bims-pideca 2026-07-05 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2026–07–05
seventeen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Dissecting autonomous enzymatic variability in single cells.
spammR: an R package designed for analysis and integration of spatial multi-omic measurements.
A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells.
Scalable phosphotyrosine enrichment with SH2 superbinder enables deep profiling of EGF responses.
Endocardial TIE2 orchestrates cardiac trabeculation via sequestering FOXO1 within the cytoplasm and stimulating versican cleavage.
Matrix Stiffness Induces Endothelial Network Senescence.
Adipocyte Pten Inhibition Improves Metabolic Health Associated with Expanded Lipid Storage Capacity and Reduced Inflammation.
ERG function in prostate cells is regulated by distinct positive feedback loops depending on AKT signaling status.
Endothelial NPR-C promotes insulin resistance via Caveolin-1-mediated insulin transcytosis.
Scaling of Neuronal Growth and Excitability Through Separable mTORC1 and mTORC2 Pathways.
Vascular Anomalies: A Comprehensive Review of Etiology, Complications, and Management Strategies.
Two-step mechanism of Bruton's tyrosine kinase membrane recruitment and activation.
PTEN Subcellular Localization Dictates Function.
Genome-wide copy number analysis identifies AKT as a novel therapeutic target in pleural mesothelioma.
CapMux: a Snakemake pipeline for early demultiplexing of split-pool scRNA-seq data into sample-resolved outputs.
Retargeted serine integrases for one-step, precise integration of large DNA sequences in human cells.
Covalent pan-TEAD inhibitors block YAP activity and demonstrate brain penetrance in a Hippo-dependent cancer model.

Nat Commun. 2026 Jul 02. pii: 5788. [Epub ahead of print]17(1):

Dissecting autonomous enzymatic variability in single cells.

Christian Gnann, Alina Sigaeva, Trang Le, Anthony J Cesnik, Sanem Sariyar, Diana Mahdessian, Rutger Schutten, Preethi Raghavan, Manuel D Leonetti, Cecilia Lindskog, Mathias Uhlén, Ulrika Axelsson, Emma Lundberg.

Metabolic enzymes perform life-sustaining functions in various cellular compartments. Anecdotally, metabolic activity is observed to vary between genetically identical cells, which impacts drug resistance, differentiation, and immune cell activation. However, no large-scale resource systematically reporting metabolic cellular heterogeneity exists. Here, we leverage imaging-based single-cell spatial proteomics to reveal the extent of non-genetic variability of the human enzymatic proteome, as a proxy for metabolic states. Nearly two fifths of enzymes exhibit cell-to-cell variable expression, and half localize to multiple cellular compartments. Metabolic heterogeneity arises largely autonomously of cell cycling, and individual cells reestablish these myriad metabolic phenotypes over several cell divisions. We reveal through multiplexed imaging that metabolic states are continuous and that the correlation between metabolic pathways is metabolic state dependent. These results establish cell-to-cell enzymatic heterogeneity as an organizing principle of cell biology that may rewire our understanding of drug resistance, treatment design, and other aspects of medicine.

DOI: https://doi.org/10.1038/s41467-026-74172-z
Bioinform Adv. 2026 ;6(1): vbag163

spammR: an R package designed for analysis and integration of spatial multi-omic measurements.

Yannick Mahlich, Harkirat Sohi, Marija Veličković, Paul D Piehowski, Jason E McDermott, Sara J C Gosline.

Motivation: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics.
Results: To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with the goal of integration across multiple data types (e.g. sequencing, metabolites, proteins) within the same tissue.
Availability and implementation: spammR is implemented in R. The package is currently installable from GitHub (https://pnnl-compbio.github.io/spammR/).

DOI: https://doi.org/10.1093/bioadv/vbag163
Nat Biotechnol. 2026 Jul 01.

A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells.

Sami Nourreddine, Yesh Doctor, Amir Dailamy, Yi-Hung Lee, Jan N Hansen, Rebecca Chinn, Antoine Forget, Benjamin Polacco, Monita Muralidharan, Alina Sigaeva, Sushant Sunder, Emily Pan, Jiahao Gao, Jake Y Chen, Timothy Clark, Jillian Parker, Kirsten Obernier, Christian Metallo, Trey Ideker, Emma Lundberg, Nevan Krogan, Prashant Mali.

