bims-pideca 2025-08-17 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2025–08–17
twenty papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Multicondition and multimodal temporal profile inference during mouse embryonic development.
The insulin signalling network.
Complementary cytoskeletal feedback loops control signal transduction excitability and cell polarity.
Systematic pegRNA design with PRIDICT2.0 and ePRIDICT for efficient prime editing.
The glycosyltransferase ALG3 is an AKT substrate that regulates protein N-glycosylation.
The Notch1 intracellular domain orchestrates mechanotransduction of fluid shear stress.
A growing problem: the many unsolved mysteries of cell growth.
Generation and evaluation of a novel PI3K-targeting gene therapy in the failing mouse heart and healthy sheep heart.
Exploiting an Epigenetic Resistance Mechanism to PI3 Kinase Inhibition in Leukemic Stem Cells.
CRISPR-Cas9 Single Nucleotide Editing of Tuberous Sclerosis Complex 2 Gene in Mesenchymal Stem Cells.
Targeting the MYC oncogene with a selective bi-steric mTORC1 inhibitor elicits tumor regression in MYC-driven cancers.
mTORC1-selective inhibitors rescue cellular phenotypes in TSC iPSC-derived neurons.
PTEN restricts IL-21R signaling in GC B cells and suppresses their differentiation to plasma cells.
TOR signalling mediates the collective movement of Border cells in Drosophila oogenesis.
Breast Cancer Cell Line-Specific Responses to Insulin: Effects on Proliferation and Migration.
Human-Induced Pluripotent Stem Cells (iPSCs) for Disease Modeling and Insulin Target Cell Regeneration in the Treatment of Insulin Resistance: A Review.
YAP charge patterning mediates signal integration through transcriptional co-condensates.
Engineering morphogenesis of cell clusters with differentiable programming.
Extracellular Vesicles of Adipose Multipotent Mesenchymal Stromal Cells Propagate Senescent Phenotype by Affecting PTEN Nuclear Import.
In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies.

Genome Res. 2025 Aug 14. pii: gr.279997.124. [Epub ahead of print]

Multicondition and multimodal temporal profile inference during mouse embryonic development.

Ran Zhang, Chengxiang Qiu, Galina Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, William Stafford Noble, Christine Disteche.

The emergence of single-cell time-series datasets enables modeling of changes in various types of cellular profiles over time. However, due to the disruptive nature of single-cell measurements, it is impossible to capture the full temporal trajectory of a particular cell. Furthermore, single-cell profiles can be collected at mismatched time points across different conditions (e.g., sex, batch, disease) and data modalities (e.g., scRNA-seq, scATAC-seq), which makes modeling challenging. Here we propose a joint modeling framework, Sunbear, for integrating multicondition and multimodal single-cell profiles across time. Sunbear can be used to impute single-cell temporal profile changes, align multidataset and multimodal profiles across time, and extrapolate single-cell profiles in a missing modality. We applied Sunbear to reveal sex-biased transcription during mouse embryonic development and predict dynamic relationships between epigenetic priming and transcription for cells in which multimodal profiles are unavailable. Sunbear thus enables the projection of single-cell time-series snapshots to multimodal and multicondition views of cellular trajectories.

DOI: https://doi.org/10.1101/gr.279997.124
Nat Metab. 2025 Aug 11.

The insulin signalling network.

James G Burchfield, Alexis Diaz-Vegas, David E James.

Insulin signalling is a central regulator of metabolism, orchestrating nutrient homeostasis and coordinating carbohydrate, protein and lipid metabolism. This network operates through dynamic, tightly regulated protein phosphorylation events involving key kinases such as AKT, shaping cellular responses with remarkable precision. Advances in phosphoproteomics have expanded our understanding of insulin signalling, revealing its intricate regulation and links to disease, particularly cardiometabolic disease. Major insights, such as the mechanisms of AKT activation and the influence of genetic and environmental factors, have emerged from studying this network. In this Review, we examine the architecture of insulin signalling, focusing on its precise temporal regulation. We highlight AKT's central role in insulin action and its vast substrate repertoire, which governs diverse cellular functions. Additionally, we explore feedback and crosstalk mechanisms, such as insulin receptor substrate protein signalling, which integrates inputs through phosphorylation at hundreds of distinct sites. Crucially, phosphoproteomics has uncovered complexities in insulin-resistant states, where network rewiring is characterized by disrupted phosphorylation and the emergence of novel sites that are absent in healthy cells. These insights redefine insulin signalling and its dysfunction, highlighting new therapeutic opportunities.

