bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–02–02
25 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Paradoxical dominant negative activity of an immunodeficiency-associated activating PIK3R1 variant.
  2. Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation.
  3. A genome-wide atlas of human cell morphology.
  4. Inhibition of Src signaling induces autophagic killing of Toxoplasma gondii via PTEN-mediated deactivation of Akt.
  5. Microenvironmental determinants of endothelial cell heterogeneity.
  6. Human TSC2 mutant cells exhibit aberrations in early neurodevelopment accompanied by changes in the DNA Methylome.
  7. Reproducibility and transparency: what's going on and how can we help.
  8. SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation.
  9. A single-cell atlas of normal and KRASG12D-malformed lymphatic vessels.
  10. CytoNorm 2.0: A flexible normalization framework for cytometry data without requiring dedicated controls.
  11. OpenMS WebApps: Building User-Friendly Solutions for MS Analysis.
  12. Oncogenic competence: balancing mutations, cellular state, and microenvironment.
  13. A novel rapalog shows improved safety vs. efficacy in a human organoid model of polycystic kidney disease.
  14. GraphVelo allows for accurate inference of multimodal omics velocities and molecular mechanisms for single cells.
  15. A phase II double-blind multicentre, placebo-controlled trial to assess the efficacy and safety of alpelisib (BYL719) in paediatric and adult patients with Megalencephaly-CApillary malformation Polymicrogyria syndrome (MCAP): the SESAM study protocol.
  16. A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology.
  17. How can we make sound replication decisions?
  18. Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach.
  19. Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data.
  20. Regulating Nrf2 activity: ubiquitin ligases and signaling molecules in redox homeostasis.
  21. PAX3-FOXO1 drives targetable cell state-dependent metabolic vulnerabilities in rhabdomyosarcoma.
  22. DeST-OT: Alignment of spatiotemporal transcriptomics data.
  23. Downregulation of the Phosphatase PHLPP1 Contributes to NNK-induced Malignant Transformation of Human Bronchial Epithelial Cells (HBECs).
  24. Expanding the phenotypic spectrum of PROS: reclassifying isolated lateralised overgrowth.
  25. Cell Storage Conditions Impact Single-Cell Proteomic Landscapes.
  1. Elife. 2025 Jan 21. pii: RP94420. [Epub ahead of print]13
    Paradoxical dominant negative activity of an immunodeficiency-associated activating PIK3R1 variant.
    Patsy R Tomlinson, Rachel G Knox, Olga Perisic, Helen Su, Gemma V Brierley, Roger L Williams, Robert K Semple.
      PIK3R1 encodes three regulatory subunits of class IA phosphoinositide 3-kinase (PI3K), each associating with any of three catalytic subunits, namely p110α, p110β, or p110δ. Constitutional PIK3R1 mutations cause diseases with a genotype-phenotype relationship not yet fully explained: heterozygous loss-of-function mutations cause SHORT syndrome, featuring insulin resistance and short stature attributed to reduced p110α function, while heterozygous activating mutations cause immunodeficiency, attributed to p110δ activation and known as APDS2. Surprisingly, APDS2 patients do not show features of p110α hyperactivation, but do commonly have SHORT syndrome-like features, suggesting p110α hypofunction. We sought to investigate this. In dermal fibroblasts from an APDS2 patient, we found no increased PI3K signalling, with p110δ expression markedly reduced. In preadipocytes, the APDS2 variant was potently dominant negative, associating with Irs1 and Irs2 but failing to heterodimerise with p110α. This attenuation of p110α signalling by a p110δ-activating PIK3R1 variant potentially explains co-incidence of gain-of-function and loss-of-function PIK3R1 phenotypes.
    Keywords:  APDS2; PIK3R1; SHORT syndrome; genetics; genomics; human; immunodeficiency; immunology; inflammation; insulin resistance; mouse; phosphoinositide 3-kinase
    DOI:  https://doi.org/10.7554/eLife.94420
  2. Nat Commun. 2025 Jan 09. 16(1): 525
    Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation.
    Daniel Czyzyk, Wupeng Yan, Simon Messing, William Gillette, Takashi Tsuji, Mitsuhiro Yamaguchi, Shinji Furuzono, David M Turner, Dominic Esposito, Dwight V Nissley, Frank McCormick, Dhirendra K Simanshu.
      Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.
    DOI:  https://doi.org/10.1038/s41467-024-55766-x
  3. Nat Methods. 2025 Jan 27.
    A genome-wide atlas of human cell morphology.
    Meraj Ramezani, Erin Weisbart, Julia Bauman, Avtar Singh, John Yong, Maria Lozada, Gregory P Way, Sanam L Kavari, Celeste Diaz, Eddy Leardini, Gunjan Jetley, Jenlu Pagnotta, Marzieh Haghighi, Thiago M Batista, Joaquín Pérez-Schindler, Melina Claussnitzer, Shantanu Singh, Beth A Cimini, Paul C Blainey, Anne E Carpenter, Calvin H Jan, James T Neal.