Comprehensively mapping the relationship between genotype and phenotype offers essential insights into how a cell's state arises from its genetic components. Toward this goal, we generated an expressed genome-scale CRISPRi perturbation cell atlas in KOLF2.1J human induced pluripotent stem cells, mapping transcriptional phenotypes associated with 11,692 perturbed genes across >2.5 million single cells. Using correlations among perturbed phenotypes, we created a cell map of the pluripotent state, demonstrating rich recapitulation of functionally related protein complexes. We then explored the atlas to uncover metabolic factor ZBTB41 and pluripotency regulator RNF7, validating their functions through metabolic tracing, immunofluorescence and protein-protein interaction assays. Lastly, we leveraged the atlas to generate a genome-scale screen of A-to-I RNA-editing modulators assayed through direct transcriptome-wide RNA editing, uncovering and mechanistically validating DBR1 as a potent regulator. Taken together, our data provide a comprehensive resource for interrogating the regulatory networks governing pluripotency, which is accessible at https://y-doctor.github.io/KOLF2.1J_Perturbation_Cell_Atlas/ .

DOI: https://doi.org/10.1038/s41587-026-03199-w
EMBO J. 2026 Jul 03.

Scalable phosphotyrosine enrichment with SH2 superbinder enables deep profiling of EGF responses.

Alexis T Chang, Ricard A Rodriguez-Mias, Matthew D Berg, Sophie Moggridge, Judit Villén.

Phosphotyrosine signaling plays a critical role in many biological processes, from cell proliferation to immune response. Despite its importance, proteomic studies of tyrosine phosphorylation have been limited in scale and throughput due to the need for specialized enrichment with costly reagents and labor-intensive protocols. To address these challenges, we developed R2HaPpY, a phosphotyrosine enrichment method that combines highly simplified phosphotyrosine superbinder reagent preparation and automated high-throughput enrichment. Our new reagent binds phosphotyrosine peptides at higher efficiency than other enrichment reagents and reduces both cost and preparation time by 20-fold. We generalized the R2HaPpY method to samples of low and high levels of phosphotyrosine. We benchmarked biological application to study EGF signaling dynamics in HeLa cells. Using only ~1 mg of input peptides, we detect and quantify 1651 unique phosphotyrosine sites. These include 878 regulated pY sites, many of which are novel or not previously annotated as EGF-responsive. Our results reveal differential temporal regulation and represent the largest phosphotyrosine dataset of cellular response to EGF stimulation to date. This streamlined, cost-effective, and sensitive method enables quantitative mapping of tyrosine phosphorylation dynamics at a scale of hundreds of samples, facilitating integration of phosphotyrosine signaling into multiomic studies across diverse biological systems and disease states.

DOI: https://doi.org/10.1038/s44318-026-00843-8
Development. 2026 Jun 29. pii: dev.205674. [Epub ahead of print]

Endocardial TIE2 orchestrates cardiac trabeculation via sequestering FOXO1 within the cytoplasm and stimulating versican cleavage.

H Scott Baldwin, Kevin Tompkins, Yan Gong, Bryan Helm, Qi Liu, Xianghu Qu.

  Abnormal cardiac trabeculation often leads to congenital heart disease (CHD). TIE2-ANG1 signaling is a key regulator of endocardial growth during trabeculation. However, little is known about the underlying mechanisms. Here we demonstrate that loss of endocardial Tie2 via Nfatc1Cre resulted in increased nuclear localization of Forkhead box O1 (FOXO1), reduced phosphorylation of AKT (the direct regulator of FOXO1) and reduced expression of several proliferation promoting genes in endocardial cells (EdCs). The cardiac defects seen in endocardial Tie2-deficient hearts were phenocopied by forced activation of FOXO1 within the endocardium and partially rescued by loss of FoxO1. Conversely, excessive PI3K signaling (the direct regulator of phosphorylation of AKT) in EdCs caused cardiac hypotrabeculation. Further, we identify that endocardial loss of Tie2 resulted in impaired cleavage of versican, which was associated with enhanced expression of ADAMTS endogenous inhibitor TIMP3 in Tie2-cko EdCs. Thus, our results suggest that TIE2 signaling in the early embryonic endocardium promotes endocardial growth via sequestering FOXO1 within the cytoplasm and modulates cardiomyocyte proliferation via stimulating versican cleavage to orchestrate myocardial trabeculation, providing insights into the pathogenesis of CHD.

