bims-pideca 2026-10-04 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2026–10–04
twenty-two papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

PI(3,5)P2 controls the signaling activity of class I PI3K.
Dietary protein governs the role of insulin signaling in the postprandial regulation of hepatic mTORC1.
Synergistic role of TFEB/TFE3 and mTORC1 in kidney cystogenesis and tumorigenesis.
A phosphoproteome atlas of human cell lines reveals the landscape of kinase activity.
Loss of Smad4 drives vascular malformations via c-KIT-dependent high-fluid shear stress mimicry.
TCR-mTORC1 signaling promotes epigenetic stabilization of Foxp3 expression in regulatory T cells via TET protein translation.
Clinical and molecular characterization of non-PIK3CA-related vascular malformations with overgrowth in a pediatric cohort.
HIF-1-mediated PPME1 expression promotes breast cancer progression via AKT activation and β-catenin recruitment.
A TBK1/ULK1 signalling axis couples lysosomal stress to TFEB activation.
Real-Time Monitoring of Mass and Mechanical Properties in Single Cells and Multicellular Spheroids.
Cellular senescence: six decades of discovery and reinvention.
Depot-Specific Insulin Receptor Isoform Dynamics During Human Adipose-Derived Stem Cell Adipogenesis.
Kidney Epithelial AKT Controls Potassium Homeostasis and Metabolic Adaptation.
Recognition of negative charge arrays by pleckstrin homology (PH) domains.
Exploiting an epigenetic resistance mechanism to PI3-kinase inhibition in leukemic stem cells.
Pop-Corn: Predicting Perturbation Phenotype Effects Across Single-Cell and Spatial Contexts.
A single-nucleus multi-omic atlas of gene regulation across 21 adult human tissues.
RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.
Spatial modulation of RAF by RAF/MEK glue enables full-dose combination with pan-RAF inhibitor and potent RAS-mutant tumor-selective MAPK and growth inhibition.
Hidden Outcomes of CRISPR-Cas9 Genome Editing Revealed by Targeted Sequencing in Isogenic Human iPSC Clones.
ACTB promotes ESCC progression by regulating the AKT-mTOR signaling pathway through an m6A-dependent mechanism.
SLC4A7/NBCn1 maintains intracellular pH to support mTORC1 activity and antibody-secreting cell differentiation.

Sci Adv. 2026 Oct 02. 12(40): eaeh8582

PI(3,5)P2 controls the signaling activity of class I PI3K.

Jiachen Sun, Julian Zalejski, Seohyeon Song, Ashutosh Sharma, Wei Wang, Yusi Hu, Wen-Ting Lo, Philipp Alexander Koch, Duy-Viet Vo, Jagriti Singh, Indira Singaram, Baoshu An, Hirushi Gunasekara, Jean J Zhao, Liang-Wei Gong, Ying S Hu, Volker Haucke, Ruixuan Gao, Wonhwa Cho.

3-Phosphoinositides are essential cellular lipids regulating health and disease. Among them, phosphatidylinositol-3,5-bisphosphate [PI(3,5)P2] remains the least understood. Using a newly developed ratiometric PI(3,5)P2 sensor that enables spatiotemporally resolved PI(3,5)P2 quantification, we demonstrate that growth factor stimulation generates a distinct PI(3,5)P2 pool on lysosomes and late endosomes. Formed sequentially by class II PI3KC2β and PIKfyve, this PI(3,5)P2 pool terminates growth factor-stimulated class I phosphatidylinositol 3-kinase (PI3K) activity through a specific interaction with its regulatory p85 subunit. Disrupting this p85-PI(3,5)P2 interaction via a small-molecule inhibitor or cancer-causing mutations blocks feedback inhibition, driving sustained class I PI3K activation and promoting neurite growth. Our findings uncover a spatiotemporally specific regulatory function of PI(3,5)P2 that links class I and II PI3Ks to tune growth factor signaling. This mechanism offers therapeutic strategies for treating p85-mutant cancers and advancing tissue regeneration.

DOI: https://doi.org/10.1126/sciadv.aeh8582
Nat Commun. 2026 08 31. pii: 10359. [Epub ahead of print]17(1):

Dietary protein governs the role of insulin signaling in the postprandial regulation of hepatic mTORC1.

Krystle C Kalafut, Yann Cormerais, Madi Y Cissé, Samuel C Lapp, Karen E Inouye, Gökhan S Hotamışlıgil, Brendan D Manning.

The nutrient-sensing mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway controls cellular and organismal growth and metabolism, and aberrant activation is linked to human disease, including metabolic disease. Cellular studies have established regulatory mechanisms influencing mTORC1 activation, but the physiological signals that control mTORC1 at the organismal and tissue levels are less well-defined. mTORC1 is dynamically regulated by fasting and feeding in metabolic tissues, with both nutrients and insulin proposed to activate mTORC1 in response to feeding. Here, studies employing a liver-specific genetic mouse model demonstrate that AKT-mediated TSC2 phosphorylation is the predominant mechanism of hepatic mTORC1 induction by insulin but is dispensable for activation by feeding. Furthermore, postprandial activation of hepatic mTORC1 requires dietary protein, which dictates the insulin-responsiveness of the pathway. Contrary to dogma, hepatic mTORC1 signaling was not elevated in response to diet-induced obesity, despite overt impairments in insulin and glucose homeostasis, and blocking hepatic AKT-TSC-mTORC1 signaling did not affect these metabolic phenotypes. Evidence is also provided supporting a role for glucagon in hepatic mTORC1 suppression during fasting. This study reveals a hierarchy of physiological signals regulating hepatic mTORC1.

