bims-pideca 2026-10-18 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2026–10–18
twenty-two papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Zovegalisib for PIK3CA-driven vascular and lymphatic malformations: a drug evaluation.
PIK3CA Mutations in Advanced or Recurrent Endometrial Cancer: An Exploratory Molecular Profiling From the Phase II MITO END-3 Study.
Integrative proximity labeling and multiomic profiling uncover domain-specific interactomes and molecular vulnerabilities of oncogenic PI3K.
YAP/TAZ-controlled ERK dynamics coordinate progenitor expansion and differentiation commitment.
PI3K signaling in breast cancer: therapeutic advances versus adaptive resistance.
Open-label extension study of leniolisib in activated PI3Kδ syndrome: Long-term efficacy and safety.
Charting the silent variation within us.
Recent developments of fluorescent proteins and biosensors driven by cross-disciplinary insights.
AKT Phosphorylation of FOXK2 at Ser398 Impacts Breast Cancer Cell Growth and Viability.
Manganese availability determines hepatic insulin sensitivity by enhancing Akt activity.
VPS34 regulation in pulmonary arterial vascular smooth muscle cells in pulmonary hypertension.
EGFR activity governs stage-dependent fibrotic responses in recessive dystrophic epidermolysis bullosa.
Dynamic remodeling of the KRAS interactome by direct RAS inhibitors with distinct mechanism of action reveals convergent responses.
Modeling human neurodegeneration with iPSCs: opportunities, limitations, and the challenge of aging.
Seumetry: a versatile and comprehensive R toolkit to accelerate high-dimensional flow and mass cytometry data analysis.
Design and Evolution of an Orthogonal HaloTag for Multiplexed Labeling in Cells.
FKBP12 determines ligand-specific SMAD signaling in individual living endothelial cells.
Comprehensive assessment of the genotype-phenotype spectrum and treatment for monoallelic insulin receptoropathy in a cohort of 505 people.
Reviewing reproducibility and replicability in 'Deconstructing gastrulation at single-cell resolution' by Stern et al. (2022).
Disease-associated mutations directionally modulate epigenetic age in iPSC-derived tissues.
An Open Infrastructure for Mass Spectrometry Data in R.
Endothelial metabolic plasticity in infantile hemangioma: evidence strength, disease phase and therapeutic readiness.

Expert Opin Investig Drugs. 2026 Oct 14.

Zovegalisib for PIK3CA-driven vascular and lymphatic malformations: a drug evaluation.

Emmanuel Seront, An Van Damme, Julien Coulie, Miikka Vikkula, Laurence M Boon.

   INTRODUCTION: PIK3CA-driven overgrowth and vascular malformations are mosaic developmental disorders in which chronic pathway inhibition may be required from childhood into adulthood. Alpelisib established PI3Kα as a clinically actionable target, but inhibition of wild-type PI3Kα can produce on-target toxicities, principally hyperglycemia, diarrhea and stomatitis, that are relevant to long-term therapy. Zovegalisib (RLY-2608) is an oral allosteric, pan-mutant-selective PI3Kα inhibitor designed to preferentially inhibit mutant over wild-type PI3Kα.
AREAS COVERED: This Drug Evaluation reviews PIK3CA biology, the current systemic-treatment landscape, zovegalisib pharmacology, and the preliminary Phase 2 ReInspire data. PubMed/MEDLINE, ClinicalTrials.gov, regulatory sources, and publicly available conference materials and company disclosures were reviewed through 20 August 2026.
EXPERT OPINION: At the formal 15 April 2026 cutoff, early ReInspire results showed a 60% week-12 volumetric response rate in 20 evaluable adults/adolescents; one unconfirmed response reported after the cutoff in a sponsor press release increased the descriptive rate to 65%. Activity after prior sirolimus and/or alpelisib and encouraging short-term tolerability support further development. Mutant selectivity could be especially valuable in chronic nonmalignant disease, but superiority over alpelisib is unproven.

Keywords:  Alpelisib; PIK3CA; PIK3CA-related overgrowth spectrum; lymphatic malformation; precision medicine; vascular anomalies; zovegalisib

DOI:  https://doi.org/10.1080/13543784.2026.2750463
JCO Precis Oncol. 2026 Oct;10(10): e2600484

PIK3CA Mutations in Advanced or Recurrent Endometrial Cancer: An Exploratory Molecular Profiling From the Phase II MITO END-3 Study.

Anna Passarelli, Giovanni Luca Scaglione, Daniela Califano, Michele Bartoletti, Domenica Lorusso, Sabrina Chiara Cecere, Anna Fagotti, Alberto Farolfi, Claudia Andreetta, Jole Ventriglia, Laura Arenare, Carmela Pisano, Daniela Russo, Maria Teresa Perri, Saverio Cinieri, Simona Scalone, Ugo De Giorgi, Valentina Arcangeli, Elena Zafarana, Maria Chiara Cannizzaro, Serafina Mammoliti, Tommaso Ambrosio, Rossella De Cecio, Clorinda Schettino, Francesco Perrone, Sandro Pignata.

