.104632
Elife. 2025 Jan 30. pii: RP98353. [Epub ahead of print]13

Cold induces brain region-selective cell activity-dependent lipid metabolism.

Hyeonyoung Min, Yale Y Yang, Yunlei Yang.

  It has been well documented that cold is an enhancer of lipid metabolism in peripheral tissues, yet its effect on central nervous system lipid dynamics is underexplored. It is well recognized that cold acclimations enhance adipocyte functions, including white adipose tissue lipid lipolysis and beiging, and brown adipose tissue thermogenesis in mammals. However, it remains unclear whether and how lipid metabolism in the brain is also under the control of ambient temperature. Here, we show that cold exposure predominantly increases the expressions of the lipid lipolysis genes and proteins within the paraventricular nucleus of the hypothalamus (PVH) in male mice. Mechanistically, by using innovatively combined brain-region selective pharmacology and in vivo time-lapse photometry monitoring of lipid metabolism, we find that cold activates cells within the PVH and pharmacological inactivation of cells blunts cold-induced effects on lipid peroxidation, accumulation of lipid droplets, and lipid lipolysis in the PVH. Together, these findings suggest that PVH lipid metabolism is cold sensitive and integral to cold-induced broader regulatory responses.

Keywords:  cold; lipid metabolism; medicine; mouse; neuroscience; paraventricular of hypothalamus; photometry

DOI:  https://doi.org/10.7554/eLife.98353
Cell Rep Med. 2025 Jan 27. pii: S2666-3791(25)00001-1. [Epub ahead of print] 101928

Targeting pancreatic cancer glutamine dependency confers vulnerability to GPX4-dependent ferroptosis.

Xuqing Shen, Yueyue Chen, Yingying Tang, Ping Lu, Mingzhu Liu, Tiebo Mao, Yawen Weng, Feier Yu, Yimei Liu, Yujie Tang, Liwei Wang, Ningning Niu, Jing Xue.

  Pancreatic ductal adenocarcinoma (PDAC) relies heavily on glutamine (Gln) utilization to meet its metabolic and biosynthetic needs. How epigenetic regulators contribute to the metabolic flexibility and PDAC's response and adaptation to Gln scarcity in the tumor milieu remains largely unknown. Here, we elucidate that prolonged Gln restriction or treatment with the Gln antagonist, 6-diazo-5-oxo-L-norleucine (DON), leads to growth inhibition and ferroptosis program activation in PDAC. A CRISPR-Cas9 screen identifies an epigenetic regulator, Paxip1, which promotes H3K4me3 upregulation and Hmox1 transcription upon DON treatment. Additionally, ferroptosis-related repressors (e.g., Slc7a11 and Gpx4) are increased as an adaptive response, thereby predisposing PDAC cells to ferroptosis upon Gln deprivation. Moreover, DON sensitizes PDAC cells to GPX4 inhibitor-induced ferroptosis, both in vitro and in patient-derived xenografts (PDXs). Taken together, our findings reveal that targeting Gln dependency confers susceptibility to GPX4-dependent ferroptosis via epigenetic remodeling and provides a combination strategy for PDAC therapy.

Keywords:  PDAC; combination therapy; epigenetic remodeling; ferroptosis; pancreatic ductal adenocarcinoma; prolonged glutamine starvation

DOI:  https://doi.org/10.1016/j.xcrm.2025.101928
Nat Commun. 2025 Jan 31. 16(1): 1201

Cell adhesion and spreading on fluid membranes through microtubules-dependent mechanotransduction.

Oleg Mikhajlov, Ram M Adar, Maria Tătulea-Codrean, Anne-Sophie Macé, John Manzi, Fanny Tabarin, Aude Battistella, Fahima di Federico, Jean-François Joanny, Guy Tran van Nhieu, Patricia Bassereau.

Integrin clusters facilitate mechanical force transmission (mechanotransduction) and regulate biochemical signaling during cell adhesion. However, most studies have focused on rigid substrates. On fluid substrates like supported lipid bilayers (SLBs), integrin ligands are mobile, and adhesive complexes are traditionally thought unable to anchor for cell spreading. Here, we demonstrate that cells spread on SLBs coated with Invasin, a high-affinity integrin ligand. Unlike SLBs functionalized with RGD peptides, integrin clusters on Invasin-SLBs grow in size and complexity comparable to those on glass. While actomyosin contraction dominates adhesion maturation on stiff substrates, we find that on fluid SLBs, integrin mechanotransduction and cell spreading rely on dynein pulling forces along microtubules perpendicular to the membranes and microtubules pushing on adhesive complexes, respectively. These forces, potentially present on non-deformable surfaces, are revealed in fluid substrate systems. Supported by a theoretical model, our findings demonstrate a mechanical role for microtubules in integrin clustering.