DOI: https://doi.org/10.1038/s42255-025-01349-z
Nat Commun. 2025 Aug 12. 16(1): 7482

Complementary cytoskeletal feedback loops control signal transduction excitability and cell polarity.

Jonathan Kuhn, Parijat Banerjee, Andrew Haye, Douglas N Robinson, Pablo A Iglesias, Peter N Devreotes.

To navigate complex environments, cells integrate chemical and mechanical cues through dynamic feedback between signaling networks and the cytoskeleton. Using synthetic tools to manipulate cytoskeletal components in Dictyostelium and human neutrophils, we uncover feedback mechanisms that regulate Ras/PI3K signaling and control front- and back-states of the cell. Increased branched actin and actin polymerization enhance Ras/PI3K activity. Similarly, decreased myosin II assembly also elevates signaling and chemotactic sensitivity. Conversely, inhibiting branched actin increases cortical actin and blocks Ras/PI3K activation-an effect lessened by decreasing filamentous actin or in myosin II-null cells. Activating RacE to increase actin crosslinking suppresses Ras activity without triggering branched actin nucleators, yet promotes spreading and protrusion. These results informed a computational model incorporating positive cytoskeletal feedback loops, which predicts shifts in polarity and migration with cytoskeletal changes. We propose that such feedback locally tunes signal network excitability, enabling cells to navigate tissues, extracellular matrix, and fluid environments.

DOI: https://doi.org/10.1038/s41467-025-62799-3
Nat Protoc. 2025 Aug 14.

Systematic pegRNA design with PRIDICT2.0 and ePRIDICT for efficient prime editing.

Nicolas Mathis, Kim Fabiano Marquart, Ahmed Allam, Michael Krauthammer, Gerald Schwank.

Prime editing is a versatile genome editing technology that enables precise genetic modifications without inducing DNA double-strand breaks. Owing to numerous variables in the prime editing guide RNA (pegRNA) design, experimentally identifying the most efficient pegRNA for a specific locus and edit is laborious. Therefore, we have developed computational tools to streamline this process. Here we present a comprehensive protocol detailing how to use PRIDICT2.0 and ePRIDICT, machine-learning models that assess the influence of the pegRNA design and chromatin context on prime editing. PRIDICT2.0 is an ensemble of attention-based bidirectional recurrent neural networks that predicts pegRNA efficiencies for replacements, insertions or deletions in different cellular contexts. Compared with other pegRNA design tools, PRIDICT2.0 accommodates larger edits-up to 40 base pairs-across diverse edit types, also allowing the introduction of silent bystander edits that can enhance editing efficiency. ePRIDICT, a gradient-boosting algorithm, further accounts for the local chromatin environments and assesses how the genomic location of the target site affects prime editing rates. Both tools are available at www.pridict.it for individual predictions or can be installed locally for batch processing of multiple edits and target sites. The protocol provides step-by-step instructions on using PRIDICT2.0 and ePRIDICT, covering sequence input, prediction generation and interpretation. Web-based predictions take under a minute, while local installation and batch processing may take up to several hours, depending on the dataset size. By streamlining pegRNA selection and chromatin context analysis, these tools promote the adoption of prime editing in basic and translational research.

DOI: https://doi.org/10.1038/s41596-025-01244-7
J Biol Chem. 2025 Aug 09. pii: S0021-9258(25)02433-0. [Epub ahead of print] 110582

The glycosyltransferase ALG3 is an AKT substrate that regulates protein N-glycosylation.

Adrija J Navarro-Traxler, Laura Ghisolfi, Evan C Lien, Alex Toker.

  The PI3K/AKT signaling pathway is frequently dysregulated in cancer and controls key cellular processes such as survival, proliferation, metabolism and growth. Protein glycosylation is essential for proper protein folding and is also often deregulated in cancer. Cancer cells depend on increased protein folding to sustain oncogene-driven proliferation rates. The N-glycosyltransferase asparagine-linked glycosylation 3 homolog (ALG3), a rate-limiting enzyme during glycan biosynthesis, catalyzes the addition of the first mannose to glycans in an alpha-1,3 linkage. Here we show that ALG3 is phosphorylated downstream of the PI3K/AKT pathway in both growth factor-stimulated cells and PI3K/AKT-hyperactive cancer cells. AKT directly phosphorylates ALG3 in the amino terminal region at Ser11/Ser13. CRISPR/Cas9-mediated depletion of ALG3 leads to improper glycan formation and induction of endoplasmic reticulum stress, the unfolded protein response, and impaired cell proliferation. Phosphorylation of ALG3 at Ser11/Ser13 is required for glycosylation of cell surface receptors EGFR, HER3 and E-cadherin. These findings provide a direct link between PI3K/AKT signaling and protein glycosylation in cancer cells.

