bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2022–01–23
sixteen papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Orofacial overgrowth with peripheral nerve enlargement and perineuriomatous pseudo-onion bulb proliferations is part of the PIK3CA-related overgrowth spectrum.
  2. Oncogenic potential of BEST4 in colorectal cancer via activation of PI3K/Akt signaling.
  3. A Causal Link between Disrupted AKT Signaling and Hyperproliferative Endometrial Diseases.
  4. High-speed fluorescence image-enabled cell sorting.
  5. Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment.
  6. Sensing of RNA stress by mTORC1 drives autoinflammation.
  7. Statistics or biology: the zero-inflation controversy about scRNA-seq data.
  8. Engineering solutions for biological studies of flow-exposed endothelial cells on orbital shakers.
  9. Comparison and evaluation of statistical error models for scRNA-seq.
  10. An autonomous TCR signal-sensing switch influences CD4/CD8 lineage choice in mice.
  11. Circulating metabolite homeostasis achieved through mass action.
  12. A PDK-1 allosteric agonist neutralizes insulin signaling derangements and beta-amyloid toxicity in neuronal cells and in vitro.
  13. New horizons in the stormy sea of multimodal single-cell data integration.
  14. A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer.
  15. The new era of quantitative cell imaging-challenges and opportunities.
  16. Massively parallel phenotyping of coding variants in cancer with Perturb-seq.
  1. HGG Adv. 2020 Oct 22. 1(1): 100009
    Orofacial overgrowth with peripheral nerve enlargement and perineuriomatous pseudo-onion bulb proliferations is part of the PIK3CA-related overgrowth spectrum.
    Ioannis G Koutlas, Ana-Lia Anbinder, Rana Alshagroud, Ana Sueli Rodrigues Cavalcante, Mohammed Al Kindi, Molly M Crenshaw, Julie C Sapp, Hannah Kondolf, Marjorie J Lindhurst, Jeffrey N Dudley, Jennifer J Johnston, Elyse Ryan, Keith Rafferty, Arupa Ganguly, Leslie G Biesecker.
      Individuals with orofacial asymmetry due to mucosal overgrowths, ipsilateral bone and dental aberrations with perineurial hyperplasia and/or perineuriomatous pseudo-onion bulb proliferations, comprise a recognizable clinical entity. In this article, we describe three individuals with this clinical entity and mosaic PIK3CA variants c.3140A>G (p. His1047Arg), c.328_330delGAA (p. Glu110del), and c.1353_1364del (p.Glu453_Leu456del). We conclude that the identification of these mosaic variants in individuals with orofacial asymmetry presenting histopathologically perineurial hyperplasia and/or intraneural pseudo-onion bulb perineurial cell proliferations supports the inclusion of this clinical entity in the PIK3CA-related overgrowth spectrum.
    Keywords:  PIK3CA; face; oral mucosa; overgrowth; perineurium; peripheral nerve; pseudo-onion bulbs
    DOI:  https://doi.org/10.1016/j.xhgg.2020.100009
  2. Oncogene. 2022 Jan 21.
    Oncogenic potential of BEST4 in colorectal cancer via activation of PI3K/Akt signaling.
    Xiao-Shun He, Wen-Long Ye, Yu-Juan Zhang, Xiao-Qin Yang, Feng Liu, Jing-Ru Wang, Xiao-Lu Ding, Yun Yang, Ruo-Nan Zhang, Yuan-Yuan Zhao, Hai-Xia Bi, Ling-Chuan Guo, Wen-Juan Gan, Hua Wu.
      BEST4 is a member of the bestrophin protein family that plays a critical role in human intestinal epithelial cells. However, its role and mechanism in colorectal cancer (CRC) remain largely elusive. Here, we investigated the role and clinical significance of BEST4 in CRC. Our results demonstrate that BEST4 expression is upregulated in clinical CRC samples and its high-level expression correlates with advanced TNM (tumor, lymph nodes, distant metastasis) stage, LNM (lymph node metastasis), and poor survival. Functional studies revealed that ectopic expression of BEST4 promoted CRC cell proliferation and metastasis, whereas the depletion of BEST4 had the opposite effect both in vitro and in vivo. Mechanistically, BEST4 binds to the p85α regulatory subunit of phosphatidylinositol-3-kinase (PI3K) and promotes p110 kinase activity; this leads to activation of Akt signaling and expression of MYC and CCND1, which are critical regulators of cell proliferation and metastasis. In clinical samples, the expression of BEST4 is positively associated with the expression of phosphorylated Akt, MYC and CCND1. Pharmacological inhibition of Akt activity markedly repressed BEST4-mediated Akt signaling and proliferation and metastasis of CRC cells. Importantly, the interaction between BEST4 and p85α was also enhanced by epidermal growth factor (EGF) in CRC cells. Therapeutically, BEST4 suppression effectively sensitized CRC cells to gefitinib treatment in vivo. Taken together, our findings indicate the oncogenic potential of BEST4 in colorectal carcinogenesis and metastasis by modulating BEST4/PI3K/Akt signaling, highlighting a potential strategy for CRC therapy.