DOI: https://doi.org/10.1038/s41467-025-56343-6
Curr Opin Cell Biol. 2025 Jan 25. pii: S0955-0674(25)00001-8. [Epub ahead of print]93 102463

Autophagic flux measurement: Cargo degradation versus generation of degradation products.

Noboru Mizushima.

Autophagy is the cellular processes that transport cytoplasmic components to lysosomes for degradation. It plays essential physiological roles, including in adaptation to environmental changes such as starvation and maintaining intracellular quality control. Recently, its links to aging and disease have garnered substantial attention. Although various methods to measure autophagic activity (autophagic flux) have been developed, accurate measurement remains challenging and often contentious. This review presents a discussion of techniques to measure the flux of autophagy, particularly macroautophagy, utilizing two contrasting approaches-assaying cargo degradation versus assaying the generation of degradation products-with an emphasis on the advantages of the latter.

DOI: https://doi.org/10.1016/j.ceb.2025.102463
Biol Methods Protoc. 2025 ;10(1): bpae094

ImmuNet: a segmentation-free machine learning pipeline for immune landscape phenotyping in tumors by multiplex imaging.

Shabaz Sultan, Mark A J Gorris, Evgenia Martynova, Lieke L van der Woude, Franka Buytenhuijs, Sandra van Wilpe, Kiek Verrijp, Carl G Figdor, I Jolanda M de Vries, Johannes Textor.

  Tissue specimens taken from primary tumors or metastases contain important information for diagnosis and treatment of cancer patients. Multiplex imaging allows in situ visualization of heterogeneous cell populations, such as immune cells, in tissue samples. Most image processing pipelines first segment cell boundaries and then measure marker expression to assign cell phenotypes. In dense tissue environments, this segmentation-first approach can be inaccurate due to segmentation errors or overlapping cells. Here, we introduce the machine-learning pipeline "ImmuNet", which identifies positions and phenotypes of cells without segmenting them. ImmuNet is easy to train: human annotators only need to click on an immune cell and score its expression of each marker-drawing a full cell outline is not required. We trained and evaluated ImmuNet on multiplex images from human tonsil, lung cancer, prostate cancer, melanoma, and bladder cancer tissue samples and found it to consistently achieve error rates below 5%-10% across tissue types, cell types, and tissue densities, outperforming a segmentation-based baseline method. Furthermore, we externally validate ImmuNet results by comparing them to flow cytometric cell count measurements from the same tissue. In summary, ImmuNet is an effective, simpler alternative to segmentation-based approaches when only cell positions and phenotypes, but not their shapes, are required for downstream analyses. Thus, ImmuNet helps researchers to analyze cell positions in multiplex tissue images more easily and accurately.

Keywords:  cell detection; click annotations; deep learning; multiplex immunohistochemistry

DOI:  https://doi.org/10.1093/biomethods/bpae094
Elife. 2025 Jan 28. pii: RP92635. [Epub ahead of print]13

Progesterone induces meiosis through two obligate co-receptors with PLA2 activity.

Nancy Nader, Lama Assaf, Lubna Zarif, Anna Halama, Sharan Yadav, Maya Dib, Nabeel Attarwala, Qiuying Chen, Karsten Suhre, Steven Gross, Khaled Machaca.

  The steroid hormone progesterone (P4) regulates multiple aspects of reproductive and metabolic physiology. Classical P4 signaling operates through nuclear receptors that regulate transcription. In addition, P4 signals through membrane P4 receptors (mPRs) in a rapid nongenomic modality. Despite the established physiological importance of P4 nongenomic signaling, the details of its signal transduction cascade remain elusive. Here, using Xenopus oocyte maturation as a well-established physiological readout of nongenomic P4 signaling, we identify the lipid hydrolase ABHD2 (α/β hydrolase domain-containing protein 2) as an essential mPRβ co-receptor to trigger meiosis. We show using functional assays coupled to unbiased and targeted cell-based lipidomics that ABHD2 possesses a phospholipase A2 (PLA2) activity that requires mPRβ. This PLA2 activity bifurcates P4 signaling by inducing clathrin-dependent endocytosis of mPRβ, resulting in the production of lipid messengers that are G-protein coupled receptor agonists. Therefore, P4 drives meiosis by inducing an ABHD2 PLA2 activity that requires both mPRβ and ABHD2 as obligate co-receptors.

