bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2026–07–12
eighteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU



  1. Nat Commun. 2026 Jul 09.
      Obtaining a precise genetic tuberous sclerosis complex diagnosis is a challenge as many missense TSC2 variants are variants of uncertain significance. Variants of uncertain significance in TSC2 have been resolved by one-at-a-time functional assays, but these assays cannot scale to the 3634 TSC2 missense variants of uncertain significance observed so far. To address this challenge, we use massively parallel sequencing to measure the steady-state abundance of almost 9000 TSC2 missense variants and develop an mTOR pathway activity assay using genome editing and cell sorting to generate activity scores for 391 missense variants. We observe that 1256 of 8864 (14.17%) missense variants assayed have altered TSC2 abundance, and 69 of 391 (17.65%) missense variants assayed have altered mTOR pathway activity. Calibration and integration of these data into classification of variants identified in a clinical cohort putatively reclassifies 212 of 276 (76.8%) TSC2 missense variants of uncertain significance. These datasets will lead to improved genetic diagnosis of tuberous sclerosis complex with potential positive impacts on the clinical management of patients and their families.
    DOI:  https://doi.org/10.1038/s41467-026-75442-6
  2. J Cachexia Sarcopenia Muscle. 2026 Aug;17(4): e70335
       BACKGROUND: The serine/threonine kinase AKT is a key regulator of glucose and energy metabolism. Prevailing dogma suggests that AKT is an obligate intermediate for glucose uptake in all metabolic tissues and that impaired AKT signalling is a major molecular driver of insulin resistance in obesity. However, whether AKT is universally required for insulin-stimulated glucose uptake across tissues in vivo has remained unresolved.
    METHOD: Several mouse models of adipose-specific AKT2 deletion (F-AKT2KO) and skeletal muscle-specific AKT1, AKT2 and combined AKT1/AKT2 knockout mice (M-AKT1KO, M-AKT2KO and M-AKTDKO) were generated. Skeletal muscle and adipose tissues were analysed following in vivo administration of insulin (2 U/kg), using Western blotting, phosphoproteomics, PI(3,4,5)P3 ELISA and mitochondrial respiration assays. Glucose metabolism was assessed using [3H]-2-deoxyglucose uptake, hyperinsulinemic-euglycemic clamps, glucose and insulin tolerance tests. Global phosphoproteomics was performed in insulin-stimulated skeletal muscle lacking AKT isoforms.
    RESULTS: Loss of AKT2 in adipose tissue impaired insulin signalling, including reduced pAS160Thr649, and markedly decreased insulin-stimulated glucose uptake (~2-3 fold reduction in F-AKT2KO vs F-Control, p < 0.001, n = 7-11), resulting in systemic insulin resistance. In contrast, M-AKTDKO mice exhibited a robust increase in insulin-stimulated glucose uptake (~3-4 fold increase) despite complete loss of AKT signalling, including pAS160Thr649. Phosphoproteomic analysis of M-AKTDKO (n = 3-4) identified ~7088 phosphosites, with 795 uniquely upregulated in insulin-stimulated M-AKTDKO muscle (fold change > 2, p < 0.05), enriched in PI3K and AMPK pathways. Consistently, ~8-fold (p < 0.05) increase in PIP3 levels was observed in M-AKTDKO muscle in response to insulin. Additionally, AKT deficiency was associated with reduced complex I-dependent mitochondrial respiration (~37% decrease in state 3 respiration), consistent with altered energetic status and AMPK activation. Genetic epistasis experiments demonstrated that both AKT and AMPK activity are required for insulin-stimulated glucose uptake, systemic glucose homeostasis and whole body insulin sensitivity.
    CONCLUSION: These findings challenge the long-standing assumption that AKT is universally required for insulin-stimulated glucose uptake in vivo. The study demonstrates that while AKT is essential in adipose tissue, it is dispensable for insulin-stimulated glucose uptake in skeletal muscle. AKT exerts negative feedback on PI3K signalling in both tissues; however, only skeletal muscle engages AMPK in the abscence of AKT to preserve glucose uptake. These findings redefine tissue-specific insulin signalling mechanisms and identify AMPK as a critical downstream target of PI3K that coordinates with AKT to regulate glucose uptake.
