bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2026–06–14
twenty-one papers selected by
Ralitsa Radostinova Madsen, MRC-PPU



  1. Res Sq. 2026 Jun 03. pii: rs.3.rs-9293424. [Epub ahead of print]
      For over three decades, we have known that oncogenic RAS alters the actin cytoskeleton organization and cell surface morphology. RAS activates the GTPase RAC1, which triggers the growth of branched actin networks to promote cell membrane protrusions. In melanoma, the hyperactive RAC1 mutant, Rac1P29S, was recently shown to drive extended lamellipodia, which then empower cell proliferation through sequestration and localized inhibition of the merlin tumor suppressor. 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/10.21203/rs.3.rs-9293424/v1
  2. Proc Natl Acad Sci U S A. 2026 Jun 16. 123(24): e2523183123
      Protein phosphorylation is dynamically regulated by the opposing activities of phosphowriter enzymes (kinases) and phosphoeraser enzymes (phosphatases and phospholyases). While significant progress has been made toward defining the sequence preferences of kinases, the selectivity of phosphoerasers has not been explored at scale. Here, we develop an experimental platform based on tandem mass spectrometry analysis of phosphoproteome-derived peptide libraries (PhosPropels) to map phosphoeraser activity across thousands of biologically relevant phosphosites. We extract positional residue preferences to rapidly define sequence motifs recognized by eight phosphoerasers spanning diverse species of origin, protein folds, and enzymatic mechanisms, yielding biological insights into pathways targeted by these enzymes. Taking advantage of the throughput of our approach, we profiled 20 variants of the phosphothreonine lyase OspF from Shigella flexneri, uncovering an intrinsic preference for p38 and Erk MAP kinase activation loops and revealing the enzyme residues that influence its selectivity for phosphothreonine. Our results establish a general method for linking phosphorylation sites to the enzymes that remove them, providing a means to dissect a key component of cellular regulatory networks.
    Keywords:  chemical biology; phosphatases; phospholyases; phosphoproteomics; phosphorylation
    DOI:  https://doi.org/10.1073/pnas.2523183123
  3. Orphanet J Rare Dis. 2026 Jun 12. pii: 216. [Epub ahead of print]21(1):
       BACKGROUND: Tuberous sclerosis complex (TSC) is a rare genetic neurocutaneous disorder resulting from mutations in the TSC1 or TSC2 genes, characterized by overgrowth and lesions in multiple organs. While renal angiomyolipomas are commonly seen, lipomas located elsewhere are rarely reported in these patients.
    RESULTS: We identified a heterozygous TSC1 mutation in a pediatric patient, who developed a lipoma in the gluteal region, which recurred after surgical resection. We observed a loss of heterozygosity in the lipoma tissue, resulting in TSC1 deficiency and subsequent activation of the mechanistic target of rapamycin (mTOR) signaling pathway. Further in vitro experiments showed that silencing TSC1 in adipocyte progenitors led to increased cell proliferation, supporting the hypothesis that TSC1 deficiency contributes to lipoma formation. Treatment with mTOR inhibitors, such as sirolimus and torin-1, as well as the phosphoinositide 3-kinase (PI3K) inhibitor alpelisib reduced cell proliferation and pathway activation in TSC1-deficient cells.
    CONCLUSIONS: This study highlights the need for further investigation into the efficacy of pathway inhibitors in managing TSC-related lipomas in vivo and offers a potential treatment avenue for patients suffering from recurrent lipomatosis.
