bims-pideca 2024-06-02 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2024–06–02
23 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Genomic dissection and mutation-specific target discovery for breast cancer PIK3CA hotspot mutations.
Patterning, regulation, and role of FoxO/DAF-16 in the early embryo.
Endogenous oncogenic KRAS expression increases cell proliferation and motility in near-diploid hTERT RPE-1 cells.
Differential endothelial cell cycle status in postnatal retinal vessels revealed using a novel PIP-FUCCI reporter and zonation analysis.
Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry.
Nonlinear dynamics in phosphoinositide metabolism.
Building and analyzing metacells in single-cell genomics data.
SGLT2 inhibition eliminates senescent cells and alleviates pathological aging.
MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions.
Regulation of TSC2 lysosome translocation and mitochondrial turnover by TSC2 acetylation status.
AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.
Regulation of Foxo1 expression is critical for central B cell tolerance and allelic exclusion.
mosaicMPI: a framework for modular data integration across cohorts and -omics modalities.
Detection of differential bait proteoforms through immunoprecipitation-mass spectrometry data analysis.
ReactomeGSA: New features to simplify public data reuse.
Hippo and PI5P4K signaling intersect to control the transcriptional activation of YAP.
Mechanical activation of VE-cadherin stimulates AMPK to increase endothelial cell metabolism and vasodilation.
Hyperactive mTORC1/4EBP1 Signaling Dysregulates Proteostasis and Accelerates Cardiac Aging.
Duration of Morning Hyperinsulinemia is Key to the Enhancement of Hepatic Glucose Uptake and Glycogen Storage Later in the Day.
Joint multi-omics discriminant analysis with consistent representation learning using PANDA.
Unveiling gene regulatory networks during cellular state transitions without linkage across time points.
Hippo-YAP/TAZ signalling coordinates adipose plasticity and energy balance by uncoupling leptin expression from fat mass.
PIK3CA mutations in endocrine-resistant breast cancer.

BMC Genomics. 2024 May 27. 25(1): 519

Genomic dissection and mutation-specific target discovery for breast cancer PIK3CA hotspot mutations.

Adam X Miranda, Justin Kemp, Brad A Davidson, Sara Erika Bellomo, Verda E Miranda, Alexandra Manoni, Caterina Marchiò, Sarah Croessmann, Ben H Park, Emily Hodges.

   BACKGROUND: Recent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype.
RESULTS: In this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspot PIK3CA mutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with each PIK3CA hotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated through in vitro analysis and publicly available patient databases.
CONCLUSIONS: Using our multi-modal genomics framework, we discover distinct differences in genomic regulation between PIK3CA hotspot mutations, suggesting the PIK3CA mutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.

Keywords:   PIK3CA ; Breast cancer; Chromatin accessibility; Epigenomics; Gene expression; Integrative analysis; Isogenic cell lines

DOI:  https://doi.org/10.1186/s12864-024-10368-1
bioRxiv. 2024 May 14. pii: 2024.05.13.594029. [Epub ahead of print]

Patterning, regulation, and role of FoxO/DAF-16 in the early embryo.

Michael S Mauro, Sophia L Martin, Julien Dumont, Mimi Shirasu-Hiza, Julie C Canman.

Insulin resistance and diabetes are associated with many health issues including higher rates of birth defects and miscarriage during pregnancy. Because insulin resistance and diabetes are both associated with obesity, which also affects fertility, the role of insulin signaling itself in embryo development is not well understood. A key downstream target of the insulin/insulin-like growth factor signaling (IIS) pathway is the forkhead family transcription factor FoxO (DAF-16 in C. elegans ). Here, we used quantitative live imaging to measure the patterning of endogenously tagged FoxO/DAF-16 in the early worm embryo. In 2-4-cell stage embryos, FoxO/DAF-16 initially localized uniformly to all cell nuclei, then became dramatically enriched in germ precursor cell nuclei beginning at the 8-cell stage. This nuclear enrichment in early germ precursor cells required germ fate specification, PI3K (AGE-1)- and PTEN (DAF-18)-mediated phospholipid regulation, and the deubiquitylase USP7 (MATH-33), yet was unexpectedly insulin receptor (DAF-2)- and AKT-independent. Functional analysis revealed that FoxO/DAF-16 acts as a cell cycle pacer for early cleavage divisions-without FoxO/DAF-16 cell cycles were shorter than in controls, especially in germ lineage cells. These results reveal the germ lineage specific patterning, upstream regulation, and cell cycle role for FoxO/DAF-16 during early C. elegans embryogenesis.

DOI: https://doi.org/10.1101/2024.05.13.594029
J Biol Chem. 2024 May 23. pii: S0021-9258(24)01910-0. [Epub ahead of print] 107409

Endogenous oncogenic KRAS expression increases cell proliferation and motility in near-diploid hTERT RPE-1 cells.

