bims-pideca 2025-05-11 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2025–05–11
23 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Limiting the impact of protein leakage in single-cell proteomics.
mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.
Live Cell Painting: image-based profiling in live cells using Acridine Orange.
Lymphatic endothelial mTORC1 instructs metabolic and developmental signaling during lymphangiogenesis.
Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry.
Leveraging CRISPR activation for rapid assessment of gene editing products in human pluripotent stem cells.
BiDAC-dependent degradation of plasma membrane proteins by the endolysosomal system.
Tie-2 regulates endothelial morphological responses to shear stress by FOXO1-triggered autophagy.
Ligand-activated EGFR/MAPK signaling but not PI3K, are key resistance mechanisms to EGFR-therapy in colorectal cancer.
scMINER: a mutual information-based framework for clustering and hidden driver inference from single-cell transcriptomics data.
Protocol for characterizing cell motility and extracellular signal-regulated kinase dynamics in epithelial monolayers using FRET imaging data.
Quantitative Label-Free Single-Cell Proteomics on the Orbitrap Astral MS.
Artery regeneration: Molecules, mechanisms and impact on organ function.
CellRomeR: an R package for clustering cell migration phenotypes from microscopy data.
Endothelial cell metabolism in cardiovascular physiology and disease.
Capivasertib plus fulvestrant in patients with HR-positive/HER2-negative advanced breast cancer: phase 3 CAPItello-291 study extended Chinese cohort.
Effective integration of multi-omics with prior knowledge to identify biomarkers via explainable graph neural networks.
The rise of RAS: how gradual oncogene activation shapes the OIS spectrum.
GelGenie: an AI-powered framework for gel electrophoresis image analysis.
A cost-effective vessel-on-a-chip for high shear stress applications in vascular biology.
High-content screening (HCS) workflows for FAIR image data management with OMERO.
Molecular circuits for genomic recording of cellular events.
Targeting the SHOC2-RAS interaction in RAS-mutant cancers.

Nat Commun. 2025 May 05. 16(1): 4169

Limiting the impact of protein leakage in single-cell proteomics.

Andrew Leduc, Yanxin Xu, Gergana Shipkovenska, Zhixun Dou, Nikolai Slavov.

Limiting artifacts during sample preparation can significantly increase data quality in single-cell proteomics experiments. Towards this goal, we characterize the impact of protein leakage by analyzing thousands of primary single cells from mouse trachea. The cells were prepared either fresh immediately after dissociation or first cryopreserved and prepared at a later date. We directly identify permeabilized cells by imaging a cell permeable dye and use the data to define a signature for protein leakage. This signature is similar across diverse cell types and reflects increased leakage propensities for cytosolic and nuclear proteins compared to membrane and mitochondrial proteins. A classifier based on the signature allowed for the accurate identification of permeabilized cells across cell types and species. The classifier is integrated into QuantQC ( scp.slavovlab.net/QuantQC ) to support its application to diverse samples and workflows.

DOI: https://doi.org/10.1038/s41467-025-56736-7
Nat Commun. 2025 May 06. 16(1): 4201

mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.

Julia Hermann, Toman Borteçen, Robert Kalis, Alexander Kowar, Catarina Pechincha, Vivien Vogt, Martin Schneider, Dominic Helm, Jeroen Krijgsveld, Fabricio Loayza-Puch, Johannes Zuber, Wilhelm Palm.

Synthesizing the cellular proteome is a demanding process that is regulated by numerous signaling pathways and RNA modifications. How precisely these mechanisms control the protein synthesis machinery to generate specific proteome subsets remains unclear. Here, through genome-wide CRISPR screens we identify genes that enable mammalian cells to adapt to inactivation of the kinase mechanistic target of rapamycin complex 1 (mTORC1), the central driver of protein synthesis. When mTORC1 is inactive, enzymes that modify tRNAs at wobble uridines (U34-enzymes), Elongator and Ctu1/2, become critically essential for cell growth in vitro and in tumors. By integrating quantitative nascent proteomics, steady-state proteomics and ribosome profiling, we demonstrate that the loss of U34-enzymes particularly impairs the synthesis of ribosomal proteins. However, when mTORC1 is active, this biosynthetic defect only mildly affects steady-state protein abundance. By contrast, simultaneous suppression of mTORC1 and U34-enzymes depletes cells of ribosomal proteins, globally inhibiting translation. Thus, mTORC1 cooperates with tRNA U34-enzymes to sustain the protein synthesis machinery and support the high translational requirements of cell growth.

DOI: https://doi.org/10.1038/s41467-025-59185-4
Mol Biol Cell. 2025 May 06. mbcE24070308

Live Cell Painting: image-based profiling in live cells using Acridine Orange.

Fernanda Garcia-Fossa, Thaís Moraes-Lacerda, Mariana Rodrigues-da-Silva, Barbara Diaz-Rohrer, Shantanu Singh, Anne E Carpenter, Beth A Cimini, Marcelo Bispo de Jesus.

