bims-cagime 2025-01-26 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–01–26
38 papers selected by
Kıvanç Görgülü, Technical University of Munich

SMAD4 and KRAS Status Shape Cancer Cell-Stromal Crosstalk and Therapeutic Response in Pancreatic Cancer.
FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis.
Pancreatic cancer cells infiltrate nerves through TGFbeta1-driven perineural epithelial-to-mesenchymal-like transdifferentiation.
Metabolic interplays between the tumour and the host shape the tumour macroenvironment.
Intercellular TIMP-1-CD63 signaling directs the evolution of immune escape and metastasis in KRAS-mutated pancreatic cancer cells.
Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response.
Ribosome Biogenesis, Altered Metabolism and Ribotoxic Stress Response in Pancreatic Ductal Adenocarcinoma Tumor Microenvironment.
Loss or inhibition of lysosomal acid lipase in vitro leads to cholesteryl ester accumulation without affecting muscle formation or mitochondrial function.
Punctuational evolution is pervasive in distal site metastatic colonization.
Multiplexed single-cell imaging reveals diverging subpopulations with distinct senescence phenotypes during long-term senescence induction.
Impaired oxidative phosphorylation drives primary tumor escape and metastasis.
Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.
Protocol for generating liver metastasis microtissues to decipher cellular interactions between metastatic intestinal cancer and liver tissue.
Accumulation of CD38 in Hybrid Epithelial/Mesenchymal Cells Promotes Immune Remodeling and Metastasis in Breast Cancer.
A Roadmap of Responses to Asymmetry Stress in Lipid Membranes.
Selective deficiency of mitochondrial respiratory complex I subunits Ndufs4/6 causes tumor immunogenicity.
Experimental tools and emerging principles of organellar mechanotransduction.
Hypoxia as a medicine.
Visualization of Apical-Basal Stress Polarity Regulating Directed Cell Migration with a FRET-Based Biosensor.
Stretch-induced endogenous electric fields drive directed collective cell migration in vivo.
Cryo-electron tomography pipeline for plasma membranes.
Membrane Surface Charge, Phospholipids, and Protein Localization.
A temperature-inducible protein module for control of mammalian cell fate.
Mapping cells through time and space with moscot.
Mitochondrial protein import stress.
Mammalian nucleophagy: process and function.
Targeting aldolase A in hepatocellular carcinoma leads to imbalanced glycolysis and energy stress due to uncontrolled FBP accumulation.
Evolving Paradigms in the Treatment of Oligometastatic Pancreatic Ductal Adenocarcinoma.
Sympathetic nerve signaling rewires the tumor microenvironment: a shift in "microenvironmental-ity".
Molecular determinants of condensate composition.
Capture of membrane proteins in their native membrane milieu.
Chronic intermittent fasting impairs β cell maturation and function in adolescent mice.
Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations.
Palmitoylation-dependent regulation of GPX4 suppresses ferroptosis.
Bypassing senescence.
Lineage tracing of pancreatic cells for mechanistic and therapeutic insights.
Single-cell RNA flow cytometry to assess intratumoral production of cytokines/chemokines.
Flamingo participates in multiple models of cell competition.

Cancer Res. 2025 Jan 22.

SMAD4 and KRAS Status Shape Cancer Cell-Stromal Crosstalk and Therapeutic Response in Pancreatic Cancer.

Eloise G Lloyd, Muntadher Jihad, Judhell S Manansala, Wenlong Li, Priscilla S W Cheng, Gianluca Mucciolo, Marta Zaccaria, Sara Pinto Teles, Joaquín Araos Henríquez, Sneha Harish, Rebecca Brais, Sally Ashworth, Weike Luo, Paul M Johnson, Lisa Veghini, Mireia Vallespinos, Vincenzo Corbo, Giulia Biffi.

Pancreatic ductal adenocarcinoma (PDAC) contains an extensive stroma that modulates response to therapy, contributing to the dismal prognosis associated with this cancer. Evidence suggests that PDAC stromal composition is shaped by mutations within malignant cells, but most previous work has focused on pre-clinical models driven by KrasG12D and mutant Trp53. Elucidation of the contribution of additional known oncogenic drivers, including KrasG12V mutation and Smad4 loss, is needed to increase understanding of malignant cell-stroma crosstalk in PDAC. Here, we used single-cell RNA-sequencing to analyze the cellular landscape of Trp53-mutant mouse models driven by KrasG12D or KrasG12V in which Smad4 was wild-type or deleted. KrasG12D Smad4-deleted PDAC developed a fibro-inflammatory rich stroma with increased malignant JAK/STAT cell signaling and enhanced therapeutic response to JAK/STAT inhibition. SMAD4 loss in KrasG12V PDAC differently altered the tumor microenvironment compared to KrasG12D PDAC, and the malignant compartment lacked JAK/STAT signaling dependency. Thus, malignant cell genotype impacts cancer cell and stromal cell phenotypes in PDAC, directly affecting therapeutic efficacy.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-2330
bioRxiv. 2025 Jan 06. pii: 2025.01.06.631537. [Epub ahead of print]

FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis.

Mike Lange, Michele Wölk, Cody E Doubravsky, Joseph M Hendricks, Shunji Kato, Yurika Otoki, Benjamin Styler, Kiyotaka Nakagawa, Maria Fedorova, James A Olzmann.

Lipid droplets (LDs) are organelles that store and supply lipids based on cellular needs. While mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here, we identify LD-localized Ferroptosis Suppressor Protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidation in vitro. Notably, polyunsaturated fatty acid (PUFA)-rich triacylglycerols enhance cancer cell sensitivity to FSP1 loss and inducing PUFA-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the buildup of oxidized lipids and induction of ferroptosis.

DOI: https://doi.org/10.1101/2025.01.06.631537
Neoplasia. 2025 Jan 21. pii: S1476-5586(25)00005-3. [Epub ahead of print]60 101126

Pancreatic cancer cells infiltrate nerves through TGFbeta1-driven perineural epithelial-to-mesenchymal-like transdifferentiation.

Theresa Krauss, Ibrahim Halil Gürcinar, Ulrike Bourquain, Maren Hieber, Evelyn N Krohmer, Nan Wu, Sergey Tokalov, Rüdiger Goess, Carmen Mota Reyes, Dieter Saur, Helmut Friess, Güralp O Ceyhan, Ihsan Ekin Demir, Okan Safak.