    Keywords:  Alpelisib; Lipoma; Sirolimus; TSC1; Tuberous sclerosis; mTOR
    DOI:  https://doi.org/10.1186/s13023-026-04442-y
  4. Proc Natl Acad Sci U S A. 2026 Jun 16. 123(24): e2523043123
      Tumor initiation requires the integration of oncogenic signals with environmental cues to enable anabolic growth. MYC is central to tumorigenesis, with its deregulation observed in over 60% of human cancers. Oncogenic MYC profoundly rewires transcription, enabling cells to bypass cell cycle checkpoints and reset metabolism. A cornerstone of this rewiring is the upregulation of biomass-producing pathways, particularly ribosome biogenesis. How and when MYC's oncogenic program is translationally executed-either immediately or until a favorable metabolic context emerges-remains a central unanswered question in tumor initiation, limiting our understanding of tumor latency and early intervention. Here, we identify LARP1 as a critical effector of MYC-driven transformation, connecting MYC oncogenic activity with mTOR signaling. Mechanistically, MYC represses miR-26a/b, relieving posttranscriptional repression of LARP1 and leading to its upregulation. LARP1 associates with the translational machinery, loading it with the anabolic translatome induced by MYC in a translationally poised state. Upon permissive mTOR signaling, and dependent on the phosphorylation of LARP1 at serines 689 and 697, this program is rapidly translated, fueling the biosynthetic processes essential for tumor development. Importantly, genetic deletion of LARP1 or pharmacological mTOR inhibition completely abrogates tumor initiation in a genetically engineered colorectal organoid model of MYC-driven tumorigenesis. This underscores the physiological relevance of this two-step mechanism in which LARP1 bridges the anabolic translatome primed by MYC with its metabolic execution controlled by mTOR. By temporally uncoupling transformation from metabolic permissiveness, this mechanism defines a critical checkpoint in early tumorigenesis, revealing a potential vulnerability for intercepting MYC-driven cancer before biomass expansion.
    Keywords:  MYC; mTOR; oncogenic translational program; tumor anabolism; tumor initiation
    DOI:  https://doi.org/10.1073/pnas.2523043123
  5. Stem Cell Res. 2026 Jun 06. pii: S1873-5061(26)00124-8. [Epub ahead of print]95 104028
      The STRAIGHT-IN platform is designed for facile genomic integration of DNA payloads into human induced pluripotent stem cells (hiPSCs) that contain a pre-inserted landing pad (LP). Here, we expanded the versatility of STRAIGHT-IN by introducing an additional, orthogonal LP into the unmodified allele of the safe harbor locus AAVS1. Specifically, we targeted the hiPSC line LUMC0099iCTRL04_AAVS1-bxb-v2 (hPSCreg LUMCi004-A-1), which already carried one LP. The resulting STRAIGHT-IN AAVS1 Dual line can integrate two independent DNA payloads in parallel, expanding the applicability of the platform for complex genomic engineering applications.
    DOI:  https://doi.org/10.1016/j.scr.2026.104028
  6. Cell. 2026 Jun 11. pii: S0092-8674(26)00587-8. [Epub ahead of print]189(12): 3501-3505
    NIH SenNet consortium
      Cellular senescence comprises diverse cell states emerging across human tissues during aging and disease. Integrating single-cell and spatial multi-omics with AI-driven analyses enables systematic mapping of senescent cell heterogeneity ("senotypes"), revealing tissue-specific programs and microenvironmental interactions. These advances provide frameworks for biomarker discovery and development of targeted senotherapeutic strategies.
    DOI:  https://doi.org/10.1016/j.cell.2026.05.028
  7. Nat Cell Biol. 2026 Jun 10.
      In migrating cells, the GTPase Rac organizes a protrusive front, whereas Rho organizes a contractile back. How these GTPases are positioned at opposite poles remains unclear. We leverage optogenetics, mechanical perturbations, and mathematical modelling to reveal a surprising mechanochemical long-range mutual activation between front and back polarity programmes that complements their well-known local mutual inhibition. Rac-based protrusions elevate membrane tension, stimulating an mTORC2-dependent activation of Rho at the opposite side of the cell. Conversely, Rho-mediated contractility induces cortical-flow-based regulation of phosphoinositide signalling that triggers Rac activation distally. We develop a minimal mechanochemical model to explain how long-range facilitation, together with local inhibition, enables robust Rho and Rac partitioning. Our findings demonstrate how the actin cortex and plasma membrane interact as an integrated mechanochemical system for long-range Rac-Rho patterning. This circuit is required for efficient polarity and migration in primary human T cells and is conserved in epithelial cells, highlighting the generality of this mechanism.
