bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–03–16
fifteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Defining the Protein Phosphatase 2A (PP2A) Subcomplexes That Regulate FoxO Transcription Factor Localization.
  2. Adapting systems biology to address the complexity of human disease in the single-cell era.
  3. Enhancing our understanding of endothelial cells.
  4. Direct sensing of dietary ω-6 linoleic acid through FABP5-mTORC1 signaling.
  5. Genetically encoded protein oscillators for FM streaming of single-cell data.
  6. Dynamic Modeling of Cell Cycle Arrest Through Integrated Single-Cell and Mathematical Modelling Approaches.
  7. Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment.
  8. High-dimensional signalling analysis of organoids.
  9. Integration of therapeutic cargo into the human genome with programmable type V-K CAST.
  10. Metaboloepigenetics: Role in the Regulation of Flow-Mediated Endothelial (Dys)Function and Atherosclerosis.
  11. Multiplexed dynamic control of temperature to probe and observe mammalian cells.
  12. SR-A3 suppresses AKT activation to protect against MAFLD by inhibiting XIAP-mediated PTEN degradation.
  13. Protein profiles predict treatment responses to the PI3K inhibitor umbralisib in patients with chronic lymphocytic leukemia.
  14. Subcellular proteomics and iPSC modeling uncover reversible mechanisms of axonal pathology in Alzheimer's disease.
  15. Protocol for monitoring the endosomal trafficking of membrane proteins in mammalian cells.
  1. Cells. 2025 Feb 27. pii: 342. [Epub ahead of print]14(5):
    Defining the Protein Phosphatase 2A (PP2A) Subcomplexes That Regulate FoxO Transcription Factor Localization.
    Adeline M Luperchio, Daniel J Salamango.
      The family of forkhead box O (FoxO) transcription factors regulate cellular processes involved in glucose metabolism, stress resistance, DNA damage repair, and tumor suppression. FoxO transactivation activity is tightly regulated by a complex network of signaling pathways and post-translational modifications. While it has been well established that phosphorylation promotes FoxO cytoplasmic retention and inactivation, the mechanism underlying dephosphorylation and nuclear translocation is less clear. Here, we investigate the role of protein phosphatase 2A (PP2A) in regulating this process. We demonstrate that PP2A and AMP-activated protein kinase (AMPK) combine to regulate nuclear translocation of multiple FoxO family members following inhibition of metabolic signaling or induction of oxidative stress. Moreover, chemical inhibitor studies indicate that nuclear accumulation of FoxO proteins occurs through inhibition of nuclear export as opposed to promoting nuclear import as previously speculated. Functional, genetic, and biochemical studies combine to identify the PP2A complexes that regulate FoxO nuclear translocation, and the binding motif required. Mutating the FoxO-PP2A interface to enhance or diminish PP2A binding alters nuclear translocation kinetics accordingly. Together, these studies shed light on the molecular mechanisms regulating FoxO nuclear translocation and provide insights into how FoxO regulation is integrated with metabolic and stress-related stimuli.
    Keywords:  AKT; FoxO; PI3K; PP2A; subcellular localization; transcription factor; tumor suppressors
    DOI:  https://doi.org/10.3390/cells14050342
  2. Nat Rev Genet. 2025 Mar 10.
    Adapting systems biology to address the complexity of human disease in the single-cell era.
    David S Fischer, Martin A Villanueva, Peter S Winter, Alex K Shalek.
      Systems biology aims to achieve holistic insights into the molecular workings of cellular systems through iterative loops of measurement, analysis and perturbation. This framework has had remarkable success in unicellular model organisms, and recent experimental and computational advances - from single-cell and spatial profiling to CRISPR genome editing and machine learning - have raised the exciting possibility of leveraging such strategies to prevent, diagnose and treat human diseases. However, adapting systems-inspired approaches to dissect human disease complexity is challenging, given that discrepancies between the biological features of human tissues and the experimental models typically used to probe function (which we term 'translational distance') can confound insight. Here we review how samples, measurements and analyses can be contextualized within overall multiscale human disease processes to mitigate data and representation gaps. We then examine ways to bridge the translational distance between systems-inspired human discovery loops and model system validation loops to empower precision interventions in the era of single-cell genomics.
    DOI:  https://doi.org/10.1038/s41576-025-00821-6
  3. Elife. 2025 Mar 11. pii: e106133. [Epub ahead of print]14
    Enhancing our understanding of endothelial cells.
    Guillermo Luxán.
      What determines whether an endothelial cell becomes part of an artery, a vein or a capillary?