Naushin L Hindul, Lauren R Abbott, Sumaya M D Adan, Kornelis R Straatman, Andrew M Fry, Kouji Hirota, Kayoko Tanaka.

  About 18% of all human cancers carry a mutation in the KRAS gene making it among the most sought-after anti-cancer targets. However, mutant KRas protein has proved remarkably undruggable. The recent approval of the first generation of RAS inhibitors therefore marks a seminal milestone in the history of cancer research. Inevitably though, it also raises the predictable challenges of limited drug efficacies and acquired resistance. Hence, new approaches that improve our understanding of the tumorigenic mechanisms of oncogenic RAS within more physiological settings continue to be essential. Here, we have employed the near-diploid human hTERT RPE-1 cells to generate isogenic cell lines in which one of the endogenous KRAS alleles carries an oncogenic KRAS mutation at glycine 12. Cells with a KRASG12V/+, KRASG12C/+, or KRASG12D/+ genotype, together with wild-type KRASG12G(WT)/+ cells, reveal that oncogenic KRAS.G12X mutations increase cell proliferation rate and cell motility and reduced focal adhesions in KRASG12V/+ cells. EGF-induced phosphorylation of ERK and AKT was comparable between KRASG12V/+, KRASG12C/+, KRASG12D/+, and KRASG12G(WT)/+ cells. Interestingly, KRASG12X/+ cells showed varying responses to distinct inhibitors with the KRASG12V/+ and KRASG12D/+ cells more sensitive to hydroxyurea and MEK inhibitors, U0126 and trametinib, but more resistant to PI3K inhibitor, PIK-90, than the KRASG12G(WT)/+ cells. A combination of low doses of hydroxyurea and U0126 showed an additive inhibition on growth rate that was greater in KRASG12V/+ than wild-type cells. Collectively, these cell lines will be a valuable resource for studying oncogenic RAS signalling and developing effective anti-KRAS reagents with minimum cytotoxicity on wild-type cells.

Keywords:  Small GTPase; cell cycle; cell motility; cell proliferation; cell signalling; focal adhesion

DOI:  https://doi.org/10.1016/j.jbc.2024.107409
Angiogenesis. 2024 May 25.

Differential endothelial cell cycle status in postnatal retinal vessels revealed using a novel PIP-FUCCI reporter and zonation analysis.

Ziqing Liu, Natalie T Tanke, Alexandra Neal, Tianji Yu, Tershona Branch, Arya Sharma, Jean G Cook, Victoria L Bautch.

  Cell cycle regulation is critical to blood vessel formation and function, but how the endothelial cell cycle integrates with vascular regulation is not well-understood, and available dynamic cell cycle reporters do not precisely distinguish all cell cycle stage transitions in vivo. Here we characterized a recently developed improved cell cycle reporter (PIP-FUCCI) that precisely delineates S phase and the S/G2 transition. Live image analysis of primary endothelial cells revealed predicted temporal changes and well-defined stage transitions. A new inducible mouse cell cycle reporter allele was selectively expressed in postnatal retinal endothelial cells upon Cre-mediated activation and predicted endothelial cell cycle status. We developed a semi-automated zonation program to define endothelial cell cycle status in spatially defined and developmentally distinct retinal areas and found predicted cell cycle stage differences in arteries, veins, and remodeled and angiogenic capillaries. Surprisingly, the predicted dearth of S-phase proliferative tip cells relative to stalk cells at the vascular front was accompanied by an unexpected enrichment for endothelial tip and stalk cells in G2, suggesting G2 stalling as a contribution to tip-cell arrest and dynamics at the front. Thus, this improved reporter precisely defines endothelial cell cycle status in vivo and reveals novel G2 regulation that may contribute to unique aspects of blood vessel network expansion.

Keywords:  Blood vessel; Cell cycle; Endothelial cells; G2 arrest; HUVEC

DOI:  https://doi.org/10.1007/s10456-024-09920-0
ArXiv. 2024 May 15. pii: arXiv:2405.09699v1. [Epub ahead of print]

Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry.

Prashant Kaushal, Manisha R Ummadi, Gwendolyn M Jang, Yennifer Delgado, Sara K Makanani, Sophie F Blanc, Decan M Winters, Jiewei Xu, Benjamin Polacco, Yuan Zhou, Erica Stevenson, Manon Eckhardt, Lorena Zuliani-Alvarez, Robyn Kaake, Danielle L Swaney, Nevan Krogan, Mehdi Bouhaddou.

Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular signaling changes in response to molecular cues. Here, we present an affinity purification mass spectrometry (APMS) proteomics protocol to quantify and visualize global changes in protein protein interaction (PPI) networks between pairwise conditions. We describe steps for expressing affinity tagged bait proteins in mammalian cells, identifying purified protein complexes, quantifying differential PPIs, and visualizing differential PPI networks. Specifically, this protocol details steps for designing affinity tagged bait gene constructs, transfection, affinity purification, mass spectrometry sample preparation, data acquisition, database search, data quality control, PPI confidence scoring, cross run normalization, statistical data analysis, and differential PPI visualization. Our protocol discusses caveats and limitations with applicability across cell types and biological areas.
Curr Opin Cell Biol. 2024 May 24. pii: S0955-0674(24)00052-8. [Epub ahead of print]88 102373

Nonlinear dynamics in phosphoinositide metabolism.

Suet Yin Sarah Fung, X J Xǔ, Min Wu.

Phosphoinositides broadly impact membrane dynamics, signal transduction and cellular physiology. The orchestration of signaling complexity by this seemingly simple metabolic pathway remains an open question. It is increasingly evident that comprehending the complexity of the phosphoinositides metabolic network requires a systems view based on nonlinear dynamics, where the products of metabolism can either positively or negatively modulate enzymatic function. These feedback and feedforward loops may be paradoxical, leading to counterintuitive effects. In this review, we introduce the framework of nonlinear dynamics, emphasizing distinct dynamical regimes such as the excitable state, oscillations, and mixed-mode oscillations-all of which have been experimentally observed in phosphoinositide metabolisms. We delve into how these dynamical behaviors arise from one or multiple network motifs, including positive and negative feedback loops, coherent and incoherent feedforward loops. We explore the current understanding of the molecular circuits responsible for these behaviors. While mapping these circuits presents both conceptual and experimental challenges, redefining cellular behavior based on dynamical state, lipid fluxes, time delay, and network topology is likely essential for a comprehensive understanding of this fundamental metabolic network.

DOI: https://doi.org/10.1016/j.ceb.2024.102373
Mol Syst Biol. 2024 May 29.

Building and analyzing metacells in single-cell genomics data.

Mariia Bilous, Léonard Hérault, Aurélie Ag Gabriel, Matei Teleman, David Gfeller.

  The advent of high-throughput single-cell genomics technologies has fundamentally transformed biological sciences. Currently, millions of cells from complex biological tissues can be phenotypically profiled across multiple modalities. The scaling of computational methods to analyze and visualize such data is a constant challenge, and tools need to be regularly updated, if not redesigned, to cope with ever-growing numbers of cells. Over the last few years, metacells have been introduced to reduce the size and complexity of single-cell genomics data while preserving biologically relevant information and improving interpretability. Here, we review recent studies that capitalize on the concept of metacells-and the many variants in nomenclature that have been used. We further outline how and when metacells should (or should not) be used to analyze single-cell genomics data and what should be considered when analyzing such data at the metacell level. To facilitate the exploration of metacells, we provide a comprehensive tutorial on the construction and analysis of metacells from single-cell RNA-seq data ( https://github.com/GfellerLab/MetacellAnalysisTutorial ) as well as a fully integrated pipeline to rapidly build, visualize and evaluate metacells with different methods ( https://github.com/GfellerLab/MetacellAnalysisToolkit ).

Keywords:  Coarse-graining; Metacells; Single-cell Data Analysis; Single-cell Genomics; Tutorial

DOI:  https://doi.org/10.1038/s44320-024-00045-6
Nat Aging. 2024 May 30.

SGLT2 inhibition eliminates senescent cells and alleviates pathological aging.

Goro Katsuumi, Ippei Shimizu, Masayoshi Suda, Yohko Yoshida, Takaaki Furihata, Yusuke Joki, Chieh-Lun Hsiao, Liang Jiaqi, Shinya Fujiki, Manabu Abe, Masataka Sugimoto, Tomoyoshi Soga, Tohru Minamino.

It has been reported that accumulation of senescent cells in various tissues contributes to pathological aging and that elimination of senescent cells (senolysis) improves age-associated pathologies. Here, we demonstrate that inhibition of sodium-glucose co-transporter 2 (SGLT2) enhances clearance of senescent cells, thereby ameliorating age-associated phenotypic changes. In a mouse model of dietary obesity, short-term treatment with the SGLT2 inhibitor canagliflozin reduced the senescence load in visceral adipose tissue and improved adipose tissue inflammation and metabolic dysfunction, but normalization of plasma glucose by insulin treatment had no effect on senescent cells. Canagliflozin extended the lifespan of mice with premature aging even when treatment was started in middle age. Metabolomic analyses revealed that short-term treatment with canagliflozin upregulated 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside, enhancing immune-mediated clearance of senescent cells by downregulating expression of programmed cell death-ligand 1. These findings suggest that inhibition of SGLT2 has an indirect senolytic effect by enhancing endogenous immunosurveillance of senescent cells.

DOI: https://doi.org/10.1038/s43587-024-00642-y
Bioinformatics. 2024 May 02. pii: btae315. [Epub ahead of print]40(5):

MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions.

