bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2025–04–20
twenty-six papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. Targeting Signaling Excitability in Cervical and Pancreatic Cancer Cells Through Combined Inhibition of FAK and PI3K.
  2. KRIT1 heterozygous mutations are sufficient to induce a pathological phenotype in patient-derived iPSC models of cerebral cavernous malformation.
  3. Fate and state transitions during human blood vessel organoid development.
  4. In toto live imaging of Erk signaling dynamics in developing zebrafish hepatocytes.
  5. Towards multimodal foundation models in molecular cell biology.
  6. Long range mutual activation establishes Rho and Rac polarity during cell migration.
  7. Substrate stiffness regulates triple-negative breast cancer signaling through CXCR4 receptor dynamics.
  8. Metabolic rewiring caused by mitochondrial dysfunction promotes mTORC1-dependent skeletal aging.
  9. Embryological cellular origins and hypoxia-mediated mechanisms in PIK3CA-driven refractory vascular malformations.
  10. Emerging roles of transcriptional condensates as temporal signal integrators.
  11. A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling.
  12. Liver gene expression and its rewiring in hepatic steatosis are controlled by PI3Kα-dependent hepatocyte signaling.
  13. scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions.
  14. PTEN and novel TEK germline variants associated with the phenotypes of PTEN hamartoma tumor syndrome.
  15. Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets.
  16. Phosphoinositide signaling at the cytoskeleton in the regulation of cell dynamics.
  17. UnitedMet harnesses RNA-metabolite covariation to impute metabolite levels in clinical samples.
  18. Deciphering Akt activation: Insights from a mean-field model.
  19. Representation of high-dimensional cell morphology and morphodynamics in 2-D latent space.
  20. Imaging 3D cell cultures with optical microscopy.
  21. Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling.
  22. CREPE (CREate Primers and Evaluate): a computational tool for large-scale primer design and specificity analysis.
  23. Automated Quality Control of Time-Course Imaging from 3D in vitro cultures.
  24. Unveiling cellular communications through rapid pan-membrane-protein labeling.
  25. Sustained mTORC1 activation in activated T cells impairs vaccine responses in older individuals.
  26. A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments.
  1. Int J Mol Sci. 2025 Mar 26. pii: 3040. [Epub ahead of print]26(7):
    Targeting Signaling Excitability in Cervical and Pancreatic Cancer Cells Through Combined Inhibition of FAK and PI3K.
    Chao-Cheng Chen, Suyang Wang, Jr-Ming Yang, Chuan-Hsiang Huang.
      The Ras/PI3K/ERK signaling network is frequently mutated and overactivated in various human cancers. Focal adhesion kinase (FAK) is commonly overexpressed in several cancer types and has been implicated in treatment resistance mechanisms. A positive feedback loop between Ras, PI3K, the cytoskeleton, and FAK was previously shown to drive Ras signaling excitability. In this study, we investigated the effectiveness of targeting Ras signaling excitability by concurrently inhibiting FAK and PI3K in cervical and pancreatic cancer cells, which depend on activation Ras/PI3K signaling. We found that the combination of FAK and PI3K inhibitors synergistically suppressed the growth of cervical and pancreatic cancer cell lines through increased apoptosis and decreased mitosis. PI3K inhibitors alone caused only a transient suppression of downstream AKT activity and paradoxically increased FAK signaling in cancer cells. The addition of an FAK inhibitor effectively counteracted this PI3K-inhibitor-induced FAK activation. Furthermore, PI3K inhibitors were found to activate multiple receptor tyrosine kinases (RTKs), including insulin receptor, IGF-1R, EGFR, HER2, HER3, AXL, and EphA2. Taken together, our results suggest that FAK inhibition is necessary to counteract the compensatory RTK activation induced by PI3K inhibitors, thereby achieving more effective suppression of cancer cell growth. These findings highlight the therapeutic potential of combined FAK and PI3K inhibition in cancer treatment.
    Keywords:  RTK/Ras/PI3K/ERK signaling network; drug combination; excitability; synergy; targeted therapy
    DOI:  https://doi.org/10.3390/ijms26073040
  2. Cell Rep. 2025 Apr 14. pii: S2211-1247(25)00347-X. [Epub ahead of print]44(5): 115576
    KRIT1 heterozygous mutations are sufficient to induce a pathological phenotype in patient-derived iPSC models of cerebral cavernous malformation.
    Maximiliano Arce, Iza Erzar, Fan Yang, Neeharika Senthilkumar, Favour C Onyeogaziri, Dario Ronchi, Frida C Ahlstrand, Nora Noll, Roberta Lugano, Mark Richards, Elisa Scola, Monica Corada, Francesca Lazzaroni, Linda Meggiolaro, Jens Schuster, Niklas Dahl, Mika Niemelä, Behnam Rezai Jahromi, Anna Dimberg, Silvia Lanfraconi, Roberto Latini, Peetra U Magnusson.
