bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2024‒03‒24
twenty-two papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes.
  2. Presence of active AKT in the nucleus upon adipocyte differentiation of 3T3-L1 cells.
  3. scPROTEIN: a versatile deep graph contrastive learning framework for single-cell proteomics embedding.
  4. Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver.
  5. Progress in single-cell multimodal sequencing and multi-omics data integration.
  6. Minimizing Shear Stress in Cell Signaling Studies.
  7. A real-world disproportionality analysis of FDA adverse event reporting system (FAERS) events for alpelisib.
  8. Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data.
  9. Expanding TheCellVision.org: A Central Repository for Visualizing and Mining High-Content Cell Imaging Projects.
  10. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation.
  11. Multi-condition and multi-modal temporal profile inference during mouse embryonic development.
  12. Cancer cells hijack physiological metabolic signals to seed liver metastasis.
  13. Substrate preference of protein kinase B isoforms can vary depending on the cell line.
  14. Modeling gene expression cascades during cell state transitions.
  15. PTEN decreases NR2F1 expression to inhibit ciliogenesis during EGFRL858R-induced lung cancer progression.
  16. E-cadherin interacts with EGFR resulting in hyper-activation of ERK in multiple models of breast cancer.
  17. FOXO1 promotes cancer cell growth through MDM2-mediated p53 degradation.
  18. Single-cell lineage tracing with endogenous markers.
  19. A fast-acting lipid checkpoint in G1 prevents mitotic defects.
  20. Integrating the response to stressed mitochondria.
  21. Proteome-scale discovery of protein degradation and stabilization effectors.
  22. Self-organization of PIP3 waves is controlled by the topology and curvature of cell membranes.
  1. Nat Commun. 2024 Mar 20. 15(1): 2474
    One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes.
    Zilu Ye, Pierre Sabatier, Javier Martin-Gonzalez, Akihiro Eguchi, Maico Lechner, Ole Østergaard, Jingsheng Xie, Yuan Guo, Lesley Schultz, Rafaela Truffer, Dorte B Bekker-Jensen, Nicolai Bache, Jesper V Olsen.
      Mass spectrometry (MS)-based proteomics workflows typically involve complex, multi-step processes, presenting challenges with sample losses, reproducibility, requiring substantial time and financial investments, and specialized skills. Here we introduce One-Tip, a proteomics methodology that seamlessly integrates efficient, one-pot sample preparation with precise, narrow-window data-independent acquisition (nDIA) analysis. One-Tip substantially simplifies sample processing, enabling the reproducible identification of >9000 proteins from ~1000 HeLa cells. The versatility of One-Tip is highlighted by nDIA identification of ~6000 proteins in single cells from early mouse embryos. Additionally, the study incorporates the Uno Single Cell Dispenser™, demonstrating the capability of One-Tip in single-cell proteomics with >3000 proteins identified per HeLa cell. We also extend One-Tip workflow to analysis of extracellular vesicles (EVs) extracted from blood plasma, demonstrating its high sensitivity by identifying >3000 proteins from 16 ng EV preparation. One-Tip expands capabilities of proteomics, offering greater depth and throughput across a range of sample types.
    DOI:  https://doi.org/10.1038/s41467-024-46777-9
  2. MicroPubl Biol. 2024 ;2024
    Presence of active AKT in the nucleus upon adipocyte differentiation of 3T3-L1 cells.
    Marianne Goris, Rhîan G Jacobsen, Aurélia E Lewis.
      AKT is an essential player in the phosphoinositide 3-kinase (PI3K) signalling pathway. Although the mechanisms of its action are well understood at the plasma membrane, AKT can also be found in the nucleus. In adipocytes, this pathway is activated during the process of adipogenesis and solicits both plasma membrane and nuclear AKT activity. However, the endogenous presence of active AKT in the nucleus during adipogenesis has not been shown. Here, we show that the levels of active AKT phosphorylated at Ser-473 increase rapidly after the induction of differentiation in 3T3-L1 cells, both in the cytoplasm and in the nucleus, and tend to remain elevated over the course of differentiation. In conclusion, these results support the notion that nuclear AKT plays an important role in this process.