  Neural invasion is a prognostic hallmark of pancreatic ductal adenocarcinoma (PDAC), yet the underlying mechanisms behind the disruption of perineural barriers and access of cancer cells into intrapancreatic nerves remain poorly understood. This study aimed to investigate the role of epithelial-mesenchymal transformation (EMT) in perineural epithelial cells during neural invasion.Histopathological analysis of human and murine primary tumors using perineurium-specific GLUT1 antibody revealed a reduction in perineural integrity, which positively correlated with the extent of neural invasion in human PDAC cases. Human pancreatic cancer cell lines were found to secrete TGFbeta1, which induced EMT of perineural epithelial cells, characterized by the loss of epithelial markers (CK19-9) and the acquisition of mesenchymal markers (alphaSMA, N-Cadherin). Additionally, these transitioning perineural epithelial cells demonstrated increased matrix-degrading capabilities through the upregulation of matrix-metalloproteases 3 and 9 via SMAD2. In an autochthonous mouse model with elevated endogenous TGFbeta1 levels in addition to oncogenic Kras activation (Ptf1aCre/+, LSL-KrasG12D/+, LSL-R26Tgfβ/+), decreased perineural integrity could be reproduced in vivo.Collectively, these findings underscore the role played by TGFbeta1-overexpressing pancreatic cancer cells in the dismantling of perineural barriers during neural invasion.

Keywords:  Epithelial-to-mesenchymal-like transdifferentiation; Nerve infiltration; Pancreatic cancer; TGFbeta1

DOI:  https://doi.org/10.1016/j.neo.2025.101126
Nat Rev Cancer. 2025 Jan 20.

Metabolic interplays between the tumour and the host shape the tumour macroenvironment.

Patricia Altea-Manzano, Amanda Decker-Farrell, Tobias Janowitz, Ayelet Erez.

Metabolic reprogramming of cancer cells and the tumour microenvironment are pivotal characteristics of cancers, and studying these processes offer insights and avenues for cancer diagnostics and therapeutics. Recent advancements have underscored the impact of host systemic features, termed macroenvironment, on facilitating cancer progression. During tumorigenesis, these inherent features of the host, such as germline genetics, immune profile and the metabolic status, influence how the body responds to cancer. In parallel, as cancer grows, it induces systemic effects beyond the primary tumour site and affects the macroenvironment, for example, through inflammation, the metabolic end-stage syndrome of cachexia, and metabolic dysregulation. Therefore, understanding the intricate metabolic interplay between the tumour and the host is a growing frontier in advancing cancer diagnosis and therapy. In this Review, we explore the specific contribution of the metabolic fitness of the host to cancer initiation, progression and response to therapy. We then delineate the complex metabolic crosstalk between the tumour, the microenvironment and the host, which promotes disease progression to metastasis and cachexia. The metabolic relationships among the host, cancer pathogenesis and the consequent responsive systemic manifestations during cancer progression provide new perspectives for mechanistic cancer therapy and improved management of patients with cancer.

DOI: https://doi.org/10.1038/s41568-024-00786-4
Mol Cancer. 2025 Jan 18. 24(1): 25

Intercellular TIMP-1-CD63 signaling directs the evolution of immune escape and metastasis in KRAS-mutated pancreatic cancer cells.

Chu-An Wang, Ya-Chin Hou, Yi-Kai Hong, Yu-Jing Tai, Chieh Shen, Pei-Chi Hou, Jhao-Lin Fu, Cheng-Lin Wu, Siao Muk Cheng, Daw-Yang Hwang, Yung-Yeh Su, Yan-Shen Shan, Shaw-Jenq Tsai.

BACKGROUND AND AIMS: Oncogenic KRAS mutations are present in approximately 90% of pancreatic ductal adenocarcinoma (PDAC). However, Kras mutation alone is insufficient to transform precancerous cells into metastatic PDAC. This study investigates how KRAS-mutated epithelial cells acquire the capacity to escape senescence or even immune clearance, thereby progressing to advanced PDAC.
METHODS: Single-cell RNA sequencing and analysis of primary PDAC tumors were conducted. Genetically engineered pancreas-specific Kras-mutated, dual specificity phosphatase-2 (Dusp2) knockout mouse models were established. Human and mouse primary pancreatic cancer cell lines were used for in vitro assessment of cancer characteristics. Tumor progression was studied via pancreas orthotopic and portal vein injection in the immune-competent mice. Clinical relevance was validated by digital spatial transcriptomic analysis of PDAC tumors.
RESULTS: Kras mutation induces the formation of pancreatic intraepithelial neoplasia (PanIN), these lesions also exhibit significant apoptotic signals. Single-cell RNA sequencing identified a subset of ERKactiveDUSP2low cells continuing to expand from early to advanced stage PDAC. In vitro and in vivo studies reveal that early infiltrating macrophage-derived tissue inhibitor of metallopeptidase 1 (TIMP-1) is the key factor in maintaining the ERKactiveDUSP2low cell population in a CD63-dependent manner. The ERKactiveDUSP2low cancer cells further exacerbate macrophage-mediated cancer malignancy, including loss of epithelial trait, increased lymphangiogenesis, and immune escape. Digital spatial profiling analysis of PDAC samples demonstrates the colocalization of TIMP-1high macrophages and CD63high cancer cells. The presence of TIMP-1high macrophages and CD63high epithelial cells correlates with poor prognosis in PDAC.
CONCLUSIONS: Our study reveals the vicious cycle between early infiltrating macrophages and pancreatic cancer cells, providing a mechanistic insight into the dynamic regulation directing pancreatic cancer progression.

DOI: https://doi.org/10.1186/s12943-024-02207-4
Mol Syst Biol. 2025 Jan 21.

Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response.

Stefanie Höfer, Larissa Frasch, Sarah Brajkovic, Kerstin Putzker, Joe Lewis, Hendrik Schürmann, Valentina Leone, Amirhossein Sakhteman, Matthew The, Florian P Bayer, Julian Müller, Firas Hamood, Jens T Siveke, Maximilian Reichert, Bernhard Kuster.

  The DNA-damaging agent Gemcitabine (GEM) is a first-line treatment for pancreatic cancer, but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs, including kinase inhibitors, but the experimental evidence for such rationale is often unclear. Here, we phenotypically screened 13 human pancreatic adenocarcinoma (PDAC) cell lines against GEM in combination with 146 clinical inhibitors and observed strong synergy for the ATR kinase inhibitor Elimusertib in most cell lines. Dose-dependent phosphoproteome profiling of four ATR inhibitors following DNA damage induction by GEM revealed a strong block of the DNA damage response pathway, including phosphorylated pS468 of CHEK1, as the underlying mechanism of drug synergy. The current work provides a strong rationale for why the combination of GEM and ATR inhibition may be useful for the treatment of PDAC patients and constitutes a rich phenotypic and molecular resource for further investigating effective drug combinations.

Keywords:  DNA Damage Response; Drug Combination Screening; Kinase Inhibitors; Pancreatic Cancer; Phosphoproteomics

DOI:  https://doi.org/10.1038/s44320-025-00085-6
Cancer Lett. 2025 Jan 20. pii: S0304-3835(25)00048-5. [Epub ahead of print] 217484

Ribosome Biogenesis, Altered Metabolism and Ribotoxic Stress Response in Pancreatic Ductal Adenocarcinoma Tumor Microenvironment.