      Cerebral cavernous malformation (CCM) is a neurovascular disease distinguished by clusters of leaky, mulberry-like blood vessels. KRIT1 bi-allelic loss-of-function mutations in endothelial cells are known to trigger brain cavernomas; however, human preclinical models are needed to unveil the importance of germline KRIT1 heterozygous mutations in CCM pathogenesis. We generated three induced pluripotent stem cells (iPSCs) from patients with CCM with hereditary KRIT1 heterozygous mutations. Patient-derived vascularized organoids exhibited intricate and abnormal vascular structures with cavernoma-like morphology, and iPSC-derived endothelial cells displayed phenotypic abnormalities at the junctional and transcriptional levels. Upon injection into brain explants, CCM endothelial cells integrated into the normal vasculature and created vascular anomalies. Lastly, transcriptional analysis showed that the endothelial progenitor marker paternally expressed gene 3 (PEG3) was highly expressed in iPSC-derived CCM endothelial cells, and this was further confirmed in familial and sporadic cavernoma biopsies. Overall, our study sheds light on the molecular consequence of KRIT1 heterozygous mutations in endothelial cells and the potential implications in cavernoma pathogenesis.
    Keywords:  BBB; CCM; CP: Stem cell research; KRIT1; endothelial cells; iPSCs; vascular malformations; vascularized organoids
    DOI:  https://doi.org/10.1016/j.celrep.2025.115576
  3. Cell. 2025 Apr 16. pii: S0092-8674(25)00387-3. [Epub ahead of print]
    Fate and state transitions during human blood vessel organoid development.
    Marina T Nikolova, Zhisong He, Makiko Seimiya, Gustav Jonsson, Wuji Cao, Ryo Okuda, Reiner A Wimmer, Ryoko Okamoto, Josef M Penninger, J Gray Camp, Barbara Treutlein.
      Human blood vessel organoids (hBVOs) have emerged as a system to model human vascular development and disease. Here, we use single-cell multi-omics together with genetic and signaling pathway perturbations to reconstruct hBVO development. Mesodermal progenitors bifurcate into endothelial and mural fates in vitro, and xenografted BVOs acquire definitive arteriovenous endothelial cell specification. We infer a gene regulatory network and use single-cell genetic perturbations to identify transcription factors (TFs) and receptors involved in cell fate specification, including a role for MECOM in endothelial and mural specification. We assess the potential of BVOs to generate organotypic states, identify TFs lacking expression in hBVOs, and find that induced LEF1 overexpression increases brain vasculature specificity. Finally, we map vascular disease-associated genes to hBVO cell states and analyze an hBVO model of diabetes. Altogether, we provide a comprehensive cell state atlas of hBVO development and illuminate the power and limitation of hBVOs for translational research.
    Keywords:  arteriovenous specification; human blood vessel organoid; human development; organoid cell atlas; single-cell genomics; single-cell perturbation screen
    DOI:  https://doi.org/10.1016/j.cell.2025.03.037
  4. Dev Biol. 2025 Apr 12. pii: S0012-1606(25)00104-6. [Epub ahead of print]523 43-50
    In toto live imaging of Erk signaling dynamics in developing zebrafish hepatocytes.
    Faraz Ahmed Butt, Alessandro De Simone, Stefano Di Talia, Kenneth D Poss.
      Regional and tissue-wide regulation of signaling pathways orchestrates cellular proliferation and differentiation during organ development. In this study, we established an imaging platform for longitudinal analysis of liver development in live developing zebrafish. We generated hepatocyte-specific transgenic lines for kinase translocation reporters of extracellular signal-regulated kinase (Erk) and c-Jun N-terminal kinase (Jnk) signaling, and with these we captured signaling dynamics that govern rapid expansion of hepatocytes toward creation of the functioning liver at single-cell resolution. Our findings reveal Erk signaling fluctuations as the liver develops and introduce methodology for investigating cell-type specific signaling dynamics during organ morphogenesis.
    DOI:  https://doi.org/10.1016/j.ydbio.2025.04.009
  5. Nature. 2025 Apr;640(8059): 623-633
    Towards multimodal foundation models in molecular cell biology.
    Haotian Cui, Alejandro Tejada-Lapuerta, Maria Brbić, Julio Saez-Rodriguez, Simona Cristea, Hani Goodarzi, Mohammad Lotfollahi, Fabian J Theis, Bo Wang.
      The rapid advent of high-throughput omics technologies has created an exponential growth in biological data, often outpacing our ability to derive molecular insights. Large-language models have shown a way out of this data deluge in natural language processing by integrating massive datasets into a joint model with manifold downstream use cases. Here we envision developing multimodal foundation models, pretrained on diverse omics datasets, including genomics, transcriptomics, epigenomics, proteomics, metabolomics and spatial profiling. These models are expected to exhibit unprecedented potential for characterizing the molecular states of cells across a broad continuum, thereby facilitating the creation of holistic maps of cells, genes and tissues. Context-specific transfer learning of the foundation models can empower diverse applications from novel cell-type recognition, biomarker discovery and gene regulation inference, to in silico perturbations. This new paradigm could launch an era of artificial intelligence-empowered analyses, one that promises to unravel the intricate complexities of molecular cell biology, to support experimental design and, more broadly, to profoundly extend our understanding of life sciences.
    DOI:  https://doi.org/10.1038/s41586-025-08710-y
  6. bioRxiv. 2024 Oct 02. pii: 2024.10.01.616161. [Epub ahead of print]
    Long range mutual activation establishes Rho and Rac polarity during cell migration.