    Keywords:  arterial enhancer; arterial gene transcription; arteriovenous differentiation; developmental biology; genetics; genomics; mouse; transcriptional regulation; vascular development; zebrafish
    DOI:  https://doi.org/10.7554/eLife.106133
  4. Science. 2025 Mar 14. 387(6739): eadm9805
    Direct sensing of dietary ω-6 linoleic acid through FABP5-mTORC1 signaling.
    Nikos Koundouros, Michal J Nagiec, Nayah Bullen, Evan K Noch, Guillermo Burgos-Barragan, Zhongchi Li, Long He, Sungyun Cho, Bobak Parang, Dominique Leone, Eleni Andreopoulou, John Blenis.
      Diet influences macronutrient availability to cells, and although mechanisms of sensing dietary glucose and amino acids are well characterized, less is known about sensing lipids. We defined a nutrient signaling mechanism involving fatty acid-binding protein 5 (FABP5) and mechanistic target of rapamycin complex 1 (mTORC1) that is activated by the essential polyunsaturated fatty acid (PUFA) ω-6 linoleic acid (LA). FABP5 directly bound to the regulatory-associated protein of mTOR (Raptor) to enhance formation of functional mTORC1 and substrate binding, ultimately converging on increased mTOR signaling and proliferation. The amounts of FABP5 protein were increased in tumors and serum from triple-negative compared with those from receptor-positive breast cancer patients, which highlights its potential role as a biomarker that mediates cellular responses to ω-6 LA intake in this disease subtype.
    DOI:  https://doi.org/10.1126/science.adm9805
  5. bioRxiv. 2025 Feb 28. pii: 2025.02.28.640587. [Epub ahead of print]
    Genetically encoded protein oscillators for FM streaming of single-cell data.
    Rohith Rajasekaran, Thomas M Galateo, Zhejing Xu, Dennis T Bolshakov, Elliott W Z Weix, Scott M Coyle.
      Radios and cellphones use frequency modulation (FM) of an oscillating carrier signal to reliably transmit multiplexed data while rejecting noise. Here, we establish a biochemical analogue of this paradigm using genetically encoded protein oscillators (GEOs) as carrier signals in circuits that enable continuous, real-time FM streaming of single-cell data. GEOs are constructed from evolutionarily diverse MinDE-family ATPase and activator modules that generate fast synthetic protein oscillations when co-expressed in human cells. These oscillations serve as a single-cell carrier signal, with frequency and amplitude controlled by GEO component levels and activity. We systematically characterize 169 ATPase/activator GEO pairs and engineer composite GEOs with multiple competing activators to develop a comprehensive platform for waveform programming. Using these principles, we design circuits that modulate GEO frequency in response to cellular activity and decode their responses using a calibrated machine-learning model to demonstrate sensitive, real-time FM streaming of transcription and proteasomal degradation dynamics in single cells. GEOs establish a dynamically controllable biochemical carrier signal, unlocking noise-resistant FM data-encoding paradigms that open new avenues for dynamic single-cell analysis.
    DOI:  https://doi.org/10.1101/2025.02.28.640587
  6. bioRxiv. 2025 Feb 26. pii: 2025.02.20.639240. [Epub ahead of print]
    Dynamic Modeling of Cell Cycle Arrest Through Integrated Single-Cell and Mathematical Modelling Approaches.
    Javiera Cortés-Ríos, Maria Rodriguez-Fernandez, Peter K Sorger, Fabian Fröhlich.
      Highly multiplexed imaging assays allow simultaneous quantification of multiple protein and phosphorylation markers, providing a static snapshots of cell types and states. Pseudo-time techniques can transform these static snapshots of unsynchronized cells into dynamic trajectories, enabling the study of dynamic processes such as development trajectories and the cell cycle. Such ordering also enables training of mathematical models on these data, but technical challenges have hitherto made it difficult to integrate multiple experimental conditions, limiting the predictive power and insights these models can generate. In this work, we propose data processing and model training approaches for integrating multiplexed, multi-condition immunofluorescence data with mathematical modelling. We devise training strategies that are applicable to datasets where cells exhibit oscillatory as well as arrested dynamics and use them to train a cell cycle model on a dataset of MCF-10A mammary epithelial exposed to cell-cycle arresting small molecules. We validate the model by investigating predicted growth factor sensitivities and responses to inhibitors of cells at different initial conditions. We anticipate that our framework will generalise to other highly multiplexed measurement techniques such as mass-cytometry, rendering larger bodies of data accessible to dynamic modelling and paving the way to deeper biological insights.