DOI: https://doi.org/10.1038/s41467-026-77216-6
Cell Death Differ. 2026 Sep 30.

Synergistic role of TFEB/TFE3 and mTORC1 in kidney cystogenesis and tumorigenesis.

Marco Ferniani, Irene Sambri, Tuong Huynh, Rossella Pennella, Gennaro Tufano, Niculin J Herz, Barbara Rossi, Antonella Iannaccone, Francesco Trepiccione, Alessia Calcagnì, Andrea Ballabio.

Birt-Hogg-Dubé (BHD) and Tuberous Sclerosis (TSC) are inherited cancer syndromes associated with kidney cystogenesis and tumorigenesis and caused by mutations of the folliculin (FLCN) and TSC1/2 genes, respectively. We and others previously showed that Transcription Factors EB (TFEB) and E3 (TFE3) are the main drivers of the kidney phenotypes observed in mouse models of these conditions. These transcription factors are also responsible for the feedback hyperactivation of the mechanistic Target of Rapamycin Complex 1 (mTORC1), a known tumorigenic factor. This raises the question of whether TFEB/TFE3 exert their oncogenic activity by inducing mTORC1 or by mTORC1-independent pathways. To address this question, we generated kidney-specific mouse models in which we knocked out factors that differentially control mTORC1 and TFEB/TFE3, thus uncoupling their activities. Specifically, we generated three kidney-specific conditional knockout lines: (1) Depdc5-KO mice in which loss of GATOR1 activity leads to mTORC1 hyperactivation and TFEB/TFE3 inhibition, (2) RagC-KO mice in which TFEB/TFE3 are constitutively active and mTORC1 activity is partially inhibited due to impaired Rag heterodimer formation, and (3) Flcn/RagC double KO mice to test whether mTORC1 inhibition induced by RagC loss ameliorates the aggressive kidney phenotype of FLCN KO mice. Comparison between these models revealed that mTORC1 hyperactivation is a key driver of cystogenesis and tumorigenesis, while TFEB/TFE3 constitutive activation further enhances and accelerates pathology by establishing a transcriptional program that integrates metabolic and stress-response pathways. Together, our findings define an oncogenic mechanism by which both mTORC1 and TFEB/TFE3 hyperactivation cooperate in kidney tumorigenesis.

DOI: https://doi.org/10.1038/s41418-026-01881-9
Nat Struct Mol Biol. 2026 Sep 30.

A phosphoproteome atlas of human cell lines reveals the landscape of kinase activity.

Claire Koenig, Hayoung Cho, Kristina B Emdal, Ilaria Piga, Pierre Sabatier, Samuel Lozano-Juárez, Ana Martinez-Val, Jesper V Olsen.

Protein phosphorylation orchestrates cellular signaling and controls most biological processes, with its dysregulation driving diseases, notably cancer. Comprehensive, high-throughput phosphoproteomics remains limited by detection sensitivity, data completeness and computational bottlenecks, especially in low-input settings. Here we present a comprehensive empirical human phosphoproteome resource, regrouping over 200,000 class I phosphosites across 33 diverse human cell lines. We demonstrate that this spectral library dramatically improves single-shot phosphoproteomics with 30-fold faster data processing compared with library-free approaches and enhances confidence in phosphosite localization even from minimal sample input. Integrating proteome and phosphoproteome data, we develop a combined kinase activity score (Cscore), revealing cell line- and cancer-specific signaling vulnerabilities, many correlating with drug sensitivity. This resource accelerates deep and reproducible phosphoproteomics, enables the systematic mapping of cellular signaling networks and may empower precision oncology by highlighting actionable kinase targets in diverse cell states.

DOI: https://doi.org/10.1038/s41594-026-01877-6
J Clin Invest. 2026 Oct 01. pii: e197609. [Epub ahead of print]136(19):

Loss of Smad4 drives vascular malformations via c-KIT-dependent high-fluid shear stress mimicry.

Johannes Gahn, Fan Wu, Qing Zhang, Yuxi Di, Tanmaya Behera, Yonggang Ren, Zohrah Hashemi, Kuheli Banerjee, Julio Cordero, Claudia Gherman, Kornelia Andorfer, Caroline T Seebauer, Fatemeh Mirzapour-Shafiyi, Gergana Dobreva, Martin A Schwartz, Roxana Ola.

  Vascular endothelial cells (ECs) encode a homeostatic fluid shear stress (FSS) set point that is essential for vascular stability. Deviations above or below this threshold trigger adaptive remodeling to restore physiological shear levels. Disruption of this control mechanism leads to enlarged arteriovenous malformations (AVMs) in hereditary hemorrhagic telangiectasia, a vascular disorder caused by heterozygous loss-of-function (LOF) mutation in ALK1, ENG, or SMAD4. Mechanistically, Smad4-deficient ECs are reset to a lower FSS set point value, resulting in AVMs that show characteristics of high-FSS remodeling with elevated KLF4 and high activation of the downstream Akt. Here, we investigated the KLF4/Akt upstream mechanisms by which SMAD4 sets the physiological FSS set point. We identified the receptor tyrosine kinase c-KIT as a component and regulator of the junctional mechanosensory receptor complex, which is highly upregulated in murine and human AVMs. SMAD4 restrains flow signaling by limiting c-KIT-dependent ERK5 activation and KLF4 induction. Thus, SMAD4 LOF leads to sustained c-KIT engagement in the sensory junctional apparatus, driving enhanced and prolonged activation of the ERK5/KLF4/Akt signaling axis. These results show that Smad4-LOF mutations induce malformations by disabling a key homeostatic mechanism and identify c-KIT as a potentially previously unrecognized therapeutic target.