Sanjib Chaudhary, Jawed Akhtar Siddiqui, Ramesh Pothuraju, Rakesh Bhatia.

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a poor overall survival rate. Cellular stress response pathways promoting cancer cell fitness in harsh tumor microenvironment (TME) play a critical role in cancer growth and survival. The influence of oncogenic Kras, multi-functional heterogeneous cancer-associated fibroblasts (CAFs), and immunosuppressive TME on cancer cells makes the disease more complex and difficult to treat. The desmoplastic reaction by CAFs comprises approximately 90% of the tumor, with only 10% of cancer cells making things even more complicated, resulting in therapy resistance. Consistently increasing fibrosis creates a hypoxic environment and elevated interstitial fluid pressure inside the tumor constraining vascular supply. Stress conditions in TME alter translation efficiency and metabolism to fulfill the energy requirements of rapidly growing cancer cells. Extensive research has been conducted on multiple molecular and metabolic regulators in PDAC TME. However, the role of TME in influencing translation programs, a prerequisite for cell cycle progression and functional/growth requirements for cancer cells, remains elusive. This review highlights the recent advancements in understanding altered translational programs in PDAC TME. We emphasize the role of ribosome biogenesis, ribosome-induced stress response, and the concept of specialized ribosomes and their probable role in mutationally rewiring the pancreatic TME.

DOI: https://doi.org/10.1016/j.canlet.2025.217484
BBA Adv. 2025 ;7 100135

Loss or inhibition of lysosomal acid lipase in vitro leads to cholesteryl ester accumulation without affecting muscle formation or mitochondrial function.

Alena Akhmetshina, Laszlo Schooltink, Melina Amor, Katharina B Kuentzel, Silvia Rainer, Ananya Nandy, Hansjoerg Habisch, Tobias Madl, Elizabeth Rendina-Ruedy, Katharina Leithner, Nemanja Vujić, Dagmar Kratky.

  Skeletal muscle (SM) is essential for movement, stability, and overall body function, and it readily adapts to changes in energy demand. Myogenesis is energy-intensive and involves complex molecular and cellular events. We recently demonstrated that the absence of lysosomal acid lipase (LAL) in vivo significantly impacts the SM phenotype, primarily by disrupting energy homeostasis and reducing ATP production. As systemic LAL deficiency affects multiple organs, we hypothesized that the altered SM phenotype resulted from systemic rather than SM-specific loss of LAL activity. To distinguish between systemic and cell-intrinsic effects, we used primary myoblasts isolated from Lal-deficient (-/-) mice as well as C2C12 cells treated with the pharmacological inhibitor of LAL, Lalistat-2. We found a significant accumulation of cholesteryl esters in both models studied, highlighting the central role of LAL in lipid catabolism in the SM. However, lipid accumulation was absent under lipoprotein-deficient culture conditions. Neither genetic loss nor pharmacological inhibition of LAL affected myofiber formation or mitochondrial function in vitro, in contrast to what we observed in SM isolated from Lal-/- mice. Tracing [13C6]-labeled glucose in both cell culture models revealed only minor changes in tricarboxylic acid cycle metabolites. These results suggest that although LAL plays an essential role in lipid metabolism, its impact on the processes involved in muscle differentiation and cellular energy production is minor. We conclude that the cell-intrinsic effects of Lal-/- SM are unlikely to drive the SM phenotype observed in vivo.

Keywords:  C2C12 cells; Energy metabolism; LAL; LAL deficiency; Myogenesis; Primary myoblast; Skeletal muscle

DOI:  https://doi.org/10.1016/j.bbadva.2024.100135
Proc Biol Sci. 2025 Jan;292(2039): 20242850

Punctuational evolution is pervasive in distal site metastatic colonization.

George Butler, Sarah R Amend, Chris Venditti, Kenneth J Pienta.

  The evolution of metastasis, the spread of cancer to distal sites within the body, represents a lethal stage of cancer progression. Yet, the evolutionary dynamics that shape the emergence of metastatic disease remain unresolved. Here, using single-cell lineage tracing data in combination with phylogenetic statistical methods, we show that the evolutionary trajectory of metastatic disease is littered with bursts of rapid molecular change as new cellular subpopulations appear, a pattern known as punctuational evolution. Next, by measuring punctuational evolution across the metastatic cascade, we show that punctuational effects are concentrated within the formation of secondary tumours at distal metastatic sites, suggesting that qualitatively different modes of evolution may drive primary and metastatic tumour progression. Taken as a whole, our findings provide empirical evidence for distinct patterns of molecular evolution at early and late stages of metastatic disease and our approach provides a framework to study the evolution of metastasis at a more nuanced level than has been previously possible.

Keywords:  cancer evolution; metastasis; punctuational evolution

DOI:  https://doi.org/10.1098/rspb.2024.2850
Geroscience. 2025 Jan 23.

Multiplexed single-cell imaging reveals diverging subpopulations with distinct senescence phenotypes during long-term senescence induction.

Garrett A Sessions, Madeline V Loops, Brian O Diekman, Jeremy E Purvis.

  Cellular senescence is a phenotypic state that contributes to the progression of age-related disease through secretion of pro-inflammatory factors known as the senescence-associated secretory phenotype (SASP). Understanding the process by which healthy cells become senescent and develop SASP factors is critical for improving the identification of senescent cells and, ultimately, understanding tissue dysfunction. Here, we reveal how the duration of cellular stress modulates the SASP in distinct subpopulations of senescent cells. We used multiplex, single-cell imaging to build a proteomic map of senescence induction in human epithelial cells induced to senescence over the course of 31 days. We map how the expression of SASP proteins increases alongside other known senescence markers such as p53, p21, and p16INK4a. The aggregated population of cells responded to etoposide with an accumulation of stress response factors over the first 11 days, followed by a plateau in most proteins. At the single-cell level, however, we identified two distinct senescence cell populations, one defined primarily by larger nuclear area and the second by higher protein concentrations. Trajectory inference suggested that cells took one of two discrete molecular paths from unperturbed healthy cells, through a common transitional subpopulation, and ending at the discrete terminal senescence phenotypes. Our results underscore the importance of using single-cell proteomics to identify the mechanistic pathways governing the transition from senescence induction to a mature state of senescence characterized by the SASP.

Keywords:  Cellular senescence; DNA damage; Senescence induction; Senescence-associated secretory phenotype (SASP)

DOI:  https://doi.org/10.1007/s11357-024-01503-7
bioRxiv. 2025 Jan 09. pii: 2025.01.08.631936. [Epub ahead of print]

Impaired oxidative phosphorylation drives primary tumor escape and metastasis.