    Author Summary: Advanced imaging techniques allow us to see detailed pictures of different proteins and cell changes. By using computational algorithms, we turn these static pictures into dynamic sequences to understand processes like the cell cycle better. However, combining data from different experiments is difficult and limits how well our models can predict outcomes. This study introduces new ways to process data and train models to handle complex data from various conditions.The approach is tested by using data from untreated and treated cells to create a model of the cell cycle. This model was then checked for accuracy by seeing how well it could predict how cells respond to growth factors and drugs from different starting points. In the future, this method could be used with other data types, allowing for more detailed and accurate models of cellular behavior.
    DOI:  https://doi.org/10.1101/2025.02.20.639240
  7. bioRxiv. 2025 Feb 27. pii: 2025.02.24.640007. [Epub ahead of print]
    Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment.
    Lambda Moses, Alik Huseynov, Joseph M Rich, Lior Pachter.
      SpatialFeatureExperiment is a Bioconductor package that leverages the versatility of Simple Features for spatial data analysis and SpatialExperiment for single-cell -omics to provide an expansive and convenient S4 class for working with spatial -omics data. SpatialFeatureExperiment can be used to store and analyze a variety of spatial -omics data types, including data from the Visium, Xenium, MERFISH, SeqFish, and Slide-seq platforms, bringing spatial operations to the SingleCellExperiment ecosystem.
    DOI:  https://doi.org/10.1101/2025.02.24.640007
  8. Curr Opin Cell Biol. 2025 Mar 09. pii: S0955-0674(25)00026-2. [Epub ahead of print]94 102488
    High-dimensional signalling analysis of organoids.
    Aurélie Dobric, Christopher J Tape.
      Cellular phenotypes are regulated by dynamic signalling processes that involve proteins, post-translational modifications, epigenetic events, and transcriptional responses. Functional perturbation studies are required to understand cell signalling mechanisms and organoids have recently emerged as scalable biomimetic models amenable to large-scale perturbation. Here, we review the recent advances in high-dimensional analysis of cell signalling in organoids. Single-cell technologies provide cell-type specific analysis of multiple biochemical modalities, enabling a deeper understanding of the signalling mechanisms driving cell-fate dynamics. Emerging multimodal techniques are further revealing coordination between signalling layers and are poised to increase our mechanistic understanding of cell signalling.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102488
  9. Nat Commun. 2025 Mar 13. 16(1): 2427
    Integration of therapeutic cargo into the human genome with programmable type V-K CAST.
    Jason Liu, Daniela S Aliaga Goltsman, Lisa M Alexander, Khak Khak Khayi, Jennifer H Hong, Drew T Dunham, Christine A Romano, Morayma M Temoche-Diaz, Shailaja Chadha, Rodrigo Fregoso Ocampo, Jennifer Oki-O'Connell, Owen P Janson, Keirstinne Turcios, Liliana Gonzalez-Osorio, Jared Muysson, Jenat Rahman, Sarah M Laperriere, Audra E Devoto, Cindy J Castelle, Cristina N Butterfield, Gregory J Cost, Christopher T Brown, Brian C Thomas.
      CRISPR-associated (Cas) transposases (CAST) are RNA-guided systems capable of programmable integration of large segments of DNA without creating double-strand breaks. Engineered Cascade CAST function in human cells but are challenging to deploy due to the complexity of the targeting components. Unlike Cascade, which require three Cas proteins, type V-K CAST require a single Cas12k effector for targeting. Here, we show that compact type V-K CAST from uncultivated microbes are repurposable for programmable DNA integration into the genome of human cells. Engineering for nuclear localization and function enables integration of a therapeutically relevant transgene at a safe-harbor site in multiple human cell types. Notably, off-targets are rare events reproducibly found in specific genomic regions. These CAST advancements are expected to accelerate applications of genome editing to therapeutic development, biotechnology, and synthetic biology.
    DOI:  https://doi.org/10.1038/s41467-025-57416-2
  10. Cells. 2025 Mar 05. pii: 378. [Epub ahead of print]14(5):
    Metaboloepigenetics: Role in the Regulation of Flow-Mediated Endothelial (Dys)Function and Atherosclerosis.
    Francisco Santos, Hashum Sum, Denise Cheuk Lee Yan, Alison C Brewer.