    DOI:  https://doi.org/10.1038/s41388-021-02160-2
  3. Endocrinology. 2022 Jan 18. pii: bqac006. [Epub ahead of print]
    A Causal Link between Disrupted AKT Signaling and Hyperproliferative Endometrial Diseases.
    James K Pru.
      
    DOI:  https://doi.org/10.1210/endocr/bqac006
  4. Science. 2022 Jan 21. 375(6578): 315-320
    High-speed fluorescence image-enabled cell sorting.
    Daniel Schraivogel, Terra M Kuhn, Benedikt Rauscher, Marta Rodríguez-Martínez, Malte Paulsen, Keegan Owsley, Aaron Middlebrook, Christian Tischer, Beáta Ramasz, Diana Ordoñez-Rueda, Martina Dees, Sara Cuylen-Haering, Eric Diebold, Lars M Steinmetz.
      Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. Here, we address this by establishing high-speed image-enabled cell sorting (ICS), which records multicolor fluorescence images and sorts cells based on measurements from image data at speeds up to 15,000 events per second. We show that ICS quantifies cell morphology and localization of labeled proteins and increases the resolution of cell cycle analyses by separating mitotic stages. We combine ICS with CRISPR-pooled screens to identify regulators of the nuclear factor κB (NF-κB) pathway, enabling the completion of genome-wide image-based screens in about 9 hours of run time. By assessing complex cellular phenotypes, ICS substantially expands the phenotypic space accessible to cell-sorting applications and pooled genetic screening.
    DOI:  https://doi.org/10.1126/science.abj3013
  5. J Proteome Res. 2022 Jan 19.
    Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment.
    Tian Zhang, Anne Fassl, Laura P Vaites, Sipei Fu, Piotr Sicinski, Joao A Paulo, Steven P Gygi.
      Kinases govern many cellular responses through the reversible transfer of a phosphate moiety to their substrates. However, pairing a substrate with a kinase is challenging. In proximity labeling experiments, proteins proximal to a target protein are marked by biotinylation, and mass spectrometry can be used for their identification. Here, we combine ascorbate peroxidase (APEX) proximity labeling and a phosphorylation enrichment-based workflow, Phospho-APEX (pAPEX), to rapidly identify phosphorylated and biotinylated neighbor proteins which can be considered for candidate substrates. The pAPEX strategy enriches and quantifies differences in proximity for proteins and phosphorylation sites proximal to an APEX2-tagged kinase under the kinase "ON" and kinase "OFF" conditions. As a proof of concept, we identified candidate substrates of MAPK1 in HEK293T and HCT116 cells and candidate substrates of PKA in HEK293T cells. In addition to many known substrates, C15orf39 was identified and confirmed as a novel MAPK1 substrate. In all, we adapted the proximity labeling-based platform to accommodate phosphorylation analysis for kinase substrate identification.
    Keywords:  MAPK1; PKA; kinases; phosphopeptide enrichment; proximity labeling; substrates identification
    DOI:  https://doi.org/10.1021/acs.jproteome.1c00865
  6. J Clin Invest. 2022 Jan 18. pii: e156119. [Epub ahead of print]132(2):
    Sensing of RNA stress by mTORC1 drives autoinflammation.
    Min Ae Lee-Kirsch.
      Loss-of-function mutations in SKIV2L underlie trichohepatoenteric syndrome (THES2), a rare inborn error of immunity characterized by diarrhea, skin lesions, brittle hair, and immunodeficiency. SKIV2L is part of a multiprotein complex required for exosome-mediated RNA surveillance through RNA decay. In this issue of the JCI, Yang et al. delineate a mechanism underlying autoinflammatory skin disease in Skiv2l-deficient mice. Thus, a lack of SKIV2L activates mTORC1 signaling in keratinocytes and T cells, impeding skin barrier integrity and T cell homeostasis. Interestingly, treatment with the mTOR inhibitor rapamycin improves skin symptoms in Skiv2l-deficient mice, suggesting a possible therapeutic avenue for patients with THES2.
    DOI:  https://doi.org/10.1172/JCI156119
  7. Genome Biol. 2022 Jan 21. 23(1): 31
    Statistics or biology: the zero-inflation controversy about scRNA-seq data.
