bims-cagime 2025-06-15 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2025–06–15
forty-two papers selected by
Kıvanç Görgülü, Technical University of Munich

Pancreatic cancer cachexia is mediated by PTHrP-driven disruption of adipose de novo lipogenesis.
Glycosaminoglycan-driven lipoprotein uptake protects tumours from ferroptosis.
Three-dimensional assessments are necessary to determine the true, spatially resolved composition of tissues.
Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis.
Emerin is an effector of oncogenic KRAS-driven nuclear dynamics in pancreatic cancer.
Leveraging autophagy and pyrimidine metabolism to target pancreatic cancer.
NINJ1 regulates plasma membrane fragility under mechanical strain.
Statin-dye conjugates for selective targeting of KRAS mutant cancer cells.
Dietary lipids, not ketone body metabolites, influence intestinal tumorigenesis in a ketogenic diet.
RalGAP complexes control secretion and primary cilia in pancreatic disease.
Cell death: Dynamics and compartmentalization of NADH and FSP1 in ferroptosis.
Targeting cancer cell stiffness and metastasis with clinical therapeutics.
Laurdan Adopts Distinct, Phase-Specific Orientations in Lipid Membranes.
Tirzepatide differentially affects body weight in mice and humans.
Probing Field Cancerization in the Gastrointestinal Tract Using a Hybrid Raman and Partial Wave Spectroscopy Microscope.
Metabolic adaptations direct cell fate during tissue regeneration.
Mast cells modulate macrophage biology through release of pre-stored CSF1.
Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing.
An adaptive organelle triad houses lipid droplets for dynamic regulation.
Disabling PSGL-1 abrogates immune suppression and resistance to PD-1 blockade in pancreatic cancer.
The lysosomal membrane protein LAMP2B mediates microlipophagy to target obesity-related disorders.
Super-Resolution FLIM Imaging of Intracellular Lipid Microenvironments with a Dual-Responsive Polarity- and pH-Sensitive Fluorescent Probe.
When essential metal elements become culprits-Cuproptosis in focus.
Conformational Dynamics and Activation of Membrane-Associated Human Group IVA Cytosolic Phospholipase A2 (cPLA2).
CDADC1 is a vertebrate-specific dCTP deaminase that metabolizes gemcitabine and decitabine to prevent cellular toxicity.
Clinical utility and tissue concordance of circulating tumor DNA in pancreatic ductal adenocarcinoma.
Promising preclinical approaches to combating cancer-associated cachexia/tissue wasting.
Targeting GRPR for sex hormone-dependent cancer after loss of E-cadherin.
GCLM lactylation mediated by ACAT2 promotes ferroptosis resistance in KRASG12D-mutant cancer.
Reproducible Sectioning and Sample Preparation for Mass Spectrometry Imaging of Cancer Metabolism in Frozen Lung Tissue.
Tumorous cholesterol biosynthesis curtails anti-tumor immunity by preventing MTOR-TFEB-mediated lysosomal degradation of CD274/PD-L1.
Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization.
Unconventional role of ATG16L1 in the control of ATP compartmentalization during apoptosis.
Epithelial-to-mesenchymal transition (EMT) and cancer metastasis: the status quo of methods and experimental models 2025.
Aging reduces the number and function of L-type calcium channels in the membrane of cardiac pacemaker cells.
Ligand-specific regulation of a binary enhancer code dictating cellular senescence.
The NAMPT enzyme employs a switch that directly senses AMP/ATP and regulates cellular responses to energy stress.
Robust statistical assessment of Oncogenotype to Organotropism translation in xenografted zebrafish.
CellNEST reveals cell-cell relay networks using attention mechanisms on spatial transcriptomics.
Aging on Chip: Harnessing the Potential of Microfluidic Technologies in Aging and Rejuvenation Research.
cGAS-STING are responsible for premature aging of telomerase-deficient zebrafish.
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression.

bioRxiv. 2025 Jun 07. pii: 2025.06.03.657464. [Epub ahead of print]

Pancreatic cancer cachexia is mediated by PTHrP-driven disruption of adipose de novo lipogenesis.

Nikita Bhalerao, Yamini Ogoti, Jessica Peura, Calvin Johnson, Qingbo Chen, Ekaterina D Korobkina, Faith N Keller, Maximilian Wengyn, Robert J Norgard, Claire Shamber, Kelsey Klute, Dominick DiMaio, Karine Sellin, Paul M Grandgenett, Rui Li, Michael A Hollingsworth, Adilson Guilherme, Michael P Czech, Richard Kremer, Lihua Julie Zhu, Emma V Watson, Marcus Ruscetti, David A Guertin, Jason R Pitarresi.

Pancreatic cancer patients have the highest rates and most severe forms of cancer cachexia, yet cachexia etiologies remain largely elusive, leading to a lack of effective intervening therapies. PTHrP has been clinically implicated as a putative regulator of cachexia, with serum PTHrP levels correlating with increased weight loss in PDAC patients. Here we show that cachectic PDAC patients have high expression of tumor PTHrP and use a genetically engineered mouse model to functionally demonstrate that deletion of Pthlh (encoding the PTHrP protein) blocks cachectic wasting, dramatically extending overall survival. The re-expression of PTHrP in lowly cachectic models is sufficient to induce wasting and reduce survival in mice, which is reversed by the conditional deletion of the PTHrP receptor, Pth1r , in adipocytes. Mechanistically, tumor-derived PTHrP suppresses de novo lipogenesis in adipocytes, leading to a molecular rewiring of adipose depots to promote wasting in the cachectic state. Finally, the pharmacological disruption of the PTHrP-PTH1R signaling axis abrogates wasting, highlighting that a targeted disruption of tumor-adipose crosstalk is an effective means to limit cachexia.
STATEMENT OF SIGNIFICANCE: Pancreatic ductal adenocarcinoma (PDAC) is the prototypical cancer type associated with cancer cachexia, a debilitating wasting syndrome marked by adipose tissue loss and muscle atrophy. Herein, we establish that PTHrP is a tumor-derived factor that facilitates cachexia by downregulating de novo lipogenesis in adipocytes and that blocking PTHrP is an effective means to limit wasting in preclinical mouse models.

DOI: https://doi.org/10.1101/2025.06.03.657464
Nature. 2025 Jun 11.

Glycosaminoglycan-driven lipoprotein uptake protects tumours from ferroptosis.

Dylan Calhoon, Lingjie Sang, Fubo Ji, Divya Bezwada, Sheng-Chieh Hsu, Feng Cai, Nathaniel Kim, Amrita Basu, Renfei Wu, Anastasia Pimentel, Bailey Brooks, Konnor La, Ana Paulina Serrano, Daniel L Cassidy, Ling Cai, Vanina Toffessi-Tcheuyap, Maryam E Moussa, Winnie Uritboonthai, Linh Truc Hoang, Meghana Kolli, Brooklyn Jackson, Vitaly Margulis, Gary Siuzdak, James Brugarolas, Ian Corbin, Derek A Pratt, Ryan J Weiss, Ralph J DeBerardinis, Kıvanç Birsoy, Javier Garcia-Bermudez.

Lipids are essential components of cancer cells due to their structural and signalling roles1. To meet metabolic demands, many cancers take up extracellular lipids2-5; however, how these lipids contribute to cancer growth and progression remains poorly understood. Here, using functional genetic screens, we identify uptake of lipoproteins-the primary mechanism for lipid transport in circulation-as a key determinant of ferroptosis sensitivity in cancer. Lipoprotein supplementation robustly inhibits ferroptosis across diverse cancer types, primarily through the delivery of α-tocopherol (α-toc), the most abundant form of vitamin E in human lipoproteins. Mechanistically, cancer cells take up lipoproteins through a pathway dependent on sulfated glycosaminoglycans (GAGs) linked to cell-surface proteoglycans. Disrupting GAG biosynthesis or acutely degrading surface GAGs reduces lipoprotein uptake, sensitizes cancer cells to ferroptosis and impairs tumour growth in mice. Notably, human clear cell renal cell carcinomas-a lipid-rich malignancy-exhibit elevated levels of chondroitin sulfate and increased lipoprotein-derived α-toc compared with normal kidney tissue. Together, our study establishes lipoprotein uptake as a critical anti-ferroptotic mechanism in cancer and implicates GAG biosynthesis as a therapeutic target.

DOI: https://doi.org/10.1038/s41586-025-09162-0
Cell Rep Methods. 2025 Jun 02. pii: S2667-2375(25)00111-0. [Epub ahead of print] 101075

Three-dimensional assessments are necessary to determine the true, spatially resolved composition of tissues.

André Forjaz, Eduarda Vaz, Valentina Matos Romero, Saurabh Joshi, Vasco Queiroga, Alicia M Braxton, Ann C Jiang, Kohei Fujikura, Toby Cornish, Seung-Mo Hong, Ralph H Hruban, Pei-Hsun Wu, Laura D Wood, Ashley L Kiemen, Denis Wirtz.

  Methods for spatially resolved cellular profiling of tissue sections enable in-depth study of inter- and intra-sample heterogeneity but often profile small regions, requiring evaluation of many samples to compensate for limited assessment. Recent advances in three-dimensional (3D) tissue mapping offer deeper insights; however, attempts to quantify the information gained in transitioning to 3D remains limited. Here, to compare inter- and intra-sample tissue heterogeneity, we analyze >100 pancreas samples as cores, whole-slide images (WSIs), and cm3-sized 3D samples. We show that tens of WSIs and hundreds of tissue microarrays are needed to approximate the compositional tissue heterogeneity of tumors. Additionally, spatial correlations of pancreatic structures decay significantly within microns, demonstrating that isolated two-dimensional (2D) sections poorly represent their surroundings. Through 3D simulations, we determined the number of slides necessary to accurately measure tumor burden. These results quantify the power of 3D mapping and establish sampling methods for biological studies prioritizing composition or incidence.