    DOI:  https://doi.org/10.17912/micropub.biology.001140
  3. Nat Methods. 2024 Mar 19.
    scPROTEIN: a versatile deep graph contrastive learning framework for single-cell proteomics embedding.
    Wei Li, Fan Yang, Fang Wang, Yu Rong, Linjing Liu, Bingzhe Wu, Han Zhang, Jianhua Yao.
      Single-cell proteomics sequencing technology sheds light on protein-protein interactions, posttranslational modifications and proteoform dynamics in the cell. However, the uncertainty estimation for peptide quantification, data missingness, batch effects and high noise hinder the analysis of single-cell proteomic data. It is important to solve this set of tangled problems together, but the existing methods tailored for single-cell transcriptomes cannot fully address this task. Here we propose a versatile framework designed for single-cell proteomics data analysis called scPROTEIN, which consists of peptide uncertainty estimation based on a multitask heteroscedastic regression model and cell embedding generation based on graph contrastive learning. scPROTEIN can estimate the uncertainty of peptide quantification, denoise protein data, remove batch effects and encode single-cell proteomic-specific embeddings in a unified framework. We demonstrate that scPROTEIN is efficient for cell clustering, batch correction, cell type annotation, clinical analysis and spatially resolved proteomic data exploration.
    DOI:  https://doi.org/10.1038/s41592-024-02214-9
  4. Nat Commun. 2024 Mar 18. 15(1): 1878
    Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver.
    Ana Belén Plata-Gómez, Lucía de Prado-Rivas, Alba Sanz, Nerea Deleyto-Seldas, Fernando García, Celia de la Calle Arregui, Camila Silva, Eduardo Caleiras, Osvaldo Graña-Castro, Elena Piñeiro-Yáñez, Joseph Krebs, Luis Leiva-Vega, Javier Muñoz, Ajay Jain, Guadalupe Sabio, Alejo Efeyan.
      The metabolic functions of the liver are spatially organized in a phenomenon called zonation, linked to the differential exposure of portal and central hepatocytes to nutrient-rich blood. The mTORC1 signaling pathway controls cellular metabolism in response to nutrients and insulin fluctuations. Here we show that simultaneous genetic activation of nutrient and hormone signaling to mTORC1 in hepatocytes results in impaired establishment of postnatal metabolic and zonal identity of hepatocytes. Mutant hepatocytes fail to upregulate postnatally the expression of Frizzled receptors 1 and 8, and show reduced Wnt/β-catenin activation. This defect, alongside diminished paracrine Wnt2 ligand expression by endothelial cells, underlies impaired postnatal maturation. Impaired zonation is recapitulated in a model of constant supply of nutrients by parenteral nutrition to piglets. Our work shows the role of hepatocyte sensing of fluctuations in nutrients and hormones for triggering a latent metabolic zonation program.
    DOI:  https://doi.org/10.1038/s41467-024-46032-1
  5. Biophys Rev. 2024 Feb;16(1): 13-28
    Progress in single-cell multimodal sequencing and multi-omics data integration.
    Xuefei Wang, Xinchao Wu, Ni Hong, Wenfei Jin.
      With the rapid advance of single-cell sequencing technology, cell heterogeneity in various biological processes was dissected at different omics levels. However, single-cell mono-omics results in fragmentation of information and could not provide complete cell states. In the past several years, a variety of single-cell multimodal omics technologies have been developed to jointly profile multiple molecular modalities, including genome, transcriptome, epigenome, and proteome, from the same single cell. With the availability of single-cell multimodal omics data, we can simultaneously investigate the effects of genomic mutation or epigenetic modification on transcription and translation, and reveal the potential mechanisms underlying disease pathogenesis. Driven by the massive single-cell omics data, the integration method of single-cell multi-omics data has rapidly developed. Integration of the massive multi-omics single-cell data in public databases in the future will make it possible to construct a cell atlas of multi-omics, enabling us to comprehensively understand cell state and gene regulation at single-cell resolution. In this review, we summarized the experimental methods for single-cell multimodal omics data and computational methods for multi-omics data integration. We also discussed the future development of this field.
