bims-cagime 2025-02-23 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–02–23
43 papers selected by
Kıvanç Görgülü, Technical University of Munich

c-Rel drives pancreatic cancer metastasis through Fibronectin-Integrin signaling-induced isolation stress resistance and EMT activation.
RNA neoantigen vaccines prime long-lived CD8+ T cells in pancreatic cancer.
Biophysical modeling of membrane curvature generation and curvature sensing by the glycocalyx.
Solute carriers: The gatekeepers of metabolism.
An organism-level quantitative flux model of energy metabolism in mice.
Cooperative nutrient scavenging is an evolutionary advantage in cancer.
Exploring the Regulation of Lipid Droplet Catabolism through Lipophagy.
Ergothioneine controls mitochondrial function and exercise performance via direct activation of MPST.
Characterization of single neurons reprogrammed by pancreatic cancer.
TREM2 depletion in pancreatic cancer elicits pathogenic inflammation and accelerates tumor progression via enriching IL-1β+ macrophages.
Calcium release from damaged lysosomes triggers stress granule formation for cell survival.
ImmuneLENS characterizes systemic immune dysregulation in aging and cancer.
Recovery of plasma membrane tension after a hyperosmotic shock.
RBM43 controls PGC1α translation and a PGC1α-STING signaling axis.
Measuring plasma membrane fluidity using confocal microscopy.
A decision point between transdifferentiation and programmed cell death priming controls KRAS-dependent pancreatic cancer development.
Gemcitabine Alters Phosphatidylcholine Metabolism in Mouse Pancreatic Tumors.
Early identification of weight loss trajectories in advanced cancer and associations with survival.
Target cell tension regulates macrophage trogocytosis.
High Glucose Contribution to the TCA Cycle Is a Feature of Aggressive Non-Small Cell Lung Cancer in Patients.
The mutational landscape and functional effects of noncoding ultraconserved elements in human cancers.
Direct ionic stress sensing and mitigation by the transcription factor NFAT5.
Lysosomal Quality Control.
Trafficking of K63-polyubiquitin modified membrane proteins in a macroautophagy-independent pathway is linked to ATG9A.
Cell fusion as a driver of metastasis: re-evaluating an old hypothesis in the age of cancer heterogeneity.
Palmitoylation of PD-L1 Regulates Its Membrane Orientation and Immune Evasion.
Understanding the coarse-grained free energy landscape of phospholipids and their phase separation.
HypoxyStat, a small-molecule form of hypoxia therapy that increases oxygen-hemoglobin affinity.
Visualization of Ferroptosis-Induced Lipid Peroxidation Using Plasma Membrane-Specific Fluorescent Probe LipoxPM.
Proteomics profiling of research models for studying pancreatic ductal adenocarcinoma.
Hexokinase detachment from mitochondria drives the Warburg effect to support compartmentalized ATP production.
Cachexia Alters Central Nervous System Morphology and Functionality in Cancer Patients.
A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity.
adiposetissue.org: A knowledge portal integrating clinical and experimental data from human adipose tissue.
Visualizing bulk autophagy in vivo by tagging endogenous LC3B.
Clonal driver neoantigen loss under EGFR TKI and immune selection pressures.
Spectrally Resolved Single-Molecule Orientation Imaging Reveals a Direct Correspondence between the Polarity and Microviscosity Experienced by Nile Red in Supported Lipid Bilayer Membranes.
ABCA1-mediated nascent HDL formation is precisely regulated by the plasma membrane cholesterol.
Swirling motion of breast cancer cells radially aligns collagen fibers to enable collective invasion.
Membrane Association of Intrinsically Disordered Proteins.
Lipid probes to study ion channels.
GDF15 Neutralization Ameliorates Muscle Atrophy and Exercise Intolerance in a Mouse Model of Mitochondrial Myopathy.
Multiplexed Lectin-PAINT super-resolution microscopy enables cell glycotyping.

bioRxiv. 2025 Feb 01. pii: 2025.01.29.635445. [Epub ahead of print]

c-Rel drives pancreatic cancer metastasis through Fibronectin-Integrin signaling-induced isolation stress resistance and EMT activation.

D Bakırdöğen, K Görgülü, J Xin, S Alcalá, L Ruiz-Cañas, K Frank, N Wu, K N Diakopoulos, C Dai, H Öztürk, D Demircioğlu, K Peschke, R Ranjan, F Fusco, J Martinez-Useros, M J Fernandez-Aceñero, N F Chhabra, J C López-Gil, J Ai, D A Ruess, E Kaya-Aksoy, K Steiger, F Schmidt, L Kohlmann, A Berninger, R M Schmid, M Reichert, M Adli, M Lesina, B Sainz, H Algül.

Pancreatic ductal adenocarcinoma remains one of the deadliest malignancies, with limited treatment options and a high recurrence rate. Recurrence happens often with metastasis, for which cancer cells must adapt to isolation stress to successfully colonize distant organs. While the fibronectin-integrin axis has been implicated in this adaptation, its regulatory mechanisms require further elaboration. Here, we identify c-Rel as an oncogenic driver in PDAC, promoting epithelial-to-mesenchymal transition (EMT) plasticity, extracellular matrix (ECM) remodeling, and resistance to isolation stress. Mechanistically, c-Rel directly regulates fibronectin ( Fn1 ) and CD61 ( itgb3 ) transcription, enhancing cellular plasticity and survival under anchorage-independent conditions. Fibronectin is not essential for EMT, but its absence significantly impairs metastatic colonization, highlighting a tumor-autonomous role for FN1 in isolation stress adaptation. These findings establish c-Rel as a key regulator of PDAC metastasis by controlling circulating tumor cell (CTC) niche and survival, suggesting that targeting the c-Rel-fibronectin-integrin axis could provide new therapeutic strategies to mitigate disease progression and recurrence.

DOI: https://doi.org/10.1101/2025.01.29.635445
Nature. 2025 Feb 19.

RNA neoantigen vaccines prime long-lived CD8+ T cells in pancreatic cancer.

Zachary Sethna, Pablo Guasp, Charlotte Reiche, Martina Milighetti, Nicholas Ceglia, Erin Patterson, Jayon Lihm, George Payne, Olga Lyudovyk, Luis A Rojas, Nan Pang, Akihiro Ohmoto, Masataka Amisaki, Abderezak Zebboudj, Zagaa Odgerel, Emmanuel M Bruno, Siqi Linsey Zhang, Charlotte Cheng, Yuval Elhanati, Evelyna Derhovanessian, Luisa Manning, Felicitas Müller, Ina Rhee, Mahesh Yadav, Taha Merghoub, Jedd D Wolchok, Olca Basturk, Mithat Gönen, Andrew S Epstein, Parisa Momtaz, Wungki Park, Ryan Sugarman, Anna M Varghese, Elizabeth Won, Avni Desai, Alice C Wei, Michael I D'Angelica, T Peter Kingham, Kevin C Soares, William R Jarnagin, Jeffrey Drebin, Eileen M O'Reilly, Ira Mellman, Ugur Sahin, Özlem Türeci, Benjamin D Greenbaum, Vinod P Balachandran.

A fundamental challenge for cancer vaccines is to generate long-lived functional T cells that are specific for tumour antigens. Here we find that mRNA-lipoplex vaccines against somatic mutation-derived neoantigens may solve this challenge in pancreatic ductal adenocarcinoma (PDAC), a lethal cancer with few mutations. At an extended 3.2-year median follow-up from a phase 1 trial of surgery, atezolizumab (PD-L1 inhibitory antibody), autogene cevumeran1 (individualized neoantigen vaccine with backbone-optimized uridine mRNA-lipoplex nanoparticles) and modified (m) FOLFIRINOX (chemotherapy) in patients with PDAC, we find that responders with vaccine-induced T cells (n = 8) have prolonged recurrence-free survival (RFS; median not reached) compared with non-responders without vaccine-induced T cells (n = 8; median RFS 13.4 months; P = 0.007). In responders, autogene cevumeran induces CD8+ T cell clones with an average estimated lifespan of 7.7 years (range 1.5 to roughly 100 years), with approximately 20% of clones having latent multi-decade lifespans that may outlive hosts. Eighty-six percent of clones per patient persist at substantial frequencies approximately 3 years post-vaccination, including clones with high avidity to PDAC neoepitopes. Using PhenoTrack, a novel computational strategy to trace single T cell phenotypes, we uncover that vaccine-induced clones are undetectable in pre-vaccination tissues, and assume a cytotoxic, tissue-resident memory-like T cell state up to three years post-vaccination with preserved neoantigen-specific effector function. Two responders recurred and evidenced fewer vaccine-induced T cells. Furthermore, recurrent PDACs were pruned of vaccine-targeted cancer clones. Thus, in PDAC, autogene cevumeran induces de novo CD8+ T cells with multiyear longevity, substantial magnitude and durable effector functions that may delay PDAC recurrence. Adjuvant mRNA-lipoplex neoantigen vaccines may thus solve a pivotal obstacle for cancer vaccination.

DOI: https://doi.org/10.1038/s41586-024-08508-4
Proc Natl Acad Sci U S A. 2025 Feb 25. 122(8): e2418357122

Biophysical modeling of membrane curvature generation and curvature sensing by the glycocalyx.

Ke Xiao, Sujeong Park, Jeanne C Stachowiak, Padmini Rangamani.