      Endothelial dysfunction is the main initiating factor in atherosclerosis. Through mechanotransduction, shear stress regulates endothelial cell function in both homeostatic and diseased states. Accumulating evidence reveals that epigenetic changes play critical roles in the etiology of cardiovascular diseases, including atherosclerosis. The metabolic regulation of epigenetics has emerged as an important factor in the control of gene expression in diseased states, but to the best of our knowledge, this connection remains largely unexplored in endothelial dysfunction and atherosclerosis. In this review, we (1) summarize how shear stress (or flow) regulates endothelial (dys)function; (2) explore the epigenetic alterations that occur in the endothelium in response to disturbed flow; (3) review endothelial cell metabolism under different shear stress conditions; and (4) suggest mechanisms which may link this altered metabolism to the regulation of the endothelial epigenome by modulations in metabolite availability. We believe that metabolic regulation plays an important role in endothelial epigenetic reprogramming and could pave the way for novel metabolism-based therapeutic strategies.
    Keywords:  atherosclerosis; endothelial dysfunction; epigenetics; mechanotransduction; metabolism; metaboloepigenetics; shear stress
    DOI:  https://doi.org/10.3390/cells14050378
  11. Cell Syst. 2025 Mar 07. pii: S2405-4712(25)00067-5. [Epub ahead of print] 101234
    Multiplexed dynamic control of temperature to probe and observe mammalian cells.
    William Benman, Pavan Iyengar, Thomas R Mumford, Zikang Huang, Manya Kapoor, Grace Liu, Lukasz J Bugaj.
      Temperature is an important biological stimulus, yet there is a lack of approaches to modulate the temperature of biological samples in a dynamic and high-throughput manner. The thermoPlate is a device for programmable control of temperature in a 96-well plate, compatible with cell culture and microscopy. The thermoPlate maintains feedback control of temperature independently in each well, with minutes-scale heating and cooling through ΔT = 15-20°C. We first used the thermoPlate to characterize the rapid temperature-dependent phase separation of a synthetic elastin-like polypeptide (ELP53). We then examined stress granule (SG) formation in response to dynamic heat stress, revealing adaptation of SGs to persistent heat and formation of a memory of stress that prevented SG formation in response to subsequent heat shocks. The capabilities and open-source nature of the thermoPlate will empower the study and engineering of a wide range of thermoresponsive phenomena. A record of this paper's transparent peer review process is included in the Supplemental information.
    Keywords:  adaptation; devices; elastin-like polypeptides; heat shock; open source; stress dynamics; stress granules; stress signaling; temperature modulation; thermogenetics
    DOI:  https://doi.org/10.1016/j.cels.2025.101234
  12. Nat Commun. 2025 Mar 11. 16(1): 2430
    SR-A3 suppresses AKT activation to protect against MAFLD by inhibiting XIAP-mediated PTEN degradation.
    Pingping Lai, Guolin Miao, Yinqi Zhao, Yufei Han, Yanwei Li, Yiran Liu, Jiabao Guo, Wenxi Zhang, Xin Guo, Yitong Xu, Lianxin Zhang, Gonglie Chen, Zihao Zhou, Si Mei, Jingxuan Chen, Jinxuan Chen, Luzheng Xu, Chong Zhang, Yang Ding, Xiaoguang Dou, Shengmei Wen, Sin Man Lam, Guanghou Shui, Yuhui Wang, Wei Huang, Dongyu Zhao, Xunde Xian.
      Scavenger receptor class A member 3 (SR-A3) is implicated in metabolic diseases; however, the relationship between SR-A3 and metabolic dysfunction-associated fatty liver disease (MAFLD) has not been documented. Here, we show that hepatic SR-A3 expression is significantly reduced in human and animal models in the context of MAFLD. Genetic inhibition of SR-A3 in hamsters elicits hyperlipidemia, hyperglycemia, insulin resistance, and hepatic steatosis under chow-diet condition, yet escalates in diet-induced MAFLD. Mechanistically, SR-A3 ablation enhances E3 ligase XIAP-mediated proteasomal ubiquitination of PTEN, leading to AKT hyperactivation. By contrast, hepatic overexpression of human SR-A3 is sufficient to attenuate metabolic disorders in WT hamsters fed a high-fat-high-cholesterol diet and ob/ob mice via suppressing the XIAP/PTEN/AKT axis. In parallel, pharmacological intervention by PTEN agonist oroxin B or lipid lowering agent ezetimibe differentially corrects MAFLD in hamsters.
    DOI:  https://doi.org/10.1038/s41467-025-57585-0
  13. Clin Cancer Res. 2025 Mar 14.
    Protein profiles predict treatment responses to the PI3K inhibitor umbralisib in patients with chronic lymphocytic leukemia.
    Yanping Yin, Haifeng Xu, Liye He, Jennifer R Brown, Anthony R Mato, Tero Aittokallio, Sigrid S Skånland.
