bims-pideca 2026-05-03 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2026–05–03
25 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Cellular responses to FGF1 are modulated by palmitoylation of the docking protein FRS2α.
Pleiotropic germline PTEN mutations influence gastrulation through dysregulated AKT activation.
Single-cell hit calling in high-content imaging screens with Buscar.
Single-cell trajectory inference for detecting transient events in biological processes.
STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.
Cell Painting PLUS: An Iterative Staining-Elution Protocol for High-Content Phenotypic Screenings.
STRAIGHT-IN Dual: a platform for dual single-copy integrations of DNA payloads and gene circuits into human induced pluripotent stem cells.
Ras promotes macropinocytic nutrient uptake by suppressing the albumin recycling receptor FcRn.
Shrinking spleens and nodes, expanding horizons: leniolisib and the future of activated phosphoinositide 3-kinase delta syndrome (APDS).
BEstimate: a computational tool for the design and interpretation of CRISPR base editing experiments.
Neudesin modulates IGF1 and insulin signaling pathways by regulating the surface expression of IGF1R through a conserved WPE motif.
ErbB family receptor dimerization dynamics and dysregulation via long-term single-molecule imaging.
Somatic mutation landscape revealed by non-invasive iPSC derivation from urine cells.
Localized heat induces ERK activation and signal propagation in solid tumors.
Modulation of Oncogenic KRAS Signaling by Branched Actin-driven Cell Membrane Protrusions.
The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease.
Leveraging training expertise to build capacity in computational personalised medicine.
Tracing cell communication programs across conditions at single cell resolution with CCC-RISE.
Potassium suppresses allosteric activation of ZAP-70-dependent T Cell Receptor signaling.
CRL4AMBRA1 is a key mediator for AKT-dependent cell cycle control in neural progenitor cells.
The atypical E3 ligase HOIL-1 safeguards the ribosome during cellular stress.
Aged differentiated cells reverse into native stemness-like state by niche cytokines to sustain lifelong homeostasis and tissue repair.
Mechanism by which a linoleic acid metabolite suppresses cancer cell growth by inhibiting mTOR.
ERG is a regulator of dynamic and reversible endothelial plasticity.
Single-cell lineage tracing identifies hemogenic endothelial cells in the adult mouse bone marrow.

Proc Natl Acad Sci U S A. 2026 May 05. 123(18): e2605311123

Cellular responses to FGF1 are modulated by palmitoylation of the docking protein FRS2α.

Seong J An, Yoshihisa Suzuki, Jyotidarsini Mohanty, Francisco Tome, Irit Lax, Joseph Schlessinger.

  An important mechanism by which receptor tyrosine kinases (RTKs) mediate cellular responses involves the formation of signaling complexes through direct interactions with membrane-associated docking proteins, followed by phosphorylation of multiple tyrosine residues. These docking proteins recruit and activate downstream signaling molecules and enzymes following ligand stimulation. The docking protein FRS2α has been established as a major signaling hub activated by fibroblast growth factors (FGFs), neurotrophic factors, and other extracellular cues. Here, we show that palmitoylation of FRS2α at two sites is essential for stabilizing its myristoylation-dependent association with the plasma membrane. FGF1-induced mitogen-activated protein kinase (MAPK) activation and other cellular responses are partially restored in cells expressing FRS2α mutants deficient in either one of the two palmitoylation sites. However full restoration of signal strength including MAPK response and other FGF1-induced cellular activities requires palmitoylation at both FRS2α sites. In addition to enhancing signaling robustness, anchoring of FRS2α to the plasma membrane creates a structural platform for assembling multiprotein complexes essential for cytoskeletal reorganization associated with membrane ruffling, macropinocytosis, and other FGF1-induced processes. Finally, we demonstrate that while PC12 cells lacking FRS2α or deficient in FRS2α palmitoylation can proliferate, FGF1-induced neuronal differentiation strictly depends on the palmitoylation of the docking protein.

Keywords:  cell signaling; myristoylation; palmitoylation; phosphorylation; receptor tyrosine kinases

DOI:  https://doi.org/10.1073/pnas.2605311123
NPJ Genom Med. 2026 Apr 28.

Pleiotropic germline PTEN mutations influence gastrulation through dysregulated AKT activation.

Omer Enes Onur, Juan Andres Venegas, Arda Durmaz, Shin Chung Kang, Masahiro Hitomi, Charis Eng.

PTEN hamartoma tumor syndrome (PHTS), caused by germline PTEN mutations, exhibits pleiotropic manifestations, including hamartomas, cancers, and neurodevelopmental disorders, posing challenges in patient management. We hypothesized that mutant PTEN allele-dependent alterations during gastrulation impact PHTS pleiotropism. We generated gastruloids from isogenic human induced pluripotent stem cells with clinically relevant heterozygous PTEN mutations, PTENG132D/WT found in PHTS patients with cancer, hamartoma, and autism spectrum disorder, and PTENM134R/WT associated with cancer-only patients. PTENG132D/WTgastruloids exhibited axial over-elongation driven by AKT hyperactivation, upregulation of Snail, a key regulator of epithelial-to-mesenchymal transition (EMT), and enrichments in mesoderm and endoderm-related gene signatures, compared to those with PTENM134R/WT or PTENWT/WT. Our machine-learning algorithm accurately recognized the over-elongated PTENG132D/WT gastruloids and morphological reversal with AKT inhibitor treatment. Our data suggest a potential link between the mutant PTEN allele-specific early developmental alterations and the clinical outcomes of PHTS, and provide a platform for pathogenic mutation and drug screening.

DOI: https://doi.org/10.1038/s41525-026-00574-z
bioRxiv. 2026 Apr 19. pii: 2026.04.15.718737. [Epub ahead of print]

Single-cell hit calling in high-content imaging screens with Buscar.

Erik Serrano, Wei-Shan Li, Gregory Way.