Keywords:  Cardiac trabeculation; Endocardial cells; FOXO1; TIE2; Timp3; versican

DOI:  https://doi.org/10.1242/dev.205674
Adv Sci (Weinh). 2026 Jul 02. e76304

Matrix Stiffness Induces Endothelial Network Senescence.

Jiyeon Song, Alexandra N Rindone, Ya Guan, Connor D Amelung, Prarthana Sanjay Daswani, Jennifer H Elisseeff, Sharon Gerecht.

  Identifying the drivers of cellular senescence that contribute to the decline in vascular function with age and disease is critical for developing restorative interventions. Here, we investigated how increased mechanical stress from extracellular matrix (ECM) stiffening shapes endothelial cell (EC) senescence. We developed a 3D human in vitro model that decouples mechanical stress from inflammatory or biochemical signals, enabling the study of senescence responses to tissue stiffening alone. We found that matrix stiffening induces an EC senescence phenotype with elevated p16/p21 and an immunomodulatory senescence-associated secretory phenotype (SASP), in the absence of inflammatory signals. This mechano-induced senescence activates Notch signaling, and treatment with an FDA-approved γ-secretase inhibitor attenuates stiffness-induced senescence. Analysis of fibrotic capsule tissue from patients with synthetic breast implants, a model of localized, mechanically driven fibrosis, validated an increase in p16+Notch1+ endothelial populations. Complementary single-cell RNA sequencing data further confirmed enrichment of Notch- and SASP-related gene programs. Our work provides a human-relevant platform for studying targetable stages of endothelial mechanoaging and identifies potential therapeutic targets associated with stiffness-induced endothelial senescence for mechanically remodeled tissues.

Keywords:  biomaterial; cell biology; endothelial stem cell; engineered tissue; extracellular matrix; fibrosis; hydrogel scaffold; notch signaling pathway; phenotype; senescence

DOI:  https://doi.org/10.1002/advs.76304
bioRxiv. 2026 Jun 25. pii: 2026.06.20.733549. [Epub ahead of print]

Adipocyte Pten Inhibition Improves Metabolic Health Associated with Expanded Lipid Storage Capacity and Reduced Inflammation.

Yumei Zhou, Yubo Wang, Jessica E Meerson, Zhiyong Cheng, Shihuan Kuang, Feng Yue.

Adipose tissue dysfunction drives obesity-associated insulin resistance, but whether expanding adipocyte lipid storage can improve metabolic health remains unclear. Here, we generated adipocyte-specific Pten knockout mice ( Pten AKO ) using Adipoq -Cre to determine how chronic Pten loss affects adipose tissue remodeling and systemic metabolism. Pten AKO mice exhibit increased adiposity and adipocyte hypertrophy under chow and high-fat diet feeding, yet showing lower blood glucose and insulin levels, enhanced insulin sensitivity, and reduced hepatic lipid accumulation during basal growth and diet-induced obesity without systemic metabolic deterioration. Despite lipid enrichment in brown adipose tissue, Pten-deficient adipocytes maintain UCP1 expression, OXPHOS protein abundance, and mitochondrial ultrastructure. Transcriptomic analysis of inguinal white adipose tissue reveals activation of adipogenesis, lipid metabolism, insulin response, oxidative phosphorylation, lipid storage, vascular and extracellular matrix pathways, together with suppression of immune and inflammatory programs. Mechanistically, Pten deficiency increases Cav1 expression, caveolae abundance, collagen expression, and extracellular matrix remodeling, suggesting coordinated structural adaptation to support adipocyte expansion. These findings demonstrate that adipocyte Pten deficiency promotes metabolically healthy adipose expansion by enhancing lipid storage capacity, preserving adipocyte function, and reducing inflammation.