    Henry De Belly, Andreu Fernandez Gallen, Evelyn Strickland, Dorothy C Estrada, Patrick J Zager, Janis K Burkhardt, Hervé Turlier, Orion D Weiner.
      In migrating cells, the GTPase Rac organizes a protrusive front, whereas Rho organizes a contractile back. How these GTPases are appropriately positioned at the opposite poles of a migrating cell is unknown. Here we leverage optogenetics, manipulation of cell mechanics, and mathematical modeling to reveal a surprising long-range mutual activation of the front and back polarity programs that complements their well-known local mutual inhibition. This long-range activation is rooted in two distinct modes of mechanochemical crosstalk. Local Rac-based protrusion stimulates Rho activation at the opposite side of the cell via membrane tension-based activation of mTORC2. Conversely, local Rho-based contraction induces cortical-flow-based remodeling of membrane-to-cortex interactions leading to PIP2 release, PIP3 generation, and Rac activation at the opposite side of the cell. We develop a minimal unifying mechanochemical model of the cell to explain how this long-range mechanical facilitation complements local biochemical inhibition to enable robust global Rho and Rac partitioning. Finally, we validate the importance of this long-range facilitation in the context of chemoattractant-based cell polarization and migration in primary human lymphocytes. Our findings demonstrate that the actin cortex and plasma membrane function as an integrated mechanochemical system for long-range partitioning of Rac and Rho during cell migration and likely other cellular contexts.
    DOI:  https://doi.org/10.1101/2024.10.01.616161
  7. bioRxiv. 2025 Apr 02. pii: 2025.03.28.645920. [Epub ahead of print]
    Substrate stiffness regulates triple-negative breast cancer signaling through CXCR4 receptor dynamics.
    Kenneth K Y Ho, Johanna M Buschhaus, Anne Zhang, Alyssa C Cutter, Brock Humphries, Gary D Luker.
      Biophysical properties of the extracellular matrix (ECM), such as mechanical stiffness, directly regulate behaviors of cancer cells linked to cancer initiation and progression. Cells sense and respond to ECM stiffness in the context of dynamic changes in biochemical inputs, such as growth factors and chemokines. While commonly studied as isolated inputs, mechanisms by which combined effects of mechanical stiffness and biochemical factors affect functions of cancer cells remain poorly defined. Using a combination of elastically supportive surface (ESS) culture dishes with defined stiffnesses and single-cell imaging, we report here that culturing cells on a stiff (28 kPa) versus soft (1.5 kPa) substrate increases CXCR4 and EGFR expression and promotes greater ligand-dependent internalization of CXCR4. In addition to increased CXCR4 expression, a stiff ECM also increases basal activation of Akt and ERK as well as signaling through these kinases in response to CXCL12-α and EGF and promotes migration of triple negative breast cancer (TNBC) cells. These data implicate receptor dynamics as a key mediator of Akt and ERK signaling as a mechanism for adverse effects of enhanced ECM stiffness on disease progression in TNBC.
    DOI:  https://doi.org/10.1101/2025.03.28.645920
  8. Sci Adv. 2025 Apr 18. 11(16): eads1842
    Metabolic rewiring caused by mitochondrial dysfunction promotes mTORC1-dependent skeletal aging.
    Kristina Bubb, Julia Etich, Kristina Probst, Tanvi Parashar, Maximilian Schuetter, Frederik Dethloff, Susanna Reincke, Janica L Nolte, Marcus Krüger, Ursula Schlötzer-Schrehard, Julian Nüchel, Constantinos Demetriades, Patrick Giavalisco, Jan Riemer, Bent Brachvogel.
      Decline of mitochondrial respiratory chain (mtRC) capacity is a hallmark of mitochondrial diseases. Patients with mtRC dysfunction often present reduced skeletal growth as a sign of premature cartilage degeneration and aging, but how metabolic adaptations contribute to this phenotype is poorly understood. Here we show that, in mice with impaired mtRC in cartilage, reductive/reverse TCA cycle segments are activated to produce metabolite-derived amino acids and stimulate biosynthesis processes by mechanistic target of rapamycin complex 1 (mTORC1) activation during a period of massive skeletal growth and biomass production. However, chronic hyperactivation of mTORC1 suppresses autophagy-mediated organelle recycling and disturbs extracellular matrix secretion to trigger chondrocytes death, which is ameliorated by targeting the reductive metabolism. These findings explain how a primarily beneficial metabolic adaptation response required to counterbalance the loss of mtRC function, eventually translates into profound cell death and cartilage tissue degeneration. The knowledge of these dysregulated key nutrient signaling pathways can be used to target skeletal aging in mitochondrial disease.
    DOI:  https://doi.org/10.1126/sciadv.ads1842
  9. EMBO Mol Med. 2025 Apr 16.
    Embryological cellular origins and hypoxia-mediated mechanisms in PIK3CA-driven refractory vascular malformations.
    Sota Torii, Keiki Nagaharu, Nanako Nakanishi, Hidehito Usui, Yumiko Hori, Katsutoshi Hirose, Satoru Toyosawa, Eiichi Morii, Mitsunaga Narushima, Yoshiaki Kubota, Osamu Nakagawa, Kyoko Imanaka-Yoshida, Kazuaki Maruyama.