      A key challenge of the modern genomics era is developing empirical data-driven representations of gene function. Here we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-wide genotype-phenotype maps comprising CRISPR-Cas9-based knockouts of >20,000 genes in >30 million cells. Our optical pooled cell profiling platform (PERISCOPE) combines a destainable high-dimensional phenotyping panel (based on Cell Painting) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This perturbation atlas comprises high-dimensional phenotypic profiles of individual cells with sufficient resolution to cluster thousands of human genes, reconstruct known pathways and protein-protein interaction networks, interrogate subcellular processes and identify culture media-specific responses. Using this atlas, we identify the poorly characterized disease-associated TMEM251/LYSET as a Golgi-resident transmembrane protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes. In sum, this perturbation atlas and screening platform represents a rich and accessible resource for connecting genes to cellular functions at scale.
    DOI:  https://doi.org/10.1038/s41592-024-02537-7
  4. PLoS Pathog. 2025 Jan 27. 21(1): e1012907
    Inhibition of Src signaling induces autophagic killing of Toxoplasma gondii via PTEN-mediated deactivation of Akt.
    Alyssa Hubal, Anusha Vendhoti, Charles N Shaffer, Sarah Vos, Yalitza Lopez Corcino, Carlos S Subauste.
      The intracellular protozoan Toxoplasma gondii manipulates host cell signaling to avoid targeting by autophagosomes and lysosomal degradation. Epidermal Growth Factor Receptor (EGFR) is a mediator of this survival strategy. However, EGFR expression is limited in the brain and retina, organs affected in toxoplasmosis. This raises the possibility that T. gondii activates a signaling mechanism independently of EGFR to avoid autophagic targeting. We report T. gondii activates Src to promote parasite survival even in cells that lack EGFR. Blockade of Src triggered LC3 and LAMP-1 recruitment around the parasitophorous vacuole (PV) and parasite killing dependent on the autophagy protein, ULK1, and lysosomal enzymes. Src promoted PI3K activation and recruitment of activated Akt to the PV membrane. T. gondii promoted Src association with PTEN, and PTEN phosphorylation at Y240, S380, T382, and T383, hallmarks of an inactive PTEN conformation known to maintain Akt activation. Blockade of parasite killing was dependent of activated Akt. Src knockdown or treatment with the Src family kinase inhibitor, Saracatinib, impaired these events, leading to PTEN accumulation around the PV and a reduction in activated Akt recruitment at this site. Saracatinib treatment in mice with pre-established cerebral and ocular toxoplasmosis promoted PTEN recruitment around tachyzoites in neural tissue impairing recruitment of activated Akt, profoundly reducing parasite load and neural histopathology that were dependent of the autophagy protein, Beclin 1. Our studies uncovered an EGFR-independent pathway activated by T. gondii that enables its survival and is central to the development of neural toxoplasmosis.
    DOI:  https://doi.org/10.1371/journal.ppat.1012907
  5. Nat Rev Mol Cell Biol. 2025 Jan 28.
    Microenvironmental determinants of endothelial cell heterogeneity.
    Jesus M Gomez-Salinero, David Redmond, Shahin Rafii.
      During development, endothelial cells (ECs) undergo an extraordinary specialization by which generic capillary microcirculatory networks spanning from arteries to veins transform into patterned organotypic zonated blood vessels. These capillary ECs become specialized to support the cellular and metabolic demands of each specific organ, including supplying tissue-specific angiocrine factors that orchestrate organ development, maintenance of organ-specific functions and regeneration of injured adult organs. Here, we illustrate the mechanisms by which microenvironmental signals emanating from non-vascular niche cells induce generic ECs to acquire specific inter-organ and intra-organ functional attributes. We describe how perivascular, parenchymal and immune cells dictate vascular heterogeneity and capillary zonation, and how this system is maintained through tissue-specific signalling activated by vasculogenic and angiogenic factors and deposition of matrix components. We also discuss how perturbation of organotypic vascular niche cues lead to erasure of EC signatures, contributing to the pathogenesis of disease processes. We also describe approaches that use reconstitution of tissue-specific signatures of ECs to promote regeneration of damaged organs.
    DOI:  https://doi.org/10.1038/s41580-024-00825-w
  6. Hum Mol Genet. 2025 Jan 29. pii: ddae199. [Epub ahead of print]
    Human TSC2 mutant cells exhibit aberrations in early neurodevelopment accompanied by changes in the DNA Methylome.
    Mary-Bronwen L Chalkley, Lindsey N Guerin, Tenhir Iyer, Samantha Mallahan, Sydney Nelson, Mustafa Sahin, Emily Hodges, Kevin C Ess, Rebecca A Ihrie.