Keywords:  AKT; ALG3; N-glycosylation; PI3-kinase; glycans; phosphorylation; signaling

DOI:  https://doi.org/10.1016/j.jbc.2025.110582
bioRxiv. 2025 Jul 14. pii: 2025.07.13.663563. [Epub ahead of print]

The Notch1 intracellular domain orchestrates mechanotransduction of fluid shear stress.

Tania Singh, Kyle A Jacobs, William J Polacheck, Matthew L Kutys.

Hemodynamic shear stress regulates endothelial phenotype through activation of Notch1 signaling, yet the mechanistic basis for this activation is unclear. Here, we establish a fluid shear stress-dependent mechanism of Notch1 activation that is distinct from canonical ligand trans-endocytosis. Application of laminar flow triggers the rapid spatial polarization of full-length Notch1 heterodimers into downstream membrane microdomains. Unlike canonical transactivation, this response occurs independently of ligand redistribution, and Notch1 receptors are cis-endocytosed into the receptor-bearing cell within polarized microdomains prior to proteolytic activation. We discover that the Notch1 intracellular domain (ICD) critically orchestrates receptor polarization and proteolytic activation in response to flow but is dispensable for canonical ligand transactivation. Shear stress increases ICD interaction with annexin A2 and caveolar proteins which control Notch1 endocytosis and proteolytic compartmentalization. These findings define a flow-specific Notch1 mechanotransduction pathway linking receptor polarization and endocytosis with proteolytic activation and establish new mechanisms regulating Notch receptor activation.

DOI: https://doi.org/10.1101/2025.07.13.663563
Mol Biol Cell. 2025 Aug 13. mbcE21070359

A growing problem: the many unsolved mysteries of cell growth.

Douglas R Kellogg.

Growth is the essential vital process that drives life forward and always occurs within cells. Cell growth fuels the cell divisions that drive proliferation of single-celled organisms and growth of multi-cellular organisms. Mechanisms that control the extent and location of growth within cells generate the extraordinary diversity of cell sizes and shapes seen across the tree of life and within the human body, and nearly all cancers show profound defects in control of cell growth that lead to severe aberrations in cell size and shape. Yet we know little about how cell growth occurs or how it is controlled. For decades we have known how basic building blocks such as amino acids and lipids are built, but an enormous gap has always remained in our understanding of how these building blocks are used to build out cells of highly diverse sizes and shapes under varying environmental conditions and in diverse developmental contexts. Given the fundamental importance of growth in biology and cancer, our minimal understanding of cell growth is a growing problem. Here, a few of the intriguing and important questions about cell growth are considered.

DOI: https://doi.org/10.1091/mbc.E21-07-0359
J Mol Cell Cardiol Plus. 2025 Sep;13 100478

Generation and evaluation of a novel PI3K-targeting gene therapy in the failing mouse heart and healthy sheep heart.

Sebastian Bass-Stringer, Daniel G Donner, Clive N May, Aya Matsumoto, Emma I Masterman, Aascha A D'Elia, Yi Ching Chen, Helen Kiriazis, Jieting Luo, Roger Chooi, Clara Liu Chung Ming, Paul Gregorevic, Colleen J Thomas, Bianca C Bernardo, Kate L Weeks, Julie R McMullen.

