bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–06–01
eighteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Differential activation of the inositol 5-phosphatase SHIP2 by EGF and insulin signaling pathways.
  2. Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics.
  3. Accessible and accurate cytometry analysis of adherent cells using fluorescence microscopes.
  4. Methods for multiplexing single-cell multi-omics.
  5. Screening for variable drug responses using human iPSC cohorts.
  6. Optogenetic control of a GEF of RhoA uncovers a signaling switch from retraction to protrusion.
  7. Practical guide to fluorescence lifetime imaging microscopy.
  8. YTHDF1 differentiates the contributing roles of mTORC1 in aging.
  9. mTOR pathway diseases: challenges and opportunities from bench to bedside and the mTOR node.
  10. Small Molecule-Induced Alterations of Protein Polyubiquitination Revealed by Mass-Spectrometric Ubiquitome Analysis.
  11. Endosomal H2O2 Molecules Act as Signaling Mediators in Akt/PKB Activation.
  12. hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments.
  13. PI3K in the VMH Attenuates Diet-Induced Obesity and Participates in the Effects of E2 on Energy Expenditure in Mice.
  14. Assessing and improving reliability of neighbor embedding methods: a map-continuity perspective.
  15. Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells.
  16. WNK1 signalling regulates amino acid transport and mTORC1 activity to sustain acute myeloid leukaemia growth.
  17. Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-Seq Data Analysis.
  18. Adipogenic Differentiation Assay for the Study of Insulin Signaling.
  1. J Biol Chem. 2025 May 22. pii: S0021-9258(25)02125-8. [Epub ahead of print] 110275
    Differential activation of the inositol 5-phosphatase SHIP2 by EGF and insulin signaling pathways.
    Amir Damouni, Dániel J Tóth, Szilvia Barsi, Dániel Károly Nagy, Alexander Kasbary, László Hunyady, Miklós Cserző, Péter Várnai.
      The importance of phosphatidylinositol 3,4,5- trisphosphate (PIP3) in cell signaling has been well established. Despite phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] emerging as an actor independent of PIP3, its exact signaling role remains poorly understood and the precise dynamics of PI(3,4)P2 and PIP3 upon receptor tyrosine kinase (RTK) stimulation are still inadequately investigated. In this study, we employed bioluminescence resonance energy transfer (BRET) sensors to monitor plasma membrane phosphoinositide (PIP) dynamics in HEK293-derived and HeLa cells following stimulation with epidermal growth factor (EGF) and insulin. Our findings reveal significant differences in PIP regulation: the increase in PI(3,4)P2 compared to PIP3 was larger with EGF stimulation relative to insulin. Using siRNA-mediated knockdown, we identified SH2-domain containing inositol polyphosphate 5-phosphatase 2 (SHIP2) as the key enzyme responsible for PI(3,4)P2 production in the EGF pathway, which was further supported by a bioinformatics analysis. Moreover, we detected increased phosphorylation at two tyrosine sites in SHIP2 upon EGF stimulation which was shown to be dependent on PI3K activation and PLC-induced calcium signal. These findings help refine our understanding of receptor-specific phosphoinositide dynamics and the enzymatic machinery involved as well as their potential influence on downstream cellular responses.
    Keywords:  SHIP2; bioluminescence resonance energy transfer; biosensor; epidermal growth factor receptor; insulin receptor; phosphatidylinositide 3‐kinase; phosphatidylinositol 3,4-bisphosphate; phosphoinositide; receptor tyrosine kinase
    DOI:  https://doi.org/10.1016/j.jbc.2025.110275
  2. Nat Methods. 2025 May 26.
    Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics.
    Sara Lobato-Moreno, Umut Yildiz, Annique Claringbould, Nila H Servaas, Evi P Vlachou, Christian Arnold, Hanke Gwendolyn Bauersachs, Víctor Campos-Fornés, Minyoung Kim, Ivan Berest, Karin D Prummel, Kyung-Min Noh, Mikael Marttinen, Judith B Zaugg.