    Keywords:  AKT signalling; AMPK signalling; GLUT4 translocation; PI3K‐PIP3 pathway; insulin signalling
    DOI:  https://doi.org/10.1002/jcsm.70335
  3. J Mol Cell Cardiol. 2026 Jul 09. pii: S0022-2828(26)00102-1. [Epub ahead of print]
      ErbB receptor tyrosine kinases orchestrate phosphorylation-based signaling in response to extracellular ligands and are key drivers in cancer biology. Although ErbB-targeted therapies have transformed cancer care, some agents cause cardiac adverse events. Yet, the acute phosphorylation programs engaged by ErbB ligands in the adult heart remain incompletely defined. Here, we applied in vivo quantitative phosphoproteomics with dual enrichment using TiO₂ and anti-phosphotyrosine antibodies to map acute cardiac phosphorylation responses to epidermal growth factor (EGF; EGFR/ErbB1) and neuregulin-1β (NRG1β; ErbB3/ErbB4) in adult mouse hearts. EGF triggered robust receptor tyrosine kinase signaling, convergence with insulin-associated nodes independent of insulin receptor activation, and phosphorylation of calcium-handling proteins including phospholamban, SERCA, NCX1, and CaV1.2, implicating CaMK2δ. NRG1β elicited a coordinated ErbB-dependent response featuring activation of Akt, MAPK, and stress kinases, with engagement of sarcomere and metabolic modules. Comparative analysis identified shared core signaling alongside ligand-specific differences in kinase and transcription factor phosphorylation, with EGF displaying broader network breadth. These data provide a phosphorylation-centric framework for ligand-resolved ErbB signaling in the heart and offer mechanistic insight into how ErbB-targeted therapies may influence cardiac function.
    Keywords:  Cardiac signaling; EGF signaling; ErbB signaling; NRG1β signaling; Phosphoproteomics
    DOI:  https://doi.org/10.1016/j.yjmcc.2026.07.006
  4. Bio Protoc. 2026 Jul 05. 16(13): e5724
      Protein kinase B, more commonly known as Akt, is a family of three serine/threonine kinases (Akt1, Akt2, and Akt3) that play a central role in regulating processes such as proliferation, survival, metabolism, and migration through phosphorylation of downstream targets. Given its involvement in numerous cellular processes, aberrant Akt signaling is prevalent across multiple cancer types, underscoring the need for Akt kinase assays to assess activity, regulatory mechanisms, and the efficacy of targeted interventions. Most existing Akt kinase assays rely on expensive commercial kits, some of which employ pre-purified, constitutively active Akt expressed in insect cells, bypassing physiologic autoinhibition of Akt; therefore, they are not suitable for evaluating allosteric inhibitors or context-dependent regulation. Here, we describe a detailed, step-by-step protocol for a nonradioactive Akt kinase assay using epitope-tagged, recombinant Akt1 expressed in a mammalian cell line and isolated by immunoprecipitation. This method eliminates the need to co-express Akt with upstream regulatory kinases or to purify active enzyme from insect cells, a time-consuming and technically demanding process, particularly when analyzing multiple Akt mutants. Because Akt is assayed in a regulated, autoinhibited state, this protocol enables direct evaluation of allosteric inhibitors that cannot be assessed using active Akt purified from insect cells. We note, however, that Akt1 kinase activity in this assay is measured from epitope-tagged, transiently overexpressed protein, which could influence cellular signaling dynamics. Despite this limitation, the cellular context preserves key regulatory features of Akt1 autoinhibition and membrane-dependent activation that are absent in assays using purified, pre-activated kinase. Together, this protocol supports analysis of Akt kinase activity under diverse experimental conditions, including receptor stimulation, pharmacologic treatment, allosteric inhibitor exposure, and mutations, using an accessible, economical, and physiologically relevant approach. Key features • This protocol is broadly accessible, requiring only standard laboratory equipment and commonly used techniques without specialized instrumentation or purified kinase preparations. • This protocol measures Akt1 catalytic output by assessing substrate phosphorylation following immunoprecipitation of transiently expressed, epitope-tagged Akt1 from cells. • The assay is performed in a low-throughput format and provides a semiquantitative readout. • This protocol can be adapted to other mammalian cell lines and optimized for other protein kinases of choice.