High-content screening (HCS) enables the systematic quantification of single-cell morphology features across thousands of perturbations, capturing rich phenotypic heterogeneity. Image-based profiling is a critical bioinformatics processing step in this pipeline, as researchers use it to predict mechanisms of action, assess toxicity, perform hit calling, and more. However, current image-based profiling workflows rely on aggregate statistics, such as calculating mean or median feature values per well, implicitly assuming cell homogeneity. This limitation obscures subpopulation effects, reducing sensitivity to subtle or heterogeneous effects of perturbations. Here we present Buscar, a method that leverages the full heterogeneity of single-cell image-based profiles to call hits. Buscar requires two reference, single-cell populations that define distinct morphology states: a reference state (e.g., disease cells) and a target state (e.g., healthy cells). Buscar then compares these two groups to define on- and off-morphology signatures, which it then uses to score every perturbation in a given screen. The scores quantify perturbation efficacy and off-target effects, or specificity, in an interpretable manner, clarifying which morphologies are appropriately altered and which may arise from off-target activity. We apply Buscar to three datasets. First, as a proof of concept, we applied Buscar to a Cell Painting dataset of cardiac fibroblasts from patients with heart failure. Buscar quantifies both morphology rescue and off-target morphology activity in these cells treated with a TGFβ receptor inhibitor. Second, we show that Buscar recovers biologically coherent gene-phenotype associations across 16 manually-labeled phenotypes in the MitoCheck dataset. Lastly, applied to CPJUMP1, we show that Buscar is robust to technical replicates collected across plates in both small-molecule and CRISPR-Cas9 perturbations. Together, these results establish Buscar as a reproducible and interpretable hit calling method that overcomes aggregation bias, enabling the simultaneous quantification of compound efficacy and specificity to enhance hit calling in HCS. We release Buscar as an open-source python package.

DOI: https://doi.org/10.64898/2026.04.15.718737
Nucleic Acids Res. 2026 Apr 23. pii: gkag368. [Epub ahead of print]54(8):

Single-cell trajectory inference for detecting transient events in biological processes.

Alexandre Hutton, Jesús Muñoz-Estrada, Jesse G Meyer.

Transient changes in gene or protein expression often mark the key regulatory checkpoints that propel cells from one functional state to the next, yet they are easy to miss in sparse, noisy single-cell omics data. We introduce scTransient, which transforms single-cell expression profiles into continuous pseudotime signals and uses wavelet-based signal processing to isolate short-lived but biologically meaningful bursts of gene activity. After ordering cells with supervised pseudotime, scTransient windows expression values with supervised pseudotime, applies a continuous wavelet transform, and assigns every gene a transient-event score (TES) that rewards sharp, isolated coefficients while penalizing background fluctuations. Synthetic benchmarks demonstrate that TES robustly recovers transient events (TE) across a wide range of parameters, including cell numbers, signal-to-noise ratios, and event widths. Applying scTransient to two real datasets-induced neuron development and single-cell cell cycle-demonstrates scTransient's ability to detect TEs along pseudotime and identify proteins known to be related to the biological process under study. These include stem cell regulators in induced neuronal development and S-phase DNA replication factors in A549 cells. By extending trajectory inference from descriptive ordering to quantitative detection of fleeting regulatory programs, scTransient offers a practical route to uncover transient molecular events that drive development, differentiation, and disease.

DOI: https://doi.org/10.1093/nar/gkag368
PLoS Comput Biol. 2026 Apr 27. 22(4): e1013689

STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.

Nicholas J Bradley, Sriram Pendyala, Katie Partington, Douglas M Fowler.

Fluorescent in situ sequencing involves imaging-based sequencing by synthesis in intact cells or tissues to reveal target nucleotide sequences inside each cell. Often, the target sequences are barcodes that indicate a perturbation (e.g., CRISPR guide or genetic variant) delivered to the cell. However, processing in situ sequencing data presents a considerable challenge, requiring stitching and aligning tens of thousands of images with millions of cells, detecting small amplicon colonies across sequencing cycles, and calling reads. To address these challenges, we introduce STARCall: STitching, Alignment and Read Calling for in situ sequencing, a software package that analyzes raw in situ sequencing images to produce a genotype-to-phenotype mapping for each cell. STARCall improves upon previous solutions by combining stitching and alignment of images into a single step that minimizes both inter-cycle and intra-cycle alignment error. STARCall also improves detection and extraction of sequencing reads, incorporating filters and normalization to combat background fluorophore signal. We compare STARCall to other methods using a diverse set of images that include commonly encountered imaging problems such as variable intensity across channels and cycles and high levels of background. Specifically, this comprises ~250,000 images from a pooled screen of ~3,500 barcoded LMNA variants expressed in U2OS cells and ~1,200 barcoded PTEN variants in induced pluripotent stem cells (iPSC) and iPSC-derived neurons. Overall, STARCall aligned more than 50% of tiles with <1 pixel residual misalignment on all nine image sets, outperforming alternative packages by 14-35%. STARCall also yielded an 8-40% increase in genotyped cells due to improved filtering and normalization methods that address background fluorescence. STARCall can call tools like CellPose to segment cells and CellProfiler to compute cell features from the phenotyping images. STARcall is open-source and freely available, providing a robust solution for the analysis of in situ sequencing data.

DOI: https://doi.org/10.1371/journal.pcbi.1013689
Curr Protoc. 2026 Apr;6(4): e70368

Cell Painting PLUS: An Iterative Staining-Elution Protocol for High-Content Phenotypic Screenings.

Marlene Wedler, Elena von Coburg, Jose M Muino, Lars Valentin, Nils Körber, Sebastian Dunst, Shu Liu.