Emily N Arner, Erin Q Jennings, Daniel R Crooks, Christopher J Ricketts, Melissa M Wolf, Matthew A Cottam, Emilie L Fisher-Gupta, Martin Lang, Nunziata Maio, Yuki Shibata, Evan S Krystofiak, Logan M Vlach, Zaid Hatem, Alexander M Blatt, Darren R Heintzman, Allison E Sewell, Emma S Hathaway, KayLee K Steiner, Xiang Ye, Samuel Schaefer, Zachary A Bacigalupa, W Marston Linehan, Kathryn E Beckermann, Frank M Mason, Kamran Idrees, W Kimryn Rathmell, Jeffrey C Rathmell.

Metastasis causes most cancer deaths and reflects transitions from primary tumor escape to seeding and growth at metastatic sites. Epithelial-to-mesenchymal transition (EMT) is important early in metastasis to enable cancer cells to detach from neighboring cells, become migratory, and escape the primary tumor. While different phases of metastasis expose cells to variable nutrient environments and demands, the metabolic requirements and plasticity of each step are uncertain. Here we show that EMT and primary tumor escape are stimulated by disrupted oxidative metabolism. Using Renal Cell Carcinoma (RCC) patient samples, we identified the mitochondrial electron transport inhibitor NDUFA4L2 as upregulated in cells undergoing EMT. Deletion of NDUFA4L2 enhanced oxidative metabolism and prevented EMT and metastasis while NDUFA4L2 overexpression enhanced these processes. Mechanistically, NDUFA4L2 suppressed oxidative phosphorylation and caused citric acid cycle intermediates to accumulate, which modified chromatin accessibility of EMT-related loci to drive primary tumor escape. The effect of impaired mitochondrial metabolism to drive EMT appeared general, as renal cell carcinoma patient tumors driven by fumarate hydratase mutations with disrupted oxidative phosphorylation were highly metastatic and also had robust EMT. These findings highlight the importance of dynamic shifts in metabolism for cell migration and metastasis, with mitochondrial impairment driving early phases of this process. Understanding mitochondrial dynamics may have important implications in both basic and translational efforts to prevent cancer deaths.

DOI: https://doi.org/10.1101/2025.01.08.631936
Sci Adv. 2025 Jan 24. 11(4): eadu5787

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.

Felix Kraus, Yuchen He, Sharan Swarup, Katherine A Overmyer, Yizhi Jiang, Johann Brenner, Cristina Capitanio, Anna Bieber, Annie Jen, Nicole M Nightingale, Benton J Anderson, Chan Lee, Joao A Paulo, Ian R Smith, Jürgen M Plitzko, Steven P Gygi, Brenda A Schulman, Florian Wilfling, Joshua J Coon, J Wade Harper.

Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multiomic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lysophosphatidylcholine species and multilamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.

DOI: https://doi.org/10.1126/sciadv.adu5787
STAR Protoc. 2025 Jan 20. pii: S2666-1667(24)00740-8. [Epub ahead of print]6(1): 103575

Protocol for generating liver metastasis microtissues to decipher cellular interactions between metastatic intestinal cancer and liver tissue.

Maria Lamprou, Ana Krotenberg Garcia, Saskia Jacoba Elisabeth Suijkerbuijk.

  Cell competition is a quality control mechanism that promotes elimination of suboptimal cells relative to fitter neighbors. Cancer cells exploit these mechanisms for expansion, but the underlying molecular pathways remain elusive. Here, we present a protocol for generating matrix-free microtissues recapitulating cellular interactions between intestinal cancer and hepatocyte-like cells using microscopy or transcriptomics/proteomics. We describe steps for generating and differentiating liver progenitor organoids and microtissue formation. We then detail procedures for immunofluorescence staining, mounting microtissues, and sorting cells. For complete details on the use and execution of this protocol, please refer to Krotenberg Garcia et al.1.

Keywords:  Cancer; Microscopy; Organoids

DOI:  https://doi.org/10.1016/j.xpro.2024.103575
Cancer Res. 2025 Jan 24. OF1-OF18

Accumulation of CD38 in Hybrid Epithelial/Mesenchymal Cells Promotes Immune Remodeling and Metastasis in Breast Cancer.

Tanvi H Visal, Recep Bayraktar, Petra den Hollander, Michael A Attathikhun, Tieling Zhou, Jing Wang, Li Shen, Corina-Elena Minciuna, Meng Chen, Elizve Barrientos-Toro, Harsh Batra, Maria Gabriela Raso, Fei Yang, Edwin R Parra, Aysegul A Sahin, George A Calin, Sendurai A Mani.

Triple-negative breast cancer (TNBC) is a highly metastatic subtype of breast cancer. The epithelial-to-mesenchymal transition is a nonbinary process in the metastatic cascade that generates tumor cells with both epithelial and mesenchymal traits known as hybrid EM cells. Recent studies have elucidated the enhanced metastatic potential of cancers featuring the hybrid EM phenotype, highlighting the need to uncover molecular drivers and targetable vulnerabilities of the hybrid EM state. Here, we discovered that hybrid EM breast tumors are enriched in CD38, an immunosuppressive molecule associated with worse clinical outcomes in liquid malignancies. Altering CD38 expression in tumor cell impacted migratory, invasive, and metastatic capabilities of hybrid EM cells. Abrogation of CD38 expression stimulated an antitumor immune response, thereby preventing the generation of an immunosuppressive microenvironment in hybrid EM tumors. CD38 levels positively correlated with PD-L1 expression in samples from patients with TNBC. Moreover, targeting CD38 potentiated the activity of anti-PD-L1, eliciting strong antitumor immunity, with reduced tumor growth in hybrid EM models. Overall, this research exposes upregulation of CD38 as a specific survival strategy utilized by hybrid EM breast tumors to suppress immune cell activity and sustain metastasis, with strong implications in other carcinomas that have hybrid EM properties. Significance: Hybrid cells co-featuring epithelial and mesenchymal traits in triple-negative breast cancer express elevated levels of CD38 to induce immunosuppression and metastasis, indicating CD38 inhibition as potential strategy for treating breast cancer.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-0400
J Phys Chem B. 2025 Jan 20.

A Roadmap of Responses to Asymmetry Stress in Lipid Membranes.

Lisa Hua, Sevda Akcesme, Kira Müller, Heiko Heerklotz.

The selective insertion of membrane-impermeant amphiphiles such as detergents, (lipo)peptides, drugs, etc. into the cis leaflet of a membrane causes an imbalance between the intrinsic areas of the cis and trans leaflet, referred to as asymmetry stress or differential stress. The literature provides individual mechanisms of how membranes respond to such stress, which are relevant to membrane remodeling processes and leakage phenomena. By studying vesicle budding, membrane leakage, and isothermal titration calorimetry of liposomes interacting with digitonin, alkyl maltosides, miltefosine, and octyl glucoside, we developed a roadmap linking the stress-response mechanisms to each other. Initially, lateral compression or stretching of the leaflets accommodates a minor asymmetry stress. Then, either molecules flip to the trans leaflet or the membrane bends to form buds. Fast flip leads to the classic three-stage model. Budding proceeds up to its limit at 20-40% of the lipid. Beyond, insertion of further detergent is opposed by the pressure in the overpopulated leaflet. This "staying out" state can persist over hours or days and up to high detergent concentrations before detergent micelles induce "micellar solubilization". Alternatively, the stress can be reduced by a transient failure of the membrane, allowing for "cracking in" of molecules, transferring them to the trans side.