DOI: https://doi.org/10.64898/2026.06.20.733549
Res Sq. 2026 Jun 15. pii: rs.3.rs-9941989. [Epub ahead of print]

ERG function in prostate cells is regulated by distinct positive feedback loops depending on AKT signaling status.

Peter Hollenhorst, Saranya Rajendran, Ethan Golditch, Renee Kinne, Nicholas Downing, Kenneth P Nephew, Sean McCabe.

A chromosomal rearrangement that causes aberrant expression of the ERG transcription factor is the most common genomic alteration in prostate cancer. Expression of ERG in prostate cells can promote either luminal epithelial or mesenchymal cell fates depending on the status of the PI3K/AKT signaling pathway. Phosphorylation of ERG by ERK is important for oncogenic activity and can be regulated by the TLR4 signaling pathway. Here we found that the PI3K/AKT pathway not only regulated how ERG promoted distinct cell types within prostate cells, but also altered the positive-feedback loops that drove ERG phosphorylation. Activation of AKT signaling switched the upstream pathway that promotes ERG phosphorylation from TLR4 to VEGF. Inhibition of the PI3K/AKT pathway in ERG-positive prostate cells resulted in loss of androgen receptor expression, gain of mesenchymal markers and loss of sensitivity to androgen receptor inhibition. Further, androgen depletion reduced PI3K/AKT activity while increasing MEK/ERK activity and relative ERG phosphorylation. In a xenograft model, single agent inhibition of TLR4 or VEGFA reduced ERG phosphorylation, tumor size, and luminal marker expression but increased mesenchymal marker expression. Combination TLR4/VEGFA inhibition reduced tumor size and reduced both luminal and mesenchymal markers. These findings suggest novel combinatorial treatments for ERG-positive prostate cancer.

DOI: https://doi.org/10.21203/rs.3.rs-9941989/v1
Metabolism. 2026 Jun 30. pii: S0026-0495(26)00197-6. [Epub ahead of print] 156686

Endothelial NPR-C promotes insulin resistance via Caveolin-1-mediated insulin transcytosis.

Zi-Qi Xu, Xin-Yi Yu, Jin-Qiu Wei, Qian-Wan Deng, Wen-Hui Zhai, Wu-Wei Rong, Meng-Yao Li, Qi-Rong Zhang, Ping-Jin Gao, Xiao-Dong Li, Ji-Guang Wang.

Obesity-induced insulin resistance contributes to metabolic dysfunction and type 2 diabetes, yet the endothelial mechanisms involved remain incompletely understood. Here, we identify endothelial natriuretic peptide receptor C (NPRC) as a key regulator of insulin transport and insulin sensitivity. NPR-C expression was increased in endothelial cells from adipose tissue and skeletal muscle of obese mice. Endothelial-specific deletion of NPR-C improved insulin sensitivity, whereas endothelial NPR-C overexpression aggravated insulin resistance, as demonstrated by glucose tolerance, insulin tolerance, and hyperinsulinemic-euglycemic clamp. Mechanistically, NPR-C impaired insulin uptake and transendothelial transport by reducing insulin receptor (IR) membrane localization and altering intracellular trafficking. NPR-C directly interacted with Caveolin-1 and promoted Tyr14 phosphorylation-dependent K48-linked ubiquitination and proteasomal degradation of Caveolin-1, disrupting caveolae function and impairing IR trafficking. Importantly, Cdh5 promoter-driven adeno-associated virus-mediated NPR-C knockdown improved insulin sensitivity in mice with established obesity. Together, these findings identify endothelial NPR-C as a regulator of Caveolin-1 stability and IR trafficking and suggest NPR-C as a potential therapeutic target for obesity-associated insulin resistance.

DOI: https://doi.org/10.1016/j.metabol.2026.156686
bioRxiv. 2026 Jun 26. pii: 2026.06.22.733785. [Epub ahead of print]

Scaling of Neuronal Growth and Excitability Through Separable mTORC1 and mTORC2 Pathways.

