bims-cagime 2025-01-12 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–01–12
thirty-one papers selected by
Kıvanç Görgülü, Technical University of Munich

Apoptotic priming in senescence predicts specific senolysis by quantitative analysis of mitochondrial dependencies.
De novo lipogenesis protects dormant breast cancer cells from ferroptosis and promotes metastasis.
Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response in pancreatic cancer.
Metastatic patterns stratify patients with pancreatic cancer.
Adaptation to cystine limitation stress promotes PDAC tumor growth and metastasis through translational upregulation of OxPPP.
Phase separation of initiation hubs on cargo is a trigger switch for selective autophagy.
Targeting pancreatic cancer cell stemness by blocking fibronectin-binding integrins on cancer-associated fibroblasts.
Confined cell migration along extracellular matrix space in vivo.
Bile acid synthesis impedes tumor-specific T cell responses during liver cancer.
Predicting protein curvature sensing across membrane compositions with a bilayer continuum model.
Systemic metabolic crosstalk as driver of cancer cachexia.
Ongoing replication stress tolerance and clonal T cell responses distinguish liver and lung recurrence and outcomes in pancreatic cancer.
Multi-dimensional analyses identify genes of high priority for pancreatic cancer research.
Migrasome formation is initiated preferentially in tubular junctions by membrane tension.
Lymphatic collection and cell isolation from mouse models for multiomic profiling.
Chronic viral mimicry induction following p53 loss promotes immune evasion.
Triacylglycerol mobilization underpins mitochondrial stress recovery.
MPicker: visualizing and picking membrane proteins for cryo-electron tomography.
Molecular dynamics at immune synapse lipid rafts influence the cytolytic behavior of CAR T cells.
PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways.
Chemically engineered antibodies for autophagy-based receptor degradation.
Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function.
Cellular and organismal function of choline metabolism.
Multiomic quantification of the KRAS mutation dosage improves the preoperative prediction of survival and recurrence in patients with pancreatic ductal adenocarcinoma.
Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing.
ATG9 promotes autophagosome formation through interaction with LC3.
Estrogens increase cancer cell efferocytosis to establish an immunosuppressive tumor microenvironment.
Pharmacological reduction of lipid hydroperoxides as a potential modulator of sarcopenia.
SQLE-mediated squalene metabolism promotes tumor immune evasion in pancreatic cancer.
KRAS Mutation Status and Treatment Outcomes in Patients With Metastatic Pancreatic Adenocarcinoma.
Stress responses induced by perturbation of the ubiquitin-proteasome system.

Cell Death Differ. 2025 Jan 06.

Apoptotic priming in senescence predicts specific senolysis by quantitative analysis of mitochondrial dependencies.

Julie A MacDonald, Gary A Bradshaw, Fleur Jochems, René Bernards, Anthony Letai.

Cellular senescence contributes to a variety of pathologies associated with aging and is implicated as a cellular state in which cancer cells can survive treatment. Reported senolytic drug treatments act through varying molecular mechanisms, but heterogeneous efficacy across the diverse contexts of cellular senescence indicates a need for predictive biomarkers of senolytic activity. Using multi-parametric analyses of commonly reported molecular features of the senescent phenotype, we assayed a variety of models, including malignant and nonmalignant cells, using several triggers of senescence induction and found little univariate predictive power of these traditional senescence markers to identify senolytic drug sensitivity. We sought to identify novel drug targets in senescent cells that were insensitive to frequently implemented senolytic therapies, such as Navitoclax (ABT-263), using quantitative mass spectrometry to measure changes in the senescent proteome, compared to cells which acquire an acute sensitivity to ABT-263 with senescence induction. Inhibition of the antioxidant GPX4 or the Bcl-2 family member MCL-1 using small molecule compounds in combination with ABT-263 significantly increased the induction of apoptosis in some, but not all, previously insensitive senescent cells. We then asked if we could use BH3 profiling to measure differences in mitochondrial apoptotic priming in these models of cellular senescence and predict sensitivity to the senolytics ABT-263 or the combination of dasatinib and quercetin (D + Q). We found, despite being significantly less primed for apoptosis overall, the dependence of senescent mitochondria on BCL-XL was significantly correlated to senescent cell killing by both ABT-263 and D + Q, despite no significant changes in the gene or protein expression of BCL-XL. However, our data caution against broad classification of drugs as globally senolytic and instead provide impetus for context-specific senolytic targets and propose BH3 profiling as an effective predictive biomarker.

DOI: https://doi.org/10.1038/s41418-024-01431-1
Redox Biol. 2024 Dec 31. pii: S2213-2317(24)00458-0. [Epub ahead of print]80 103480

De novo lipogenesis protects dormant breast cancer cells from ferroptosis and promotes metastasis.

Beatriz Puente-Cobacho, Cintia Esteo, Patricia Altea-Manzano, Jose Luis Garcia-Perez, José L Quiles, Pedro Sanchez-Rovira, María D Martín-Salvago, Lucía Molina-Jiménez, Rafael J Luque, Sarah-Maria Fendt, Laura Vera-Ramirez.

  Dormant disseminated tumor cells (DTCs) remain viable for years to decades before establishing a clinically overt metastatic lesion. DTCs are known to be highly resilient and able to overcome the multiple biological hurdles imposed along the metastatic cascade. However, the specific metabolic adaptations of dormant DTCs remain to be elucidated. Here, we reveal that dormant DTCs upregulate de novo lipogenesis and favor the activation and incorporation of monounsaturated fatty acids (MUFAs) to their cellular membranes through the activation of acyl-coenzyme A synthetase long-chain family member 3 (ACSL3). Pharmacologic inhibition of de novo lipogenesis or genetic knockdown of ACSL3 results in lipid peroxidation and non-apoptotic cell death through ferroptosis. Clinically, ACSL3 was found to be overexpressed in quiescent DTCs in the lymph nodes of breast cancer patients and to significantly correlate with shorter disease-free and overall survival. Our work provides new insights into the molecular mechanisms enabling the survival of dormant DTCs and supports the use of de novo lipogenesis inhibitors to prevent breast cancer metastasis.

Keywords:  Breast cancer; Ferroptosis; Lipid metabolism; Lipid peroxidation; Metastasis; Monounsaturated fatty acids activation; Tumor cell dormancy

DOI:  https://doi.org/10.1016/j.redox.2024.103480
Nat Commun. 2025 Jan 06. 16(1): 335

Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response in pancreatic cancer.

Lukas Klein, Mengyu Tu, Niklas Krebs, Laura Urbach, Daniela Grimm, Muhammad Umair Latif, Frederike Penz, Anna Blandau, Xueyan Wu, Rebecca Diya Samuel, Stefan Küffer, Florian Wegwitz, Nathan Chan, Kazeera Aliar, Foram Vyas, Uday Kishore, Elisabeth Hessmann, Andreas Trumpp, Elisa Espinet, Argyris Papantonis, Rama Khokha, Volker Ellenrieder, Barbara T Grünwald, Shiv K Singh.