      Tuberous Sclerosis Complex (TSC) is a debilitating developmental disorder characterized by a variety of clinical manifestations. While benign tumors in the heart, lungs, kidney, and brain are all hallmarks of the disease, the most severe symptoms of TSC are often neurological, including seizures, autism, psychiatric disorders, and intellectual disabilities. TSC is caused by loss of function mutations in the TSC1 or TSC2 genes and consequent dysregulation of signaling via mechanistic Target of Rapamycin Complex 1 (mTORC1). While TSC neurological phenotypes are well-documented, it is not yet known how early in neural development TSC1/2-mutant cells diverge from the typical developmental trajectory. Another outstanding question is the contribution of homozygous-mutant cells to disease phenotypes and whether phenotypes are also present in the heterozygous-mutant populations that comprise the vast majority of cells in patients. Using TSC patient-derived isogenic induced pluripotent stem cells (iPSCs) with defined genetic changes, we observed aberrant early neurodevelopment in vitro, including misexpression of key proteins associated with lineage commitment and premature electrical activity. These alterations in differentiation were coincident with hundreds of differentially methylated DNA regions, including loci associated with key genes in neurodevelopment. Collectively, these data suggest that mutation or loss of TSC2 affects gene regulation and expression at earlier timepoints than previously appreciated, with implications for whether and how prenatal treatment should be pursued.
    Keywords:  DNA methylation; iPS cells; neurodevelopment; tuberous sclerosis
    DOI:  https://doi.org/10.1093/hmg/ddae199
  7. Nat Commun. 2025 Jan 27. 16(1): 1082
    Reproducibility and transparency: what's going on and how can we help.
      
    DOI:  https://doi.org/10.1038/s41467-024-54614-2
  8. Nat Commun. 2025 Jan 30. 16(1): 1176
    SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation.
    Ella Doron-Mandel, Benjamin J Bokor, Yanzhe Ma, Lena A Street, Lauren C Tang, Ahmed A Abdou, Neel H Shah, George Rosenberger, Marko Jovanovic.
      A protein's molecular interactions and post-translational modifications (PTMs), such as phosphorylation, can be co-dependent and reciprocally co-regulate each other. Although this interplay is central for many biological processes, a systematic method to simultaneously study assembly states and PTMs from the same sample is critically missing. Here, we introduce SEC-MX (Size Exclusion Chromatography fractions MultipleXed), a global quantitative method combining Size Exclusion Chromatography and PTM-enrichment for simultaneous characterization of PTMs and assembly states. SEC-MX enhances throughput, allows phosphopeptide enrichment, and facilitates quantitative differential comparisons between biological conditions. Conducting SEC-MX on HEK293 and HCT116 cells, we generate a proof-of-concept dataset, mapping thousands of phosphopeptides and their assembly states. Our analysis reveals intricate relationships between phosphorylation events and assembly states and generates testable hypotheses for follow-up studies. Overall, we establish SEC-MX as a valuable tool for exploring protein functions and regulation beyond abundance changes.
    DOI:  https://doi.org/10.1038/s41467-025-56303-0
  9. JCI Insight. 2025 Jan 28. pii: e185181. [Epub ahead of print]
    A single-cell atlas of normal and KRASG12D-malformed lymphatic vessels.
    Lorenzo M Fernandes, Danielle Griswold-Wheeler, Jeffrey D Tresemer, Angelica Vallejo, Neda Vishlaghi, Benjamin Levi, Abigail Shapiro, Joshua P Scallan, Michael T Dellinger.
      Somatic activating mutations in KRAS can cause complex lymphatic anomalies (CLAs). However, the specific processes that drive KRAS-mediated CLAs have yet to be fully elucidated. Here, we used single-cell RNA sequencing to construct an atlas of normal and KrasG12D-malformed lymphatic vessels. We identified six subtypes of lymphatic endothelial cells (LECs) in the lungs of adult wild-type mice (Ptx3, capillary, collecting, valve, mixed, and proliferating). To determine when the LEC subtypes were specified during development, we integrated our data with data from four stages of development. We found that proliferating and Ptx3 LECs were prevalent during early lymphatic development and that collecting and valve LECs emerged later in development. Additionally, we discovered that the proportion of Ptx3 LECs decreased as the lymphatic network matured but remained high in KrasG12D mice. We also observed that the proportion of collecting and valve LECs was lower in KrasG12D mice than in wild-type mice. Last, we found that immature lymphatic vessels in young mice were more sensitive to the pathologic effects of KrasG12D than mature lymphatic vessels in older mice. Together, our results expand the current model for the development of the lymphatic system and suggest that KRAS mutations impair the maturation of lymphatic vessels.
    Keywords:  Angiogenesis; Development; Endothelial cells; Vascular biology
    DOI:  https://doi.org/10.1172/jci.insight.185181
  10. Cytometry A. 2025 Jan 28.
    CytoNorm 2.0: A flexible normalization framework for cytometry data without requiring dedicated controls.
    Katrien L A Quintelier, Marcella Willemsen, Victor Bosteels, Joachim G J V Aerts, Yvan Saeys, Sofie Van Gassen.