    Keywords:  Data integration; Multi-omics; Multi-omics data integration; Single-cell multimodal omics; Single-cell sequencing
    DOI:  https://doi.org/10.1007/s12551-023-01092-3
  6. Curr Protoc. 2024 Mar;4(3): e1019
    Minimizing Shear Stress in Cell Signaling Studies.
    Josefina Mendez, Alex Toker.
      Cellular signal transduction comprises a complex series of biochemical reactions by which extracellular signals such as growth factors, hormones, cytokines, and neurotransmitters are translated into specific intracellular responses. Signal transduction is mediated by protein kinase phosphorylation cascades that culminate in the regulation of numerous cellular responses, including division, differentiation, migration, and survival. Importantly, signal relay pathways are dysregulated in human diseases, making the study of signal transduction important for both uncovering basic biology and understanding pathophysiology. Established laboratory cell culture models are useful for studying signal transduction mechanisms, but differences in sample handling procedures can introduce unwanted variability in experimental outcomes and conclusions. One such potential source of experimental variability is the introduction of fluid shear stress upon handling of tissue culture cells. Fluid shear stress triggers a wide range of cellular responses in adherent cell culture, including stimulating the production of cyclic AMP, potentiating the activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2), and ultimately inducing changes in the gene expression of growth and remodeling factors. Further, mechanical stress on cells is physiologically relevant to the development of many pathologies. Here, we describe a detailed protocol for cell lysis and protein extraction that minimizes shear stress induced by classical cell harvest protocols. We also highlight the impact of fluid shear stress by using immunoblotting to assess ERK pathway activation as a readout for this protocol. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Gentle cell lysis and protein extraction Basic Protocol 2: Immunoblotting for cell signaling readouts by SDS-PAGE.
    Keywords:  ERK1/2; SDS-PAGE; cell signaling; lysis; protein extraction; shear stress
    DOI:  https://doi.org/10.1002/cpz1.1019
  7. Heliyon. 2024 Mar 30. 10(6): e27529
    A real-world disproportionality analysis of FDA adverse event reporting system (FAERS) events for alpelisib.
    Yu Lin, Xinlei Zheng, Yan Chen, Qichun Nian, Li Lin, Maohua Chen.
      In this study, we delved into the safety profile of alpelisib, an FDA-approved treatment for hormone receptor-positive, HER2-negative, PIK3CA-mutated advanced or metastatic breast cancer, and PIK3CA-Related Overgrowth Spectrum (PROS). Despite its approval, real-world, long-term safety data is lacking. Our research scrutinizes the FDA database to assess alpelisib 's safety. We retrospectively analyzed data from April 2019 to June 2023 using four algorithms. Among 7,609,450 reports, 6692 implicated alpelisib as the primary suspected drug, uncovering adverse events (AEs) across 26 organ systems. Notably, we identified 21 previously unlisted AEs. Furthermore, differences in AEs emerged between patients with PIK3CA-mutated breast cancer and those with PROS. This study provides vital insights for healthcare professionals to navigate AEs in clinical practice and informs future research for enhancing alpelisib 's safety profile.
    Keywords:  Adverse event; Alpelisib; Disproportionality analysis; FAERS database; Pharmacovigilance
    DOI:  https://doi.org/10.1016/j.heliyon.2024.e27529
  8. Brief Bioinform. 2024 Jan 22. pii: bbae095. [Epub ahead of print]25(2):
    Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data.
    Chuxi Xiao, Yixin Chen, Qiuchen Meng, Lei Wei, Xuegong Zhang.
      Recent advancements in single-cell sequencing technologies have generated extensive omics data in various modalities and revolutionized cell research, especially in the single-cell RNA and ATAC data. The joint analysis across scRNA-seq data and scATAC-seq data has paved the way to comprehending the cellular heterogeneity and complex cellular regulatory networks. Multi-omics integration is gaining attention as an important step in joint analysis, and the number of computational tools in this field is growing rapidly. In this paper, we benchmarked 12 multi-omics integration methods on three integration tasks via qualitative visualization and quantitative metrics, considering six main aspects that matter in multi-omics data analysis. Overall, we found that different methods have their own advantages on different aspects, while some methods outperformed other methods in most aspects. We therefore provided guidelines for selecting appropriate methods for specific scenarios and tasks to help obtain meaningful insights from multi-omics data integration.