    Keywords:  Akt; Allosteric inhibitors; Immunoprecipitation; Nonradioactive kinase assay; Phosphorylation
    DOI:  https://doi.org/10.21769/BioProtoc.5724
  5. Nature. 2026 Jul 08.
    Tabula Sapiens Consortium
      Developing a universal representation space for cells that encompasses the tremendous molecular diversity of cell types across species would be transformative for cell biology. Recent work using single-cell transcriptomic approaches to create molecular definitions of cell types in the form of cell atlases has provided the necessary data for such an endeavour1-3. Here we present the universal cell embedding (UCE) foundation model. UCE was trained on a large corpus of cell data using self-supervision, creating a unified biological latent space that can represent cells across diverse tissues and species. This latent space captures important biological variation despite the presence of experimental noise. UCE's universality means that new cells can be embedded with no data labelling, model training or fine-tuning. We used UCE to create the Integrated Mega-scale Atlas, embedding 36 million cells, with more than 1,000 uniquely named cell types, from hundreds of experiments, dozens of tissues and eight species. We gain insights into the organization of cell types and tissues within the space. UCE's embedding space exhibits emergent behaviour, identifying biology that it was never trained for, such as identifying developmental lineages and embedding data from species that were not included in the training set. Overall, by enabling a universal representation for every cell state and type, UCE is a valuable tool for analysis, annotation and hypothesis generation over single-cell data.
    DOI:  https://doi.org/10.1038/s41586-026-10689-z
  6. Cell Signal. 2026 Jul 09. pii: S0898-6568(26)00391-8. [Epub ahead of print] 112734
      How glucose and one‑carbon metabolism converge on Rag GTPase-dependent mechanistic target of rapamycin complex 1 (mTORC1) remains poorly defined, particularly in the absence of AMP-activated protein kinase (AMPK). This study mapped an AMPK-independent glucose-response pathway in human cells using CRISPR editing, rescue assays, proteomics, thermal stability analysis, and RNA sequencing. In AMPK-deficient human cells, glucose refeeding rapidly reactivated mTORC1, and proteomics of mTORC1-associated complexes identified NSUN2 as a glucose-associated factor. NSUN2 loss markedly reduced glucose-induced mTORC1 activation, whereas re-expression restored it. Genetic analyses placed NSUN2 upstream of the lysosomal Rag module because constitutively active Rag GTPases bypassed NSUN2 deficiency. Structure-function studies showed that the acute signaling role of NSUN2 was largely independent of its catalytic cysteines, but required an N-terminal nutrient-responsive motif and a predicted S-adenosylmethionine (SAM)-responsive segment. SAM increased the thermal stability of wild-type NSUN2, and proteomics and Immunoprecipitation identified methionine adenosyltransferase 2 A (MAT2A), a SAM-producing enzyme, as a glucose-responsive NSUN2 partner. MAT2A knockout reproduced the signaling defect. Transcriptomics further linked NSUN2 to glucose-responsive programs in proteostasis, secretion, and stress adaptation. These results identify NSUN2 as a noncanonical signaling factor that couples glucose and methyl-donor availability to Rag-dependent mTORC1 control and transcriptional adaptation.