    DOI:  https://doi.org/10.1038/s41556-026-01965-1
  8. Stem Cell Res Ther. 2026 Jun 09.
      Cerebral cavernous malformation (CCM) is a rare cerebrovascular disorder characterized by abnormal endothelial architecture and clinically manifests as hemorrhage, epilepsy, and neurological deficits. Two primary factors have constrained the advancement of research in the field of CCM. Firstly, the utilization of animal models, which do not fully recapitulate human neurovascular biology, has been a major impediment. Secondly, the restricted access to patient lesion tissue has hindered progress. These constraints impede mechanistic dissection and therapeutic translation. This review discusses how models derived from human pluripotent stem cells (hPSCs), particularly induced pluripotent stem cells (iPSCs), are advancing research on cardiovascular endothelial cells by enabling human-specific and patient-tailored disease modeling. These stem cell models complement classical mouse models, creating a synergistic approach. The following section summarizes recent advances in three key areas: disease etiology, model development, and translational applications. In particular, the iPSC-derived endothelial cell system has provided mechanistic insights into how mutations in CCM1/2/3 and PIK3CA disrupt endothelial homeostasis in both two-dimensional and three-dimensional contexts, leading to aberrant activation of downstream signaling pathways. The discussion extends to more advanced platforms, including vascular organoids and blood-brain barrier models that more faithfully recapitulate the neurovascular microenvironment and pathological cell-cell interactions. Furthermore, iPSC-based high-throughput drug screening facilitates target validation, drug repurposing, and the development of personalized therapeutic strategies. Although challenges remain regarding model maturity and standardization, stem cell-derived vascular models provide a robust framework for CCM research. This review provides a concise overview of the fundamental iPSC models frequently employed in CCM research and proposes a hierarchical mechanistic framework of "mutation-driven, signal amplification, and lesion evolution." The advantages of 2D and 3D iPSC models for elucidating early endothelial abnormalities, cell-cell interactions, and tissue-level lesion formation are highlighted, and the applicability of various models for reconstructing the CCM microenvironment is emphasized. In conclusion, a model selection strategy for translational research is proposed: iPSC models should be used to elucidate human-derived mechanisms and for drug screening, while animal and chimeric models should be employed to study long-term disease progression, immune involvement, and in vivo validation.
    Keywords:  CCM; Disease modeling; Stem cells; Vascular malformation; iPSCs
    DOI:  https://doi.org/10.1186/s13287-026-05081-7
  9. Cell Rep Methods. 2026 Jun 10. pii: S2667-2375(26)00184-0. [Epub ahead of print] 101484
      Fluorescence lifetime imaging microscopy (FLIM) is sensitive to molecular environments and enables high-resolution mapping of cellular heterogeneity. Yet, the journey from raw photon decays to biological insight remains fragmented by multi-step data extraction and siloed analyses, creating burdens for experts and non-experts alike. This work presents FLIM Playground, the first interactive graphical platform that unifies single-cell FLIM workflows. Modularly designed to encompass data extraction (if desired) and data analysis, FLIM Playground can check field-of-view metadata, calibrate and extract fluorescence lifetime features per region of interest along with morphology and texture features across channels, merge multiple datasets, and provide real-time visual analytic modules. Lifetime extraction was validated against commercial software and published results, and both data extraction and analysis were demonstrated on a FLIM dataset of cancer cell lines. By adopting best practices and offering interactivity, FLIM Playground promotes reproducibility, allows for expansion to new imaging modalities, and accelerates hypothesis-driven discovery.
    Keywords:  CP: imaging; FLIM; GUI; TCSPC; fluorescence lifetime imaging microscopy; image analysis; interactive visualization; lifetime fitting; metabolic imaging; open-source software; phasor analysis
    DOI:  https://doi.org/10.1016/j.crmeth.2026.101484
  10. Nat Methods. 2026 Jun 09.
      The success of transformer-based foundation models on natural language and images has motivated their use in single-cell biology. Single-cell foundation models have been trained on increasingly larger transcriptomic datasets, scaling from initial studies with 1 million cells to newer atlases with over 100 million cells. Here we investigate the role of pretraining dataset size and diversity on the performance of single-cell foundation models on both zero-shot and fine-tuned tasks. Using a large corpus of 22.2 million cells, we pretrain a total of 400 models, which we evaluate by conducting 6,400 experiments. Our results show that current methods tend to plateau in performance with pretraining datasets that are only a fraction of the size of current training corpora. Unlike large language models, single-cell foundation models show no clear data scaling laws, indicating that developers should focus on balancing model capacity, dataset size and computational resources rather than indiscriminately increasing all three.