  Heart failure (HF) remains a clinical challenge with cardiac dysfunction typically progressing even with treatment, and heart transplants only available to small numbers. We previously identified phosphoinositide 3-kinase (PI3K, p110α) as a master regulator of exercise-induced cardioprotection, and showed that gene therapy, incorporating a constitutively active form of PI3K (caPI3K) improved function of the failing mouse heart. However, this approach was not cardiac-specific and the gene therapy was challenging to manufacture. The aim of this study was to develop new PI3K-based gene therapies with more optimal properties for clinical translation. We generated and assessed adeno-associated viruses (AAV6) encoding various PI3K constructs, with different enhancers, promoters and transgene components in healthy adult male mice. The most promising AAV construct based on AAV expression, cardiac-specificity, and ease of manufacture contained a cardiac troponin T (cTnT) promoter together with a small region of the regulatory subunit of PI3K (iSH2), and an intron from the β-globin gene which enhances transcription (IVS2). This AAV (1 × 1012, 2 × 1012 vg) was administered to mice with myocardial ischemia/reperfusion injury (I/R: 1 h ischemia with reperfusion; AAV delivered 24 h post-I/R). Direct cardiac injections of PI3K-based AAVs were also performed in healthy adult female sheep. I/R mouse hearts treated with the AAV6-cTnT-IVS2-iSH2 displayed increased phosphorylation of Akt, but no improvement in cardiac function or structure was observed. AAV6-cTnT-IVS2-iSH2 successfully transduced healthy sheep hearts which increased endogenous PI3K catalytic activity. Further testing/optimization of the AAV (time of delivery and/or duration) will be required to assess the therapeutic potential of this approach.

Keywords:  AAV; Gene therapy; Heart failure; Large animal; Mouse; PI3K

DOI:  https://doi.org/10.1016/j.jmccpl.2025.100478
bioRxiv. 2025 Jul 15. pii: 2025.07.11.663968. [Epub ahead of print]

Exploiting an Epigenetic Resistance Mechanism to PI3 Kinase Inhibition in Leukemic Stem Cells.

Shira G Glushakow-Smith, Imit Kaur, Simone Sidoli, Shayda Hemmati, Ellen Angeles, Taneisha Sinclair, Samarpana Chakraborty, Aaliyah Battle, Kristina Ames, Swathi-Rao Narayanagari, Rotila Hyka, Mark Soto, Melissa Tracy, Jayaram Vankudoth, Seiya Kitamura, Linde Miles, Ulrich Steidl, Aditi Shastri, Amit Verma, Kira Gritsman.

Acquired non-genetic resistance mechanisms to existing therapies contribute to poor outcomes for acute myeloid leukemia (AML) patients, and inability to target leukemic stem cells (LSCs) can lead to relapse. To overcome these challenges, we tested whether LSCs have dependencies on PI3 kinase (PI3K). We found that LSCs are susceptible to isoform-selective targeting of PI3K and are particularly dependent on the P110 alpha isoform of PI3K. We discovered that PI3K inactivation leads to dynamic changes in EZH2/PRC2 function in leukemic cells, and we uncovered downregulation of EZH2 protein levels as a resistance mechanism in response to PI3K inhibition. We found that PI3K inhibition in AML cells can lead to compensatory upregulation of EZH1, and that EZH1 knockdown can sensitize AML cells to PI3K inhibition. We leveraged this resistance mechanism by combining a PI3K inhibitor with an EZH1/2 dual inhibitor, which successfully overcomes the acquired resistance and leads to sustained targeting of AML cells ex vivo and in murine AML and PDX models in vivo. This study identifies a promising novel therapeutic regimen for targeting LSCs in AML.

DOI: https://doi.org/10.1101/2025.07.11.663968
CRISPR J. 2025 Aug 14.

CRISPR-Cas9 Single Nucleotide Editing of Tuberous Sclerosis Complex 2 Gene in Mesenchymal Stem Cells.

Abdallah Salemdawod, Brandon Cooper, Yajie Liang, Piotr Walczak, Hartmut Vatter, Jaroslaw Maciaczyk, Miroslaw Janowski.

The tuberous sclerosis complex (TSC)2 gene regulates the mammalian target of rapamycin (mTOR) pathway, impacting cell proliferation and growth. The loss-of-function mutations, especially in mesenchymal progenitors, drive the development multiple benign and malignant tumors. TSC2 mutations in certain cancer types, e.g., breast cancer, are also associated with poorer prognosis. The databases of TSC2-mutations report point mutations as the most prevalent. We aimed to test the feasibility of inducing point mutations in mesenchymal stem cells (MSCs), targeting the most frequent point mutations of the TSC2 gene, TSC2. c.1864 C>T (p.Arg622Trp), TSC2. c.1832 G>A (p.Arg611Glu), and TSC2. c.5024 C>T (p.Pro1675Leu) using two delivery methods for CRISPR-Cas9. We report a high editing efficiency of up to 85% inducing TSC2 point mutations in hMSCs using lipofectamine-based transfection. Overall, the high editing efficiency of some TSC2 mutations enables the induction and reversal of mutations in primary hMSCs without needing resource-consuming derivation of cell lines frequently distinct from their primary counterparts.