DOI: https://doi.org/10.1021/acs.jpcb.4c05868
Nat Cancer. 2025 Jan 17.

Selective deficiency of mitochondrial respiratory complex I subunits Ndufs4/6 causes tumor immunogenicity.

Jiaxin Liang, Tevis Vitale, Xixi Zhang, Thomas D Jackson, Deyang Yu, Mark Jedrychowski, Steve P Gygi, Hans R Widlund, Kai W Wucherpfennig, Pere Puigserver.

Cancer cells frequently rewire their metabolism to support proliferation and evade immune surveillance, but little is known about metabolic targets that could increase immune surveillance. Here we show a specific means of mitochondrial respiratory complex I (CI) inhibition that improves tumor immunogenicity and sensitivity to immune checkpoint blockade (ICB). Targeted genetic deletion of either Ndufs4 or Ndufs6, but not other CI subunits, induces an immune-dependent growth attenuation in melanoma and breast cancer models. We show that deletion of Ndufs4 induces expression of the major histocompatibility complex (MHC) class I co-activator Nlrc5 and antigen presentation machinery components, most notably H2-K1. This induction of MHC-related genes is driven by a pyruvate dehydrogenase-dependent accumulation of mitochondrial acetyl-CoA, which leads to an increase in histone H3K27 acetylation within the Nlrc5 and H2-K1 promoters. Taken together, this work shows that selective CI inhibition restricts tumor growth and that specific targeting of Ndufs4 or Ndufs6 increases T cell surveillance and ICB responsiveness.

DOI: https://doi.org/10.1038/s43018-024-00895-x
Trends Cell Biol. 2025 Jan 18. pii: S0962-8924(24)00279-4. [Epub ahead of print]

Experimental tools and emerging principles of organellar mechanotransduction.

Kai Li, Yuh Nung Jan.

  Mechanotransduction is the process by which cells detect mechanical forces and convert them into biochemical or electrical signals. This process occurs across various cellular compartments, including the plasma membrane, cytoskeleton, and intracellular organelles. While research has focused mainly on force sensing at the plasma membrane, the mechanisms and significance of intracellular mechanotransduction are just beginning to be understood. This review summarizes current techniques for studying organellar mechanobiology, and highlights advances in our understanding of the mechanosensitive events occurring in organelles such as the endoplasmic reticulum (ER), Golgi apparatus, and endolysosomes. Additionally, some open questions and promising directions are identified for future research.

Keywords:  mechanobiology; mechanosensitive ion channel; mechanotransduction; organelle

DOI:  https://doi.org/10.1016/j.tcb.2024.12.011
Sci Transl Med. 2025 Jan 22. 17(782): eadr4049

Hypoxia as a medicine.

Robert S Rogers, Vamsi K Mootha.

Oxygen is essential for human life, yet a growing body of preclinical research is demonstrating that chronic continuous hypoxia can be beneficial in models of mitochondrial disease, autoimmunity, ischemia, and aging. This research is revealing exciting new and unexpected facets of oxygen biology, but translating these findings to patients poses major challenges, because hypoxia can be dangerous. Overcoming these barriers will require integrating insights from basic science, high-altitude physiology, clinical medicine, and sports technology. Here, we explore the foundations of this nascent field and outline a path to determine how chronic continuous hypoxia can be safely, effectively, and practically delivered to patients.

DOI: https://doi.org/10.1126/scitranslmed.adr4049
ACS Sens. 2025 Jan 23.

Visualization of Apical-Basal Stress Polarity Regulating Directed Cell Migration with a FRET-Based Biosensor.

Cunli Wang, Dengyue Xu, Shuai Shao, Jinxin Han, Na Li, Zhengyao Zhang, Hangyu Zhang, Bo Liu.

  Intracellular morphological apical-basal polarity, regulated by conserved polarity proteins, plays a crucial role in cell migration and metastasis. In this study, using a genetically encoded Förster resonance energy transfer (FRET) biosensor to visually present the spatiotemporal stress state between the lipid rafts on the membrane and the linked actin, we first provide the evidence for the existence of intrinsic apical-basal stress polarity in tumor cells and demonstrate that this polarity is a prerequisite for the formation of flow-induced front-back stress polarity. Interestingly, our study revealed that the front-back stress polarity disappeared upon the disruption of intrinsic apical-basal stress discrepancy, resulting in a large attenuated cell migration activity reduced from 76.2 ± 3.5% to 10 ± 4.9%. This unexpected discovery not only highlights the significance of apical-basal stress polarity as another factor influencing cell migration but also indicates that the disruption of apical-basal polarity in stress might be a novel therapeutic approach for tumor metastasis.

Keywords:  FRET biosensor; cell membrane; cell migration; cytoskeleton; stress polarity

DOI:  https://doi.org/10.1021/acssensors.4c00628
Nat Mater. 2025 Jan 17.

Stretch-induced endogenous electric fields drive directed collective cell migration in vivo.

Fernando Ferreira, Sofia Moreira, Min Zhao, Elias H Barriga.

Directed collective cell migration is essential for morphogenesis, and chemical, electrical, mechanical and topological features have been shown to guide cell migration in vitro. Here we provide in vivo evidence showing that endogenous electric fields drive the directed collective cell migration of an embryonic stem cell population-the cephalic neural crest of Xenopus laevis. We demonstrate that the voltage-sensitive phosphatase 1 is a key component of the molecular mechanism, enabling neural crest cells to specifically transduce electric fields into a directional cue in vivo. Finally, we propose that endogenous electric fields are mechanically established by the convergent extension movements of the ectoderm, which generate a membrane tension gradient that opens stretch-activated ion channels. Overall, these findings establish a role for electrotaxis in tissue morphogenesis, highlighting the functions of endogenous bioelectrical stimuli in non-neural contexts.

DOI: https://doi.org/10.1038/s41563-024-02060-2
Nat Commun. 2025 Jan 20. 16(1): 855

Cryo-electron tomography pipeline for plasma membranes.

Willy W Sun, Dennis J Michalak, Kem A Sochacki, Prasanthi Kunamaneni, Marco A Alfonzo-Méndez, Andreas M Arnold, Marie-Paule Strub, Jenny E Hinshaw, Justin W Taraska.

Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with subtomogram averaging and employs a genetically encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cellular environment. The pipeline provides efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of mammalian cells.

DOI: https://doi.org/10.1038/s41467-025-56045-z
Rev Physiol Biochem Pharmacol. 2025 ;187 89-101

Membrane Surface Charge, Phospholipids, and Protein Localization.