    Keywords:  benchmarking; integration; multi-omics; single cell
    DOI:  https://doi.org/10.1093/bib/bbae095
  9. Genetics. 2024 Mar 22. pii: iyae044. [Epub ahead of print]
    Expanding TheCellVision.org: A Central Repository for Visualizing and Mining High-Content Cell Imaging Projects.
    Myra Paz David Masinas, Athanasios Litsios, Anastasia Razdaibiedina, Matej Usaj, Charles Boone, Brenda J Andrews.
      We previously constructed TheCellVision.org, a central repository for visualizing and mining data from yeast high-content imaging projects. At its inception, TheCellVision.org housed two high-content screening (HCS) projects providing genome-scale protein abundance and localization information for the budding yeast Saccharomyces cerevisiae, as well as a comprehensive analysis of the morphology of its endocytic compartments upon systematic genetic perturbation of each yeast gene. Here, we report on the expansion of TheCellVision.org by the addition of two new HCS projects and the incorporation of new global functionalities. Specifically, TheCellVision.org now hosts images from the Cell Cycle Omics project, which describes genome-scale cell cycle-resolved dynamics in protein localization, protein concentration, gene expression, and translational efficiency in budding yeast. Moreover, it hosts PIFiA, a computational tool for image-based predictions of protein functional annotations. Across all its projects, TheCellVision.org now houses > 800,000 microscopy images along with computational tools for exploring both the images and their associated datasets. Together with the newly added global functionalities, which include the ability to query genes in any of the hosted projects using either yeast or human gene names, TheCellVision.org provides an expanding resource for single-cell eukaryotic biology.
    Keywords:  PIFiA; TheCellVision.org; cell cycle omics; cell vision; high-content screening; image analysis tools; protein abundance; quantitative image analysis; subcellular localization; subcellular morphology
    DOI:  https://doi.org/10.1093/genetics/iyae044
  10. Elife. 2024 Mar 22. pii: RP90579. [Epub ahead of print]12
    Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation.
    Wayne Mitchell, Ludger J E Goeminne, Alexander Tyshkovskiy, Sirui Zhang, Julie Y Chen, Joao A Paulo, Kerry A Pierce, Angelina H Choy, Clary B Clish, Steven P Gygi, Vadim N Gladyshev.
      Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
    Keywords:  aging; biological age; cell biology; mitochondria; mouse; oxidative phosphorylation; reprogramming
    DOI:  https://doi.org/10.7554/eLife.90579
  11. bioRxiv. 2024 Mar 04. pii: 2024.03.03.583179. [Epub ahead of print]
    Multi-condition and multi-modal temporal profile inference during mouse embryonic development.
    Ran Zhang, Chengxiang Qiu, Gala Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, Christine Disteche, William Stafford Noble.
      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 multi-condition and multi-modal single-cell profiles across time. Sunbear can be used to impute single-cell temporal profile changes, align multi-dataset and multi-modal 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 multi-modal profiles are unavailable. Sunbear thus enables the projection of single-cell time-series snapshots to multi-modal and multi-condition views of cellular trajectories.
    DOI:  https://doi.org/10.1101/2024.03.03.583179
  12. Cancer Res. 2024 Mar 19.
    Cancer cells hijack physiological metabolic signals to seed liver metastasis.
    Andres Rettig, Karuna Ganesh.
      Metastasis arises from cancer-cell intrinsic adaptations and permissive tumor microenvironments (TME) that are distinct across different organs. Deciphering the mechanisms underpinning organotropism could provide novel preventive and therapeutic strategies for cancer patients. Rogava and colleagues identified Pip4kc as a driver of liver metastasis, acting by sensitizing cancer cells to insulin-dependent PI3K/AKT signaling, which could be reversed by dual pharmacological inhibition of PI3K and SGLT2 or a ketogenic diet. The study highlights the importance of tumor: microenvironment communication in the context of systemic physiology and points towards potential combination therapies.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-0835
  13. PLoS One. 2024 ;19(3): e0298322
    Substrate preference of protein kinase B isoforms can vary depending on the cell line.
    Miguel S Palma, Samantha R Perez, Aida Husain, Deepali Bhandari.