Asan F Abdulkareem, Noah H Elste, Rain Younger, Mackenzi L Prina, Evan Dennis, Jessica Urbanczyk, Mohsen Bayat, Hassaan A Malik, Shahriar A Tafti, Hunter S Holoubek, Dylan Marchand, Karen E Beenken, Dennis W Province, Kristopher T Kahle, Matthew C Weston, Jeremy M Barry, Bryan W Luikart.

As neurons grow, they must regulate intrinsic excitability to maintain an appropriate level of spiking based on synaptic inputs. Using gene knockouts, phosphoproteomics, and electrophysiology we show PTEN regulates neuronal growth and intrinsic excitability through separable downstream mechanisms. Pten loss induces cellular hypertrophy, increased excitatory synaptic input, reduced fast afterhyperpolarization, and burst firing. Deleting the mTORC1 scaffold, Raptor, rescues overgrowth and synaptic input but fails to normalize firing, while deleting Akt or the mTORC2 scaffold, Rictor, restores firing without rescuing growth. This dissociation identifies an AKT-mTORC2 mechanism that regulates voltage-gated calcium and BK potassium channels to set spike repolarization and burst firing. In vivo , Pten knockout produces altered network synchrony, lethal seizures, and impaired object and location behavior; Raptor co-deletion display non-lethal hyperexcitability with improved object-location coupling. The biological and pathophysiological significance of these mechanisms is demonstrated by overlap of the PTEN-regulated phosphoproteome with ASD and epilepsy.

DOI: https://doi.org/10.64898/2026.06.22.733785
Ann Plast Surg. 2026 Jun 29.

Vascular Anomalies: A Comprehensive Review of Etiology, Complications, and Management Strategies.

Jordan Johnson, Mehul Prabha, Zariah Hadnot, Anvith P Reddy, Franklin R Gergoudis, Emmanuel Giannas, Izabela Galdyn.

  Vascular anomalies encompass a group of disorders involving abnormalities of blood and lymphatic vessels, ranging from benign cutaneous lesions to complex, life-threatening conditions. These anomalies are broadly classified into vascular tumors and malformations based on underlying pathophysiology. Despite their clinical prevalence, the management of vascular anomalies remains challenging due to their diverse presentations, variable progression, and potential for significant functional and aesthetic morbidity. This review provides a comprehensive overview of the etiology, clinical presentation, complications, and management strategies of vascular anomalies, with a focus on their relevance to plastic and reconstructive surgery. Vascular tumors, including infantile hemangiomas, congenital hemangiomas, pyogenic granulomas, and kaposiform hemangioendothelioma, are characterized by abnormal cellular proliferation and demonstrate variable natural histories ranging from spontaneous involution to aggressive growth requiring intervention. In contrast, vascular malformations arise from embryologic errors in vasculogenesis and persist throughout life, progressively enlarging without regression. These include capillary, venous, lymphatic, and arteriovenous malformations, each with distinct clinical features and treatment considerations. Management is highly individualized and often necessitates a multidisciplinary approach. Treatment modalities include pharmacologic therapy (eg, beta-blockers, sirolimus, and targeted molecular agents), laser therapy, sclerotherapy, embolization, and surgical intervention. Plastic surgeons play a critical role in addressing deformity, restoring function, and optimizing aesthetic outcomes through reconstructive techniques. Given the complexity of these conditions, a thorough understanding of classification systems, disease progression, and available treatment options is essential. This review synthesizes current evidence to guide clinicians in the evaluation and management of vascular anomalies, emphasizing a patient-centered, multidisciplinary approach to optimize both functional and cosmetic outcomes.

Keywords:  arteriovenous malformations; infantile hemangioma; lymphatic malformations; reconstructive surgery; vascular anomalies; vascular malformations; vascular tumors

DOI:  https://doi.org/10.1097/SAP.0000000000004791
Proc Natl Acad Sci U S A. 2026 Jul 07. 123(27): e2528109123

Two-step mechanism of Bruton's tyrosine kinase membrane recruitment and activation.