PURPOSE: Immunotherapy with chemotherapy significantly improves progression-free survival in advanced endometrial cancer (EC), especially in microsatellite instability-high (MSI-H) cases. Despite this, for recurrent EC in the postimmunotherapy setting, new treatment options are urgently needed. The PI3K pathway is frequently altered in gynecologic cancers, including EC, representing a potential treatment target.
PATIENTS AND METHODS: In a preplanned translational analysis of the MITO END-3, we retrospectively analyzed the genomic abnormalities of 107 patients with samples eligible for next-generation sequencing (NGS) analysis (FoundationOne CDx) with a focus on PIK3CA mutational status.
RESULTS: In our analysis, the four most frequently mutated genes were TP53, PIK3CA, ARID1A, and PTEN. PIK3CA mutations were detected in 51.4% (55/107 patients) of tissue samples. A total of 68 different PIK3CA mutations were observed, of which 64 were considered pathogenic and four were classified as variants of unknown significance, with the co-occurrence of two different pathogenic mutations in 2 patients. The most frequent PIK3CA mutations were found in the kinase domain, most commonly H1047R (11/68) and H1047Y (3/68), and in the helical domain, including E545K (4/68) and E542K (3/68). Notably, 24 different PIK3CA mutations out of 68 reported in MITO END-3 are considered predictive of response to PI3K inhibition with alpelisib according to current literature in breast cancer. Interestingly, PIK3CA mutations were observed in all The Cancer Genome Atlas categories.
CONCLUSION: In this post hoc analysis from the MITO END-3 trial, we confirmed the high frequency of PIK3CA mutations in EC, establishing this tumor as an ideal candidate for testing of PI3K inhibitors in clinical trials.

DOI: https://doi.org/10.1200/PO-26-00484
J Biol Chem. 2026 Oct 16. pii: S0021-9258(26)02527-5. [Epub ahead of print] 113655

Integrative proximity labeling and multiomic profiling uncover domain-specific interactomes and molecular vulnerabilities of oncogenic PI3K.

Donghee Lee, Jin Koh, Sun Hee Choi, Jong Hyuk Kim.

  Activating mutations in PIK3CA (encoding the p110α kinase) are among the most frequent oncogenic drivers in human tumors. The two major hotspot mutations, E545K (helical domain) and H1047R (kinase domain), both hyperactivate PI3K-AKT signaling, yet they exhibit distinct functional behaviors and differential drug sensitivities. The mutation-specific protein-protein interaction (PPI) networks underlying the differences, however, remain largely unexplored. In this study, we established experimental approaches to identify proteins in proximity to oncogenic PI3K using biotin ligase-based proximity labeling. Our data revealed that the PIK3CA H1047R and E545K mutants fused to BioID2 formed structurally distinct complexes, each associating with unique proximal proteins identified by liquid chromatography-tandem mass spectrometry. Further integration of the PPI networks with CRISPR dependency screens and multiomic profiling mapped the divergent functional interactomes of p110α hotspot mutants. H1047R exhibited a synthetic lethal dependency on the adaptor protein TAB2, which is associated with aggressive clinical phenotypes in breast cancer. Distinctly, E545K interacted with core subunits of the SWI/SNF chromatin remodeling complex, corresponding to a globally repressive chromatin state at distal enhancers. This SWI/SNF association also revealed a mutation-specific epigenetic vulnerability, with E545K-mutant cells displaying increased sensitivity to EZH2 inhibitors. Collectively, these findings demonstrate that the molecular network complexity of oncogenic PI3K can be interrogated through proximity labeling and that distinct PIK3CA point mutations rewire non-overlapping PPI networks, revealing domain-specific dependencies. Our study provides a framework for mapping mutation-specific interactomes and offers molecular insights and potential therapeutic strategies for PIK3CA-mutant tumors.

Keywords:  PI3K; PIK3CA mutation; multiomic profiling; protein-protein interaction; proximity labeling; synthetic lethality

DOI:  https://doi.org/10.1016/j.jbc.2026.113655
bioRxiv. 2026 Sep 28. pii: 2026.09.24.753950. [Epub ahead of print]

YAP/TAZ-controlled ERK dynamics coordinate progenitor expansion and differentiation commitment.

Sanjeev Sharma, Henri Berger, Zhibo Zhang, Tobias Meyer, Mary N Teruel.

Progenitor cells must proliferate to expand the cell population, yet terminal differentiation requires this proliferative state to end. How signaling controls the duration of this proliferative window remains poorly understood. Using adipogenesis and live single-cell imaging of differentiation, cell-cycle, and ERK-activity reporters, we show that YAP and TAZ coordinate progenitor expansion with differentiation commitment by regulating ERK dynamics. YAP/TAZ maintain cells in a fluctuating high-ERK state that promotes proliferation while actively keeping the differentiation driver PPARG below the threshold for irreversible commitment. Crucially, this differentiation block is not explained by proliferation alone: inhibiting CDK4/6 or AKT suppressed proliferation without restoring differentiation, whereas MEK-ERK inhibition restored differentiation even when YAP/TAZ activity remained high. As YAP/TAZ activity decreases, dampened ERK fluctuations trigger PPARG activation. These findings support a self-limiting model in which YAP/TAZ-driven progenitor expansion progressively increases cell density and contact-dependent Hippo signaling, reducing YAP/TAZ activity and terminating the proliferative phase. Consequently, transient YAP/TAZ activation expands the progenitor pool while preserving subsequent differentiation, whereas sustained activation suppresses commitment. Together, these findings identify YAP/TAZ-controlled ERK dynamics as the nexus coordinating progenitor expansion with terminal differentiation and suggest that slower density-dependent Hippo feedback may set the duration of this proliferative window to regulate differentiated cell-number output.