Keywords:  3D digital pathology; 3D modeling; CP: imaging; PDAC; pancreatic cancer; tissue composition; tissue heterogeneity; tissue sampling; tumor heterogeneity; tumor microenvironment

DOI:  https://doi.org/10.1016/j.crmeth.2025.101075
bioRxiv. 2025 Jun 01. pii: 2025.05.28.656689. [Epub ahead of print]

Molecular dynamics driving phenotypic divergence among KRAS mutants in pancreatic tumorigenesis.

Adrien Grimont, David J Falvo, Whitney J Sisso, Paul Zumbo, Christopher W Chan, Francisco Santos, Grace Pan, Megan Cleveland, Tomer M Yaron, Alexa Osterhoudt, Yinuo Meng, Maria Paz Zafra, William B Fall, Andre F Rendeiro, Erika Hissong, Rhonda K Yantiss, Doron Betel, Mark A Magnuson, Steven D Leach, Anil K Rustgi, Lukas E Dow, Rohit Chandwani.

Inflammation in the pancreas drives acinar-to-ductal metaplasia (ADM), a progenitor-like state that can be hijacked by mutant Kras in the formation of pancreatic cancer (PDAC). How these cell fate decisions vary according to KRAS mutation remains poorly understood. To define mutation-specific lineage reversion and tumor initiation, we implement novel Ptf1a-TdTomato mice and multiple KRAS mutants across an array of genetic, pharmacologic, and inflammatory perturbations in vivo . Whereas KRAS G12D co-opts injury to enable lineage reversion, enhancer reprogramming, and tumor initiation, KRAS G12R/V can initiate but not sustain dedifferentiated and neoplastic transcriptional and epigenetic programs. We find the KRAS G12R/V defects consist of a failure to invoke robust EGFR signaling and activate Rac1/Vav1, with constitutive Akt activation in vivo sufficient to rescue the tumorigenic potential of KRAS G12R . As the marked heterogeneity among KRAS variants begins early in tumorigenesis, these data are crucial to understanding mutation-specific oncogenic trajectories and directing the implementation of KRAS -directed therapeutics.
SIGNIFICANCE: Defining how KRAS mutants drive distinct outcomes in human pancreatic cancer is critical for developing allele-specific therapeutic approaches. This study unveils a hierarchy among KRAS G12D , KRAS G12V , and KRAS G12R to drive tumor initiation, owing to heterogeneous activation of EGFR, PI3K/AKT, and RAC1 signaling, thus revealing mutation-specific evolutionary paths in pancreatic tumorigenesis.

DOI: https://doi.org/10.1101/2025.05.28.656689
JCI Insight. 2025 Jun 10. pii: e187799. [Epub ahead of print]

Emerin is an effector of oncogenic KRAS-driven nuclear dynamics in pancreatic cancer.

Luis F Flores, David L Marks, Renzo E Vera, Ashley N Sigafoos, Ezequiel J Tolosa, Luciana L Almada, David R Pease, Merih D Toruner, Brian Chang, Brooke R Tader, Kayla C LaRue-Nolan, Ryan M Carr, Rondell P Graham, Catherine E Hagen, Matthew R Brown, Aleksey V Matveyenko, Katherine L Wilson, David W Dawson, Christopher L Pin, Kyle J Roux, Martin E Fernandez-Zapico.

  For over a century, scientists reported the disruption of normal nuclear shape and size in cancer. These changes have long been used as tools for diagnosis and staging of malignancies. However, to date, the mechanisms underlying these aberrant nuclear phenotypes and their biological significance remain poorly understood. Using a model of pancreatic ductal adenocarcinoma (PDAC), the major histological subtypes of pancreatic cancer, we found oncogenic mutant KRAS reduces nuclear size. Transcriptomic and protein expression analysis of mutant KRAS-expressing PDAC cells revealed differential levels of several nuclear envelope-associated genes. Further analysis demonstrated the nuclear lamina protein, Emerin (EMD), acted downstream of KRAS to mediate nuclear size reduction in PDAC. Analysis of human PDAC samples showed that increased EMD expression associates with reduced nuclear size. Finally, in vivo genetic depletion of EMD in a mutant KRAS-driven PDAC model resulted in an increased nuclear size and a reduced incidence of poorly differentiated PDAC. Thus, our data provides evidence of a novel mechanism underlying nuclear size regulation and its impact in PDAC carcinogenesis.

Keywords:  Cancer; Cell biology; Oncology

DOI:  https://doi.org/10.1172/jci.insight.187799
bioRxiv. 2025 Jun 05. pii: 2025.05.29.656904. [Epub ahead of print]

Leveraging autophagy and pyrimidine metabolism to target pancreatic cancer.

Suzanne Dufresne, Ramya S Kuna, Kristiana Wong, Anvita Komarla, Angelica Rock, Joel Rosada-Encarnación, Celina Shen, Payel Mondal, Louis R Parham, Fabiana Izidro Layng, Kristina L Peck, Alexandra Fowler, Andrew M Lowy, Dannielle Engle, Herve Tiriac, Reuben Shaw, Nicholas Cosford, Christian Metallo, Christina Towers.

Autophagy inhibitors are promising compounds to treat pancreatic ductal adenocarcinoma (PDA) but their efficacy in patients is unclear, highlighting a need to understand mechanisms of resistance. We used a novel approach to uncover metabolic adaptations that bypass autophagy inhibition. Utilizing PDA cells with acquired resistance to different autophagy inhibitors, we found that severe autophagy depletion induces metabolic rewiring to sustain TCA intermediates and nucleotides for biosynthesis. Long-term autophagy inhibition results in altered pyruvate metabolism likely regulated by lower pyrimidine pools. Cells adapting to loss of autophagy preferentially salvage pyrimidines to replenish these pools instead of synthesizing them de novo. Exploiting this metabolic vulnerability, we found that acquired resistance to autophagy inhibition promotes increased salvage and therefore sensitivity to pyrimidine analogues, including gemcitabine and trifluridine/tipiracil leading to combinatory effects with autophagy inhibitors and pyrimidine analogs. These studies provide mechanistic insight defining how autophagy inhibition can be leveraged to treat pancreatic cancer.

DOI: https://doi.org/10.1101/2025.05.29.656904
Nature. 2025 Jun 09.

NINJ1 regulates plasma membrane fragility under mechanical strain.

Yunfeng Zhu, Fang Xiao, Yiling Wang, Yufang Wang, Jialin Li, Dongmei Zhong, Zhilei Huang, Miao Yu, Zhirong Wang, Joshua Barbara, Christopher Plunkett, Mengxue Zeng, Yiyan Song, Tian Tan, Ruibin Zhang, Kezhen Xu, Zhongxing Wang, Changjie Cai, Xiangdong Guan, Scott Hammack, Liang Zhang, Zheng Shi, Fu-Li Xiang, Feng Shao, Jie Xu.

Plasma membrane integrity is vital for nearly all aspects of cell functioning1. Mechanical forces can cause plasma membrane damage2, but it is not known whether there are large molecules that regulate plasma membrane integrity under mechanical strain. Here we constructed a 384-well cellular stretch system that delivers precise, reproducible strain to cultured cells. Using the system, we screened 10,843 siRNAs targeting 2,726 multi-pass transmembrane proteins for strain-induced membrane permeability changes. The screen identified NINJ1, a protein recently proposed to regulate pyroptosis and other lytic cell death3,4, as the top hit. We demonstrate that NINJ1 is a critical regulator for mechanical strain-induced plasma membrane rupture (PMR), without the need of stimulating any cell death programs. NINJ1 level on the plasma membrane is inversely correlated to the amount of force required to rupture the membrane. In the pyroptosis context, NINJ1 on its own is not sufficient to fully rupture the membrane, and additional mechanical force is required for full PMR. Our work establishes that NINJ1 functions as a bona fide determinant of membrane biomechanical properties. Our study also suggests that PMR across tissues of distinct mechanical microenvironments is subjected to fine tuning by differences in NINJ1 expression and external forces.

DOI: https://doi.org/10.1038/s41586-025-09222-5
bioRxiv. 2025 Jun 06. pii: 2025.06.03.657329. [Epub ahead of print]

Statin-dye conjugates for selective targeting of KRAS mutant cancer cells.

Hye-Ran Moon, Zhenying Cai, Bo Kyung Cho, Hyeyoun Chang, Seung Taek Hong, Jean J Zhao, Ick Chan Kwon, Thomas M Roberts, Bumsoo Han, Ju Hee Ryu.

Over 90% of pancreatic ductal adenocarcinoma (PDAC) patients involve KRAS mutations ( KRAS MUT ), for which current treatment options are limited. Statins, commonly used to lower cholesterol, have demonstrated certain selective toxicity towards KRAS -transformed cells, prompting the question of whether statins could achieve selective uptake specifically in KRAS MUT cells. To investigate this, we synthesized statin-dye conjugates by attaching a fluorescent dye (Cy5.5) to two statins: simvastatin and pravastatin, aiming to assess whether selective uptake indeed occurs. Our findings revealed that these conjugates exhibited markedly enhanced uptake in KRAS MUT cells compared to KRAS wild-type ( KRAS WT ) cells. Given the magnitude of the selective uptake, we realized that the uptake of these conjugates itself is of considerable intrinsic interests. We evaluated the uptake of these conjugates in both KRAS MUT and KRAS WT cells and examined their potential to selectively target KRAS MUT pancreatic cancer cells (PCCs) using an engineered PDAC tumor model co-cultured with PCCs and cancer-associated fibroblasts (CAFs). Our findings indicate that KRAS MUT cancer cells exhibited higher uptake of statin-Cy5.5 conjugates via enhanced macropinocytosis compared to KRAS WT cancer cells and CAFs. We also found enhanced uptake of the statin-Cy5.5 conjugate in MCF10A cells with PTEN deficiency, a condition known to elevate macropinocytosis, compared to control MCF10A cells with wild-type PTEN . Notably, in the PCC and CAF co-culture model, the pravastatin-Cy5.5 conjugate selectively killed KRAS MUT PCCs without affecting the KRAS WT CAFs. These findings highlight the potential of stain-drug conjugates as targeted delivery vehicles for KRAS MUT cancer therapy.