    Keywords:  Glucose sensing; NSUN2; Nutrient signaling; Rag GTPases; S-adenosylmethionine; mTORC1
    DOI:  https://doi.org/10.1016/j.cellsig.2026.112734
  7. Proc Natl Acad Sci U S A. 2026 Jul 14. 123(28): e2615120123
      Brain capillaries sense neural activity and direct blood flow to active regions-a process termed neurovascular coupling that underlies activity-dependent increases in local perfusion (functional hyperemia). A key contributor to functional hyperemic responses is the capillary endothelial cell (cEC) inward rectifier K+ (Kir2.1) channel, which, when activated by neuronal activity-derived extracellular K+, initiates vasodilatory electrical signals that propagate through the vascular network. Kir2.1 channel function requires continual production of its lipid cofactor, phosphatidylinositol-4,5-bisphosphate (PIP2), and is compromised in mouse models of cerebral small vessel (cSVD). Although decreased PIP2 availability is a common feature of cSVDs, mechanisms underlying PIP2 synthesis remain poorly understood. We hypothesized that Arf6, a small GTPase expressed in cECs that stimulates PIP2 production, is critical for this process. Using patch-clamp electrophysiology, we demonstrate that inhibiting Arf6 activity progressively decreased cEC Kir2.1 channel activity. This deficit manifested as loss of capillary-to-arteriole electrical signaling in isolated vessels and diminished functional hyperemia in vivo. Exogenously provided PIP2 restored Kir2.1 currents and functional hyperemia after Arf6 inhibition or genetic knockdown. Collectively, our data suggest that cEC Arf6 sustains Kir2.1 activity by maintaining PIP2 levels and demonstrate that diminished PIP2 synthesis is sufficient to impair functional hyperemia. Furthermore, we identify Arf6 as a mechanistic link between PIP2 production and endothelial electrical signaling, highlighting Arf6 as a potential therapeutic target for restoring functional hyperemia.
    Keywords:  ADP-ribosylation factor 6; Kir2.1 channels; cerebral blood flow; endothelial cells; phosphatidylinositol-4,5-bisphosphate
    DOI:  https://doi.org/10.1073/pnas.2615120123
  8. Nat Commun. 2026 Jul 06. pii: 5631. [Epub ahead of print]17(1):
      Thoracic aortic aneurysms and dissections (TAAD), a life-threatening complication of Marfan syndrome (MFS), lack curative therapies. Our previous studies revealed that versican accumulation drives MFS aortopathy through AKT-NO pathway overactivation, but the upstream mechanisms remained unclear. Here, we show that versican-driven fibronectin (FN) accumulation activates an αVβ3-PI3K-PIP3-PDK1-ILK signaling cascade leading to AKT-NOS2 upregulation and aortic disease. FN accumulates in aortas of MFS patients and mice of both sexes and correlates with increased αVβ3 integrin and ILK expression. Disrupting FN assembly or inhibiting αVβ3, PI3K, PIP3, PDK1 or ILK prevents FN-induced AKT activation and NOS2 upregulation, restores vascular contractility, and limits aortic dilation in MFS mice. Inhibition of ILK or PDK1, aortic silencing of Ilk, or smooth muscle-specific deletion of Ilk reverses or prevents aortic growth. Together, these findings define a mechanistically integrated FN-αVβ3-PI3K-PIP3-PDK1-ILK-AKT-NOS2 signaling cascade in MFS and support its causative role in human TAAD, highlighting its components as potential targets for therapeutic intervention.
    DOI:  https://doi.org/10.1038/s41467-026-74707-4
  9. Development. 2026 Jul 01. pii: dev205643. [Epub ahead of print]153(13):
      The intestinal epithelial lining is highly dynamic, with size and cellular composition adapting to nutrient status. This requires regulation of intestinal stem cell (ISC) proliferation and enterocyte size. How the intestinal absorptive area matches physiological nutrient conditions remains unclear. Here, we show that the transcription factor Nuclear Factor Y (NF-Y) plays a role in this process. NF-Y loss of function in ISCs led to high proliferation and cell growth, a phenotype influenced by dietary nutrients. NF-Y loss of function also increased nutrient metabolism, as shown by more mitochondria and larger lipid droplets in progenitors. Mechanistically, NF-Y restrains mTOR complex 1 (mTORC1) activity in ISCs by controlling transcription of mTORC1 signaling components such as Pras40 and Sestrin. Overall, our results demonstrate that NF-Y limits excessive nutrient-adaptive intestinal epithelial growth.