DOI: https://doi.org/10.64898/2026.09.24.753950
J Clin Invest. 2026 Oct 15. pii: e207635. [Epub ahead of print]136(20):

PI3K signaling in breast cancer: therapeutic advances versus adaptive resistance.

Fabiana Napolitano, Nisha Unni, Carlos L Arteaga.

Somatic alterations in the phosphoinositide 3-kinase (PI3K) pathway are frequent oncogenic drivers in cancer and are particularly relevant in estrogen receptor-positive breast cancer, where PI3K signaling integrates hormonal, growth factor, and metabolic inputs. Therapeutic targeting of PI3K has been limited by toxicity, pathway crosstalk, and adaptive resistance. Recent advances in structural and functional characterization of PIK3CA mutations have enabled the development of more selective inhibitors, including PI3K isoform-selective and emerging allosteric PI3Ka mutant-targeted compounds. These approaches aim to improve the therapeutic index while maintaining pathway inhibition. In parallel, combination strategies with endocrine therapy and CDK4/6 inhibitors have demonstrated clinical benefit in selected patient populations. However, responses are often transient owing to compensatory signaling and pathway reactivation. Additional metabolic and transcriptional adaptations further contribute to sustaining tumor cell survival. Overall, PI3K-targeted therapy is evolving along two complementary paths: increased mutant-selective inhibition to improve therapeutic index and broader pathway-level strategies designed to overcome adaptive resistance and achieve more durable responses. Ongoing efforts focus on optimizing combination strategies, enhancing development of predictive biomarkers, and improving therapeutic sequencing to achieve durable responses while minimizing toxicity.

DOI: https://doi.org/10.1172/JCI207635
J Hum Immun. 2027 Jan 04. pii: e20260040. [Epub ahead of print]3(1):

Open-label extension study of leniolisib in activated PI3Kδ syndrome: Long-term efficacy and safety.

V Koneti Rao, Anna Šedivá, Virgil A S H Dalm, Alessandro Plebani, Catharina Schuetz, Anna Shcherbina, Antonio Trizzino, Yulia Zharankova, Alanvin Orpia, Elaine Kulm, Julia Körholz, Vassilios Lougaris, Yulia Rodina, Jason Bradt, Anurag Relan, Gulbu Uzel.

Activated phosphoinositide 3-kinase delta syndrome (APDS) is an inborn error of immunity characterized by immune deficiency and dysregulation. Leniolisib is a selective phosphoinositide 3-kinase delta inhibitor approved to treat APDS in patients ≥12 years old. We report final results from a single-arm, open-label extension study in 37 patients with APDS (NCT02859727). Median leniolisib exposure was 4.3 years (range, 1.2-7.0 years). Adverse events (AE) were reported in 34 patients; 87% were grade 1. Serious AEs, reported in 10 patients, were deemed unrelated to leniolisib. Two patients discontinued treatment due to AEs: cardiac arrest and Hodgkin's lymphoma. There were significant reductions in annual infection (P = 0.0005) and respiratory infection (P = 0.0017) rates per year of treatment. Immunoglobulin replacement therapy (IRT) use significantly decreased per year of treatment (P = 0.0095). Clinically meaningful improvements in general health scores from the 36-Item Short Form Survey were observed. Overall, long-term use of leniolisib was generally well tolerated, and infections and IRT use reduced over time.

DOI: https://doi.org/10.70962/jhi.20260040
Cell. 2026 Oct 15. pii: S0092-8674(26)01187-6. [Epub ahead of print]189(21): 6589-6593

Charting the silent variation within us.

Jacey R Pridgen, Margaret A Goodell.

Every cell in the human body carries its own genome, shaped by mutations acquired over a lifetime, yet this vast somatic variation has been nearly impossible to measure. The SMaHT Network now delivers benchmarked tools and the first body-wide map of somatic mosaicism, establishing a baseline of "normal" against which its roles in development, aging, and disease can finally be tested.

DOI: https://doi.org/10.1016/j.cell.2026.09.046
Nat Methods. 2026 Oct 16.

Recent developments of fluorescent proteins and biosensors driven by cross-disciplinary insights.

Anneliese M M Gest, Sohum Mehta, Jin Zhang.

Since the discovery and application of green fluorescent protein for use as an optical tag, fluorescent proteins (FPs) have changed the way we observe biological signals and processes. FP and fluorescent biosensor design has continued to advance, facilitated by new technologies and developments in chemistry, physics, engineering and screening technologies. We summarize some of the recent developments in FP engineering, focusing on insights that have led to improved photostability or longer wavelengths, among other improvements, highlighting mScarlet as a case study. We also discuss the engineering of new fluorescent biosensors, focusing on the ways in which screening, quantitative imaging, spatial resolution and multiplexing have been improved in recent years. Finally, we conclude with a perspective on what the future holds for the next generation of FPs and biosensors.

DOI: https://doi.org/10.1038/s41592-026-03268-7
FASEB J. 2026 Oct 31. 40(20): e72373

AKT Phosphorylation of FOXK2 at Ser398 Impacts Breast Cancer Cell Growth and Viability.

L T Carneiro, J M R C Nunes, G De Gregoriis, B S Mendonça, W M Araújo, R C Maia, E W F Lam, R S Carvalho, M A Carvalho, A D Sharrocks, G Nestal de Moraes.