      Congenital vascular malformations, affecting 0.5% of the population, often occur in the head and neck, complicating treatment due to the critical functions in these regions. Our previous research identified distinct developmental origins for blood and lymphatic vessels in these areas, tracing them to the cardiopharyngeal mesoderm (CPM), which contributes to the development of the head, neck, and cardiovascular system in both mouse and human embryos. In this study, we investigated the pathogenesis of these malformations by expressing Pik3caH1047R in the CPM. Mice expressing Pik3caH1047R in the CPM developed vascular abnormalities restricted to the head and neck. Single-cell RNA sequencing revealed that Pik3caH1047R upregulates Vegf-a expression in endothelial cells through HIF-mediated hypoxia signaling. Human samples supported these findings, showing elevated HIF-1α and VEGF-A in malformed vessels. Notably, inhibition of HIF-1α and VEGF-A in the mouse model significantly reduced abnormal vasculature. These results highlight the role of embryonic origins and hypoxia-driven mechanisms in vascular malformations, providing a foundation for the development of therapies targeting these difficult-to-treat conditions.
    Keywords:  Cardiopharyngeal Mesoderm; Endothelial Cellular Origin; Hypoxia; PIK3CA Mutation; Vascular Malformations
    DOI:  https://doi.org/10.1038/s44321-025-00235-1
  10. Nat Rev Genet. 2025 Apr 16.
    Emerging roles of transcriptional condensates as temporal signal integrators.
    Kirstin Meyer, Bo Huang, Orion D Weiner.
      Transcription factors relay information from the external environment to gene regulatory networks that control cell physiology. To confer signalling specificity, robustness and coordination, these signalling networks use temporal communication codes, such as the amplitude, duration or frequency of signals. Although much is known about how temporal information is encoded, a mechanistic understanding of how gene regulatory networks decode signalling dynamics is lacking. Recent advances in our understanding of phase separation of transcriptional condensates provide new biophysical frameworks for both temporal encoding and decoding mechanisms. In this Perspective, we summarize the mechanisms by which transcriptional condensates could enable temporal decoding through signal adaptation, memory and persistence. We further outline methods to probe and manipulate dynamic communication codes of transcription factors and condensates to rationally control gene activation.
    DOI:  https://doi.org/10.1038/s41576-025-00837-y
  11. bioRxiv. 2025 Apr 02. pii: 2025.03.31.645599. [Epub ahead of print]
    A computational workflow for assessing drug effects on temporal signaling dynamics reveals robustness in stimulus-specific NFκB signaling.
    Emily R Bozich, Xiaolu Guo, Jennifer L Wilson, Alexander Hoffmann.
      Single-cell studies of signal transduction have revealed complex temporal dynamics that determine downstream biological function. For example, the stimulus-specific dynamics of the transcription factor NFκB specify stimulus-specific gene expression programs, and loss of specificity leads to disease. Thus, it is intriguing to consider drugs that may restore signaling specificity in disease contexts, or reduce activity but maintain signaling specificity to avoid unwanted side effects. However, while steady-state dose-response relationships have been the focus of pharmacological studies, there are no established methods for quantifying drug impact on stimulus-response signaling dynamics. Here we evaluated how drug treatments affect the stimulus-specificity of NFκB activation dynamics and its ability to accurately code ligand identity and dose. Specifically, we simulated the dynamic NFκB trajectories in response to 15 stimuli representing various immune threats under treatment of 10 representative drugs across 20 dosage levels. To quantify the effects on coding capacity, we introduced a Stimulus Response Specificity (SRS) score and a stimulus confusion score. We constructed stimulus confusion maps by employing epsilon network clustering in the trajectory space and in various dimensionally reduced spaces: canonical polyadic decomposition (CPD), functional principal component analysis (fPCA), and NFκB signaling codons (i.e. established, informative dynamic features). Our results indicated that the SRS score and the stimulus confusion map based on signaling codons are best-suited to quantify stimulus-specific NFκB dynamics confusion under pharmacological perturbations. Using these tools we found that temporal coding capacity of the NFκB signaling network is generally robust to a variety of pharmacological perturbations, thereby enabling the targeting of stimulus-specific dynamics without causing broad side-effects.
    DOI:  https://doi.org/10.1101/2025.03.31.645599
  12. PLoS Biol. 2025 Apr 14. 23(4): e3003112
    Liver gene expression and its rewiring in hepatic steatosis are controlled by PI3Kα-dependent hepatocyte signaling.
    Marion Régnier, Arnaud Polizzi, Tiffany Fougeray, Anne Fougerat, Prunelle Perrier, Karen Anderson, Yannick Lippi, Sarra Smati, Céline Lukowicz, Frédéric Lasserre, Edwin Fouche, Marine Huillet, Clémence Rives, Blandine Tramunt, Claire Naylies, Géraldine Garcia, Elodie Rousseau-Bacquié, Justine Bertrand-Michel, Cécile Canlet, Sylvie Chevolleau-Mege, Laurent Debrauwer, Christophe Heymes, Rémy Burcelin, Thierry Levade, Pierre Gourdy, Walter Wahli, Yuna Blum, Laurence Gamet-Payrastre, Sandrine Ellero-Simatos, Julie Guillermet-Guibert, Phillip Hawkins, Len Stephens, Catherine Postic, Alexandra Montagner, Nicolas Loiseau, Hervé Guillou.