      Enhancers and transcription factors (TFs) are crucial in regulating cellular processes. Current multiomic technologies to study these elements in gene regulatory mechanisms lack multiplexing capability and scalability. Here we present single-cell ultra-high-throughput multiplexed sequencing (SUM-seq) for co-assaying chromatin accessibility and gene expression in single nuclei. SUM-seq enables profiling hundreds of samples at the million cell scale and outperforms current high-throughput single-cell methods. We demonstrate the capability of SUM-seq to (1) resolve temporal gene regulation of macrophage M1 and M2 polarization to bridge TF regulatory networks and immune disease genetic variants, (2) define the regulatory landscape of primary T helper cell subsets and (3) dissect the effect of perturbing lineage TFs via arrayed CRISPR screens in spontaneously differentiating human induced pluripotent stem cells. SUM-seq offers a cost-effective, scalable solution for ultra-high-throughput single-cell multiomic sequencing, accelerating the unraveling of complex gene regulatory networks in cell differentiation, responses to perturbations and disease studies.
    DOI:  https://doi.org/10.1038/s41592-025-02700-8
  3. Sci Rep. 2025 May 28. 15(1): 18691
    Accessible and accurate cytometry analysis of adherent cells using fluorescence microscopes.
    Daniel Foyt, Yiming Kuang, Samma Rehem, Klaus Yserentant, Bo Huang.
      We have developed a method along with a Python-based analysis tool to capture images and produce flow-cytometry-like data for adherent cell culture utilizing simple accessible microscopes. Leveraging the recently developed generalist algorithms for cell segmentation, our approach efficiently quantifies single-cell fluorescence signals. We demonstrated the utility of this method by screening a set of 88 prime editing conditions using the integration of mNeonGreen211 as a reporter.
    DOI:  https://doi.org/10.1038/s41598-025-01957-5
  4. Nat Methods. 2025 May 26.
    Methods for multiplexing single-cell multi-omics.
    Laura C Kida, Caleb A Lareau.
      
    DOI:  https://doi.org/10.1038/s41592-025-02657-8
  5. PLoS One. 2025 ;20(5): e0323953
    Screening for variable drug responses using human iPSC cohorts.
    Melpomeni Platani, Hao Jiang, Lindsay Davidson, Santosh Hariharan, Regis Doyonnas, Angus I Lamond, Jason R Swedlow.
      We have developed a laboratory-based drug screening platform that uses a cohort of human induced pluripotent stem cell (hiPSC) lines, derived from different donors, to predict variable drug responses of potential clinical relevance. This builds on recent findings that pluripotent hiPSC lines express a broad repertoire of gene transcripts and proteins, whose expression levels reflect the genetic identity of the donor. We demonstrate that a cohort of hiPSC lines from different donors can be screened efficiently in their pluripotent state, using high-throughput Cell Painting assays. Variable phenotypic responses between hiPSC lines were detected with a wide range of clinically approved drugs, in use across multiple disease areas. Furthermore, information on mechanisms of drug-cell interactions underlying the observed variable responses was derived by using quantitative proteomic analysis to compare sets of hiPSC lines that had been stratified objectively, based upon variable response, Cell Painting data. We propose that information derived from comparative drug screening, using curated libraries of hiPSC lines from different donors, can help to improve the delivery of safe new drugs suitable for a broad range of genetic backgrounds and sexual diversity within human populations.
    DOI:  https://doi.org/10.1371/journal.pone.0323953
  6. Elife. 2025 May 27. pii: RP93180. [Epub ahead of print]12
    Optogenetic control of a GEF of RhoA uncovers a signaling switch from retraction to protrusion.
    Jean de Seze, Maud Bongaerts, Benoit Boulevard, Mathieu Coppey.
      The ability of a single protein to trigger different functions is an assumed key feature of cell signaling, yet there are very few examples demonstrating it. Here, using an optogenetic tool to control membrane localization of RhoA nucleotide exchange factors (GEFs), we present a case where the same protein can trigger both protrusion and retraction when recruited to the plasma membrane, polarizing the cell in two opposite directions. We show that the basal concentration of the GEF prior to activation predicts the resulting phenotype. A low concentration leads to retraction, whereas a high concentration triggers protrusion. This unexpected protruding behavior arises from the simultaneous activation of Cdc42 by the GEF and sequestration of active RhoA by the GEF PH domain at high concentrations. We propose a minimal model that recapitulates the phenotypic switch, and we use its predictions to control the two phenotypes within selected cells by adjusting the frequency of light pulses. Our work exemplifies a unique case of control of antagonist phenotypes by a single protein that switches its function based on its concentration or dynamics of activity. It raises numerous open questions about the link between signaling protein and function, particularly in contexts where proteins are highly overexpressed, as often observed in cancer.