Image-based profiling has been used to analyze cell health, drug mechanism of action, CRISPR-edited cells, and overall cytotoxicity. Cell Painting is a broadly used image-based assay that uses morphological features to capture how cells respond to treatments. However, this method requires cell fixation for staining, which prevents examining live cells. To address this limitation, here we present Live Cell Painting (LCP), a high-content method based on Acridine orange, a metachromatic dye that labels different organelles and cellular structures. We began by showing that LCP can be applied to follow acidic vesicle redistribution of cells exposed to acidic vesicles inhibitors. Next, we show that LCP can identify subtle changes in cells exposed to silver nanoparticles that are not detected by techniques such as MTT assay. In drug treatments, LCP was helpful in assessing the dose-response relationship and creating profiles that allow clustering of drugs that cause liver injury. Here, we present an affordable and easy-to-use image-based assay capable of assessing overall cell health and showing promise for use in various applications such as assessing drugs and nanoparticles. We envisage the use of Live Cell Painting as an initial screening of overall cell health while providing insights into new biological questions.

DOI: https://doi.org/10.1091/mbc.E24-07-0308
Dev Cell. 2025 May 02. pii: S1534-5807(25)00250-3. [Epub ahead of print]

Lymphatic endothelial mTORC1 instructs metabolic and developmental signaling during lymphangiogenesis.

Fei Han, Summer Simeroth, Jie Zhu, Irma Gryniuk, Atul Pranay, Weiqing Chen, Yuan Wang, Yuanyuan Cai, Zhiyuan Shen, Guangyu Wang, Courtney T Griffin, Lijun Xia, Pengchun Yu.

  The lymphatic vasculature comprises lymphatic capillaries and collecting vessels. To support lymphatic development, lymphatic endothelial cells (LECs) utilize nutrients to fuel lymphangiogenic processes. Meanwhile, LECs maintain constant prospero homeobox 1 (PROX1) expression critical for lymphatic specification. However, molecular mechanisms orchestrating nutrient metabolism while sustaining PROX1 levels in LECs remain unclear. Here, we show that loss of RAPTOR, an indispensable mechanistic target of rapamycin complex 1 (mTORC1) component, downregulates PROX1 and impairs lymphatic capillary growth and differentiation of collecting lymphatics in mice. Mechanistically, mTORC1 inhibition in mouse and human LECs causes Myc reduction, which decreases hexokinase 2 (HK2) and glutaminase (GLS), inhibiting glycolysis and glutaminolysis. Myc or HK2/GLS ablation impedes lymphatic capillary and collecting vessel formation. Interestingly, mTORC1 regulation of PROX1 is independent of Myc-HK2/GLS signaling. Moreover, genetic interaction analysis indicates that Myc and PROX1 play crucial roles in mTORC1-regulated lymphatic development. Collectively, our findings identify mTORC1 as a key regulator of metabolic programs and PROX1 expression during lymphangiogenesis.

Keywords:  Myc; PROX1; glutaminase; glutaminolysis; glycolysis; hexokinase 2; lymphangiogenesis; lymphatic endothelial cell; lymphatic vessel; mTORC1

DOI:  https://doi.org/10.1016/j.devcel.2025.04.012
ACS Synth Biol. 2025 May 06.

Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry.

Xiaoming Lu, Daniel J Pritko, Megan E Abravanel, Jonah R Huggins, Oluwaferanmi Ogunleye, Tirthankar Biswas, Katia C Ashy, Semaj K Woods, Mariclaire W T Livingston, Mark A Blenner, Marc R Birtwistle.

  Genetically encoded, single-cell barcodes are broadly useful for experimental tasks such as lineage tracing or genetic screens. For such applications, a barcode library would ideally have high diversity (many unique barcodes), nondestructive identification (repeated measurements in the same cells or population), and fast, inexpensive readout (many cells and conditions). Current nucleic acid barcoding methods generate high diversity but require destructive and slow/expensive readout, and current fluorescence barcoding methods are nondestructive, fast, and inexpensive to readout but lack high diversity. We recently proposed a theory for how fluorescent protein combinations may generate a high-diversity barcode library with nondestructive, fast, and inexpensive identification. Here, we present an initial experimental proof-of-concept by generating a library of ∼150 barcodes from two-way combinations of 18 fluorescent proteins, 61 of which are tested experimentally. We use a pooled cloning strategy to generate a barcode library that is validated to contain every possible combination of the 18 fluorescent proteins. Experimental results using single mammalian cells and spectral flow cytometry demonstrate excellent classification performance of individual fluorescent proteins, with the exception of mTFP1, and of most evaluated barcodes, with many true positive rates >99%. The library is compatible with genetic screening for hundreds of genes (or gene pairs) and lineage tracing hundreds of clones. This work lays a foundation for greater diversity libraries (potentially ∼105 and more) generated from hundreds of spectrally resolvable tandem fluorescent protein probes.