Colin D McCaig.

  Cell membranes contain multiple charged lipids that bind proteins dynamically and their spatial organization on the inner/outer membrane leaflet, or in spatially localized areas has considerable biological importance. Myristoylated alanine-rich C kinase substrate (MARCKS) proteins and their roles as electrostatic switches are one example covered. Cell surface charge needs to be monitored and regulated continually and the roles of lipid flippases and scramblases and their electrical regulation also are considered.

Keywords:  Angiogenesis; Lipid flippases; Lipid scramblases; Membrane surface charge; Phospholipids

DOI:  https://doi.org/10.1007/978-3-031-68827-0_9
Nat Methods. 2025 Jan 23.

A temperature-inducible protein module for control of mammalian cell fate.

William Benman, Zikang Huang, Pavan Iyengar, Delaney Wilde, Thomas R Mumford, Lukasz J Bugaj.

Inducible protein switches are currently limited for use in tissues and organisms because common inducers cannot be controlled with precision in space and time in optically dense settings. Here, we introduce a protein that can be reversibly toggled with a small change in temperature, a stimulus that is both penetrant and dynamic. This protein, called Melt (Membrane localization using temperature) oligomerizes and translocates to the plasma membrane when temperature is lowered. We generated a library of Melt variants with switching temperatures ranging from 30 °C to 40 °C, including two that operate at and above 37 °C. Melt was a highly modular actuator of cell function, permitting thermal control over diverse processes including signaling, proteolysis, nuclear shuttling, cytoskeletal rearrangements and cell death. Finally, Melt permitted thermal control of cell death in a mouse model of human cancer. Melt represents a versatile thermogenetic module for straightforward, non-invasive and spatiotemporally defined control of mammalian cells with broad potential for biotechnology and biomedicine.

DOI: https://doi.org/10.1038/s41592-024-02572-4
Nature. 2025 Jan 22.

Mapping cells through time and space with moscot.

Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Lama Saber, Changying Jing, Aimée Bastidas-Ponce, Perla Cota, Marta Tarquis-Medina, Shrey Parikh, Ilan Gold, Heiko Lickert, Mostafa Bakhti, Mor Nitzan, Marco Cuturi, Fabian J Theis.

Single-cell genomic technologies enable the multimodal profiling of millions of cells across temporal and spatial dimensions. However, experimental limitations hinder the comprehensive measurement of cells under native temporal dynamics and in their native spatial tissue niche. Optimal transport has emerged as a powerful tool to address these constraints and has facilitated the recovery of the original cellular context1-4. Yet, most optimal transport applications are unable to incorporate multimodal information or scale to single-cell atlases. Here we introduce multi-omics single-cell optimal transport (moscot), a scalable framework for optimal transport in single-cell genomics that supports multimodality across all applications. We demonstrate the capability of moscot to efficiently reconstruct developmental trajectories of 1.7 million cells from mouse embryos across 20 time points. To illustrate the capability of moscot in space, we enrich spatial transcriptomic datasets by mapping multimodal information from single-cell profiles in a mouse liver sample and align multiple coronal sections of the mouse brain. We present moscot.spatiotemporal, an approach that leverages gene-expression data across both spatial and temporal dimensions to uncover the spatiotemporal dynamics of mouse embryogenesis. We also resolve endocrine-lineage relationships of delta and epsilon cells in a previously unpublished mouse, time-resolved pancreas development dataset using paired measurements of gene expression and chromatin accessibility. Our findings are confirmed through experimental validation of NEUROD2 as a regulator of epsilon progenitor cells in a model of human induced pluripotent stem cell islet cell differentiation. Moscot is available as open-source software, accompanied by extensive documentation.

DOI: https://doi.org/10.1038/s41586-024-08453-2
Nat Cell Biol. 2025 Jan 22.

Mitochondrial protein import stress.

Nikolaus Pfanner, Fabian den Brave, Thomas Becker.

Mitochondria have to import a large number of precursor proteins from the cytosol. Chaperones keep these proteins in a largely unfolded state and guide them to the mitochondrial import sites. Premature folding, mitochondrial stress and import defects can cause clogging of import sites and accumulation of non-imported precursors, representing a critical burden for cellular proteostasis. Here we discuss how cells respond to mitochondrial protein import stress by regenerating clogged import sites and inducing stress responses. The mitochondrial protein import machinery has a dual role by serving as sensor for detecting mitochondrial dysfunction and inducing stress-response pathways. The production of chaperones that fold or sequester precursor proteins in deposits is induced and the proteasomal activity is increased to remove the excess precursor proteins. Together, these pathways reveal how mitochondria are tightly integrated into a cellular proteostasis and stress response network to maintain cell viability.

DOI: https://doi.org/10.1038/s41556-024-01590-w
Autophagy. 2025 Jan 19.

Mammalian nucleophagy: process and function.

Fujian Ji, Enyong Dai, Rui Kang, Daniel J Klionsky, Tong Liu, Yu Hu, Daolin Tang, Kun Zhu.

  The nucleus is a highly specialized organelle that houses the cell's genetic material and regulates key cellular activities, including growth, metabolism, protein synthesis, and cell division. Its structure and function are tightly regulated by multiple mechanisms to ensure cellular integrity and genomic stability. Increasing evidence suggests that nucleophagy, a selective form of autophagy that targets nuclear components, plays a critical role in preserving nuclear integrity by clearing dysfunctional nuclear materials such as nuclear proteins (lamins, SIRT1, and histones), DNA-protein crosslinks, micronuclei, and chromatin fragments. Impaired nucleophagy has been implicated in aging and various pathological conditions, including cancer, neurodegeneration, autoimmune disorders, and neurological injury. In this review, we focus on nucleophagy in mammalian cells, discussing its mechanisms, regulation, and cargo selection, as well as evaluating its therapeutic potential in promoting human health and mitigating disease.

Keywords:  Autophagy; disease; micronucleus; nuclear quality control; nucleophagy

DOI:  https://doi.org/10.1080/15548627.2025.2455158
Nat Metab. 2025 Jan 20.

Targeting aldolase A in hepatocellular carcinoma leads to imbalanced glycolysis and energy stress due to uncontrolled FBP accumulation.

Marteinn T Snaebjornsson, Philipp Poeller, Daria Komkova, Florian Röhrig, Lisa Schlicker, Alina M Winkelkotte, Adriano B Chaves-Filho, Kamal M Al-Shami, Carolina Dehesa Caballero, Ioanna Koltsaki, Felix C E Vogel, Roberto Carlos Frias-Soler, Ramona Rudalska, Jessica D Schwarz, Elmar Wolf, Daniel Dauch, Ralf Steuer, Almut Schulze.