  Generation of membrane curvature is fundamental to cellular function. Recent studies have established that the glycocalyx, a sugar-rich polymer layer at the cell surface, can generate membrane curvature. While there have been some theoretical efforts to understand the interplay between the glycocalyx and membrane bending, there remain open questions about how the properties of the glycocalyx affect membrane bending. For example, the relationship between membrane curvature and the density of glycosylated proteins on its surface remains unclear. In this work, we use polymer brush theory to develop a detailed biophysical model of the energetic interactions of the glycocalyx with the membrane. Using this model, we identify the conditions under which the glycocalyx can both generate and sense curvature. Our model predicts that the extent of membrane curvature generated depends on the grafting density of the glycocalyx and the backbone length of the polymers constituting the glycocalyx. Furthermore, when coupled with the intrinsic membrane properties such as spontaneous curvature and a line tension along the membrane, the curvature generation properties of the glycocalyx are enhanced. These predictions were tested experimentally by examining the propensity of glycosylated transmembrane proteins to drive the assembly of highly curved filopodial protrusions at the plasma membrane of adherent mammalian cells. Our model also predicts that the glycocalyx has curvature-sensing capabilities, in agreement with the results of our experiments. Thus, our study develops a quantitative framework for mapping the properties of the glycocalyx to the curvature generation capability of the membrane.

Keywords:  curvature generation; curvature sensing; glycocalyx; membrane bending; polymer brush theory

DOI:  https://doi.org/10.1073/pnas.2418357122
Cell. 2025 Feb 20. pii: S0092-8674(25)00044-3. [Epub ahead of print]188(4): 869-884

Solute carriers: The gatekeepers of metabolism.

Artem Khan, Yuyang Liu, Mark Gad, Timothy C Kenny, Kıvanç Birsoy.

  Solute carrier (SLC) proteins play critical roles in maintaining cellular and organismal homeostasis by transporting small molecules and ions. Despite a growing body of research over the past decade, physiological substrates and functions of many SLCs remain elusive. This perspective outlines key challenges in studying SLC biology and proposes an evidence-based framework for defining SLC substrates. To accelerate the deorphanization process, we explore systematic technologies, including human genetics, biochemistry, and computational and structural approaches. Finally, we suggest directions to better understand SLC functions beyond substrate identification in physiology and disease.

Keywords:  SLC; deorphanization; metabolism; solute carriers

DOI:  https://doi.org/10.1016/j.cell.2025.01.015
Cell Metab. 2025 Feb 13. pii: S1550-4131(25)00008-7. [Epub ahead of print]

An organism-level quantitative flux model of energy metabolism in mice.

Bo Yuan, Will Doxsey, Özlem Tok, Young-Yon Kwon, Yanshan Liang, Karen E Inouye, Gökhan S Hotamışlıgil, Sheng Hui.

  Mammalian tissues feed on nutrients in the blood circulation. At the organism level, mammalian energy metabolism is comprised of the oxidation, storage, interconversion, and release of circulating nutrients. Here, by integrating isotope tracer infusion, mass spectrometry, and isotope gas analyzer measurement, we developed a framework to systematically quantify fluxes through these metabolic processes for 10 major circulating energy nutrients in mice, resulting in an organism-level quantitative flux model of energy metabolism. This model revealed in wild-type mice that circulating nutrients have metabolic cycling fluxes dominant to their oxidation fluxes, with distinct partitions between cycling and oxidation for individual circulating nutrients. Applications of this framework in obese mouse models showed extensive elevation of metabolic cycling fluxes in ob/ob mice but not in diet-induced obese mice on a per-animal or per-lean mass basis. Our framework is a valuable tool to reveal new features of energy metabolism in physiological and disease conditions.

Keywords:  energy metabolism; futile cycle; high-fat diet; isotope tracing; metabolic flux analysis; ob/ob; obesity

DOI:  https://doi.org/10.1016/j.cmet.2025.01.008
Nature. 2025 Feb 19.

Cooperative nutrient scavenging is an evolutionary advantage in cancer.

Gizem Guzelsoy, Setiembre D Elorza, Manon Ros, Logan T Schachtner, Makiko Hayashi, Spencer Hobson-Gutierrez, Parker Rundstrom, Julia S Brunner, Ray Pillai, William E Walkowicz, Lydia W S Finley, Maxime Deforet, Thales Papagiannakopoulos, Carlos Carmona-Fontaine.

The survival of malignant cells within tumours is often seen as depending on ruthless competition for nutrients and other resources1,2. Although competition is certainly critical for tumour evolution and cancer progression, cooperative interactions within tumours are also important, albeit poorly understood3,4. Cooperative populations at all levels of biological organization risk extinction if their population size falls below a critical tipping point5,6. Here we examined whether cooperation among tumour cells may be a potential therapeutic target. We identified a cooperative mechanism that enables tumour cells to proliferate under the amino acid-deprived conditions found in the tumour microenvironment. Disruption of this mechanism drove cultured tumour populations to the critical extinction point and resulted in a marked reduction in tumour growth in vivo. Mechanistically, we show that tumour cells collectively digest extracellular oligopeptides through the secretion of aminopeptidases. The resulting free amino acids benefit both aminopeptidase-secreting cells and neighbouring cells. We identified CNDP2 as the key enzyme that hydrolyses these peptides extracellularly, and loss of this aminopeptidase prevents tumour growth in vitro and in vivo. These data show that cooperative scavenging of nutrients is key to survival in the tumour microenvironment and reveal a targetable cancer vulnerability.

DOI: https://doi.org/10.1038/s41586-025-08588-w
J Vis Exp. 2025 Jan 31.

Exploring the Regulation of Lipid Droplet Catabolism through Lipophagy.

Carolina Lagos, Diego Tapia, Cristina Silva, Jorge Cancino.

Macroautophagy, commonly referred to as autophagy, is a highly conserved cellular process responsible for the degradation of cellular components. This process is particularly prominent under conditions such as fasting, cellular stress, organelle damage, cellular damage, or aging of cellular components. During autophagy, a segment of the cytoplasm is enclosed within double-membrane vesicles known as autophagosomes, which then fuse with lysosomes. Following this fusion, the contents of autophagosomes undergo non-selective bulk degradation facilitated by lysosomes. However, autophagy also exhibits selective functionality, targeting specific organelles, including mitochondria, peroxisomes, lysosomes, nuclei, and lipid droplets (LDs). Lipid droplets are enclosed by a phospholipid monolayer that isolates neutral lipids from the cytoplasm, protecting cells from the harmful effects of excess sterols and free fatty acids (FFAs). Autophagy is implicated in various conditions, including neurodegenerative diseases, metabolic disorders, and cancer. Specifically, lipophagy -- the autophagy-dependent degradation of lipid droplets -- plays a crucial role in regulating intracellular FFA levels across different metabolic states. This regulation supports essential processes such as membrane synthesis, signaling molecule formation, and energy balance. Consequently, impaired lipophagy increases cellular vulnerability to death stimuli and contributes to the development of diseases such as cancer. Despite its significance, the precise mechanisms governing lipid droplet metabolism regulated by lipophagy in cancer cells remain poorly understood. This article aims to describe confocal imaging acquisition and quantitative imaging analysis protocols that enable the investigation of lipophagy associated with metabolic changes in cancer cells. The results obtained through these protocols may shed light on the intricate interplay between autophagy, lipid metabolism, and cancer progression. By elucidating these mechanisms, novel therapeutic targets may emerge for combating cancer and other metabolic-related diseases.

DOI: https://doi.org/10.3791/67287
Cell Metab. 2025 Feb 11. pii: S1550-4131(25)00024-5. [Epub ahead of print]

Ergothioneine controls mitochondrial function and exercise performance via direct activation of MPST.

Hans-Georg Sprenger, Melanie J Mittenbühler, Yizhi Sun, Jonathan G Van Vranken, Sebastian Schindler, Abhilash Jayaraj, Sumeet A Khetarpal, Amanda L Smythers, Ariana Vargas-Castillo, Anna M Puszynska, Jessica B Spinelli, Andrea Armani, Tenzin Kunchok, Birgitta Ryback, Hyuk-Soo Seo, Kijun Song, Luke Sebastian, Coby O'Young, Chelsea Braithwaite, Sirano Dhe-Paganon, Nils Burger, Evanna L Mills, Steven P Gygi, Joao A Paulo, Haribabu Arthanari, Edward T Chouchani, David M Sabatini, Bruce M Spiegelman.

  Ergothioneine (EGT) is a diet-derived, atypical amino acid that accumulates to high levels in human tissues. Reduced EGT levels have been linked to age-related disorders, including neurodegenerative and cardiovascular diseases, while EGT supplementation is protective in a broad range of disease and aging models. Despite these promising data, the direct and physiologically relevant molecular target of EGT has remained elusive. Here, we use a systematic approach to identify how mitochondria remodel their metabolome in response to exercise training. From these data, we find that EGT accumulates in muscle mitochondria upon exercise training. Proteome-wide thermal stability studies identify 3-mercaptopyruvate sulfurtransferase (MPST) as a direct molecular target of EGT; EGT binds to and activates MPST, thereby boosting mitochondrial respiration and exercise training performance in mice. Together, these data identify the first physiologically relevant EGT target and establish the EGT-MPST axis as a molecular mechanism for regulating mitochondrial function and exercise performance.

Keywords:  MPST; ergothioneine; exercise; mitochondria

DOI:  https://doi.org/10.1016/j.cmet.2025.01.024
Nature. 2025 Feb 17.

Characterization of single neurons reprogrammed by pancreatic cancer.

Vera Thiel, Simon Renders, Jasper Panten, Nicolas Dross, Katharina Bauer, Daniel Azorin, Vanessa Henriques, Vanessa Vogel, Corinna Klein, Aino-Maija Leppä, Isabel Barriuso Ortega, Jonas Schwickert, Iordanis Ourailidis, Julian Mochayedi, Jan-Philipp Mallm, Carsten Müller-Tidow, Hannah Monyer, John Neoptolemos, Thilo Hackert, Oliver Stegle, Duncan T Odom, Rienk Offringa, Albrecht Stenzinger, Frank Winkler, Martin Sprick, Andreas Trumpp.