Keywords:  fluorescent protein; genetically-encoded fluorescence barcodes; nanopore sequencing; single-cell analysis; spectral deconvolution; spectral flow cytometry

DOI:  https://doi.org/10.1021/acssynbio.4c00807
Stem Cell Reports. 2025 Apr 25. pii: S2213-6711(25)00103-1. [Epub ahead of print] 102499

Leveraging CRISPR activation for rapid assessment of gene editing products in human pluripotent stem cells.

Youjun Wu, Aaron Zhong, Alessandro Evangelisti, Mega Sidharta, Huangfu Danwei, Lorenz Studer, Ting Zhou.

  Verification of genome editing in human pluripotent stem cells (hPSCs), particularly at silent loci, is desirable but challenging, as it often requires complex and time-intensive differentiation to induce their expression. Here, we establish a rapid and effective workflow for verifying genome-edited hPSC lines targeting unexpressed genes using CRISPR-mediated transcriptional activation (CRISPRa). We systematically compared the efficiency of various CRISPRa systems and identified the synergistic activation mediator (SAM) system as the most potent for activating silent genes in hPSCs. Furthermore, combining SAM with TET1, a demethylation module, enhanced the activation of methylated genes. By inducing targeted gene activation in undifferentiated hPSCs using CRISPRa, we successfully verified single- and dual-reporter lines, functionally tested degradation tag (dTAG) knockins, and validated silent gene knockouts within 48 h. This approach bypasses the need to induce target gene expression through differentiation, providing a rapid and effective assay for verifying silent gene editing at the hPSC stage.

Keywords:  CRISPR-mediated transcriptional activation; dTAG system; human pluripotent stem cells; knockins; knockouts; reporter lines; silent gene editing

DOI:  https://doi.org/10.1016/j.stemcr.2025.102499
Nat Commun. 2025 May 10. 16(1): 4345

BiDAC-dependent degradation of plasma membrane proteins by the endolysosomal system.

Sammy Villa, Qumber Jafri, Julia R Lazzari-Dean, Manjot Sangha, Niclas Olsson, Austin E Y T Lefebvre, Mark E Fitzgerald, Katrina Jackson, Zhenghao Chen, Brian Y Feng, Aaron H Nile, David Stokoe, Kirill Bersuker.

The discovery of bifunctional degradation activating compounds (BiDACs) has led to the development of a new class of drugs that promote the clearance of their protein targets. BiDAC-induced ubiquitination is generally believed to direct cytosolic and nuclear proteins to proteolytic destruction by proteasomes. However, pathways that govern the degradation of other classes of BiDAC targets, such as integral membrane and intraorganellar proteins, have not been investigated in depth. In this study we use morphological profiling and CRISPR/Cas9 genetic screens to investigate the mechanisms by which BiDACs induce the degradation of plasma membrane receptor tyrosine kinases (RTKs) EGFR and Her2. We find that BiDAC-dependent ubiquitination triggers the trafficking of RTKs from the plasma membrane to lysosomes for degradation. Notably, functional proteasomes are required for endocytosis of RTKs upstream of the lysosome. Additionally, our screen uncovers a non-canonical function of the lysosome-associated arginine/lysine transporter PQLC2 in EGFR degradation. Our data show that BiDACs can target proteins to proteolytic machinery other than the proteasome and motivate further investigation of mechanisms that govern the degradation of diverse classes of BiDAC targets.

DOI: https://doi.org/10.1038/s41467-025-59627-z
PLoS One. 2025 ;20(5): e0322869

Tie-2 regulates endothelial morphological responses to shear stress by FOXO1-triggered autophagy.

Mana Ghanbarpour Houshangi, Keisuke Shirakura, Dietmar Vestweber.

INTRODUCTION: Endothelial cells respond to flow-induced shear stress by morphological changes, a process which is important for vascular development and physiology. High laminar shear stress activates Tie-2 which supports endothelial junction integrity and protects against vascular leaks and the generation of atherosclerotic plaques.
METHODS: We have examined the role of Tie-2 and FOXO1 in controlling vascular endothelial cell morphology under physiological shear stress. To address this, we exposed human umbilical vein endothelial cells (HUVECs) transfected with siRNA to 15 dyn/cm2 of shear stress for 24 hours. The resulting cells were analyzed by immunofluorescence staining.
RESULTS: We found that shear stress-induced activation of Tie-2 is required for endothelial cell alignment and elongation in the direction of flow. Mechanistically, we found that FOXO1 is an essential target downstream of Tie-2, which becomes translocated from the nucleus into the cytosol. There, FOXO1 stimulates the formation of autophagosomes, and both FOXO1 and autophagy stimulation are needed for Tie-2-dependent cell alignment.
CONCLUSION: In conclusion, laminar fluid shear stress stimulates a novel Tie-2-FOXO1-autophagy signaling axis which is required for endothelial cell alignment. This represents a new mechanism by which Tie-2 contributes to vascular protection under laminar shear stress.