DOI: https://doi.org/10.1101/2025.06.03.657329
bioRxiv. 2025 Jun 07. pii: 2025.06.06.658169. [Epub ahead of print]

Dietary lipids, not ketone body metabolites, influence intestinal tumorigenesis in a ketogenic diet.

Jessica E S Shay, Fangtao Chi, Constantine N Tzouanas, Johanna Ten Hoeve, Kevin J Williams, Tolga Sever, Isabela Fuentes, Ömer H Yilmaz.

Diet composition shapes tissue function and disease risk by modulating nutrient availability, metabolic state, and cellular dynamics. In the gastrointestinal tract, obesogenic high-fat diets enhance intestinal stem cell activity and tumorigenesis. However, the impact of ketogenic diets (KD), which contain even higher lipid content but induce ketogenesis, remains poorly understood. This is particularly relevant for patients with familial adenomatous polyposis (FAP), who face a high risk of small intestinal tumours. Here, we combine dietary, genetic, and metabolic manipulations in mouse models of spontaneous intestinal adenoma formation to dissect the role of systemic and epithelial ketogenesis in intestinal cancer. We show that KD accelerates tumour burden and shortens survival, independent of ketone body production. Through genetic manipulation of the ketogenic pathway, we modulate local and systemic ketone body production; however, neither inhibition nor augmentation of the ketogenic enzyme HMGCS2 nor disruption of ketolysis altered tumour progression. In contrast, inhibition of fatty acid oxidation did limit adenomatous formation. These findings reveal that dietary lipid content, through FAO rather than ketone body metabolism, influences intestinal tumorigenesis and highlight the need for nuanced consideration of dietary strategies for cancer prevention in genetically susceptible populations.

DOI: https://doi.org/10.1101/2025.06.06.658169
Life Sci Alliance. 2025 Aug;pii: e202403123. [Epub ahead of print]8(8):

RalGAP complexes control secretion and primary cilia in pancreatic disease.

Lisa H Apken, Hannah Barz, Stephanie Beel, Esther Michalke, René Rasche, Archana Verma, Andrea Ricker, Harald Nüsse, Jürgen Klingauf, Kornelius Kerl, Eva Wardelmann, Daniel Kümmel, Konrad Steinestel, Zoltán Pethő, Michael Meisterernst, Andrea Oeckinghaus.

κB-Ras/RalGAP complexes limit the activity of Ral GTPases, which function in EGFR/Ras signaling. RalGAP expression is down-regulated in pancreatic cancer; however, the role of RalGAP and Ral GTPases in tumor development in vivo remained unclear. Here, we show that pancreatic RalGAPβ deficiency alone is sufficient to induce inflammation and neoplasia in vivo. We identify that this phenotype is triggered by disturbance of the secretory pathway and polarized exocytosis in acinar cells, demonstrating that RalGAP complexes uphold spatial control of Ral activity. We furthermore show that RALGAPβ deficiency results in defective primary cilium assembly, a process required for efficient acinar regeneration upon inflammation. Only primary cilium formation depends on κB-Ras proteins, suggesting that κB-Ras proteins are not essential for all RalGAP complex-controlled processes. In combination with an oncogenic KRAS G12D mutation, RalGAPβ deficiency leads to a dramatic shortening of tumor latency and median survival. Our results highlight an important role of RalGAP/Ral signaling in upholding acinar cell identity and preventing pancreatic cancer development.

DOI: https://doi.org/10.26508/lsa.202403123
Curr Biol. 2025 Jun 09. pii: S0960-9822(25)00441-5. [Epub ahead of print]35(11): R406-R409

Cell death: Dynamics and compartmentalization of NADH and FSP1 in ferroptosis.

Amalia H Megarioti, Kirandeep K Deol, James A Olzmann.

A new study identifies the aldehyde dehydrogenase ALDH7A1 as a key regulator of ferroptosis. ALDH7A1 generates a pool of membrane-associated NADH, which is used by ferroptosis suppressor protein 1 to recycle the lipid antioxidant coenzyme Q10 and suppress ferroptosis.

DOI: https://doi.org/10.1016/j.cub.2025.04.012
Clin Exp Metastasis. 2025 Jun 11. 42(4): 34

Targeting cancer cell stiffness and metastasis with clinical therapeutics.

Alexa M Gajda, Raymundo Rodríguez-López, Ekrem Emrah Er.

  Tumorigenesis and metastasis of solid tumors are coupled to profound biophysical changes that alter cancer cells' mechanobiology, critically impacting metastatic progression. In particular, cell stiffness determines the ability of cancer cells to invade surrounding tissues, withstand shear fluid stress and evade immune surveillance. Here, we summarize the biological factors, pathological factors, and therapeutic modalities that affect the mechanobiology of cancer cells. We focus on clinically utilized chemotherapeutics and targeted therapies that show direct and indirect modulation of cancer cells' stiffness and discuss how these treatments can be used in combination with other treatment modalities to improve patient outcomes. Finally, we list the outstanding challenges in the field and provide a perspective on expanding the clinical utilization of experimental therapeutics that can act as "mechanotherapeutics" by regulating mechanobiology of cancer cells.

Keywords:  Cell stiffness; Compliance; Mechanobiology; Mechanotherapeutics; Metastasis; Tumor microenvironment

DOI:  https://doi.org/10.1007/s10585-025-10353-2
J Phys Chem B. 2025 Jun 10.

Laurdan Adopts Distinct, Phase-Specific Orientations in Lipid Membranes.

Agnieszka Lester, Hanna Orlikowska-Rzeznik, Emilia Krok, Lukasz Piatkowski.

For over 40 years, Laurdan has been widely used as a universal fluorescent probe for the study of lipid membranes. However, recent molecular dynamics simulations have uncovered previously unknown properties of Laurdan, revealing that it can adopt distinct conformations within the lipid bilayer, thereby influencing its molecular orientation. Despite these findings, experimental and quantitative validation has been lacking. Here, we present the first experimental study of the orientation of Laurdan in a phase-separated supported lipid bilayer, directly linking its spatial orientation to its emission spectra in liquid-ordered (Lo) and liquid-disordered (Ld) phases. Using azimuthally and radially polarized excitation beams, we show that in the Lo phase, Laurdan molecules align more parallel to the membrane normal, whereas in the Ld phase, they adopt a more planar orientation within the membrane. Interestingly, the emission spectra for both excitation modes converge at shorter wavelengths, but show deviations at longer wavelengths, particularly in the Ld phase. By refining our understanding of the behavior of Laurdan in lipid membranes, this study underlines the critical role of the molecular orientation of the dye in fluorescence-based membrane studies and highlights the need for orientation-sensitive analysis in biophysical investigations.

DOI: https://doi.org/10.1021/acs.jpcb.5c02384
Nat Rev Endocrinol. 2025 Jun 09.

Tirzepatide differentially affects body weight in mice and humans.

Aaron Novikoff, Timo D Müller.

DOI: https://doi.org/10.1038/s41574-025-01139-3
Anal Chem. 2025 Jun 11.

Probing Field Cancerization in the Gastrointestinal Tract Using a Hybrid Raman and Partial Wave Spectroscopy Microscope.

Elena Kriukova, Mikhail Mazurenka, Sabrina Marcazzan, Markus Tschurtschenthaler, Gerwin Puppels, Sarah Glasl, Dieter Saur, Moritz Jesinghaus, Marialena Pouliou, Marios Agelopoulos, Apostolos Klinakis, Michael Quante, Jorge Ripoll, Vasilis Ntziachristos, Dimitris Gorpas.

Field cancerization (FC) refers to spatially distributed premalignant tissue changes that lead to the appearance of local malignancy, and its detection can improve cancer screening. In this work, we employ combined Raman and partial wave spectroscopy (RS-PWS) to detect FC in gastroesophageal (L2-IL1B) and intestinal (Villin-Cre, Apcfl/wt) tumor mouse models. Using a hybrid RS-PWS microscope, we acquire both molecular and morphological information from macroscopically normal tumor-adjacent tissue and investigate the individual and combined performance of each modality. For data analysis, we use partial least-squares discriminant analysis (PLS-DA). In the normal tissue of L2-IL1B mice, we demonstrate a statistically significant increase (p < 0.001) in Raman band intensities associated with free amino acids and a decrease in bands associated with lipids (p < 0.005) and carotenoids (p < 0.001) compared to healthy controls. Similarly, in the normal mucosa of Villin-Cre, Apcfl/wt mice, the intensities of RS bands associated with amino acids increase significantly (p < 0.05) compared to controls, while the intensities of lipid-associated bands decrease significantly (p < 0.05). Transcriptomic profiling using RNA-sequencing analysis on these samples identified a significant correlation between gene expression and optical findings. Moreover, we demonstrate that combining RS and PWS data further improves the significance of our classification results. When macroscopically normal tumor-adjacent tissue is compared with tissue from healthy controls, we observe that PWS increases the R2 of RS results by ∼9% in L2-IL1B mice and ∼5% in Villin-Cre, Apcfl/wt mice. Combining molecular RS with structural PWS information enhances the ability to detect precancerous changes and provides insights into tissue alterations during cancer development.