Keywords:  ABHD2; PLA2; cell biology; lipid messengers; membrane progesterone receptor beta; nongenomic signaling; progesterone; xenopus

DOI:  https://doi.org/10.7554/eLife.92635
Clin Nutr. 2024 Dec 30. pii: S0261-5614(24)00469-2. [Epub ahead of print]45 262-269

Brown adipose tissue is associated with reduced weight loss and risk of cancer cachexia: A retrospective cohort study.

Grigorios Panagiotou, Demsina Babazadeh, Dario F Mazza, Soheila Azghadi, Joseph M Cawood, Aaron S Rosenberg, Fumiaki Imamura, Nita G Forouhi, Abhijit J Chaudhari, Yasser G Abdelhafez, Ramsey D Badawi, Maria Chondronikola.

   BACKGROUND & AIMS: Brown adipose tissue (BAT) has been mainly investigated as a potential target against cardiometabolic disease, but it has also been linked to cancer-related outcomes. Although preclinical data support that BAT and the thermogenic adipocytes in white adipose tissue may play an adverse role in the pathogenesis of cancer cachexia, results from studies in patients have reported inconsistent results. The purpose of this study was to examine the interrelationship between presence of detectable BAT, changes in body weight, and cachexia in patients with cancer. We hypothesized that evidence of BAT at cancer diagnosis would be associated with greater weight loss and risk of cancer cachexia up to a year after cancer diagnosis.
METHODS: We conducted a retrospective cohort study in treatment-naïve patients with detectable BAT (BAT+, n = 57) and without evidence of BAT (BAT-, n = 73) on 2-deoxy-2-[18F]fluoro-d-glucose positron emission tomography-computed tomography (18F-FDG-PET-CT) imaging performed for cancer staging (2004-2020). Patients' clinical, demographic, and anthropometric characteristics were extracted from their electronic medical record for up to a year after diagnosis. The two groups were a priori matched for demographic, anthropometric, and disease-related characteristics at diagnosis, as well as for season and outdoor temperature on the day of the PET-CT scan. Cancer cachexia was defined as weight loss greater than 5 % or 2 % if body mass index was lower than 20 kg/m2. Poisson regression models were fitted to estimate the relative risk (RR) for developing cancer cachexia over the 1-year follow-up among BAT+ compared to BAT- patients.
RESULTS: The BAT+ group experienced a lower magnitude of weight loss compared with the BAT- group during the 1-year follow-up (p = 0.014 for interaction between BAT status and time). The risk for cancer cachexia was 44 % lower in the BAT+ than the BAT- group, adjusted for age, sex, outdoor temperature on the day of the 18F-FDG-PET-CT imaging, cancer site and stage (RR: 0.56, 95 % CI: 0.32 to 0.97).
CONCLUSION: Contrary to our original hypothesis, evidence of BAT assessed by 18F-FDG-PET-CT imaging at cancer diagnosis was associated with greater body weight maintenance and lower risk for developing cancer cachexia up to one year after diagnosis. Larger, prospective studies and mechanistic experiments are needed to expand and identify the causal factors of our observations.

Keywords:  Brown adipose tissue; Cachexia; Cancer; Muscle; Obesity

DOI:  https://doi.org/10.1016/j.clnu.2024.12.028
Nat Commun. 2025 Jan 25. 16(1): 1011

Mechanisms of RCD-1 pore formation and membrane bending.

Keli Ren, James Daniel Farrell, Yueyue Li, Xinrui Guo, Ruipei Xie, Xin Liu, Qiaozhen Kang, Qihui Fan, Fangfu Ye, Jingjin Ding, Fang Jiao.

Regulator of cell death-1 (RCD-1) governs the heteroallelic expression of RCD-1-1 and RCD-1-2, a pair of fungal gasdermin (GSDM)-like proteins, which prevent cytoplasmic mixing during allorecognition and safeguard against mycoparasitism, genome exploitation, and deleterious cytoplasmic elements (e.g., senescence plasmids) by effecting a form of cytolytic cell death. However, the underlying mechanisms by which RCD-1 acts on the cell membrane remain elusive. Here, we demonstrate that RCD-1 binds acidic lipid membranes, forms pores, and induces membrane bending. Using atomic force microscopy (AFM) and AlphaFold, we show that RCD-1-1 and RCD-1-2 form heterodimers that further self-assemble into ~14.5 nm-wide transmembrane pores (~10 heterodimers). Moreover, through AFM force spectroscopy and micropipette aspiration, we reveal that RCD-1 proteins bend membranes with low bending moduli. This combined action of pore formation and membrane deformation may constitute a conserved mechanism within the broader GSDM family.