The peripheral nervous system (PNS) orchestrates organ function in health and disease. Most cancers including pancreatic ductal adenocarcinoma (PDAC) are infiltrated by PNS neurons, contributing to the complex tumor microenvironment (TME)1,2. However, neuronal cell bodies reside in various PNS ganglia, far from the tumor mass. Thus, cancer or healthy organ-innervating neurons elude current tissue sequencing datasets. To molecularly characterize pancreas- and PDAC-innervating neurons at single cell resolution, we developed "Trace-n-seq". This method employs retrograde tracing of axons from tissues to their respective ganglia followed by single-cell isolation and transcriptomic analysis. By characterizing >5.000 individual sympathetic and sensory neurons with about 4.000 innervating PDAC or healthy pancreas we reveal novel neuronal cell types and unique molecular networks distinct to pancreas, pancreatitis, PDAC, or melanoma metastasis. We integrate single-cell datasets of innervating neurons and the TME to establish a neuro-cancer-microenvironment interactome, delineate cancer-driven neuronal reprogramming and generate a pancreatic cancer-nerve signature. Pharmacological denervation induces a proinflammatory TME and increases immune-checkpoint inhibitor effectiveness. Nab-Paclitaxel causes intra-tumor neuropathy which attenuated PDAC growth and in combination with sympathetic denervation results in synergistic tumor regression. Our multi-dimensional data reveal new insights into the networks and functions of PDAC-innervating neurons, supporting inclusion of denervation in future therapies.

DOI: https://doi.org/10.1038/s41586-025-08735-3
Gastroenterology. 2025 Feb 14. pii: S0016-5085(25)00368-3. [Epub ahead of print]

TREM2 depletion in pancreatic cancer elicits pathogenic inflammation and accelerates tumor progression via enriching IL-1β+ macrophages.

Daowei Yang, Xinlei Sun, Hua Wang, Ignacio I Wistuba, Huamin Wang, Anirban Maitra, Yang Chen.

   BACKGROUND & AIMS: Pancreatic ductal adenocarcinoma (PDAC) has a complex tumor microenvironment enriched with tumor-associated macrophages. Triggering receptor expressed on myeloid cells 2 (TREM2) is highly expressed by a subset of macrophages in PDAC. However, the functional role of TREM2 in PDAC progression remains elusive.
METHODS: We generated a novel transgenic mouse model (KPPC;Trem2-/-) that enables the genetic depletion of TREM2 in the context of spontaneous PDAC development. Single-cell RNA-sequencing analysis was utilized to identify changes in the tumor immune microenvironment upon TREM2 depletion. We evaluated the impacts of TREM2 depletion on the tumor immune microenvironment to elucidate the functions of TREM2 in macrophages and PDAC development.
RESULTS: Unexpectedly, genetic depletion of TREM2 significantly accelerated spontaneous PDAC progression and shortened the survival of KPPC;Trem2-/- mice. Single-cell analysis revealed that TREM2 depletion enhanced pro-inflammatory macrophages and exacerbated pathogenic inflammation in PDAC. Specifically, TREM2 functions as a key braking mechanism for the NLRP3/NF-κB/IL-1β inflammasome pathway, opposing to microbial lipopolysaccharide (LPS) as the key activator of this pathway. TREM2 deficiency orchestrated with microbial LPS to trigger IL-1β upregulation and pathogenic inflammation, thereby fueling PDAC development. Notably, IL-1β inhibition or microbiome ablation not only reversed the accelerated PDAC progression caused by TREM2 depletion, but also further inhibited PDAC progression in the TREM2-depleted context.
CONCLUSIONS: TREM2 depletion accelerates tumor progression by enhancing pro-inflammatory macrophages and IL-1β-mediated pathogenic inflammation in PDAC. The accelerated tumor progression by TREM2 depletion can be reversed by blocking IL-1β-associated pathogenic inflammation.

Keywords:  Genetically engineered mouse models; Macrophages; Pancreatic cancer; Single-cell RNA-sequencing; TREM2; Tumor immune microenvironment

DOI:  https://doi.org/10.1053/j.gastro.2025.01.244
Autophagy. 2025 Feb 17.

Calcium release from damaged lysosomes triggers stress granule formation for cell survival.

Aravinth Kumar Jayabalan, Aanuoluwakiitan Ayeni, Jingyue Jia.

  Lysosomes are essential membrane-bound organelles that integrate intracellular needs and external signals through multiple functions, including autophagy-mediated degradation and MTORC1 signaling. The integrity of the lysosomal membrane is therefore crucial for maintaining cellular homeostasis. Various endogenous and exogenous factors can damage lysosomes, contributing to diseases such as infections, cancer, and neurodegeneration. In response, cells mount defensive mechanisms to cope with such stress, including the formation of stress granules (SGs) - membraneless organelles composed of RNAs and protein complexes. While SGs have emerged as key players in repairing damaged lysosomes, how lysosomal damage triggers their formation and influences cell fate remains unclear. Here we report that the calcium signal from damaged lysosomes mediates SG formation and protects cells from lysosomal damage-induced cell death. Mechanistically, calcium leakage from damaged lysosomes signals the recruitment of calcium-activating protein PDCD6IP/ALIX and its partner PDCD6/ALG2. This complex recruits protein kinase EIF2AK2/PKR and its activator PRKRA/PACT, which phosphorylates translation initiator factor EIF2S1, stalling global translation initiation. This translation arrest leads to the accumulation of inactive messenger ribonucleoprotein complexes (mRNPs), resulting in SG formation. Cells deficient in SG formation show increased cell death when exposed to lysosomal damage from disease-associated factors including SARS-CoV-2ORF3a, adenovirus, malarial pigment, proteopathic MAPT/tau, or environmental hazards. Collectively, this study reveals how damaged lysosomes signal through calcium to trigger SG assembly, promoting cell survival. This establishes a novel link between membrane-bound and membraneless organelles, with implications for diseases involving lysosomal damage and SG dysfunction.

Keywords:  Calcium signaling; cell survival; lysosomal damage; stress granules

DOI:  https://doi.org/10.1080/15548627.2025.2468910
Nat Genet. 2025 Feb 18.

ImmuneLENS characterizes systemic immune dysregulation in aging and cancer.

TRACERx Consortium

Recognition and elimination of pathogens and cancer cells depend on the adaptive immune system. Thus, accurate quantification of immune subsets is vital for precision medicine. We present immune lymphocyte estimation from nucleotide sequencing (ImmuneLENS), which estimates T cell and B cell fractions, class switching and clonotype diversity from whole-genome sequencing data at depths as low as 5× coverage. By applying ImmuneLENS to the 100,000 Genomes Project, we identify genes enriched with somatic mutations in T cell-rich tumors, significant sex-based differences in circulating T cell fraction and demonstrated that the circulating T cell fraction in patients with cancer is significantly lower than in healthy individuals. Low circulating B cell fraction was linked to increased cancer incidence. Finally, circulating T cell abundance was more prognostic of 5-year cancer survival than infiltrating T cells.

DOI: https://doi.org/10.1038/s41588-025-02086-5
Mol Biol Cell. 2025 Feb 19. mbcE24100436

Recovery of plasma membrane tension after a hyperosmotic shock.

Jasmine Phan, Malan Silva, Robin Kohlmeyer, Romy Ruethemann, Lincoln Gay, Erik Jorgensen, Markus Babst.

Maintaining proper tension is critical for the organization and function of the plasma membrane. To study the mechanisms by which yeast restores normal plasma membrane tension, we used a microfluidics device to expose yeast to hyperosmotic conditions, which reduced cell volume and caused a ∼20% drop in cell surface area. The resulting low tension plasma membrane exhibited large clusters of negatively-charged glycerophospholipids together with nutrient transporters, suggesting phase segregation of the membrane. We found that endocytosis was blocked by the phase segregation and thus was not involved in removing excess membrane. In contrast, rapid recovery of plasma membrane tension was dependent on 1) eisosome morphology changes that were able to absorb most of the excess surface area and 2) lipid transport from the plasma membrane to the endoplasmic reticulum, where lipids were shunted into newly formed lipid droplets.

DOI: https://doi.org/10.1091/mbc.E24-10-0436
Cell Metab. 2025 Feb 11. pii: S1550-4131(25)00013-0. [Epub ahead of print]

RBM43 controls PGC1α translation and a PGC1α-STING signaling axis.

Phillip A Dumesic, Sarah E Wilensky, Symanthika Bose, Jonathan G Van Vranken, Steven P Gygi, Bruce M Spiegelman.

  Obesity is associated with systemic inflammation that impairs mitochondrial function. This disruption curtails oxidative metabolism, limiting adipocyte lipid metabolism and thermogenesis, a metabolically beneficial program that dissipates chemical energy as heat. Here, we show that PGC1α, a key governor of mitochondrial biogenesis, is negatively regulated at the level of its mRNA translation by the RNA-binding protein RBM43. RBM43 is induced by inflammatory cytokines and suppresses mitochondrial biogenesis in a PGC1α-dependent manner. In mice, adipocyte-selective Rbm43 disruption elevates PGC1α translation and oxidative metabolism. In obesity, Rbm43 loss improves glucose tolerance, reduces adipose inflammation, and suppresses activation of the innate immune sensor cGAS-STING in adipocytes. We further identify a role for PGC1α in safeguarding against cytoplasmic accumulation of mitochondrial DNA, a cGAS ligand. The action of RBM43 defines a translational regulatory axis by which inflammatory signals dictate cellular energy metabolism and contribute to metabolic disease pathogenesis.

Keywords:  PGC1α; adipocyte; adipose thermogenesis; adipose tissue; cGAS-STING; inflammation; mRNA translation; mitochondria; obesity; oxidative metabolism

DOI:  https://doi.org/10.1016/j.cmet.2025.01.013
Nat Protoc. 2025 Feb 19.

Measuring plasma membrane fluidity using confocal microscopy.