Rodolphe Loubaton, Nicolas Champagnat, Pierre Vallois, Laurent Vallat.

MOTIVATION: The dynamic transcriptional mechanisms that govern eukaryotic cell function can now be analyzed by RNA sequencing. However, the packages currently available for the analysis of raw sequencing data do not provide automatic analysis of complex experimental designs with multiple biological conditions and multiple analysis time-points.
RESULTS: The MultiRNAflow suite combines several packages in a unified framework allowing exploratory and supervised statistical analyses of temporal data for multiple biological conditions.
AVAILABILITY AND IMPLEMENTATION: The R package MultiRNAflow is freely available on Bioconductor (https://bioconductor.org/packages/MultiRNAflow/), and the latest version of the source code is available on a GitHub repository (https://github.com/loubator/MultiRNAflow).

DOI: https://doi.org/10.1093/bioinformatics/btae315
Sci Rep. 2024 May 31. 14(1): 12521

Regulation of TSC2 lysosome translocation and mitochondrial turnover by TSC2 acetylation status.

Patricia Marqués, Jesús Burillo, Carlos González-Blanco, Beatriz Jiménez, Gema García, Ana García-Aguilar, Sarai Iglesias-Fortes, Ángela Lockwood, Carlos Guillén.

  Sirtuin1 (SIRT1) activity decreases the tuberous sclerosis complex 2 (TSC2) lysine acetylation status, inhibiting the mechanistic target of rapamycin complex 1 (mTORC1) signalling and concomitantly, activating autophagy. This study analyzes the role of TSC2 acetylation levels in its translocation to the lysosome and the mitochondrial turnover in both mouse embryonic fibroblast (MEF) and in mouse insulinoma cells (MIN6) as a model of pancreatic β cells. Resveratrol (RESV), an activator of SIRT1 activity, promotes TSC2 deacetylation and its translocation to the lysosome, inhibiting mTORC1 activity. An improvement in mitochondrial turnover was also observed in cells treated with RESV, associated with an increase in the fissioned mitochondria, positive autophagic and mitophagic fluxes and an enhancement of mitochondrial biogenesis. This study proves that TSC2 in its deacetylated form is essential for regulating mTORC1 signalling and the maintenance of the mitochondrial quality control, which is involved in the homeostasis of pancreatic beta cells and prevents from several metabolic disorders such as Type 2 Diabetes Mellitus.

Keywords:  Acetylation; Lysosome; Mitophagy; Pancreatic β cells; TSC2; mTORC1

DOI:  https://doi.org/10.1038/s41598-024-63525-7
Res Sq. 2024 May 15. pii: rs.3.rs-4370115. [Epub ahead of print]

AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.

Sehyun Oh, Kai Gravel-Pucillo, Marcel Ramos, Sean Davis, Vince Carey, Martin Morgan, Levi Waldron.

Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows. Here we present the AnVILWorkflow R package, which enables the convenient execution of bioinformatics workflows hosted on AnVIL directly from an R environment. AnVILWorkflowsimplifies the setup of the cloud computing environment, input data formatting, workflow submission, and retrieval of results through intuitive functions. We demonstrate the utility of AnVILWorkflowfor three use cases: bulk RNA-seq analysis with Salmon, metagenomics analysis with bioBakery, and digital pathology image processing with PathML. The key features of AnVILWorkflow include user-friendly browsing of available data and workflows, seamless integration of R and non-R tools within a reproducible analysis pipeline, and accessibility to scalable computing resources without direct management overhead. While some limitations exist around workflow customization, AnVILWorkflowlowers the barrier to taking advantage of AnVIL's resources, especially for exploratory analyses or bulk processing with established workflows. This empowers a broader community of researchers to leverage the latest genomics tools and datasets using familiar R syntax. This package is distributed through the Bioconductor project (https://bioconductor.org/packages/AnVILWorkflow), and the source code is available through GitHub (https://github.com/shbrief/AnVILWorkflow).

DOI: https://doi.org/10.21203/rs.3.rs-4370115/v1
Cell Rep. 2024 May 25. pii: S2211-1247(24)00611-9. [Epub ahead of print]43(6): 114283

Regulation of Foxo1 expression is critical for central B cell tolerance and allelic exclusion.

Megan R McCaleb, Anjelica M Miranda, Hadeel A Khammash, Raul M Torres, Roberta Pelanda.