  FOXK2 is a transcription factor known to mediate drug sensitivity in breast cancer. However, poor prognosis patients and drug-resistant cells exhibit constitutively elevated levels of FOXK2 protein, which appears functionally inactive. Although emerging evidence suggests that FOXK2 is regulated by post-translational modifications, the underlying mechanisms in breast cancer remain poorly understood. An in silico analysis identified AKT as a putative regulator of FOXK2, prompting the investigation of AKT-mediated phosphorylation of FOXK2 in cancer. Our results show that elevated FOXK2 protein levels are associated with increased AKT phosphorylation and doxorubicin resistance. Modulation of AKT levels reduces FOXK2 at protein but not mRNA levels. Consistently, analysis of public breast tumor datasets revealed increased FOXK2 phosphorylation at different sites, including serine 398. Immunoblotting with an antibody against AKT substrates and lambda phosphatase treatment indicates that serine 398 in FOXK2 is an AKT phosphorylation site. Notably, the phosphodeficient FOXK2 mutant (S398A) impaired cell growth, metabolic cell viability, and clonogenic capacity, even in the presence of chemotherapeutic drugs. In summary, AKT regulates FOXK2 in drug-resistant breast cancer cells, with serine 398 emerging as a novel phosphorylation site. Our findings reveal key insights into FOXK2 regulation and the contribution to understanding breast cancer cell biology.

Keywords:  AKT oncogenic kinase; FOXK2 phosphorylation; FOXK2 transcription factor; breast cancer cell growth; drug resistance

DOI:  https://doi.org/10.1096/fj.202600413RRR
J Clin Invest. 2026 Oct 08. pii: e200951. [Epub ahead of print]

Manganese availability determines hepatic insulin sensitivity by enhancing Akt activity.

Jennifer R Gamarra, Sei Higuchi, Timothy L Yuan, Yuke Xie, Cong Liu, Niroshan Shanmugarajah, Hang Yang, Meredith O Kelly, Sarah A Hannou, Kathrin Schilling, Ana Navas-Acien, Eunhee Choi, Anum Glasgow, Inna I Astapova, Mark A Herman, Rebecca A Haeusler.

  Insulin signaling is a critical determinant of metabolic health, and impairments in insulin action contribute to the development of type 2 diabetes. The kinase Akt is a central mediator of insulin signaling and is required for insulin's suppression of hepatic glucose output. Although the regulation of Akt by the insulin receptor-PI3K pathway is well understood, there are instances in which signaling downstream of Akt is dissociated from proximal insulin signaling, for example in insulin resistance. Nonetheless, little is known about PI3K-independent mechanisms of Akt regulation. Here, we discovered that hepatocyte manganese concentrations are a key determinant of PI3K-independent Akt function in vivo. We further demonstrated that manganese increases Akt's catalytic efficiency, and quantitative phosphoproteomics revealed that manganese and insulin act additively to enhance Akt activity. Moreover, we uncovered that hepatic manganese concentrations fluctuate during fasting and feeding via carbohydrate-dependent transcriptional regulation of the manganese efflux transporter Slc30a10. This dynamic metal-signaling axis provides a mechanistic link between nutrient status and Akt activation, and suggests a molecular explanation for the glucose-lowering effects of manganese observed in humans. Our findings establish manganese as a physiologically regulated cofactor for Akt and position metal bioavailability as a previously unrecognized layer of insulin signaling control.

Keywords:  Cell biology; Glucose metabolism; Insulin; Metabolism; Protein kinases

DOI:  https://doi.org/10.1172/JCI200951
bioRxiv. 2026 Sep 29. pii: 2026.09.28.752142. [Epub ahead of print]

VPS34 regulation in pulmonary arterial vascular smooth muscle cells in pulmonary hypertension.

Anthony Natoli, Benjamin Reinhard, Logan Hallee, Huan Zhang, Kaylin Piza-Taylor, Felix Aung, Andrianna Poznahovska, Jason P Gleghorn, Rachel Lucas, Maggie DiVita, Yuanjun Shen.

Pulmonary arterial hypertension (PAH) is characterized by the hyperproliferative phenotype of pulmonary arterial smooth muscle cells (PAVSMCs) and extensive extracellular matrix (ECM) remodeling. Vacuolar protein sorting 34 (VPS34), a Class III Phosphatidylinositol-3 Kinase (PI3K), regulates cell proliferation, but its specific function in pulmonary vascular remodeling remains poorly understood. We aim to determine the role of VPS34 activation and regulation in PAVSMC proliferation, matrix deposition, and the progression of PAH. First, we found a marked decrease in the inhibitory phosphorylation of VPS34 at Ser164 (P-S164-VPS34)-indicative of constitutive VPS34 activation-in remodeled pulmonary arteries (PAs) from human PAH patients and male mice exposed to Sugen/Hypoxia (SuHx). In human PAH PAVSMCs, siRNA-mediated knockdown of VPS34 or pharmacological inhibition via the selective inhibitor SAR405 significantly blunted cell proliferation and reduced the production of fibronectin, a major component of the remodeled ECM. Mechanistically, we found that Akt activation in PAH PAVSMCs promotes VPS34 activation; Protein Phosphatase 1 Catalytic Subunit Alpha is a potential effector in VPS34 activation; and active VPS34 led to the activation of the mTOR/S6 signaling pathway with tuberous sclerosis complex 2 downregulation. Finally, in vivo treatment with SAR405 attenuated right ventricular systolic pressure, right ventricular hypertrophy, and pulmonary vascular remodeling in SuHx mice, while concurrently decreasing vascular fibronectin deposition. Our study demonstrates that VPS34 activation, driven by an Akt-mediated loss of the inhibitory P-S164, is crucial in PAVSMC proliferation and fibrotic vascular remodeling in PAH. Targeting the VPS34 axis represents a promising anti-remodeling therapeutic strategy for the treatment of PAH.
Clinical Relevance: What is new?: This study identifies VPS34 activation via loss of the inhibitory Ser164 Phosphorylation as a previously unrecognized mechanism promoting pulmonary arterial smooth muscle cell (PAVSMC) hyperproliferation, pulmonary vascular remodeling, and pulmonary hypertension.VPS34 activation increases PAVSMC-derived fibronectin production, highlighting the potential role of VPS34 in regulating extracellular matrix remodeling.Pharmacological inhibition of VPS34 by SAR405 decreased PAH PAVSMC proliferation and pulmonary vascular remodeling.What are the clinical implications?: There is no FDA-approved VPS34 inhibitor, but chemicals or macromolecules targeting VPS34 activation, at least in PAVSMC, could be beneficial against pulmonary vascular remodeling and pulmonary hypertension progression.Further understanding the regulation of extracellular matrix remodeling by VPS34 can also spark new therapies for pulmonary vascular diseases.