Pablo Carravilla, Luca Andronico, Jan Schlegel, Yagmur B Urem, Ellen Sjule, Franziska Ragaller, Florian Weber, Cenk O Gurdap, Yavuz Ascioglu, Taras Sych, Joseph Lorent, Erdinc Sezgin.

Membrane fluidity is a crucial parameter for cellular physiology. Recent evidence suggests that fluidity varies between cell types and states and in diseases. As membrane fluidity has gradually become an important consideration in cell biology and biomedicine, it is essential to have reliable and quantitative ways to measure it in cells. In the past decade, there has been substantial progress both in chemical probes and in imaging tools to make membrane fluidity measurements easier and more reliable. We have recently established a robust pipeline, using confocal imaging and new environment-sensitive probes, that has been successfully used for several studies. Here we present our detailed protocol for membrane fluidity measurement, from labeling to imaging and image analysis. The protocol takes ~4 h and requires basic expertise in cell culture, wet lab and microscopy.

DOI: https://doi.org/10.1038/s41596-024-01122-8
Nat Commun. 2025 Feb 19. 16(1): 1765

A decision point between transdifferentiation and programmed cell death priming controls KRAS-dependent pancreatic cancer development.

Anne T Schneider, Christiane Koppe, Emilie Crouchet, Aristeidis Papargyriou, Michael T Singer, Veronika Büttner, Leonie Keysberg, Marta Szydlowska, Frank Jühling, Julien Moehlin, Min-Chun Chen, Valentina Leone, Sebastian Mueller, Thorsten Neuß, Mirco Castoldi, Marina Lesina, Frank Bergmann, Thilo Hackert, Katja Steiger, Wolfram T Knoefel, Alex Zaufel, Jakob N Kather, Irene Esposito, Matthias M Gaida, Ahmed Ghallab, Jan G Hengstler, Henrik Einwächter, Kristian Unger, Hana Algül, Nikolaus Gassler, Roland M Schmid, Roland Rad, Thomas F Baumert, Maximilian Reichert, Mathias Heikenwalder, Vangelis Kondylis, Mihael Vucur, Tom Luedde.

KRAS-dependent acinar-to-ductal metaplasia (ADM) is a fundamental step in the development of pancreatic ductal adenocarcinoma (PDAC), but the involvement of cell death pathways remains unclear. Here, we show that key regulators of programmed cell death (PCD) become upregulated during KRAS-driven ADM, thereby priming transdifferentiated cells to death. Using transgenic mice and primary cell and organoid cultures, we show that transforming growth factor (TGF)-β-activated kinase 1 (TAK1), a kinase regulating cell survival and inflammatory pathways, prevents the elimination of transdifferentiated cells through receptor-interacting protein kinase 1 (RIPK1)-mediated apoptosis and necroptosis, enabling PDAC development. Accordingly, pharmacological inhibition of TAK1 induces PCD in patient-derived PDAC organoids. Importantly, cell death induction via TAK1 inhibition does not appear to elicit an overt injury-associated inflammatory response. Collectively, these findings suggest that TAK1 supports cellular plasticity by suppressing spontaneous PCD activation during ADM, representing a promising pharmacological target for the prevention and treatment of PDAC.

DOI: https://doi.org/10.1038/s41467-025-56493-7
J Proteome Res. 2025 Feb 19.

Gemcitabine Alters Phosphatidylcholine Metabolism in Mouse Pancreatic Tumors.

Nav Raj Phulara, Chiaki Tsuge Ishida, Peter John Espenshade, Herana Kamal Seneviratne.

  Pancreatic ductal adenocarcinoma (PDAC) is among the deadliest diseases, despite advancements in elucidating tumor biology and developing novel therapeutics. Importantly, lipids, such as phospholipids, are crucial for the survival and proliferation of tumor cells. However, the impact of chemotherapeutic drugs on phospholipid metabolism in PDAC remains poorly understood. Gemcitabine (a nucleoside analogue) is a first-line drug in PDAC treatment, but its clinical effectiveness is limited by multiple factors. Herein, we employed matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) and proteomics approaches to investigate gemcitabine-induced lipid metabolism alterations in mouse pancreatic tumors following gemcitabine treatment (n = 3, control tumors; n = 3, gemcitabine-treated tumors). From MALDI MSI experiments, we observed elevated levels of several phosphatidylcholines (PCs), PC(30:0), PC(32:3), PC(34:2), PC(36:1), and PC(36:2), in gemcitabine-treated tumor tissues compared to the control. In addition, proteomics data revealed the differential abundance of several phospholipid-binding proteins in response to gemcitabine treatments. Furthermore, several endoplasmic reticulum stress-related proteins exhibited high expression in gemcitabine-treated tumor tissues. Altogether, our MALDI MSI and proteomics data provide important insights into alterations in PC metabolism in pancreatic tumors in response to gemcitabine treatment. Importantly, targeting the altered PC metabolism during gemcitabine therapy might help combat pancreatic cancer.

Keywords:  MALDI mass spectrometry imaging; gemcitabine; lipid metabolism; phosphatidylcholine; proteomics

DOI:  https://doi.org/10.1021/acs.jproteome.4c00839
J Natl Cancer Inst. 2025 Feb 18. pii: djaf030. [Epub ahead of print]

Early identification of weight loss trajectories in advanced cancer and associations with survival.

Sophia Fuller, Stacey Alexeeff, Bette Caan, Marcus Dasilva Goncalves, Richard F Dunne, Tobias Janowitz, Mariam Jamal-Hanjani, Tilak K Sundaresan, Elizabeth M Cespedes Feliciano.

Consensus criteria to diagnose unintentional weight loss, a condition often termed cachexia that affects most patients with advanced cancer, are based on 6-month changes by which time intervention is often ineffective. Leveraging the large and diverse population in Kaiser Permanente Northern California's community oncology practice, we studied 8,338 patients with advanced lung, pancreatic, or colorectal cancers. We calculated weekly weight change measurements from 2-months pre- to 6-months post-diagnosis to identify 4 weight change trajectories (Gain, Stable, Moderate Loss, and Severe Loss) and associated these trajectories with survival. With high agreement, we classified patients into these trajectories after 3 months and found them to be prognostic; those classified in Moderate (HR = 1.55; 95%CI: 1.45-1.67) or Severe Loss (HR = 2.20; 95%CI: 2.01-2.41) at 3 months had significantly increased risk of death compared to the Stable trajectory. Weight loss at 3 months post-diagnosis can accurately classify deleterious weight trajectories, allowing for earlier clinical intervention.

DOI: https://doi.org/10.1093/jnci/djaf030
Res Sq. 2025 Feb 05. pii: rs.3.rs-5806746. [Epub ahead of print]

Target cell tension regulates macrophage trogocytosis.

Daniel Fletcher, Caitlin Cornell, Aymeric Chorlay, Deepak Krishnamurthy, Nicholas Martin, Lucia Baldauf.

Macrophages are known to engulf small membrane fragments, or trogocytose, target cells and pathogens, rather than fully phagocytose them. However, little is known about what causes macrophages to choose trogocytosis versus phagocytosis. Here, we report that cortical tension of target cells is a key regulator of macrophage trogocytosis. At low tension, macrophages will preferentially trogocytose antibody-opsonized cells, while at high tension they tend towards phagocytosis. Using model vesicles, we demonstrate that macrophages will rapidly switch from trogocytosis to phagocytosis when membrane tension is increased. Stiffening the cortex of target cells also biases macrophages to phagocytose them, a trend that can be countered by increasing antibody surface density and is captured in a mechanical model of trogocytosis. This work suggests that the target cell, rather than the macrophage, determines phagocytosis versus trogocytosis, and that macrophages do not require a distinct molecular pathway for trogocytosis.

DOI: https://doi.org/10.21203/rs.3.rs-5806746/v1
Cancer Discov. 2025 Feb 17. OF1-OF15

High Glucose Contribution to the TCA Cycle Is a Feature of Aggressive Non-Small Cell Lung Cancer in Patients.

Ling Cai, Nia G Hammond, Alpaslan Tasdogan, Massar Alsamraae, Chendong Yang, Robert B Cameron, Peiran Quan, Ashley Solmonson, Wen Gu, Panayotis Pachnis, Mayher Kaur, Brianna K Chang, Qin Zhou, Christopher T Hensley, Quyen N Do, Luiza Martins Nascentes Melo, Jessalyn M Ubellacker, Akash Kaushik, Maia G Clare, Isabel N Alcazar, Katarzyna Kurylowicz, Joseph D Marcuccilli, Gabriele Allies, Andrea Kutritz, Joachim Klode, Vijayashree Ramesh, Thomas J Rogers, Aparna D Rao, Hannah E Crentsil, Hong Li, Fang Brister, Phyllis McDaniel, Xiaohong Xu, Bret M Evers, Lauren G Zacharias, Jessica Sudderth, Jian Xu, Thomas P Mathews, Dwight Oliver, John D Minna, John Waters, Sean J Morrison, Kemp H Kernstine, Brandon Faubert, Ralph J DeBerardinis.

SIGNIFICANCE: Intraoperative 13C-glucose infusions in patients with NSCLC show that tumors with high labeling of TCA cycle intermediates progress rapidly, resulting in metastasis and early death. Blocking this pathway suppresses metastasis of human NSCLC cells in mice.

DOI: https://doi.org/10.1158/2159-8290.CD-23-1319
Sci Adv. 2025 Feb 21. 11(8): eado2830

The mutational landscape and functional effects of noncoding ultraconserved elements in human cancers.