  Resolving the molecular mechanisms of central B cell tolerance might unveil strategies that prevent autoimmunity. Here, using a mouse model of central B cell tolerance in which Forkhead box protein O1 (Foxo1) is either deleted or over-expressed in B cells, we show that deleting Foxo1 blocks receptor editing, curtails clonal deletion, and decreases CXCR4 expression, allowing high-avidity autoreactive B cells to emigrate to the periphery whereby they mature but remain anergic and short lived. Conversely, expression of degradation-resistant Foxo1 promotes receptor editing in the absence of self-antigen but leads to allelic inclusion. Foxo1 over-expression also restores tolerance in autoreactive B cells harboring active PI3K, revealing opposing roles of Foxo1 and PI3K in B cell selection. Overall, we show that the transcription factor Foxo1 is a major gatekeeper of central B cell tolerance and that PI3K drives positive selection of immature B cells and establishes allelic exclusion by suppressing Foxo1.

Keywords:  B cells; CP: Immunology; Foxo1; PI3K; bone marrow; mice; receptor editing; tolerance

DOI:  https://doi.org/10.1016/j.celrep.2024.114283
Nucleic Acids Res. 2024 May 30. pii: gkae442. [Epub ahead of print]

mosaicMPI: a framework for modular data integration across cohorts and -omics modalities.

Theodore B Verhey, Heewon Seo, Aaron Gillmor, Varsha Thoppey-Manoharan, David Schriemer, Sorana Morrissy.

Advances in molecular profiling have facilitated generation of large multi-modal datasets that can potentially reveal critical axes of biological variation underlying complex diseases. Distilling biological meaning, however, requires computational strategies that can perform mosaic integration across diverse cohorts and datatypes. Here, we present mosaicMPI, a framework for discovery of low to high-resolution molecular programs representing both cell types and states, and integration within and across datasets into a network representing biological themes. Using existing datasets in glioblastoma, we demonstrate that this approach robustly integrates single cell and bulk programs across multiple platforms. Clinical and molecular annotations from cohorts are statistically propagated onto this network of programs, yielding a richly characterized landscape of biological themes. This enables deep understanding of individual tumor samples, systematic exploration of relationships between modalities, and generation of a reference map onto which new datasets can rapidly be mapped. mosaicMPI is available at https://github.com/MorrissyLab/mosaicMPI.

DOI: https://doi.org/10.1093/nar/gkae442
Sci Data. 2024 May 29. 11(1): 551

Detection of differential bait proteoforms through immunoprecipitation-mass spectrometry data analysis.

Savvas Kourtis, Damiano Cianferoni, Luis Serrano, Sara Sdelci.

Proteins are often referred to as the workhorses of cells, and their interactions are necessary to facilitate specific cellular functions. Despite the recognition that protein-protein interactions, and thus protein functions, are determined by proteoform states, such as mutations and post-translational modifications (PTMs), methods for determining the differential abundance of proteoforms across conditions are very limited. Classically, immunoprecipitation coupled with mass spectrometry (IP-MS) has been used to understand how the interactome (preys) of a given protein (bait) changes between conditions to elicit specific cellular functions. Reversing this concept, we present here a new workflow for IP-MS data analysis that focuses on identifying the differential peptidoforms of the bait protein between conditions. This method can provide detailed information about specific bait proteoforms, potentially revealing pathogenic protein states that can be exploited for the development of targeted therapies.

DOI: https://doi.org/10.1038/s41597-024-03394-x
Bioinformatics. 2024 May 28. pii: btae338. [Epub ahead of print]

ReactomeGSA: New features to simplify public data reuse.

Alexander Grentner, Eliot Ragueneau, Chuqiao Gong, Adrian Prinz, Sabina Gansberger, Inigo Oyarzun, Henning Hermjakob, Johannes Griss.

MOTIVATION: ReactomeGSA is part of the Reactome knowledgebase and one of the leading multi-omics pathway analysis platforms. ReactomeGSA provides access to quantitative pathway analysis methods supporting different 'omics data types. Additionally, ReactomeGSA can process different datasets simultaneously, leading to a comparative pathway analysis that can also be performed across different species.
RESULTS: We present a major update to the ReactomeGSA analysis platforms that greatly simplifies the reuse and direct integration of public data. In order to increase the number of available datasets, we developed the new grein_loader Python application that can directly fetch experiments from the GREIN resource. This enabled us to support both EMBL-EBI's Expression Atlas and GEO RNA-seq Experiments Interactive Navigator (GREIN) within ReactomeGSA. To further increase the visibility and simplify the reuse of public datasets, we integrated a novel search function into ReactomeGSA that enables users to search for public datasets across both supported resources. Finally, we completely re-developed ReactomeGSA's web-frontend and R/Bioconductor package to support the new search and loading features, and greatly simplify the use of ReactomeGSA.
AVAILABILITY: The new ReactomeGSA web frontend is available at https://www.reactome.org/gsa with an built-in, interactive tutorial. The ReactomeGSA R package (https://bioconductor.org/packages/release/bioc/html/ReactomeGSA.html) is available through Bioconductor and shipped with detailed documentation and vignettes. The grein_loader Python application is available through the Python Package Index (pypi). The complete source code for all applications is available on GitHub at https://github.com/grisslab/grein_loader and https://github.com/reactome.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btae338
Sci Signal. 2024 May 28. 17(838): eado6266

Hippo and PI5P4K signaling intersect to control the transcriptional activation of YAP.