Rachel A McAllister, Amy L Stiegler, Keerthana Chari, Meera Chari, Moitrayee Bhattacharyya, Kallol Gupta.

  Peripheral membrane proteins (PMPs) are critical mediators of signaling cascades initiated at the cell surface. Their functions depend on their innate ability to interact dynamically with membranes in response to changing cellular conditions. This membrane recruitment may occur via high-affinity interactions with specific lipids/proteins or via transient, low-affinity interactions with the membrane. These weak and dynamic interactions, which are critical regulators of PMP function, are challenging to capture. Taking Bruton's tyrosine kinase (BTK), a nonreceptor tyrosine kinase essential for B cell activation, we demonstrate a native mass spectrometry platform to understand lipid-mediated recruitment of PMPs by directly studying it from lipid bilayers customized to target membranes. Our data demonstrate that BTK recognizes phosphatidylserine (PS) independently of phosphatidylinositol (3, 4, 5) phosphate (PIP3) binding. We show that PS-bound BTK retains PIP3 binding via high-affinity sites, while exhibiting PIP3-independent basal membrane recruitment. Biochemical assays show that this PS-mediated recruitment sensitizes BTK to PIP3-mediated activation at near-physiological PIP3 concentrations. Thus, we propose a two-step model for BTK membrane recruitment and activation. A low-affinity interaction with high-copy number PS enables plasma membrane recruitment of BTK and increases its membrane-bound concentration. Upon B cell activation, this prerecruited, membrane-bound BTK population localizes to PIP3-rich domains via electrostatic gliding along the membrane, driven by low-affinity PS and high-affinity PIP3 binding. This indicates a cooperative mechanism in which PS can amplify B cell signaling by increasing membrane-bound BTK levels. Our work demonstrates a general model of regulation of PH domain-containing proteins by weak protein-lipid interactions, which can be extended to other PMPs.

Keywords:  B cell signaling; kinase regulation; native mass spectrometry; protein–lipid interaction

DOI:  https://doi.org/10.1073/pnas.2528109123
bioRxiv. 2026 Jun 18. pii: 2026.06.16.732743. [Epub ahead of print]

PTEN Subcellular Localization Dictates Function.

Nicole M Desmet, Cheyenne F Griffin, Helena Seo, Annaliese OuYang, Penelope Tir, Mackenzi L Prina, Wei Wang, Meijie Li, Bryan W Luikart.

Mutations in phosphatase and tensin homolog (PTEN) drive unregulated activation of the phosphatidylinositol-3-kinase (PI3K) pathway, resulting in neuronal hypertrophy, and are strongly associated with autism spectrum disorder (ASD). Several PTEN mutations alter subcellular localization, yet how localization governs PTEN function in developing neurons remains unclear. Although PTEN has been reported broadly distributed throughout neurons, here, live imaging of HaloTagged PTEN reveals dynamically regulated localization, suggesting spatial control of its signaling. We then used retroviral-mediated genetic manipulation to delete endogenous Pten in developing hippocampal neurons while simultaneously expressing PTEN fused to defined localization motifs, allowing us to directly test how subcellular targeting regulates neuronal morphology. Loss of Pten produces neurons characterized by enlarged somata, more elaborate dendritic arbors, and increased spine density, length, and head area. Nuclear-excluded PTEN fully rescued these phenotypes, whereas targeting PTEN to filopodia via fusion to the FBAR domain of srGAP3 or to the postsynaptic density via Homer1C corrected or corrected all morphological abnormalities in PTEN-deficient neurons and simplified dendritic arborization compared to wild-type. In contrast, nuclear-localized PTEN produced only partial rescue, normalizing soma size and spine head area but not dendritic complexity or spine density. These findings indicate that PTEN acts locally to restrain growth and structural connectivity, whereas regulation of spine head size can be mediated by PTEN both inside and outside the nucleus, potentially through transcriptional or splicing-dependent mechanisms. Together, our results identify subcellular localization as a critical determinant of PTEN function and reveal spatially distinct mechanisms through which PTEN sculpts neuronal development.