DOI: https://doi.org/10.64898/2026.09.28.752142
J Invest Dermatol. 2026 Oct 16. pii: S0022-202X(26)03781-4. [Epub ahead of print]

EGFR activity governs stage-dependent fibrotic responses in recessive dystrophic epidermolysis bullosa.

Bing Hang, Alexander Nyström.

  Repeated injury can impair transitions between cellular phenotypes, potentially leading to pathological tissue repair. In recessive dystrophic epidermolysis bullosa (RDEB), collagen VII deficiency predisposes to repeated tissue injury, driving inflammation and fibrosis. Although fibroblasts are major effector cells in RDEB fibrosis, their phenotypic and molecular changes underlying disease progression remain elusive. Through cellular and in situ analyses of clinical samples and tissue from an RDEB mouse model, we disclose a phenotypic switch in dermal fibroblasts during disease progression. At early stages, fibroblasts display a contractile phenotype, whereas at later stages they transition toward a less contractile phenotype with increased production of a fibrosis-promoting extracellular matrix, indicated by high tenascin-C levels. Dysregulated epidermal growth factor receptor (EGFR) signaling through AKT appears central to this switch. At early stages, EGFR signaling and AKT support fibroblast contractility, whereas at later stages this signaling becomes intrinsically blunted, with ADAM17 implicated in the transition. The type of inflammation modulates this phenotypic switch. Thus, RDEB fibroblasts transition from a contractile to a less contractile but pro-fibrotic phenotype during disease progression. These findings suggest that reducing cellular contractility may be advantageous at earlier disease stages, whereas extracellular matrix-targeting strategies may have higher priority at later stages.

Keywords:  AKT; Collagen VII; contractility; inflammation; myofibroblasts

DOI:  https://doi.org/10.1016/j.jid.2026.10.007
Oncogene. 2026 Oct 16.

Dynamic remodeling of the KRAS interactome by direct RAS inhibitors with distinct mechanism of action reveals convergent responses.

Yang Yang, Tingyu Liu, Charles Y Cho, Xianzhong Liu, Ansgar Brock, Doug Quackenbush, Kaisheng Chen, Frederick Lo, Cyril H Benes, Jacob R Haling.

KRAS is mutated in 30% of all human cancers. Small molecule inhibitors targeting KRAS with distinct mechanisms-of-action and variable specificities have entered the clinic, but their full effect on the RAS signaling network remains unclear. Here, we described the impact of RAS inhibition on the KRAS interactome using Proximity-dependent Biotin Identification. Two inhibitors were used: panRAS-ON, which forms a ternary complex between cyclophilin and RAS in the GTP-bound state; panKRAS-off, which binds to the KRAS switch II pocket. RAS inhibitors were found to significantly alter 16.5% of proteins in proximity to KRAS. Despite their distinct modality, the KRAS inhibitors induced highly correlated changes in the KRAS interactomes. Among KRAS-proximal proteins, Afadin was highly affected by RAS inhibition. AFDN is a key regulator of cell motility, invasion, and metastasis. Analysis of AFDN phosphorylation revealed that AKT only partially modulates p-Ser1718, while KRAS inhibition sufficiently abolished EGF-mediated AFDN phosphorylation. Silencing AFDN in a KRAS-driven non-small cell lung cancer model abolished chemotaxis and disrupted directional migration in an EGF-driven wound healing model. We demonstrated that KRAS is a central node in regulating growth factor-induced cell migration, and that KRAS inhibition plays a broader role than MAPK-mediated cell proliferation and survival.

DOI: https://doi.org/10.1038/s41388-026-04017-y
J Clin Invest. 2026 Oct 15. pii: e209602. [Epub ahead of print]136(20):

Modeling human neurodegeneration with iPSCs: opportunities, limitations, and the challenge of aging.

Shijie Wang, Lisa Elia, Weiyi Liu, Steven Finkbeiner.