      Insulin and other growth factors are key regulators of liver gene expression, including in metabolic diseases. Most of the phosphoinositide 3-kinase (PI3K) activity induced by insulin is considered to be dependent on PI3Kα. We used mice lacking p110α, the catalytic subunit of PI3Kα, to investigate its role in the regulation of liver gene expression in health and in metabolic dysfunction-associated steatotic liver disease (MASLD). The absence of hepatocyte PI3Kα reduced maximal insulin-induced PI3K activity and signaling, promoted glucose intolerance in lean mice and significantly regulated liver gene expression, including insulin-sensitive genes, in ad libitum feeding. Some of the defective regulation of gene expression in response to hepatocyte-restricted insulin receptor deletion was related to PI3Kα signaling. In addition, though PI3Kα deletion in hepatocytes promoted insulin resistance, it was protective against steatotic liver disease in diet-induced obesity. In the absence of hepatocyte PI3Kα, the effect of diet-induced obesity on liver gene expression was significantly altered, with changes in rhythmic gene expression in liver. Altogether, this study highlights the specific role of p110α in the control of liver gene expression in physiology and in the metabolic rewiring that occurs during MASLD.
    DOI:  https://doi.org/10.1371/journal.pbio.3003112
  13. Nat Methods. 2025 Apr 17.
    scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions.
    Hechen Li, Ziqi Zhang, Michael Squires, Xi Chen, Xiuwei Zhang.
      Simulated single-cell data are essential for designing and evaluating computational methods in the absence of experimental ground truth. Here we present scMultiSim, a comprehensive simulator that generates multimodal single-cell data encompassing gene expression, chromatin accessibility, RNA velocity and spatial cell locations while accounting for the relationships between modalities. Unlike existing tools that focus on limited biological factors, scMultiSim simultaneously models cell identity, gene regulatory networks, cell-cell interactions and chromatin accessibility while incorporating technical noise. Moreover, it allows users to adjust each factor's effect easily. Here we show that scMultiSim generates data with expected biological effects, and demonstrate its applications by benchmarking a wide range of computational tasks, including multimodal and multi-batch data integration, RNA velocity estimation, gene regulatory network inference and cell-cell interaction inference using spatially resolved gene expression data. Compared to existing simulators, scMultiSim can benchmark a much broader range of existing computational problems and even new potential tasks.
    DOI:  https://doi.org/10.1038/s41592-025-02651-0
  14. Genes Dis. 2025 Jul;12(4): 101466
    PTEN and novel TEK germline variants associated with the phenotypes of PTEN hamartoma tumor syndrome.
    Hongrui Chen, Bin Sun, Yanchun Zhou, Chen Hua, Xiaoxi Lin.
      
    DOI:  https://doi.org/10.1016/j.gendis.2024.101466
  15. Cell Genom. 2025 Apr 15. pii: S2666-979X(25)00107-7. [Epub ahead of print] 100851
    Proteomic-based stemness score measures oncogenic dedifferentiation and enables the identification of druggable targets.
    Clinical Proteomic Tumor Analysis Consortium
      Cancer progression and therapeutic resistance are closely linked to a stemness phenotype. Here, we introduce a protein-expression-based stemness index (PROTsi) to evaluate oncogenic dedifferentiation in relation to histopathology, molecular features, and clinical outcomes. Utilizing datasets from the Clinical Proteomic Tumor Analysis Consortium across 11 tumor types, we validate PROTsi's effectiveness in accurately quantifying stem-like features. Through integration of PROTsi with multi-omics, including protein post-translational modifications, we identify molecular features associated with stemness and proteins that act as active nodes within transcriptional networks, driving tumor aggressiveness. Proteins highly correlated with stemness were identified as potential drug targets, both shared and tumor specific. These stemness-associated proteins demonstrate predictive value for clinical outcomes, as confirmed by immunohistochemistry in multiple samples. The findings emphasize PROTsi's efficacy as a valuable tool for selecting predictive protein targets, a crucial step in customizing anti-cancer therapy and advancing the clinical development of cures for cancer patients.
    Keywords:  biomarkers; cancer; drug targets; kinase activity; machine learning; mass spectrometry; multiomics; proteomics; stemness; tumor plasticity
    DOI:  https://doi.org/10.1016/j.xgen.2025.100851
  16. Cell Death Dis. 2025 Apr 14. 16(1): 296
    Phosphoinositide signaling at the cytoskeleton in the regulation of cell dynamics.
    Xiaoting Hou, Yu Chen, Noah D Carrillo, Vincent L Cryns, Richard A Anderson, Jichao Sun, Songlin Wang, Mo Chen.