Recep Bayraktar, Yitao Tang, Mihnea P Dragomir, Cristina Ivan, Xinxin Peng, Linda Fabris, Jianhua Zhang, Alessandro Carugo, Serena Aneli, Jintan Liu, Mei-Ju M Chen, Sanjana Srinivasan, Iman Sahnoune, Emine Bayraktar, Kadir C Akdemir, Meng Chen, Pranav Narayanan, Wilson Huang, Leonie Florence Ott, Agda Karina Eterovic, Oscar Eduardo Villarreal, Mohammad Moustaf Mohammad, Michael D Peoples, Danielle M Walsh, Jon Andrew Hernandez, Margaret B Morgan, Kenna R Shaw, Jennifer S Davis, David Menter, Constantine S Tam, Paul Yeh, Sarah-Jane Dawson, Laura Z Rassenti, Thomas J Kipps, Tanja Kunej, Zeev Estrov, Simon A Joosse, Luca Pagani, Catherine Alix-Panabières, Klaus Pantel, Alessandra Ferajoli, Andrew Futreal, Ignacio I Wistuba, Milan Radovich, Scott Kopetz, Michael J Keating, Giulio F Draetta, John S Mattick, Han Liang, George A Calin.

The mutational landscape of phylogenetically ultraconserved elements (UCEs), especially those in noncoding DNAs (ncUCEs), and their functional relevance in cancers remain poorly characterized. Here, we perform a systematic analysis of whole-genome and in-house targeted UCE sequencing datasets from more than 3000 patients with cancer of 13,736 UCEs and demonstrate that ncUCE somatic alterations are common. Using a multiplexed CRISPR knockout screen in colorectal cancer cells, we show that the loss of several altered ncUCEs significantly affects cell proliferation. In-depth functional studies in vitro and in vivo further reveal that specific ncUCEs can be enhancers of tumor suppressors (such as ARID1B) and silencers of oncogenic proteins (such as RPS13). Moreover, several miRNAs located in ncUCEs are recurrently mutated. Mutations in miR-142 locus can affect the Drosha-mediated processing of precursor miRNAs, resulting in the down-regulation of the mature transcript. These results provide systematic evidence that specific ncUCEs play diverse regulatory roles in cancer.

DOI: https://doi.org/10.1126/sciadv.ado2830
Sci Adv. 2025 Feb 21. 11(8): eadu3194

Direct ionic stress sensing and mitigation by the transcription factor NFAT5.

Chandni B Khandwala, Parijat Sarkar, H Broder Schmidt, Mengxiao Ma, Ganesh V Pusapati, Frederic Lamoliatte, Maia Kinnebrew, Bhaven B Patel, Desiree Tillo, Andres M Lebensohn, Rajat Rohatgi.

Rising temperatures and water scarcity caused by climate change are increasingly exposing our cells and tissues to ionic stress, a consequence of elevated cytoplasmic ionic strength that can disrupt protein, organelle, and genome function. Here, we unveil a single-protein mechanism for ionic strength sensing and mitigation in animal cells, one that is notably different from the analogous high osmolarity glycerol kinase cascade in yeast. The Rel family transcription factor NFAT5 directly senses intracellular ionic strength using a C-terminal prion-like domain (PLD). In response to elevated intracellular ionic strength, this PLD is necessary and sufficient to coordinate an adaptive gene expression program by recruiting the transcriptional coactivator BRD4. The purified NFAT5 PLD forms condensates in response to elevated solution ionic strength in vitro, and human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic stress in yeast. We propose that ion-sensitive conformational changes in a PLD directly regulate transcription to maintain ionic strength homeostasis in animal cells.

DOI: https://doi.org/10.1126/sciadv.adu3194
Autophagy. 2025 Feb 19.

Lysosomal Quality Control.

Danielle Henn, Xi Yang, Ming Li.

  Healthy cells need functional lysosomes to degrade cargo delivered by autophagy and endocytosis. Defective lysosomes can lead to severe conditions such as lysosomal storage diseases (LSDs) and neurodegeneration. To maintain lysosome integrity and functionality, cells have evolved multiple quality control pathways corresponding to different types of stress and damage. These can be divided into five levels: regulation, reformation, repair, removal, and replacement. The different levels of lysosome quality control often work together to maintain the integrity of the lysosomal network. This review summarizes the different quality control pathways and discusses the less-studied area of lysosome membrane protein regulation and degradation, highlighting key unanswered questions in the field.

Keywords:  ESCRT; Lysophagy; lysosome membrane protein regulation; lysosome membrane repair; lysosome quality control

DOI:  https://doi.org/10.1080/15548627.2025.2469206
Mol Biol Cell. 2025 Feb 19. mbcE24120535

Trafficking of K63-polyubiquitin modified membrane proteins in a macroautophagy-independent pathway is linked to ATG9A.

Francesco Scavone, Sharon Lian, Eeva-Liisa Eskelinen, Robert E Cohen, Tingting Yao.

Cytoplasmic K63-linked polyubiquitin signals have well-established roles in endocytosis and selective autophagy. However, how these signals help to direct different cargos to different intracellular trafficking routes is unclear. Here we report that, when the K63-polyubiquitin signal is blocked by intracellular expression of a high-affinity sensor (named Vx3), many proteins originating from the plasma membrane are found trapped in clusters of small vesicles that co-localize with ATG9A, a transmembrane protein that plays an essential role in autophagy. Importantly, whereas ATG9A is required for cluster formation, other core autophagy machinery as well as selective autophagy cargo receptors are not required. Although the cargos are sequestered in the vesicular clusters in an ATG9-dependent manner, additional signals are needed to induce LC3 conjugation. Upon removal of the Vx3 block, K63-polyubiquitylated cargos are rapidly delivered to lysosomes. These observations suggest that ATG9A plays an unexpected role in the trafficking of K63-polyubiquitin modified membrane proteins. [Media: see text] [Media: see text] [Media: see text].

DOI: https://doi.org/10.1091/mbc.E24-12-0535
Front Immunol. 2025 ;16 1524781

Cell fusion as a driver of metastasis: re-evaluating an old hypothesis in the age of cancer heterogeneity.

Eduardo López-Collazo, Laura Hurtado-Navarro.

  Numerous studies have investigated the molecular mechanisms and signalling pathways underlying cancer metastasis, as there is still no effective treatment for this terminal stage of the disease. However, the exact processes that enable primary cancer cells to acquire a metastatic phenotype remain unclear. Increasing attention has been focused on the fusion of cancer cells with myeloid cells, a phenomenon that may result in hybrid cells, so-called Tumour Hybrid Cells (THCs), with enhanced migratory, angiogenic, immune evasion, colonisation, and metastatic properties. This process has been shown to potentially drive tumour progression, drug resistance, and cancer recurrence. In this review, we explore the potential mechanisms that govern cancer cell fusion, the molecular mediators involved, the metastatic characteristics acquired by fusion-derived hybrids, and their clinical significance in human cancer. Additionally, we discuss emerging pharmacological strategies aimed at targeting fusogenic molecules as a means to prevent metastatic dissemination.

Keywords:  cancer cell hybrid; cancer recurrence; cell fusion; macrophages; metastasis; oncogenic resistance; tumour hybrid cell

DOI:  https://doi.org/10.3389/fimmu.2025.1524781
Langmuir. 2025 Feb 18.

Palmitoylation of PD-L1 Regulates Its Membrane Orientation and Immune Evasion.

Siya Zhang, Hong-Yin Wang, Xuan Tao, Zhongwen Chen, Ilya Levental, Xubo Lin.

Recently identified palmitoylation of PD-L1 is essential for immune regulation. To elucidate the underlying molecular mechanism, we performed giant plasma membrane vesicle (GPMV) experiments, μs-scale all-atom molecular dynamics (MD) simulations, fluorescence resonance energy transfer (FRET) experiments, and immune killing experiments. GPMV experiments indicated that PD-L1 palmitoylation enhanced its lipid raft affinity. MD simulations revealed dramatically different membrane orientation states of PD-L1 in liquid-ordered (Lo, lipid raft) compared to liquid-disordered (Ld, nonraft) membrane environments, which was validated by FRET experiments. The Ld region promoted the "lie-down" orientation of PD-L1, which could inhibit its association with the PD-1 protein on immune cells and thus promote the immune killing of cancer cells. This hypothesis was supported by immune killing experiments using γδT cells as effector cells and NCI-H1299 lung cancer cells as target cells. In short, our study demonstrates that the palmitoylation affects PD-L1's membrane localization and then membrane orientation, which thus regulates its binding with T cell PD-1 and the immune regulation. These observations may guide therapeutic strategies by explicating the regulation of immune checkpoint proteins by post-translational modifications and membrane environments.

DOI: https://doi.org/10.1021/acs.langmuir.4c04441
Biophys J. 2025 Feb 18. pii: S0006-3495(24)04125-0. [Epub ahead of print]124(4): 620-636

Understanding the coarse-grained free energy landscape of phospholipids and their phase separation.

Patrick G Sahrmann, Gregory A Voth.

The cell membrane exhibits lateral heterogeneity due to the preferential association among the large number of lipid species that constitute the membrane. In particular, the preferential association of cholesterol (CHOL) with saturated lipids into ordered domains has been an area of intense investigation. The large spatiotemporal scales that comprise spontaneous domain formation largely precludes computational investigation via conventional all-atom molecular dynamics. We demonstrate here that molecular coarse-grained (CG) models, obtained from the bottom-up, i.e., via statistical mechanical renormalization of atomistic models, are capable of spontaneous assembly and phase separation for two model raft-like systems, DLiPC/DPPC/CHOL and DOPC/DPPC/CHOL. The resulting bottom-up CG models exhibit spontaneous self-assembly and phase separation and recapitulate the structural correlations of the underlying atomistic models. The accuracy and fast dynamics of these CG models constitute an effective means of bypassing the limited spatiotemporal scales of atomistic simulations. As the first bottom-up CG models of lipid phase separation, the CG models in this work provide an informative analysis for further construction of bottom-up CG models transferable across a range of lipid compositions.