    DOI:  https://doi.org/10.1038/s41592-026-03120-y
  11. Cell Stem Cell. 2026 Jun 08. pii: S1934-5909(26)00196-7. [Epub ahead of print]
      Principles of developmental biology have inspired efforts for directed differentiation of human pluripotent stem cells (hPSCs), leading to the first generation of organoids that are now well established as models of human development and disease. However, first-generation organoid models were missing many cell types that would be needed to study normal and pathological processes. Here, we discuss how designing next-generation organoids with increased cellular complexity has been possible by better reproducing developmental processes in play during organogenesis in vivo. We focus on recent conceptual and technical advances in reconstructing appropriate cellular diversity in organoids, dissecting the importance of tissue-tissue interactions and specialized cell addition, and how engineering technologies can further enhance our ability to control how cells are brought together to mimic human development in vitro.
    Keywords:  assembloid; developmental biology; engineering organoid; organogenesis; organoid; self-organization
    DOI:  https://doi.org/10.1016/j.stem.2026.05.004
  12. Arterioscler Thromb Vasc Biol. 2026 Jun 11.
      Phosphoregulatory events underlie vascular responses to environmental and pathological stimuli, regulate hemostasis and thrombosis, and drive vascular remodeling in health and disease. Consequently, defining phosphorylation-dependent signaling networks in vascular physiology and pathology has enabled biomarker discovery and informed therapeutic interventions. Advances in mass spectrometry-based phosphoproteomics have enabled accurate and high-resolution mapping of dynamic phosphorylation events at the systems level, providing comprehensive mechanistic insights into vascular signaling and pathology. In this review, we contextualize phosphorylation in the vascular niche and summarize the current state of phosphoproteomics in vascular research, highlighting experimental design considerations, technological advances, quantification strategies, and data analysis approaches to uncover biological insights from large-scale phosphoproteomic data sets. Finally, we discuss recent discoveries in vascular signaling and disease, along with current challenges and emerging directions for applying phosphoproteomics to critical questions in vascular biology.
    Keywords:  biology; data analysis; hemostasis; phosphorylation; vascular remodeling
    DOI:  https://doi.org/10.1161/ATVBAHA.126.323845
  13. Diabetologia. 2026 Jun 09.
       AIMS/HYPOTHESIS: Maternal diabetes confers two opposing risks to fetal growth, resulting in macrosomia in mild cases and intrauterine growth restriction (IUGR) in severe cases. The mechanisms governing these divergent responses are poorly understood, given the intimate regulation of insulin by glucose and insulin's fetal growth-promoting effects. We hypothesised that the degree of maternal hyperglycaemia dictates a bimodal pattern of fetal insulin secretion that determines fetal growth, and that use of a ketogenic diet (KD) as a nutritional intervention could modify this outcome.
    METHODS: We used the Insulin-rtTA;TET-DTA mouse model to induce preconception diabetes. Dams were stratified based on maternal blood glucose, namely non-diabetes (glucose <9.6 mmol/l), mild diabetes (glucose range 9.6-16.7 mmol/l) or severe diabetes (glucose >16.7 mmol/l), and maintained on either a normal diet or a KD. We assessed fetal growth and plasma C-peptide, performed islet functional assays ex vivo, and characterised changes in plasma metabolites. Fetal pancreases were analysed by immunohistochemistry for beta cell area, proliferation, maturation and mechanistic target of rapamycin complex 1 (mTORC1) activity.
    RESULTS: Mild maternal diabetes induced fetal macrosomia, driven by beta cell hyperplasia, hyperinsulinaemia and premature beta cell functional maturation, as reflected by glucose-stimulated insulin secretion and upregulated MafA expression. This was associated with strong activation of the mTORC1 pathway. In contrast, severe diabetes caused IUGR associated with reduced beta cell mass and profound functional impairment. The KD had divergent effects: it normalised fetal growth in the mild diabetes group by preventing beta cell proliferation and premature maturation, thereby reducing insulin secretion, but failed to rescue IUGR in the severe diabetes group, despite partially restoring beta cell function. Notably, the KD uncoupled the positive correlation between fetal insulin and body weight, revealing a primary, insulin-independent, growth-restrictive effect.