Increased glycolytic flux is a hallmark of cancer; however, an increasing body of evidence indicates that glycolytic ATP production may be dispensable in cancer, as metabolic plasticity allows cancer cells to readily adapt to disruption of glycolysis by increasing ATP production via oxidative phosphorylation. Using functional genomic screening, we show here that liver cancer cells show a unique sensitivity toward aldolase A (ALDOA) depletion. Targeting glycolysis by disrupting the catalytic activity of ALDOA led to severe energy stress and cell cycle arrest in murine and human hepatocellular carcinoma cell lines. With a combination of metabolic flux analysis, metabolomics, stable-isotope tracing and mathematical modelling, we demonstrate that inhibiting ALDOA induced a state of imbalanced glycolysis in which the investment phase outpaced the payoff phase. Targeting ALDOA effectively converted glycolysis from an energy producing into an energy-consuming process. Moreover, we found that depletion of ALDOA extended survival and reduced cancer cell proliferation in an animal model of hepatocellular carcinoma. Thus, our findings indicate that induction of imbalanced glycolysis by targeting ALDOA presents a unique opportunity to overcome the inherent metabolic plasticity of cancer cells.

DOI: https://doi.org/10.1038/s42255-024-01201-w
J Gastrointest Cancer. 2025 Jan 18. 56(1): 47

Evolving Paradigms in the Treatment of Oligometastatic Pancreatic Ductal Adenocarcinoma.

Enoch Chang, Alexander D Sherry, Jakob Liermann, Amir Abdollahi, Ching-Wei D Tzeng, Chad Tang, Todd A Aguilera, Eugene J Koay, Prajnan Das, Albert C Koong, Shubham Pant, Ethan B Ludmir.

  Multiple randomized trials have suggested that the addition of comprehensive metastasis-directed therapy to best systemic therapy improves disease control and survival among patients with oligometastatic disease, even for histologies with a high propensity for rapid spread. Here, we review the growing literature supporting the oligometastatic paradigm in pancreatic ductal adenocarcinoma. We summarize key details from nascent institutional series and reflect on the recently reported phase II randomized EXTEND trial. We discuss various strategies for enhancing the clinical and technical implementation of metastasis-directed therapy in this patient population. Lastly, we highlight multiple ongoing landmark trials seeking to optimize and validate the role of metastasis-directed therapy in oligometastatic pancreatic cancer. Ultimately, these and other continued clinical and translational research efforts will be critical to improve care and outcomes for patients with oligometastatic pancreatic ductal adenocarcinoma.

Keywords:  Metastasis-directed therapy; Oligometastatic pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.1007/s12029-024-01145-0
Cancer Metastasis Rev. 2025 Jan 20. 44(1): 25

Sympathetic nerve signaling rewires the tumor microenvironment: a shift in "microenvironmental-ity".

Ariana Sattler, Tetiana Korzun, Kasmira Gupta, Parham Diba, Natasha Kyprianou, Sebnem Ece Eksi.

  Nerve signaling within the tumor microenvironment (TME) plays a critical role in the initiation, progression, and metastasis of solid tumors. Due to their highly responsive behavior and activation upon injury and cancer onset, this review specifically focuses on how sympathetic nerves rewire the TME. Within tumors, sympathetic nerves closely interact with various TME components, and their combined signaling often shifts tumor-intrinsic physiology toward tumor-supportive phenotypes. In turn, the TME components, such as myeloid cells, lymphoid cells, extracellular matrix (ECM), endothelial cells, cancer associated fibroblasts (CAFs), and Schwann cells, secrete neurotrophic and axon guidance factors that influence both sympathetic outgrowth and tumor cell behavior, further exacerbating tumor progression and metastasis. Here, we review the current evidence on the multidirectional impacts of sympathetic nerves and both immune and non-immune TME components, the nature of these communication processes, and how exploring these interactions may inform future therapeutics to impair cancer progression and metastasis.

Keywords:  Cancer neuroscience; Neuro-immune axis; Sympathetic signaling; Tumor microenvironment

DOI:  https://doi.org/10.1007/s10555-025-10241-x
Mol Cell. 2025 Jan 16. pii: S1097-2765(24)01039-6. [Epub ahead of print]85(2): 290-308

Molecular determinants of condensate composition.

Alex S Holehouse, Simon Alberti.

  Cells use membraneless compartments to organize their interiors, and recent research has begun to uncover the molecular principles underlying their assembly. Here, we explore how site-specific and chemically specific interactions shape the properties and functions of condensates. Site-specific recruitment involves precise interactions at specific sites driven by partially or fully structured interfaces. In contrast, chemically specific recruitment is driven by complementary chemical interactions without the requirement for a persistent bound-state structure. We propose that site-specific and chemically specific interactions work together to determine the composition of condensates, facilitate biochemical reactions, and regulate enzymatic activities linked to metabolism, signaling, and gene expression. Characterizing the composition of condensates requires novel experimental and computational tools to identify and manipulate the molecular determinants guiding condensate recruitment. Advancing this research will deepen our understanding of how condensates regulate cellular functions, providing valuable insights into cellular physiology and organization.

Keywords:  binding; biomolecular condensates; cellular organization; chemical specificity; disordered protein regions; phase separation; specificity

DOI:  https://doi.org/10.1016/j.molcel.2024.12.021
Nat Methods. 2025 Jan 20.

Capture of membrane proteins in their native membrane milieu.

DOI: https://doi.org/10.1038/s41592-024-02518-w
Cell Rep. 2025 Jan 18. pii: S2211-1247(24)01576-6. [Epub ahead of print]44(2): 115225

Chronic intermittent fasting impairs β cell maturation and function in adolescent mice.

Leonardo Matta, Peter Weber, Suheda Erener, Alina Walth-Hummel, Daniela Hass, Lea K Bühler, Katarina Klepac, Julia Szendroedi, Joel Guerra, Maria Rohm, Michael Sterr, Heiko Lickert, Alexander Bartelt, Stephan Herzig.

  Intermittent fasting (IF) is a nutritional lifestyle intervention with broad metabolic benefits, but whether the impact of IF depends on the individual's age is unclear. Here, we investigated the effects of IF on systemic metabolism and β cell function in old, middle-aged, and young mice. Short-term IF improves glucose homeostasis across all age groups without altering islet function and morphology. In contrast, while chronic IF is beneficial for adult mice, it results in impaired β cell function in the young. Using single-cell RNA sequencing (scRNA-seq), we delineate that the β cell maturation and function scores are reduced in young mice. In human islets, a similar pattern is observed in type 1 (T1D), but not type 2 (T2D), diabetes, suggesting that the impact of chronic IF in adolescence is linked to the development of β cell dysfunction. Our study suggests considering the duration of IF in younger persons, as it may worsen rather than reduce diabetes outcomes.

Keywords:  CP: Metabolism; Langerhans’ islets; diabetes; glucose metabolism; insulin; intermittent fasting; pancreas; weight loss; β cells

DOI:  https://doi.org/10.1016/j.celrep.2024.115225
J Phys Chem B. 2025 Jan 23.