      Cytometry is a single cell, high-dimensional, high-throughput technique that is being applied across a range of disciplines. However, many elements alongside the data acquisition process might give rise to technical variation in the dataset, called batch effects. CytoNorm is a normalization algorithm for batch effect removal in cytometry data that was originally published in 2020 and has been applied on a variety of datasets since then. Here, we present CytoNorm 2.0, discussing new, illustrative use cases to increase the applicability of the algorithm and showcasing new visualizations that enable thorough quality control and understanding of the normalization process. We explain how CytoNorm can be used without the need for technical replicates or controls, show how the goal distribution can be tailored toward the experimental design and we elaborate on the choice of markers for CytoNorm's internal FlowSOM clustering step.
    Keywords:  CytoNorm; batch effects; data integration; normalization; quality control
    DOI:  https://doi.org/10.1002/cyto.a.24910
  11. J Proteome Res. 2025 Jan 29.
    OpenMS WebApps: Building User-Friendly Solutions for MS Analysis.
    Tom David Müller, Arslan Siraj, Axel Walter, Jihyung Kim, Samuel Wein, Johannes von Kleist, Ayesha Feroz, Matteo Pilz, Kyowon Jeong, Justin Cyril Sing, Joshua Charkow, Hannes Luc Röst, Timo Sachsenberg.
      Liquid chromatography-mass spectrometry (LC-MS) is an indispensable analytical technique in proteomics, metabolomics, and other life sciences. While OpenMS provides advanced open-source software for MS data analysis, its complexity can be challenging for nonexperts. To address this, we have developed OpenMS WebApps, a framework for creating user-friendly MS web applications based on the Streamlit Python package. OpenMS WebApps simplifies MS data analysis through an intuitive graphical user interface, interactive result visualizations, and support for both local and online execution. Key features include workspace management, automatic generation of input widgets, and parallel execution of tools, resulting in high performance and ready-to-use solutions for online and local deployment. This framework benefits both researchers and developers: scientists can focus on their research without the burden of complex software setups, and developers can rapidly create and distribute custom WebApps with novel algorithms. Several applications built on the OpenMS WebApps template demonstrate its utility across diverse MS-related fields, enhancing the OpenMS ecosystem for developers and a wider range of users. Furthermore, it integrates seamlessly with third-party software, extending its benefits to developers beyond the OpenMS community.
    Keywords:  OpenMS; Streamlit; mass spectrometry; metabolomics; proteomics; pyOpenMS; web applications
    DOI:  https://doi.org/10.1021/acs.jproteome.4c00872
  12. Trends Cancer. 2025 Jan 28. pii: S2405-8033(25)00004-4. [Epub ahead of print]
    Oncogenic competence: balancing mutations, cellular state, and microenvironment.
    Lisa Pavinato, Arianna Baggiolini.
      Cancer development is driven by mutations, yet tumor-causing mutations only lead to tumor formation within specific cellular contexts. The reasons why certain mutations trigger malignant transformation in some contexts but not others remain often unclear. Both intrinsic and extrinsic factors play a key role in driving carcinogenesis by leading the cells toward a state of 'oncogenic competence'. This state is shaped by the transcriptional and epigenetic programs that define a specific cell in time and space. These programs arise from the interplay between genetic mutations, cellular lineage, differentiation state, and microenvironment. A deeper understanding of oncogenic competence is essential to uncover the mechanisms behind tumor initiation and, ultimately, advance the development of novel targeted therapies for cancer treatment and prevention.
    Keywords:  cellular lineage; differentiation state; microenvironment; mutations; oncogenic competence
    DOI:  https://doi.org/10.1016/j.trecan.2025.01.002
  13. Stem Cell Reports. 2025 Jan 09. pii: S2213-6711(24)00355-2. [Epub ahead of print] 102395
    A novel rapalog shows improved safety vs. efficacy in a human organoid model of polycystic kidney disease.
    Ramila E Gulieva, Parvaneh Ahmadvand, Benjamin S Freedman.
      The mammalian target of rapamycin (mTOR) pathway is a therapeutic target in polycystic kidney disease (PKD), but mTOR inhibitors such as everolimus have failed to show efficacy at tolerated doses in clinical trials. Here, we introduce AV457, a novel rapalog developed to reduce side effects, and assess its dose-dependent safety and efficacy versus everolimus in PKD1-/- and PKD2-/- human kidney organoids, which form cysts in a PKD-specific way. Both AV457 and everolimus reduce cyst growth over time. At intermediate doses, AV457 exhibits an improved safety profile relative to everolimus, with comparable efficacy. Target engagement assays confirm mTOR pathway inhibition and greater selectivity of AV457 for mTOR complex 1 versus complex 2, compared to everolimus. AV457 thus provides a more favorable balance of safety and efficacy for PKD compared to everolimus and merits further consideration as an investigational therapeutic.