    CONCLUSIONS/INTERPRETATION: Fetal growth in a mouse model of diabetes in pregnancy is governed by a bimodal beta cell response to the maternal glycaemic environment, orchestrated at the molecular level by the mTORC1 pathway. A KD can prevent diabetes-derived macrosomia by reducing beta cell stimulation and through insulin-independent mechanisms, but cannot reverse IUGR, warranting further studies of its role in diabetes during pregnancy.
    Keywords:  Beta cell maturation; Fetal beta cell; Fetal growth; IUGR; Insulin secretion; Ketogenic diet; Macrosomia; Maternal diabetes; Pregnancy; mTORC1
    DOI:  https://doi.org/10.1007/s00125-026-06771-w
  14. bioRxiv. 2026 Jun 01. pii: 2026.05.31.729073. [Epub ahead of print]
      Synthetic gene-regulation logic is established in immortalized cell lines but remains largely aspirational in human induced pluripotent stem cells (hiPSCs) and derivatives. This gap constrains both mechanistic discovery and translational engineering in physiologically relevant models. We developed CIRI ( C ombinatorial I nducible C R ISPR in I PSCs), an isogenic, safe-harbor-engineered platform in which tetracycline-responsive single guide RNAs (sgR-NAs) carry modular RNA aptamers that recruit RNA-binding proteins and effector domains. This design enables multimodal regulation from a single catalytically inactive Cas9 (dCas9), exemplified by orthogonal CRISPR activation and interference (CRISPRa/i). After optimizing sgRNA-aptamer architectures, we achieved robust CRISPRa and CRISPRi in hiPSCs and hiPSC-derived cardiac organoids. CIRI rapidly channels hiPSC forward programming into skeletal myocytes by activating MYOD1 while repressing NANOG , POU5F1/OCT4 , and SOX2 . Combinatorial pooled dual-guide single-cell RNA sequencing screens identify ID3 as a road-block and KDM6B and SMARCD3 as synergistic enhancers of myogenic maturation. Together, CIRI establishes a programmable synthetic biology framework in human stem cell models.
    GRAPHICAL ABSTRACT:
    DOI:  https://doi.org/10.64898/2026.05.31.729073
  15. Adv Biol (Weinh). 2026 Jun;10(6): e70133
      Liver fibrosis is characterized by excessive collagen accumulation, the principal component of the extracellular matrix (ECM), produced by activated hepatic stellate cells (HSCs). While the catabolic role of mannose receptor C-type 2 (MRC2) in binding and degradation of collagen is established, its role in regulating pro-fibrotic signaling remains undefined. We investigated the novel, non-canonical signaling function of the collagen receptor MRC2 as a regulator of HSC activation. Using doxycycline-inducible knockdown and overexpression systems in human HSCs, we show that MRC2 deficiency enhances activation phenotypes, including proliferation, migration, contraction, and collagen overproduction. Conversely, MRC2 overexpression suppressed these effects. Transcriptomic analysis of MRC2 knockdown cells revealed a pro-fibrotic transcriptional shift, with enrichment of pathways related to ECM organization, collagen biosynthesis, and the PI3K/AKT signaling axis. Mechanistically, MRC2 depletion induced transcriptional upregulation of ECM genes and components of the integrin/PI3K/AKT axis, accompanied by increased AKT phosphorylation. Pharmacological inhibition of either PI3K or integrins reversed ECM gene expression and collagen phenotypes induced by MRC2 depletion, establishing these pathways as required mediators. Our findings identify a novel, non-canonical signaling function of MRC2 as a negative regulator of HSC activation.