    Keywords:  cell biology; cell migration; human; optogenetics; signaling
    DOI:  https://doi.org/10.7554/eLife.93180
  7. Mol Biol Cell. 2025 Jun 01. 36(6): tp1
    Practical guide to fluorescence lifetime imaging microscopy.
    Nadia Sarfraz, Esther Braselmann.
      Fluorescence lifetime imaging microscopy (FLIM) has emerged as a powerful modality that offers sensitivity to molecular environments, fluorophore concentration independence, local environment sensing, characterization of molecular binding events with multiplexing capabilities, and monitoring metabolism. Recently, we adapted FLIM for quantitatively sensing RNAs in live cells, establishing the Riboglow-FLIM platform. More broadly, FLIM has the potential to complement and advance traditional intensity-based microscopy platforms. Here, we provide a practical guide to make use of FLIM for diverse fluorescence sensors. We discuss FLIM basics, the experimental setup, data-fitting principles, and real-world case studies of well-understood fluorescent proteins to demonstrate the applicability of these workflows. This perspective provides a basic "best practices" guide for designing and executing FLIM experiments, with the goal of introducing researchers to concepts that will help empower them to utilize this emerging technology.
    DOI:  https://doi.org/10.1091/mbc.E24-03-0110
  8. Mol Cell. 2025 May 22. pii: S1097-2765(25)00408-3. [Epub ahead of print]
    YTHDF1 differentiates the contributing roles of mTORC1 in aging.
    Chenzhong Xu, Cong Yu, Jie Zhang, Zhen Zhang, Jin Zhang, Yuan Meng, Ming Wang, Minting Wen, Junhao Chen, Yuping Ning, Xinchun Chen, Jinke Gu, Wen Su, Baohua Liu.
      The mechanistic target of rapamycin (mTOR) serves as an essential hub in sensing metabolic stress and regulating aging, although the differential contributions of mTOR-regulated protein and cholesterol synthesis are unclear. Post-transcriptional modifications of mRNAs, such as N6-methyladenosine (m6A), occur rapidly in response to acute environmental changes to maintain tissue homeostasis. Here, we showed that loss of YTH m6A RNA-binding protein 1 (YTHDF1) accelerated murine aging. Mechanistically, YTHDF1 is anchored to the lysosome surface by lysosome-associated membrane protein (LAMP2), whereby it recruits tuberous sclerosis complex (TSC2) to inhibit mTOR complex 1 (mTORC1). Ythdf1 loss activated mTORC1-sterol regulatory element-binding protein 2 (SREBP2)-axis-mediated cholesterol biosynthesis but not m6A-reader-regulated protein translation. Rapamycin restored murine healthspan in contrast to the maximum lifespan shortening caused by Ythdf1 depletion. Our data reveal an m6A-independent function of YTHDF1, which differentiates the contributing roles of mTORC1 in the regulation of aging.
    Keywords:  SREBP2; TSC2; YTHDF1; aging; m6A; mTORC1; rapamycin
    DOI:  https://doi.org/10.1016/j.molcel.2025.05.003
  9. Orphanet J Rare Dis. 2025 May 27. 20(1): 256
    mTOR pathway diseases: challenges and opportunities from bench to bedside and the mTOR node.