      Many proteins in higher eukaryotes, especially those with crucial functions, have multiple isoforms with redundant roles providing protection against potential functional deficiencies in one isoform. However, these isoforms can also have some unique roles. Protein kinase B, also known as Akt, is one such protein that has three isoforms encoded on different genes. Due to high sequence similarity and the general lack of specific reagents, most studies on Akt generalize their findings and do not distinguish between the isoforms. Using an established chemical genetic strategy and a set of known Akt substrates, this work explores substrate specificity of Akt isoforms under steady state conditions in two commonly used cell lines. This strategy can be applied to study any Akt isoform-specific substrates of interest in any cell line of choice as long as the cell line can be transfected.
    DOI:  https://doi.org/10.1371/journal.pone.0298322
  14. iScience. 2024 Apr 19. 27(4): 109386
    Modeling gene expression cascades during cell state transitions.
    Daniel Rosebrock, Martin Vingron, Peter F Arndt.
      During cellular processes such as differentiation or response to external stimuli, cells exhibit dynamic changes in their gene expression profiles. Single-cell RNA sequencing (scRNA-seq) can be used to investigate these dynamic changes. To this end, cells are typically ordered along a pseudotemporal trajectory which recapitulates the progression of cells as they transition from one cell state to another. We infer transcriptional dynamics by modeling the gene expression profiles in pseudotemporally ordered cells using a Bayesian inference approach. This enables ordering genes along transcriptional cascades, estimating differences in the timing of gene expression dynamics, and deducing regulatory gene interactions. Here, we apply this approach to scRNA-seq datasets derived from mouse embryonic forebrain and pancreas samples. This analysis demonstrates the utility of the method to derive the ordering of gene dynamics and regulatory relationships critical for proper cellular differentiation and maturation across a variety of developmental contexts.
    Keywords:  Biological constraints; Cell biology; Classification of bioinformatical subject; Systems biology; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2024.109386
  15. Cell Death Dis. 2024 Mar 18. 15(3): 225
    PTEN decreases NR2F1 expression to inhibit ciliogenesis during EGFRL858R-induced lung cancer progression.
    Thi Thanh Truc Tran, Jan-Jong Hung.
      Lung cancer is the major cause of death worldwide. Activation of oncogenes or inhibition of tumor suppressors causes cancer formation. Previous studies have indicated that PTEN, as a tumor suppressor, inhibits cancer formation. In this study, we studied the role of PTEN in EGFRL858R-induced lung cancer in vivo. Interestingly, loss of PTEN increased bronchial cell hyperplasia but decreased alveolar cell hyperplasia in EGFRL858R*PTEN-/--induced lung cancer. Systematic analysis of gene expression by RNA-seq showed that several genes related to ciliogenesis were upregulated in EGFRL858R*PTEN-/--induced lung cancer and subsequently showed that bronchial ciliated cells were hyperplastic. Several critical ciliogenesis-related genes, such as Mucin5A, DNAI2, and DNAI3, were found to be regulated by NR2F1. Next, NR2F1 was found to be inhibited by overexpression of PTEN, indicating that PTEN negatively regulates NR2F1, thereby inhibiting the expression of ciliogenesis-related genes and leading to the inhibition of bronchial cell hyperplasia during EGFRL858R-induced lung cancer progression. In addition, we also found that PTEN decreased AKT phosphorylation in A549, KRAS mutant, and H1299 cells but increased AKT phosphorylation in PC9, EGFRL858R, and H1299L858R cells, suggesting that PTEN may function as a tumor suppressor and an oncogene in lung cancers with KRAS mutation and EGFR mutation, respectively. PTEN acts as a double-edged sword that differentially regulates EGFRL858R-induced lung cancer progression in different genomic backgrounds. Understanding the PTEN in lung cancer with different genetic backgrounds will be beneficial for therapy in the future.
    DOI:  https://doi.org/10.1038/s41419-024-06610-z
  16. Oncogene. 2024 Mar 20.
    E-cadherin interacts with EGFR resulting in hyper-activation of ERK in multiple models of breast cancer.