DOI: https://doi.org/10.1371/journal.pone.0322869
Nat Commun. 2025 May 09. 16(1): 4332

Ligand-activated EGFR/MAPK signaling but not PI3K, are key resistance mechanisms to EGFR-therapy in colorectal cancer.

Xueping Qu, Habib Hamidi, Radia M Johnson, Ethan S Sokol, Eva Lin, Cathy Eng, Tae Won Kim, Johanna Bendell, Smruthy Sivakumar, Benjamin Kaplan, Felipe de Sousa E Melo, Andrew Mancini, Matthew Wongchenko, Yi Shi, David Shames, Yibing Yan, Fortunato Ciardiello, Carlos Bais.

Understanding mechanisms of resistance to active therapies is crucial for developing more effective treatments. Here, we investigate resistance to anti-EGFR and anti-VEGF plus chemotherapy treatment in colorectal cancer (CRC) patients from the IMblaze370 trial (NCT02788279). While anti-VEGF does not select for secondary mutations, anti-EGFR leads to simultaneous mutations in EGFR and MAPK, but not PI3K pathway genes. Notably, we observe frequent acquired mutations in the EGFR extracellular but not intracellular domain and that patients with higher baseline expression of EGFR-ligands are prone to acquire resistant mutations. This data reveals a ligand-activated EGFR/MAPK-signaling dependency in CRC. We also observe enrichment for 8q gains in anti-EGFR treated patients, potentially linked to MYC amplification, a finding further supported by baseline expression analysis. This work adds to the evidence supporting broader evaluation of EGFR and pan-KRAS inhibitor combinations in CRC patients. It also underscores the utility of EGFR ligands as anti-EGFR efficacy biomarkers and provides a rationale for developing ligand blockers to complement and/or improve conventional anti-EGFR therapies in CRC.

DOI: https://doi.org/10.1038/s41467-025-59588-3
Nat Commun. 2025 May 08. 16(1): 4305

scMINER: a mutual information-based framework for clustering and hidden driver inference from single-cell transcriptomics data.

Qingfei Pan, Liang Ding, Siarhei Hladyshau, Xiangyu Yao, Jiayu Zhou, Lei Yan, Yogesh Dhungana, Hao Shi, Chenxi Qian, Xinran Dong, Chad Burdyshaw, Joao Pedro Veloso, Alireza Khatamian, Zhen Xie, Isabel Risch, Xu Yang, Jiyuan Yang, Xin Huang, Jason Fang, Anuj Jain, Arihant Jain, Michael Rusch, Michael Brewer, Junmin Peng, Koon-Kiu Yan, Hongbo Chi, Jiyang Yu.

Single-cell transcriptomics data present challenges due to their inherent stochasticity and sparsity, complicating both cell clustering and cell type-specific network inference. To address these challenges, we introduce scMINER (single-cell Mutual Information-based Network Engineering Ranger), an integrative framework for unsupervised cell clustering, transcription factor and signaling protein network inference, and identification of hidden drivers from single-cell transcriptomic data. scMINER demonstrates superior accuracy in cell clustering, outperforming five state-of-the-art algorithms and excelling in distinguishing closely related cell populations. For network inference, scMINER outperforms three established methods, as validated by ATAC-seq and CROP-seq. In particular, it surpasses SCENIC in revealing key transcription factor drivers involved in T cell exhaustion and Treg tissue specification. Moreover, scMINER enables the inference of signaling protein networks and drivers with high accuracy, which presents an advantage in multimodal single cell data analysis. In addition, we establish scMINER Portal, an interactive visualization tool to facilitate exploration of scMINER results.

DOI: https://doi.org/10.1038/s41467-025-59620-6
STAR Protoc. 2025 May 07. pii: S2666-1667(25)00222-9. [Epub ahead of print]6(2): 103816

Protocol for characterizing cell motility and extracellular signal-regulated kinase dynamics in epithelial monolayers using FRET imaging data.

Julio Cesar Sanchez-Rendon, Lara Hundsdorfer, Effie E Bastounis.

  Extracellular signal-regulated kinase (ERK) activity waves regulate critical processes like wound healing and bacterial pathogen dissemination by altering host cell motility and biomechanics. Here, we present a protocol for fluorescence resonance energy transfer (FRET) imaging of ERK activity in the nuclei of epithelial cells in a monolayer using an ERK biosensor. Moreover, we outline all image processing steps for the spatiotemporal quantification of single-cell ERK oscillations and wave propagation. Modifications, especially with respect to FRET imaging, may be necessary if different ERK biosensors are used. For complete details on the use and execution of this protocol, please refer to Hundsdorfer et al.1.