DOI: https://doi.org/10.1021/acs.analchem.5c00954
Nature. 2025 Jun 11.

Metabolic adaptations direct cell fate during tissue regeneration.

Almudena Chaves-Perez, Scott E Millman, Sudha Janaki-Raman, Yu-Jui Ho, Clemens Hinterleitner, Valentin J A Barthet, John P Morris, Francisco M Barriga, Jose Reyes, Aye Kyaw, H Amalia Pasolli, Dana Pe'er, Craig B Thompson, Lydia W S Finley, Justin R Cross, Scott W Lowe.

Although cell-fate specification is generally attributed to transcriptional regulation, emerging data also indicate a role for molecules linked with intermediary metabolism. For example, α-ketoglutarate (αKG), which fuels energy production and biosynthetic pathways in the tricarboxylic acid (TCA) cycle, is also a co-factor for chromatin-modifying enzymes1-3. Nevertheless, whether TCA-cycle metabolites regulate cell fate during tissue homeostasis and regeneration remains unclear. Here we show that TCA-cycle enzymes are expressed in the intestine in a heterogeneous manner, with components of the αKG dehydrogenase complex4-6 upregulated in the absorptive lineage and downregulated in the secretory lineage. Using genetically modified mouse models and organoids, we reveal that 2-oxoglutarate dehydrogenase (OGDH), the enzymatic subunit of the αKG dehydrogenase complex, has a dual, lineage-specific role. In the absorptive lineage, OGDH is upregulated by HNF4 transcription factors to maintain the bioenergetic and biosynthetic needs of enterocytes. In the secretory lineage, OGDH is downregulated through a process that, when modelled, increases the levels of αKG and stimulates the differentiation of secretory cells. Consistent with this, in mouse models of colitis with impaired differentiation and maturation of secretory cells, inhibition of OGDH or supplementation with αKG reversed these impairments and promoted tissue healing. Hence, OGDH dependency is lineage-specific, and its regulation helps to direct cell fate, offering insights for targeted therapies in regenerative medicine.

DOI: https://doi.org/10.1038/s41586-025-09097-6
J Allergy Clin Immunol. 2025 Jun 04. pii: S0091-6749(25)00617-7. [Epub ahead of print]

Mast cells modulate macrophage biology through release of pre-stored CSF1.

Daniel Kovacs, Klaus Heger, Piero Giansanti, Caterina Iuliano, Felix Meissner, Matthias Mann, Jan Böttcher, Ruppert Öllinger, Roland Rad, Freya Tammer, Vanessa Gölling, Theodor Zeng, Ali Masjedi, Tanja Groll Dr Med Vet, Axel Roers, Magda Babina, Maria S Robles, Markus Moser, Susanne Kaesler, Katja Steiger Dr Med Vet, Tilo Biedermann, Marc Schmidt-Supprian.

   BACKGROUND: Mast cells are tissue-resident immune cells present in connective tissues throughout the body. They exert diverse functions in immunity by rapidly releasing a plethora of preformed mediators, including proteoglycans, cytokines, and proteases, which are stored in cytoplasmic granules.
OBJECTIVE: Our aim was to systematically and globally identify mast cell-released protein mediators and elucidate their functions.
METHODS: We analysed the secretomes of antigen-activated primary mouse mast cells using quantitative mass spectrometry-based proteomics and conducted follow-up studies in vitro, ex vivo and using mast cell-specific genetic mouse models.
RESULTS: We identified CSF1 as a novel preformed mast cell mediator present in the granules of all connective tissue-type mast cells. We further show that the mast cell secretome can induce macrophage differentiation and a unique polarisation pattern via CSF1 and other mediators. Mast cell-derived CSF1 has systemic functions, as mast cell-specific CSF1-deficient mice have lower serum CSF1 levels and reduced numbers of circulating monocytes. In addition, using an orthotopic transplantation-based melanoma mouse model, we show that loss of mast cell-derived CSF1 promotes cancer cell expansion. Finally, we demonstrate that CSF1 is also prestored and released by human mast cells.
CONCLUSION: CSF1 is an evolutionarily conserved, constitutive mast cell granule component. Mast cell degranulation induces macrophage differentiation and a unique polarisation state, the former being completely dependent on CSF1, while the latter is only modulated.

Keywords:  CSF1; mast cell; mast cell mediator; melanoma; proteome

DOI:  https://doi.org/10.1016/j.jaci.2025.05.022
ACS Nano. 2025 Jun 09.

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

Yujun Feng, Donglai Chen, Catherine Applegate, Natalia 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 of heterogeneous cell populations. Here, we describe nanocoding, a technology that applies 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 upon cell lysis. In cultured cell lines and heterogeneous cells from tissue digests, nanocoding occurs in 40 min with stability after sample mixing and requires only commercially available reagents without complex chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples from adipose tissue of obese rodents containing lipid-rich debris and heterogeneous cells 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. The ease of generating and tuning these constructs may afford efficient and robust sample multiplexing with minimal crosstalk.

Keywords:  adipose tissue; aging; immune cell; macrophage; multiplexed single-cell RNA sequencing; obesity; t cell

DOI:  https://doi.org/10.1021/acsnano.5c02111
Cell Rep. 2025 Jun 11. pii: S2211-1247(25)00584-4. [Epub ahead of print]44(6): 115813

An adaptive organelle triad houses lipid droplets for dynamic regulation.

Hong Qiu, Can Miao, Cunqi Ye.

  Cell organelles compartmentalize metabolic reactions and require inter-organelle communications to coordinate metabolic activities in fluctuating nutrient environments. While membrane contacts enable this communication by facilitating metabolite exchange, the functional organization of organelles through these contacts remains underexplored. Here, we show that excess lactate induces severe metabolic stress under nutrient deprivation in the budding yeast Saccharomyces cerevisiae, necessitating a rapid life cycle of lipid droplets (LDs) for cellular adaptation. This process uncovers a previously uncharacterized subcellular architecture-an organelle triad-comprising the vacuole, LDs, and the nuclear endoplasmic reticulum (ER). The vacuole undergoes expansion and deformation, enveloping the entire nucleus that is encircled by an orbit of LDs. Formation of this organelle triad depends on the timely and abundant expression of membrane-tethering proteins that mediate vacuole-LD contact sites and nuclear ER-vacuole junctions. This dynamic and reversible subcellular organization ensures efficient LD metabolism to support cell survival under nutrient stress.

Keywords:  CP: Cell biology; LDO proteins; lipid droplet; membrane contact; nutrient stress; nvj1; subcellular architecture; the nucleus–vacuole junction; vac8; vacuole deformation

DOI:  https://doi.org/10.1016/j.celrep.2025.115813
bioRxiv. 2025 May 27. pii: 2025.05.22.655365. [Epub ahead of print]

Disabling PSGL-1 abrogates immune suppression and resistance to PD-1 blockade in pancreatic cancer.

Jennifer L Hope, Yijuan Zhang, Hannah A F Hetrick, Evelyn S Sanchez-Hernandez, Beatrice Silvestri, Brianna J Smith, Sanmati H Nakil, Sreeja Roy, Michelle Lin, Ashley B Palete, Swetha Maganti, Lily Ling, Dennis C Otero, Katelyn T Byrne, Gabriele Romano, Yu Xin Wang, Cosimo Commisso, Linda M Bradley.

Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer for which there is a critical need to identify novel therapeutic targets. Herein we define PSGL-1 as a checkpoint inhibitor using a syngeneic orthotopic model of PDAC. As with PDAC patients, CD8 + T cells within murine PDAC tumors expressed high levels of PSGL-1. PSGL-1 -/- mice displayed striking T cell-dependent control of primary tumors and lung metastases. Extensive spatial remodeling within PDAC tumors occurred in PSGL-1 -/- mice with a dramatic loss of proliferating tumor cells and an increase in CD8 + T cell engagement of antigen-presenting cells. The prominent CD8 + T cell infiltrates included subsets of pre-exhausted T cells retaining hallmarks of stemness and multifunctional effector capacity. These changes enabled a near complete response of PDAC to therapeutic PD-1 blockade. Our findings identify PSGL-1 as a key regulator of anti-tumor immunity in PDAC, highlighting its potential as a therapeutic target to limit CD8 + T cell exhaustion and enhance immunotherapy response.
Summary: Hope et al describe a pivotal function of PSGL-1 in CD8 + T cell responses to pancreatic ductal adenocarcinoma. Genetic deletion of PSGL-1 elicits tumor control by increasing T cell infiltration and maintaining functional subsets, thereby promoting sensitivity to PD-1 blockade.

DOI: https://doi.org/10.1101/2025.05.22.655365
Cell Rep. 2025 Jun 10. pii: S2211-1247(25)00600-X. [Epub ahead of print]44(6): 115829

The lysosomal membrane protein LAMP2B mediates microlipophagy to target obesity-related disorders.

Ryohei Sakai, Shu Aizawa, Hyeon-Cheol Lee-Okada, Katsunori Hase, Hiromi Fujita, Hisae Kikuchi, Yukiko U Inoue, Takayoshi Inoue, Chihana Kabuta, Takehiko Yokomizo, Tadafumi Hashimoto, Keiji Wada, Tatsuo Mano, Ikuko Koyama-Honda, Tomohiro Kabuta.