Lavinia Palamiuc, Jared L Johnson, Zeinab Haratipour, Ryan M Loughran, Woong Jae Choi, Gurpreet K Arora, Vivian Tieu, Kyanh Ly, Alicia Llorente, Sophia Crabtree, Jenny C Y Wong, Archna Ravi, Thorsten Wiederhold, Rabi Murad, Raymond D Blind, Brooke M Emerling.

Phosphoinositides are essential signaling molecules. The PI5P4K family of phosphoinositide kinases and their substrates and products, PI5P and PI4,5P2, respectively, are emerging as intracellular metabolic and stress sensors. We performed an unbiased screen to investigate the signals that these kinases relay and the specific upstream regulators controlling this signaling node. We found that the core Hippo pathway kinases MST1/2 phosphorylated PI5P4Ks and inhibited their signaling in vitro and in cells. We further showed that PI5P4K activity regulated several Hippo- and YAP-related phenotypes, specifically decreasing the interaction between the key Hippo proteins MOB1 and LATS and stimulating the YAP-mediated genetic program governing epithelial-to-mesenchymal transition. Mechanistically, we showed that PI5P interacted with MOB1 and enhanced its interaction with LATS, thereby providing a signaling connection between the Hippo pathway and PI5P4Ks. These findings reveal how these two important evolutionarily conserved signaling pathways are integrated to regulate metazoan development and human disease.

DOI: https://doi.org/10.1126/scisignal.ado6266
bioRxiv. 2024 May 13. pii: 2024.05.09.593171. [Epub ahead of print]

Mechanical activation of VE-cadherin stimulates AMPK to increase endothelial cell metabolism and vasodilation.

Nicholas M Cronin, Logan W Dawson, Kris A DeMali.

Endothelia cells respond to mechanical force by stimulating cellular signaling, but how these pathways are linked to elevations in cell metabolism and whether metabolism supports the mechanical response remains poorly understood. Here, we show that application of force to VE-cadherin stimulates liver kinase B1 (LKB1) to activate AMP-activated protein kinase (AMPK), a master regulator of energy homeostasis. VE-cadherin stimulated AMPK increases eNOS activity and localization to the plasma membrane as well as reinforcement of the actin cytoskeleton and cadherin adhesion complex, and glucose uptake. We present evidence for the increase in metabolism being necessary to fortify the adhesion complex, actin cytoskeleton, and cellular alignment. Together these data extend the paradigm for how mechanotransduction and metabolism are linked to include a connection to vasodilation, thereby providing new insight into how diseases involving contractile, metabolic, and vasodilatory disturbances arise.

DOI: https://doi.org/10.1101/2024.05.09.593171
bioRxiv. 2024 May 14. pii: 2024.05.13.594044. [Epub ahead of print]

Hyperactive mTORC1/4EBP1 Signaling Dysregulates Proteostasis and Accelerates Cardiac Aging.

Weronika Zarzycka, Kamil A Kobak, Catherine J King, Frederick F Peelor, Benjamin F Miller, Ying Ann Chiao.

The mechanistic target of rapamycin complex 1 (mTORC1) has a major impact on aging by regulation of proteostasis. It is well established that mTORC1 signaling is hyperactivated with aging and age-related diseases. Previous studies have shown that partial inhibition of mTOR signaling by rapamycin reverses the age-related decline in cardiac function and structure in old mice. However, the downstream signaling pathways involved in this protection against cardiac aging have not been established. TORC1 phosphorylates 4E-binding protein 1 (4EBP1) to promote the initiation of cap-dependent translation. The aim of this project is to examine the role of the mTORC1/4EBP1 axis in age-related cardiac dysfunction. We utilized a whole-body 4EBP1 KO mouse model, which mimics a hyperactive 4EBP1/eIF4E axis, to investigate the effects of hyperactive mTORC1/4EBP1 axis in cardiac aging. Echocardiographic measurements revealed that young 4EBP1 KO mice have no difference in cardiac function at baseline compared to WT mice. Interestingly, middle-aged (14-15-month-old) 4EBP1 KO mice show impaired diastolic function and myocardial performance compared to age-matched WT mice and their diastolic function and myocardial performance are at similar levels as 24-month-old WT mice, suggesting that 4EBP1 KO mice experience accelerated cardiac aging. Old 4EBP1 KO mice show further declines in systolic and diastolic function compared to middle-aged 4EBP1 KO mice and have worse systolic and diastolic function than age-matched old WT mice. Gene expression levels of heart failure markers are not different between 4EBP1 KO and WT mice at these advanced ages. However, ribosomal biogenesis and overall protein ubiquitination are significantly increased in 4EBP1 KO mice when compared to WT, which suggests dysregulated proteostasis. Together, these results show that a hyperactive 4EBP1/eIF4E axis accelerates cardiac aging, potentially by dysregulating proteostasis.