Keywords:  cell biology; cell-based assays; computer sciences; microscopy

DOI:  https://doi.org/10.1016/j.xpro.2025.103816
Mol Cell Proteomics. 2025 May 05. pii: S1535-9476(25)00080-5. [Epub ahead of print] 100982

Quantitative Label-Free Single-Cell Proteomics on the Orbitrap Astral MS.

Valdemaras Petrosius, Pedro Aragon-Fernandez, Tabiwang N Arrey, Jakob Woessman, Nil Üresin, Bauke de Boer, Jinyu Su, Benjamin Furtwängler, Hamish Stewart, Eduard Denisov, Johannes Petzoldt, Amelia C Peterson, Christian Hock, Eugen Damoc, Alexander Makarov, Vlad Zabrouskov, Bo T Porse, Erwin M Schoof.

Single-cell proteomics by mass spectrometry (scp-MS) holds the potential to provide unprecedented insights into molecular features directly linked to the cellular phenotype, while deconvoluting complex organisms into their basic building blocks. Tailored sample preparation that maximizes the extracted amount of material that is introduced into the mass spectrometer has rapidly propelled the field forward. However, the measured signal is still at the lower edge of detection approaching the sensitivity boundary of current instrumentation. Here, we investigate the capacity of the enhanced sensitivity of the Orbitrap Astral mass spectrometer to facilitate deeper proteome profiles from low-input to single-cell samples. We carry out a comprehensive data acquisition method survey to pinpoint which parameters provide most sensitivity. Furthermore, we explore the quantitative accuracy of the obtained measurements to ensure that the obtained abundances are in line with expected ground truth values. We culminate our technical exploration by generating small datasets from two cultured cell lines and a primary bone marrow sample, to showcase obtainable proteome coverage differences from different source materials. Finally, as a proof of concept we explore protein covariation to showcase how information on known protein complexes is captured inherently in our scp-MS data.

DOI: https://doi.org/10.1016/j.mcpro.2025.100982
Semin Cell Dev Biol. 2025 May 02. pii: S1084-9521(25)00021-7. [Epub ahead of print]171 103611

Artery regeneration: Molecules, mechanisms and impact on organ function.

Swarnadip Ghosh, Bhavnesh Bishnoi, Soumyashree Das.

  Replenishment of artery cells to repair or create new arteries is a promising strategy to re-vascularize ischemic tissue. However, limited understanding of cellular and molecular programs associated with artery (re-)growth impedes our efforts towards designing optimal therapeutic approaches. In this review, we summarize different cellular mechanisms that drive injury-induced artery regeneration in distinct organs and organisms. Artery formation during embryogenesis includes migration, self-amplification, and changes in cell fates. These processes are coordinated by multiple signaling pathways, like Vegf, Wnt, Notch, Cxcr4; many of which, also involved in injury-induced vascular responses. We also highlight how physiological and environmental factors determine the extent of arterial re-vascularization. Finally, we discuss different in vitro cellular reprogramming and tissue engineering approaches to promote artery regeneration, in vivo. This review provides the current understanding of endothelial cell fate reprogramming and explores avenues for regenerating arteries to restore organ function through efficient revascularization.

Keywords:  Artery; Cellular reprogramming; Collateral arteries; Development; Endothelial cells; Genetic lineage tracing; Regeneration

DOI:  https://doi.org/10.1016/j.semcdb.2025.103611
Bioinform Adv. 2025 ;5(1): vbaf069

CellRomeR: an R package for clustering cell migration phenotypes from microscopy data.

Iivari Kleino, Mats Perk, António G G Sousa, Markus Linden, Julia Mathlin, Daniel Giesel, Paulina Frolovaite, Sami Pietilä, Sini Junttila, Tomi Suomi, Laura L Elo.

Motivation: The analysis of cell migration using time-lapse microscopy typically focuses on track characteristics for classification and statistical evaluation of migration behaviour. However, considerable heterogeneity can be seen in cell morphology and microscope signal intensity features within the migrating cell populations.
Results: To utilize this information in cell migration analysis, we introduce here an R package CellRomeR, designed for the phenotypic clustering of cells based on their morphological and motility features from microscopy images. Utilizing machine learning techniques and building on an iterative clustering projection method, CellRomeR offers a new approach to identify heterogeneity in cell populations. The clustering of cells along the migration tracks allows association of distinct cellular phenotypes with different cell migration types and detection of migration patterns associated with stable and unstable cell phenotypes. The user-friendly interface of CellRomeR and multiple visualization options facilitate an in-depth understanding of cellular behaviour, addressing previous challenges in clustering cell trajectories using microscope cell tracking data.
Availability and implementation: CellRomeR is available as an R package from https://github.com/elolab/CellRomeR.

DOI: https://doi.org/10.1093/bioadv/vbaf069
Nat Rev Cardiol. 2025 May 09.

Endothelial cell metabolism in cardiovascular physiology and disease.

Alessandra Pasut, Eleonora Lama, Amaryllis H Van Craenenbroeck, Jeffrey Kroon, Peter Carmeliet.