Pancreatic ductal adenocarcinoma (PDAC) displays a high degree of spatial subtype heterogeneity and co-existence, linked to a diverse microenvironment and worse clinical outcome. However, the underlying mechanisms remain unclear. Here, by combining preclinical models, multi-center clinical, transcriptomic, proteomic, and patient bioimaging data, we identify an interplay between neoplastic intrinsic AP1 transcription factor dichotomy and extrinsic macrophages driving subtype co-existence and an immunosuppressive microenvironment. ATAC-, ChIP-, and RNA-seq analyses reveal that JUNB/AP1- and HDAC-mediated epigenetic programs repress pro-inflammatory signatures in tumor cells, antagonizing cJUN/AP1 signaling, favoring a therapy-responsive classical neoplastic state. This dichotomous regulation is amplified via regional TNF-α+ macrophages, which associates with a reactive phenotype and reduced CD8+ T cell infiltration in patients. Consequently, combined preclinical anti-TNF-α immunotherapy and chemotherapy reduces macrophages and promotes CD3+/CD8+ T cell infiltration in basal-like PDAC, improving survival. Hence, tumor cell-intrinsic epigenetic programs, together with extrinsic microenvironmental cues, facilitate intratumoral subtype heterogeneity and disease progression.

DOI: https://doi.org/10.1038/s41467-024-55330-7
Nat Cancer. 2025 Jan 09.

Metastatic patterns stratify patients with pancreatic cancer.

John Nguyen, Francisco Sanchez-Vega.

DOI: https://doi.org/10.1038/s43018-024-00846-6
bioRxiv. 2024 Dec 17. pii: 2024.12.12.628246. [Epub ahead of print]

Adaptation to cystine limitation stress promotes PDAC tumor growth and metastasis through translational upregulation of OxPPP.

Yunzhan Li, Zekun Li, Dongxiao Sun, Bo Ni, Mingjun Tan, Ashley E Shay, Min Wang, Chenyang Meng, Guangcong Shen, Boyang Fu, Yueying Shan, Tianxin Zhou, Yongjie Xie, Kun-Ming Chen, Bin Qiao, Yunkun Dang, Scot R Kimball, Pankaj K Singh, Xiuchao Wang, Jihui Hao, Shengyu Yang.

Cystine/cysteine is critical for antioxidant response and sulfur metabolism in cancer cells and is one of the most depleted amino acids in the PDAC microenvironment. The effects of cystine limitation stress (CLS) on PDAC progression are poorly understood. Here we report that adaptation to CLS (CLSA) promotes PDAC cell proliferation and tumor growth through translational upregulation of the oxidative pentose phosphate pathway (OxPPP). OxPPP activates the de novo synthesis of nucleotides and fatty acids to support tumor growth. Our data suggested that much like hypoxia, CLS in the tumor microenvironment could promote PDAC tumor growth and metastasis through upregulating anabolic metabolism of nucleotides and lipids.

DOI: https://doi.org/10.1101/2024.12.12.628246
Nat Cell Biol. 2025 Jan 07.

Phase separation of initiation hubs on cargo is a trigger switch for selective autophagy.

Mariya Licheva, Jeremy Pflaum, Riccardo Babic, Hector Mancilla, Jana Elsässer, Emily Boyle, David M Hollenstein, Jorge Jimenez-Niebla, Jonas Pleyer, Mio Heinrich, Franz-Georg Wieland, Joachim Brenneisen, Christopher Eickhorst, Johann Brenner, Shan Jiang, Markus Hartl, Sonja Welsch, Carola Hunte, Jens Timmer, Florian Wilfling, Claudine Kraft.

Autophagy is a key cellular quality control mechanism. Nutrient stress triggers bulk autophagy, which nonselectively degrades cytoplasmic material upon formation and liquid-liquid phase separation of the autophagy-related gene 1 (Atg1) complex. In contrast, selective autophagy eliminates protein aggregates, damaged organelles and other cargoes that are targeted by an autophagy receptor. Phase separation of cargo has been observed, but its regulation and impact on selective autophagy are poorly understood. Here, we find that key autophagy biogenesis factors phase separate into initiation hubs at cargo surfaces in yeast, subsequently maturing into sites that drive phagophore nucleation. This phase separation is dependent on multivalent, low-affinity interactions between autophagy receptors and cargo, creating a dynamic cargo surface. Notably, high-affinity interactions between autophagy receptors and cargo complexes block initiation hub formation and autophagy progression. Using these principles, we converted the mammalian reovirus nonstructural protein µNS, which accumulates as particles in the yeast cytoplasm that are not degraded, into a neo-cargo that is degraded by selective autophagy. We show that initiation hubs also form on the surface of different cargoes in human cells and are key to establish the connection to the endoplasmic reticulum, where the phagophore assembly site is formed to initiate phagophore biogenesis. Overall, our findings suggest that regulated phase separation underscores the initiation of both bulk and selective autophagy in evolutionarily diverse organisms.

DOI: https://doi.org/10.1038/s41556-024-01572-y
Cancer Res Commun. 2025 Jan 09.

Targeting pancreatic cancer cell stemness by blocking fibronectin-binding integrins on cancer-associated fibroblasts.

Chengsheng Wu, Tami von Schalscha, Diva Sansanwal, Chen Qian, Qinlin Jiang, Ryan M Shepard, Hiromi I Wettersten, Stephen McCormack, Sara M Weis, David A Cheresh.

Cancer-associated fibroblasts (CAF) generate an extracellular matrix (ECM) which provides a repository for factors that promote pancreatic cancer progression. Here, we establish that CAF contribution to pancreatic tumor initiation, i.e. stemness, depends on fibronectin (FN) as a scaffold required for assembly of a collagen-containing fibrotic ECM with a critical dependence on the FN-binding integrins, α5β1 and αvβ3. CAF matrix assembly can be prevented by knockdown of FN, ITGA5, or ITGB3, or by a bispecific antibody with dual recognition of α5β1 and αvβ3 that can also destabilize a pre-existing matrix. In mice, the ability of CAFs to produce a stiff collagenous matrix and accelerate tumor initiation can be blocked by knockdown of FN or FN-binding integrins, or systemic treatment with the α5β1/αvβ3 bispecific antibody. Together, these results reveal that dual targeting of the FN-binding integrins α5β1/αvβ3 can block the ability of CAFs and their matrix from enhancing pancreatic cancer stemness and progression.

DOI: https://doi.org/10.1158/2767-9764.CRC-24-0491
Proc Natl Acad Sci U S A. 2025 Jan 07. 122(1): e2414009121

Confined cell migration along extracellular matrix space in vivo.

Oleksandr Chepizhko, Josep-Maria Armengol-Collado, Stephanie Alexander, Esther Wagena, Bettina Weigelin, Luca Giomi, Peter Friedl, Stefano Zapperi, Caterina A M La Porta.