Keywords:  Cardiovascular disease; Cell biology; Genetics; Molecular biology; Signal transduction; Vascular biology

DOI:  https://doi.org/10.1172/JCI197609
Proc Natl Acad Sci U S A. 2026 Oct 06. 123(40): e2612904123

TCR-mTORC1 signaling promotes epigenetic stabilization of Foxp3 expression in regulatory T cells via TET protein translation.

Tomohide Kinoshita, Akira Nakajima, Toru Kobayashi, Mai Ohno, Yuxi Wei, Tatsumasa Hasegawa, Norihito Hayatsu, Shoshiro Hirayama, Yu-Ichi Tsukada, Atsushi Hirao, Shigeo Murata, Shohei Hori.

  Regulatory T (Treg) cell differentiation and function rely on stable expression of the master transcription factor Foxp3. While Foxp3 expression is epigenetically stabilized through DNA demethylation of a Foxp3 enhancer (the Treg-specific demethylated region, TSDR), the mechanisms underlying this process remain unclear. Here, we show that strong and sustained T cell receptor (TCR) signaling promotes TSDR demethylation, stabilizes Foxp3 expression, and confers suppressive activity in in vitro-induced Treg (iTreg) cells through activation of mTORC1. Mechanistically, TCR-mTORC1 signaling promotes TSDR demethylation by enhancing translation of TET2, and likely TET3, enzymes that mediate DNA demethylation. Rescue of impaired TSDR demethylation under mTORC1 inhibition by the TET2 catalytic domain, together with dose-dependent impairment following heterozygous deficiency of TET2 and/or TET3, supports a causal link between TET protein abundance and TSDR demethylation. In vivo, mTORC1 inactivation increases the frequency of cells harboring a methylated TSDR among peripheral Foxp3+ T cells, but not among developing Foxp3+ thymocytes, supporting in vivo relevance of mTORC1-dependent epigenetic remodeling. Thus, TCR-mTORC1 signaling promotes epigenetic stabilization of Foxp3 expression through translational control of TET proteins, revealing an unrecognized role for mTORC1 in iTreg cell differentiation.

Keywords:  DNA demethylation; Foxp3; T cell receptor; mTORC1; regulatory T cells

DOI:  https://doi.org/10.1073/pnas.2612904123
World J Pediatr. 2026 Sep 30.

Clinical and molecular characterization of non-PIK3CA-related vascular malformations with overgrowth in a pediatric cohort.

Giuseppe Reynolds, Maria Luca, Paola Coppo, Roberta La Selva, Chiara Leoni, Iacopo Bellani, Simona Ragusa, Stefania Massuras, Sonia Perrelli, Stefania Martino, Paola Sabrina Buonuomo, Federico Rondot, Alessandro Mauro Spinelli, Carla Morando, Marilidia Piglionica, Nicoletta Resta, Alessandro Mussa.

   INTRODUCTION: Vascular malformations (VMs) associated with overgrowth represent a heterogeneous group of congenital disorders driven by somatic or germline variants in genes regulating vascular morphogenesis and cellular proliferation. While PIK3CA-related overgrowth spectrum (PROS) is relatively well characterized, non-PIK3CA VMs with overgrowth remain poorly defined, with limited genotype-phenotype correlations and no standardized therapeutic strategies. This study aimed to characterize the clinical and molecular features of this underrecognized group in a pediatric cohort.
METHODS: We conducted a multicentric retrospective study across five Italian tertiary centers. Patients were included if they presented with a vascular malformation, clinically appreciable regional overgrowth beyond the vascular lesion itself, and a confirmed pathogenic or likely pathogenic variant in genes of the PI3K/AKT/mTOR or related signalling pathways, excluding PIK3CA. Genetic testing was performed via next-generation sequencing (NGS) using a 17-gene targeted panel (read depth >2000 ×) on peripheral blood, buccal swab, or affected-tissue biopsies. Clinical data were systematically collected across six predefined domains including phenotype, imaging, hemostatic parameters, and therapeutic management.
RESULTS: A total of 41 patients were enrolled, including 20 males and 21 females. The mean age at diagnosis was 12.1 ± 1.4 years. Variants were identified in TEK (24.4%), GNAQ (21.9%), GNA11 (21.9%), PTEN (14.6%), RASA1 (12.2%), AKT3 (2.4%) and EPHB4 (2.4%). Somatic variants accounted for 65.9% of cases. Phenotypic features included skeletal anomalies (46.3%), soft tissue overgrowth (60.9%), macrocrania (19.5%), and segmental undergrowth in a subset. A syndromic diagnosis was established in 63.4% of patients; however, marked phenotypic overlap across genes was observed. Functional limitations affected 43.9% of patients. Alpelisib yielded clinical improvement in selected TEK-variant patients, whereas sirolimus showed limited efficacy.
CONCLUSIONS: Non-PIK3CA VMs with overgrowth constitute a clinically and molecularly heterogeneous spectrum with substantial phenotypic overlap across genotypes, rendering phenotype-based classification unreliable. Somatic mosaicism, variable allele frequency, and tissue-specific expression underlie this heterogeneity. Our findings advocate for broad NGS panels with tissue-based analysis, systematic parental testing, and molecularly driven classification. The observed response to alpelisib in TEK-related disease supports the concept of convergent downstream pathway activation as a rationale for targeted therapies beyond PROS.