  Cell Painting (CP) methods use a combination of fluorescent dyes to label multiple cellular compartments simultaneously, enabling the comprehensive analysis of phenotypic changes through morphological profiling. Here, we present a detailed protocol for the Cell Painting PLUS (CPP) method along with an automated image and data analysis strategy. In CPP, the iterative staining, elution, and re-staining of cells with seven fluorescent dyes enable multiplexed analysis of nine cellular compartments and organelles. Each dye is captured in individual imaging channels to specifically distinguish effects on the plasma membrane, actin cytoskeleton, cytoplasmic and nucleolar RNA, lysosomes, nuclear DNA, endoplasmic reticulum, mitochondria, and Golgi apparatus. During the image analysis procedure, 894 morphological features (readouts) are extracted from single cells to generate comprehensive phenotypic profiles that resemble morphological perturbations. For efficient processing of the extracted features, we provide an automated data analysis workflow, which includes quality control, data normalization, and various data visualization tools. This workflow is based on a customized CPPAnalyzer Jupyter notebook and a CPPManager KNIME workflow, which can be easily applied without any special bioinformatics knowledge. In this way, CPP expands the multiplexing capacity, customizability, and, importantly, organelle specificity of the available CP-based screening methods. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Seeding of U2OS, MCF-7, or HepG-2 cells in multiwell plates and treatment of cells with compounds Support Protocol 1: Preparation of assay-ready compound plate Alternate Protocol: Seeding and differentiation of primary RPTEC-TERT1 cells in multiwell plates Basic Protocol 2: Staining and imaging of cells using Cell Painting PLUS Basic Protocol 3: Image analysis Basic Protocol 4: Data normalization and data quality control Basic Protocol 5: Visualization of data using CPPManager KNIME workflow.

Keywords:  Cell Painting PLUS (CPP); cell‐based assays; high‐throughput high‐content screenings; morphological profiling; new approach methodologies (NAMs)

DOI:  https://doi.org/10.1002/cpz1.70368
Nat Biomed Eng. 2026 Apr 30.

STRAIGHT-IN Dual: a platform for dual single-copy integrations of DNA payloads and gene circuits into human induced pluripotent stem cells.

Albert Blanch-Asensio, Deon S Ploessl, Benjamin B Johnson, Sara Cascione, Myrthe R M Berndsen, Nathan B Wang, Valeria V Orlova, Anna Alemany, Christine L Mummery, Kate E Galloway, Richard P Davis.

Targeting DNA payloads into human induced pluripotent stem cells (hiPSCs) typically requires multiple inefficient steps, slowing the testing of gene circuits and cell-fate programmes. Here we show that STRAIGHT-IN Dual enables simultaneous, allele-specific, single-copy integration of two DNA constructs efficiently within 1 week. STRAIGHT-IN Dual leverages the STRAIGHT-IN platform for near-scarless payload integration, facilitating the recycling of components for further modifications. Using STRAIGHT-IN Dual, we investigate how promoter choice and gene syntax influence transgene silencing and how these design features affect reporter expression and forward programming of hiPSCs into neurons, motor neurons and endothelial cells. We also incorporate a grazoprevir-inducible synthetic gene switch that complements tetracycline-inducible control, providing tunable and temporally controlled expression of different transcription factors within the same cell. STRAIGHT-IN Dual generates homogeneous engineered hiPSC populations, accelerating synthetic biology design-build-test cycles in stem cells and enabling controlled comparisons of circuit performances.

DOI: https://doi.org/10.1038/s41551-026-01677-9
EMBO Rep. 2026 Apr 29.

Ras promotes macropinocytic nutrient uptake by suppressing the albumin recycling receptor FcRn.

Rafael Paschoal de Campos, Xuxia Wu, Aslihan Inal, Zhao Liu, Craig B Thompson, Wilhelm Palm.

Macropinocytosis and lysosomal degradation of extracellular protein constitute a nutrient acquisition pathway in Ras-driven cancers. By catabolizing albumin, the most abundant plasma protein, Ras-transformed cells sustain growth in environments where free amino acids are scarce. Under physiological conditions, however, albumin is normally protected from lysosomal degradation by the neonatal Fc receptor (FcRn), which recycles albumin back to the extracellular space. Here, by investigating how cancer cells overcome FcRn-mediated albumin recycling, we identify the Ras-Erk MAPK signaling pathway as a critical regulator of FcRn. Expression of constitutively active Ras variants or stimulation with growth factors represses FcRn transcription through activation of the MAPK pathway, leading to decreased FcRn protein abundance. Conversely, pharmacological inhibition of Ras-MAPK signaling de-represses FcRn expression. Restoring FcRn levels in Ras-transformed cells limits lysosomal albumin degradation and impairs the proliferation of cells that depend on albumin as an essential amino acid source. Thus, oncogenic Ras signaling promotes the nutritional utilization of albumin by suppressing FcRn, thereby supporting cancer cell adaptation to nutrient-poor environments.

DOI: https://doi.org/10.1038/s44319-026-00787-4
J Allergy Clin Immunol Pract. 2026 Apr 28. pii: S2213-2198(26)00327-2. [Epub ahead of print]

Shrinking spleens and nodes, expanding horizons: leniolisib and the future of activated phosphoinositide 3-kinase delta syndrome (APDS).

Kittipos Visitsunthorn, V Koneti Rao.

Activated phosphoinositide 3-kinase delta syndrome is an inborn error of immunity characterized by combination of immunodeficiency with immune dysregulation and classified within autoimmune lymphoproliferative immunodeficiencies. Early therapeutic strategies extrapolated from autoimmune lymphoproliferative syndrome, including mTOR inhibition with sirolimus, provided variable control of lymphoproliferation. Recognition of constitutive PI3Kδ signaling led to the development of leniolisib, approved by the U.S. Food and Drug Administration in 2023, marking a transition toward pathway-specific precision therapy. In this Clinical Perspective, we review the evolution of targeted therapy in APDS, the biochemical structure and selectivity of leniolisib relative to other PI3K inhibitors, and the mechanistic distinction between proximal PI3Kδ inhibition and downstream mTOR blockade. We summarize current clinical evidence and practical considerations for dosing and monitoring in the absence of serum drug-level assays. Finally, we outline key unresolved questions, including long-term disease modification, biomarker validation, pediatric outcomes, treatment sequencing and combination strategies, while positioning leniolisib relative to hematopoietic stem cell transplantation, and desirability of it's wider global access.