    Keywords:   Drosophila midgut; Intestinal stem cell; NF-Y; Tissue growth; mTOR
    DOI:  https://doi.org/10.1242/dev.205643
  10. Aging Cell. 2026 Jul;25(7): e70627
      Aging, as an intrinsic risk factor, accelerates gingival inflammation and periodontal diseases. However, the cellular and molecular mechanisms underlying gingival aging remain unclear, hindering the development of targeted therapies. In this study, we performed the first single-cell transcriptomic analysis of aging human gingiva, identifying primary cilia as potential regulators of gingival fibroblast senescence. We demonstrated that aged gingival tissues exhibit increased fibroblast senescence and enhanced ciliogenesis compared to young tissues. Suppression of ciliogenesis significantly reduced senescence markers and alleviated DNA damage in aged fibroblasts accompanied by increased AKT activation. In addition, FOXO1 inactivation and enhanced expression of DNA repair-related genes were found after suppression of ciliogenesis in aged gingival fibroblasts. Importantly, inhibition of AKT partially reversed the anti-senescent phenotypes induced by ciliogenesis suppression. Functionally, adeno-associated virus-mediated suppression of ciliogenesis in aged mice mitigated gingival fibroblast senescence, reduced inflammation, and diminished tissue fibrosis. These findings highlight that primary cilia may contribute to the regulation of gingival fibroblast senescence and identify ciliary dynamics and AKT signaling downstream of cilia as potential therapeutic targets for managing aging-related gingival diseases, providing a potential strategy to improve periodontal health in the elderly.
    Keywords:  aging; cellular senescence; fibroblasts; gingiva; periodontal diseases; primary cilia
    DOI:  https://doi.org/10.1111/acel.70627
  11. Stem Cell Reports. 2026 Jul 09. pii: S2213-6711(26)00219-5. [Epub ahead of print] 103008
      Bone marrow mesenchymal stem cell (BMSC) lineage commitment contributes to metabolic bone diseases, but whether glucagon-like peptide-1 (GLP-1) regulates osteo-adipogenic fate remains unclear. Here, RNA sequencing was performed to identify potential pathways regulated by GLP-1 in BMSCs, followed by gain- and loss-of-function experiments. Furthermore, BMSC-specific Hif-2α knockout mice with glucocorticoid-induced osteoporosis were treated with semaglutide to evaluate skeletal effects. GLP-1 suppressed adipogenesis and promoted osteogenesis of BMSCs in a dose-dependent manner. Transcriptomic analysis identified PI3K-AKT and hypoxia signaling as major GLP-1-regulated pathways. Mechanistically, GLP-1 inhibited AKT activation during adipogenesis and reshaped AKT signaling dynamics during osteogenesis. Loss of HIF-2α largely abolished GLP-1-mediated regulation of AKT activity. In vivo, semaglutide improved trabecular bone mass in osteoporotic mice, whereas this bone-protective effect was markedly diminished in Hif-2α-knockout mice. Our findings suggest that GLP-1 modulates BMSC lineage commitment by inhibiting adipogenesis and enhancing osteogenesis through HIF-2α-associated regulation of AKT signaling.
    DOI:  https://doi.org/10.1016/j.stemcr.2026.103008
  12. Nat Genet. 2026 Jul 10.
      Phenotypically healthy cells frequently harbor somatic variants at cancer-associated genes, indicating that malignant transformation requires the selection of several alterations. Predicting which combinations of mutations, or co-mutations, exhibit oncogenic capacity requires identifying co-mutations that occur more or less frequently than expected. However, statistical frameworks to solve this problem are hampered by tumor heterogeneity and data availability. Here we curated putative oncogenic mutations in >70,000 human tumors from 119 subtypes, and designed a strategy to search for co-mutations based on in silico simulation of mutagenesis (SelectSim). Using this dataset and tool, we discovered and validated co-mutations across independent human cohorts, compared co-mutations across different tumor types and identified potential risk factors of metastatic progression. Notably, across several cohorts of phenotypically normal tissue samples, we show that, unlike individual oncogenic variants, significantly co-occurring mutations are largely cancer-specific and are observed rarely in healthy tissues, providing clues about the paths to tumorigenesis.