DOI: https://doi.org/10.1177/25731599251367059
Cell Chem Biol. 2025 Aug 11. pii: S2451-9456(25)00227-2. [Epub ahead of print]

Targeting the MYC oncogene with a selective bi-steric mTORC1 inhibitor elicits tumor regression in MYC-driven cancers.

Wadie D Mahauad-Fernandez, Yu Chi Yang, Ian Lai, Jangho Park, Lilian Yao, James W Evans, Danielle F Atibalentja, Xinyu Chen, Vishnupriya Kanakaveti, Zihui Zhao, G Leslie Burnett, Bianca J Lee, Nuntana Dinglasan, Nataliya Tovbis Shifrin, Ethan Ahler, Elsa Quintana, Adrian L Gill, Jacqueline A M Smith, Mallika Singh, Dean W Felsher.

  The MYC oncogene is causally involved in the pathogenesis of most human cancers. The mTORC1 complex regulates MYC translation through 4EBP1 and S6K. However, agents that selectively target mTORC1 (without affecting mTORC2) have so far failed to reactivate 4EBP1 and, thus, cannot effectively suppress MYC in vivo. In contrast, nonselective inhibitors that block both mTOR complexes can activate 4EBP1, but often lack tolerability and induce immunosuppression. Here, we introduce bi-steric mTORC1-selective inhibitors, including the clinical candidate RMC-5552, which potently reactivate 4EBP1 and decrease MYC protein expression levels. Consequently, suppression of MYC signaling occurs, resulting in tumor growth inhibition through both direct effects on tumor cells and immune activation. RMC-5552 exhibits anti-tumor activity in human patient-derived xenografts models harboring genomic MYC amplifications and reduces MYC protein levels in vivo. Furthermore, bi-steric mTORC1-selective inhibitors enhance the efficacy of immune checkpoint blockade, leading to tumor regression.

Keywords:  4EBP1; HCC; MYC; MYC-driven cancers; S6k; hepatocellular carcinoma; immune activation; immune checkpoint blockade; mTORC1-selective inhibitors; tumor immune microenvironment; tumor regression

DOI:  https://doi.org/10.1016/j.chembiol.2025.07.004
Front Neurosci. 2025 ;19 1595880

mTORC1-selective inhibitors rescue cellular phenotypes in TSC iPSC-derived neurons.

Elizabeth D Buttermore, Gayathri Rajaram Srinivasan, Hellen Jumo, Amanda C Swanson, Benjamin O'Kelly, Nina R Makhortova, Mustafa Sahin, Stelios T Tzannis.

  The mechanistic target of rapamycin (mTOR) pathway plays an important role in regulating multiple cellular processes, including cell growth, autophagy, proliferation, protein synthesis, and lipid synthesis, among others. Given the central role of this pathway in multiple cellular processes, it is not surprising that mTOR pathway dysregulation is a key mechanism underlying several neurological disorders, including Tuberous Sclerosis Complex (TSC). TSC patients typically present with pathogenic variants in the TSC1 or TSC2 genes, which encode proteins forming a complex that plays an important role in modulating mTOR activity. We previously reported cellular and functional deficits in induced pluripotent stem cell (iPSC)-derived neurons from TSC patients. These deficits were reversed by inhibiting mTOR activity using rapamycin treatment, revealing the role of mTOR signaling in the regulation of cell morphology and hyperexcitability phenotypes in TSC patient-derived neurons. However, chronic rapamycin treatment inhibits both mTORC1 and mTORC2 activity and its clinical use is associated with significant side effects. With the development of novel mTORC1-selective compounds, we aimed to assess whether selective inhibition of mTORC1 likewise reversed the cellular and functional deficits found in TSC patient-derived neurons. Our results indicate that the novel, selective mTORC1 inhibitors nearly fully reversed the cellular and functional deficits of TSC2 -/ - iPSC-derived neurons in a fashion and magnitude similar to rapamycin, as they all reversed and near-normalized their neuronal hyperexcitability and abnormal morphology as compared to the DMSO-treated cells. These data suggest that mTORC1-specific compounds could provide clinical therapeutic benefit similar to rapamycin without the same side effects.

Keywords:  TSC2; hyperexcitability; iPSC-derived neurons; mTOR; mTORC1; mTORC2; soma size

DOI:  https://doi.org/10.3389/fnins.2025.1595880
J Immunol. 2025 Aug 07. pii: vkaf160. [Epub ahead of print]

PTEN restricts IL-21R signaling in GC B cells and suppresses their differentiation to plasma cells.