    Laura Mantoan Ritter, Nicholas M P Annear, Emma L Baple, Leila Y Ben-Chaabane, Istvan Bodi, Lauren Brosson, Jill E Cadwgan, Bryn Coslett, Andrew H Crosby, D Mark Davies, Nicola Daykin, Stefanie Dedeurwaerdere, Christina Dühring Fenger, Elaine A Dunlop, Frances V Elmslie, Marie Girodengo, Sophie Hambleton, Anna C Jansen, Simon R Johnson, Kelly C Kearley, John C Kingswood, Liisi Laaniste, Katherine Lachlan, Andrew Latchford, Ralitsa R Madsen, Sahar Mansour, Simeon R Mihaylov, Louwai Muhammed, Claire Oliver, Tom Pepper, Lettie E Rawlins, Ina Schim van der Loeff, Ata Siddiqui, Pooja Takhar, Katrina Tatton-Brown, Andrew R Tee, Priyanka Tibarewal, Charlotte Tye, Sila K Ultanir, Bart Vanhaesebroeck, Benjamin Zare, Deb K Pal, Joseph M Bateman.
      Mechanistic target of rapamycin (mTOR) is a highly conserved serine/threonine kinase that regulates key cellular processes including cell growth, autophagy and metabolism. Hyperactivation of the mTOR pathway causes a group of rare and ultrarare genetic diseases. mTOR pathway diseases have diverse clinical manifestations that are managed by distinct medical disciplines but share a common underlying molecular basis. There is a now a deep understanding of the molecular underpinning that regulates the mTOR pathway but effective treatments for most mTOR pathway diseases are lacking. Translating scientific knowledge into clinical applications to benefit the unmet clinical needs of patients is a major challenge common to many rare diseases. In this article we expound how mTOR pathway diseases provide an opportunity to coordinate basic and translational disease research across the group, together with industry, medical research foundations, charities and patient groups, by pooling expertise and driving progress to benefit patients. We outline the germline and somatic mutations in the mTOR pathway that cause rare diseases and summarise the prevalence, genetic basis, clinical manifestations, pathophysiology and current treatments for each disease in this group. We describe the challenges and opportunities for progress in elucidating the underlying mechanisms, improving diagnosis and prognosis, as well as the development and approval of new therapies for mTOR pathway diseases. We illustrate the crucial role of patient public involvement and engagement in rare disease and mTOR pathway disease research. Finally, we explain how the mTOR Pathway Diseases node, part of the Research Disease Research UK Platform, will address these challenges to improve the understanding, diagnosis and treatment of mTOR pathway diseases.
    Keywords:  AKT; Birt-Hogg-Dubé; Everolimus; PI3K; PTEN; Peutz-Jeghers; Rapamycin; Rare diseases; Tuberous sclerosis complex; mTOR
    DOI:  https://doi.org/10.1186/s13023-025-03740-1
  10. Angew Chem Int Ed Engl. 2025 May 30. e202508916
    Small Molecule-Induced Alterations of Protein Polyubiquitination Revealed by Mass-Spectrometric Ubiquitome Analysis.
    Siska Führer, Kai Gallant, Farnusch Kaschani, Markus Kaiser, Petra Janning, Herbert Waldmann, Malte Gersch.
      Small molecules which alter protein ubiquitination are emerging as therapeutics due to their ability to modulate targets previously deemed undruggable. These compounds comprise PROTACs, molecular glue degraders and DUB inhibitors, among others. However, methods for the proteome-wide monitoring of compound-induced changes in protein polyubiquitination, which may also detect non-degradative modifications, are lacking. Here, we report the utilization of polyubiquitin enrichment coupled to mass spectrometry to monitor small molecule-induced changes in cellular protein ubiquitination. We established enrichment through tandem ubiquitin binding entities (TUBEs) following semi-denaturing cell lysis and devised an elution protocol compatible with downstream LC-MS/MS analysis. We demonstrate broad applicability of the workflow by assessing ubiquitination changes induced by a PROTAC, a p97 inhibitor and deubiquitinase inhibitors. Application of the assay to compounds inhibiting the deubiquitinase USP7 revealed the induction of non-degradative ubiquitination on the UBE3A E3 ligase. Collectively, we established a versatile proteomics method to facilitate the direct investigation of cellular polyubiquitination, with high relevance for the identification and characterization of protein degraders, stabilizers and other molecules with ubiquitin-mediated bioactivity.