    Keywords:  Akt; IC50; S6; ciliopathy; drug discovery; immunoblot; mTORC1; mTORC2; sirolimus; therapeutic screening
    DOI:  https://doi.org/10.1016/j.stemcr.2024.102395
  14. Res Sq. 2025 Jan 15. pii: rs.3.rs-5613372. [Epub ahead of print]
    GraphVelo allows for accurate inference of multimodal omics velocities and molecular mechanisms for single cells.
    Jianhua Xing, Yuhao Chen, Yan Zhang, Jiaqi Gan, Ke Ni, Ming Chen, Ivet Bahar.
      RNA velocities and generalizations emerge as powerful approaches for extracting time-resolved information from high-throughput snapshot single-cell data. Yet, several inherent limitations restrict applying the approaches to genes not suitable for RNA velocity inference due to complex transcriptional dynamics, low expression, or lacking splicing dynamics, or data of non-transcriptomic modality. Here, we present GraphVelo, a graph-based machine learning procedure that uses as input the RNA velocities inferred from existing methods and infers velocity vectors lying in the tangent space of the low-dimensional manifold formed by the single cell data. GraphVelo preserves vector magnitude and direction information during transformations across different data representations. Tests on multiple synthetic and experimental scRNA-seq data including viral-host interactome and multi-omics datasets demonstrate that GraphVelo, together with downstream generalized dynamo analyses, extends RNA velocities to multi-modal data and reveals quantitative nonlinear regulation relations between genes, virus and host cells, and different layers of gene regulation.
    DOI:  https://doi.org/10.21203/rs.3.rs-5613372/v1
  15. BMJ Open. 2024 Dec 20. 14(12): e084614
    A phase II double-blind multicentre, placebo-controlled trial to assess the efficacy and safety of alpelisib (BYL719) in paediatric and adult patients with Megalencephaly-CApillary malformation Polymicrogyria syndrome (MCAP): the SESAM study protocol.
    SESAM study group
       INTRODUCTION: The megalencephaly capillary malformation polymicrogyria (MCAP syndrome) results from mosaic gain-of-function PIK3CA variants. The main clinical features are macrocephaly, somatic overgrowth, neurodevelopmental delay and brain anomalies. Alpelisib (Vijoice) is a recently FDA-approved PI3Kα-specific inhibitor for patients with PIK3CA-related overgrowth spectrum (PROS). During its development, in patients with the MCAP subgroup of PROS, there was no specific, standardised evaluation of the effect on neuro-cognitive functioning. Moreover, it remains unknown if the molecule crosses the blood-brain barrier. Our objective is to evaluate the efficacy of a 24 month treatment with alpelisib on adaptive behaviour in patients with MCAP syndrome.
    METHODS AND ANALYSIS: SESAM is an industry-sponsored two-period multicentre French academic phase II trial, with a 6-month double-blind, placebo-controlled period followed by an open-label period. The primary endpoint is a ≥4-point improvement in the Vineland II Adaptive Behaviour Scale (VABS), 24 months after treatment initiation. Secondary objectives are safety, VABS improvement at 6 months, impact on the quality of life, epilepsy and hypotonia. 20 patients aged 2 to 40 years with an MCAP diagnosis and neurodevelopmental disorders of various degrees, will be followed monthly in local centres, centrally assessed (clinical, biological, neuropsychological and functional evaluation) at baseline and every 6 months. Patients will be evaluated by volumetric MRI at baseline and at 24 months. An optional lumbar puncture will be performed to investigate blood-brain barrier crossing. Inclusions were completed by April 2024, with the end of follow-up in November 2026.Given the efficacy of alpelisib in patients with PROS, if the drug crosses the blood-brain barrier, we can expect a clinical benefit for patients with neurocognitive disorders.
    ETHICS AND DISSEMINATION: Ethical approval was given by CPP Sud-Ouest et Outre-Mer I (reference: 2022-500197-34-01). Findings from this study will be disseminated via publication, reports and conference presentations.
    TRIAL REGISTRATION NUMBER: NCT05577754.
    Keywords:  Clinical trials; Developmental neurology & neurodisability; Neurogenetics; Paediatric clinical genetics & dysmorphology
    DOI:  https://doi.org/10.1136/bmjopen-2024-084614
  16. Nat Commun. 2025 Jan 24. 16(1): 975
    A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology.
    Yingying Zhang, Alden K Leung, Jin Joo Kang, Yu Sun, Guanxi Wu, Le Li, Jiayang Sun, Lily Cheng, Tian Qiu, Junke Zhang, Shayne D Wierbowski, Shagun Gupta, James G Booth, Haiyuan Yu.
      A major goal of cancer biology is to understand the mechanisms driven by somatically acquired mutations. Two distinct methodologies-one analyzing mutation clustering within protein sequences and 3D structures, the other leveraging protein-protein interaction network topology-offer complementary strengths. We present NetFlow3D, a unified, end-to-end 3D structurally-informed protein interaction network propagation framework that maps the multiscale mechanistic effects of mutations. Built upon the Human Protein Structurome, which incorporates the 3D structures of every protein and the binding interfaces of all known protein interactions, NetFlow3D integrates atomic, residue, protein and network-level information: It clusters mutations on 3D protein structures to identify driver mutations and propagates their impacts anisotropically across the protein interaction network, guided by the involved interaction interfaces, to reveal systems-level impacts. Applied to 33 cancer types, NetFlow3D identifies 2 times more 3D clusters and incorporates 8 times more proteins in significantly interconnected network modules compared to traditional methods.