Alexander R Maldeney, Wenxia Jiang, Laura Conter, Daniel J Wikenheiser, William F Hawse, Anandkumar Patel, Weixun Peng, Mark J Shlomchik, Wei Luo.

  The germinal center (GC) reaction is essential for generating high-quality humoral memory. Positively selected GC B cells must decide whether to remain in the GC for further affinity maturation or differentiate into memory or plasma cells (PCs). Previously, we identified IL-21R and CD40 signaling as critical promoters of GC B cell effector differentiation. However, the mechanisms regulating the strength of these signals remain unclear. PTEN, a negative regulator of PI3K signaling, is markedly upregulated in GC B cells. To explore the role of PTEN in GC B cell fate decisions, we used a tamoxifen-driven Cre system to delete PTEN in B cells after GC reaction was fully established. We found that PTEN deletion in ongoing GC B cells led to significantly increased differentiation into PCs, while having limited effects on class switching or memory precursor differentiation. These results were further confirmed using a GC B cell transfer system, where wild-type and PTEN-deficient GC B cells were transferred into the same recipient mice. Mechanistically, PTEN deletion or inhibition in established GC B cells resulted in more sustained IL-21R signaling and enhanced CD40 signaling-both known to promote PC differentiation. Interestingly, Peyer's patch GC B cells exhibited higher PTEN levels than de novo GC B cells generated through immunization. Notably, PTEN deficiency selectively expanded GC B cells in Peyer's patches but had no impact on those induced by immunization. These findings reveal previously unrecognized roles for PTEN in regulating GC B cell signaling and limiting their differentiation into PCs.

Keywords:  PTEN; germinal center B cell; plasma cell differentiation; signaling

DOI:  https://doi.org/10.1093/jimmun/vkaf160
Development. 2025 Aug 11. pii: dev.204612. [Epub ahead of print]

TOR signalling mediates the collective movement of Border cells in Drosophila oogenesis.

Sudipta Halder, Adhisree Sharma, Sayan Acharjee, Neha Biju, Mincy Kunjumon, Rohan Jayant Khadilkar, Mohit Prasad.

  Collective cell migration is seen in various biological processes spanning embryonic development, organogenesis, wound healing and, unfortunately, cancer metastasis. Here, we have examined the role of the evolutionary conserved Target of Rapamycin signalling (TOR) in mediating collective cell movement employing the model of migrating BCs in Drosophila oogenesis. Though TOR signalling is classically linked to cell growth, cell proliferation and metabolism, here we demonstrate TOR Complex1 (TORC1) regulates efficient group cell movement of BCs. Employing live cell imaging, genetics, and tissue immunohistochemistry, we demonstrate TOR functions through transcription factor Reptor to modulate the Death-associated inhibitor of apoptosis 1 (DIAP1) in mediating efficient movement of BCs. Coincidentally, Rapamycin-treated myeloblast Kasumi-1 cells exhibit lower levels of transcript for DIAP-1 homolog, Baculoviral IAP repeat-containing 2 (BIRC2), similar to what is observed in flies.

Keywords:   Drosophila oogenesis; BC migration; BIRC2; Collective cell movement; DIAP1; REPTOR; TOR signalling

DOI:  https://doi.org/10.1242/dev.204612
Int J Mol Sci. 2025 Aug 04. pii: 7523. [Epub ahead of print]26(15):

Breast Cancer Cell Line-Specific Responses to Insulin: Effects on Proliferation and Migration.

Mattia Melloni, Domenico Sergi, Angelina Passaro, Luca Maria Neri.

  Breast cancer (BC) progression appears to be significantly influenced by the diabetic microenvironment, characterised by hyperglycaemia and hyperinsulinemia, though the exact cellular mechanisms remain partly unclear. This study investigated the effects of exposure to supra-physiological levels of glucose and insulin on two distinct BC cell models: hormone-responsive MCF-7 cells and triple-negative MDA-MB-231 cells. To evaluate the effects triggered by high insulin level in different BC cell subtypes, we analysed the activation status of PI3K/AKT and MAPK pathways, cell proliferation, cell distribution in cell cycle phases and cell migration. High insulin level significantly activates the insulin metabolic pathway via AKT phosphorylation in both cell lines while inducing pro-proliferative stimulus and modulation of cell distribution in cell cycle phases only in the hormone-responsive MCF-7 cell line. On the contrary, high-glucose containing medium alone did not modulate proliferation nor further increased it when combined with high insulin level in both the investigated cell lines. However, following insulin treatment, the MAPK pathway remained unaffected, suggesting that the proliferation effects in the MCF-7 cell line are mediated by AKT activation. This linkage was also demonstrated by AKT phosphorylation blockade, driven by the AKT inhibitor MK-2206, which negated the proliferative stimulus. Interestingly, while MDA-MB-231 cells, following chronic hyperinsulinemia exposure, did not exhibit enhanced proliferation, they displayed a marked increase in migratory behaviour. These findings suggest that chronic hyperinsulinemia, but not hyperglycaemia, exerts subtype-specific effects in BC, highlighting the potential of targeting insulin pathways for therapeutic intervention.