Most neurodegenerative diseases reflect patient-specific combinations of polygenic risk variants interacting with aging and environmental factors, rather than a single causative mutation. Phase III clinical trial failure rates for neurodegenerative indications exceed 95%, reflecting in part the limitations of existing preclinical systems to fully model the human genetic context of disease. Patient-derived induced pluripotent stem cells (iPSCs) have the potential to address this shortcoming by faithfully recapitulating human cell biology and preserving each patient's complete genetic architecture. This Review examines iPSC-based models of neurodegeneration across three themes. First, we discuss mechanisms revealed by these models, from convergent pathways uncovered by familial mutations to early evidence that sporadic disease biology is accessible at sufficient cohort scale. Second, we evaluate culture systems from 2-dimensional monocultures to organoids, examining how increasing complexity expands addressable biological questions while introducing trade-offs. Third, we address the aging problem: reprogramming erases epigenetic signatures of donor aging, removing the cellular context in which late-onset sporadic neurodegeneration emerges. We discuss strategies approximating aging in iPSC-derived neurons and highlight direct conversion strategies that preserve native epigenetic age, enabling access to age-dependent phenotypes. We propose a framework matching model systems to biological questions, improving mechanistic understanding and therapeutic development.

DOI: https://doi.org/10.1172/JCI209602
Bioinformatics. 2026 Oct 02. pii: btag730. [Epub ahead of print]42(10):

Seumetry: a versatile and comprehensive R toolkit to accelerate high-dimensional flow and mass cytometry data analysis.

Hamburg Intestinal Tissue Study Group

MOTIVATION: Recent progress in flow and mass cytometry technologies enables the simultaneous measurement of over 50 parameters for an individual cell. The resulting increase in data volume and complexity present challenges for conventional analysis methods, which are based on manual gating, are time-consuming and fail to capture unknown or minor cell populations. Advances in single-cell RNA sequencing (scRNAseq) technologies have prompted the development of computational analysis tools designed to process and analyze high-dimensional biological data. Building on these advances, we here present Seumetry, a framework that combines flow and mass cytometry data-specific analysis methods with the capabilities of Seurat, a powerful tool for the analysis of scRNAseq data.
RESULTS: Seumetry offers methods for advanced quality control, data visualizations, and differential population abundance and protein expression analysis. We tested Seumetry on an in-house generated complex dataset of immune cells from different layers of human intestines, demonstrating that Seumetry accurately identifies distinct immune cell populations. Furthermore, benchmarking against public datasets showed that Seumetry aligns with manual-gated results, further validating its use for high-dimensional flow and mass cytometry data. In summary, Seumetry provides a new scalable framework for the comprehensive analysis of high-dimensional cytometry data with seamless integration into commonly used scRNAseq analysis tools, enabling in-depth analysis methods to facilitate biological interpretations.
AVAILABILITY: Seumetry code is available open source under an MIT license and the current version can be viewed and used via Github: https://github.com/imsb-uke/Seumetry; and archived on Zenodo: https://doi.org/10.5281/zenodo.21216681. Flow cytometry data generated for this manuscript is available via Zenodo: https://doi.org/10.5281/zenodo.11935872.

DOI: https://doi.org/10.1093/bioinformatics/btag730
bioRxiv. 2026 Sep 30. pii: 2026.05.14.725131. [Epub ahead of print]

Design and Evolution of an Orthogonal HaloTag for Multiplexed Labeling in Cells.

Benjamin J Goldberg, Bryan J Lampkin, Alexander T Stead, Siena Stanten, Patrick Rabe, Joshua A Kritzer.

The self-labeling protein HaloTag is used to install a wide variety of functional small molecules in cells and living organisms with exquisite specificity with respect to cell type and subcellular localization. HaloTag is a core part of many biotechnology-based tools for sensing, tracking, and manipulating biological systems with a high degree of spatial and temporal control. Due to the limitations of fluorescent proteins and other self-labeling proteins, most of these tools have historically been restricted to a single channel. In this work, we used structure-guided rational design and directed evolution to produce an orthogonal HaloTag protein called OrthoTag which reacts selectively with a modified chloroalkane substrate. OrthoTag retains many of HaloTag's superior properties, and reaction rate measurements with purified proteins show OrthoTag and its substrate have 109-fold mutual orthogonality to HaloTag with respect to substrate concentration. We demonstrate the application of OrthoTag for multiplexed labeling experiments in mammalian cells with minimal optimization. Going forward, OrthoTag should be straightforward to incorporate into HaloTag-based systems to allow simultaneous measurement or manipulation of two biological targets or processes. The availability of multiple high-performance self-labeling proteins will enable the continued development of new multiplexed biotechnology methods.

DOI: https://doi.org/10.64898/2026.05.14.725131
iScience. 2026 Oct 16. 29(10): 117728

FKBP12 determines ligand-specific SMAD signaling in individual living endothelial cells.

Zixin Huang, Sonja Lenhardt, Petra Snyder, Ahmed Bulldan, Felix Hausch, Alexander Loewer.

  The BMP signaling pathway plays a pivotal role in regulating the formation and maintenance of our vascular system, employing a diverse set of ligands, receptors, and cytoplasmic mediators. However, little is known about how the interplay of these elements is regulated dynamically in individual living endothelial cells. Here, we developed fluorescent reporter to quantify BMP signaling and used a combination of time-resolved microscopy and computer-aided analysis to demonstrate ligand-specific dynamics of SMAD1, SMAD5, and SMAD9. Using this approach, we identified FKBP12 as a critical regulator of receptor complex activity that determines the balance of SMAD1/5/9 and SMAD2/3 signaling upon treatment with angiogenic ligands such as BMP7 and Activin A. This provides insights into the regulation of the BMP pathway in endothelial cells and offers a potential node for modulating vascular pathologies where the SMAD1/5/9-SMAD2/3 balance is disrupted.