Endothelial cells are multifunctional cells that form the inner layer of blood vessels and have a crucial role in vasoreactivity, angiogenesis, immunomodulation, nutrient uptake and coagulation. Endothelial cells have unique metabolism and are metabolically heterogeneous. The microenvironment and metabolism of endothelial cells contribute to endothelial cell heterogeneity and metabolic specialization. Endothelial cell dysfunction is an early event in the development of several cardiovascular diseases and has been shown, at least to some extent, to be driven by metabolic changes preceding the manifestation of clinical symptoms. Diabetes mellitus, hypertension, obesity and chronic kidney disease are all risk factors for cardiovascular disease. Changes in endothelial cell metabolism induced by these cardiometabolic stressors accelerate the accumulation of dysfunctional endothelial cells in tissues and the development of cardiovascular disease. In this Review, we discuss the diversity of metabolic programmes that control endothelial cell function in the cardiovascular system and how these metabolic programmes are perturbed in different cardiovascular diseases in a disease-specific manner. Finally, we discuss the potential and challenges of targeting endothelial cell metabolism for the treatment of cardiovascular diseases.

DOI: https://doi.org/10.1038/s41569-025-01162-x
Nat Commun. 2025 May 09. 16(1): 4324

Capivasertib plus fulvestrant in patients with HR-positive/HER2-negative advanced breast cancer: phase 3 CAPItello-291 study extended Chinese cohort.

Xichun Hu, Qingyuan Zhang, Tao Sun, Huihua Xiong, Wei Li, Yuee Teng, Yen-Shen Lu, Ling-Ming Tseng, Min Yan, Hongsheng Li, Danmei Pang, Shin-Cheh -Chen, Wenyan Chen, Ou Jiang, Jingfen Wang, Xinhong Wu, Xian Wang, Aimin Zang, Xiaojia Wang, Julie M Collins, Ethan Fan, Lin Jiang, Xiaoling Zeng, Nicholas C Turner.

In the global CAPItello-291 randomized phase 3 study (NCT04305496) in patients with hormone receptor-positive/HER2-negative advanced breast cancer and progression during/after aromatase inhibitor treatment, capivasertib-fulvestrant significantly improved progression-free survival (PFS) in the overall population and patients with PIK3CA/AKT1/PTEN-altered tumors versus placebo-fulvestrant. We assessed efficacy and safety of capivasertib-fulvestrant in a prespecified exploratory analysis of a Chinese cohort (n = 24) and extended study with the same protocol (n = 110). Clinically meaningful PFS benefit for capivasertib-fulvestrant was observed in the overall population (median PFS: 6.9 [capivasertib-fulvestrant] versus 2.8 [placebo-fulvestrant] months; hazard ratio 0.51, 95% CI 0.34-0.76), patients with PIK3CA/AKT1/PTEN-altered tumors (n = 46; 5.7 versus 1.9 months; hazard ratio 0.41, 95% CI 0.19-0.85) and PIK3CA/AKT1/PTEN-non-altered tumors (patients with confirmed next-generation sequencing results [n = 68]; 9.2 versus 2.7 months; hazard ratio 0.38; 95% CI 0.21-0.68). The most frequent adverse events (AEs) with capivasertib-fulvestrant were diarrhea (60.6% versus 11.3% with placebo-fulvestrant) and hyperglycemia (57.7% versus 17.7%). AEs leading to capivasertib-fulvestrant discontinuation were reported in 11.3% of patients versus 3.2% for placebo-fulvestrant. The benefit-risk profile of capivasertib-fulvestrant in the Chinese cohort was favorable; further exploration in patients with PIK3CA/AKT1/PTEN-non-altered tumors is warranted.

DOI: https://doi.org/10.1038/s41467-025-59210-6
NPJ Syst Biol Appl. 2025 May 08. 11(1): 43

Effective integration of multi-omics with prior knowledge to identify biomarkers via explainable graph neural networks.

Rohit K Tripathy, Zachary Frohock, Hong Wang, Gregory A Cary, Stephen Keegan, Gregory W Carter, Yi Li.

The rapid growth of multi-omics datasets and the wealth of biological knowledge necessitates the development of effective methods for their integration. Such methods are essential for building predictive models and identifying drug targets based on a limited number of samples. We propose a framework called GNNRAI for the supervised integration of multi-omics data with biological priors represented as knowledge graphs. Our framework leverages graph neural networks (GNNs) to model the correlation structures among features from high-dimensional 'omics data, which reduces the effective dimensions in data and enables us to analyze thousands of genes simultaneously using hundreds of samples. Furthermore, our framework incorporates explainability methods to elucidate informative biomarkers. We apply our framework to Alzheimer's disease (AD) multi-omics data, showing that the integration of transcriptomics and proteomics data with prior AD knowledge is effective, improving the prediction accuracy of AD status over single-omics analyses and highlighting both known and novel AD-predictive biomarkers.