      The cytoskeleton, composed of microfilaments, intermediate filaments, and microtubules, provides the structural basis for cellular functions such as motility and adhesion. Equally crucial, phosphoinositide (PIPn) signaling is a critical regulator of these processes and other biological activities, though its precise impact on cytoskeletal dynamics has yet to be systematically investigated. This review explores the complex interplay between PIPn signaling and the cytoskeleton, detailing how PIPn modulates the dynamics of actin, intermediate filaments, and microtubules to shape cellular behavior. Dysregulation of PIPn signaling is implicated in various diseases, including cancer, highlighting promising therapeutic opportunities through targeted modulation of these pathways. Future research should aim to elucidate the intricate molecular interactions and broader cellular responses to PIPn signaling perturbations, particularly in disease contexts, to devise effective strategies for restoring cytoskeletal integrity.
    DOI:  https://doi.org/10.1038/s41419-025-07616-x
  17. Nat Cancer. 2025 Apr 18.
    UnitedMet harnesses RNA-metabolite covariation to impute metabolite levels in clinical samples.
    Amy X Xie, Wesley Tansey, Ed Reznik.
      Comprehensively studying metabolism requires metabolite measurements. Such measurements, however, are often unavailable in large cohorts of tissue samples. To address this basic barrier, we propose a Bayesian framework ('UnitedMet') that leverages RNA-metabolite covariation to impute otherwise unmeasured metabolite levels from widely available transcriptomic data. UnitedMet is equally capable of imputing whole pool sizes and outcomes of isotope tracing experiments. We apply UnitedMet to investigate the metabolic impact of driver mutations in kidney cancer, identifying an association between BAP1 and a highly oxidative tumor phenotype. We similarly apply UnitedMet to determine that advanced kidney cancers upregulate oxidative phosphorylation relative to early-stage disease, that oxidative metabolism in kidney cancer is associated with inferior outcomes to anti-angiogenic therapy and that kidney cancer metastases demonstrate elevated oxidative phosphorylation. UnitedMet provides a scalable tool for assessing metabolic phenotypes when direct measurements are infeasible, facilitating unexplored avenues for metabolite-focused hypothesis generation.
    DOI:  https://doi.org/10.1038/s43018-025-00943-0
  18. Math Biosci. 2025 Apr 11. pii: S0025-5564(25)00060-4. [Epub ahead of print]384 109434
    Deciphering Akt activation: Insights from a mean-field model.
    Catheryn W Gray, Adelle C F Coster.
      Being at the right place at the right time is vital for any signalling system component. Akt/PKB is a well-known low-threshold switch in the mammalian insulin signalling pathway. The activation of Akt is essential for the uptake of glucose, however, data concerning this vital system is very sparse, particularly with regards to cellular location and activation state. Here we present a parsimonious mathematical model that captures the current experimental understanding of Akt dynamics. The system operates on two distinct timescales (signalling and physical transport), with the transportation of Akt constituting the rate-limiting step in most circumstances. The model outputs are consistent with observations of the steady state behaviour of the system and display the transient overshoot behaviour which is a necessary characteristic of the activation of Akt.
    Keywords:  Activation; Akt/PKB; ODE model; Signalling; Transport
    DOI:  https://doi.org/10.1016/j.mbs.2025.109434
  19. Phys Biol. 2025 Apr 15.
    Representation of high-dimensional cell morphology and morphodynamics in 2-D latent space.
    Christian T Cunningham, Bo Sun.
      he morphology and morphodynamics of cells as important biomarkers of the cellular state are widely appreciated in both fundamental research and clinical applications. Quantification of cell morphology often requires a large number of geometric measures that form a high-dimensional feature vector. This mathematical representation creates barriers to communicating, interpreting, and visualizing data. Here, we develop a deep learning-based algorithm to project 13-dimensional (13D) morphological feature vectors into 2-dimensional (2D) morphological latent space. We show that the projection has less than 5\% information loss and separates the different migration phenotypes of metastatic breast cancer cells. Using the projection, we demonstrate the phenotype-dependent motility of breast cancer cells in the 3D extracellular matrix, and the continuous cell state change upon drug treatment. We also find that dynamics in the 2D morphological latent space quantitatively agrees with the morphodynamics of cells in the 13D feature space, preserving the diffusive power and the Lyapunov exponent of cell shape fluctuations even though the dimensional reduction projection is highly nonlinear. Our results suggest that morphological latent space is a powerful tool to represent and understand the cell morphology and morphodynamics.
    Keywords:  deep learning; dimensional reduction; morphodynamics; morphology
    DOI:  https://doi.org/10.1088/1478-3975/adcd37
  20. Nat Methods. 2025 Apr 17.
    Imaging 3D cell cultures with optical microscopy.
    Huai-Ching Hsieh, Qinghua Han, David Brenes, Kevin W Bishop, Rui Wang, Yuli Wang, Chetan Poudel, Adam K Glaser, Benjamin S Freedman, Joshua C Vaughan, Nancy L Allbritton, Jonathan T C Liu.
      Three-dimensional (3D) cell cultures have gained popularity in recent years due to their ability to represent complex tissues or organs more faithfully than conventional two-dimensional (2D) cell culture. This article reviews the application of both 2D and 3D microscopy approaches for monitoring and studying 3D cell cultures. We first summarize the most popular optical microscopy methods that have been used with 3D cell cultures. We then discuss the general advantages and disadvantages of various microscopy techniques for several broad categories of investigation involving 3D cell cultures. Finally, we provide perspectives on key areas of technical need in which there are clear opportunities for innovation. Our goal is to guide microscope engineers and biomedical end users toward optimal imaging methods for specific investigational scenarios and to identify use cases in which additional innovations in high-resolution imaging could be helpful.