       PURPOSE: The management of chronic lymphocytic leukemia (CLL) has significantly improved with targeted therapies. However, many patients experience a suboptimal response. To optimally select the best therapy, predictive biomarkers are necessary. Here, we used the PI3K inhibitor umbralisib as a model to (i) understand how targeted treatment affects cell signaling and immunophenotypes in responders and non-responders; (ii) identify molecular features that predict individual treatment responses; and (iii) suggest alternative treatment options for the non-responders.
    EXPERIMENTAL DESIGN: We performed functional phenotyping of CLL cells from patients enrolled in two clinical trials with umbralisib, administered either as a monotherapy (NCT02742090, n=55) or in combination with the BTK inhibitor acalabrutinib (NCT04624633, n=12).
    RESULTS: We found that umbralisib monotherapy led to significant changes in (phospho)protein levels, including AKT (pS473), in responders but not in non-responders. Furthermore, the proportion of cytotoxic natural killer cells increased at the end of study, but only in responders, suggesting a role in the anti-tumor response. To identify molecular predictors of response, we used the baseline levels of 30 (phospho)proteins in the monotherapy cohort as input features for a machine learning model, which achieved a significant prediction accuracy in cross-validation and maintained its predictive power in the combination cohort. Drug sensitivity profiling of the CLL cells at baseline suggested that PI3K + Bcl-2 inhibitors are effective in umbralisib non-responders.
    CONCLUSIONS: Functional phenotyping reveals differential cellular responses to umbralisib treatment in responders and non-responders; predicts treatment response of individual CLL patients; and suggests alternative treatment options for the non-responders.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-24-2911
  14. Nat Aging. 2025 Mar 10.
    Subcellular proteomics and iPSC modeling uncover reversible mechanisms of axonal pathology in Alzheimer's disease.
    Yifei Cai, Jean Kanyo, Rashaun Wilson, Shveta Bathla, Pablo Leal Cardozo, Lei Tong, Shanshan Qin, Lukas A Fuentes, Iguaracy Pinheiro-de-Sousa, Tram Huynh, Liyuan Sun, Mohammad Shahid Mansuri, Zichen Tian, Hao-Ran Gan, Amber Braker, Hoang Kim Trinh, Anita Huttner, TuKiet T Lam, Evangelia Petsalaki, Kristen J Brennand, Angus C Nairn, Jaime Grutzendler.
      Dystrophic neurites (also termed axonal spheroids) are found around amyloid deposits in Alzheimer's disease (AD), where they impair axonal electrical conduction, disrupt neural circuits and correlate with AD severity. Despite their importance, the mechanisms underlying spheroid formation remain incompletely understood. To address this, we developed a proximity labeling approach to uncover the proteome of spheroids in human postmortem and mouse brains. Additionally, we established a human induced pluripotent stem cell (iPSC)-derived AD model enabling mechanistic investigation and optical electrophysiology. These complementary approaches revealed the subcellular molecular architecture of spheroids and identified abnormalities in key biological processes, including protein turnover, cytoskeleton dynamics and lipid transport. Notably, the PI3K/AKT/mTOR pathway, which regulates these processes, was activated in spheroids. Furthermore, phosphorylated mTOR levels in spheroids correlated with AD severity in humans. Notably, mTOR inhibition in iPSC-derived neurons and mice ameliorated spheroid pathology. Altogether, our study provides a multidisciplinary toolkit for investigating mechanisms and therapeutic targets for axonal pathology in neurodegeneration.
    DOI:  https://doi.org/10.1038/s43587-025-00823-3
  15. STAR Protoc. 2025 Mar 08. pii: S2666-1667(25)00092-9. [Epub ahead of print]6(1): 103686
    Protocol for monitoring the endosomal trafficking of membrane proteins in mammalian cells.
    Peng Xu, Jianbo Yue.
      Here, we present a protocol to study epidermal growth factor (EGF) receptor (EGFR) or transferrin trafficking in mammalian cells. We describe steps for using fluorescent ligands or antibodies, confocal imaging, and quantitative analysis to track their movement. We detail procedures for cell culture preparation, labeling membrane proteins, optimizing imaging, and isolating cell lysates for the biochemical analysis of EGFR degradation after EGF treatment. This protocol is adaptable to various cell types and for assessing genetic or pharmacological impacts on endosomal trafficking. For complete details on the use and execution of this protocol, please refer to Ye et al.,1 Ye et al.,2 and Wang et al.3.
    Keywords:  Cell culture; Cell-based assays; Microscopy; Signal transduction
    DOI:  https://doi.org/10.1016/j.xpro.2025.103686
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