DOI: https://doi.org/10.1101/2024.05.13.594044
bioRxiv. 2024 May 18. pii: 2024.05.10.593551. [Epub ahead of print]

Duration of Morning Hyperinsulinemia is Key to the Enhancement of Hepatic Glucose Uptake and Glycogen Storage Later in the Day.

Hannah L Waterman, Mary Courtney Moore, Marta S Smith, Ben Farmer, Melanie Scott, Dale S Edgerton, Alan D Cherrington.

The second meal phenomenon refers to the improvement in glucose tolerance seen following a second identical meal. We previously showed that 4 hours of morning (AM) hyperinsulinemia, but not hyperglycemia, enhanced hepatic glucose uptake (HGU) and glycogen storage during an afternoon (PM) hyperinsulinemic hyperglycemic clamp (HIHG). Our current aim was to determine if the duration or pattern of morning hyperinsulinemia is important for the PM response to a HIHG clamp. To determine this, we administered the same total amount of insulin either over 2h in the first half of the morning (Ins2h-A), over 2h in the 2nd half of the morning (Ins2h-B), or over the entire 4h (Ins4h) of the morning. In the 4h PM period, all three groups had 4x basal insulin, 2x basal glycemia, and portal glucose infusion to simulate a meal. During the PM clamp, there was a marked increase in the mean hepatic glucose uptake and hepatic glycogen synthesis in the Ins4h group compared to the Ins2h-A and Ins2h-B groups, despite matched hepatic glucose and insulin loads. Thus, the longer duration (Ins4h) of mild hyperinsulinemia in the morning seems to be the key to much greater liver glucose uptake during the PM clamp.
New and noteworthy: Morning insulin exposure primes the liver for increased hepatic glucose uptake and glycogen storage during a subsequent meal. This study addressed whether the pattern and/or duration of meal-associated insulin delivery in the morning influences insulin's ensuing priming effect. We found that in the morning, a smaller amount of insulin delivered over a longer duration is more effective than a larger amount over a shorter duration in improving liver glucose metabolism in the afternoon.

DOI: https://doi.org/10.1101/2024.05.10.593551
Res Sq. 2024 May 17. pii: rs.3.rs-4353037. [Epub ahead of print]

Joint multi-omics discriminant analysis with consistent representation learning using PANDA.

Jia Wu, Muhammad Aminu, Lingzhi Hong, Natalie Vokes, Stephanie Schmidt, Maliazurina B Saad, Bo Zhu, Xiuning Li, Tina Cascone, Ajay Sheshadri, David Jaffray, Andrew Futreal, Jack Lee, Lauren Byers, Don Gibbons, John Heymach, Ken Chen, Chao Cheng, Jianjun Zhang, Bo Wang.

Integrative multi-omics analysis provides deeper insight and enables better and more realistic modeling of the underlying biology and causes of diseases than does single omics analysis. Although several integrative multi-omics analysis methods have been proposed and demonstrated promising results in integrating distinct omics datasets, inconsistent distribution of the different omics data, which is caused by technology variations, poses a challenge for paired integrative multi-omics methods. In addition, the existing discriminant analysis-based integrative methods do not effectively exploit correlation and consistent discriminant structures, necessitating a compromise between correlation and discrimination in using these methods. Herein we present PAN-omics Discriminant Analysis (PANDA), a joint discriminant analysis method that seeks omics-specific discriminant common spaces by jointly learning consistent discriminant latent representations for each omics. PANDA jointly maximizes between-class and minimizes within-class omics variations in a common space and simultaneously models the relationships among omics at the consistency representation and cross-omics correlation levels, overcoming the need for compromise between discrimination and correlation as with the existing integrative multi-omics methods. Because of the consistency representation learning incorporated into the objective function of PANDA, this method seeks a common discriminant space to minimize the differences in distributions among omics, can lead to a more robust latent representations than other methods, and is against the inconsistency of the different omics. We compared PANDA to 10 other state-of-the-art multi-omics data integration methods using both simulated and real-world multi-omics datasets and found that PANDA consistently outperformed them while providing meaningful discriminant latent representations. PANDA is implemented using both R and MATLAB, with codes available at https://github.com/WuLabMDA/PANDA.

DOI: https://doi.org/10.21203/rs.3.rs-4353037/v1
Sci Rep. 2024 05 29. 14(1): 12355

Unveiling gene regulatory networks during cellular state transitions without linkage across time points.

Ruosi Wan, Yuhao Zhang, Yongli Peng, Feng Tian, Ge Gao, Fuchou Tang, Jinzhu Jia, Hao Ge.