Keywords:  Children; Overgrowth; PIK3CA/mTOR pathway; Vascular malformations

DOI:  https://doi.org/10.1007/s12519-026-01098-3
J Clin Invest. 2026 Oct 01. pii: e205415. [Epub ahead of print]136(19):

HIF-1-mediated PPME1 expression promotes breast cancer progression via AKT activation and β-catenin recruitment.

Yajing Lyu, Varen Talwar, Yongkang Yang, Si-Sim Kang, Shuyi Li, Shaima Salman, Daiana Drehmer, Yufeng Wang, Chelsey Chen, Vijay Ramu, Sujin Kim, Dylan Park, Tina Yi-Ting Huang, Emmanuel Datan, Dominic Dordai, Jonathan P Schneck, Gregg L Semenza.

  Hypoxia-inducible factor 1 (HIF-1) orchestrates the transcriptional regulation of thousands of genes involved in breast cancer (BC) progression. Here, we identified protein phosphatase 2A (PP2A) methylesterase 1 (PPME1) as a critical HIF-1 target gene that drives oncogenic signaling under hypoxic conditions. In BC cells, HIF-1-dependent PPME1 expression caused inhibition of the PP2A catalytic subunit (PP2Ac), thereby diminishing PP2A activity, which led to AKT activation, phosphorylation of β-catenin, and its nuclear translocation. Nuclear β-catenin cooperates with HIF-1 to promote BC stem cell specification by activating transcription of the NANOG and KLF4 genes, which encode pluripotency factors, and to drive immune evasion by activating transcription of VEGFA, which recruits and polarizes immunosuppressive tumor-associated macrophages and ISG20, which represses STAT1/IRF1-dependent expression of CXCL10, thereby impairing CD8+ T cell recruitment. In vivo, PPME1 knockdown altered the tumor immune microenvironment, enhanced antitumor immunity, and synergized with anti-CTLA-4 immunotherapy to enable complete tumor eradication. These findings establish PPME1 as a critical regulator linking hypoxia signaling, stemness, and immune evasion and highlight its potential as a BC therapeutic target in combination with immune checkpoint blockade.

Keywords:  Breast cancer; Genetics; Oncology

DOI:  https://doi.org/10.1172/JCI205415
Nature. 2026 Sep 30.

A TBK1/ULK1 signalling axis couples lysosomal stress to TFEB activation.

Alessandra Esposito, Ibrahim Bayramoglu, Chiara Varriale, Maria Pia Cavaliere, Maria Elsa Brunetti, Rossella Agostinis, Rachel M Jansen, Dan A Tudorica, Yongjia Duan, Martina Spacci, Alessia Calcagnì, Carolin D Strobl, Verena Passerini, Fabrizio Andreone, Jlenia Monfregola, Julia Richter, Francesca Sacco, Wolfram Klapper, Oliver Weigert, Andrea Ballabio, Roberto Zoncu, James H Hurley, Joern Dengjel, Gennaro Napolitano.

Lysosomal adaptation to environmental changes is critical for cellular and metabolic homeostasis and requires coordination by the mTORC1 kinase, which conveys nutritional and stress signals into distinct, substrate-specific outputs1,2. The FLCN-FNIP complex (FLCN:FNIP) serves as a crucial regulator of lysosomal function by selectively controlling the ability of mTORC1 to inhibit transcription factor EB (TFEB), a master regulator of catabolic programs and a known oncogene3. Yet how FLCN:FNIP activity is regulated has remained unclear. Here we identify a nutrient-independent lysosomal signalling pathway that regulates FLCN through v-ATPase-driven recruitment of TBK1 or ULK1 (TBK1/ULK1) to lysosomes, via the TAX1BP1 adaptor. This enables TBK1/ULK1-mediated FNIP1 phosphorylation at S296, resulting in inhibition of FLCN and nuclear translocation of TFEB. Recurrent ATP6V1B2 v-ATPase mutations, found in patients with follicular lymphoma, constitutively activate this pathway, leading to hyperactivation of TFEB and follicular lymphoma proliferation. Our work uncovers a lysosomal signalling pathway that is critical for lysosomal adaptation and tumorigenesis.

DOI: https://doi.org/10.1038/s41586-026-11093-3
Adv Sci (Weinh). 2026 Sep 27. e77926

Real-Time Monitoring of Mass and Mechanical Properties in Single Cells and Multicellular Spheroids.

Ilaria Incaviglia, Giulia E M Ammirati, Sophie Herzog, Tommy Krug, Nico Strohmeyer, Miguel Camacho Rufino, Matthias P Lutolf, David A Weitz, Daniel J Müller.

  Cell state, growth, and mechanics are tightly connected properties underpinned by fundamental biological processes. Yet methods to quantify them simultaneously under physiologically relevant conditions, at resolutions sufficient to follow (sub)cellular processes, are still lacking. In particular, the correlation between cell state, mass, and mechanical properties during dynamic processes such as growth, differentiation, development, and disease remains poorly understood. Here, we develop experimental and theoretical approaches based on photothermally actuated microcantilevers integrated with optical microscopy to simultaneously monitor the morphology, mass, and quality (Q)-factor of single mammalian cells and larger cellular systems under culture conditions, with millisecond time resolution. We find that the Q-factor, a measure of mechanical energy dissipation, mirrors the mechanical properties of the cell, with the cytoplasm dominating as the largest and softest compartment. Our method reveals how cellular mechanical properties correlate with mass and depend on cell type, state, and growth. Applied to human spheroids, it further monitors how larger cellular systems regulate mechanical properties during development. Together, these measurements quantify mechanobiological parameters that have so far remained inaccessible, opening the way to a more complete characterization of how cellular systems regulate mechanics during fundamental processes of life.