DOI: https://doi.org/10.1016/j.jaip.2026.03.040
Genome Biol. 2026 Apr 27.

BEstimate: a computational tool for the design and interpretation of CRISPR base editing experiments.

Cansu Dinçer, Bo Fussing, Mathew J Garnett, Matthew A Coelho.

  CRISPR base editors enable scalable targeted DNA mutagenesis and are a powerful tool for analysing the function of variants of uncertain significance and disease modelling. Existing guide RNA (gRNA) design tools lack comprehensive functional annotation of target sequences. Here we developed BEstimate, a flexible computational pipeline that systematically specifies base editor gRNA target sites, generates on-target activity and off-target predictions, and provides functional, structural and clinical annotations of installed variants. BEstimate supports custom gRNA design against variant alleles and reversion of disease variants. BEstimate is a freely available, versatile tool for designing gRNA libraries and analysing base editor screens.

Keywords:  Base editing; CRISPR; Library design; Screening; guideRNA

DOI:  https://doi.org/10.1186/s13059-026-04077-z
FEBS J. 2026 Apr 25.

Neudesin modulates IGF1 and insulin signaling pathways by regulating the surface expression of IGF1R through a conserved WPE motif.

Yoshiaki Nakayama, Motohiro Nonaka, Yuki Masuda, Hikaru Matsumoto, Katsuaki Higashi, Yangha Pak, Satsuki Komoda, Ayami Tagawa, Ryohei Shimizu, Tadahisa Mikami, Satomi Nadanaka, Toshihide Yamasaki, Kohei Sano, Takahiro Mukai, Hiroshi Kitagawa, Morichika Konishi.

  Neudesin, a secreted protein implicated in diverse physiological processes, such as metabolism and immunity, lacks an identified receptor, which has prevented a detailed understanding of its molecular mechanisms. In this study, we aimed to elucidate the function of neudesin by identifying its cognate receptor and investigating its effects on cellular signaling. Using a combination of phage display, bioinformatics, and biochemical analysis, we identified insulin-like growth factor 1 receptor (IGF1R) as a high-affinity receptor for neudesin, with a binding affinity of 1.78 ± 1.87 nm. This interaction was mediated by a conserved tryptophan-proline-glutamic acid (WPE) motif in the IGF1R extracellular domain. Our cellular assays revealed that, while neudesin binding to IGF1R induces basal phosphorylation of the downstream signaling molecules extracellular signal-regulated kinase (ERK) and AKT (also known as Protein Kinase B, or PKB) in a cell-line-specific manner, it consistently acts as a negative modulator, attenuating both IGF1- and insulin-induced signaling. Mechanistically, neudesin promoted the downregulation of cell surface IGF1R, thereby reducing the receptor pool available for ligand stimulation. Furthermore, neudesin inhibited insulin signaling, likely through the co-internalization of IGF1R/insulin receptor (INSR) hybrid complexes. The physiological significance of this role was underscored in 3 T3-L1 adipocytes, where neudesin knockdown enhanced insulin-induced signaling and accelerated triglyceride accumulation. These results establish a novel molecular link between neudesin and the IGF1/insulin signaling axis, suggesting that neudesin may serve as an endogenous modulator of IGF1R/insulin activity, with potential implications for metabolic and growth-related diseases.

Keywords:  IGF1R; cell signaling; insulin; neudesin; phage display

DOI:  https://doi.org/10.1111/febs.70566
Cell. 2026 Apr 28. pii: S0092-8674(26)00399-5. [Epub ahead of print]

ErbB family receptor dimerization dynamics and dysregulation via long-term single-molecule imaging.

Kaibo Ma, Xiaojie Ma, João F Shida, Zijian Niu, Yuzhu Karlie Lin, Saptarshi Mandal, Alexandra Dobbins, Lior Golomb, Michael J Eck, Heidi Greulich, Matthew Meyerson, Chunte Sam Peng.

  Dimerization is crucial for the activation of ErbB family receptors, yet the real-time dynamics and effects of oncogenic mutations remain unclear. Here, we performed long-term, multicolor single-particle tracking (SPT) of EGFR, HER2, and HER3 in living cells using upconverting nanoparticles (UCNPs), which do not photobleach. Our technique enables continuous observation of receptor interactions, revealing details of their dimerization dynamics. Oncogenic EGFR mutations promote stable, ligand-independent dimerization. Unexpectedly, both HER2 and HER3 exhibit constitutive homodimerization, prompting a revised model for their activation mechanisms. HER2 mutations modestly enhance homodimer stability compared with EGFR mutations, while HER3 mutations destabilize homodimers, suggesting that HER3 homodimerization sequesters HER3 and limits heterodimerization with other receptors. We also identified stable, ligand-independent heterodimers among all three receptors, further stabilized by ligand stimulation. These insights offer a comprehensive ErbB interaction network, elucidating diverse dimerization mechanisms and implications for oncogenic signaling.

Keywords:  ErbB receptor family; dimerization network; long-term single-particle tracking; oncogenic signaling; upconverting nanoparticles

DOI:  https://doi.org/10.1016/j.cell.2026.04.010
bioRxiv. 2026 Apr 14. pii: 2026.04.11.717904. [Epub ahead of print]

Somatic mutation landscape revealed by non-invasive iPSC derivation from urine cells.

Taejeong Bae, Livia Tomasini, Leszek J Klimczak, Merit Kayastha, Milovan Suvakov, Yeongjun Jang, Alexandre Jourdon, Dmitry A Gordenin, Flora M Vaccarino, Alexej Abyzov.