    DOI:  https://doi.org/10.1038/s41588-026-02661-4
  13. Nat Cell Biol. 2026 Jul 06.
      Cells under high confinement migrate efficiently in low-adhesion environments by forming stable, polarized, hydrostatic pressure-driven leader blebs. Here we investigated the basis of polarized bleb morphology in metastatic melanoma cells migrating under low-adhesive and highly confined microenvironments. Using high-resolution live imaging, molecular perturbations and biosensors, we show that EGF signalling through PI3K stabilizes and maintains polarized leader blebs. EGFR and PI3K activities form a gradient within leader blebs that decreases from rear to front, promoting phosphatidylinositol 3,4,5-trisphosphate and Rac1-GTP accumulation at the bleb rear, whereas phosphatidylinositol 4,5-bisphosphate and RhoA-GTP concentrate at the bleb tip, the inverse of the organization observed in integrin-dependent mesenchymal migration. Optogenetic disruption of this gradient triggers bleb retraction, underscoring its functional importance. Mathematical modelling and experiments identified a mechanism whereby during bleb initiation, CD44 and ERM proteins restrict EGFR mobility within a membrane-apposed cortical actin meshwork at the bleb rear, establishing the EGFR-PI3K-Rac gradient. Together, these findings define the biophysical and molecular mechanisms that underlie polarity in bleb-based migration and highlight how alternative spatial organization of signalling modules supports distinct migration modes in different microenvironments.
    DOI:  https://doi.org/10.1038/s41556-026-01981-1
  14. Elife. 2026 07 08. pii: RP105302. [Epub ahead of print]14
      Analysis of multimodal and multidimensional data capturing dynamic interactions between diverse cell populations is a current challenge in bioimaging, especially in the context of immunology and immunotherapy research. Here, we introduce Celldetective, an open-source Python-based software tool designed for high-performance end-to-end analysis of image-based in vitro immune and immunotherapy assays. Celldetective is purpose-built for multicondition, 2D multi-channel time-lapse microscopy of mixed cell populations. Although it is optimised for the needs of immunology assays, it is nevertheless broadly applicable to any biological system involving interacting cell populations. The software seamlessly integrates AI-based segmentation, tracking, and automated single-cell event detection, all within an intuitive graphical interface that supports interactive visualisation, annotation, and training options. We showcase its capabilities with original datasets of single immune effector cell interactions with an activating surface mediated by bispecific antibodies and pairwise interactions in antibody-dependent cell cytotoxicity events.
    Keywords:  bioimage analysis; bispecific antibody; cancer cell line; computational biology; deep learning; human; immune cells interactions; immunology; inflammation; multimodal microscopy; primary immune cells; systems biology
    DOI:  https://doi.org/10.7554/eLife.105302
  15. Cell Rep. 2026 Jul 09. pii: S2211-1247(26)00753-9. [Epub ahead of print]45(7): 117675
      ERK1/2 play crucial roles in diverse cellular processes, yet their functions and underlying mechanisms in human embryonic stem cells (hESCs) remain incompletely defined. Here, we generate hESC lines with graded ERK1/2 activities and demonstrate that moderate ERK1/2 activation, with intact kinase activity and nuclear localization capacity, is optimal for sustaining the primed pluripotency state. Specifically, ERK1/2 hyperactivation induces mesendoderm differentiation, whereas their depletion drives trophoblast-like differentiation. Mechanistically, ERK1/2 govern pluripotency primarily through directly controlling key transcription factors (e.g., MYC, ZIC2, and FOS) and crosstalking with Hippo and BMP signaling pathways. Additionally, ERK1/2 preserve the homeostasis of the MYC-Ac-CoA-H3K27ac axis and constrain the CDK1-EZH2-H3K27me3 axis, thereby activating pluripotency genes and repressing trophoblast lineage genes. Collectively, this study systematically deciphers direct and indirect regulatory functions of ERK1/2 in hESCs, revealing a holistic regulatory network, in which ERK1/2 act as a central hub, to govern pluripotency of primed hESCs.