    Gabriella C Russo, Ashleigh J Crawford, David Clark, Julie Cui, Ryan Carney, Michelle N Karl, Boyang Su, Bartholomew Starich, Tung-Shing Lih, Pratik Kamat, Qiming Zhang, Praful R Nair, Pei-Hsun Wu, Meng-Horng Lee, Hon S Leong, Hui Zhang, Vito W Rebecca, Denis Wirtz.
      The loss of intercellular adhesion molecule E-cadherin is a hallmark of the epithelial-mesenchymal transition (EMT), during which tumor cells transition into an invasive phenotype. Accordingly, E-cadherin has long been considered a tumor suppressor gene; however, E-cadherin expression is paradoxically correlated with breast cancer survival rates. Using novel multi-compartment organoids and multiple in vivo models, we show that E-cadherin promotes a hyper-proliferative phenotype in breast cancer cells via interaction with the transmembrane receptor EGFR. The E-cad and EGFR interaction results in activation of the MEK/ERK signaling pathway, leading to a significant increase in proliferation via activation of transcription factors, including c-Fos. Pharmacological inhibition of MEK activity in E-cadherin positive breast cancer significantly decreases both tumor growth and macro-metastasis in vivo. This work provides evidence for a novel role of E-cadherin in breast tumor progression and identifies a new target to treat hyper-proliferative E-cadherin-positive breast tumors, thus providing the foundation to utilize E-cadherin as a biomarker for specific therapeutic success.
    DOI:  https://doi.org/10.1038/s41388-024-03007-2
  17. J Biol Chem. 2024 Mar 20. pii: S0021-9258(24)01704-6. [Epub ahead of print] 107209
    FOXO1 promotes cancer cell growth through MDM2-mediated p53 degradation.
    Haruki Tomiyasu, Makoto Habara, Shunsuke Hanaki, Yuki Sato, Yosei Miki, Midori Shimada.
      FOXO1 is a transcription factor and potential tumor suppressor that is negatively regulated downstream of PI3K-PKB/AKT signaling. Paradoxically, FOXO also promotes tumor growth, but the detailed mechanisms behind this role of FOXO are not fully understood. In this study, we revealed a molecular cascade by which the Thr24 residue of FOXO1 is phosphorylated by AKT and is dephosphorylated by calcineurin, which is a Ca2+-dependent protein phosphatase. Curiously, single nucleotide somatic mutations of FOXO1 in cancer occur frequently at and near Thr24. Using a calcineurin inhibitor and shRNA directed against calcineurin, we revealed that calcineurin-mediated dephosphorylation of Thr24 regulates FOXO1 protein stability. We also found that FOXO1 binds to the promoter region of MDM2 and activates transcription, which in turn promotes MDM2-mediated ubiquitination and degradation of p53. FOXO3a and FOXO4 are shown to control p53 activity, however, the significance of FOXO1 in p53 regulation remains largely unknown. Supporting this notion, FOXO1 depletion increased p53 and p21 protein levels in association with inhibition of cell proliferation. Taken together, these results indicate that FOXO1 is stabilized by calcineurin-mediated dephosphorylation, and that FOXO1 supports cancer cell proliferation by promoting MDM2 transcription and subsequent p53 degradation.
    Keywords:  FOXO1; MDM2; calcineurin; p53; protein degradation
    DOI:  https://doi.org/10.1016/j.jbc.2024.107209
  18. Biophys Rev. 2024 Feb;16(1): 125-139
    Single-cell lineage tracing with endogenous markers.
    Yan Xue, Zezhuo Su, Xinyi Lin, Mun Kay Ho, Ken H O Yu.
      Resolving lineage relationships between cells in an organism provides key insights into the fate of individual cells and drives a fundamental understanding of the process of development and disease. A recent rapid increase in experimental and computational advances for detecting naturally occurring somatic nuclear and mitochondrial mutation at single-cell resolution has expanded lineage tracing from model organisms to humans. This review discusses the advantages and challenges of experimental and computational techniques for cell lineage tracing using somatic mutation as endogenous DNA barcodes to decipher the relationships between cells during development and tumour evolution. We outlook the advantages of spatial clonal evolution analysis and single-cell lineage tracing using endogenous genetic markers.