    DOI:  https://doi.org/10.1038/s41467-024-54176-3
  17. Proc Natl Acad Sci U S A. 2025 Feb 04. 122(5): e2401236121
    How can we make sound replication decisions?
    Clintin P Davis-Stober, Alexandra Sarafoglou, Balazs Aczel, Suyog H Chandramouli, Timothy M Errington, Sarahanne M Field, Ayelet Fishbach, Juliana Freire, John P A Ioannidis, Klaus Oberauer, Franco Pestilli, Susanne Ressl, Daniel J Schad, Judith Ter Schure, Katya Tentori, Don van Ravenzwaaij, Joachim Vandekerckhove, Odd Erik Gundersen.
      Replication and the reported crises impacting many fields of research have become a focal point for the sciences. This has led to reforms in publishing, methodological design and reporting, and increased numbers of experimental replications coordinated across many laboratories. While replication is rightly considered an indispensable tool of science, financial resources and researchers' time are quite limited. In this perspective, we examine different values and attitudes that scientists can consider when deciding whether to replicate a finding and how. We offer a conceptual framework for assessing the usefulness of various replication tools, such as preregistration.
    Keywords:  methodology; reform; replication; reproducibility
    DOI:  https://doi.org/10.1073/pnas.2401236121
  18. Bioinformatics. 2025 Jan 31. pii: btaf046. [Epub ahead of print]
    Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach.
    Mateusz Staniak, Ting Huang, Amanda M Figueroa-Navedo, Devon Kohler, Meena Choi, Trent Hinkle, Tracy Kleinheinz, Robert Blake, Christopher M Rose, Yingrong Xu, Pierre M Jean Beltran, Liang Xue, Małgorzata Bogdan, Olga Vitek.
       MOTIVATION: Bottom-up mass spectrometry-based proteomics studies changes in protein abundance and structure across conditions. Since the currency of these experiments are peptides, ie subsets of protein sequences that carry the quantitative information, conclusions at a different level must be computationally inferred. The inference is particularly challenging in situations where the peptides are shared by multiple proteins or post-translational modifications. While many approaches infer the underlying abundances from unique peptides, there is a need to distinguish the quantitative patterns when peptides are shared.
    RESULTS: We propose a statistical approach for estimating protein abundances, as well as site occupancies of post-translational modifications, based on quantitative information from shared peptides. The approach treats the quantitative patterns of shared peptides as convex combinations of abundances of individual proteins or modification sites, and estimates the abundance of each source in a sample together with the weights of the combination. In simulation-based evaluations, the proposed approach improved the precision of estimated fold changes between conditions. We further demonstrated the practical utility of the approach in experiments with diverse biological objectives, ranging from protein degradation and thermal proteome stability, to changes in protein post-translational modifications.
    AVAILABILITY: The approach is implemented in an open-source R package MSstatsWeightedSummary. The package is currently available at https://github.com/Vitek-Lab/MSstatsWeightedSummary (doi:10.5281/zenodo.14662989). Code required to reproduce the results presented in this article can be found in a repository https://github.com/mstaniak/MWS_reproduction (doi:10.5281/zenodo.14656053).
    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
    DOI:  https://doi.org/10.1093/bioinformatics/btaf046
  19. Nat Commun. 2025 Jan 29. 16(1): 1141
    Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data.
    Guanao Yan, Shuo Harper Hua, Jingyi Jessica Li.
      In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review 34 state-of-the-art methods, classifying SVGs into three categories: overall, cell-type-specific, and spatial-domain-marker SVGs. Our review explains the intuitions underlying these methods, summarizes their applications, and categorizes the hypothesis tests they use in the trade-off between generality and specificity for SVG detection. We discuss challenges in SVG detection and propose future directions for improvement. Our review offers insights for method developers and users, advocating for category-specific benchmarking.
    DOI:  https://doi.org/10.1038/s41467-025-56080-w
  20. Trends Biochem Sci. 2025 Jan 27. pii: S0968-0004(24)00282-2. [Epub ahead of print]
    Regulating Nrf2 activity: ubiquitin ligases and signaling molecules in redox homeostasis.
    John D Hayes, Sharadha Dayalan Naidu, Albena T Dinkova-Kostova.