    Ruochen Jiang, Tianyi Sun, Dongyuan Song, Jingyi Jessica Li.
      Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as missing data to be corrected. To help address the controversy, here we discuss the sources of biological and non-biological zeros; introduce five mechanisms of adding non-biological zeros in computational benchmarking; evaluate the impacts of non-biological zeros on data analysis; benchmark three input data types: observed counts, imputed counts, and binarized counts; discuss the open questions regarding non-biological zeros; and advocate the importance of transparent analysis.
    DOI:  https://doi.org/10.1186/s13059-022-02601-5
  8. PLoS One. 2022 ;17(1): e0262044
    Engineering solutions for biological studies of flow-exposed endothelial cells on orbital shakers.
    Andreia Fernandes, Vahid Hosseini, Viola Vogel, Robert D Lovchik.
      Shear stress is extremely important for endothelial cell (EC) function. The popularity of 6-well plates on orbital shakers to impose shear stress on ECs has increased among biologists due to their low cost and simplicity. One characteristic of such a platform is the heterogeneous flow profile within a well. While cells in the periphery are exposed to a laminar and high-velocity pulsatile flow that mimics physiological conditions, the flow in the center is disturbed and imposes low shear stress on the cells, which is characteristic of atheroprone regions. For studies where such heterogeneity is not desired, we present a simple cell-patterning technique to selectively prevent cell growth in the center of the well and facilitate the exclusive collection and analysis of cells in the periphery. This guarantees that cell phenotypes will not be influenced by secreted factors from cells exposed to other shear profiles nor that interesting results are obscured by mixing cells from different regions. We also present a multi-staining platform that compartmentalizes each well into 5 smaller independent regions: four at the periphery and one in the center. This is ideal for studies that aim to grow cells on the whole well surface, for comparison with previous work and minimal interference in the cell culture, but require screening of markers by immunostaining afterwards. It allows to compare different regions of the well, reduces antibody-related costs, and allows the exploration of multiple markers essential for high-content screening of cell response. By increasing the versatility of the 6-well plate on an orbital shaker system, we hope that these two solutions motivate biologists to pursue studies on EC mechanobiology and beyond.
    DOI:  https://doi.org/10.1371/journal.pone.0262044
  9. Genome Biol. 2022 Jan 18. 23(1): 27
    Comparison and evaluation of statistical error models for scRNA-seq.
    Saket Choudhary, Rahul Satija.
       BACKGROUND: Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple sources, including biological variation in cellular state as well as technical variation introduced during experimental processing. Deconvolving these effects is a key challenge for preprocessing workflows. Recent work has demonstrated the importance and utility of count models for scRNA-seq analysis, but there is a lack of consensus on which statistical distributions and parameter settings are appropriate.
    RESULTS: Here, we analyze 59 scRNA-seq datasets that span a wide range of technologies, systems, and sequencing depths in order to evaluate the performance of different error models. We find that while a Poisson error model appears appropriate for sparse datasets, we observe clear evidence of overdispersion for genes with sufficient sequencing depth in all biological systems, necessitating the use of a negative binomial model. Moreover, we find that the degree of overdispersion varies widely across datasets, systems, and gene abundances, and argues for a data-driven approach for parameter estimation.
    CONCLUSIONS: Based on these analyses, we provide a set of recommendations for modeling variation in scRNA-seq data, particularly when using generalized linear models or likelihood-based approaches for preprocessing and downstream analysis.
    Keywords:  Differential expression; Dimension reduction; Feature selection; Normalization; Single-cell RNA-seq; Variable genes
    DOI:  https://doi.org/10.1186/s13059-021-02584-9
  10. Commun Biol. 2022 Jan 21. 5(1): 84
    An autonomous TCR signal-sensing switch influences CD4/CD8 lineage choice in mice.
    Jayati Basu, Jikun Zha, Emmanuelle Nicolas, Michael Coulton, Philip Czyzewicz, Xiang Hua, Lu Ge, Dietmar J Kappes.
      How multipotential cells initiate distinct gene expression programs in response to external cues to instruct cell fate choice remains a fundamental question in biology. Establishment of CD4 and CD8 T cell fates during thymocyte development is critically regulated by T cell receptor (TCR) signals, which in turn control expression of the CD4-determining transcription factor ThPOK. However, the mechanism whereby differential TCR signals are molecularly interpreted to promote or antagonize ThPOK expression, and thereby CD4 versus CD8 lineage fates remains unknown. Here we show, using reverse genetic and molecular approaches that an autonomous, position-independent TCR-sensing switch is embedded within the ThPOK locus. Further, using an in vivo mutagenesis approach, we demonstrate that differential TCR signals are interpreted during lineage commitment by relative binding of EGR, NFAT and Ebox factors to this bistable switch. Collectively our study reveals the central molecular mechanism whereby TCR signaling influences differential lineage choice. Ultimately, these findings may provide an important new tool for skewing T cell fate to treat cancer and autoimmune diseases.