DOI: https://doi.org/10.1038/s41467-025-56398-5
Cancer Commun (Lond). 2025 Jan 25.

Cuproplasia and cuproptosis, two sides of the coin.

Kaizhong Lu, Chandra Sugiarto Wijaya, Qinghua Yao, Hongchuan Jin, Lifeng Feng.

  Copper is an essential micronutrient in the human body, mainly acting as a crucial cofactor required for a wide range of physiological processes across nearly all cell types. Recent advances revealed that tumor cells seize copper to fulfill their rapid proliferation, metastasis, immune evasion, and so on by reprogramming the copper regulatory network, defined as cuproplasia. Thus, targeting copper chelation to reduce copper levels has been considered a rational tumor therapy strategy. However, overloaded copper ions could be toxic, which leads to the aggregation of lipoylated mitochondrial proteins and the depletion of iron-sulfur clusters, ultimately resulting in cell death, termed cuproptosis. Upon its discovery, cuproptosis has attracted great interest from oncologists, and targeting cuproptosis by copper ionophores exhibits as a potential anti-tumor therapy. In this review, we present the underlying mechanisms involved in cuproplasia and cuproptosis. Additionally, we sum up the chemicals targeting either cuproplasia or cuproptosis for cancer therapy. Further attention should be paid to distinguishing cancer patients who are suitable for targeting cuproplasia or cuproptosis.

Keywords:  copper homeostasis; cuproplasia; cuproptosis; therapeutics targeting copper; tumor

DOI:  https://doi.org/10.1002/cac2.70001
Cell. 2025 Jan 23. pii: S0092-8674(24)01476-4. [Epub ahead of print]188(2): 273-274

Cell after 50.

John W Pham.

DOI: https://doi.org/10.1016/j.cell.2024.12.033
Nanoscale. 2025 Jan 27.

Atomic force microscopy combined with microfluidics for label-free sorting and automated nanomechanics of circulating tumor cells in liquid biopsy.

Xiaoqun Qi, Sen Lin, Mi Li.

Liquid biopsies are expected to advance cancer management, and particularly physical cues are gaining attention for indicating tumorigenesis and metastasis. Atomic force microscopy (AFM) has become a standard and important tool for detecting the mechanical properties of single living cells, but studies of developing AFM-based methods to efficiently measure the mechanical properties of circulating tumor cells (CTCs) in liquid biopsy for clinical utility are still scarce. Herein, we present a proof-of-concept study based on the complementary combination of AFM and microfluidics, which allows label-free sorting of individual CTCs and subsequent automated AFM measurements of the mechanical properties of CTCs. With the use of a microfluidic system containing contraction-expansion microchannels, specific cancer cell types were separated and harvested in a marker-independent manner. Subsequently, automated AFM indentation and force spectroscopy experiments were performed on the enriched cells under the precise guidance of the label-free identification of cells using a deep learning optical image recognition model. The effectiveness of the presented method was verified on three experimental sample systems, including mixed microspheres with different sizes, a mixture of different types of cancer cells, and a mixture of cancer cells and blood cells. The study illustrates a feasible framework based on the integration of AFM and microfluidics for non-destructive and efficient nanomechanical phenotyping of CTCs in bodily fluids, which offers additional possibilities for the clinical applications of AFM-based nanomechanical analysis and will also benefit the field of mechanobiology as well as cancer liquid biopsy.

DOI: https://doi.org/10.1039/d4nr04033c
Nat Commun. 2025 Jan 24. 16(1): 978

SLC25A38 is required for mitochondrial pyridoxal 5'-phosphate (PLP) accumulation.

Izabella A Pena, Jeffrey S Shi, Sarah M Chang, Jason Yang, Samuel Block, Charles H Adelmann, Heather R Keys, Preston Ge, Shveta Bathla, Isabella H Witham, Grzegorz Sienski, Angus C Nairn, David M Sabatini, Caroline A Lewis, Nora Kory, Matthew G Vander Heiden, Myriam Heiman.