      Transcription factor NF-E2 p45-related factor 2 (Nrf2) orchestrates defenses against oxidants and thiol-reactive electrophiles. It is controlled at the protein stability level by several E3 ubiquitin ligases (CRL3Keap1, CRL4DCAF11, SCFβ-TrCP, and Hrd1). CRL3Keap1 is of the greatest importance because it constitutively targets Nrf2 for proteasomal degradation under homeostatic conditions but is prevented from doing so by oxidative stressors. Repression of Nrf2 by CRL3Keap1 is attenuated by SQSTM1/p62, and this is reinforced by phosphorylation of SQSTM1/p62. Repression by SCFβ-TrCP requires phosphorylation of Nrf2 by GSK3, the activity of which is inhibited by PKB/Akt and other kinases. We discuss how Nrf2 activity is controlled by the ubiquitin ligases under different circumstances. We also describe endogenous signaling molecules that inactivate CRL3Keap1 to alleviate stress and restore homeostasis.
    Keywords:  KEAP1; NRF2; SQSTM1/p62; redox switch; signaling; β-TrCP
    DOI:  https://doi.org/10.1016/j.tibs.2024.12.010
  21. bioRxiv. 2025 Jan 19. pii: 2025.01.15.633227. [Epub ahead of print]
    PAX3-FOXO1 drives targetable cell state-dependent metabolic vulnerabilities in rhabdomyosarcoma.
    Katrina I Paras, Julia S Brunner, Jacob A Boyer, Angela M Montero, Benjamin T Jackson, Sangita Chakraborty, Abigail Xie, Kristina Guillan, Armaan Siddiquee, Lourdes Pajuelo Torres, Joshua D Rabinowitz, Andrew Kung, Daoqi You, Filemon Dela Cruz, Lydia W S Finley.
      PAX3-FOXO1, an oncogenic transcription factor, drives a particularly aggressive subtype of rhabdomyosarcoma (RMS) by enforcing gene expression programs that support malignant cell states. Here we show that PAX3-FOXO1 + RMS cells exhibit altered pyrimidine metabolism and increased dependence on enzymes involved in de novo pyrimidine synthesis, including dihydrofolate reductase (DHFR). Consequently, PAX3-FOXO1 + cells display increased sensitivity to inhibition of DHFR by the chemotherapeutic drug methotrexate, and this dependence is rescued by provision of pyrimidine nucleotides. Methotrexate treatment mimics the metabolic and transcriptional impact of PAX3-FOXO1 silencing, reducing expression of genes related to PAX3-FOXO1-driven malignant cell states. Accordingly, methotrexate treatment slows growth of multiple PAX3-FOXO1 + tumor xenograft models, but not fusion-negative counterparts. Taken together, these data demonstrate that PAX3-FOXO1 induces cell states characterized by altered pyrimidine dependence and nominate methotrexate as an addition to the current therapeutic arsenal for treatment of these malignant pediatric tumors.
    DOI:  https://doi.org/10.1101/2025.01.15.633227
  22. Cell Syst. 2025 Jan 20. pii: S2405-4712(24)00365-X. [Epub ahead of print]
    DeST-OT: Alignment of spatiotemporal transcriptomics data.
    Peter Halmos, Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J Raphael.
      Spatially resolved transcriptomics (SRT) measures mRNA transcripts at thousands of locations within a tissue slice, revealing spatial variations in gene expression and cell types. SRT has been applied to tissue slices from multiple time points during the development of an organism. We introduce developmental spatiotemporal optimal transport (DeST-OT), a method to align spatiotemporal transcriptomics data using optimal transport (OT). DeST-OT uses semi-relaxed OT to model cellular growth, death, and differentiation processes. We also derive a growth distortion metric and a migration metric to quantify the plausibility of spatiotemporal alignments. DeST-OT outperforms existing methods on the alignment of spatiotemporal transcriptomics data from developing mouse kidney and axolotl brain. DeST-OT estimated growth rates also provide insights into the gene expression programs governing the growth and differentiation of cells over space and time.
    Keywords:  alignment; development; developmental biology; growth rates; optimal transport; semi-relaxed optimal transport; spatially resolved transcriptomics; spatiotemporal; trajectory inference
    DOI:  https://doi.org/10.1016/j.cels.2024.12.001
  23. J Biol Chem. 2025 Jan 23. pii: S0021-9258(25)00068-7. [Epub ahead of print] 108221
    Downregulation of the Phosphatase PHLPP1 Contributes to NNK-induced Malignant Transformation of Human Bronchial Epithelial Cells (HBECs).
    Xuelei Liu, Shirui Huang, Xiaozhen Gu, Ziyi Yang, Jiajun Xiu, Xiaodan Xu, Yaxin Cao, Jingjing Wang, Yunping Zhao, Minggang Peng, Zhongxian Tian, Xiaohui Hua, Hui-Li Wang, Chuanshu Huang.