    Keywords:  BMP–SMAD1/5; CP: cell biology; CP: stem cell research; ERK1/2; H3K27ac; H3K27me3; Hippo–YAP1; human embryonic stem cells
    DOI:  https://doi.org/10.1016/j.celrep.2026.117675
  16. Nucleic Acids Res. 2026 Jul 03. pii: gkag627. [Epub ahead of print]54(13):
      Start-stop elements are translation regulatory elements in 5' untranslated regions (UTR) of eukaryotic transcripts, consisting of a start codon immediately followed by a stop codon. In contrast to canonical upstream Translons (uTranslons), they exclude elongation which creates unique properties. We conducted a comprehensive, carefully controlled comparison of human start-stop elements and uTranslons both at a genome-wide level and with targeted reporter assays. We found that start-stops and uTranslons were similar with respect to their presence in the 5' UTRs of hundreds of genes, in particular transcription factors and signaling molecules, the low transcript levels of the corresponding genes, short RNA half-lives, and the negative effect on downstream translation. However, start-stop containing genes were translationally even more repressed than genes with uTranslons. Analysing the start-stop architecture and diverse ribosome footprinting datasets, we found evidence for a start-stop-specific mechanism that involves repeat cycling between initiation, termination, ribosome splitting, and 60S rejoining-a process possibly modulated by ASCC3 and eIF1. This cycling explained increased ribosome retention at start-stops and was-in contrast to ribosome retention at uTranslons-independent of the global initiation state. Finally, we showed that the start-stop element in human ATF4 augments the core regulatory model by controlling translation of the uTranslons.
    DOI:  https://doi.org/10.1093/nar/gkag627
  17. EMBO J. 2026 Jul 06.
      Identifying senescent cells via single-cell transcriptome profiling data remains challenging due to cellular heterogeneity and overlap with other cellular states. Here, we present SenFlag, a streamlined gene signature for enhanced identification of senescent cells based on integration of core gene expression features. SenFlag was derived through systematic assessment of bulk and single-cell RNA-sequencing datasets across multiple senescence models. It captures a conserved transcriptional program characterized by reduced expression of proliferation-associated genes and chromatin-associated genes (HMGB1/2, HMGN2), combined with upregulation of cell-cycle inhibitors (CDKN1A/CDKN2A) and of CCND1. Additionally, SenFlag incorporates lysosomal features, including increased expression of V-ATPase subunits and cathepsins. SenFlag identifies a rare but progressively accumulating population of senescent cells across tissues in both mice and humans in vivo, with enrichment in epithelial and endothelial compartments. SenFlag-positive cells increase with age and following tissue injury, and are reduced in datasets involving senescence-targeting interventions, supporting its specificity in vivo. Together, SenFlag provides a robust and interpretable signature for identifying senescent cells in single-cell datasets and facilitates the study of senescence across physiological and pathological contexts.
    DOI:  https://doi.org/10.1038/s44318-026-00845-6
  18. Sci Transl Med. 2026 Jul 08. 18(857): eaec4386
      Primary enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles, known as congenital cerebral ventriculomegaly (CCV), is a hallmark of congenital hydrocephalus. CCV is also enigmatically but frequently associated with autism and other neurodevelopmental disorders. To gain insight into the developmental genetic regulation of the human CSF-ventricular system, we conducted an integrated, multiomic study of about 2700 trio-based exomes from patients with primary CCV. We found that about 25% of cases were associated with rare, damaging de novo variants in mutation-intolerant genes, many of which are linked to other dominant Mendelian disorders. Thirty-five exome-wide significant CCV genes and dozens of other high-confidence CCV genes converged on pathways involved in ATP-dependent Brahma-related gene 1/Brahma-associated factor chromatin remodeling, histone H3 lysine 4 methylation, and phosphoinositide 3-kinase signaling. Knockout of selected CCV genes in mouse models supported that de novo variants in CCV genes caused ventriculomegaly by impairing both CSF dynamics and cortical cytoarchitecture through dysregulation of neuroprogenitor cell growth and maturation in the ventricular and subventricular zones. These findings indicated that genetic and epigenetic programs coordinate the "hand-in-glove" development of the CSF-ventricular system with that of the cerebral cortex and establish a genetic connection between CCV and neurodevelopmental disorders, potentially explaining why some patients with hydrocephalus continue to exhibit CCV and neurodevelopmental disorders despite CSF shunting. We suggest that combined brain imaging and whole-exome sequencing could enable early detection of, and intervention for, autism and other neurodevelopmental disorders.
    DOI:  https://doi.org/10.1126/scitranslmed.aec4386