    DOI:  https://doi.org/10.1038/s41592-025-02647-w
  21. Cell Stem Cell. 2025 Apr 10. pii: S1934-5909(25)00101-8. [Epub ahead of print]
    Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling.
    Kristina S Stapornwongkul, Elisa Hahn, Patryk Poliński, Laura Salamó Palau, Krisztina Arató, LiAng Yao, Kate Williamson, Nicola Gritti, Kerim Anlas, Mireia Osuna Lopez, Kiran R Patil, Idse Heemskerk, Miki Ebisuya, Vikas Trivedi.
      Metabolic pathways can influence cell fate decisions, yet their regulative role during embryonic development remains poorly understood. Here, we demonstrate an instructive role of glycolytic activity in regulating signaling pathways involved in mesoderm and endoderm specification. Using a mouse embryonic stem cell (mESC)-based in vitro model for gastrulation, we found that glycolysis inhibition increases ectodermal cell fates at the expense of mesodermal and endodermal lineages. We demonstrate that this relationship is dose dependent, enabling metabolic control of germ layer proportions through exogenous glucose levels. We further show that glycolysis acts as an upstream regulator of Nodal and Wnt signaling and that its influence on cell fate specification can be decoupled from its effects on growth. Finally, we confirm the generality of our findings using a human gastrulation model. Our work underscores the dependence of signaling pathways on metabolic conditions and provides mechanistic insight into the nutritional regulation of cell fate decision-making.
    Keywords:  Nodal signaling; Wnt signaling; endoderm; gastruloid; germ layer specification; glycolysis; mesoderm; metabolic signaling; nutritional environment; stem cell model of development
    DOI:  https://doi.org/10.1016/j.stem.2025.03.011
  22. bioRxiv. 2025 Apr 02. pii: 2025.03.28.646040. [Epub ahead of print]
    CREPE (CREate Primers and Evaluate): a computational tool for large-scale primer design and specificity analysis.
    Jonathan W Pitsch, Sara A Wirth, Nicole T Costantino, Josh Mejia, Rose M Doss, Xiaoxu Yang, Martin W Breuss.
      Polymerase chain reaction (PCR) is ubiquitous in biological research labs, as it is a fast, flexible, and cost-effective technique to amplify a DNA region of interest. Novel applications often leverage this ease of implementation and parallelize reactions for multiplexed approaches, such as next-generation sequencing. However, manual primer design can be an error-prone and time-consuming process depending on the number and composition of target sites. While Primer3 has emerged as an accessible tool to solve some of these issues and increase reproducibility, additional computational pipelines are required for appropriate scaling. Moreover, this does not replace the manual confirmation of primer specificity (i.e., the assessment of off-targets). To overcome the challenges associated with large-scale primer design, we fused the functionality of Primer3 and In-Silico PCR (ISPCR); this integrated pipeline, which we call CREPE ( CRE ate P rimers and E valuate), performs primer design and specificity analysis through a custom evaluation script for any given number of target sites at scale. Its final output summarizes the lead forward and reverse primer pair for each target site, a measure of the likelihood of binding to off-targets, and additional information to aid a user's decision-making. We provide this through a customized workflow for targeted amplicon sequencing (TAS) on a 150bp paired-end Illumina platform. Experimental testing of this application on clinically relevant loci showed successful amplification for more than 90% of primers deemed acceptable by CREPE. Together, we believe that CREPE represents a useful bioinformatic tool that supports the important scaling of PCR-based applications.
    DOI:  https://doi.org/10.1101/2025.03.28.646040
  23. bioRxiv. 2025 Apr 05. pii: 2025.03.31.646437. [Epub ahead of print]
    Automated Quality Control of Time-Course Imaging from 3D in vitro cultures.
    Eric Cramer, Tamara Lopez-Vidal, Jeanette Johnson, Vania Wang, Daniel Bergman, Ashani Weeraratna, Richard Burkhart, Elana J Fertig, Jacquelyn W Zimmerman, Laura M Heiser, Young Hwan Chang.
      Longitudinal imaging of 3D cell cultures like tumor organoids and spheroids offers crucial insights into cancer progression and treatment. However, spatial displacement during time-course imaging, caused by matrix detachment or experimental artifacts, can confound analyses. Existing computational methods struggle to address this issue. We present a new algorithm to evaluate data integrity and rectify mislabeling in longitudinal imaging of 3D cell culture. Our algorithm integrates permutation-based optimization with Procrustes analysis. By using X and Y coordinates of images, it accurately reorders, matches, and aligns object positions across time points, correcting for rotation, translation, and small movements. Validation with simulated data confirmed its accuracy and robustness. Applied to longitudinal imaging of tumor spheroids, our algorithm revealed frequent displacement amongst the spheroids between time points and corrected many mislabeled images. This computationally efficient and adaptable method needs no experimental adjustments and presents a readily accessible solution for data quality control.