  Collective migration of cancer cells is often interpreted using concepts derived from the physics of active matter, but the experimental evidence is mostly restricted to observations made in vitro. Here, we study collective invasion of metastatic cancer cells injected into the mouse deep dermis using intravital multiphoton microscopy combined with a skin window technique and three-dimensional quantitative image analysis. We observe a multicellular but low-cohesive migration mode characterized by rotational patterns which self-organize into antiparallel persistent tracks with orientational nematic order. We analyze the deformations induced by the cells in the extracellular matrix and find broadly distributed strain bands with a prevalence of compression. A model of active nematic hydrodynamics is able to describe several statistical features of the experimentally observed flow, suggesting that collective cancer cell invasion can be interpreted as a nematic active fluid in the turbulent regime. Our results help elucidate the migration patterns of cancer cells in vivo and provide quantitative guidance for the development of realistic in vitro and in silico models for collective cell migration.

Keywords:  active nematic turbulence; collective cell migration; extracellular matrix confinement; quantitative image analysis

DOI:  https://doi.org/10.1073/pnas.2414009121
Science. 2025 Jan 10. 387(6730): 192-201

Bile acid synthesis impedes tumor-specific T cell responses during liver cancer.

Siva Karthik Varanasi, Dan Chen, Yingluo Liu, Melissa A Johnson, Cayla M Miller, Souradipta Ganguly, Kathryn Lande, Michael A LaPorta, Filipe Araujo Hoffmann, Thomas H Mann, Marcos G Teneche, Eduardo Casillas, Kailash C Mangalhara, Varsha Mathew, Ming Sun, Isaac J Jensen, Yagmur Farsakoglu, Timothy Chen, Bianca Parisi, Shaunak Deota, Aaron Havas, Jin Lee, H Kay Chung, Andrea Schietinger, Satchidananda Panda, April E Williams, Donna L Farber, Debanjan Dhar, Peter D Adams, Gen-Sheng Feng, Gerald S Shadel, Mark S Sundrud, Susan M Kaech.

The metabolic landscape of cancer greatly influences antitumor immunity, yet it remains unclear how organ-specific metabolites in the tumor microenvironment influence immunosurveillance. We found that accumulation of primary conjugated and secondary bile acids (BAs) are metabolic features of human hepatocellular carcinoma and experimental liver cancer models. Inhibiting conjugated BA synthesis in hepatocytes through deletion of the BA-conjugating enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) enhanced tumor-specific T cell responses, reduced tumor growth, and sensitized tumors to anti-programmed cell death protein 1 (anti-PD-1) immunotherapy. Furthermore, different BAs regulated CD8+ T cells differently; primary BAs induced oxidative stress, whereas the secondary BA lithocholic acid inhibited T cell function through endoplasmic reticulum stress, which was countered by ursodeoxycholic acid. We demonstrate that modifying BA synthesis or dietary intake of ursodeoxycholic acid could improve tumor immunotherapy in liver cancer model systems.

DOI: https://doi.org/10.1126/science.adl4100
bioRxiv. 2024 Dec 21. pii: 2024.01.15.575755. [Epub ahead of print]

Predicting protein curvature sensing across membrane compositions with a bilayer continuum model.

Yiben Fu, David H Johnson, Andrew H Beaven, Alexander J Sodt, Wade F Zeno, Margaret E Johnson.

Cytoplasmic proteins must recruit to membranes to function in processes such as endocytosis and cell division. Many of these proteins recognize not only the chemical structure of the membrane lipids, but the curvature of the surface, binding more strongly to more highly curved surfaces, or 'curvature sensing'. Curvature sensing by amphipathic helices is known to vary with membrane bending rigidity, but changes to lipid composition can simultaneously alter membrane thickness, spontaneous curvature, and leaflet symmetry, thus far preventing a systematic characterization of lipid composition on such curvature sensing through either experiment or simulation. Here we develop and apply a bilayer continuum membrane model that can tractably address this gap, quantifying how controlled changes to each material property can favor or disfavor protein curvature sensing. We evaluate both energetic and structural changes to vesicles upon helix insertion, with strong agreement to new in vitro experiments and all-atom MD simulations, respectively. Our membrane model builds on previous work to include both monolayers of the bilayer via representation by continuous triangular meshes. We introduce a coupling energy that captures the incompressibility of the membrane and the established energetics of lipid tilt. In agreement with experiment, our model predicts stronger curvature sensing in membranes with distinct tail groups (POPC vs DOPC vs DLPC), despite having identical head-group chemistry; the model shows that the primary driving force for weaker curvature sensing in DLPC is that it is thinner, and more wedge shaped. Somewhat surprisingly, asymmetry in lipid shape composition between the two leaflets has a negligible contribution to membrane mechanics following insertion. Our multi-scale approach can be used to quantitatively and efficiently predict how changes to membrane composition in flat to highly curved surfaces alter membrane energetics driven by proteins, a mechanism that helps proteins target membranes at the correct time and place.
Significance: Proteins must recruit to membranes for essential biological functions including endocytosis and cell division. In addition to recognizing specific lipid head-groups, many of these proteins also 'sense' the curvature of the membrane, but the strength of sensing is known to vary with distinct membrane compositions. Predicting the dependence of sensing on changes to lipid composition cannot be done a priori due to the multiple material properties, including bilayer thickness, bending rigidity, tilt modulus, spontaneous curvature, and leaflet asymmetry that vary with lipid type. Here we use a multi-scale approach to systematically address this gap, developing a double-leaflet continuum model that is informed by structural deformations from all-atom MD and validated against in vitro experiments. This efficient approach can be applied and extended to quantify how proteins sense and drive membrane curvature across a wide range of membrane bilayers, including distinct leaflet compositions and membrane geometries.

DOI: https://doi.org/10.1101/2024.01.15.575755
Trends Endocrinol Metab. 2025 Jan 04. pii: S1043-2760(24)00327-8. [Epub ahead of print]

Systemic metabolic crosstalk as driver of cancer cachexia.

Elisabeth Wyart, Giovanna Carrà, Elia Angelino, Fabio Penna, Paolo E Porporato.

  Cachexia is a complex metabolic disorder characterized by negative energy balance due to increased consumption and lowered intake, leading to progressive tissue wasting and inefficient energy distribution. Once considered as passive bystander, metabolism is now acknowledged as a regulator of biological functions and disease progression. This shift in perspective mirrors the evolving understanding of cachexia itself, no longer viewed merely as a secondary consequence of cancer but as an active process. However, metabolic dysregulations in cachexia are currently studied in an organ-specific manner, failing to be fully integrated into a comprehensive framework that explains their functional roles in disease progression. Thus, in this review, we aim to provide a general overview of the various metabolic alterations with a potential systemic impact.

Keywords:  cachexia; cross-talk; metabolism; muscle wasting

DOI:  https://doi.org/10.1016/j.tem.2024.12.005
Nat Cancer. 2025 Jan 09.

Ongoing replication stress tolerance and clonal T cell responses distinguish liver and lung recurrence and outcomes in pancreatic cancer.

Jason M Link, Jennifer R Eng, Carl Pelz, Kevin MacPherson-Hawthorne, Patrick J Worth, Shamaline Sivagnanam, Dove J Keith, Sydney Owen, Ellen M Langer, Alison Grossblatt-Wait, Gustavo Salgado-Garza, Allison L Creason, Sara Protzek, Julian Egger, Hannah Holly, Michael B Heskett, Koei Chin, Nell Kirchberger, Konjit Betre, Elmar Bucher, David Kilburn, Zhi Hu, Michael W Munks, Isabel A English, Motoyuki Tsuda, Jeremy Goecks, Emek Demir, Andrew C Adey, Adel Kardosh, Charles D Lopez, Brett C Sheppard, Alex Guimaraes, Brian Brinkerhoff, Terry K Morgan, Gordon B Mills, Lisa M Coussens, Jonathan R Brody, Rosalie C Sears.