    Keywords:  HSC activation; extracellular matrix; liver fibrosis; transcriptional regulation
    DOI:  https://doi.org/10.1002/adbi.70133
  16. Ann Biomed Eng. 2026 Jun 10.
      Cells respond to extracellular matrices (ECMs) and generate internal signals associated with genomic and epigenomic changes. Currently, many studies employ direct intracellular chemical, genomic, or epigenomic modulation, which may not always be the optimal avenue for directing cell transitions and fate decisions in therapeutic contexts. This paper aims to conceptualize adhesion-niche-based mechanobiological strategies that are free from direct intracellular modulation, but effective in controlling cell transitions and fate decisions, such as endothelial-to-mesenchymal transition (EndMT), epithelial-to-mesenchymal transition (EMT), as well as reprogramming and differentiation processes associated with them. To this end, we review the molecular and biophysical mechanisms of cellular interactions with two-dimensional ECMs. Across ECMs, focal adhesions, the cytoplasm, and the nuclear envelope, we discuss how mechanical signals propagate and generate biological events. By providing an integrated picture of the mechanobiological responses of contractile cells on two-dimensional ECMs, our review offers novel perspectives on anti-EndMT and anti-EMT, based on adhesion-niche-dependent modulation of biphasic mechanotransduction.
    Keywords:  Adhesion; Biphasic mechanotransduction; Cell fate decision; Endothelial-to-mesenchymal transition; Epithelial-to-mesenchymal transitions; Extracellular matrix rigidity
    DOI:  https://doi.org/10.1007/s10439-026-04218-2
  17. Commun Biol. 2026 Jun 09.
      Cells are exposed to a variety of mechanical forces, including flow and stretch. Several transmembrane receptors have been implicated in mechanosignaling, but most cell-cell adhesion receptors have not been tested. Here, we use a siRNA screen targeting cell-cell junction-associated proteins to identify novel force-sensing receptors, measuring nuclear localization of the mechanosensitive transcription factor YAP. This screen identifies Nectin family cell-cell adhesion receptors as mechansensors. Of the Nectins, NECL5 depletion shows the lowest levels of YAP nuclear localization and reduces actin filament alignment. Nectin-3 (a known NECL5 interactor) also decreases YAP nuclear localization. In response to flow or stretch forces, NECL5 knockdown in endothelial cells reduces YAP signaling, acting through the PI3K/AKT pathway. NECL5 also mediates actin filament alignment induced by flow. Mechanical stimuli increase NECL5 localization to cell-cell junctions in vitro and in aortas in vivo. Together, these results indicate that the Nectin NECL5 plays a central role in mechanosignaling.
    DOI:  https://doi.org/10.1038/s42003-026-10455-x
  18. Mol Cell. 2026 Jun 11. pii: S1097-2765(26)00323-0. [Epub ahead of print]
      There is an urgent need to comprehensively catalog senescence markers across cell types in an organism in order to characterize senescent-cell heterogeneity. Here, we profiled the transcriptomes and proteomes in 14 different primary human cell types undergoing over 30 senescence paradigms to create a senescence catalog we termed "SenCat." We found that while senescent cells from all primary cell types did not share a single unique marker, they did activate shared specific metabolic and damage-response pathways implicated in tissue repair. Moreover, machine-learning-refined SenCat signatures enabled senescence scoring and identification across multiple human and mouse datasets, both at bulk and single-cell levels. In sum, SenCat represents a much-needed resource to identify senescence across multiple cell types and tissues in the body.
    Keywords:  aging; machine learning; mass spectrometry; proteomics; senolytics; senotype; single-nuclei RNA-sequencing; transcriptomics
    DOI:  https://doi.org/10.1016/j.molcel.2026.05.017
  19. FASEB J. 2026 Jun 30. 40(12): e71837
      Clinical therapies targeting mammalian target of rapamycin (mTOR) are associated with high rates of pneumonitis. Recent studies independently revealed the upregulation of the proinflammatory transcription factor interferon regulatory factor-1 (IRF-1) by mTOR inhibition (mTORi) of endothelial cells (EC) and further highlighted a mechanism converging on myosin light chain (MLC) phosphorylation-dependent cytoskeletal dynamics in promoting the endothelial hyperpermeability and pulmonary inflammation caused by mTORi. This study investigated a role for this mechanism in linking the regulation of IRF-1 expression with downstream responses in mTOR-inhibited EC. IRF-1 was transcriptionally upregulated in cultured EC by treatment with mTOR inhibitor rapamycin or torin 1, or by silencing either Raptor or Rictor expression to disrupt mTOR complex 1 (mTORC1) or 2 (mTORC2). Inhibition of MLC kinase (MLCK) activity or activation of MLC phosphatase (MLCP) to suppress MLC phosphorylation, or direct inhibition of actin polymerization, attenuated IRF-1 expression as well as transcription of an array of proinflammatory cytokines. Moreover, IRF-1 in turn upregulated MLCK expression to enhance MLC phosphorylation and promote endothelial hyperpermeability in mTOR-inhibited EC. Consistent with these observations in culture, targeted endothelial deficiency of IRF-1 in mice significantly reduced lung edema and inflammation elicited by separate or combined treatment of rapamycin and lipopolysaccharide. In conclusion, activation of actomyosin contractility by mTORi upregulated IRF-1, which promoted the development of lung injury by mediating inflammation and hyperpermeability responses in EC.