    Motivation: Three-dimensional (3D) in vitro models, such as tumor organoids and spheroids embedded in an extracellular matrix, are increasingly vital for studying normal and disease biology, including drug responses. 1-3 A key advantage of these models is that imaging platforms can perform continuous longitudinal imaging to track phenotypic changes. However, common issues in 3D techniques, such as matrix shifts during experimental setup or image capture, can introduce technical artifacts that affect downstream analyses. Currently, no automated analytical approaches exist for assessing or correcting technical artifacts. Here, we introduce a robust, automated algorithm for assessing the quality of time-course image data and, in some cases, correcting object mislabeling to enable accurate tracking of individual spheroids over time. This approach relies only on image metadata, requiring no experimental modifications. It offers a readily implementable solution for improving data integrity and reproducibility and enhancing the reliability of longitudinal 3D cell culture studies.
    DOI:  https://doi.org/10.1101/2025.03.31.646437
  24. Nat Commun. 2025 Apr 15. 16(1): 3584
    Unveiling cellular communications through rapid pan-membrane-protein labeling.
    Hirushi Gunasekara, Yu-Shiuan Cheng, Vanessa Perez-Silos, Alejandro Zevallos-Morales, Daniel Abegg, Alyssa Burgess, Liang-Wei Gong, Richard D Minshall, Alexander Adibekian, Carlos Murga-Zamalloa, Alison E Ondrus, Ying S Hu.
      Dynamic protein distribution within and across the plasma membrane is pivotal in regulating cell communication. However, rapid, high-density labeling methods for multiplexed live imaging across diverse cell types remain scarce. Here, we demonstrate N-hydroxysuccinimide (NHS)-ester-based amine crosslinking of fluorescent dyes to uniformly label live mammalian cell surface proteins. Using model cell systems, we capture previously elusive membrane topology and cell-cell interactions. Live imaging shows transient membrane protein accumulation at cell-cell contacts and bidirectional migration patterns guided by membrane fibers in DC2.4 dendritic cells. Multiplexed superresolution imaging reveals the biogenesis of membrane tunneling nanotubes that facilitate intercellular transfer in DC2.4 cells, and caveolin 1-dependent endocytosis of insulin receptors in HEK293T cells. 3D superresolution imaging reveals membrane topology remodeling in response to stimulation, generation of microvesicles, and phagocytic activities in Jurkat T cells. Furthermore, NHS-labeling remains stable in vivo, enabling visualization of intercellular transfer among splenocytes using a T cell lymphoma mouse model.
    DOI:  https://doi.org/10.1038/s41467-025-58779-2
  25. Sci Adv. 2025 Apr 18. 11(16): eadt4881
    Sustained mTORC1 activation in activated T cells impairs vaccine responses in older individuals.
    Xiaorong Lin, Yanhua Du, Shuo Kan, Junjie Chen, Yunxue Yin, Linlin Li, Jingwen Chen, Wenrong Jiang, Wenqiang Cao, Chulwoo Kim, Liang Chen, Shiwen Wang, Jorg J Goronzy, Jun Jin.
      T cell aging contributes to the lower vaccine efficacy in older adults, yet the molecular mechanism remains elusive. Here, we show the density of initially responding naïve CD4+ T cells is instructive in T follicular helper (TFH) cell fate decisions and declines with age. A lower number of initially responding cells did not affect TFH differentiation at peak responses after immunization but accounted for an increased contraction phase manifesting as a larger loss of CXCR5 expression. Mechanistically, cells activated at a lower initial density had more sustained mammalian target of rapamycin complex 1 (mTORC1) activities that impair CXCR5 maintenance. YAP-dependent regulation of SLC7A5 involved in the cell density-dependent regulation of mTORC1 activities and TFH loss. Old mice fed with a leucine-restricted diet after peak responses showed smaller TFH loss and improved humoral immune responses. Attenuating mTORC1 signaling after peak response is a strategy to boost vaccine responses in older individuals.
    DOI:  https://doi.org/10.1126/sciadv.adt4881
  26. bioRxiv. 2025 Apr 03. pii: 2025.04.03.646654. [Epub ahead of print]
    A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments.
    Madeleine Duran, Eliza Barkan, Amy Tresenrider, Heidi Lee, Ryan Z Friedman, Nicholas Lammers, Marazzano Colón, Jennifer Franks, Brent Ewing, David Kimelman, Cole Trapnell.
      Improvements in single-cell sequencing protocols have democratized their use for phenotyping at organism-scale and molecular resolution, but interpreting such experiments poses computational challenges. Identifying the genes and cell types directly impacted by genetic, chemical, or environmental perturbations requires explicit modeling of lineage relationships amongst many cell types, over time, from datasets with millions of cells collected from thousands of specimens. We describe two software tools, "Hooke" and "Platt", which exploit the rich statistical patterns within single-cell datasets to characterize the direct molecular and cellular consequences of experimental perturbations. We apply Hooke and Platt to a single-cell atlas of thousands of perturbed zebrafish embryos to synthesize a coherent map of lineage dependencies and leverage it to reveal previously unappreciated roles for fate-determining transcription factors. We show that the co-variation between cell types in single-cell datasets is a powerful source of information for inferring how cells depend on genes and one another in the program of vertebrate development.
    DOI:  https://doi.org/10.1101/2025.04.03.646654
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