Somatic mutations that arise post-zygotically create genetic diversity among normal human cells and provide key insights into human development and aging. Fibroblast-derived induced pluripotent stem cells (iPSCs) have proved to be a useful system for disease modelling; however, due to their clonal nature, iPSC lines carry somatic mutations inherited from the founder cells, raising concerns about their genomic integrity. At the same time, this clonality enables single-cell-level discovery of somatic mutations and the reconstruction of developmental lineages. In living individuals, though, this approach requires invasive biopsies and is limited to skin-derived lineages. Here, we generated 33 urine-derived iPSC lines from four males representing two father- son relationships, performed shallow whole-genome sequencing of the lines and analyzed somatic mutations. Derived iPSCs representing single cells from urine carried a few hundred of somatic single-nucleotide variants per genome, dominated by endogenous, clock-like mutational signatures and lacking environmental imprints such as UV-associated mutations. Copy-number analysis identified somatic CNVs in most of the lines and revealed higher CNV burdens in fathers than in sons, consistent with age-related structural mosaicism. Shared mutations across lines enabled reconstruction of cell lineage phylogenetic trees. In summary, urine-derived iPSCs showed genomic alterations comparable to those in fibroblast-derived iPSC lines and represent a valuable non-invasive alternative for disease modeling. Overall, this study provides the first genome-wide characterization of somatic mutations in urine-derived iPSCs and establishes them as a practical and non-invasive platform for charting somatic mutation landscapes and tracing developmental lineages in living humans.

DOI: https://doi.org/10.64898/2026.04.11.717904
Sci Rep. 2026 Apr 30.

Localized heat induces ERK activation and signal propagation in solid tumors.

Farsai Taemaitree, Yuta Takano, Daisuke Yamaguchi, Kazushi Yamaguchi, Yudai Yamashita, Motosuke Tsutsumi, Chentao Wen, Kohei Otomo, Kenji Hirai, James Hutchison, Indra Van Zundert, Sandra Krzyzowska, Maria Bravo, Sayuki Hirano, Koutarou D Kimura, Kazuhiro Aoki, Susana Rocha, Tomomi Nemoto, Beatrice Fortuni, Hiroshi Uji-I.

  Localized plasmonic heating by metallic nanoparticles offers a promising strategy to destroy cancer cells through controlled thermal stress. However, how cells sense and respond to microscale temperature variations within complex tissue environments remains unclear. Here, we investigate how plasmon-induced local heating reshapes intercellular signaling and cell fate within tumor spheroids, focusing on the extracellular signal-regulated kinase (ERK) pathway. HeLa spheroids expressing a FRET-based ERK biosensor were subjected to defined photothermal stimuli using gold nanostars as nanoscale heat sources, while ERK activity was tracked with a deep-learning algorithm (3DeeCellTracker). Local heating triggered marked alterations in ERK signaling dynamics compared to spontaneous activity, including changes in activation frequency, timing, and duration. Remarkably, heat-induced ERK activation spread across neighboring cells, revealing thermally mediated intercellular propagation. Quantitative analysis further showed that temperature elevation modulates cell death and division in a power-dependent manner. These results uncover how nanoscale heat generation governs signaling networks and collective cellular behavior, providing a mechanistic framework to understand and optimize heat-based cancer treatment strategies.

Keywords:  ERK signaling; Gold nanoparticles; Photothermal therapy; Tumor spheroids

DOI:  https://doi.org/10.1038/s41598-026-49009-w
bioRxiv. 2026 Apr 13. pii: 2026.04.09.717047. [Epub ahead of print]

Modulation of Oncogenic KRAS Signaling by Branched Actin-driven Cell Membrane Protrusions.

Gabriel Muhire Gihana, Kushal Bhatt, Bo-Jui Chang, Vasanth Murali, Felix Zhou, Jungsik Noh, Roshan Ravishankar, Hazel Borges, Jinlong Lin, Jessica Oceguera, Pedro Augusto Nogueira, Lizbeth Perez Castro, Niranjan Venkateswaran, Bingying Chen, Reto Fiolka, Maralice Conacci-Sorrell, Kevin Dean, Gaudenz Danuser.

For over three decades, we have known that oncogenic RAS alters the actin cytoskeleton organization and cell surface morphology 1,2 . RAS activates the GTPase RAC1, which triggers the growth of branched actin networks to promote cell membrane protrusions 3,4 . In melanoma, the hyperactive RAC1 mutant, Rac1 P29S , was recently shown to drive extended lamellipodia, which then empower cell proliferation through sequestration and localized inhibition of the merlin tumor suppressor 5 . This discovery illustrates cell morphological programs not only as outputs but also as regulators of human oncogenic signals. Hence, we wondered whether the pronounced branched actin-driven membrane protrusions (BAMPs) downstream of oncogenic RAS are not mere outputs of RAS signaling but rather an active component in mediating the oncogenic penetrance of RAS mutants. We used volumetric light sheet microscopy and biochemical approaches to investigate the role of BAMPs in regulating the molecular signaling of oncogenic KRAS in pancreatic and lung cancer models. We found that elevated BAMP formation regulated the interaction of oncogenic KRAS with downstream effectors, specifically with the RAC1 GEF TIAM1. This implies that BAMPs amplify their own upstream regulators in a positive feedback. This meritorious cycle upregulates cyclin D1 expression by inactivating the merlin tumor suppressor, independently of the mitogen activated protein kinase pathway (MAPK). In the absence of BAMPs, cells carrying oncogenic KRAS mutations are unable to attain their full penetrance in proliferation. Overall, this work unveils the long-overlooked role of branched actin-driven cell morphology in the functionalization of KRAS mutants as potent oncogenes.

DOI: https://doi.org/10.64898/2026.04.09.717047
NPJ Syst Biol Appl. 2026 Apr 25.

The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease.