DOI: https://doi.org/10.64898/2026.06.16.732743
Lung Cancer. 2026 Jun 28. pii: S0169-5002(26)00573-8. [Epub ahead of print]218 109512

Genome-wide copy number analysis identifies AKT as a novel therapeutic target in pleural mesothelioma.

Claudia Kalla, Dina Mönch, Sophia Steinlein, Alessandro Pastore, Heike Horn, Roger Falkenstern-Ge, Julia Schüler, German Ott, Gerhard Preissler.

   PURPOSE: Targeting aberrantly activated kinases in pleural mesothelioma (PM) is a promising therapeutic strategy. To identify potential candidates, we characterized recurrent chromosomal gains in PM and subsequently evaluated the specific inhibition of kinases that were activated by amplification and/or overexpression.
METHODS: 42 primary PM were screened for chromosomal alterations using OncoScan technology and AKT expression was assessed using immunohistochemistry. The impact of Ipatasertib (pan-AKT inhibitor) and Sapanisertib (mTOR inhibitor) on cell survival, apoptosis induction, AKT/mTOR signaling, glycolysis was investigated in cell lines and primary cells. Preclinical anti-tumor efficacy was further assessed in a PDX model selected for AKT and mTOR expression.
RESULTS: OncoScan profiling identified eleven regions of significant chromosomal gains. Among them, 14q32.33 and 19q13.2 gains affected AKT1 and AKT2, members of the AKT serine/threonine protein kinase family. AKT1 protein was expressed in 66 % (60/91), AKT2 in 80 % (73/91) and AKT3 in 94 % (86/91) PM. 57 % PM co-expressed AKT1/AKT2/AKT3. Treatment with Ipatasertib impaired cell viability in PM cell lines and induced apoptosis. Combined treatment with Ipatasertib and Sapanisertib had a synergistic cytotoxic effect in all three cell lines and primary cells from two PM patients, even in Cisplatin-resistant cells. We also noted an improved response to the combination in a PDX model. Mechanistically, the combined treatment acted synergistically to inactivate AKT/mTOR downstream signaling, suppress glycolysis, and trigger ATP depletion.
CONCLUSIONS: Our study demonstrates recurrent activation of AKT kinases by copy number gains and upregulated expression in PM. Pharmacological AKT and mTOR inhibition is a promising therapeutic alternative for mesothelioma.

Keywords:  AKT; Ipatasertib; OncoScan CNV analysis; Pleural mesothelioma; Sapanisertib

DOI:  https://doi.org/10.1016/j.lungcan.2026.109512
Front Bioinform. 2026 ;6 1846065

CapMux: a Snakemake pipeline for early demultiplexing of split-pool scRNA-seq data into sample-resolved outputs.

Denis Baronas.

  Single-cell RNA sequencing methods based on split-pool combinatorial barcoding enable high-throughput profiling, yet sample identity is often encoded during early barcoding steps rather than through the library index. Consequently, reads from multiple biological samples remain pooled, complicating per-sample analysis and selective extraction of samples of interest. Here, I present CapMux, a Snakemake-based pipeline for processing split-pool scRNA-seq data from raw sequencing files to sample-resolved outputs. CapMux supports workflows starting from either BCL files or FASTQ files and reconstructs sample identity by integrating sub-library index information with the experiment-specific barcoding plate layout. The pipeline was developed for the CapSeq method but is configurable for related scRNA-seq combinatorial barcoding designs through specification of barcode positions and experimental layout. In a controlled cell line mixing scRNA-seq experiment, CapMux resolved pooled data into outputs for each sample, enabling independent quality control summaries, mapping statistics, count matrices, and downstream visualizations. Runtime benchmarking indicated that secondary demultiplexing step added only a modest computational overhead. Together, these results show that CapMux provides a practical and adaptable framework for recovering sample-level resolution from split-pool scRNA-seq data.

Keywords:  CapSeq; sample demultiplexing; sequencing data processing; single-cell RNA sequencing; split-pool combinatorial barcoding

DOI:  https://doi.org/10.3389/fbinf.2026.1846065
Nat Biotechnol. 2026 Jun 29.

Retargeted serine integrases for one-step, precise integration of large DNA sequences in human cells.