    Keywords:  Biological activity; Drug Discovery; Protein modifications; Ubiquitin proteasome system; proteomics
    DOI:  https://doi.org/10.1002/anie.202508916
  11. Antioxidants (Basel). 2025 May 16. pii: 594. [Epub ahead of print]14(5):
    Endosomal H2O2 Molecules Act as Signaling Mediators in Akt/PKB Activation.
    Sujin Park, Chaewon Kim, Sukyeong Heo, Dongmin Kang.
      Receptor-mediated endocytosis (RME) is a commonly recognized receptor internalization process of receptor degradation or recycling. However, recent studies have supported that RME is closely related to signal propagation and amplification from the plasma membrane to the cytosol. Few studies have elucidated the role of H2O2, a mild oxidant among reactive oxygen species (ROS) in RME and second messenger of signal propagation. In the present study, we investigated the regulatory function of H2O2 in early endosomes during signaling throughout receptor-mediated endocytosis. In mammalian cells with a physiological amount of H2O2 generated during epidermal growth factor (EGF) activation, fluorescence imaging showed that the levels of two activating phosphorylations on Ser473 and Thr308 of Akt were transiently increased in the plasma membrane, but the predominant p-Akt on Ser473 appeared in early endosomes. To examine the role of endosomal H2O2 molecules as signaling mediators of Akt activation in endosomes, we modulated endosomal H2O2 through the ectopic expression of an endosomal-targeting catalase (Cat-Endo). The forced removal of endosomal H2O2 inhibited the Akt phosphorylation on Ser473 but not on Thr308. The levels of mSIN and rictor, two components of mTORC2 that work as a kinase in Akt phosphorylation on Ser473, were also selectively diminished in the early endosomes of Cat-Endo-expressing cells. We also observed a decrease in the endosomal level of the adaptor protein containing the PH domain, the PTB domain, and the Leucine zipper motif 1 (APPL1) protein, which is an effector of Rab5 and key player in the assembly of signaling complexes regulating the Akt pathway in Cat-Endo-expressing cells compared with those in normal cells. Therefore, the H2O2-dependent recruitment of the APPL1 adaptor protein into endosomes was required for full Akt activation. We proposed that endosomal H2O2 is a promoter of Akt signaling.
    Keywords:  Akt/PKB; early endosome; hydrogen peroxide; receptor-mediated endocytosis; the Leucine zipper motif 1 (APPL1)
    DOI:  https://doi.org/10.3390/antiox14050594
  12. Mol Syst Biol. 2025 May 27.
    hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments.
    Samantha N Fischer, Erin R Claussen, Savvas Kourtis, Sara Sdelci, Sandra Orchard, Henning Hermjakob, Georg Kustatscher, Kevin Drew.
      Macromolecular protein complexes carry out most cellular functions. Unfortunately, we lack the subunit composition for many human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify >15,000 human protein complexes. We show our map of protein complexes is highly accurate and more comprehensive than previous maps, placing nearly 70% of human proteins into their physical contexts. We globally characterize our complexes using mass spectrometry based protein covariation data (ProteomeHD.2) and identify covarying complexes suggesting common functional associations. hu.MAP3.0 generates testable functional hypotheses for 472 uncharacterized proteins which we support using AlphaFold modeling. Additionally, we use AlphaFold modeling to identify 5871 mutually exclusive proteins in hu.MAP3.0 complexes suggesting complexes serve different functional roles depending on their subunit composition. We identify expression as the primary way cells and organisms relieve the conflict of mutually exclusive subunits. Finally, we import our complexes to EMBL-EBI's Complex Portal ( https://www.ebi.ac.uk/complexportal/home ) and provide complexes through our hu.MAP3.0 web interface ( https://humap3.proteincomplexes.org/ ). We expect our resource to be highly impactful to the broader research community.
    Keywords:  Disease Candidates; Machine Learning; Mutually Exclusive; Protein Complex; Protein Interaction
    DOI:  https://doi.org/10.1038/s44320-025-00121-5
  13. J Endocr Soc. 2025 Jul;9(7): bvaf080
    PI3K in the VMH Attenuates Diet-Induced Obesity and Participates in the Effects of E2 on Energy Expenditure in Mice.