Keywords:  Biochemistry; cell biology

DOI:  https://doi.org/10.1016/j.isci.2026.117728
Res Sq. 2026 Sep 28. pii: rs.3.rs-10884175. [Epub ahead of print]

Comprehensive assessment of the genotype-phenotype spectrum and treatment for monoallelic insulin receptoropathy in a cohort of 505 people.

Rebecca Brown, Jingxiang Xu, Jian'an Luan, Bruno Donadille, Vahid Aslanzadeh, Christine Bellané-Chantelot, Valeria Grasso, Delphine Collin-Chavagnac, Mafalda Mucciolo, Ingrid Allix, Anne Bachelot, Sabine Baron, Danila Benevento, Laurence Blanco, Muriel Bourgeon, Sophie Christin-Maître, Elaine Cochran, Régis Coutant, Lea Dheghani, Annalisa Deodati, Charlotte Djakouré, Danièle Dubois-Laforgue, Lise Duranteau, Claire-Lise Gay, Siri Atma Greeley, Tülay Guran, Balamurugan Kandasamy, Marie Laloi-Michelin, Pascale Mahot, Dominique Maiter, Viswanathan Mohan, Rinki Murphy, Estelle Nobécourt, Novella Rapini, Sylvie Salenave, Pratik Shah, Megan Startzell, Igor Tauveron, Daniel Terral, A Kemal Topaloglu, Praveen V P, Marie-Christine Vantyghem, Vankatesan Radha, Martin Wabitsch, Peter Winocour, Hannele Yki-Järvinen, Jacques Young, Rachel Williams, Kashyap Patel, Loredana Marcovecchio, Louis Lebreton, Camille Vatier, Nicholas Wareham, Anna Stears, Elise Bismuth, David Savage, Isabelle Jéru, Stephen O'Rahilly, Kevin Colclough, Gemma Brierley, Fabrizio Barbetti, Corinne Vigouroux, Robert Semple.

Background Insulin signalling is mediated by the INSR -encoded receptor tyrosine kinase. Biallelic INSR variants cause the most severe insulin resistance (IR), whereas heterozygous mutations cause less rare but still severe IR. Dominantly inherited IR has been attributed to dominant negative action of intracellular (IC) missense variants, but whether extracellular (EC) variants exert dominant-negative effects, and whether simple heterozygous loss of function (LoF) causes a metabolic phenotype, remains unresolved. We aimed to clarify the phenotypic spectrum, underlying mechanisms, and natural history of IR caused by heterozygous INSR variants. Methods We aggregated genetic and clinical data from 505 individuals with monoallelic rare INSR variants from published reports, international referral centres, ClinVar/HGMD, and the Fenland population cohort. Loss-of-function (LoF) status was assigned using in silico tools including NMDetector and SpliceAI; Insulin concentrations were compared against age-, sex-, and BMI-specific reference centiles (Fenland, NHANES, IDEFICS). The common p.M1180K variant was functionally characterised by assessing cell-surface expression, and insulin-induced autophosphorylation. Results 240 probands and 265 relatives were studied. There was marked female predominance among probands (Male:Female = 1:3.4) and earlier female presentation, most often with hyperandrogenism. Presentation with diabetes, hyperinsulinaemia, or hypoglycaemia was common in both sexes. Missense variants were 14-fold enriched in the IC domain compared to gnomAD, concentrated in key functional motifs including activation and catalytic loops, whereas LoF variants were distributed in proportion to domain length. The p.M1180K variant was normally expressed but autophosphorylation-deficient. Most EC variant carriers - including genetically-ascertained individuals with EC LoF or deleterious missense variants - showed moderate to severe IR from puberty onwards. Across the whole cohort with IC or EC variants, diabetes occurred in 56% and hypoglycaemia in 55%, the latter a presenting feature in 11% of probands and common among relatives. Birthweight standard deviation score (SDS) was reduced (-1.0) and BMI SDS modestly increased (+ 0.7). Hyperandrogenism and/or Polyendocrine Metabolic Ovarian Syndrome affected 82% of postpubertal females, while GDM affected 20-53% of pregnancies. Lipid profiles were normal. Conclusions The human INSR demonstrates haploinsufficiency, with EC LoF and deleterious missense variants causing IR with variable penetrance. Hypoglycaemia is more common than previously recognised, warranting caution with diabetes therapies.

DOI: https://doi.org/10.21203/rs.3.rs-10884175/v1
J Microsc. 2026 Oct 13.

Reviewing reproducibility and replicability in 'Deconstructing gastrulation at single-cell resolution' by Stern et al. (2022).

Gabriel G Martins, Haydee O Hernández, Lachlan Whitehead, Pradeep Rajasekhar.

  Quantitative analysis of embryonic morphogenesis often requires handling terabyte-scale 4D microscopy datasets, posing major computational and methodological challenges. Such analyses involve complex workflows for image restoration, segmentation, and tracking of thousands of cells in 3D, sometimes assembled from multiple generic tools and custom scripts. In their study 'Deconstructing gastrulation at single-cell resolution,' the authors present an integrated computational framework for cell segmentation, tracking and modelling of cell-cell interactions during Drosophila gastrulation. Their approach combines both generic tools such as ilastik, FIJI, Cellpose, MATLAB code and tools such as ImSAnE to reconstruct whole-embryo, single-cell morphogenetic atlas with unprecedented detail. While the methodology is transparent and well-documented, its implementation relies on multiple software environments and some non-open-source components, limiting full reproducibility and generalisability. Nevertheless, their 'computational framework' exemplifies rigorous data sharing, clear documentation, and methodological transparency aligned with several community guidelines for reproducible image analysis. We discuss this work in the context of reproducibility, replicability, generalisability, transparency, validity, and robustness, emphasising how emerging open-source and popular solutions could improve accessibility and replicability of similar large-scale bioimage analysis workflows in developmental biology.