    Keywords:  actin cytoskeleton; cell contraction; endothelial cell; inflammation; lung injury; mTOR inhibition; myosin light chain; permeability
    DOI:  https://doi.org/10.1096/fj.202503788R
  20. bioRxiv. 2026 Jun 04. pii: 2026.06.01.728946. [Epub ahead of print]
    DCWG Members
      Since publication of the FAIR Guiding Principles in 2016, the scientific community has increasingly sought to make experimental data findable, accessible, interoperable, and reusable. Operationalizing the FAIR principles in routine scientific workflows remains challenging without a standardized, workable infrastructure. With over 10,000 datasets from over 40 institutions, spanning more than 50 diverse assay types ranging from single-cell sequencing technologies to 2D and 3D spatial omics, the U.S. National Institutes of Health (NIH) Human Bio-Molecular Atlas Program (HuBMAP) consortium has been ideally situated to create a FAIR ecosystem. With the goal of achieving data "FAIRness," HuBMAP developed and implemented well-defined, community-endorsed metadata reporting standards across the research lifecycle. These reporting standards include detailed schemas, harmonized across a multitude of assays, that define the metadata associated with a dataset and the organization of the corresponding data files. These standards ensure documentation of the data collection process, of the data themselves, and of the manner in which the data are packaged for sharing, while remaining compliant with the Health Insurance Portability and Accountability Act (HIPAA). The use of these reporting standards, in tandem with technology to foster adherence, allows HuBMAP to fulfill its goal of generating FAIR data for open dissemination through its Data Portal and Human Reference Atlas. The procedures and simple workflow adopted by HuBMAP investigators serve as a model for other scientific communities aiming to maximize the value of varied datasets addressing a shared research question. The HuBMAP end-to-end, metadata-centered workflow has been replicated and enhanced by the NIH Cellular Senescence Network (SenNet) consortium and is readily available through open-source technology for others to utilize.
    DOI:  https://doi.org/10.64898/2026.06.01.728946
  21. Curr Opin Chem Biol. 2026 Jun 12. pii: S1367-5931(26)00054-2. [Epub ahead of print]93 102705
      By generating short-lived reactive intermediates that covalently tag nearby biomolecules, proximity labeling (PL) has become a central strategy for spatial proteomics and for probing protein-protein interactions in living systems. However, key aspects of PL performance, including labeling radius, temporal resolution, and biological compatibility, are ultimately governed by how these intermediates are produced, confined, and quenched in situ. Here we use reactive-intermediate generation as an organizing chemical framework to compare major PL modalities. We focus primarily on proteome-centered PL systems, while noting that the same framework can extend to other biomolecular readouts. We discuss peroxide- and oxygen-driven platforms that form phenoxyl radicals and quinone electrophiles, ATP-coupled ligase approaches that transfer activated intermediates to proximal nucleophiles, and light-triggered photocatalytic systems that access carbenes or nitrenes, singlet oxygen or radical reactive oxygen species, and photoredox-uncaged electrophiles. Across these manifolds, we highlight the trade-offs that set operational boundaries and outline design principles for next-generation PL that is quantitative, minimally perturbative, and increasingly in vivo compatible.
    DOI:  https://doi.org/10.1016/j.cbpa.2026.102705