    Aline Alves de Jesus, Raoni Conceição Dos-Santos, Isabelle Rodrigues-Santos, Hellen Veida-Silva, Milene Mantovani Mata, Rafaella Eduarda Volpi, Gabriel Henrique Marques Gonçalves, Luiz Carlos Navegantes, Carol Fuzeti Elias, José Antunes-Rodrigues, Lucila Leico Kagohara Elias.
      Obesity is associated with the development of several illnesses, such as diabetes mellitus, cancer, and cardiovascular diseases. Elucidating the mechanisms of body weight control is important for the development of effective therapeutic strategies against obesity. In response to the action of hormones such as leptin and 17β-estradiol (E2), the ventromedial hypothalamus (VMH) plays an essential role in protection against diet-induced obesity (DIO) through the regulation of food intake and energy expenditure. However, little is known about the intracellular mechanisms involved in these effects. To assess the role of phosphoinositide 3-kinase (PI3K) signaling in neurons that express steroidogenic factor 1 (SF1) in the VMH in energy homeostasis, we used Cre-lox technology to generate male and female mice with specific disruption of the catalytic subunit P110α in SF1 neurons in the VMH. We demonstrated that the conditional knockout of P110α in SF1 neurons in the VMH affects body weight, energy expenditure, and thermogenesis in animals fed a high-fat diet. In addition, we demonstrated that female mice with genetic disruption of PI3K activity in VMH neurons exhibited greater weight gain than their male counterparts. Furthermore, inhibition of PI3K activity in the VMH partially blocked the effects of E2 on body weight regulation, stimulation of energy expenditure, and thermogenesis in female ovariectomized mice. Collectively, our results indicate that PI3K activity in VMH neurons plays a relevant role in protecting against DIO and contributes to the effects of estradiol on energy expenditure in females.
    Keywords:  17β estradiol; PI3K; SF1; VMH; diet-induced obesity; energy expenditure
    DOI:  https://doi.org/10.1210/jendso/bvaf080
  14. Nat Commun. 2025 May 30. 16(1): 5037
    Assessing and improving reliability of neighbor embedding methods: a map-continuity perspective.
    Zhexuan Liu, Rong Ma, Yiqiao Zhong.
      Visualizing high-dimensional data is essential for understanding biomedical data and deep learning models. Neighbor embedding methods, such as t-SNE and UMAP, are widely used but can introduce misleading visual artifacts. We find that the manifold learning interpretations from many prior works are inaccurate and that the misuse stems from a lack of data-independent notions of embedding maps, which project high-dimensional data into a lower-dimensional space. Leveraging the leave-one-out principle, we introduce LOO-map, a framework that extends embedding maps beyond discrete points to the entire input space. We identify two forms of map discontinuity that distort visualizations: one exaggerates cluster separation and the other creates spurious local structures. As a remedy, we develop two types of point-wise diagnostic scores to detect unreliable embedding points and improve hyperparameter selection, which are validated on datasets from computer vision and single-cell omics.
    DOI:  https://doi.org/10.1038/s41467-025-60434-9
  15. Nat Commun. 2025 May 27. 16(1): 4884
    Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells.
    Mirjam van Bentum, Bertram Klinger, Anja Sieber, Sheyda Naghiloo, Henrik Zauber, Nadine Lehmann, Mohamed Haji, Sylvia Niquet, Philipp Mertins, Nils Blüthgen, Matthias Selbach.
      Targeted kinase inhibitors are a cornerstone of cancer therapy, but their success is often hindered by the complexity of cellular signaling networks that can lead to resistance. Overcoming this challenge necessitates a deep understanding of cellular signaling responses. While standard global phosphoproteomics offers extensive insights, lengthy processing times, the complexity of data interpretation, and frequent omission of crucial phosphorylation sites limit its utility. Here, we combine data-independent acquisition (DIA) with spike-in of synthetic heavy stable isotope-labeled phosphopeptides to facilitate the targeted detection of particularly informative phosphorylation sites. Our spike-in enhanced detection in DIA (SPIED-DIA) approach integrates the improved sensitivity of spike-in-based targeted detection with the discovery potential of global phosphoproteomics into a simple workflow. We employed this method to investigate synergistic signaling responses in colorectal cancer cell lines following MEK inhibition. Our findings highlight that combining MEK inhibition with growth factor stimulation synergistically activates JNK signaling in HCT116 cells. This synergy emphasizes the therapeutic potential of concurrently targeting MEK and JNK pathways, as evidenced by the significantly impaired growth of HCT116 cells when treated with both inhibitors. Our results demonstrate that SPIED-DIA effectively identifies synergistic signaling responses in colorectal cancer cells, presenting a valuable tool for uncovering new therapeutic targets and strategies in cancer treatment.