Free Energy, Rates, and Mechanism of Transmembrane Dimerization in Lipid Bilayers from Dynamically Unbiased Molecular Dynamics Simulations.

Emil Jackel, Gianmarco Lazzeri, Roberto Covino.

The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics simulations do not cover the time scales required to sample the typical transmembrane assembly. Hence, most studies rely on enhanced sampling schemes that steer the dynamics of transmembrane proteins along a collective variable that should encode all slow degrees of freedom. However, given the complexity of the condensed-phase lipid environment, this is far from trivial, with the consequence that free energy profiles of dimerization can be poorly converged. Here, we introduce an alternative approach, which relies only on simulating short, dynamically unbiased paths, avoiding using collective variables or biasing forces. By merging all paths, we obtain free energy profiles, rates, and mechanisms of transmembrane dimerization with the same set of simulations. We showcase our algorithm by sampling the spontaneous association and dissociation of a transmembrane protein in a lipid bilayer, the popular coarse-grained Martini force field. Our algorithm represents a promising way to investigate assembly processes in biologically relevant membranes, overcoming some of the challenges of conventional methods.

DOI: https://doi.org/10.1021/acs.jpcb.4c05242
Nat Commun. 2025 Jan 20. 16(1): 867

Palmitoylation-dependent regulation of GPX4 suppresses ferroptosis.

Bin Huang, Hui Wang, Shuo Liu, Meng Hao, Dan Luo, Yi Zhou, Ying Huang, Yong Nian, Lei Zhang, Bo Chu, Chengqian Yin.

S-palmitoylation is a reversible and widespread post-translational modification, but its role in the regulation of ferroptosis has been poorly understood. Here, we elucidate that GPX4, an essential regulator of ferroptosis, is reversibly palmitoylated on cysteine 66. The acyltransferase ZDHHC20 palmitoylates GPX4 and increases its protein stability. ZDHHC20 depletion or inhibition of protein palmitoylation by 2-BP sensitizes cancer cells to ferroptosis. Moreover, we identify APT2 as the depalmitoylase of GPX4. Genetic silencing or pharmacological inhibition of APT2 with ML349 increases GPX4 palmitoylation, thereby stabilizing the protein and conferring resistance to ferroptosis. Notably, disrupting GPX4 palmitoylation markedly potentiates ferroptosis in xenografted and orthotopically implanted tumor models, and inhibits tumor metastasis through blood vessels. In the chemically induced colorectal cancer model, knockout of APT2 significantly aggravates cancer progression. Furthermore, pharmacologically modulating GPX4 palmitoylation impacts liver ischemia-reperfusion injury. Overall, our findings uncover the intricate network regulating GPX4 palmitoylation, highlighting its pivotal role in modulating ferroptosis sensitivity.

DOI: https://doi.org/10.1038/s41467-025-56344-5
Sci Signal. 2025 Jan 21. 18(870): eadv9441

Bypassing senescence.

Annalisa M VanHook.

A metabolic switch enables hepatocytes in damaged livers to escape senescence and form tumors.

DOI: https://doi.org/10.1126/scisignal.adv9441
Trends Endocrinol Metab. 2025 Jan 18. pii: S1043-2760(24)00330-8. [Epub ahead of print]

Lineage tracing of pancreatic cells for mechanistic and therapeutic insights.

Huan Zhao, Bin Zhou.

  Recent advances in lineage-tracing technologies have significantly improved our understanding of pancreatic cell biology, particularly in elucidating the ontogeny and regenerative capacity of pancreatic cells. A deeper appreciation of the mechanisms underlying pancreatic cell identity and plasticity holds the potential to inform the development of new therapeutic modalities for conditions such as diabetes and pancreatitis. With this goal in mind, here we summarize advances, challenges, and future directions in tracing pancreatic cell origins and fates using lineage-tracing technologies. Given their essential role for blood glucose regulation, we pay particular attention on the insights gained from endocrine cells, especially β-cells.

Keywords:  lineage tracing; pancreatic cell; regeneration; β cell

DOI:  https://doi.org/10.1016/j.tem.2024.12.008
Methods Cell Biol. 2025 ;pii: S0091-679X(24)00222-X. [Epub ahead of print]191 221-246

Single-cell RNA flow cytometry to assess intratumoral production of cytokines/chemokines.

Khiem C Lam, Romina S Goldszmid.

  The tumor microenvironment (TME) consists of complex interactions between cellular and extracellular components, among which the immune system is known to play an integral role in disease progression and response to therapy. Cytokines and chemokines are cell signaling proteins used by immune cells to communicate with each other as well as with other cell types in the body. These proteins control systemic and local immune responses and levels of cytokines/chemokines in the TME have been associated with tumor outcomes. However, cytokines and chemokines have varied expression across cell types, tumors, and host conditions. Therefore, approaches to effectively study the production of these proteins at the single-cell level in the TME are needed to fully elucidate the mechanisms governing the anti-cancer immune response. Here, we detail a protocol to assess the production of cytokines/chemokines across leukocyte populations in mouse tumors using RNA flow cytometry. Importantly, this method can be adapted with minimal changes to study various mouse and human tumors, other RNA analytes, and non-tumor tissues.

Keywords:  Cancer immunology; Cytokines/chemokines; Interferon; RNA flow cytometry; Tumor microenvironment

DOI:  https://doi.org/10.1016/bs.mcb.2024.10.013
Elife. 2024 Dec 30. pii: RP98535. [Epub ahead of print]13

Flamingo participates in multiple models of cell competition.

Pablo Sanchez Bosch, Bomsoo Cho, Jeffrey D Axelrod.

  The growth and survival of cells with different fitness, such as those with a proliferative advantage or a deleterious mutation, is controlled through cell competition. During development, cell competition enables healthy cells to eliminate less fit cells that could jeopardize tissue integrity, and facilitates the elimination of pre-malignant cells by healthy cells as a surveillance mechanism to prevent oncogenesis. Malignant cells also benefit from cell competition to promote their expansion. Despite its ubiquitous presence, the mechanisms governing cell competition, particularly those common to developmental competition and tumorigenesis, are poorly understood. Here, we show that in Drosophila, the planar cell polarity (PCP) protein Flamingo (Fmi) is required by winners to maintain their status during cell competition in malignant tumors to overtake healthy tissue, in early pre-malignant cells when they overproliferate among wildtype cells, in healthy cells when they later eliminate pre-malignant cells, and by supercompetitors as they compete to occupy excessive territory within wildtype tissues. 'Would-be' winners that lack Fmi are unable to overproliferate, and instead become losers. We demonstrate that the role of Fmi in cell competition is independent of PCP, and that it uses a distinct mechanism that may more closely resemble one used in other less well-defined functions of Fmi.

Keywords:  D. melanogaster; Flamingo; cell competition; development; developmental biology

DOI:  https://doi.org/10.7554/eLife.98535