  Lifestyle diseases, such as obesity, diabetes, and metabolic syndrome, are leading health problems, most of which are related to abnormal lipid metabolism. Lysosomes can degrade lipid droplets (LDs) via microautophagy, but the regulatory factors and physiological significance of this process are not fully understood. Here, we report the molecular mechanism and pathophysiological roles of microlipophagy, regulated by the lysosomal membrane protein LAMP2B. Our study reveals that LAMP2B interacts with phosphatidic acid, facilitating lysosomal-LD interactions and enhancing lipid hydrolysis via microlipophagy depending on endosomal sorting complexes required for transport. Correlative light and electron microscopy demonstrates direct LD uptake into lysosomes at contact sites. Moreover, LAMP2B overexpression in mice prevents high-fat diet-induced obesity, insulin resistance, and adipose tissue inflammation; liver lipidomics analysis suggests enhanced triacylglycerol hydrolysis. Overall, the findings of this study elucidate the mechanism of microlipophagy, which could be promising for the treatment of obesity and related disorders.

Keywords:  CP: Cell biology; CP: Metabolism; LAMP2B; lipid droplet; lysosome; microautophagy; microlipophagy

DOI:  https://doi.org/10.1016/j.celrep.2025.115829
Anal Chem. 2025 Jun 12.

Super-Resolution FLIM Imaging of Intracellular Lipid Microenvironments with a Dual-Responsive Polarity- and pH-Sensitive Fluorescent Probe.

Shixian Cao, Caixia Sun, Wendong Jin, Dewang Jin, Xinru Hu, Zhiqiang Liu, Xiaoqiang Yu, Kang-Nan Wang.

The microenvironment is essential for the proper function of organelles and biological systems. In particular, its physical properties─such as polarity and pH profoundly influence both physiological and pathological processes. Therefore, directly visualizing and quantitatively measuring changes in the cellular microenvironment is crucial for advancing our understanding of these fundamental processes. Fluorescent probes capable of enabling direct visualization and quantitative analysis of the cellular microenvironment using STED/FLIM (stimulated emission depletion fluorescence and lifetime imaging microscopy) offer powerful tools for exploring intracellular biophysical properties with nanoscale resolution. However, such probes remain largely unexplored. Here, we present TPA-BT-CA, a highly photostable fluorescent probe that is both polarity- and pH-sensitive, enabling real-time super-resolution imaging and quantitative mapping of intracellular lipid distributions via STED/FLIM microscopy. The donor-acceptor-acceptor (D-A-A) structural design of TPA-BT-CA facilitates efficient intramolecular charge transfer, leading to strong fluorescence signals and prolonged fluorescence lifetimes in nonpolar environments, thereby allowing precise differentiation of lipid regions with varying polarity. Furthermore, protonation and deprotonation processes under acidic or alkaline conditions induce fluorescence lifetime shifts, enabling quantitative assessment of lipid distribution in living cells. This work establishes a new approach for high-resolution visualization and quantitative measurement of the cellular microenvironment, offering new insights into lipid organization and microenvironmental dynamics.

DOI: https://doi.org/10.1021/acs.analchem.5c00826
Cancer Cell. 2025 May 29. pii: S1535-6108(25)00217-X. [Epub ahead of print]

When essential metal elements become culprits-Cuproptosis in focus.

Jiachen Hu, Xuejun Jiang.

Recently, a copper-dependent form of cell death called cuproptosis has been described, distinct from apoptosis, ferroptosis, and other known pathways. Cuproptosis is defined by excessive copper binding to lipoylated proteins, causing their aggregation and leading to cell death. Here, we discuss recent advances in understanding cuproptosis, focusing on its molecular mechanisms, physiological regulators, and therapeutic potential in cancer.

DOI: https://doi.org/10.1016/j.ccell.2025.05.008
J Phys Chem Lett. 2025 Jun 09. 6059-6065

Conformational Dynamics and Activation of Membrane-Associated Human Group IVA Cytosolic Phospholipase A2 (cPLA2).

Mac Kevin E Braza, Edward A Dennis, Rommie E Amaro.

Cytosolic phospholipase A2 (cPLA2) associates with membranes, where it hydrolyzes phospholipids containing arachidonic acid to initiate an inflammatory cascade. All-atom molecular dynamics simulations were employed to understand the activation process when cPLA2 associates with the endoplasmic reticulum (ER) membrane of macrophages, where it acts. We found that membrane association causes the lid region of cPLA2 to undergo a closed-to-open state transition that is accompanied by the sideways movement of loop 495-540, allowing the exposure of a cluster of lysine residues (K488, K541, K543, and K544), which are known to bind allosteric activator PIP2 from the membrane. The active site of the open form of cPLA2, containing catalytic dyad residues S228 and D549, exhibited a 3-fold larger cavity than the closed form of cPLA2 in aqueous solution. These findings provide mechanistic insight into how cPLA2-ER membrane association promotes major transitions between conformational states critical to allosteric activation and enzymatic phospholipid hydrolysis.

DOI: https://doi.org/10.1021/acs.jpclett.5c00860
Proc Natl Acad Sci U S A. 2025 Jun 17. 122(24): e2424409122

CDADC1 is a vertebrate-specific dCTP deaminase that metabolizes gemcitabine and decitabine to prevent cellular toxicity.

Marcelo M Rodriguez, Debashree Chatterjee, Johanna Guerry, Anne-Marie Patenaude, Charles C H Cohen, Therence Bois, Ariane Larouche, Silvana R Ferreira, Thierry Bertomeu, Andrew Chatr-Aryamontri, Li Zhang, Sylvie Mader, Corey Nislow, Guillaume St-Jean, Yvan Guindon, Astrid Zahn, Javier M Di Noia.

  Cancer therapy is limited by resistance to standard-of-care chemotherapeutic and/or by treatment-associated toxicity. Identifying molecular mechanisms that modulate cellular toxicity is crucial for enhancing treatment efficacy. We characterize CDADC1, a vertebrate-specific orphan enzyme, as an unprecedented eukaryotic dCTP deaminase. CDADC1 catalyzes the conversion of dCTP into dUTP. While bacteria use this activity to sustain proliferation, CDADC1 evolved independently and is not required for mammalian cell proliferation, as demonstrated in cell lines and by the normal growth and standard lifespan of Cdadc1-deficient mice. However, we uncover a role of CDADC1 in metabolizing nucleotide analogs gemcitabine and decitabine. Gain- and loss-of-function assays in cancer cell lines, along with ectopic mouse models of pancreatic cancer, show that CDADC1 reduces these drugs' efficacy. By the same token, Cdadc1-/- mice are hypersensitive to gemcitabine. Mechanistically, CDADC1 deaminates the active triphosphate form of gemcitabine and decitabine, rendering them susceptible to inactivation by deoxyuridine triphosphatase. In contrast, the dCMP deaminase DCTD contributes to cell proliferation and promotes gemcitabine and decitabine toxicity. Thus, CDADC1 underpins a previously unrecognized mechanism of intrinsic chemoresistance in cancer cells and has a nonredundant role in protecting from gemcitabine toxicity. CDADC1 reveals a clinically relevant metabolic pathway that might be exploited to enhance the efficacy of deoxycytidine analogs but calls for assessing CDADC1 status to avoid lethal toxicities.

Keywords:  cytidine deaminase; dCTP deaminase; decitabine; gemcitabine; nucleotide metabolism

DOI:  https://doi.org/10.1073/pnas.2424409122
J Natl Cancer Inst. 2025 Jun 13. pii: djaf139. [Epub ahead of print]

Clinical utility and tissue concordance of circulating tumor DNA in pancreatic ductal adenocarcinoma.

Fergus Keane, Lily V Saadat, Catherine A O'Connor, Joanne F Chou, Anita S Bowman, Fei Xu, Fionnuala Crowley, Neha Debnath, Joshua D Schoenfeld, Anupriya Singhal, Drew Moss, Darren Cowzer, Emily Harrold, Wungki Park, Anna Varghese, Fiyinfolu Balogun, Kenneth H Yu, Alice Zervoudakis, Marinela Capanu, Michael F Berger, Alice C Wei, Angela Rose Brannon, Eileen M O'Reilly.

IMPORTANCE: The utility of ctDNA in addressing challenges of molecular tissue profiling and complementing NGS is undefined in pancreas ductal adenocarcinoma (PDAC).
OBJECTIVE: To assess ctDNA detection rates by stage, disease burden, metastasis patterns, compare overall survival (OS) between ctDNA-positive and ctDNA-negative cases, and determine concordance between ctDNA and matched-tissue biopsies.
DESIGN: Single-institution study, 2019- 2022.
SETTING: Memorial Sloan Kettering.
PARTICIPANTS: Patients with PDAC and ctDNA profiling.
MAIN OUTCOMES AND MEASURES: Clinical, survival data abstracted from medical records. NGS by MSK-ACCESS ctDNA assay.
RESULTS: Four hundred and fourteen patients with PDAC: 28% stage I/II, 21% stage III, 51% stage IV. ctDNA detection highest among patients with advanced disease: 75% stage IV, 38% stage III, 34% stage I/II disease. For stage IV, ctDNA more frequently detected with ≥2 organs involved than with <2 organs (76% vs 38%, P = .025). Higher rates ctDNA detection observed in patients with liver metastases vs without (82% vs 52%, P < .001). In untreated stage IV cohort (N = 120), median OS was 10 months for those with detectable ctDNA (95% CI 6.9, 14) vs 19 months (95% CI 13, Not Reached) for those with undetectable ctDNA (P = .1). Concordance between ctDNA and matched tissue NGS lower in untreated stage I-III disease, but high for untreated stage IV PDAC, including critical success index of 93.1% of KRAS variants.
CONCLUSION: ctDNA is a promising tool in detection of somatic variants in PDAC. Concordance between ctDNA and tissue is high for patients with untreated metastatic disease, notably for detection of KRAS variants.