DOI: https://doi.org/10.1038/s41540-025-00519-9
Genes Dev. 2025 May 05.

The rise of RAS: how gradual oncogene activation shapes the OIS spectrum.

Haoran Zhu, Adelyne Sue Li Chan, Masashi Narita.

  Excessive levels of oncogenic RAS expression in normal cells trigger reactive cellular senescence, known as oncogene-induced senescence (OIS)-a putative autonomous tumor-suppressive mechanism. However, the monoallelic expression of oncogenic RAS from the endogenous locus often fails to induce senescence, at least in the short term. Consequently, whether robust senescence characterizes the preneoplasia driven by oncogenic RAS under physiological conditions has been debated. A key challenge is the highly heterogeneous nature of senescence at both the population and single-cell levels. Notably, increasing evidence suggests that RAS levels are gradually upregulated during the development of tumors driven by oncogenic RAS. To address the complex relationship between diverse oncogenic responses, including senescence and tumor initiation, we introduce the concept of an OIS spectrum, where oncogenic dosage-dependent cellular states lie between normal cells and full senescence. Intermediate "sub-OIS" states may play a critical role in tumor initiation, potentially providing one explanation for the ongoing debate.

Keywords:  RAS; liver cancer; oncogene-induced senescence; tumor-initiating cells

DOI:  https://doi.org/10.1101/gad.352761.125
Nat Commun. 2025 May 05. 16(1): 4087

GelGenie: an AI-powered framework for gel electrophoresis image analysis.

Matthew Aquilina, Nathan J W Wu, Kiros Kwan, Filip Bušić, James Dodd, Laura Nicolás-Sáenz, Alan O'Callaghan, Peter Bankhead, Katherine E Dunn.

Gel electrophoresis is a ubiquitous laboratory method for the separation and semi-quantitative analysis of biomolecules. However, gel image analysis principles have barely advanced for decades, in stark contrast to other fields where AI has revolutionised data processing. Here, we show that an AI-based system can automatically identify gel bands in seconds for a wide range of experimental conditions, surpassing the capabilities of current software in both ease-of-use and versatility. We use a dataset containing 500+ images of manually-labelled gels to train various U-Nets to accurately identify bands through segmentation, i.e. classifying pixels as 'band' or 'background'. When applied to gel electrophoresis data from other laboratories, our system generates results that quantitatively match those of the original authors. We have publicly released our models through GelGenie, an open-source application that allows users to extract bands from gel images on their own devices, with no expert knowledge or experience required.

DOI: https://doi.org/10.1038/s41467-025-59189-0
Microvasc Res. 2025 May 03. pii: S0026-2862(25)00033-0. [Epub ahead of print] 104814

A cost-effective vessel-on-a-chip for high shear stress applications in vascular biology.

Clarissa Becher, Martin Frauenlob, Florian Selinger, Peter Ertl, Marie-José Goumans, Gonzalo Sanchez-Duffhues.

  The vascular endothelium is constantly subjected to hemodynamic forces, including tangential shear stress, which are crucial for maintaining vascular homeostasis. Pathological shear stress levels, such as those observed in pulmonary arterial hypertension (PAH) or atherosclerosis, disrupt this balance, driving vascular remodeling and endothelial dysfunction. Current microfluidic platforms for studying these conditions are limited by high costs, excessive reagent requirements, and non-physiological channel geometries. Here we introduce a novel microfluidic chip system, a Nylon Vessel-on-Chip (NVoC) which represents a cost-effective and straightforward fabrication platform that eliminates the need for specialized equipment and enables a physiologically relevant round channel geometry. The NVoC was fabricated using Polydimethylsiloxane (PDMS) and nylon threads, with surface activation achieved through polydopamine and collagen-I coating, enabling robust endothelial cell (EC) attachment and long-term culture. Immortalized endothelial colony-forming cells (iECFCs) and human umbilical vein EC (HUVECs) were used to optimize and validate the platform, demonstrating its compatibility with high shear stress conditions (up to 90 dyne/cm2) and various molecular biology techniques, including RT-qPCR, Western blotting, and immunofluorescent staining. With fabrication costs six times lower than commercial alternatives and overall experimental costs reduced threefold, the NVoC offers the ability to expose endothelial cells to physiological and pathological shear stress levels in a reproducible, accessible, and scalable manner. Its versatility and affordability make it a valuable tool for investigating shear stress-related mechanisms in microvascular diseases, particularly PAH, with potential applications in drug discovery and translational research.

Keywords:  Bone morphogenetic proteins; Endothelial cell; Hemodynamics; Microfluidics; Pulmonary arterial hypertension; Shear stress

DOI:  https://doi.org/10.1016/j.mvr.2025.104814
Sci Rep. 2025 May 09. 15(1): 16236

High-content screening (HCS) workflows for FAIR image data management with OMERO.