Keywords:  3D image segmentation; algorithmic replicability; automated cell tracking; image analysis

DOI:  https://doi.org/10.1111/jmi.70132
bioRxiv. 2026 Oct 04. pii: 2026.09.30.755445. [Epub ahead of print]

Disease-associated mutations directionally modulate epigenetic age in iPSC-derived tissues.

Nicholas J Skvir, Todd W Dowrey, Samuel F Cranston, Elise MacDonald, Richard Giadone, Dakota Jones, Carly S Golden, Braden Pate, Madeline Labott, Maria A Serrano, Konstantinos-Dionysios Alysandratos, Kim Vanuytsel, George J Murphy.

Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) resets epigenetic age, creating a major challenge for modeling age-associated cellular states and limiting the use of iPSCs in aging research beyond the genetic component. Recent work has shown that healthy organoids can re-accumulate age-associated epigenetic states over extended culture; whether disease-associated genetic states can directionally reshape these trajectories after reprogramming remains unknown. Here, we present a reproducible, in-vitro approach to re-establish epigenetic aging trajectories using iPSC-derived organoid systems, as quantified by multiple epigenetic clock models. We first demonstrate that epigenetic age progressively increases with serial passaging in a lung organoid model (alveolospheres). We then show that disease-associated mutations in multiple models drive additional, cell-intrinsic shifts in epigenetic age, implicating disease state as an independent modulator of epigenetic clocks. Together, these findings reinforce that iPSC-derived organoids recapitulate epigenetic aging trajectories over time, while highlighting disease state as a potent and potentially tractable modulator of epigenetic age in vitro. By enabling more faithful modeling of age-associated cellular states, this approach expands the utility of iPSC-based systems for dissecting the molecular mechanisms that regulate human aging.

DOI: https://doi.org/10.64898/2026.09.30.755445
Methods Mol Biol. 2027 ;3071 29-54

An Open Infrastructure for Mass Spectrometry Data in R.

Johannes Rainer, Marilyn De Graeve, Philippine Louail, Sebastien Gibb, Laurent Gatto.

  We present the Spectra software, an R/Bioconductor package, defining an efficient infrastructure for storing, handling, and visualizing mass spectrometry data. We describe how Spectra adapts to different data types, sizes, and use cases, addressing scalability while keeping a consistent user interface. We also demonstrate how it can integrate with third-party Python tools and follow modern tidyomics principles, seamlessly integrating with more general tidy data science tools.

Keywords:  Bioconductor; Mass spectrometry; Metabolomics; Proteomics; R; Reproducible research; Software

DOI:  https://doi.org/10.1007/978-1-0716-5519-1_3
J Dermatol Sci. 2026 Sep 25. pii: S0923-1811(26)00171-4. [Epub ahead of print]

Endothelial metabolic plasticity in infantile hemangioma: evidence strength, disease phase and therapeutic readiness.

Qian Lin, Ruonan Ke, Xuejun Ni, Lu Chen, Xiaofen Wan, Xiuying Shan, Biao Wang, Beichen Cai.

  Endothelial metabolism is increasingly used to explain the growth, involution and drug response of infantile hemangioma (IH), but the supporting studies differ sharply in disease relevance and validation depth. We assessed which endothelial metabolic and plasticity mechanisms are sufficiently supported to guide experiments, biomarker work or therapeutic development. We performed a structured narrative search of PubMed/MEDLINE from inception to 28 July 2026 and hand-searched the references of included studies and recent reviews. Evidence was weighted by phase-resolved human tissue, patient-derived hemangioma endothelial or stem cells, pathway-specific perturbation, orthogonal or rescue experiments, and lesion-relevant in vivo testing. PFKFB3-supported glycolysis has the most complete preclinical chain for proliferative hemangioma endothelial cells. The SOX18-mevalonate pathway is comparably well anchored during hemangioma stem-cell endothelial differentiation and supports a beta-adrenergic-receptor-independent mechanism for R(+) propranolol. AIBP/NAXE-cholesterol-HIF-1α signaling is supported by bidirectional perturbation and several animal contexts, whereas amino-acid findings remain descriptive. Endothelial-to-mesenchymal transition is not a single involution program: TGF-β1 can drive a proangiogenic state, whereas M1-associated cytokines confer mesenchymal and adipogenic competence in regression-linked models. Recent mitochondrial-targeting and cell-fate studies remain single-study, model-limited evidence. None of the proposed PFKFB3 inhibitors, statins, optically pure R(+) beta-blocker enantiomers or phase-matched combinations has established efficacy or safety for infants with IH. Current evidence prioritizes mechanisms for preclinical development, not off-label treatment. Reproducibility, infant-relevant pharmacology, developmental safety and phase-specific biomarkers are required before clinical testing.

Keywords:  EndoMT; Endothelial metabolism; Infantile hemangioma; PFKFB3; Propranolol; SOX18

DOI:  https://doi.org/10.1016/j.jdermsci.2026.09.003