Patients with metastatic pancreatic ductal adenocarcinoma survive longer if disease spreads to the lung but not the liver. Here we generated overlapping, multi-omic datasets to identify molecular and cellular features that distinguish patients whose disease develops liver metastasis (liver cohort) from those whose disease develops lung metastasis without liver metastases (lung cohort). Lung cohort patients survived longer than liver cohort patients, despite sharing the same tumor subtype. We developed a primary organotropism (pORG) gene set enriched in liver cohort versus lung cohort primary tumors. We identified ongoing replication stress response pathways in high pORG/liver cohort tumors, whereas low pORG/lung cohort tumors had greater densities of lymphocytes and shared T cell clonal responses. Our study demonstrates that liver-avid pancreatic ductal adenocarcinoma is associated with tolerance to ongoing replication stress, limited tumor immunity and less-favorable outcomes, whereas low replication stress, lung-avid/liver-averse tumors are associated with active tumor immunity that may account for favorable outcomes.

DOI: https://doi.org/10.1038/s43018-024-00881-3
JCI Insight. 2025 Jan 07. pii: e174264. [Epub ahead of print]

Multi-dimensional analyses identify genes of high priority for pancreatic cancer research.

Zeribe C Nwosu, Heather Giza, Maya Nassif, Verodia Charlestin, Rosa E Menjivar, Daeho Kim, Samantha B Kemp, Peter Sajjakulnukit, Anthony Andren, Li Zhang, William Km Lai, Ian Loveless, Nina G Steele, Jiantao Hu, Biao Hu, Shaomeng Wang, Marina Pasca di Magliano, Costas A Lyssiotis.

  Pancreatic ductal adenocarcinoma (PDAC) is a drug resistant and lethal cancer. Identification of the genes that consistently show altered expression across patients' cohorts can expose effective therapeutic targets and strategies. To identify such genes, we separately analyzed five human PDAC microarray datasets. We defined genes as 'consistent' if upregulated or downregulated in ≥ 4 datasets (adjusted P<0.05). The genes were subsequently queried in additional datasets, including single-cell RNA-sequencing data, and we analyzed their pathway enrichment, tissue-specificity, essentiality for cell viability, association with cancer features e.g., tumor subtype, proliferation, metastasis and poor survival outcome. We identified 2,010 consistently upregulated and 1,928 downregulated genes of which >50%, to our knowledge, were uncharacterized in PDAC. These genes spanned multiple processes, including cell cycle, immunity, transport, metabolism, signaling and transcriptional/epigenetic regulation - cell cycle and glycolysis being the most altered. Several upregulated genes correlated with cancer features, and their suppression impaired PDAC cell viability in prior CRISPR/Cas9 and RNA interference screens. Further, the upregulated genes predicted sensitivity to bromodomain and extraterminal (epigenetic) protein inhibition, which, in combination with gemcitabine, disrupted amino acid metabolism and in vivo tumor growth. Our results highlight genes for further studies in the quest for PDAC mechanisms, therapeutic targets and biomarkers.

Keywords:  Cancer; Gastroenterology; Glucose metabolism; Molecular genetics; Oncology

DOI:  https://doi.org/10.1172/jci.insight.174264
Biophys J. 2025 Jan 03. pii: S0006-3495(24)04110-9. [Epub ahead of print]

Migrasome formation is initiated preferentially in tubular junctions by membrane tension.

Ben Zucker, Raviv Dharan, Dongju Wang, Li Yu, Raya Sorkin, Michael M Kozlov.

  Migrasomes, the vesicle-like membrane micro-structures, arise on the retraction fibers (RFs), the branched nano-tubules pulled out of cell plasma membranes during cell migration and shaped by membrane tension. Migrasomes form in two steps: a local RF bulging is followed by a protein-dependent stabilization of the emerging spherical bulge. Here we addressed theoretically and experimentally the previously unexplored mechanism of bulging of membrane tubular systems. We assumed that the bulging could be driven by increases in membrane tension and experimentally verified this hypothesis in live cell and biomimetic systems. We exposed RF-generating live cells to a hypotonic medium, which produced water flows into the cells and a related increase in the membrane tension. We observed the formation of migrasome-like bulges with a preferential location in the RF branching sites. Next, we developed a biomimetic system of three membrane tubules pulled out of a giant vesicle (GPMV), connected by a junction, and subjected to pulling forces controlled by the GPMV membrane tension. An abrupt increase in the GPMV tension resulted in the generation of migrasome-like bulges mainly in the junctions. To understand the physical forces behind these observations, we considered theoretically the mechanical energy of a membrane system consisting of a three-way tubular junction with emerging tubular arms subjected to membrane tension. Substantiating our experimental observations, the energy minimization predicted a tension increase to drive the formation of membrane bulges, preferably, in the junction site, independently of the way of the tension application. We generalized the model to derive universal criteria of bulging in branched membrane tubules.

Keywords:  membrane elasticity; membrane pearling; membrane tension; membrane thermodynamics; migrasomes

DOI:  https://doi.org/10.1016/j.bpj.2024.12.029
Nat Protoc. 2025 Jan 08.

Lymphatic collection and cell isolation from mouse models for multiomic profiling.

Marie Sabatier, Ani Solanki, Sangeetha Thangaswamy, Pin-Ji Lei, Hengbo Zhou, Meghan O'Melia, Lutz Menzel, Samir Mitri, Jessalyn M Ubellacker.

Premetastatic cancer cells often spread from the primary lesion through the lymphatic vasculature and, clinically, the presence or absence of lymph node metastases impacts treatment decisions. However, little is known about cancer progression via the lymphatic system or of the effect that the lymphatic environment has on cancer progression. This is due, in part, to the technical challenge of studying lymphatic vessels and collecting lymph fluid. Here we provide a step-by-step procedure to collect both lymph and tumor-draining lymph in mouse models of cancer metastasis. This protocol has been adapted from established methods of lymph collection and was developed specifically for the collection of lymph from tumors. The approach involves the use of mice bearing melanoma or breast cancer orthotopic tumors. After euthanasia, the cisterna chyli and the tumor are exposed and viewed using a stereo microscope. Then, a glass cannula connected to a 1 mL syringe is inserted directly into the cisterna chyli or the tumor-draining lymphatics for collection of pure lymph. These lymph samples can be used to analyze the lymph-derived cancer cells using highly sensitive multiomics approaches to investigate the impact of the lymph environment during cancer metastasis. The procedure requires 2 h per mouse to complete and is suitable for users with minimal expertise in small animal handling and use of microsurgical tools under a stereo microscope.

DOI: https://doi.org/10.1038/s41596-024-01081-0
Cancer Discov. 2025 Jan 07.

Chronic viral mimicry induction following p53 loss promotes immune evasion.