Mainak Guharoy, Isabelle Adant, Matthew Bird, Alexander Botzki, James Collier, Jonas Dehairs, Stefaan Derveaux, Simon Devos, Geert Goeminne, Francis Impens, Andrea Jáñez Pedrayes, Rekin's Janky, Ruth Maes, Pedro Magalhães, Teresa M Maia, Wouter Meersseman, Daisy Rymen, Johannes V Swinnen, Delphi Van Haver, Dries Verdegem, Peter Witters, David Cassiman, Bart Ghesquiere.

Analyzing single omics and integrating multimodal omics datasets to capture functional dysregulation in disease remains challenging. Here, we propose a bioinformatics framework that leverages curated datasets of protein complexes ('complexome') as a foundation for proteomics data integration. Available for human and other model organisms, the complexome provides a global view of cellular function, enabling queries with proteomics datasets. We first benchmarked how protein abundances across human tissues shape distinct complexomic profiles, serving to fingerprint biological activity. Next, we analyzed complexome remodeling using disease versus control proteomics quantifications. Using proteomics data from fibroblasts of patients with genetically confirmed metabolic defects, we identified significant perturbations in mitochondrial oxidative phosphorylation complexes and additional complexes involved in wider mitochondrial functions. The complexome provides a systems-wide approach to dissect mechanisms underlying disease-related functional and phenotypic changes by mapping measured protein-level perturbations to specific molecular complexes. The software is available as a Python notebook at https://github.com/mguharoy/Complexome.

DOI: https://doi.org/10.1038/s41540-026-00716-0
Bioinform Adv. 2026 ;6(1): vbag070

Leveraging training expertise to build capacity in computational personalised medicine.

PermedCoE consortium

Summary: Rapid development of genomic technologies in recent years enables personalised medicine to become an essential part of healthcare. Advanced computational methods are required to extract relevant insights that can be applied in clinical settings. This presents a challenge for clinicians and biomedical researchers, who need specialised training to adopt these tools. Within the context of PerMedCoE, the first European Centre of Excellence in Personalised Medicine, we developed and delivered a competency-based training programme to support professionals in the life sciences to work with modelling and simulation tools that integrate omics data to identify biological processes relevant to disease. We identified a set of required competencies in the field and built a series of career profiles with specific competence levels in these. The competencies and profiles contributed to define the focus and target audience of the training activities delivered: a combination of self-paced learning resources, webinars and online and face-to-face synchronous courses. The outputs of the programme (competencies, career profiles and training materials) can be used by biomedical professionals for their own career development or to train others. In addition, the approach can be adopted by other fields with rapid technological advancements and a constant need to upskill professionals.
Availability and implementation: The competency framework is reproduced in full in this paper as supplementary material and available on the Competency Hub at https://competency.ebi.ac.uk/framework/permedcoe/2.1.

DOI: https://doi.org/10.1093/bioadv/vbag070
bioRxiv. 2026 Apr 15. pii: 2026.04.14.718551. [Epub ahead of print]

Tracing cell communication programs across conditions at single cell resolution with CCC-RISE.

Andrew Ramirez, Nathaniel Thomas, Daniel R Calabrese, John R Greenland, Aaron S Meyer.

Cell-cell communication (CCC) mediates coordinated cellular activities that vary dynamically across time, location, and biological context. While various tools exist to infer CCC, they typically aggregate data according to pre-defined cell types, obscuring critical single-cell heterogeneity. Furthermore, because signaling pathways and cell populations operate in a coordinated manner, an integrative analytical approach is essential. To address these challenges, we developed CCC-RISE, an extension of the tensor-based method Reduction and Insight in Single-cell Exploration (RISE). CCC-RISE identifies integrative patterns of single-cell variation by deconvolving communication into interpretable modules defined by unique sender cells, receiver cells, ligands, and condition associations. We applied this framework to a COVID-19 cohort with varying disease severity and a lung transplant cohort with acute allograft dysfunction. In both contexts, CCC-RISE successfully identified disease-relevant communication programs and traced them to specific cellular subpopulations, often crossing conventional cell-type boundaries. This approach offers a robust pipeline enabling the identification of disease-relevant signaling subpopulations that are invisible to aggregate methods.
Highlights: CCC-RISE enables integrative analysis of cell-cell communication across multiple conditions at single-cell resolutionCCC-RISE deconvolves signaling patterns into modules defined by their sender cells, receiver cells, LR pairs, and experimental conditions/samplesAnalysis at single-cell resolution uncovers signaling activity within and across conventional cell types.

DOI: https://doi.org/10.64898/2026.04.14.718551
J Biol Chem. 2026 Apr 27. pii: S0021-9258(26)01955-1. [Epub ahead of print] 113083

Potassium suppresses allosteric activation of ZAP-70-dependent T Cell Receptor signaling.

Swarnendu Roy, Soumee SenGupta, Kaustav Gangopadhyay, Sudipta Majumder, Jibitesh Das, Anushka Sinha, Prosad Kumar Das, Bidisha Sinha, Rahul Das.

  Ionic imbalance in the tumor microenvironment alters the function of tumor-infiltrating T lymphocytes. High extracellular K+ suppresses T cell function by negatively regulating T cell receptor (TCR) signaling. The mechanism of how monovalent cations regulate T lymphocyte function is unknown. Here, we present a mechanism that explains how cellular potassium dynamics regulate TCR function. At rest, high intracellular K+ uncouples allosteric recruitment of ZAP-70, a key signaling module, to the TCR complex. Elevated K+ concentration imparts a higher thermodynamic penalty on the binding of the ZAP-70 regulatory module to the phosphotyrosine residues in the ITAM motifs of the CD3 chain. Our data suggest that K+ functions as a key allosteric modulator, stabilizing the autoinhibited conformation of ZAP-70. Thus, it prevents spontaneous TCR activation in the resting state. Formation of the antigen-TCR complex induces K+ efflux, leading to spontaneous recruitment of ZAP-70 to the TCR. Increasing extracellular K+ concentration perturbs K+ efflux and slows ZAP-70 recruitment to the TCR complex, even upon antigen binding. Impaired ZAP-70 activation partially dampens TCR signaling, thereby altering downstream signaling. In contrast, the regulatory module in the paralogous kinase Syk, which is expressed in B cells, is insensitive to potassium concentration. At elevated K+ concentration, the interaction between the Syk regulatory module and phosphorylated ITAM motifs remains unaltered. We conclude that K+ dynamics are integral to T cell ligand discrimination and fundamental to turning off the signaling during T cell quiescence.