Keywords:  cancer; cell mass; cell mechanics; cell state; human fibroblasts; human spheroids; mechanobiology; microcantilever; mouse fibroblasts; quality‐factor

DOI:  https://doi.org/10.1002/advs.77926
EMBO J. 2026 Oct 02.

Cellular senescence: six decades of discovery and reinvention.

Myrthe Klaver, Lotte Sophie Steeneken, Naomi Veeningen, Abdullah Altulea, Marco Demaria.

Cellular senescence has undergone a remarkable conceptual evolution since its discovery in 1961. Initially described by Hayflick and Moorhead as the finite proliferative lifespan of cultured human cells, senescence was first viewed as a consequence of cellular aging. The identification of telomere shortening, senescence biomarkers, and oncogene- and damage-induced senescence subsequently established its molecular basis and role as a tumor-suppressive stress response. The discovery of the senescence-associated secretory phenotype (SASP) further transformed the field by revealing that senescent cells actively communicate with and remodel their tissue environment. Genetic mouse models later demonstrated causal roles for senescent cells in tissue repair, aging, and age-related disease, while senotherapeutics established senescence as a therapeutic target. Here, we trace the major conceptual transitions that shaped the field, from replicative endpoint to stress-response program, regulator of tissue homeostasis, driver of chronic pathology, and clinically actionable process. We discuss the discoveries, controversies, and technological advances underlying these transitions and how emerging single-cell technologies, precision biomarkers, and targeted interventions are shaping the next era of senescence research.

DOI: https://doi.org/10.1038/s44318-026-00922-w
Obesity (Silver Spring). 2026 Oct 01.

Depot-Specific Insulin Receptor Isoform Dynamics During Human Adipose-Derived Stem Cell Adipogenesis.

Valentina Annamaria Genchi, Celeste Lauriola, Cristina Caccioppoli, Rossella D'Oria, Nicola Marrano, Giuseppina Biondi, Sebastio Perrini, Annalisa Natalicchio, Luigi Laviola, Francesco Giorgino, Angelo Cignarelli.

   OBJECTIVE: The insulin receptor (IR) and the insulin-like growth factor I receptor (IGF-IR) regulate adipose tissue (AT) differentiation. This study investigated the expression of IGF-IR, IR, and the IR isoforms (IRa and IRb) in human subcutaneous (S-ASC) and visceral (V-ASC) adipose-derived stem cells.
METHODS: S-AT and V-AT biopsies were obtained from human donors and ASC were differentiated into adipocytes. mRNA levels of all receptors were quantified by qPCR at baseline and after differentiation. IR protein expression and adipogenic efficiency were assessed by flow cytometry.
RESULTS: In undifferentiated ASC, IGF-IR transcripts exceeded IR and were higher in S-ASC than V-ASC. Upon differentiation, IGF-IR decreased in S-ASC but remained unchanged in V-ASC, whereas IR increased in both depots. S-ASC displayed ~twofold higher IRa expression and greater insulin-induced Akt activation. During adipogenesis, IR expression rose in both depots, with IRb exceeding IRa particularly in V-ASC (+50%). In whole AT, IR exceeded IGF-IR, and no depot-specific differences were observed between IR isoforms. Adipogenic conversion was higher in S-ASC (60%) than V-ASC (20%). Only ~77% of S-ASC- and ~61% of V-ASC-derived adipocytes expressed surface IR.
CONCLUSIONS: Depot-specific dynamics of IR isoforms may influence adipogenic capacity and insulin responsiveness and suggest partially receptor-independent pathways of adipocyte differentiation.

Keywords:  adipogenesis; human adipose stem cells; insulin receptor isoform

DOI:  https://doi.org/10.1002/oby.70315
J Am Soc Nephrol. 2026 Oct 01.

Kidney Epithelial AKT Controls Potassium Homeostasis and Metabolic Adaptation.

Masa-Ki Inoue, Yahua Zhang, Alondra Vázquez Rivera, Clinton M Hasenour, Juan Pablo Arroyo, Fabian Bock, Alina Yu, Izumi Kaji, Mohammed Z Ferdaus, Eric Delpire, Jamey D Young, Ming-Zhi Zhang, Raymond C Harris, Andrew S Terker.

BACKGROUND: Potassium intake is strongly associated with cardiometabolic health, yet the mechanisms linking electrolyte balance to systemic metabolism remain poorly defined. We hypothesized that renal epithelial AKT acts as a potassium-responsive signaling node that coordinates potassium homeostasis and metabolic adaptation.
METHODS: Inducible nephron-wide and proximal tubule-specific AKT1/AKT2 knockout mice were generated to define the role of epithelial AKT in renal potassium handling and metabolism. Physiologic, molecular, proteomic, and metabolic analyses were performed under normal and potassium-restricted dietary conditions, complemented by mechanistic studies in cultured cells.
RESULTS: Proteomic analysis revealed that dietary potassium restriction stimulated AKT-dependent pathways in the kidney, including glycolysis and de novo lipogenesis. Nephron-wide and proximal tubule-specific AKT deletion impaired adaptation to potassium deprivation, resulting in urinary potassium wasting, reduced kidney hypertrophy, diminished proximal tubule transporter expression, and hypokalemia. Mechanistically, AKT loss suppressed low-K+-induced glycolytic and lipogenic programs, reduced de novo palmitate synthesis, and promoted a renal catabolic, ketogenic phenotype characterized by increased HMGCS2 expression and ketone production. In vitro studies showed that low-potassium-induced AKT activation required mTOR activity but was independent of Rictor, whereas Sin1 and mLST8 were essential. AKT deletion also reduced expression of the proximal tubule glucose transporters SGLT1 and SGLT2, causing glycosuria. These renal adaptations were accompanied by lower fasting glucose levels, improved glucose tolerance, enhanced insulin sensitivity, and increased AKT signaling in liver and skeletal muscle.
CONCLUSIONS: Renal epithelial AKT was required for adaptation to dietary potassium restriction. AKT deletion impaired potassium conservation, reduced kidney growth and proximal tubular transport function, and promoted a shift from anabolic to catabolic renal metabolism. These changes were accompanied by glycosuria and systemic metabolic alterations, including lower fasting glucose levels, improved glucose tolerance, and enhanced insulin sensitivity.