Keywords:  breast cancer; hyperglycaemia; hyperinsulinemia; insulin signalling; type 2 diabetes mellitus

DOI:  https://doi.org/10.3390/ijms26157523
Cells. 2025 Aug 01. pii: 1188. [Epub ahead of print]14(15):

Human-Induced Pluripotent Stem Cells (iPSCs) for Disease Modeling and Insulin Target Cell Regeneration in the Treatment of Insulin Resistance: A Review.

Sama Thiab, Juberiya M Azeez, Alekya Anala, Moksha Nanda, Somieya Khan, Alexandra E Butler, Manjula Nandakumar.

  Diabetes mellitus, both type 1 (T1D) and type 2 (T2D), has become the epidemic of the century and a major public health concern given its rising prevalence and the increasing adoption of a sedentary lifestyle globally. This multifaceted disease is characterized by impaired pancreatic beta cell function and insulin resistance (IR) in peripheral organs, namely the liver, skeletal muscle, and adipose tissue. Additional insulin target tissues, including cardiomyocytes and neuronal cells, are also affected. The advent of stem cell research has opened new avenues for tackling this disease, particularly through the regeneration of insulin target cells and the establishment of disease models for further investigation. Human-induced pluripotent stem cells (iPSCs) have emerged as a valuable resource for generating specialized cell types, such as hepatocytes, myocytes, adipocytes, cardiomyocytes, and neuronal cells, with diverse applications ranging from drug screening to disease modeling and, importantly, treating IR in T2D. This review aims to elucidate the significant applications of iPSC-derived insulin target cells in studying the pathogenesis of insulin resistance and T2D. Furthermore, recent differentiation strategies, protocols, signaling pathways, growth factors, and advancements in this field of therapeutic research for each specific iPSC-derived cell type are discussed.

Keywords:  diabetes mellitus; human-induced pluripotent stem cells; iPSC differentiation; iPSC-derived insulin target cells; insulin resistance

DOI:  https://doi.org/10.3390/cells14151188
Nat Commun. 2025 Aug 12. 16(1): 7454

YAP charge patterning mediates signal integration through transcriptional co-condensates.

Kirstin Meyer, Klaus Yserentant, Rasmi Cheloor-Kovilakam, Kiersten M Ruff, Chan-I Chung, Xiaokun Shu, Bo Huang, Orion D Weiner.

Transcription factor dynamics are used to selectively engage gene regulatory programs. Biomolecular condensates have emerged as an attractive signaling module in this process, but the underlying mechanisms are not well-understood. Here, we probe the molecular basis of YAP signal integration through transcriptional condensates. Leveraging light-sheet single-molecule imaging and synthetic condensates, we demonstrate charge-mediated co-condensation of the transcriptional regulators YAP and Mediator into transcriptionally active condensates in stem cells. Intrinsically disordered region sequence analysis and YAP protein engineering demonstrate that the signaling specificity of YAP is established, in part, through complementary electrostatic interactions between negatively charged blocks within YAP and positively charged blocks within Mediator. YAP/Mediator co-condensation is counteracted by negative feedback from transcription, driving an adaptive transcriptional response that is well-suited for decoding dynamic inputs. Our work reveals a molecular framework for YAP condensate formation and sheds light on the function of YAP condensates for emergent gene regulatory behavior.

DOI: https://doi.org/10.1038/s41467-025-62157-3
Nat Comput Sci. 2025 Aug 13.

Engineering morphogenesis of cell clusters with differentiable programming.

Ramya Deshpande, Francesco Mottes, Ariana-Dalia Vlad, Michael P Brenner, Alma Dal Co.