    DOI:  https://doi.org/10.1038/s42003-022-02999-5
  11. Nat Metab. 2022 Jan 20.
    Circulating metabolite homeostasis achieved through mass action.
    Xiaoxuan Li, Sheng Hui, Emily T Mirek, William O Jonsson, Tracy G Anthony, Won Dong Lee, Xianfeng Zeng, Cholsoon Jang, Joshua D Rabinowitz.
      Homeostasis maintains serum metabolites within physiological ranges. For glucose, this requires insulin, which suppresses glucose production while accelerating its consumption. For other circulating metabolites, a comparable master regulator has yet to be discovered. Here we show that, in mice, many circulating metabolites are cleared via the tricarboxylic acid cycle (TCA) cycle in linear proportionality to their circulating concentration. Abundant circulating metabolites (essential amino acids, serine, alanine, citrate, 3-hydroxybutyrate) were administered intravenously in perturbative amounts and their fluxes were measured using isotope labelling. The increased circulating concentrations induced by the perturbative infusions hardly altered production fluxes while linearly enhancing consumption fluxes and TCA contributions. The same mass action relationship between concentration and consumption flux largely held across feeding, fasting and high- and low-protein diets, with amino acid homeostasis during fasting further supported by enhanced endogenous protein catabolism. Thus, despite the copious regulatory machinery in mammals, circulating metabolite homeostasis is achieved substantially through mass action-driven oxidation.
    DOI:  https://doi.org/10.1038/s42255-021-00517-1
  12. PLoS One. 2022 ;17(1): e0261696
    A PDK-1 allosteric agonist neutralizes insulin signaling derangements and beta-amyloid toxicity in neuronal cells and in vitro.
    Henry Querfurth, John Marshall, Keykavous Parang, Mengia S Rioult-Pedotti, Rakesh Tiwari, Bumsup Kwon, Steve Reisinger, Han-Kyu Lee.
      The Alzheimer's brain is affected by multiple pathophysiological processes, which include a unique, organ-specific form of insulin resistance that begins early in its course. An additional complexity arises from the four-fold risk of Alzheimer's Disease (AD) in type 2 diabetics, however there is no definitive proof of causation. Several strategies to improve brain insulin signaling have been proposed and some have been clinically tested. We report findings on a small allosteric molecule that reverses several indices of insulin insensitivity in both cell culture and in vitro models of AD that emphasize the intracellular accumulation of β-amyloid (Aβi). PS48, a chlorophenyl pentenoic acid, is an allosteric activator of PDK-1, which is an Akt-kinase in the insulin/PI3K pathway. PS48 was active at 10 nM to 1 μM in restoring normal insulin-dependent Akt activation and in mitigating Aβi peptide toxicity. Synaptic plasticity (LTP) in prefrontal cortical slices from normal rat exposed to Aβ oligomers also benefited from PS48. During these experiments, neither overstimulation of PI3K/Akt signaling nor toxic effects on cells was observed. Another neurotoxicity model producing insulin insensitivity, utilizing palmitic acid, also responded to PS48 treatment, thus validating the target and indicating that its therapeutic potential may extend outside of β-amyloid reliance. The described in vitro and cell based-in vitro coupled enzymatic assay systems proved suitable platforms to screen a preliminary library of new analogs.
    DOI:  https://doi.org/10.1371/journal.pone.0261696
  13. Mol Cell. 2022 Jan 20. pii: S1097-2765(21)01074-1. [Epub ahead of print]82(2): 248-259
    New horizons in the stormy sea of multimodal single-cell data integration.
    Christopher A Jackson, Christine Vogel.
      While measurements of RNA expression have dominated the world of single-cell analyses, new single-cell techniques increasingly allow collection of different data modalities, measuring different molecules, structural connections, and intermolecular interactions. Integrating the resulting multimodal single-cell datasets is a new bioinformatics challenge. Equally important, it is a new experimental design challenge for the bench scientist, who is not only choosing from a myriad of techniques for each data modality but also faces new challenges in experimental design. The ultimate goal is to design, execute, and analyze multimodal single-cell experiments that are more than just descriptive but enable the learning of new causal and mechanistic biology. This objective requires strict consideration of the goals behind the analysis, which might range from mapping the heterogeneity of a cellular population to assembling system-wide causal networks that can further our understanding of cellular functions and eventually lead to models of tissues and organs. We review steps and challenges toward this goal. Single-cell transcriptomics is now a mature technology, and methods to measure proteins, lipids, small-molecule metabolites, and other molecular phenotypes at the single-cell level are rapidly developing. Integrating these single-cell readouts so that each cell has measurements of multiple types of data, e.g., transcriptomes, proteomes, and metabolomes, is expected to allow identification of highly specific cellular subpopulations and to provide the basis for inferring causal biological mechanisms.