DOI: https://doi.org/10.1681/ASN.0000001278
bioRxiv. 2026 Sep 22. pii: 2026.09.21.753330. [Epub ahead of print]

Recognition of negative charge arrays by pleckstrin homology (PH) domains.

Christopher K Ng, James W Murphy, Jeannine M Mendrola, Michael Sarullo, Steven E Stayrook, Kathryn M Ferguson, Mark A Lemmon.

Pleckstrin homology (PH) domains are typically assumed to be phosphoinositide-binding modules, although most lack strong lipid specificity and their broader ligand repertoire remains poorly defined. We find that many yeast PH domains bind Nsr1p, the ortholog of nucleolin - also identified as a PH domain ligand - suggesting widespread recognition of negatively charged protein regions. The phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5) P 2 )-binding PLCδ 1 PH domain also binds a highly phosphorylated region of IRBIT through the same site that recognizes PtdIns(4,5) P 2 . Using high-throughput integrated phosphopeptide (Hi-P) screening, we surveyed 38,624 mammalian sequences containing three documented phosphoserines. PLCδ 1 -PH bound numerous phosphorylated and unphosphorylated acidic peptides, and phosphorylation generally strengthened pre-existing interactions rather than conferring strict specificity - without requiring a fixed phosphoserine spacing. Instead, favored phosphopeptides combined a key phosphoserine with upstream acidic residues. Structural modeling suggests that this phosphoserine occupies the canonical inositol phosphate binding pocket, while adjacent acidic residues make delocalized electrostatic contacts. Thus, PH domains can recognize various patterns of protein negative charge, expanding their potential regulatory roles beyond membrane targeting.

DOI: https://doi.org/10.64898/2026.09.21.753330
Leukemia. 2026 Sep 28.

Exploiting an epigenetic resistance mechanism to PI3-kinase inhibition in leukemic stem cells.

Shira G Glushakow-Smith, Imit Kaur, Simone Sidoli, Shayda Hemmati, Ellen Angeles, Taneisha Sinclair, Samarpana Chakraborty, Aaliyah Battle, Kristina Ames, Swathi-Rao Narayanagari, Rotila Hyka, Mark Soto, Melissa Tracy, Jayaram Vankudoth, Seiya Kitamura, Linde A Miles, Ulrich Steidl, Aditi Shastri, Amit Verma, Kira Gritsman.

Acquired non-genetic resistance mechanisms to existing therapies contribute to poor outcomes for acute myeloid leukemia (AML) patients, and the inability to target leukemic stem cells (LSCs) can lead to relapse. To overcome these challenges, we tested whether LSCs have dependencies on PI3- kinase (PI3K). We found that LSCs are susceptible to isoform-selective targeting of PI3K and are particularly dependent on the p110 alpha isoform of PI3K. We discovered that PI3K inactivation leads to dynamic changes in EZH2/PRC2 function in leukemic cells, and we uncovered downregulation of EZH2 protein levels as an adaptive resistance mechanism in response to PI3K inhibition. We found that PI3K inhibition in AML cells can lead to compensatory upregulation of EZH1, and that EZH1 knockdown can sensitize AML cells to PI3K inhibition. We leveraged this resistance mechanism by combining a PI3K inhibitor with an EZH1/2 dual inhibitor, which successfully overcomes the acquired resistance and leads to sustained targeting of AML cells ex vivo and in murine AML and PDX models in vivo. This study identifies a promising novel therapeutic regimen for targeting LSCs in AML.

DOI: https://doi.org/10.1038/s41375-026-03145-4
bioRxiv. 2026 Sep 26. pii: 2026.09.25.754560. [Epub ahead of print]

Pop-Corn: Predicting Perturbation Phenotype Effects Across Single-Cell and Spatial Contexts.

Jiapeng Chen, Yan Cui, Yanjun Shao, Na Sun, Maria Rodriguez Martinez.

Genetic perturbations can reshape cell populations by altering the relative abundance of specific cell types and states within the profiled population, including increases, decreases and states that become detectable after perturbation. Pooled single-cell screens, such as Perturb-seq, measure such responses at scale. However, only a small fraction of possible perturbations can be tested experimentally. A central challenge is therefore to predict compositional shifts induced by unseen perturbations. Many perturbation-prediction methods do not directly optimize for this outcome; instead, they predict gene-expression responses and infer cell-type and cell-state composition downstream. Surprisingly, we find that even models that accurately predict perturbation-induced changes in average gene expression perform poorly at forecasting these compositional shifts. To address this gap, we present Pop-Corn, a method that directly predicts how a perturbation reshapes cell-type composition without reconstructing gene expression. In the primary T-cell benchmark, Pop-Corn predicted the overall cell-state composition of held-out perturbations more accurately than the evaluated expression-prediction pipelines, while better preserving the diversity of observed cell states. We further extend Pop-Corn to intact tissue, where it predicts perturbation-induced cell-type proportion changes in local cellular neighborhoods and uses attention patterns to generate hypotheses about context-dependent cellular interactions. Retrospective virtual screens support the use of Pop-Corn to prioritize perturbations for experimental follow-up according to their predicted effects on cell-state composition.