Friedrich Fauser, Sebastian Arangundy-Franklin, Jessica E Davis, Lifeng Liu, Nicola J Schmidt, Luis Rodriguez, Danny F Xia, Nga Nguyen, Yuanyue Zhou, Nicholas A Scarlott, Lynn N Truong, Rakshaa Mureli, Irene S Tan, Satria Sajuthi, Sarah J Hinkley, Bhakti N Kadam, Stephen Lam, Bryan Bourgeois, Emily Tait, Mohammad Qasim, Vishvesha Vaidya, Adeline Chen, Andrew Nguyen, Yuri R Bendaña, David A Shivak, Patrick Li, Andreas Reik, David E Paschon, Gregory D Davis, Jeffrey C Miller.

Serine integrases can precisely integrate large DNA constructs into desired chromosomal sites but only if their natural target site is first installed into the recipient genome. Here, to retarget serine integrases to a desired genomic site, we develop a modular integrase (MINT) system for genome editing. Through a combination of structural modeling, single-round directed evolution and screening in human cells, we retargeted the specificity of the serine integrase Bxb1. We demonstrate the therapeutic potential of the MINT system by retargeting Bxb1 to the human AAVS1 and TRAC loci, where wild-type Bxb1 has no detectable activity. By combining MINT constructs with both known activity-increasing Bxb1 mutants and zinc-finger DNA-binding domains, we achieve efficiencies of 29% at the AAVS1 locus and 35% at the TRAC locus in K562 cells. To further demonstrate clinical potential, we achieved 29% GFP integration efficiencies at the TRAC locus in human T cells.

DOI: https://doi.org/10.1038/s41587-026-03186-1
Nat Commun. 2026 Jun 27.

Covalent pan-TEAD inhibitors block YAP activity and demonstrate brain penetrance in a Hippo-dependent cancer model.

Thijs J Hagenbeek, Jason Zbieg, Russell Smith, Sayantanee Paul, Luca Gerosa, Consuelo Torrini, Alissa D Guarnaccia, Christy Ong, Jennifer A Lacap, Miaoran Ning, Nicole M Sodir, Marc Hafner, Julien Tremblay, James Hawley, Bryan Chan, Vishal A Verma, Ramsay E Beveridge, Peter L Hsu, Gözde Ulas, Lisha Wang, Jim Nonomiya, Shu Chen, Victoria Pham, Joshua Webster, Jessica Preston, Jeff Hung, Jeff Eastham, Debra Dunlap, Wendy Lee, Paul Beroza, Naema Nayyar, Scott Martin, Eva Lin, Julie Weng, Scott A Foster, Frances Shanahan, Rina Fong, Gladys Boenig, Paola Di Lello, Marta H Kubala, Thomas Hunsaker, Mirunalini Ravichandran, Pablo Saenz-Lopez Larrocha, Jeffrey Lau, Le An, Elizabeth Levy, Maria N Lorenzo, Jennie R Lill, Zora D Modrusan, Yi-Chen Chen, Xiaosai Yao, Priscilla K Brastianos, Danilo Maddalo, Anwesha Dey.

TEAD transcription factors enable the oncogenic activity of deregulated Hippo signaling and are a promising therapeutic target in oncology. Targeting the TEAD lipid pocket is an established path to inhibit the oncogenic activities of cofactors YAP and TAZ. Here we present two pan-TEAD inhibitors, GNE-8025 and its in vivo brain-penetrant derivative GNE-2181, that covalently bind the lipid pocket at a conserved cysteine. Both small molecules show growth inhibition of YAP-driven tumor cells in vitro and in vivo. Moreover, we show that GNE-8025 increases the activity of a broad range of MAPK pathway inhibitors in vitro as well as the KRASG12C inhibitor Divarasib both in vitro and in vivo. In addition, GNE-2181 inhibits growth of an intracranial tumor model in vivo. Altogether we present a next-generation class of TEAD inhibitors representing a significant advancement towards potent, specific, and effective Hippo-targeting cancer therapies.

DOI: https://doi.org/10.1038/s41467-026-74722-5