Keywords:  Cell Signaling; Potassium; T cell receptor; Tyrosine Kinase; ZAP-70

DOI:  https://doi.org/10.1016/j.jbc.2026.113083
EMBO Rep. 2026 Apr 27.

CRL4AMBRA1 is a key mediator for AKT-dependent cell cycle control in neural progenitor cells.

He Wang, Panmiao Liu, Runmin Wang, Hanwen Gu, Tingting Zhu, Guiquan Chen, Jian-Jun Yang.

Neural progenitor cell (NPC) proliferation is fundamental for population expansion and brain development. G1 phase control determines the cell cycle duration of NPCs and thereby affects their proliferation efficiency. However, the molecular mechanisms governing G1 phase progression in NPCs remain unclear. Here, we show that AKT gain-of-function mutations and pharmacological inhibition exert opposing effects on NPC proliferation. Consistently, Emx1-Cre-mediated deletion of Akt1/2/3 in mice impairs NPC proliferation and disrupts cortical development. We find that AKT deficiency induces G1 phase arrest and prolongs the cell cycle of NPCs. Mechanistically, we demonstrate that AKT-mediated phosphorylation inhibits the activity of CRL4AMBRA1 E3 ubiquitin ligase to safeguard cyclin D2 (CCND2) stability. Specifically, AKT phosphorylates DDB1, the adaptor of CRL4AMBRA1, which disrupts its interaction with CCND2 and reduces its degradation. These findings reveal a post-translational mechanism impacting NPC cell cycle and cortical morphogenesis, providing insight into the etiology of malformations of cortical development.

DOI: https://doi.org/10.1038/s44319-026-00768-7
Nat Cell Biol. 2026 Apr 30.

The atypical E3 ligase HOIL-1 safeguards the ribosome during cellular stress.

Todd Douglas, Pengju Nie, Jiasheng Zhang, Kyrillos S Abdallah, Zhiping Wu, Meghan McReynolds, Kazuhiro Iwai, Junmin Peng, Wendy V Gilbert, Lawrence H Young, Craig M Crews.

The ribosome has emerged as a signalling hub that can sense metabolic perturbations and coordinate responses that either restore homeostasis or initiate cell death. The range of insults that signal via the ribosome and the mechanisms governing such cell fate decisions remain uncharacterized. Here we identify the atypical E3 ligase HOIL-1 as an unexpected node in the ribosome signalling network that resolves cellular stress. We find that truncating HOIL-1 mutations associated with dilated cardiomyopathy exacerbate cardiac dysfunction in mice and broadly sensitize cells to nutrient and translational stress. These diverse signals converge on the MAP3K ZAKα, a sentinel of ribotoxic stress. Mechanistically, HOIL-1 promotes ribosome ubiquitination and facilitates cytoprotective ribosome-associated quality control. HOIL-1 loss of function causes glucose starvation to become ribotoxic, leading to ZAKα-dependent ATF4 activation and disulfidptosis driven by the cystine-glutamate antiporter xCT. These data reveal a molecular circuit controlling cell fate during nutrient stress and establish the ribosome as a signalosome that responds to cellular glucose levels.

DOI: https://doi.org/10.1038/s41556-026-01936-6
Nat Commun. 2026 Apr 25.

Aged differentiated cells reverse into native stemness-like state by niche cytokines to sustain lifelong homeostasis and tissue repair.

Shalini Dimri-Wagh, Swarnabh Bhattacharya, Gharam Yassen, Ofir Shorer, Aya Amitai-Lange, Anna Altshuler, Shira Hadad-Porat, Keren Yizhak, Yuval Shaked, Michael Mimouni, Beatrice Tiosano, Ramez Barbara, Ruby Shalom-Feuerstein.

Recent studies report that epithelial differentiated cells can undergo a reverse process called dedifferentiation in response to stem cell loss. However, the extent of this reversion and the plasticity of young versus aged-differentiated cells remain unclear. Here we show that dedifferentiated corneal epithelial cells acquire a transcriptomic state closely resembling native stem cells, sustain tissue homeostasis across lifespan and efficiently repair repeated tissue injury. Transplantation of stage-specific genetically traceable aged differentiated epithelial cells onto a denuded niche reveals reversion into a stemness-like state, restoring both quiescent and active stem cell compartments. This plasticity operates within the epithelial lineage, allowing transitions along the differentiation axis, but remains restricted across lineages, as transplanted conjunctival cells fail to regenerate the corneal stem cell pool. Mechanistically, we identify niche-derived cytokines that trigger reprogramming in vivo and enhance stemness in primary human corneal epithelial cells, revealing a conserved and therapeutically exploitable pathway for epithelial regeneration.

DOI: https://doi.org/10.1038/s41467-026-72331-w
Cell Chem Biol. 2026 Apr 30. pii: S2451-9456(26)00137-6. [Epub ahead of print]

Mechanism by which a linoleic acid metabolite suppresses cancer cell growth by inhibiting mTOR.

Seung Ju Park, Sera Kim, Hongmok Kwon, Jiyeon Choi, Ji Kwang Kim, Inhong Jung, Seol-Wa Lim, Young Ran Kim, A-Yeong Yang, Boah Lee, Haein Lee, Seung Eun Park, Seulgi Lee, Myeongsu Shin, Bernie Byunghoon Park, YunHye Kim, Jinwook Lee, Byung-Chul Oh, Daniel Deredge, Patrick L Wintrode, Mi-Young Kim, Youngjoo Byun, Seyun Kim.