DOI: https://doi.org/10.64898/2026.09.25.754560
bioRxiv. 2026 Sep 26. pii: 2026.09.25.754561. [Epub ahead of print]

A single-nucleus multi-omic atlas of gene regulation across 21 adult human tissues.

Kaili Fan, Amrita Sule, Amy Guillaumet-Adkins, Ruochi Zhang, Tianxiong Yu, Zhijie Cao, Xuting Zhang, Neva Durand, MaryKate Tellier, Laura Domenech, Francois Aguet, Jason D Buenrostro, Kristin G Ardlie.

Diverse human cell types establish specialized functions through lineage- and context-specific regulatory programs. Interpreting non-coding genetic risk requires integrated multi-omic reference maps that directly connect regulatory DNA to cellular expression across human tissues. Here we present a single-nucleus multi-omic atlas comprising 459,856 transcriptomic and chromatin accessibility profiles from 21 adult human tissues and four donors, including paired measurements from 160,688 nuclei. The atlas resolves nine cell lineages, 61 broad cell types and 313 subclusters, and identifies 1,085,062 candidate cis-regulatory elements (cCREs), including 161,270 novel elements absent from ENCODE. Regulatory activity was dominated by cell identity but refined by tissue context. Joint profiling enabled 871,177 cCRE-gene associations and revealed lineage-specific regulatory architectures. Cross-tissue accessibility further identified lineage-restricted and constitutively inaccessible chromatin domains, the latter showing preferential hypomethylation across human cancers. Furthermore, we leverage this dataset to train sequence-to-function models to predict chromatin-accessibility effects for 548,656 fine-mapped variants, identifying 18,133 high-effect variants, including 1,120 broadly active variants. Models trained for eight endothelial subtypes further resolve predicted variant effects across vascular beds. Together, this atlas provides a comprehensive cellular and computational framework for interpreting regulatory sequence, context-dependent gene control, and complex trait genetics across the human body.

DOI: https://doi.org/10.64898/2026.09.25.754561
bioRxiv. 2026 Sep 11. pii: 2026.09.07.749899. [Epub ahead of print]

RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.

Paolo Cadinu, Christian A Reardon-Lochbaum, Hao Zhang, Katerina Kalemaki, Brianna R Watson, Stelios Smirnakis, Scott B Snapper, Alan B Cantor, Jeffrey R Moffitt.

Image-based transcriptomic approaches can define, discover, and chart cell types and states within an array of tissues. However, measurement quality depends on RNA integrity, and the modern tissue preservation toolbox was not designed to protect this highly labile molecule. Here we leverage MERFISH to show that tissue-dependent differences in endogenous RNase activity can shape spatial transcriptomics data quality for different preservation methods and that RNase-activity-guided protocol optimization can improve data quality. In parallel, we introduce an RNA-aware pan-tissue preservation approach, Rapid Inhibition and Permanent Inactivation of Nucleases (RIPIN), that rapidly stabilizes samples with a broad-spectrum RNase inhibitor while permitting slow, chemical inactivation. RIPIN produces high-quality MERFISH measurements in all profiled human and mouse tissues, is compatible with clinical workflows, and is easily integrated with frozen or paraffin sectioning. By highlighting how RNA integrity can be lost during tissue processing, our work may inspire the next generation of RNA-aware histology methods.

DOI: https://doi.org/10.64898/2026.09.07.749899
Cancer Discov. 2026 Sep 29.

Spatial modulation of RAF by RAF/MEK glue enables full-dose combination with pan-RAF inhibitor and potent RAS-mutant tumor-selective MAPK and growth inhibition.

Ana Orive-Ramos, Bijaya Gaire, Christos Adamopoulos, Beau Baars, Mathieu Desaunay, Ziyue Kou, Evangelia Matenoglou, Silvia Coma, Nayeli Gutiérrez Trejo, Kevin Mohammed, Stuart A Aaronson, Jian Jin, Tiphaine C Martin, Ernesto Guccione, Evripidis Gavathiotis, Jonathan A Pachter, Poulikos I Poulikakos.

Effective MAPK-targeted therapies require greater pathway inhibition in tumors than in normal tissues. Although pan-RAF inhibitors have demonstrated activity in RAS-mutant cancers, combinations with MEK inhibitors require dose reductions because of toxicity, limiting clinical benefit. Here, we show that this toxicity results from MEK inhibitor-mediated feedback relief, which promotes RAF activation and enhances pan-RAF inhibitor binding in normal cells. We identify a distinct mechanism of RAF inhibition by RAF/MEK glues: by stabilizing RAF-MEK complexes, these compounds trap RAF in the cytosol, preventing membrane recruitment required for RAF activation. This spatial modulation mechanism preserves tumor-selective MAPK inhibition and enables full-dose combination therapy with pan-RAF inhibitors. This therapeutic strategy produced robust tumor regressions in multiple RAS-mutant tumor models, including models refractory to current RAS/MAPK-targeting therapies. Our findings underscore drug-induced proximity as a strategy to achieve tumor selectivity and support the clinical development of RAF/MEK glue plus pan-RAF inhibitor combinations for RAS-mutant tumors.