    DOI:  https://doi.org/10.1038/s41467-025-59404-y
  16. Nat Commun. 2025 May 27. 16(1): 4920
    WNK1 signalling regulates amino acid transport and mTORC1 activity to sustain acute myeloid leukaemia growth.
    Shunlei Duan, Karl Agger, Jan-Erik Messling, Koutarou Nishimura, Xuerui Han, Isabel Peña-Rømer, Pavel Shliaha, Helene Damhofer, Max Douglas, Manas Kohli, Akos Pal, Yasmin Asad, Aaron Van Dyke, Raquel Reilly, Robert Köchl, Victor L J Tybulewicz, Ronald C Hendrickson, Florence I Raynaud, Paolo Gallipoli, George Poulogiannis, Kristian Helin.
      The lack of curative therapies for acute myeloid leukaemia (AML) remains an ongoing challenge despite recent advances in the understanding of the molecular basis of the disease. Here we identify the WNK1-OXSR1/STK39 pathway as a previously uncharacterised dependency in AML. We show that genetic depletion and pharmacological inhibition of WNK1 or its downstream phosphorylation targets OXSR1 and STK39 strongly reduce cell proliferation and induce apoptosis in leukaemia cells in vitro and in vivo. Furthermore, we show that the WNK1-OXSR1/STK39 pathway controls mTORC1 signalling via regulating amino acid uptake through a mechanism involving the phosphorylation of amino acid transporters, such as SLC38A2. Our findings underscore an important role of the WNK1-OXSR1/STK39 pathway in regulating amino acid uptake and driving AML progression.
    DOI:  https://doi.org/10.1038/s41467-025-59969-8
  17. Entropy (Basel). 2025 Apr 22. pii: 453. [Epub ahead of print]27(5):
    Integrating Dynamical Systems Modeling with Spatiotemporal scRNA-Seq Data Analysis.
    Zhenyi Zhang, Yuhao Sun, Qiangwei Peng, Tiejun Li, Peijie Zhou.
      Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene expression, offering valuable insights into cellular states at a single time point. Recent advancements in temporally resolved scRNA-seq, spatial transcriptomics (ST), and time-series spatial transcriptomics (temporal-ST) have further revolutionized our ability to study the spatiotemporal dynamics of individual cells. These technologies, when combined with computational frameworks such as Markov chains, stochastic differential equations (SDEs), and generative models like optimal transport and Schrödinger bridges, enable the reconstruction of dynamic cellular trajectories and cell fate decisions. This review discusses how these dynamical system approaches offer new opportunities to model and infer cellular dynamics from a systematic perspective.
    Keywords:  cellular trajectories; computational modeling; single-cell RNA sequencing; spatiotemporal dynamics
    DOI:  https://doi.org/10.3390/e27050453
  18. Methods Mol Biol. 2025 ;2938 31-46
    Adipogenic Differentiation Assay for the Study of Insulin Signaling.
    Jonathan M Gamwell, Emily Cresswell, Katherine E Pinnick.
      In vitro models of adipogenesis are valuable tools for the study of human adipocyte development and function. Prevailing methods rely on the extended use of supraphysiological concentrations of glucose and adipogenic hormones, which can negatively impact some aspects of adipocyte function, in particular, insulin signaling. In this chapter, we present a modified adipogenic differentiation protocol which has been optimized for the study of insulin signaling and glucose uptake in human adipose-derived stem cells (hADSCs).
    Keywords:  Adipogenesis; Cell model; Glucose uptake; Insulin signaling
    DOI:  https://doi.org/10.1007/978-1-0716-4607-6_4
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