Many essential proteins require pyridoxal 5'-phosphate, the active form of vitamin B6, as a cofactor for their activity. These include enzymes important for amino acid metabolism, one-carbon metabolism, polyamine synthesis, erythropoiesis, and neurotransmitter metabolism. A third of all mammalian pyridoxal 5'-phosphate-dependent enzymes are localized in the mitochondria; however, the molecular machinery involved in the regulation of mitochondrial pyridoxal 5'-phosphate levels in mammals remains unknown. In this study, we used a genome-wide CRISPR interference screen in erythroleukemia cells and organellar metabolomics to identify the mitochondrial inner membrane protein SLC25A38 as a regulator of mitochondrial pyridoxal 5'-phosphate. Loss of SLC25A38 causes depletion of mitochondrial, but not cellular, pyridoxal 5'-phosphate, and impairs cellular proliferation under both physiological and low vitamin B6 conditions. Metabolic changes associated with SLC25A38 loss suggest impaired mitochondrial pyridoxal 5'-phosphate-dependent enzymatic reactions, including serine to glycine conversion catalyzed by serine hydroxymethyltransferase-2 as well as ornithine aminotransferase. The proliferation defect of SLC25A38-null K562 cells in physiological and low vitamin B6 media can be explained by the loss of serine hydroxymethyltransferase-2-dependent production of one-carbon units and downstream de novo nucleotide synthesis. Our work points to a role for SLC25A38 in mitochondrial pyridoxal 5'-phosphate accumulation and provides insights into the pathology of congenital sideroblastic anemia.

DOI: https://doi.org/10.1038/s41467-025-56130-3
Chem Biomed Imaging. 2025 Jan 27. 3(1): 25-34

Alteration of Lipid Metabolism in Hypoxic Cancer Cells.

Gil A Gonzalez, Ezinne U Osuji, Natalie C Fiur, Matthew G Clark, Seohee Ma, Laura L Lukov, Chi Zhang.

Due to uncontrolled cell proliferation and disrupted vascularization, many cancer cells in solid tumors have limited oxygen supply. The hypoxic microenvironments of tumors lead to metabolic reprogramming of cancer cells, contributing to therapy resistance and metastasis. To identify better targets for the effective removal of hypoxia-adaptive cancer cells, it is crucial to understand how cancer cells alter their metabolism in hypoxic conditions. Here, we studied lipid metabolic changes in cancer cells under hypoxia using coherent Raman scattering (CRS) microscopy. We discovered the accumulation of lipid droplets (LDs) in the endoplasmic reticulum (ER) in hypoxia. Time-lapse CRS microscopy revealed the release of old LDs and the reaccumulated LDs in the ER during hypoxia exposure. Additionally, we explored the impact of carbon sources on LD formation and found that MIA PaCa2 cells preferred fatty acid uptake for LD formation, while glucose was essential to alleviate lipotoxicity. Hyperspectral-stimulated Raman scattering (SRS) microscopy revealed a reduction in cholesteryl ester content and a decrease in lipid saturation levels of LDs in hypoxic MIA PaCa2 cancer cells. This alteration in LD content is linked to reduced efficacy of treatments targeting cholesteryl ester formation. This study unveils important lipid metabolic changes in hypoxic cancer cells, providing insights that could lead to better treatment strategies for hypoxia-resistant cancer cells.

DOI: https://doi.org/10.1021/cbmi.4c00050
Molecules. 2025 Jan 17. pii: 377. [Epub ahead of print]30(2):

Cell Labeling with 15-YNE Is Useful for Tracking Protein Palmitoylation and Metabolic Lipid Flux in the Same Sample.

Nadine Merz, Karin Schilling, Dominique Thomas, Lisa Hahnefeld, Sabine Grösch.

  Protein S-palmitoylation is the process by which a palmitoyl fatty acid is attached to a cysteine residue of a protein via a thioester bond. A range of methodologies are available for the detection of protein S-palmitoylation. In this study, two methods for the S-palmitoylation of different proteins were compared after metabolic labeling of cells with 15-hexadecynoic acid (15-YNE) to ascertain their relative usefulness. It was hypothesized that labeling cells with a traceable lipid would affect lipid metabolism and the cellular lipidome. In this study, we developed a method to track 15-YNE incorporation into lipids using liquid chromatography high-resolution mass spectrometry (LC-HRMS) as well as protein palmitoylation in the same sample. We observed a time- and concentration-dependent S-palmitoylation of calnexin and succinate dehydrogenase complex flavoprotein subunit A (SDHA) depending on the cell type. The detection of S-palmitoylation with a clickable fluorophore or biotin azide followed by immunoprecipitation is shown to be equally useful. 15-YNE was observed to be incorporated into a wide array of lipid classes during the process, yet it did not appear to modify the overall lipid composition of the cells. In conclusion, we show that 15-YNE is a useful tracer to detect both protein S-palmitoylation and lipid metabolism in the same sample.

Keywords:  Cy5.5-azide; LC-HRMS; Linex; alkyne; biotin; click reaction; protein palmitoylation

DOI:  https://doi.org/10.3390/molecules30020377