  Mechanistic target of rapamycin (mTOR) is a key protein kinase that integrates various internal and external signals to control biological events including cell growth. Whereas substantial efforts were made to elucidate protein subunits interacting with mTOR, endogenous metabolite-mTOR interactions remain largely unknown. Using affinity protein purification and mass spectrometry, we identified direct binding of mTOR to 13-S-hydroxyoctadecadienoic acid (13-S-HODE) which is an oxygenated metabolite of linoleic acid, a polyunsaturated essential fatty acid. Interaction of 13-S-HODE with the catalytic ATP-binding domain of mTOR prevented its kinase activity in an ATP-competitive manner. Furthermore, either 13-S-HODE treatment or expression of arachidonate 15-lipoxygenase (ALOX15), an enzyme responsible for 13-S-HODE production, reduced mTOR signaling, thereby suppressing the growth of cancer cells as well as tumor xenografts. Our results highlight the importance of 13-S-HODE serving as a tumor suppressive, mTOR-inhibiting metabolite that links polyunsaturated fatty acid metabolism and the mTOR signaling in controlling cancer cell growth.

Keywords:  13-S-HODE; ALOX15; PUFA; cancer; cell growth; linoleic acid; mTOR

DOI:  https://doi.org/10.1016/j.chembiol.2026.04.004
Genome Med. 2026 May 01. pii: 53. [Epub ahead of print]18(1):

ERG is a regulator of dynamic and reversible endothelial plasticity.

Kristen Schulz, Steven R Botts, Kai Ellis, Corey A Scipione, Nadiya Khyzha, Christy Ho, Rathnakumar Kumaragurubaran, Kyoko E Yuki, Joshua D Wythe, Clint L Miller, Michael D Wilson, Kathryn L Howe, Jason E Fish.

   BACKGROUND: Endothelial cells (ECs) orchestrate vascular homeostasis and resilience but can undergo reprogramming into a mesenchymal-like phenotype through an endothelial-to-mesenchymal transition (EndMT). Crucially, EndMT is a linchpin underlying several cardiometabolic diseases, but is almost universally studied as an endpoint. The transcription factor ERG (ETS-related gene) is critical to the maintenance of EC identity and function, yet the dynamic transcriptional and functional consequences of ERG loss on EndMT programs, and whether this can be reversed, has not been explored.
METHODS: We modeled both acute and chronic ERG loss in human aortic ECs using siRNA knockdown and CRISPR/Cas9-mediated ERG deletion. We profiled temporal changes in chromatin accessibility (ATAC-seq), transcriptomic responses (RNA-seq), and endothelial phenotypes, including migration and barrier integrity. The temporal kinetics of ERG loss and restoration was assessed by comparing stable ERG knockout to transient ERG knockdown and recovery over time. The implications to human disease were deciphered by examining ERG gene regulatory networks in human atherosclerosis and linkage with genetic variation associated with human cardiovascular disease.
RESULTS: Analysis of gene regulatory networks revealed profound and dynamic rewiring of endothelial and mesenchymal transcriptional programs upon loss of ERG. While endothelial identity was rapidly lost by 24 h of ERG knockdown, acquisition of mesenchymal identity, barrier dysfunction, and enhanced cell migration required 72 h to manifest. Loss of ERG was accompanied by a rapid reduction in accessibility of ETS motifs and an extensive gain in open chromatin containing AP1 motifs. Disease-relevant endothelial dysfunction programs were associated with dynamically reorganized transcriptional networks. Importantly, restoration of ERG expression reversed EndMT gene regulatory networks and phenotypes.
CONCLUSIONS: Overall, this study highlights the ETS factor, ERG, as an essential transcriptional safeguard of endothelial identity and function, and demonstrates that ERG loss initiates a progressive, yet reversible, EndMT program with EC identity loss preceding a gain of mesenchymal gene regulatory networks and phenotypes. This study establishes loss of ERG as an early initiating event in EndMT and suggests that ERG-targeted therapies may hold promise for promoting endothelial resilience.

Keywords:  Cardiovascular disease; Endothelial cell identity; Endothelial function; Endothelial-to-mesenchymal transition; Gene regulatory networks

DOI:  https://doi.org/10.1186/s13073-026-01638-6
Elife. 2026 Apr 27. pii: RP109553. [Epub ahead of print]15

Single-cell lineage tracing identifies hemogenic endothelial cells in the adult mouse bone marrow.

Jing-Xin Feng, Mei-Ting Yang, Lili Li, Caiyi C Li, Ferenc Livak, Jack Chen, Yongmei Zhao, Dunrui Wang, Avinash Bhandoola, Naomi Taylor, Giovanna Tosato.

  During mouse development, hematopoietic stem and progenitor cells (HSPCs) originate from hemogenic endothelial cells (ECs) through a process of endothelial-to-hematopoietic transition. These HSPCs are thought to fully sustain adult hematopoiesis. However, it remains unknown whether adult ECs retain hemogenic potential. Here, we used in vivo genetic lineage tracking at population and single-cell (sc) levels, scRNA sequencing, and bone marrow (BM) transplantation to detect hemogenic ECs in adult mice. We identify and characterize BM-resident, adult Cdh5/VE-Cadherin+ ECs that produce hematopoietic cell-progeny in vitro and in mice. These adult hemogenic ECs and their hematopoietic cell progeny give rise to hematopoietic cells following adoptive transfer into adult mice. Furthermore, blood cells generated from adult and developmental ECs comparably home to peripheral tissues, where they similarly contribute to inflammatory responses. Thus, our results identify previously unrecognized BM-derived adult hemogenic ECs that generate HSPC and functional mature blood cells.

Keywords:  bone marrow; cell biology; endothelium; hematopoiesis; mouse; transplantation

DOI:  https://doi.org/10.7554/eLife.109553