      Cigarette smoking (CS) is one of the greatest health concerns, which can cause lung cancer. 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), a tobacco-specific nitrosamine, and has been well-documented for its carcinogenic activity in both epidemiological and laboratory studies. PH domain leucine-rich repeat protein phosphatase 1 (PHLPP1) and phosphatase and tensin homolog (PTEN) are two well-known phosphatase tumor suppressors that have been reported to be downregulated in human lung cancer tissues. However, the effect of NNK exposure on the expression of PHLPP1 and PTEN is unknown, and such effects may be early events leading to lung carcinogenesis. We explored this question in current studies and found that exposure of human bronchial epithelial BEP2D cells to NNK resulted in cell malignant transformation accompanied by a remarkable downregulation of PHLPP1 and PTEN. Such downregulation of PHLPP1 and PTEN was also consistently observed in vivo in Cigarette Smoking-exposed mouse lung tissues. Our studies further showed that overexpression of PHLPP1 or PTEN alleviated NNK-induced BEP2D cell transformation. Ectopic expression of PHLPP1 promoted PTEN protein expression, while PTEN overexpression did not affect PHLPP1 expression. Mechanistic studies showed that NNK was able to inhibit PP2A-C activity, which directly attenuated c-Jun phosphorylation at Ser63/73, and subsequently inhibited the PHLPP1 transcription and expression. Further, the downregulation of PHLPP1 led to a reduction of pten mRNA stability and expression through the HUR/Jun D/miR-613/NCL axis. Taken together, our studies advance the field of tobacco-induced lung cancer research by uncovering new mechanistic insights and identifying a novel molecular axis that could inform future therapeutic strategies. It also adds a new dimension by exploring the interaction between PHLPP1 and PTEN in the context of tobacco carcinogen exposure.
    Keywords:  NNK; PHLPP1; PP2AC; PTEN; lung carcinogenesis; miR-613
    DOI:  https://doi.org/10.1016/j.jbc.2025.108221
  24. J Med Genet. 2025 Jan 27. pii: jmg-2024-110364. [Epub ahead of print]
    Expanding the phenotypic spectrum of PROS: reclassifying isolated lateralised overgrowth.
    Andrea Gazzin, Giuseppe Reynolds, Stefania Massuras, Maria Luca, Paola Coppo, Diana Carli, Marilidia Piglionica, Stefania Martino, Rosanna Bagnulo, Giovanni Battista Ferrero, Nicoletta Resta, Alessandro Mussa.
      Lateralised overgrowth (LO) is characterised by the asymmetric increase in the size of any part of the body exceeding 10% compared with the unaffected contralateral one. LO is a key feature in various syndromic overgrowth disorders, such as Beckwith-Wiedemann spectrum and PIK3CA-related overgrowth spectrum (PROS). However, it can also present as isolated (ILO). Defining the aetiology of LO is critical due to the clinical implications and management strategies required for each condition. This report presents two patients who were followed up throughout childhood for ILO and were ultimately diagnosed with PROS through molecular analysis on DNA extracted from a skin biopsy, revealing the PIK3CA:c.263G>A (p.Arg88Gln) variant at a high variant allele frequency. This variant has been described in association with macrocephaly-capillary malformation syndrome but not with ILO. In conclusion, this is the first report of patients harbouring the (p.Arg88Gln) variant with a diagnosis of ILO, thus, highlighting the importance of considering ILO within the PROS and underscoring the necessity for somatic DNA testing. An early and accurate molecular diagnosis is crucial for guiding appropriate clinical management in order to ensure access to targeted therapies, emphasising the need for further research to refine diagnostic criteria and testing recommendations for ILO.
    Keywords:  Diagnosis; Mosaicism
    DOI:  https://doi.org/10.1136/jmg-2024-110364
  25. J Proteome Res. 2025 Jan 24.
    Cell Storage Conditions Impact Single-Cell Proteomic Landscapes.
    Bora Onat, Amanda Momenzadeh, Ali Haghani, Yuming Jiang, Yang Song, Sarah J Parker, Jesse G Meyer.
      Single cell transcriptomics (SCT) has revolutionized our understanding of cellular heterogeneity, yet the emergence of single cell proteomics (SCP) promises a more functional view of cellular dynamics. A challenge is that not all mass spectrometry facilities can perform SCP, and not all laboratories have access to cell sorting equipment required for SCP, which together motivate an interest in sending bulk cell samples through the mail for sorting and SCP analysis. Shipping requires cell storage, which has an unknown effect on SCP results. This study investigates the impact of cell storage conditions on the proteomic landscape at the single cell level, utilizing Data-Independent Acquisition (DIA) coupled with Parallel Accumulation Serial Fragmentation (diaPASEF). Three storage conditions were compared in 293T cells: (1) 37 °C (control), (2) 4 °C overnight, and (3) -196 °C storage followed by liquid nitrogen preservation. Both cold and frozen storage induced significant alterations in the cell diameter, elongation, and proteome composition. By elucidating how cell storage conditions alter cellular morphology and proteome profiles, this study contributes foundational technical information about SCP sample preparation and data quality.
    Keywords:  HEK293T; LC−MS; SCP; single cell proteomics; storage conditions; timsTOF-SCP
    DOI:  https://doi.org/10.1021/acs.jproteome.4c00632
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