DOI: https://doi.org/10.1158/2159-8290.CD-25-1596
CRISPR J. 2026 Sep 30. 25731599261492640

Hidden Outcomes of CRISPR-Cas9 Genome Editing Revealed by Targeted Sequencing in Isogenic Human iPSC Clones.

Maria Tubalova, Galina Koksharova, Silvia Souza da Costa, Ana Cristina Victorino Krepischi, Veniamin Fishman, Maria Gridina.

Advances in CRISPR-Cas9-based genome editing have simplified the generation of isogenic induced pluripotent stem cell (iPSC) pairs differing by a single genetic perturbation, minimizing interindividual variability in disease modeling. However, imprecise editing can cause unintended mutations that distort genotype-phenotype interpretation. Here, we investigated the molecular consequences of CRISPR-Cas9 editing in human iPSCs carrying a tandem duplication of the STAG2 locus. Using hybridization capture-based targeted next-generation sequencing of genomic regions surrounding Cas9-induced double-strand breaks, we identified inversions, plasmid DNA integrations, and complex structural rearrangements that had been missed by conventional PCR-based genotyping. The main advance of our study is the application of a practical hybridization capture-based workflow for resolving such hidden editing outcomes during the generation of isogenic iPSC models. In the selected clones subjected to detailed analysis, targeted sequencing enabled us to revise the initial interpretation of editing outcomes and resolve discrepancies between genotypic and transcriptomic data. Our results demonstrate that complex on-target alterations can remain undetected by conventional PCR-based genotyping and show that hybridization capture-based targeted sequencing can serve as a practical quality-control approach for the characterization of edited iPSC clones.

DOI: https://doi.org/10.1177/25731599261492640
Oncogene. 2026 Sep 30.

ACTB promotes ESCC progression by regulating the AKT-mTOR signaling pathway through an m6A-dependent mechanism.

Yunshan Jiang, Dan Zhao, Dongxia Liao, Fengling Yang, Canyang Lin, Pengfei Liu, Zheyuan Chen, Fang Shaobo, Xiaoxue Deng, Xiaolei Ni, Baoling Guo.

Esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignancy with poor prognosis, and the upstream regulatory mechanisms driving oncogenic signaling remain insufficiently defined. In this study, we identify a previously unrecognized nuclear function of the cytoskeletal protein ACTB in promoting ESCC progression. We show that ACTB translocates to the nucleus and directly binds to the promoter of the m6A reader gene YTHDC2, transcriptionally activating its expression. YTHDC2, in turn, binds to m6A-modified sites on AKT mRNA, preventing its degradation and enhancing its stability. This results in sustained activation of the PI3K-AKT-mTOR signaling pathway, a key oncogenic cascade that promotes tumor growth and survival. Integrated CUT&Tag and RNA-seq analyses revealed a direct ACTB-YTHDC2 transcriptional axis, while RNA immunoprecipitation and MeRIP-qPCR confirmed YTHDC2-AKT interaction via m6A recognition. Functional assays in ESCC cell lines, patient-derived organoids, and xenograft mouse models demonstrated that both ACTB and YTHDC2 are essential for ESCC proliferation and tumorigenicity. Notably, pharmacological inhibition of mTOR with rapamycin effectively suppressed ACTB-driven tumor phenotypes in vitro and in vivo, supporting the therapeutic relevance of this signaling axis. Together, our findings define a novel ACTB-YTHDC2-AKT-mTOR regulatory network that integrates transcriptional and epitranscriptomic control in ESCC. This study reveals a noncanonical nuclear role for ACTB and identifies a mechanistically tractable pathway that may be exploited for targeted therapy in ACTB-driven esophageal cancer.

DOI: https://doi.org/10.1038/s41388-026-03995-3
Nat Commun. 2026 09 11. pii: 10407. [Epub ahead of print]17(1):

SLC4A7/NBCn1 maintains intracellular pH to support mTORC1 activity and antibody-secreting cell differentiation.

Ke Hu, Yin-Hu Wang, Anthony Y Tao, Maxwell McDermott, Miki Jishage, Li Zhong, Thomas Boehringer, Marcus J Hines, Sergei B Koralov, Ebbe Boedtkjer, Stefan Feske.

Antibody-producing plasmablasts (PB) and plasma cells (PC) are critical for humoral immunity, autoimmunity and vaccine responses. Despite the importance of environmental stressors in regulating humoral immune responses, the influence of pH on PB and PC differentiation remains elusive. Here, we identify SLC4A7/NBCn1, a Na+/HCO3- cotransporter, as a selective regulator of PB differentiation in vitro. SLC4A7 deletion also impairs the formation of antibody secreting cells (ASCs) and antibody responses in mice in vivo following immunization and influenza A virus infection. Mechanistically, SLC4A7 deletion results in intracellular acidification and lysosomal alkalinization, and is associated with impaired function of the mechanistic target of rapamycin complex 1 (mTORC1). Enforcing mTORC1 activation in SLC4A7-deficient B cells or B cells in which intracellular pH is acidified by blocking Na+/H+ exchanger (NHE) function restores PB differentiation in vitro. Moreover, ASC differentiation and antibody responses are impaired under conditions of extracellular acidosis in vitro and in a mouse model of metabolic acidosis. Altogether, we identify a critical relationship between intracellular pH regulation through SLC4A7 and mTORC1-dependent ASC differentiation and humoral immunity.

DOI: https://doi.org/10.1038/s41467-026-77588-9