Understanding the fundamental rules of organismal development is a central, unsolved problem in biology. These rules dictate how individual cellular actions coordinate over macroscopic numbers of cells to grow complex structures with exquisite functionality. We use recent advances in automatic differentiation to discover local interaction rules and genetic networks that yield emergent, systems-level characteristics in a model of development. We consider a growing tissue with cellular interactions mediated by morphogen diffusion, cell adhesion and mechanical stress. Each cell has an internal genetic network that is used to make decisions based on the cell's local environment. Here we show that one can learn the parameters governing cell interactions in the form of interpretable genetic networks for complex developmental scenarios. When combined with recent experimental advances measuring spatio-temporal dynamics and gene expression of cells in a growing tissue, the methodology outlined here offers a promising path to unraveling the cellular bases of development.

DOI: https://doi.org/10.1038/s43588-025-00851-4
Int J Mol Sci. 2025 Jul 24. pii: 7164. [Epub ahead of print]26(15):

Extracellular Vesicles of Adipose Multipotent Mesenchymal Stromal Cells Propagate Senescent Phenotype by Affecting PTEN Nuclear Import.

Elizaveta Chechekhina, Semyon Kamenkov, Vadim Chechekhin, Anna Zinoveva, Elizaveta Bakhchinyan, Anastasia Efimenko, Natalia Kalinina, Vsevolod Tkachuk, Konstantin Kulebyakin, Pyotr Tyurin-Kuzmin.

  Replicative or stress-induced senescence disrupts the functioning of multipotent mesenchymal stromal cells (MSCs) required for tissue renewal and regeneration. Aged MSCs demonstrate reduced proliferation, impaired differentiation, and aberrant secretory activity, defined as "senescence-associated secretory phenotype" (SASP). SASP is characterized by elevated secretion of proinflammatory cytokines and specific extracellular vesicles (SASP-EVs), which affect the cellular microenvironment and promote tissue dysfunction. However, molecular mechanisms responsible for senescent phenotype propagation remain largely obscure. Earlier, we demonstrated suppression of adipogenic differentiation and insulin sensitivity of young MSCs by SASP-EVs. In this study, we elucidated potential mechanisms underlying SASP-EVs' effects on MSCs. Bioinformatic analysis revealed that insulin signaling components are the most probable targets of SASP-EVs microRNA cargo. We demonstrated that SASP-EVs downregulated intracellular AGO1 levels, but surprisingly, PTEN levels were upregulated. Specifically, the increase in PTEN content was provided by its nuclear fraction. We have found that the intracellular PTEN distribution in young MSCs treated by SASP-EVs was similar to senescent MSCs. Furthermore, PTEN upregulation was accompanied by increased PTENP1 expression-a molecular sponge for PTEN-targeting microRNAs. Our findings indicate that nuclear PTEN could be a hallmark of senescent MSCs, and SASP-EVs propagate the senescent phenotype in young MSCs by promoting PTEN nuclear localization.

Keywords:  PTEN nuclear import; SASP; cellular senescence; extracellular vesicles; insulin resistance; mesenchymal stem cells; microRNAs

DOI:  https://doi.org/10.3390/ijms26157164
Commun Chem. 2025 Aug 13. 8(1): 245

In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies.

Philipp Bräuer, Laszlo Tirian, Fränze Müller, Karl Mechtler, Manuel Matzinger.

Cross-linking mass spectrometry has evolved as a powerful technique to study protein-protein interactions and to provide structural information. Low reaction efficiencies, and complex matrices lead to challenging system wide crosslink analysis. We improved and streamlined an Azide-A-DSBSO based in vivo crosslinking workflow employing two orthogonal effective enrichment steps: Affinity enrichment and size exclusion chromatography (SEC). Combined, they allow an effective enrichment of DSBSO containing peptides and remove the background of linear as well as mono-linked peptides. We found that the analysis of a single SEC fraction is effective to yield ~90% of all crosslinks, which is important whenever measurement time is limited, and sample throughput is crucial. Our workflow resulted in more than 5000 crosslinks from K562 cells and generated a comprehensive PPI network. From 393 PPI found within the nucleus, 56 are novel. We further show, that by applying DSBSO to nuclear extracts we yield more crosslinks on lower abundant proteins and showcase this on the DEAD-box RNA helicase DDX39B which is predominantly expressed in the nucleus. Our data indicates that DDX39B might be present in monomeric and dimeric forms together with DDX39A within the nuclear extracts analyzed.

DOI: https://doi.org/10.1038/s42004-025-01644-6