Charles A Ishak, Sajid A Marhon, Nairi Tchrakian, Anjelica Hodgson, Helen Loo Yau, Isabela M Gonzaga, Melanie Peralta, Ilinca M Lungu, Stephanie Gomez, Sheng-Ben Liang, Shu Yi Shen, Raymond Chen, Jocelyn Chen, Biji Chatterjee, Kevin N Wanniarachchi, Junwoo Lee, Nicholas Zehrbach, Amir Hosseini, Parinaz Mehdipour, Siyu Sun, Alexander Solovyov, Ilias Ettayebi, Kyle E Francis, Aobo He, Taiyi Wu, Shengrui Feng, Tiago da Silva Medina, Felipe Campos de Almeida, Jane Bayani, Jason Li, Spencer MacDonald, Yadong Wang, Sarah S Garcia, Elisa Arthofer, Noor Diab, Aneil Srivastava, Paul Tran Austin, Peter J B Sabatini, Benjamin D Greenbaum, Catherine A O'Brien, Trevor G Shepherd, Ming Sound Tsao, Katherine B Chiappinelli, Amit M Oza, Blaise A Clarke, Robert Rottapel, Stephanie Lheureux, Daniel D De Carvalho.

Epigenetic therapies facilitate transcription of immunogenic repetitive elements that cull cancer cells through 'viral mimicry' responses. Paradoxically, cancer-initiating events also facilitate transcription of repetitive elements. Contributions of repetitive element transcription towards cancer initiation, and the mechanisms by which cancer cells evade lethal viral mimicry responses during tumor initiation remain poorly understood. In this report, we characterize premalignant lesions of the fallopian tube along with syngeneic epithelial ovarian cancer models to explore the earliest events of tumorigenesis following loss of the p53 tumor suppressor protein. We report that p53 loss permits transcription of immunogenic repetitive elements and chronic viral mimicry activation that increases cellular tolerance of cytosolic nucleic acids and diminishes cellular immunogenicity. This selection process can be partially attenuated pharmacologically. Altogether, these results reveal that viral mimicry conditioning following p53 loss promotes immune evasion and may represent a pharmacological target for early cancer interception.

DOI: https://doi.org/10.1158/2159-8290.CD-24-0094
Nat Cell Biol. 2025 Jan 08.

Triacylglycerol mobilization underpins mitochondrial stress recovery.

Zakery N Baker, Yunyun Zhu, Rachel M Guerra, Andrew J Smith, Aline Arra, Lia R Serrano, Katherine A Overmyer, Shankar Mukherji, Elizabeth A Craig, Joshua J Coon, David J Pagliarini.

Mitochondria are central to myriad biochemical processes, and thus even their moderate impairment could have drastic cellular consequences if not rectified. Here, to explore cellular strategies for surmounting mitochondrial stress, we conducted a series of chemical and genetic perturbations to Saccharomyces cerevisiae and analysed the cellular responses using deep multiomic mass spectrometry profiling. We discovered that mobilization of lipid droplet triacylglycerol stores was necessary for strains to mount a successful recovery response. In particular, acyl chains from these stores were liberated by triacylglycerol lipases and used to fuel biosynthesis of the quintessential mitochondrial membrane lipid cardiolipin to support new mitochondrial biogenesis. We demonstrate that a comparable recovery pathway exists in mammalian cells, which fail to recover from doxycycline treatment when lacking the ATGL lipase. Collectively, our work reveals a key component of mitochondrial stress recovery and offers a rich resource for further exploration of the broad cellular responses to mitochondrial dysfunction.

DOI: https://doi.org/10.1038/s41556-024-01586-6
Nat Commun. 2025 Jan 08. 16(1): 472

MPicker: visualizing and picking membrane proteins for cryo-electron tomography.

Xiaofeng Yan, Shudong Li, Weilin Huang, Hao Wang, Tianfang Zhao, Mingtao Huang, Niyun Zhou, Yuan Shen, Xueming Li.

Advancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong contrast in cryoET tomograms, which masks the signals from membrane proteins. These factors pose difficulties in observing and revealing the structures of membrane proteins in situ. Here, we report a membrane-flattening method and the corresponding software, MPicker, designed for the visualization, localization, and orientation determination of membrane proteins in cryoET tomograms. This method improves the visualization of proteins on and around membranes by generating a flattened tomogram that eliminates membrane curvature and reduces the spatial complexity of membrane protein analysis. In MPicker, we integrated approaches for automated particle picking and coarse alignment of membrane proteins for sub-tomogram averaging. MPicker was tested on tomograms of various cells to evaluate the method for visualizing, picking, and analyzing membrane proteins.

DOI: https://doi.org/10.1038/s41467-024-55767-w
Sci Adv. 2025 Jan 10. 11(2): eadq8114

Molecular dynamics at immune synapse lipid rafts influence the cytolytic behavior of CAR T cells.

Ahmed Z Gad, Jessica S Morris, Lea Godret-Miertschin, Melisa J Montalvo, Sybrina S Kerr, Harrison Berger, Jessica C H Lee, Amr M Saadeldin, Mohammad H Abu-Arja, Shuo Xu, Spyridoula Vasileiou, Rebecca M Brock, Kristen Fousek, Mohamed F Sheha, Madhuwanti Srinivasan, Yongshuai Li, Arash Saeedi, Kandice R Levental, Ann M Leen, Maksim Mamonkin, Alexandre Carisey, Navin Varadarajan, Meenakshi Hegde, Sujith K Joseph, Ilya Levental, Malini Mukherjee, Nabil Ahmed.

Chimeric antigen receptor T cells (CART) targeting CD19 through CD28.ζ signaling induce rapid lysis of leukemic blasts, contrasting with persistent tumor control exhibited by 4-1BB.ζ-CART. We reasoned that molecular dynamics at the CART immune synapse (CARIS) could explain differences in their tumor rejection kinetics. We observed that CD28.ζ-CART engaged in brief highly lethal CARIS and mastered serial killing, whereas 4-1BB.ζ-CART formed lengthy CARIS and relied on robust expansion and cooperative killing. We analyzed CARIS membrane lipid rafts (mLRs) and found that, upon tumor engagement, CD28.ζ-CAR molecules rapidly but transiently translocated into mLRs, mobilizing the microtubular organizing center and lytic granules to the CARIS. This enabled fast CART recovery and sensitivity to low target site density. In contrast, gradual accumulation of 4-1BB.ζ-CAR and LFA-1 molecules at mLRs built mechanically tonic CARIS mediating chronic Fas ligand-based killing. The differences in CD28.ζ- and 4-1BB.ζ-CARIS dynamics explain the distinct cytolytic behavior of CART and can guide engineering of more adaptive effective cellular products.

DOI: https://doi.org/10.1126/sciadv.adq8114
Nat Commun. 2025 Jan 08. 16(1): 510

PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways.

Julian Müller, Florian P Bayer, Mathias Wilhelm, Maximilian G Schuh, Bernhard Kuster, Matthew The.

Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level. Here, we present PTMNavigator, a tool integrated into the ProteomicsDB platform that offers an interactive interface for researchers to overlay experimental PTM data with pathway diagrams. PTMNavigator provides ~3000 canonical pathways from manually curated databases, enabling users to modify and create custom diagrams tailored to their data. Additionally, PTMNavigator automatically runs kinase and pathway enrichment algorithms whose results are directly integrated into the visualization. This offers a comprehensive view of the intricate relationship between PTMs and signaling pathways. We demonstrate the utility of PTMNavigator by applying it to two phosphoproteomics datasets, showing how it can enhance pathway enrichment analysis, visualize how drug treatments result in a discernable flow of PTM-driven signaling, and aid in proposing extensions to existing pathways. By enhancing our understanding of cellular signaling dynamics and facilitating the discovery of PTM-pathway interactions, PTMNavigator advances our knowledge of PTM biology and its implications in health and disease.

DOI: https://doi.org/10.1038/s41467-024-55533-y
Nat Chem Biol. 2025 Jan 09.

Chemically engineered antibodies for autophagy-based receptor degradation.

Binghua Cheng, Meiqing Li, Jiwei Zheng, Jiaming Liang, Yanyan Li, Ruijing Liang, Hui Tian, Zeyu Zhou, Li Ding, Jian Ren, Wenli Shi, Wenjie Zhou, Hailiang Hu, Long Meng, Ke Liu, Lintao Cai, Ximing Shao, Lijing Fang, Hongchang Li.

Cell surface receptor-targeted protein degraders hold promise for drug discovery. However, their application is restricted because of the complexity of creating bifunctional degraders and the reliance on specific lysosome-shuttling receptors or E3 ubiquitin ligases. To address these limitations, we developed an autophagy-based plasma membrane protein degradation platform, which we term AUTABs (autophagy-inducing antibodies). Through covalent conjugation with polyethylenimine (PEI), the engineered antibodies acquire the capacity to degrade target receptors through autophagy. The degradation activities of AUTABs are self-sufficient, without necessitating the participation of lysosome-shuttling receptors or E3 ubiquitin ligases. The broad applicability of this platform was then illustrated by targeting various clinically important receptors. Notably, combining specific primary antibodies with a PEI-tagged secondary nanobody also demonstrated effective degradation of target receptors. Thus, our study outlines a strategy for directing plasma membrane proteins for autophagic degradation, which possesses desirable attributes such as ease of generation, independence from cell type and broad applicability.

DOI: https://doi.org/10.1038/s41589-024-01803-1
Elife. 2025 Jan 07. pii: RP100928. [Epub ahead of print]13

Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function.

Masroor Ahmad Paddar, Fulong Wang, Einar S Trosdal, Emily Hendrix, Yi He, Michelle R Salemi, Michal Mudd, Jingyue Jia, Thabata Duque, Ruheena Javed, Brett S Phinney, Vojo Deretic.

  ATG5 is one of the core autophagy proteins with additional functions such as noncanonical membrane atg8ylation, which among a growing number of biological outputs includes control of tuberculosis in animal models. Here, we show that ATG5 associates with retromer's core components VPS26, VPS29, and VPS35 and modulates retromer function. Knockout of ATG5 blocked trafficking of a key glucose transporter sorted by the retromer, GLUT1, to the plasma membrane. Knockouts of other genes essential for membrane atg8ylation, of which ATG5 is a component, affected GLUT1 sorting, indicating that membrane atg8ylation as a process affects retromer function and endosomal sorting. The contribution of membrane atg8ylation to retromer function in GLUT1 sorting was independent of canonical autophagy. These findings expand the scope of membrane atg8ylation to specific sorting processes in the cell dependent on the retromer and its known interactors.

Keywords:  active tuberculosis; atg8ylation; autophagy; cell biology; glucose transport; human; latent tuberculosis; membrane transport; mouse

DOI:  https://doi.org/10.7554/eLife.100928
Nat Metab. 2025 Jan 08.

Cellular and organismal function of choline metabolism.

Timothy C Kenny, Samantha Scharenberg, Monther Abu-Remaileh, Kıvanç Birsoy.

Choline is an essential micronutrient critical for cellular and organismal homeostasis. As a core component of phospholipids and sphingolipids, it is indispensable for membrane architecture and function. Additionally, choline is a precursor for acetylcholine, a key neurotransmitter, and betaine, a methyl donor important for epigenetic regulation. Consistent with its pleiotropic role in cellular physiology, choline metabolism contributes to numerous developmental and physiological processes in the brain, liver, kidney, lung and immune system, and both choline deficiency and excess are implicated in human disease. Mutations in the genes encoding choline metabolism proteins lead to inborn errors of metabolism, which manifest in diverse clinical pathologies. While the identities of many enzymes involved in choline metabolism were identified decades ago, only recently has the field begun to understand the diverse mechanisms by which choline availability is regulated and fuelled via metabolite transport/recycling and nutrient acquisition. This review provides a comprehensive overview of choline metabolism, emphasizing emerging concepts and their implications for human health and disease.

DOI: https://doi.org/10.1038/s42255-024-01203-8
Exp Mol Med. 2025 Jan 08.

Multiomic quantification of the KRAS mutation dosage improves the preoperative prediction of survival and recurrence in patients with pancreatic ductal adenocarcinoma.

Won-Gun Yun, Daeun Kim, Youngmin Han, Wooil Kwon, Seong-Geun Lee, Jin-Young Jang, Daechan Park.

Most cancer mutation profiling studies are laboratory-based and lack direct clinical application. For clinical use, it is necessary to focus on key genes and integrate them with relevant clinical variables. We aimed to evaluate the prognostic value of the dosage of the KRAS G12 mutation, a key pancreatic ductal adenocarcinoma (PDAC) variant and to investigate the biological mechanism of the prognosis associated with the dosage of the KRAS G12 mutation. In this retrospective cohort study, we analyzed 193 surgically treated patients with PDAC between 2009 and 2016. RNA, whole-exome, and KRAS-targeted sequencing data were used to estimate the dosage of the KRAS G12 mutant. Our prognostic scoring system included the mutation dosage from targeted sequencing ( > 0.195, 1 point), maximal tumor diameter at preoperative imaging ( > 20 mm, 1 point), and carbohydrate antigen 19-9 levels ( > 150 U/mL, 1 point). The KRAS mutation dosage exhibited comparable performance with clinical variables for survival prediction. High KRAS mutation dosages activated the cell cycle, leading to high mutation rates and poor prognosis. According to prognostic scoring systems that integrate mutation dosage with clinical factors, patients with 0 points had superior median overall survival of 97.0 months and 1-year, 3-year, and 5-year overall survival rates of 95.8%, 70.8%, and 66.4%, respectively. In contrast, patients with 3 points had worse median overall survival of only 16.0 months and 1-year, 3-year, and 5-year overall survival rates of 65.2%, 8.7%, and 8.7%, respectively. The incorporation of the KRAS G12 mutation dosage variable into prognostic scoring systems can improve clinical variable-based survival prediction, highlighting the feasibility of an integrated scoring system with clinical significance.

DOI: https://doi.org/10.1038/s12276-024-01382-0
bioRxiv. 2024 Dec 20. pii: 2024.12.16.628827. [Epub ahead of print]

Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing.