DOI: https://doi.org/10.1093/jnci/djaf139
Curr Opin Support Palliat Care. 2025 Jun 10.

Promising preclinical approaches to combating cancer-associated cachexia/tissue wasting.

Savannah A Epstein, Aneesha Dasgupta, Jason D Doles.

   PURPOSE OF REVIEW: To highlight promising pre-clinical work seeking to target cancer-associated tissue/muscle wasting.
RECENT FINDINGS: This narrative review explores recent innovations and emerging/understudied aspects of cancer cachexia biology, highlighting representative studies across three key areas: (a) novel strategies for targeting established wasting pathways, (b) multimodal/combinatorial therapeutic approaches, and (c) mechanisms involving inter-tissue communication.
SUMMARY: Though not exhaustive, this review highlights three key areas of pre-clinical research with the potential to inform and inspire future clinical trials aimed at mitigating cachexia and tissue wasting in cancer patients.

Keywords:  cachexia; muscle wasting; preclinical targets

DOI:  https://doi.org/10.1097/SPC.0000000000000763
Nature. 2025 Jun 11.

Targeting GRPR for sex hormone-dependent cancer after loss of E-cadherin.

Jérémy H Raymond, Zackie Aktary, Marie Pouteaux, Valérie Petit, Flavie Luciani, Maria Wehbe, Patrick Gizzi, Claire Bourban, Didier Decaudin, Fariba Nemati, Igor Martianov, Irwin Davidson, Catherine-Laure Tomasetto, Richard M White, Florence Mahuteau-Betzer, Béatrice Vergier, Lionel Larue, Véronique Delmas.

Sex inequalities in cancer are well documented, but the current limited understanding is hindering advances in precision medicine and therapies1. Consideration of ethnicity, age and sex is essential for the management of cancer patients because they underlie important differences in both incidence and response to treatment2,3. Age-related hormone production, which is a consistent divergence between the sexes, is underestimated in cancers that are not recognized as being hormone dependent4-6. Here, we show that premenopausal women have increased vulnerability to cancers, and we identify the cell-cell adhesion molecule E-cadherin as a crucial component in the oestrogen response in various cancers, including melanoma. In a mouse model of melanoma, we discovered an oestrogen-sensitizing pathway connecting E-cadherin, β-catenin, oestrogen receptor-α and GRPR that promotes melanoma aggressiveness in women. Inhibiting this pathway by targeting GRPR or oestrogen receptor-α reduces metastasis in mice, indicating its therapeutic potential. Our study introduces a concept linking hormone sensitivity and tumour phenotype in which hormones affect cell phenotype and aggressiveness. We have identified an integrated pro-tumour pathway in women and propose that targeting a G-protein-coupled receptor with drugs not commonly used for cancer treatment could be more effective in treating E-cadherin-dependent cancers in women. This study emphasizes the importance of sex-specific factors in cancer management and offers hope of improving outcomes in various cancers.

DOI: https://doi.org/10.1038/s41586-025-09111-x
Cell Rep. 2025 Jun 09. pii: S2211-1247(25)00545-5. [Epub ahead of print]44(6): 115774

GCLM lactylation mediated by ACAT2 promotes ferroptosis resistance in KRASG12D-mutant cancer.

Yubin Chen, Qian Yan, Shiye Ruan, Jinwei Cui, Zhenchong Li, Zhongyan Zhang, Jiayu Yang, Jike Fang, SiYang Liu, Shanzhou Huang, Baohua Hou, Chuanzhao Zhang.

  KRAS mutations drive tumorigenesis, but their role in ferroptosis regulation remains unclear. Here, we construct wild-type KRAS (KRASWT) and KRASG12D-mutant cancer cells and demonstrate that G12D-mutant cells exhibit increased viability and reduced ferroptosis upon RSL3 or erastin treatment. These cells show diminished lipid peroxidation and mitochondrial damage, indicating ferroptosis resistance. KRASG12D activates MEK/ERK signaling to phosphorylate LDHA, enhancing glycolysis and lactate production. Exogenous lactate supplementation similarly protects WT cells from ferroptosis. Mechanistically, G12D-mutation-derived lactate induces glutamate-cysteine ligase (GCL) modifier (GCLM) lactylation, a process catalyzed by acetyl-coenzyme A (CoA) acetyltransferase 2 (ACAT2). Inhibition of GCLM lactylation either through the mutation of the lactylation site or by knockdown of ACAT2 diminished the enzymatic activity of GCL and suppressed glutathione synthesis. Importantly, ACAT2 depletion overcomes ferroptosis resistance in KRASG12D-mutant tumors in vivo. Our findings reveal a KRASG12D-driven metabolic adaptation linking GCLM lactylation to ferroptosis resistance, proposing ACAT2 inhibition as a therapeutic strategy for KRAS-mutant cancers.

Keywords:  CP: Cancer; CP: Metabolism; GCLM; KRAS mutation; ferroptosis; glutamate-cysteine ligase modifier; pancreatic cancer; protein lactylation

DOI:  https://doi.org/10.1016/j.celrep.2025.115774
Methods Mol Biol. 2025 ;2925 309-328

Reproducible Sectioning and Sample Preparation for Mass Spectrometry Imaging of Cancer Metabolism in Frozen Lung Tissue.

Vanessa Y Rubio, Hayley D Ackerman, Nicole Hackel, Christina L Carr, Jaden Baldwin, John H Lockhart, Claudenir Ferrari, Jodi Balasi, Joseph O Johnson, Brooke Smedley, Eric Welsh, Oscar E Ospina, Paul A Stewart, Elsa R Flores, John M Koomen.

  Mass Spectrometry Imaging (MSI) for small molecules has emerged as the optimal technique to ascertain meaningful biology from spatial distributions of metabolites, lipids, and other classes of molecules. The success or failure of this approach rests on the sample preparation. Each tissue can have its unique challenges. In addition, the established histological processes for embedding frozen tissue, such as optimal cutting temperature medium, produce large polyethylene glycol clusters that suppress and interfere with the signal of biological molecules. To address these challenges, we provide a reproducible protocol for sectioning lung cancer tissue using a commercially available histological embedding matrix using tissues from genetically engineered mouse models of lung adenocarcinoma with a fluorescent reporter cassette to highlight additional microscopy methods used in parallel with mass spectrometry imaging to select regions of interest to compare tumor and adjacent lung tissue. These improvements to existing techniques produce high-quality sections of frozen tissue for histology and mass spectrometry imaging.

Keywords:  Frozen Tissue; Lipids; Lung Cancer; Mass Spectrometry Imaging; Matrix-Assisted Laser Desorption Ionization (MALDI); Metabolomics; Tissue Sectioning

DOI:  https://doi.org/10.1007/978-1-0716-4534-5_23
Autophagy. 2025 Jun 12.

Tumorous cholesterol biosynthesis curtails anti-tumor immunity by preventing MTOR-TFEB-mediated lysosomal degradation of CD274/PD-L1.

Huina Wang, Xiuli Yi, Di Qu, Xiangxu Wang, Hao Wang, Hengxiang Zhang, Yuqi Yang, Tianwen Gao, Weinan Guo, Chunying Li.

  Enhanced cholesterol biosynthesis is a hallmark metabolic characteristic of cancer, exerting an oncogenic role by supplying intermediate metabolites that regulate intracellular signaling pathways. The pharmacological blockade of cholesterol biosynthesis has been well documented as a promising therapeutic approach in cancer. Particularly, cholesterol biosynthesis is linked to macroautophagy/autophagy and lysosome metabolism, with the engagement of the critical autophagy regulators like MTOR to be fully activated by lysosomal cholesterol trafficking and accumulation. Previous studies have primarily focused on the role of cholesterol biosynthesis in tumor cell-intrinsic biological processes, whereas its involvement in tumor immune evasion and the underlying mechanisms related to autophagy or lysosome metabolism remain elusive. Herein, through bioinformatics analysis we discovered a negative correlation between cholesterol biosynthesis and the score of tumor-infiltrating lymphocytes in cancers. Inhibition of tumor cell cholesterol biosynthesis leads to increased infiltration and activation of CD8+ T cells in the tumor microenvironment, which is largely responsible for the impairment of tumor growth. Mechanistically, cholesterol biosynthesis inhibition impairs the activation of MTOR at lysosomes, thereby promoting the nuclear translocation of TFEB and downstream lysosome biosynthesis, facilitating the degradation of CD274/PD-L1 within lysosomes in tumor cells. Ultimately, the HMGCR-MTOR-LAMP1 axis that connects cholesterol, lysosome and tumor immunology, predicts poor response to immunotherapy and worse prognosis of patients with melanoma. These findings unveil an immunomodulatory role of tumorous cholesterol biosynthesis via the regulation of CD274 lysosomal degradation. Targeting cholesterol biosynthesis holds promise as a potential therapeutic strategy in cancer, particularly when combined with immune checkpoint blockade.

Keywords:  Cholesterol; PD-L1; TFEB; immune evasion; lysosome; protein degradation

DOI:  https://doi.org/10.1080/15548627.2025.2519066
Bioinformatics. 2025 Jun 02. pii: btaf205. [Epub ahead of print]41(6):

Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization.