DOI: https://doi.org/10.1016/j.bpj.2024.12.030
Cell. 2025 Feb 12. pii: S0092-8674(25)00098-4. [Epub ahead of print]

HypoxyStat, a small-molecule form of hypoxia therapy that increases oxygen-hemoglobin affinity.

Skyler Y Blume, Ankur Garg, Yolanda Martí-Mateos, Ayush D Midha, Brandon T L Chew, Baiwei Lin, Cecile Yu, Ryan Dick, Patrick S Lee, Eva Situ, Richa Sarwaikar, Eric Green, Vyas Ramanan, Gijsbert Grotenbreg, Maarten Hoek, Christopher Sinz, Isha H Jain.

  We have previously demonstrated that chronic inhaled hypoxia is remarkably therapeutic in the premier animal model of mitochondrial Leigh syndrome, the Ndufs4 knockout (KO) mouse. Subsequent work has extended this finding to additional mitochondrial diseases and more common conditions. However, challenges inherent to gas-based therapies have hindered the rapid translation of our findings to the clinic. Here, we tested a small molecule (hereafter termed HypoxyStat) that increases the binding affinity of hemoglobin for oxygen, thereby decreasing oxygen offloading to tissues. Daily oral dosing of HypoxyStat caused systemic hypoxia in mice breathing normoxic (21% O2) air. When administered prior to disease onset, this treatment dramatically extended the lifespan of Ndufs4 KO mice and rescued additional aspects of disease, including behavior, body weight, neuropathology, and body temperature. HypoxyStat was also able to reverse disease at a very late stage, thereby serving as a clinically tractable form of hypoxia therapy.

Keywords:  Leigh syndrome; hemoglobin; hyperoxia; hypoxia; mitochondrial disease; oxygen; red blood cells; therapy

DOI:  https://doi.org/10.1016/j.cell.2025.01.029
Chemistry. 2025 Feb 17. e202404323

Visualization of Ferroptosis-Induced Lipid Peroxidation Using Plasma Membrane-Specific Fluorescent Probe LipoxPM.

Hidefumi Iwashita, Rina Tokunaga, Kosei Shioji.

  Reactive oxygen species (ROS) play essential roles in cellular processes, but aberrant generation of ROS can damage lipids, proteins, and DNA leading to pathological events such as aging and neurodegenerative diseases. Polyunsaturated fatty acids (PUFAs) are especially susceptible to such oxidative stress. This ROS-induced lipid peroxidation is a key process of ferroptosis, an iron-dependent, non-apoptotic form of cell death. Although lipid peroxidation is an essential event in ferroptosis, current study tools for detecting the oxidation process lack specificity toward a particular membrane type such as plasma membrane. In this study, we present LipoxPM, a novel fluorescent probe that targets lipid peroxidation specifically in plasma membrane over other cellular membranes. LipoxPM features a BODIPY-based fluorophore and an anionic sulfonate group, enhancing selective accumulation in the plasma membrane. LipoxPM was able to detect ferroptosis-related lipid peroxidation in live cells, visualizing the spatial distribution of lipid peroxidation in the cell death processes. This probe would enable study of unknown mechanisms of ferroptosis and could potentially facilitate development of therapeutic strategies targeting oxidative stress-related diseases.

Keywords:  Ferroptosis; Fluorescent probe; Lipid peroxidation; Plasma membrane

DOI:  https://doi.org/10.1002/chem.202404323
Sci Data. 2025 Feb 14. 12(1): 266

Proteomics profiling of research models for studying pancreatic ductal adenocarcinoma.

Mathilde Resell, Hanne-Line Rabben, Animesh Sharma, Lars Hagen, Linh Hoang, Nan T Skogaker, Anne Aarvik, Eirik Knudsen Bjåstad, Magnus K Svensson, Manoj Amrutkar, Caroline S Verbeke, Surinder K Batra, Gunnar Qvigstad, Timothy C Wang, Anil Rustgi, Duan Chen, Chun-Mei Zhao.

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies, with a five-year survival rate of 10-15% due to late-stage diagnosis and limited efficacy of existing treatments. This study utilized proteomics-based systems modelling to generate multimodal datasets from various research models, including PDAC cells, spheroids, organoids, and tissues derived from murine and human samples. Identical mass spectrometry-based proteomics was applied across the different models. The preparation and validation of the research models and the proteomics were described in detail. The assembly datasets we present here contribute to the data collection on PDAC, which will be useful for systems modelling, data mining, knowledge discovery in databases, and bioinformatics of individual models. Further data analysis may lead to the generation of research hypotheses, predictions of targets for diagnosis and treatment, and relationships between data variables.

DOI: https://doi.org/10.1038/s41597-025-04522-x
bioRxiv. 2025 Feb 08. pii: 2025.02.07.637120. [Epub ahead of print]

Hexokinase detachment from mitochondria drives the Warburg effect to support compartmentalized ATP production.

Kimberly S Huggler, Carlos A Mellado Fritz, Kyle M Flickinger, Gavin R Chang, Meghan F McGuire, Jason R Cantor.

Hexokinase (HK) catalyzes the synthesis of glucose-6-phosphate, marking the first committed step of glucose metabolism. Most cancer cells express two homologous isoforms (HK1 and HK2) that can each bind to the outer mitochondrial membrane (OMM). CRISPR screens across hundreds of cancer cell lines indicate that both are dispensable for cell growth in traditional culture media. By contrast, HK2 deletion impairs cell growth in Human Plasma-Like Medium (HPLM). Here, we find that HK2 is required to maintain sufficient cytosolic (OMM-detached) HK activity under conditions that enhance HK1 binding to the OMM. Notably, OMM-detached rather than OMM-docked HK promotes "aerobic glycolysis" (Warburg effect), an enigmatic phenotype displayed by most proliferating cells. We show that several proposed theories for this phenotype cannot explain the HK2 dependence and instead find that HK2 deletion severely impairs glycolytic ATP production with little impact on total ATP yield for cells in HPLM. Our results reveal a basis for conditional HK2 essentiality and suggest that demand for compartmentalized ATP synthesis underlies the Warburg effect.

DOI: https://doi.org/10.1101/2025.02.07.637120
J Cachexia Sarcopenia Muscle. 2025 Feb;16(1): e13742

Cachexia Alters Central Nervous System Morphology and Functionality in Cancer Patients.

Estefania Simoes, Ricardo Uchida, Mariana P Nucci, Fabio L S Duran, Joanna D C C Lima, Leonardo R Gama, Naomi A Costa, Maria C G Otaduy, Fang C Bin, Jose P Otoch, Paulo Alcantara, Alexandre Ramos, Alessandro Laviano, Mauricio Berriel Diaz, Margaret M Esiri, Gabriele C DeLuca, Stephan Herzig, Geraldo Busatto Filho, Marilia Seelaender.

   BACKGROUND: Cachexia is a clinically challenging multifactorial and multi-organ syndrome, associated with poor outcome in cancer patients, and characterised by inflammation, wasting and loss of appetite. The syndrome leads to central nervous system (CNS) function dysregulation and to neuroinflammation; nevertheless, the mechanisms involved in human cachexia remain unclear.
METHODS: We used in vivo structural and functional magnetic resonance imaging (Cohort 1), as well as postmortem neuropathological analyses (Cohort 2) in cachectic cancer (CC) patients compared to weight stable cancer (WSC) patients. Cohort 1 included treatment-naïve adults diagnosed with colorectal cancer, further divided into WSC (n = 12; 6/6 [male/female], 61.3 ± 3.89 years) and CC (n = 10; 6/4, 63.0 ± 2.74 years). Cohort 2 was composed by human postmortem cases where gastrointestinal carcinoma was the underlying cause of death (WSC n = 6; 3/3, 82.7 ± 3.33 years and CC n = 10; 5/5, 84.2 ± 2.28 years).
RESULTS: Here we demonstrate that the CNS of CC patients presents regional structural differences within the grey matter (GM). Cachectic patients presented an augmented area within the region of the orbitofrontal cortex, olfactory tract and the gyrus rectus (coordinates X, Y, Z = 6, 20,-24; 311 voxels; pFWE = 0.023); increased caudate and putamen volume (-10, 20, -8; 110 voxel; pFWE = 0.005); and reduced GM in superior temporal gyrus and rolandic operculum (56,0,2; 156 voxels; pFWE = 0.010). Disrupted functional connectivity was found in several regions such as the salience network, subcortical and temporal cortical areas of cachectic patients (20 decreased and 5 increased regions connectivity pattern, pFDR < 0.05). Postmortem neuropathological analyses identified abnormal neuronal morphology and density, increased microglia/macrophage burden, astrocyte profile disruption and mTOR pathway related neuroinflammation (p < 0.05).
CONCLUSIONS: Our results indicate that cachexia compromises CNS morphology mostly causing changes in the GM of cachectic patients, leading to alterations in regional volume patterns, functional connectivity, neuronal morphology, neuroglia profile and inducing neuroinflammation, all of which may contribute to the loss of homeostasis control and to deficient information processing, as well as to the metabolic and behavioural derangements commonly observed in human cachexia. This first human mapping of CNS cachexia responses will now pave the way to mechanistically interrogate these pathways in terms of their therapeutic potential.

Keywords:  central nervous system; grey matter; human cachexia; neuroimaging; neuroinflammation; neuropathology

DOI:  https://doi.org/10.1002/jcsm.13742
bioRxiv. 2025 Feb 08. pii: 2025.02.03.635951. [Epub ahead of print]

A Quantitative Approach to Mapping Mitochondrial Specialization and Plasticity.

Anna S Monzel, Jack Devine, Darshana Kapri, Jose Antonio Enriquez, Caroline Trumpff, Martin Picard.