Yujun Feng, Donglai Chen, Catherine C Applegate, Natalia Y Gonzalez Medina, Chia-Wei Kuo, Opeyemi H Arogundade, Chris L Wright, Fangxiu Xu, Jenny Drnevich, Andrew M Smith.

Sample multiplexing is an emerging method in single-cell RNA sequencing (scRNA-seq) that addresses high costs and batch effects. Current multiplexing schemes use DNA labels to barcode cell samples but are limited in their stability and extent of labeling across heterogeneous cell populations. Here, we introduce Nanocoding using lipid nanoparticles (LNPs) for high barcode labeling density in multiplexed scRNA-seq. LNPs reduce dependencies on cell surface labeling mechanisms due to multiple controllable means of cell uptake, amplifying barcode loading 10-100-fold and allowing both protection and efficient release by dissolution. In cultured cell lines and heterogeneous cells from tissue digests, Nanocoding occurs in 40 minutes with stability after sample mixing and requires only commercially available reagents without novel chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples containing lipid-rich debris and heterogeneous cells from adipose tissue of obese rodents show more than 95% labeling with all known subtypes identified. Using Nanocoding, we investigate gene expression changes related to aging in adipose tissue, profiling cells that could not be readily identified with current direct conjugate methods using lipid or antibody conjugates. This ease of generating and tuning these constructs may afford efficient and robust whole-sample multiplexing with minimal sample crosstalk.

DOI: https://doi.org/10.1101/2024.12.16.628827
Biochem Biophys Res Commun. 2024 Dec 27. pii: S0006-291X(24)01790-X. [Epub ahead of print]747 151254

ATG9 promotes autophagosome formation through interaction with LC3.

Peiqi Xu, Ting Zhang, Fangfang Yu, Lixia Guo, Yanan Yang.

  The autophagosome is a double-membrane organelle that executes macroautophagy. Previous studies have shown that the autophagosome formation is driven by autophagy-related genes, among which ATG9 is the only conserved transmembrane protein and has been shown to play a critical role in the autophagosome formation. However, how ATG9 binds to the growing autophagosome membrane has remained uncertain. Herein, we report that ATG9 binds to LC3, an essential membrane component of the autophagosome, thereby allowing ATG9 to incorporate into the autophagosome membrane. Mechanistically, we show that ATG9 interacts with LC3 through its UIM motives, which bind to the UDS site of LC3. Interrupting such UIM-UDS interaction abolishes the autophagosome association of ATG9 and suppresses the autophagosome formation. Collectively, our findings reveal a novel mechanism regulating autophagosome biogenesis and suggest that the interaction of ATG9 with LC3 is critical for ATG9 binding to the growing autophagosome membrane.

Keywords:  ATG9; Autophagosome; LC3; UDS; UIM

DOI:  https://doi.org/10.1016/j.bbrc.2024.151254
bioRxiv. 2024 Dec 26. pii: 2024.12.26.630419. [Epub ahead of print]

Estrogens increase cancer cell efferocytosis to establish an immunosuppressive tumor microenvironment.

Binita Chakraborty, Prabuddha Chakraborty, Michael C Brown, Daniel Crowder, Aditi Goyal, Rachid Safi, Sandeep Artham, Megan Kirkland, Alessandro Racioppi, Patrick Juras, Debarati Mukherjee, Felicia Lim, Jovita Byemerwa, Kiana Gunn, Scott R Floyd, Georgia Beasley, Suzanne Wardell, Ching-Yi Chang, Donald P McDonnell.

Phagocytic clearance of apoptotic cancer cells (efferocytosis) by tumor-associated macrophages (TAMs) contributes in a substantial manner to the establishment of an immunosuppressive tumor microenvironment. This puts in context our observation that the female steroid hormone 17β-estradiol (E2) facilitates tumor immune resistance through cancer cell extrinsic Estrogen Receptor (ERalpha;) signaling in TAMs. Notable was the finding that E2 induces the expression of CX3CR1 in TAMs to enable efferocytosis of apoptotic cancer cells which results in the suppression of type I interferon (IFN) signaling. Mechanistically, E2 facilitates calcium-dependent activation of the transcription factor NFATC1, which in turn induces CX3CR1 expression. This drives macrophage polarization towards an immune-suppressive state, increasing the ability of TAMs to engulf pro-inflammatory apoptotic cancer cells. Genetic or pharmacological inhibition of the E2/ER/CX3CR1 axis reversed the efferocytic activity of TAMs, rescued E2-dependent suppression of type I IFN signaling, and potentiated intratumoral adaptive immune cell function. Efferocytosis following radiation-induced cancer cell apoptosis limits the efficacy of radiation therapy. Importantly, we determined that preconditioning with either ER-directed endocrine therapies or CX3CR1 inhibition enhanced the antitumor efficacy of radiation therapy by reversing macrophage suppression and reviving intratumoral T cell activation. Our work defines the mechanisms by which E2 increases the efferocytotic activity of TAMs to establish an immunosuppressive tumor microenvironment and demonstrates how this process can be reversed with endocrine therapies which target ERalpha.

DOI: https://doi.org/10.1101/2024.12.26.630419
J Physiol. 2025 Jan 08.

Pharmacological reduction of lipid hydroperoxides as a potential modulator of sarcopenia.

Jacob L Brown, Hongyang Xu, Elizabeth Duggan, Craig S Rosenfeld, Holly Van Remmen.

  We previously reported that elevated expression of phospholipid hydroperoxide glutathione peroxidase 4, an enzyme that regulates membrane lipid hydroperoxides, can mitigate sarcopenia in mice. However, it is still unknown whether a pharmacological intervention designed to modulate lipid hydroperoxides might be an effective strategy to reduce sarcopenia in aged mice. Here we asked whether a newly developed compound, CMD-35647 (CMD), can reduce muscle atrophy induced by sciatic nerve transection. We treated mice daily with vehicle or CMD (15 mg/kg, i.p. injection) starting 1 day prior to denervation. CMD treatment reduced hydroperoxide generation and blunted muscle atrophy by over 17% in denervated muscle. To test whether CMD can reduce ageing-induced muscle atrophy and weakness, we treated mice with either vehicle or CMD (15 mg/kg, i.p. injection) 3 days per week for 8 months, starting at 18 months of age until 26 months of age. We measured muscle mass, functional status of neuromuscular junctions, muscle contractile function and mitochondrial function in control and CMD-treated 26-month-old female mice. Treatment with CMD conferred protection against muscle atrophy in both tibialis anterior and extensor digitorum longus that was associated with maintenance of fibre size of MHC 2b and 2x fibres. Mitochondrial respiration was also protected in CMD-treated mice. We also found that muscle force generation was protected with CMD treatment despite denervation in ∼25% of the muscle fibres. Overall, this study shows that pharmacological interventions designed to reduce lipid hydroperoxides might be effective for preventing sarcopenia. KEY POINTS: Sarcopenia in aged mice is associated with muscle loss, contractile dysfunction, denervation, and reduced mitochondrial respiration. CMD-35647 is a pharmocological compound that can neutralize lipid hydroperoxides. 8 month treatment of CMD-35647 mitigated muscle atrophy in tibialis anterior and extensor digitorum longus. 8 month treatment of CMD-35647 improved muscle function in aged mice independent of the neuromuscular junction. Aged mice treated with CMD-35647 had greater respiration in red gastrocnemius muscle when compared to vehicle treated mice.