    Keywords:  gene regulatory network; inferrence; integration; integromics; multi-omics; multimodal
    DOI:  https://doi.org/10.1016/j.molcel.2021.12.012
  14. Sci Adv. 2022 Jan 21. 8(3): eabg6711
    A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer.
    Diogo F T Veiga, Alex Nesta, Yuqi Zhao, Anne Deslattes Mays, Richie Huynh, Robert Rossi, Te-Chia Wu, Karolina Palucka, Olga Anczukow, Christine R Beck, Jacques Banchereau.
      Tumors display widespread transcriptome alterations, but the full repertoire of isoform-level alternative splicing in cancer is unknown. We developed a long-read (LR) RNA sequencing and analytical platform that identifies and annotates full-length isoforms and infers tumor-specific splicing events. Application of this platform to breast cancer samples identifies thousands of previously unannotated isoforms; ~30% affect protein coding exons and are predicted to alter protein localization and function. We performed extensive cross-validation with -omics datasets to support transcription and translation of novel isoforms. We identified 3059 breast tumor-specific splicing events, including 35 that are significantly associated with patient survival. Of these, 21 are absent from GENCODE and 10 are enriched in specific breast cancer subtypes. Together, our results demonstrate the complexity, cancer subtype specificity, and clinical relevance of previously unidentified isoforms and splicing events in breast cancer that are only annotatable by LR-seq and provide a rich resource of immuno-oncology therapeutic targets.
    DOI:  https://doi.org/10.1126/sciadv.abg6711
  15. Mol Cell. 2022 Jan 20. pii: S1097-2765(21)01086-8. [Epub ahead of print]82(2): 241-247
    The new era of quantitative cell imaging-challenges and opportunities.
    Neda Bagheri, Anne E Carpenter, Emma Lundberg, Anne L Plant, Rick Horwitz.
      Quantitative optical microscopy-an emerging, transformative approach to single-cell biology-has seen dramatic methodological advancements over the past few years. However, its impact has been hampered by challenges in the areas of data generation, management, and analysis. Here we outline these technical and cultural challenges and provide our perspective on the trajectory of this field, ushering in a new era of quantitative, data-driven microscopy. We also contrast it to the three decades of enormous advances in the field of genomics that have significantly enhanced the reproducibility and wider adoption of a plethora of genomic approaches.
    DOI:  https://doi.org/10.1016/j.molcel.2021.12.024
  16. Nat Biotechnol. 2022 Jan 20.
    Massively parallel phenotyping of coding variants in cancer with Perturb-seq.
    Oana Ursu, James T Neal, Emily Shea, Pratiksha I Thakore, Livnat Jerby-Arnon, Lan Nguyen, Danielle Dionne, Celeste Diaz, Julia Bauman, Mariam Mounir Mosaad, Christian Fagre, April Lo, Maria McSharry, Andrew O Giacomelli, Seav Huong Ly, Orit Rozenblatt-Rosen, William C Hahn, Andrew J Aguirre, Alice H Berger, Aviv Regev, Jesse S Boehm.
      Genome sequencing studies have identified millions of somatic variants in cancer, but it remains challenging to predict the phenotypic impact of most. Experimental approaches to distinguish impactful variants often use phenotypic assays that report on predefined gene-specific functional effects in bulk cell populations. Here, we develop an approach to functionally assess variant impact in single cells by pooled Perturb-seq. We measured the impact of 200 TP53 and KRAS variants on RNA profiles in over 300,000 single lung cancer cells, and used the profiles to categorize variants into phenotypic subsets to distinguish gain-of-function, loss-of-function and dominant negative variants, which we validated by comparison with orthogonal assays. We discovered that KRAS variants did not merely fit into discrete functional categories, but spanned a continuum of gain-of-function phenotypes, and that their functional impact could not have been predicted solely by their frequency in patient cohorts. Our work provides a scalable, gene-agnostic method for coding variant impact phenotyping, with potential applications in multiple disease settings.
    DOI:  https://doi.org/10.1038/s41587-021-01160-7
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