Joanna Lenkiewicz, Christopher Churas, Mengzhou Hu, Gege Qian, Mayank Jain, Maxwell Adam Levinson, Sadnan Al Manir, Yue Qin, Dylan Fong, Keiichiro Ono, Jing Chen, Chengzhan Gao, Dexter Pratt, Jillian A Parker, Timothy Clark, Trey Ideker, Leah V Schaffer.

SUMMARY: Cells are organized as a hierarchy of macromolecular assemblies, ranging from small protein complexes to entire organelles. Various technologies have been developed to elucidate subcellular architecture at different scales, such as mass spectrometry approaches for mapping protein biophysical interactions and immunofluorescence imaging for mapping protein localization. We present the Cell Mapping Toolkit, which is designed to systematically integrate data from different modalities into unified hierarchical maps of subcellular organization. The toolkit facilitates an end-to-end pipeline including processing datasets, integrating modalities, and visualizing the final cell map with rich metadata including provenance documentation at each step. The Cell Mapping Toolkit provides researchers with tools for analyzing, integrating, and visualizing diverse protein datasets in a robust and reproducible framework.
AVAILABILITY AND IMPLEMENTATION: The code is freely available and is hosted on GitHub at https://github.com/idekerlab/cellmaps_pipeline. Comprehensive documentation and practical examples are provided at https://cellmaps-pipeline.readthedocs.io/.

DOI: https://doi.org/10.1093/bioinformatics/btaf205
Autophagy. 2025 Jun 12.

Unconventional role of ATG16L1 in the control of ATP compartmentalization during apoptosis.

Elena Terraza-Silvestre, Julia Bandera-Linero, Daniel Oña-Sánchez, Felipe X Pimentel-Muinos.

  The autophagy mediator ATG16L1 forms part of a complex that is essential for MAP1LC3/LC3 lipidation and autophagosome formation in the canonical macroautophagic/autophagic pathway. However, ATG16L1 is also involved in unconventional activities where LC3 becomes lipidated in single-membrane structures unrelated to double-membrane autophagosomes. Such atypical activities usually require the C-terminal domain of the molecule that includes 7 WD40-type repetitions (WD40 domain, WDD). The WDD acts as a docking site for upstream inducers that engage the LC3 lipidation ability of ATG16L1 in alternative membrane compartments. Given that this domain is absent in the yeast Atg16 ortholog, an intriguing idea proposes that it was added to the primitive protein during evolution to perform new physiological roles required by the appearance of multicellularity. Identification of such atypical activities and their physiological implications at the organismal level are important issues that remain to be clarified. In a recent report we describe an unconventional autophagic pathway that restrains the immunogenic potential of apoptosis, a key feature of homeostatic and developmentally regulated cell death in multicellular organisms. This signaling route emanates from apoptotic mitochondria and induces the formation of single-membrane, LC3-positive vesicles through a mechanism that requires the WDD of ATG16L1. The induced vesicles sequester ATP to inhibit the amount of ATP released from apoptotic cells and, consequently, prevent the activation of co-cultured phagocytes. Thus, this is a pathway that contributes to maintain the immunosilent nature of apoptotic cell death.

Keywords:  ATG16L1; ATP secretion; Apoptosis; BAK; immunogenic cell death; unconventional autophagy

DOI:  https://doi.org/10.1080/15548627.2025.2519051
Mol Cancer. 2025 Jun 07. 24(1): 167

Epithelial-to-mesenchymal transition (EMT) and cancer metastasis: the status quo of methods and experimental models 2025.

Heike Allgayer, Samikshya Mahapatra, Barnalee Mishra, Biswajit Swain, Suryendu Saha, Sinjan Khanra, Kavita Kumari, Venketesh K Panda, Diksha Malhotra, Nitin S Patil, Jörg H Leupold, Gopal C Kundu.

Epithelial-to-mesenchymal transition (EMT) is a crucial cellular process for embryogenesis, wound healing, and cancer progression. It involves a shift in cell interactions, leading to the detachment of epithelial cells and activation of gene programs promoting a mesenchymal state. EMT plays a significant role in cancer metastasis triggering tumor initiation and stemness, and activates metastatic cascades resulting in resistance to therapy. Moreover, reversal of EMT contributes to the formation of metastatic lesions. Metastasis still needs to be better understood functionally in its major but complex steps of migration, invasion, intravasation, dissemination, which contributes to the establishment of minimal residual disease (MRD), extravasation, and successful seeding and growth of metastatic lesions at microenvironmentally heterogeneous sites. Therefore, the current review article intends to present, and discuss comprehensively, the status quo of experimental models able to investigate EMT and metastasis in vitro and in vivo, for researchers planning to enter the field. We emphasize various methods to understand EMT function and the major steps of metastasis, including diverse migration, invasion and matrix degradation assays, microfluidics, 3D co-culture models, spheroids, organoids, or latest spatial and imaging methods to analyze complex compartments. In vivo models such as the chorionallantoic membrane (CAM) assay, cell line-derived and patient-derived xenografts, syngeneic, genetically modified, and humanized mice, are presented as a promising arsenal of tools to analyze intravasation, site specific metastasis, and treatment response. Furthermore, we give a brief overview on methods detecting dissemination and MRD in carcinomas, highlighting its significance in tracking the course of disease and response to treatment. Enhanced lineage tracking tools, dynamic in vivo imaging, and therapeutically useful in vivo models as powerful preclinical tools may still better reveal functional interdependencies between metastasis and EMT. Future directions are discussed in light of emerging views on the biology, diagnosis, and treatment of EMT and metastasis.

DOI: https://doi.org/10.1186/s12943-025-02338-2
bioRxiv. 2025 May 27. pii: 2022.06.22.497267. [Epub ahead of print]

Aging reduces the number and function of L-type calcium channels in the membrane of cardiac pacemaker cells.

Oscar Vivas, Matthias Baudot, Roxanne Madden, Sabrina Choi, Victor A Flores, L Fernando Santana, Claudia M Moreno.

Every heartbeat is initiated by a spontaneous electrical signal generated inside the cardiac pacemaker. The generation of this electrical signal depends on the coordinated opening and closing of different ion channels, where voltage-gated L-type calcium channels play a central role. Despite the reliability of the pacemaker, all mammals experience a linear slowdown of the pacemaker rate with age. In humans, this slowing can become pathological and constitutes the main cause for the requirement of the implantation of artificial pacemakers. However, the mechanisms behind the age-associated slowdown of the pacemaker are not well understood. Here, we show that age alters L-type calcium channels in pacemaker cells from mice. The age-associated alterations include: i) a reduction in the density of the channels at the plasma membrane, ii) a reduction in the clustering of the channels, and iii) a decrease in channel open probability. Altogether, these age-associated alterations result in a global reduction of the L-type calcium current density and in a slowdown of the pacemaker diastolic depolarization. Remarkably, increasing the open probability of L-type calcium channels pharmacologically was enough to restore pacemaker rate in old cells to the same levels observed in the young. Overall, our findings provide evidence that proper organization and function of L-type calcium channels is impaired by aging and that this dysfunction contributes to the slowdown of pacemaker cells in old animals.

DOI: https://doi.org/10.1101/2022.06.22.497267
Proc Natl Acad Sci U S A. 2025 Jun 17. 122(24): e2506321122

Ligand-specific regulation of a binary enhancer code dictating cellular senescence.

Thomas Suter, Meyer J Friedman, Cagdas Tazearslan, Daria Merkurjev, Kenny Ohgi, Dario Meluzzi, Michael G Rosenfeld, Yousin Suh.

  Cellular senescence, a major contributor to aging and age-related pathologies, is characterized by irreversible proliferative arrest and a disease-linked, proinflammatory profile known as the Senescence Associated Secretory Phenotype (SASP). A critical unanswered question is whether these properties are regulated by specific enhancer subsets, potentially licensing strategies that selectively block deleterious SASP components. Here, we identify two functionally distinct and independently regulated enhancer programs underlying senescence that are controlled by different TGF-β family ligands. Whereas Activin A stimulates recruitment of nuclear factor IA/C (NFIA/C) and SMAD2/3 transcription factors to an enhancer network that induces proliferation arrest, TGF-β2 promotes SMAD2/3-mediated suppression of a p65-dependent enhancer cohort driving the SASP. We have also uncovered reciprocal SMAD2/3-super-enhancer-regulated feedback loops that govern expression of the TGF-β2 (TGFB2) and Activin A (INHBA) transcription units, both of which are significantly up-regulated in replicative senescence. The characteristic enhancer usage and transcriptional landscape of high-passage senescent cells are sensitive to rapamycin treatment, discontinuation of which results in robust but selective senescent enhancer activation and exacerbation of the SASP. Collectively, this study uncovers separable enhancer programs and their key constituent transcription factors that contribute to the canonical features of cellular senescence, potentially informing the development of SASP-targeted therapies.

Keywords:  NFI; SMAD2/3; cellular senescence; enhancers; p65

DOI:  https://doi.org/10.1073/pnas.2506321122
Mol Cell. 2025 Jun 05. pii: S1097-2765(25)00461-7. [Epub ahead of print]

The NAMPT enzyme employs a switch that directly senses AMP/ATP and regulates cellular responses to energy stress.

Yumeng Zu, Chou Wu, Feifei Li, Hong Yao, Yuyue Xia, Ruoxi Zhang, Lulu Li, Shuangquan Chen, Qi Shi, Shuang Xi, Huanhuan Pang, Minghui Liu, Leibo Wang, Sandi Terpack, Weihua Wang, She Chen, Hong Zhang, Yibing Wang, Maojun Yang, Shanjin Huang, Fuling Zhou, Yu Tang, Zeping Hu, Shilong Fan, Yefeng Tang, Young-Sam Lee, Gelin Wang.