Mitochondria are a diverse family of organelles that specialize to accomplish complimentary functions 1-3 . All mitochondria share general features, but not all mitochondria are created equal 4 .Here we develop a quantitative pipeline to define the degree of molecular specialization among different mitochondrial phenotypes - or mitotypes . By distilling hundreds of validated mitochondrial genes/proteins into 149 biologically interpretable MitoPathway scores (MitoCarta 3.0 5 ) the simple mitotyping pipeline allows investigators to quantify and interpret mitochondrial diversity and plasticity from transcriptomics or proteomics data across a variety of natural and experimental contexts. We show that mouse and human multi-organ mitotypes segregate along two main axes of mitochondrial specialization, contrasting anabolic (liver) and catabolic (brain) tissues. In cultured primary human fibroblasts exhibiting robust time-dependent and treatment-induced metabolic plasticity 6-8 , we demonstrate how the mitotype of a given cell type recalibrates i) over time in parallel with hallmarks of aging, and ii) in response to genetic, pharmacological, and metabolic perturbations. Investigators can now use MitotypeExplorer.org and the associated code to visualize, quantify and interpret the multivariate space of mitochondrial biology.

DOI: https://doi.org/10.1101/2025.02.03.635951
Cell Metab. 2025 Feb 14. pii: S1550-4131(25)00012-9. [Epub ahead of print]

adiposetissue.org: A knowledge portal integrating clinical and experimental data from human adipose tissue.

Jiawei Zhong, Danae Zareifi, Sophie Weinbrenner, Mattias Hansen, Felix Klingelhuber, Pamela A Nono Nankam, Scott Frendo-Cumbo, Nayanika Bhalla, Lina Cordeddu, Thais de Castro Barbosa, Peter Arner, Ingrid Dahlman, Maheswary Muniandy, Sini Heinonen, Kirsi H Pietiläinen, Anne Hoffmann, Adhideb Ghosh, Dorit John, Anke Tönjes, Patrik L Ståhl, Yvonne Böttcher, Maria Keller, Peter Kovacs, Alastair G Kerr, Dominique Langin, Christian Wolfrum, Matthias Blüher, Natalie Krahmer, Lucas Massier, Niklas Mejhert, Mikael Rydén.

We developed the Adipose Tissue Knowledge Portal by centralizing previously dispersed datasets, integrating clinical and experimental results with transcriptomic and proteomic data from >6,000 women and men. The platform includes multiple adipose depots, resident cell types, and adipocyte perturbation studies. By providing streamlined data access, the portal enables integrative analyses and serves as a powerful tool to interrogate various dimensions of adipose biology down to the single-cell level.

DOI: https://doi.org/10.1016/j.cmet.2025.01.012
Autophagy. 2025 Feb 14. 1-17

Visualizing bulk autophagy in vivo by tagging endogenous LC3B.

Xiukui Gao, Yue Xiong, Hangbin Ma, Hao Zhou, Wei Liu, Qiming Sun.

  Macroautophagy/autophagy plays a crucial role in maintaining cellular and organismal health, making the measurement of autophagy flux in vivo essential for its study. Current tools often depend on the overexpression of autophagy probes. In this study, we developed a knock-in mouse model, termed tfLC3-KI, by inserting a tandem fluorescent tag coding sequence into the native Map1lc3b gene locus. We found that tfLC3-KI mice exhibit optimal expression of mRFP-eGFP-LC3B, allowing for convenient measurement of autophagic structures and flux at single-cell resolution, both in vivo and in primary cell cultures. Additionally, we compared autophagy in neurons and glial cells across various brain regions between tfLC3-KI mice and CAG-tfLC3 mice, the latter overexpressing the probe under the strong CMV promoter. Finally, we used tfLC3-KI mice to map the spatial and temporal dynamics of basal autophagy activity in the reproductive system. Our findings highlight the value of the tfLC3-KI mouse model for investigating autophagy flux in vivo and demonstrate the feasibility of tagging endogenous proteins to visualize autophagic structures and flux in both bulk and selective autophagy research in vivo.Abbreviation: BafA1: bafilomycin A1; CQ: chloroquine; EBSS: Earle's balanced salt solution; Es: elongating spermatids; HPF: hippocampalformation; HY: hypothalamus; LCs: leydig cells; OLF: olfactory areas; PepA: pepstatin A; Rs: round spermatids; SCs: sertoli cells; Spc: spermatocytes; Spg: spermatogonia; tfLC3: tandem fluorescently tagged mRFP-eGFP-LC3; TH: thalamus.

Keywords:  Autophagy flux; endogenous LC3B; in vivo; knock-in; tandem fluorescence protein

DOI:  https://doi.org/10.1080/15548627.2025.2457910
Nature. 2025 Feb 19.

Clonal driver neoantigen loss under EGFR TKI and immune selection pressures.

Maise Al Bakir, James L Reading, Samuel Gamble, Rachel Rosenthal, Imran Uddin, Andrew Rowan, Joanna Przewrocka, Amber Rogers, Yien Ning Sophia Wong, Amalie K Bentzen, Selvaraju Veeriah, Sophia Ward, Aaron T Garnett, Paula Kalavakur, Carlos Martínez-Ruiz, Clare Puttick, Ariana Huebner, Daniel E Cook, David A Moore, Chris Abbosh, Crispin T Hiley, Cristina Naceur-Lombardelli, Thomas B K Watkins, Marina Petkovic, Roland F Schwarz, Felipe Gálvez-Cancino, Kevin Litchfield, Peter Meldgaard, Boe Sandahl Sorensen, Line Bille Madsen, Dirk Jäger, Martin D Forster, Tobias Arkenau, Clara Domingo-Vila, Timothy I M Tree, Mohammad Kadivar, Sine Reker Hadrup, Benny Chain, Sergio A Quezada, Nicholas McGranahan, Charles Swanton.

Neoantigen vaccines are under investigation for various cancers, including epidermal growth factor receptor (EGFR)-driven lung cancers1,2. We tracked the phylogenetic history of an EGFR mutant lung cancer treated with erlotinib, osimertinib, radiotherapy and a personalized neopeptide vaccine (NPV) targeting ten somatic mutations, including EGFR exon 19 deletion (ex19del). The ex19del mutation was clonal, but is likely to have appeared after a whole-genome doubling (WGD) event. Following osimertinib and NPV treatment, loss of the ex19del mutation was identified in a progressing small-cell-transformed liver metastasis. Circulating tumour DNA analyses tracking 467 somatic variants revealed the presence of this EGFR wild-type clone before vaccination and its expansion during osimertinib/NPV therapy. Despite systemic T cell reactivity to the vaccine-targeted ex19del neoantigen, the NPV failed to halt disease progression. The liver metastasis lost vaccine-targeted neoantigens through chromosomal instability and exhibited a hostile microenvironment, characterized by limited immune infiltration, low CXCL9 and elevated M2 macrophage levels. Neoantigens arising post-WGD were more likely to be absent in the progressing liver metastasis than those occurring pre-WGD, suggesting that prioritizing pre-WGD neoantigens may improve vaccine design. Data from the TRACERx 421 cohort3 provide evidence that pre-WGD mutations better represent clonal variants, and owing to their presence at multiple copy numbers, are less likely to be lost in metastatic transition. These data highlight the power of phylogenetic disease tracking and functional T cell profiling to understand mechanisms of immune escape during combination therapies.

DOI: https://doi.org/10.1038/s41586-025-08586-y
J Phys Chem B. 2025 Feb 20.

Spectrally Resolved Single-Molecule Orientation Imaging Reveals a Direct Correspondence between the Polarity and Microviscosity Experienced by Nile Red in Supported Lipid Bilayer Membranes.

Aranyak Sarkar, Jyotsna Bhatt Mitra, Veerendra K Sharma, Vinu Namboodiri, Manoj Kumbhakar.

Molecular-level interactions among lipids, cholesterol, and water dictate the nanoscale membrane organization of lipid bilayers into liquid-ordered (Lo) and liquid-disordered (Ld) phases, characterized by different polarities and orders. Generally, solvatochromic dyes easily discriminate polarity difference between Lo and Ld phases, whereas molecular flippers and rotors show distinct photophysics depending on the membrane order. Despite progress in single-molecule spectral imaging and single-molecule orientation mapping, direct experimental proof linking polarity with microviscosity sensed by the same probe eludes us. Here, we demonstrate spectrally resolved single-molecule orientation localization microscopy to connect nanoscopic localization of a probe on a bilayer membrane with its emission spectra, three-dimensional dipole orientation, and rotational constraint offered by the local microenvironment and highlight the excellent correspondence between the polarity and order experienced by the same probe. This technique has the potential to address nanoscale heterogeneity and dynamics, especially in biology and material sciences.

DOI: https://doi.org/10.1021/acs.jpcb.4c07578
J Lipid Res. 2025 Feb 18. pii: S0022-2275(25)00022-7. [Epub ahead of print] 100762

ABCA1-mediated nascent HDL formation is precisely regulated by the plasma membrane cholesterol.

Fumihiko Ogasawara, Kazumitsu Ueda.

  Intracellular cholesterol transport is essential for maintaining cellular cholesterol homeostasis. ABCA1 continuously moves cholesterol from the inner leaflet to the outer leaflet of the plasma membrane (PM) to maintain low inner leaflet cholesterol levels. When PM inner leaflet cholesterol levels exceed ER cholesterol levels, which are maintained at approximately 5 mol% by the complex of sterol regulatory element-binding protein (SREBP) and SREBP cleavage-activating protein (SCAP), Aster-A/GramD1a transports the excess cholesterol to the ER. Furthermore, ABCA1 removes excess PM cholesterol by promoting its efflux as nascent high-density lipoprotein (HDL) particles. Thus, cellular cholesterol homeostasis is maintained by the coordinated action of SCAP-SREBP, Aster-A/GramD1a, and ABCA1. While the regulation of SCAP-SREBP and Aster-A/GramD1a is well-understood, the mechanism governing ABCA1 activity remain less understood. In this study, we investigated the impact of PM cholesterol levels on ABCA1-mediated cholesterol and phosphatidylcholine (PC) efflux. Cells were treated with various concentrations of methyl-β-cyclodextrin (MβCD) or MβCD-cholesterol for 30 minutes to modulate PM cholesterol levels. We found that the initial velocities of both cholesterol and PC efflux were dependent solely on PM cholesterol levels, despite both being substrates for ABCA1. Intriguingly, when PM cholesterol levels dropped below 70% of the level observed in cells cultured in the presence of 10% FBS, both cholesterol and PC efflux ceased, even in the presence of abundant PC in the PM. Our findings suggest that ABCA1-mediated nascent HDL formation is precisely regulated to maintain optimal PM cholesterol levels.