    Keywords:  Mitochondrial mutations; Single-cell lineage tracing; Somatic nuclear mutations; Spatial clonal evolution
    DOI:  https://doi.org/10.1007/s12551-024-01179-5
  19. Nat Commun. 2024 Mar 18. 15(1): 2441
    A fast-acting lipid checkpoint in G1 prevents mitotic defects.
    Marielle S Köberlin, Yilin Fan, Chad Liu, Mingyu Chung, Antonio F M Pinto, Peter K Jackson, Alan Saghatelian, Tobias Meyer.
      Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.
    DOI:  https://doi.org/10.1038/s41467-024-46696-9
  20. Mol Cell. 2024 Mar 21. pii: S1097-2765(24)00168-0. [Epub ahead of print]84(6): 995-997
    Integrating the response to stressed mitochondria.
    Elliot Dine, Richard J Youle.
      Chakrabarty et al.1 demonstrate that phospho-EIF2α (pEIF2α), the translation initiation factor that mediates the integrated stress response (ISR), is necessary and sufficient for the autophagic degradation of mitochondria following the addition of mitochondrial stressors.
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.026
  21. Nature. 2024 Mar 20.
    Proteome-scale discovery of protein degradation and stabilization effectors.
    Juline Poirson, Hanna Cho, Akashdeep Dhillon, Shahan Haider, Ahmad Zoheyr Imrit, Mandy Hiu Yi Lam, Nader Alerasool, Jessica Lacoste, Lamisa Mizan, Cassandra Wong, Anne-Claude Gingras, Daniel Schramek, Mikko Taipale.
      Targeted protein degradation and stabilization are promising therapeutic modalities because of their potency, versatility and their potential to expand the druggable target space1,2. However, only a few of the hundreds of E3 ligases and deubiquitinases in the human proteome have been harnessed for this purpose, which substantially limits the potential of the approach. Moreover, there may be other protein classes that could be exploited for protein stabilization or degradation3-5, but there are currently no methods that can identify such effector proteins in a scalable and unbiased manner. Here we established a synthetic proteome-scale platform to functionally identify human proteins that can promote the degradation or stabilization of a target protein in a proximity-dependent manner. Our results reveal that the human proteome contains a large cache of effectors of protein stability. The approach further enabled us to comprehensively compare the activities of human E3 ligases and deubiquitinases, identify and characterize non-canonical protein degraders and stabilizers and establish that effectors have vastly different activities against diverse targets. Notably, the top degraders were more potent against multiple therapeutically relevant targets than the currently used E3 ligases cereblon and VHL. Our study provides a functional catalogue of stability effectors for targeted protein degradation and stabilization and highlights the potential of induced proximity screens for the discovery of new proximity-dependent protein modulators.
    DOI:  https://doi.org/10.1038/s41586-024-07224-3
  22. Biophys J. 2024 Mar 21. pii: S0006-3495(24)00202-9. [Epub ahead of print]
    Self-organization of PIP3 waves is controlled by the topology and curvature of cell membranes.
    Sema Erisis, Marcel Hörning.
      PIP3 is a signaling lipid on the plasma membrane that plays a fundamental role in cell signaling with a strong impact on cell physiology and diseases. It is responsible for the protruding edge formation, cell polarization, macropinocytosis and other membrane remodeling dynamics in cells. It has been shown that the membrane confinement and curvature affects the wave formation of PIP3 and F-actin. But even in the absence of F-actin, a complex self-organization of the spatiotemporal PIP3 waves is observed. In recent findings, we have shown that these waves can be guided and pinned on strongly bended Dictyostelium membranes caused by molecular crowding and curvature limited diffusion. Based on these experimental findings, we investigate the spatiotemporal PIP3 wave dynamics on realistic 3D cell-like membranes to explore the effect of curvature limited diffusion, as observed experimentally. We use an established stochastic reaction-diffusion model with enzymatic Michaelis-Menten type reactions that mimics the dynamics of Dictyostelium cells. As these cells mimic the 3D shape and size observed experimentally, we found that the PIP3 wave directionality can be explained by a Hopf-like and a reverse periodic-doubling bifurcation for uniform diffusion and curvature limited diffusion properties. Finally, we compare the results with recent experimental findings and discuss the discrepancy between the biological and numerical results.
    DOI:  https://doi.org/10.1016/j.bpj.2024.03.022
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