  Nicotinamide adenine dinucleotide (NAD+) is a crucial compound in energy metabolism and cell signaling. Nicotinamide phosphoribosyltransferase (NAMPT) is the rate-limiting enzyme responsible for NAD+ biosynthesis from nicotinamide (NAM). Here, we report that NAMPT activity is inhibited by adenosine monophosphate (AMP) in response to energy stress. Our global metabolite-protein interaction mapping reveals that NAMPT differentially interacts with AMP from fasted mouse livers. Crystal structures of NAMPT-AMP show that AMP binds similarly to the NAMPT reaction product, nicotinamide mononucleotide (NMN). The inhibition of NAMPT by AMP can be relieved by NAMPT activators or adenosine triphosphate (ATP), likely in a competitive manner. Based on these findings, we further investigated upstream factors contributing to AMP accumulation and found that activation of purine synthesis unexpectedly promotes the rise of AMP during fasting. Notably, an increased AMP/ATP ratio correlates with NAD+ decline in ischemic stroke models, in which NAMPT activators can otherwise confer protection.

Keywords:  AMP; ATP; NAD(+) biosynthesis; NAMPT; energy stress; fasting; ischemia; purine synthesis

DOI:  https://doi.org/10.1016/j.molcel.2025.05.022
bioRxiv. 2025 Jun 01. pii: 2025.05.28.656734. [Epub ahead of print]

Robust statistical assessment of Oncogenotype to Organotropism translation in xenografted zebrafish.

David Saucier, Xuexia Jiang, Divya Rajendran, Roshan Ravishankar, Erin Butler, Aruna Marchetto, Raushan T Kurmasheva, Thomas G P Grünewald, James F Amatruda, Gaudenz Danuser.

Organotropism results from the functional versatility of metastatic cancer cells to survive and proliferate in diverse microenvironments. This adaptivity can originate in clonal variation of the spreading tumor and is often empowered by epigenetic and molecular reprogramming of cell regulatory circuits. Related to organotropic colonization of metastatic sites are environmentally-sensitive, differential responses of cancer cells to therapeutic attack. Accordingly, understanding the organotropic profile of a cancer and probing the underlying driver mechanisms are of high clinical importance. However, determining systematically the organotropism of one cancer versus the organotropism of another cancer, potentially with the granularity of comparing the same cancer type between patients or tracking the evolution of a cancer in a single patient for the purpose of personalized treatment, has remained very challenging. It requires a host organism that allows observation of the spreading pattern over relatively short experimental times. Moreover, organotropic patterns often tend to be statistically weak and superimposed by experimental variation. Thus, an assay for organotropism must give access to statistical powers that can separate 'meaningful heterogeneity', i.e., heterogeneity that determines organotropism, from 'meaningless heterogeneity', i.e., heterogeneity that causes experimental noise. Here we describe an experimental workflow that leverages the physiological properties of zebrafish larvae for an imaging-based assessment of organotropic patterns over a time-frame of 3 days. The workflow incorporates computer vision pipelines to automatically integrate the stochastic spreading behavior of a particular cancer xenograft in tens to hundreds of larvae allowing subtle trends in the colonization of particular organs to emerge above random cell depositions throughout the host organism. We validate our approach with positive control experiments comparing the spreading patterns of a metastatic sarcoma against non-transformed fibroblasts and the spreading patterns of two melanoma cell lines with previously established differences in metastatic propensity. We then show that integration of the spreading pattern of xenografts in 40 - 50 larvae is necessary and sufficient to generate a Fish Metastatic Atlas page that is representative of the organotropism of a particular oncogenotype and experimental condition. Finally, we apply the power of this assay to determine the function of the EWSR1::FLI1 fusion oncogene and its transcriptional target SOX6 as plasticity factors that enhance the adaptive capacity of metastatic Ewing sarcoma.

DOI: https://doi.org/10.1101/2025.05.28.656734
Nat Methods. 2025 Jun 06.

CellNEST reveals cell-cell relay networks using attention mechanisms on spatial transcriptomics.

Fatema Tuz Zohora, Deisha Paliwal, Eugenia Flores-Figueroa, Joshua Li, Tingxiao Gao, Faiyaz Notta, Gregory W Schwartz.

Dysregulation of communication between cells mediates complex diseases such as cancer and diabetes; however, detecting cell-cell communication at scale remains one of the greatest challenges in transcriptomics. Most current single-cell RNA sequencing and spatial transcriptomics computational approaches exhibit high false-positive rates, do not detect signals between individual cells and only identify single ligand-receptor communication. To overcome these challenges, we developed Cell Neural Networks on Spatial Transcriptomics (CellNEST) to decipher patterns of communication. Our model introduces a new type of relay-network communication detection that identifies putative ligand-receptor-ligand-receptor communication. CellNEST detects T cell homing signals in human lymph nodes, identifies aggressive cancer communication in lung adenocarcinoma and colorectal cancer, and predicts new patterns of communication that may act as relay networks in pancreatic cancer. Along with CellNEST, we provide a web-based, interactive visualization method to explore in situ communication. CellNEST is available at https://github.com/schwartzlab-methods/CellNEST .

DOI: https://doi.org/10.1038/s41592-025-02721-3
Adv Healthc Mater. 2025 Jun 12. e2500217

Aging on Chip: Harnessing the Potential of Microfluidic Technologies in Aging and Rejuvenation Research.

Limor Zwi-Dantsis, Vignesh Jayarajan, George M Church, Roger D Kamm, João Pedro de Magalhães, Emad Moeendarbary.

  Aging is a complex process and the main risk factor for many common human diseases. Traditional aging research using short-lived animal models and two-dimensional cell cultures has led to key discoveries, but their relevance to human aging remains debatable. Microfluidics, a rapidly growing field that manipulates small volumes of fluids within microscale channels, offers new opportunities for aging research. By enabling the development of advanced three-dimensional cellular models that closely mimic human tissues, microfluidics allows more accurate investigation of aging processes while reducing costs, resource use, and culture time. This review explores how microfluidic systems, particularly organ-on-chip models, can improve our understanding of aging and age-related diseases, bridge the gap between animal models and human biology, and support the discovery of rejuvenation therapies. We highlight their role in monitoring aging biomarkers, analyzing functional cellular changes, and identifying longevity-promoting compounds. The ability of microfluidics to detect, analyze, and remove senescent cells is also discussed, along with emerging applications such as partial reprogramming for cellular rejuvenation. Furthermore, we summarize how these devices support single-cell analysis and recreate specific tissue microenvironments that influence aging. Insights from microfluidic approaches hold promise for developing therapeutic strategies to extend healthspan and promote longevity.

Keywords:  aging research; microfluidics; organ‐on‐a‐chip; rejuvenation

DOI:  https://doi.org/10.1002/adhm.202500217
EMBO J. 2025 Jun 09.

cGAS-STING are responsible for premature aging of telomerase-deficient zebrafish.

Naz Şerifoğlu, Giulia Allavena, Bruno Lopes-Bastos, Marta Marzullo, Andreia Marques, Pauline Colibert, Pavlos Bousounis, Eirini Trompouki, Miguel Godinho Ferreira.

  Telomere shortening occurs in multiple tissues throughout aging. When telomeres become critically short, they trigger DNA-damage responses and p53 stabilization, leading to apoptosis or replicative senescence. In vitro, cells with short telomeres activate the cGAS-STING innate immune pathway resulting in type-I interferon-based inflammation and senescence. However, the consequences of these events for the organism are not yet understood. Here, we show that sting is responsible for premature aging of telomerase-deficient zebrafish. We generated sting-/- tert-/- double-mutant animals and observed a thorough rescue of tert-/- phenotypes. At the cellular level, lack of cGAS-STING in tert mutants resulted in reduced senescence, increased cell proliferation, and decreased inflammation despite similarly short telomeres. Critically, absence of sting function resulted in dampening of the DNA damage response and reduced p53 levels. At the organism level, sting-/- tert-/- zebrafish regained fertility, showed delayed cachexia, and decreased cancer incidence, resulting in increased healthspan and lifespan of telomerase mutant animals.

Keywords:  Aging; Inflammation; Telomerase; Zebrafish; cGAS-STING

DOI:  https://doi.org/10.1038/s44318-025-00482-5
Nat Methods. 2025 Jun 06.

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression.

Albert Dominguez Mantes, Antonio Herrera, Irina Khven, Anjalie Schlaeppi, Eftychia Kyriacou, Georgios Tsissios, Evangelia Skoufa, Luca Santangeli, Elena Buglakova, Emine Berna Durmus, Suliana Manley, Anna Kreshuk, Detlev Arendt, Can Aztekin, Joachim Lingner, Gioele La Manno, Martin Weigert.

Identification of spot-like structures in large, noisy microscopy images is a crucial step for many life-science applications. Imaging-based spatial transcriptomics (iST), in particular, relies on the precise detection of millions of transcripts in low signal-to-noise images. Despite recent advances in computer vision, most of the currently used spot detection techniques are still based on classical signal processing and require tedious manual tuning per dataset. Here we introduce Spotiflow, a deep learning method for subpixel-accurate spot detection that formulates spot detection as a multiscale heatmap and stereographic flow regression problem. Spotiflow supports 2D and 3D images, generalizes across different imaging conditions and is more time and memory efficient than existing methods. We show the efficacy of Spotiflow by extensive quantitative experiments on diverse datasets and demonstrate that its increased accuracy leads to meaningful improvements in biological insights obtained from iST and live imaging experiments. Spotiflow is available as an easy-to-use Python library as well as a napari plugin at https://github.com/weigertlab/spotiflow .

DOI: https://doi.org/10.1038/s41592-025-02662-x