Time-stamped cross-sectional data, which lack linkage across time points, are commonly generated in single-cell transcriptional profiling. Many previous methods for inferring gene regulatory networks (GRNs) driving cell-state transitions relied on constructing single-cell temporal ordering. Introducing COSLIR (COvariance restricted Sparse LInear Regression), we presented a direct approach to reconstructing GRNs that govern cell-state transitions, utilizing only the first and second moments of samples between two consecutive time points. Simulations validated COSLIR's perfect accuracy in the oracle case and demonstrated its robust performance in real-world scenarios. When applied to single-cell RT-PCR and RNAseq datasets in developmental biology, COSLIR competed favorably with existing methods. Notably, its running time remained nearly independent of the number of cells. Therefore, COSLIR emerges as a promising addition to GRN reconstruction methods under cell-state transitions, bypassing the single-cell temporal ordering to enhance accuracy and efficiency in single-cell transcriptional profiling.

DOI: https://doi.org/10.1038/s41598-024-62850-1
Nat Metab. 2024 May;6(5): 847-860

Hippo-YAP/TAZ signalling coordinates adipose plasticity and energy balance by uncoupling leptin expression from fat mass.

Sungwoo Choi, Ju-Gyeong Kang, Yen T H Tran, Sun-Hye Jeong, Kun-Young Park, Hyemi Shin, Young Hoon Kim, Myungsun Park, Hahn Nahmgoong, Taejun Seol, Haeyon Jeon, Yeongmin Kim, Sanghee Park, Hee-Joo Kim, Min-Seob Kim, Xiaoxu Li, Maroun Bou Sleiman, Eries Lee, Jinhyuk Choi, David Eisenbarth, Sang Heon Lee, Suhyeon Cho, David D Moore, Johan Auwerx, Il-Young Kim, Jae Bum Kim, Jong-Eun Park, Dae-Sik Lim, Jae Myoung Suh.

Adipose tissues serve as an energy reservoir and endocrine organ, yet the mechanisms that coordinate these functions remain elusive. Here, we show that the transcriptional coregulators, YAP and TAZ, uncouple fat mass from leptin levels and regulate adipocyte plasticity to maintain metabolic homeostasis. Activating YAP/TAZ signalling in adipocytes by deletion of the upstream regulators Lats1 and Lats2 results in a profound reduction in fat mass by converting mature adipocytes into delipidated progenitor-like cells, but does not cause lipodystrophy-related metabolic dysfunction, due to a paradoxical increase in circulating leptin levels. Mechanistically, we demonstrate that YAP/TAZ-TEAD signalling upregulates leptin expression by directly binding to an upstream enhancer site of the leptin gene. We further show that YAP/TAZ activity is associated with, and functionally required for, leptin regulation during fasting and refeeding. These results suggest that adipocyte Hippo-YAP/TAZ signalling constitutes a nexus for coordinating adipose tissue lipid storage capacity and systemic energy balance through the regulation of adipocyte plasticity and leptin gene transcription.

DOI: https://doi.org/10.1038/s42255-024-01045-4
Sci Rep. 2024 May 31. 14(1): 12542

PIK3CA mutations in endocrine-resistant breast cancer.

Caroline Schagerholm, Stephanie Robertson, Hosein Toosi, Emmanouil G Sifakis, Johan Hartman.

  Around 75% of breast cancer (BC) patients have tumors expressing the predictive biomarker estrogen receptor α (ER) and are offered endocrine therapy. One-third eventually develop endocrine resistance, a majority with retained ER expression. Mutations in the phosphatidylinositol bisphosphate 3-kinase (PI3K) catalytic subunit encoded by PIK3CA is a proposed resistance mechanism and a pharmacological target in the clinical setting. Here we explore the frequency of PIK3CA mutations in endocrine-resistant BC before and during treatment and correlate to clinical features. Patients with ER-positive (ER +), human epidermal growth factor receptor 2 (HER2)-negative primary BC with an ER + relapse within 5 years of ongoing endocrine therapy were retrospectively assessed. Tissue was collected from primary tumors (n = 58), relapse tumors (n = 54), and tumor-free lymph nodes (germline controls, n = 62). Extracted DNA was analyzed through panel sequencing. Somatic mutations were observed in 50% (31/62) of the patients, of which 29% occurred outside hotspot regions. The presence of PIK3CA mutations was significantly associated with nodal involvement and mutations were more frequent in relapse than primary tumors. Our study shows the different PIK3CA mutations in endocrine-resistant BC and their fluctuations during therapy. These results may aid investigations of response prediction, facilitating research deciphering the mechanisms of endocrine resistance.

Keywords:  Breast cancer; Endocrine-resistance; PIK3CA

DOI:  https://doi.org/10.1038/s41598-024-62664-1