Keywords:  Aging; Mitochondria; Neuromuscular junction; lipid hydroperoxide; muscle atrophy; muscle weakness; oxylipin; sarcopenia

DOI:  https://doi.org/10.1113/JP287090
Front Immunol. 2024 ;15 1512981

SQLE-mediated squalene metabolism promotes tumor immune evasion in pancreatic cancer.

Junchen Pan, Haixi Liang, Lin Zhou, Wenhua Lu, Bitao Huo, Rui Liu, Peng Huang.

   Background: Squalene epoxidase (SQLE) is a key enzyme in cholesterol biosynthesis and has been shown to negatively affect tumor immunity and is associated with poor outcomes of immunotherapy in various cancers. While most research in this area has focused on the impact of cholesterol on immune functions, the influence of SQLE-mediated squalene metabolism within the tumor immune microenvironment (TIME) remains unexplored.
Methods: We established an immune-competent mouse model (C57BL/6) bearing mouse pancreatic cancer xenografts (KPC cells) with or without stable SQLE-knockdown (SQLE-KD) to evaluate the impact of SQLE-mediated metabolism on pancreatic cancer growth and immune functions. The effect of squalene on tumor growth and immune cells was tested by direct administration of squalene to C57BL/6 mice bearing KPC tumors. Flow cytometry analysis and immunohistochemical (IHC) staining of immune cells from the tumor tissues were performed to evaluate changes in immune function. We also employed RNA-sequencing to analyze the gene expression profiles in pancreatic cancer cells (PANC-1) treated with or without squalene. RT-PCR and Western blot analyses were used to investigate the relevant molecular mechanisms.
Results: We show that SQLE is significantly overexpressed in pancreatic cancer, and abrogation of SQLE results in a significant increase in squalene accumulation within tumor cells. The elevated squalene inhibits CXCL1 transcription through its impact on the NF-κB pathway via p65, and thus reduces the recruitment of myeloid-derived suppressor cells (MDSCs) and tumor-associated macrophages (TAMs) into the tumor microenvironment. Silencing of SQLE also leads to an increased proportion of CD8+ T cells in the tumor tissues and suppresses tumor growth in vivo. Importantly, direct administration of squalene, the metabolic substrate of SQLE, to immune-competent mice bearing KPC pancreatic cancer tumors causes a substantial decrease in CD206+ TAMs and MDSCs, thus releasing immune suppression and inhibiting tumor growth.
Conclusion: Our study shows that squalene is an important immune-modulating metabolite that inhibits the infiltration of immune-suppressive cells in TIME, and that SQLE exerts its tumor immune evasion effect by metabolic removal of squalene. Thus, SQLE-mediated squalene metabolic pathway could be a potential target to enhance antitumor immunity in pancreatic cancer.

Keywords:  MDSCs; NF-κB; SQLE; TAMs; pancreatic cancer; squalene

DOI:  https://doi.org/10.3389/fimmu.2024.1512981
JAMA Netw Open. 2025 Jan 02. 8(1): e2453588

KRAS Mutation Status and Treatment Outcomes in Patients With Metastatic Pancreatic Adenocarcinoma.

Carter Norton, Matthew Steven Shaw, Zachary Rubnitz, Jarrod Smith, Heloisa P Soares, Christopher D Nevala-Plagemann, Ignacio Garrido-Laguna, Vaia Florou.

Importance: Despite the high prevalence of KRAS alterations in pancreatic ductal adenocarcinoma (PDAC), the clinical impact of common KRAS mutations with different cytotoxic regimens is unknown. This evidence is important to inform current treatment and provide a benchmark for emergent targeted KRAS therapies in metastatic PDAC.
Objective: To assess the clinical implications of common KRAS G12 mutations in PDAC and to compare outcomes of standard-of-care multiagent therapies across these common mutations.
Design, Setting, and Participants: This retrospective cohort study obtained deidentified clinical data for 5382 patients from a nationwide (US-based) clinicogenomic database. The deidentified data originated from approximately 280 US cancer clinics (approximately 800 sites of care). Patients diagnosed with metastatic PDAC from February 9, 2010, to September 20, 2022, and with sufficient follow-up and treatment data were included.
Main Outcomes and Measures: Median overall survival (OS) and time to next treatment (TTNT) were calculated for each KRAS mutation group. Hazard ratios (HRs) were generated using multivariate Cox proportional hazards models for KRAS mutations and mutation-treatment combinations.
Results: A total of 2433 patients with PDAC were included in the analysis (mean age at first treatment, 67.0 [range, 66.0-68.0] years; 1340 male [55.1%]). Among 2023 patients with KRAS mutations, those with G12R had the longest median TTNT (6.0 [95% CI, 5.2-6.6] months) and the longest median OS (13.2 [95% CI, 10.6-15.2] months). Patients with KRAS G12D and G12V mutations had a significantly higher risk of disease progression (HRs, 1.15; [95% CI, 1.04-1.29; P = .009] and 1.16 [95% CI, 1.04-1.30; P = .01], respectively) and death (HRs, 1.29 [95% CI, 1.15-1.45; P < .001] and 1.23 [95% CI, 1.09-1.39; P < .001], respectively) compared with KRAS wild type. The FOLFIRINOX regimen (fluorouracil, irinotecan, oxaliplatin, and leucovorin) had a significantly lower risk of treatment progression and death than gemcitabine with (HRs, 1.19 [95% CI, [1.09-1.29; P < .001] and 1.18 [95% CI, 1.07-1.29; P < .001], respectively) or without (HRs, 1.37 [95% CI, 1.11-1.69; P = .003] and 1.41 [95% CI 1.13-1.75; P = .002], respectively) nab-paclitaxel across all patients.
Conclusions and Relevance: In this cohort study of 2433 patients with PDAC, KRAS G12D and G12V mutations were associated with worse patient outcomes compared with KRAS wild type. KRAS G12R was associated with more favorable patient outcomes, and FOLFIRINOX was associated with better patient outcomes than gemcitabine-based therapies. These findings highlight the need for more effective systemic therapies for these groups of patients.

DOI: https://doi.org/10.1001/jamanetworkopen.2024.53588
Trends Biochem Sci. 2025 Jan 07. pii: S0968-0004(24)00283-4. [Epub ahead of print]

Stress responses induced by perturbation of the ubiquitin-proteasome system.

Mamta Rai, Liam C Hunt, Fabio Demontis.

  The ubiquitin-proteasome system is key for proteostasis and its disruption can induce several cellular adaptations. Here, we summarize the range of cellular responses that are induced by perturbation of distinct components of the ubiquitin-proteasome system, and how proteasome stress in a tissue can induce systemic responses in distant tissues.

Keywords:  E2 ubiquitin-conjugating enzymes; UBA1; ingrained stress response; proteasome; systemic stress response; ubiquitination

DOI:  https://doi.org/10.1016/j.tibs.2024.12.011