Keywords:  ABC protein; ABCA7; ATP-binding cassette A1 (ABCA1); SREBP cleavage–activating protein (SCAP); apolipoprotein A-I (apoA-I): Aster-A/GramD1a; cholesterol; high-density lipoprotein (HDL); phosphatidylcholine (PC); plasma membrane; sterol regulatory element–binding protein (SREBP)

DOI:  https://doi.org/10.1016/j.jlr.2025.100762
bioRxiv. 2025 Feb 06. pii: 2025.01.31.635980. [Epub ahead of print]

Swirling motion of breast cancer cells radially aligns collagen fibers to enable collective invasion.

Aashrith Saraswathibhatla, Md Foysal Rabbi, Sushama Varma, Vasudha Srivastava, Olga Ilina, Naomi Hassan Kahtan Alyafei, Louis Hodgson, Zev Gartner, Peter Friedl, Robert West, Taeyoon Kim, Ovijit Chaudhuri.

In breast cancer (BC), radial alignment of collagen fibers at the tumor-matrix interface facilitates collective invasion of cancer cells into the surrounding stromal matrix, a critical step toward metastasis. Collagen remodeling is driven by proteases and cellular forces, mediated by matrix mechanical plasticity, or irreversible matrix deformation in response to force. However, the specific mechanisms causing collagen radial alignment remain unclear. Here, we study collective invasion of BC tumor spheroids in collagen-rich matrices. Increasing plasticity to BC-relevant ranges facilitates invasion, with increasing stiffness potentiating a transition from single cell to collective invasion. At enhanced plasticity, cells radially align collagen at the tumor-matrix interface prior to invasion. Surprisingly, cells migrate tangentially to the tumor-matrix interface in a swirling-like motion, perpendicular to the direction of alignment. Mechanistically, swirling generates local shear stresses, leading to distally propagating contractile radial stresses due to negative normal stress, an underappreciated property of collagen-rich matrices. These contractile stresses align collagen fibers radially, facilitating collective invasion. The basement membrane (BM), which separates epithelia from stroma in healthy tissues, acts as a mechanical insulator by preventing swirling cells from aligning collagen. Thus, after breaching the BM, swirling of BC cells at the tumor-stroma interface radially aligns collagen to facilitate invasion.

DOI: https://doi.org/10.1101/2025.01.31.635980
Annu Rev Biophys. 2025 Feb 14.

Membrane Association of Intrinsically Disordered Proteins.

Matthew MacAinsh, Fidha Nazreen Kunnath Muhammedkutty, Ramesh Prasad, Huan-Xiang Zhou.

It is now clear that membrane association of intrinsically disordered proteins or intrinsically disordered regions regulates many cellular processes, such as membrane targeting of Src family kinases and ion channel gating. Residue-specific characterization by nuclear magnetic resonance spectroscopy, molecular dynamics simulations, and other techniques has shown that polybasic motifs and amphipathic helices are the main drivers of membrane association; sequence-based prediction of residue-specific membrane association propensity has become possible. Membrane association facilitates protein-protein interactions and protein aggregation-these effects are due to reduced dimensionality but are similar to those afforded by condensate formation via liquid-liquid phase separation (LLPS). LLPS at the membrane surface provides a powerful means for recruiting and clustering proteins, as well as for membrane remodeling.

DOI: https://doi.org/10.1146/annurev-biophys-070124-092816
Curr Opin Chem Biol. 2025 Feb 19. pii: S1367-5931(25)00013-4. [Epub ahead of print]85 102581

Lipid probes to study ion channels.

Helene Jahn, Show-Ling Shyng, Carsten Schultz.

  Lipids can have specific interaction partners and act as small molecule regulators of proteins, especially for transmembrane proteins. Transmembrane proteins, such as ion channels, can be influenced by lipids in four ways; lipids can be direct ligands, localize effector proteins or domains, affect protein-protein interaction, or change the biophysical properties of the surrounding membrane. In this article, we will give examples of how lipids directly interact with ion channels and address the complex aspect of indirect regulation via lipids of the surrounding membrane bilayer. In addition, we discuss current and propose future molecular tools and experiments elucidating the many roles lipids play in ion channel function.

Keywords:  Caged lipids; Interactome; Ligand; Photo-crosslinkable lipids; Protein structure

DOI:  https://doi.org/10.1016/j.cbpa.2025.102581
J Cachexia Sarcopenia Muscle. 2025 Feb;16(1): e13715

GDF15 Neutralization Ameliorates Muscle Atrophy and Exercise Intolerance in a Mouse Model of Mitochondrial Myopathy.

Stephen E Flaherty, LouJin Song, Bina Albuquerque, Anthony Rinaldi, Mary Piper, Dinesh Hirenallur Shanthappa, Xian Chen, John Stansfield, Shoh Asano, Evanthia Pashos, Trenton Thomas Ross, Srinath Jagarlapudi, Abdul Sheikh, Bei Zhang, Zhidan Wu.

   BACKGROUND: Primary mitochondrial myopathies (PMMs) are disorders caused by mutations in genes encoding mitochondrial proteins and proteins involved in mitochondrial function. PMMs are characterized by loss of muscle mass and strength as well as impaired exercise capacity. Growth/Differentiation Factor 15 (GDF15) was reported to be highly elevated in PMMs and cancer cachexia. Previous studies have shown that GDF15 neutralization is effective in improving skeletal muscle mass and function in cancer cachexia. It remains to be determined if the inhibition of GDF15 could be beneficial for PMMs. The purpose of the present study is to assess whether treatment with a GDF15 neutralizing antibody can alleviate muscle atrophy and physical performance impairment in a mouse model of PMM.
METHODS: The effects of GDF15 neutralization on PMM were assessed using PolgD257A/D257A (POLG) mice. These mice express a proofreading-deficient version of the mitochondrial DNA polymerase gamma, leading to an increased rate of mutations in mitochondrial DNA (mtDNA). These animals display increased circulating GDF15 levels, reduced muscle mass and function, exercise intolerance, and premature aging. Starting at 9 months of age, the mice were treated with an anti-GDF15 antibody (mAB2) once per week for 12 weeks. Body weight, food intake, body composition, and muscle mass were assessed. Muscle function and exercise capacity were evaluated using in vivo concentric max force stimulation assays, forced treadmill running and voluntary home-cage wheel running. Mechanistic investigations were performed via muscle histology, bulk transcriptomic analysis, RT-qPCR and western blotting.
RESULTS: Anti-GDF15 antibody treatment ameliorated the metabolic phenotypes of the POLG animals, improving body weight (+13% ± 8%, p < 0.0001), lean mass (+13% ± 15%, p < 0.001) and muscle mass (+35% ± 24%, p < 0.001). Additionally, the treatment improved skeletal muscle max force production (+35% ± 43%, p < 0.001) and exercise performance, including treadmill (+40% ± 29%, p < 0.05) and voluntary wheel running (+320% ± 19%, p < 0.05). Mechanistically, the beneficial effects of GDF15 neutralization are linked to the reversal of the transcriptional dysregulation in genes involved in autophagy and proteasome signalling. The treatment also appears to dampen glucocorticoid signalling by suppressing circulating corticosterone levels in the POLG animals.
CONCLUSIONS: Our findings highlight the potential of GDF15 neutralization with a monoclonal antibody as a therapeutic avenue to enhance physical performance and mitigate adverse clinical outcomes in patients with PMM.

Keywords:  GDF15; antibody; mice; mitochondria; muscle; primary mitochondrial myopathy

DOI:  https://doi.org/10.1002/jcsm.13715
Commun Biol. 2025 Feb 20. 8(1): 267

Multiplexed Lectin-PAINT super-resolution microscopy enables cell glycotyping.

Marrit M E Tholen, Roger Riera, Cristina Izquierdo-Lozano, Lorenzo Albertazzi.

Glycosylation profoundly influences cellular function, yet deciphering its intricate patterns remains a formidable challenge. Current techniques often compromise sensitivity, multiplexing, or the ability to capture in-situ cell-to-cell variations. To address these limitations, we introduce 'Lectin-PAINT,' a super-resolution imaging method enabling multiplexed live-cell visualization of the cellular glycocalyx at the single-cell and single-molecule levels. Lectin-PAINT leverages the reversible binding of lectins to specific carbohydrate families to perform point accumulation in nanoscale topography (PAINT), enabling the identification, mapping, and tracking of carbohydrates with a resolution beyond the diffraction limit. Our technique harnesses a tailored lectin library, spanning key carbohydrate recognition, offering insights into their abundance, affinity, and mobility. Through 8-color super-resolution imaging, we extract more than 350 glycosylation parameters with single-cell resolution, creating a cell's 'glycotype' or glycan fingerprint. We showcase the power of this approach by glycotyping and categorizing a diverse set of cancer cell types, shedding light on the heterogeneity and variability of the glycocalyx in cancer. In the future, this research will contribute to the more fundamental understanding of changes in the glycocalyx due to disease.

DOI: https://doi.org/10.1038/s42003-025-07626-7