Riccardo Massei, Wibke Busch, Beatriz Serrano-Solano, Matthias Bernt, Stefan Scholz, Elena K Nicolay, Hannes Bohring, Jan Bumberger.

High-content screening (HCS) for bioimaging is a powerful approach to studying biological processes, enabling the acquisition of large amounts of images from biological samples. However, it generates massive amounts of metadata, making HCS experiments a unique data management challenge. This data includes images, reagents, protocols, analytic outputs, and phenotypes, all of which must be stored, linked, and made accessible to users, scientists, collaborators, and the broader community to ensure sharable results. This study showcases different approaches using Workflow Management Systems (WMS) to create reusable semi-automatic workflows for HCS bioimaging data management, leveraging the image data management platform OMERO. The three developed workflows demonstrate the transition from a local file-based storage system to an automated and agile image data management framework. These workflows facilitate the management of large amounts of data, reduce the risk of human error, and improve the efficiency and effectiveness of image data management. We illustrate how applying WMS to HCS data management enables us to consistently transfer images across different locations in a structured and reproducible manner, reducing the risk of errors and increasing data consistency and reproducibility. Furthermore, we suggest future research direction, including developing new workflows and integrating machine learning algorithms for automated image analysis. This study provides a blueprint for developing efficient and effective image data management systems for HCS experiments and demonstrates how different WMS approaches can be applied to create reusable, semi-automated workflows for HCS bioimaging data management using OMERO.

DOI: https://doi.org/10.1038/s41598-025-00720-0
Trends Genet. 2025 May 06. pii: S0168-9525(25)00079-4. [Epub ahead of print]

Molecular circuits for genomic recording of cellular events.

Wei Chen, Junhong Choi.

  Advances in precise genome editing are enabling genomic recordings of cellular events. Since the initial demonstration of CRISPR-based genome editing, the field of genomic recording has witnessed key strides in lineage recording, where clonal lineage relationships among cells are indirectly recorded as synthetic mutations. However, methods for directly recording and reconstructing past cellular events are still limited, and their potential for revealing new insights into cell fate decisions has yet to be realized. The field needs new sensing modules and genetic circuit architectures that faithfully encode past cellular states into genomic DNA recordings to achieve such goals. Here we review recently developed strategies to construct diverse sensors and explore how emerging synthetic biology tools may help to build molecular circuits for genomic recording of diverse cellular events.

Keywords:  CRISPR; genomic recording; molecular circuits; synthetic biology

DOI:  https://doi.org/10.1016/j.tig.2025.04.004
Nature. 2025 May 07.

Targeting the SHOC2-RAS interaction in RAS-mutant cancers.

Zachary J Hauseman, Frédéric Stauffer, Kim S Beyer, Sandra Mollé, Elena Cavicchioli, Jean-Remy Marchand, Michelle Fodor, Jessica Viscomi, Anxhela Dhembi, Stéphanie Katz, Beatrice Faggion, Mylene Lanter, Grainne Kerr, Daniela Schildknecht, Cornelia Handl, Danilo Maddalo, Carole Pissot Soldermann, Jacob Brady, Om Shrestha, Zachary Nguyen, Lukas Leder, Gregor Cremosnik, Sandra Lopez Romero, Ulrich Hassiepen, Travis Stams, Markus Linder, Giorgio G Galli, Daniel A Guthy, Daniel A King, Sauveur-Michel Maira, Claudio R Thoma, Veronika Ehmke, Luca Tordella.

Activating mutations in the rat sarcoma (RAS) genes HRAS, NRAS and KRAS collectively represent the most frequent oncogenic driver in human cancer1. They have previously been considered undruggable, but advances in the past few years have led to the clinical development of agents that target KRAS(G12C) and KRAS(G12D) mutants, yielding promises of therapeutic responses at tolerated doses2. However, clinical agents that selectively target NRAS(Q61*) mutants (* represents 'any'), the second-most-frequent oncogenic driver in melanoma, are still lacking. Here we identify SHOC2, a component of the SHOC2-MRAS-PP1C complex, as a dependency of RAS(Q61*) tumours in a nucleotide-state-dependent and isoform-agnostic manner. Mechanistically, we found that oncogenic NRAS(Q61R) forms a direct interaction with SHOC2, evidenced by X-ray co-crystal structure. In vitro high-throughput screening enabled the discovery of small molecules that bind to SHOC2 and disrupt the interaction with NRAS(Q61*). Structure-based optimization led to a cellularly active tool compound that shows inhibition of mitogen-activated protein kinase (MAPK) signalling and proliferation in RAS-mutant cancer models, most notably in NRAS(Q61*) settings. These findings provide evidence for a neomorph SHOC2-(canonical)RAS protein interaction that is pharmacologically actionable and relevant to cancer sustenance. Overall, this work provides the concept validation and foundation for developing new therapies at the core of the RAS signalling pathway.

DOI: https://doi.org/10.1038/s41586-025-08931-1