bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–01–29
eightteen papers selected by
Ralitsa Radostinova Madsen, University College London
  1. Immune-interacting lymphatic endothelial subtype at capillary terminals drives lymphatic malformation.
  2. TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.
  3. RIPK1 blocks T cell senescence mediated by RIPK3 and caspase-8.
  4. Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival.
  5. Stochastic phenotypes in RAS-dependent developmental diseases.
  6. Editorial: Somatic mutations, genome mosaicism and aging.
  7. Primary cilia are WNT-transducing organelles whose biogenesis is controlled by a WNT-PP1 axis.
  8. Mosaic pathogenic variants in AKT3 cause capillary malformation and undergrowth.
  9. Endoderm-derived islet1-expressing cells differentiate into endothelial cells to function as the vascular HSPC niche in zebrafish.
  10. Epithelial disruption drives mesendoderm differentiation in human pluripotent stem cells by enabling TGF-β protein sensing.
  11. scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data.
  12. Early insight into spontaneous mutations.
  13. scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection.
  14. The fidelity of transcription in human cells.
  15. CLASH enables large-scale parallel knock-in for cell engineering.
  16. Proteomics Update and Perspectives from the Proteomics in Cell Biology and Disease Mechanisms Conference.
  17. Direct lysis of 3D cell cultures for RT-qPCR gene expression quantification.
  18. Precise transcript targeting by CRISPR-Csm complexes.
  1. J Exp Med. 2023 Apr 03. pii: e20220741. [Epub ahead of print]220(4):
    Immune-interacting lymphatic endothelial subtype at capillary terminals drives lymphatic malformation.
    Milena Petkova, Marle Kraft, Simon Stritt, Ines Martinez-Corral, Henrik Ortsäter, Michael Vanlandewijck, Bojana Jakic, Eulàlia Baselga, Sandra D Castillo, Mariona Graupera, Christer Betsholtz, Taija Mäkinen.
      Oncogenic mutations in PIK3CA, encoding p110α-PI3K, are a common cause of venous and lymphatic malformations. Vessel type-specific disease pathogenesis is poorly understood, hampering development of efficient therapies. Here, we reveal a new immune-interacting subtype of Ptx3-positive dermal lymphatic capillary endothelial cells (iLECs) that recruit pro-lymphangiogenic macrophages to promote progressive lymphatic overgrowth. Mouse model of Pik3caH1047R-driven vascular malformations showed that proliferation was induced in both venous and lymphatic ECs but sustained selectively in LECs of advanced lesions. Single-cell transcriptomics identified the iLEC population, residing at lymphatic capillary terminals of normal vasculature, that was expanded in Pik3caH1047R mice. Expression of pro-inflammatory genes, including monocyte/macrophage chemokine Ccl2, in Pik3caH1047R-iLECs was associated with recruitment of VEGF-C-producing macrophages. Macrophage depletion, CCL2 blockade, or anti-inflammatory COX-2 inhibition limited Pik3caH1047R-driven lymphangiogenesis. Thus, targeting the paracrine crosstalk involving iLECs and macrophages provides a new therapeutic opportunity for lymphatic malformations. Identification of iLECs further indicates that peripheral lymphatic vessels not only respond to but also actively orchestrate inflammatory processes.
    DOI:  https://doi.org/10.1084/jem.20220741
  2. EMBO J. 2023 Jan 24. e112344
    TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.
    Sunil Shetty, Jon Hofstetter, Stefania Battaglioni, Danilo Ritz, Michael N Hall.
      Target of rapamycin complex 1 (TORC1) promotes biogenesis and inhibits the degradation of ribosomes in response to nutrient availability. To ensure a basal supply of ribosomes, cells are known to preserve a small pool of dormant ribosomes under nutrient-limited conditions. However, the regulation of these dormant ribosomes is poorly characterized. Here, we show that upon inhibition of yeast TORC1 by rapamycin or nitrogen starvation, the ribosome preservation factor Stm1 mediates the formation of nontranslating, dormant 80S ribosomes. Furthermore, Stm1-bound 80S ribosomes are protected from proteasomal degradation. Upon nutrient replenishment, TORC1 directly phosphorylates and inhibits Stm1 to reactivate translation. Finally, we find that SERBP1, a mammalian ortholog of Stm1, is likewise required for the formation of dormant 80S ribosomes upon mTORC1 inhibition in mammalian cells. These data suggest that TORC1 regulates ribosomal dormancy in an evolutionarily conserved manner by directly targeting a ribosome preservation factor.
    Keywords:  SERBP1; Stm1; TORC1; dormant ribosomes; proteasome
    DOI:  https://doi.org/10.15252/embj.2022112344
  3. Sci Adv. 2023 Jan 25. 9(4): eadd6097
    RIPK1 blocks T cell senescence mediated by RIPK3 and caspase-8.
    Takayuki Imanishi, Midori Unno, Natsumi Yoneda, Yasutaka Motomura, Miho Mochizuki, Takaharu Sasaki, Manolis Pasparakis, Takashi Saito.
      Receptor-interacting protein kinase 1 (RIPK1) regulates cell death and inflammation. Here, we show that T cell-specific RIPK1 deficiency in mice leads to the premature senescence of T cells and induces various age-related diseases, resulting in premature death. RIPK1 deficiency causes higher basal activation of mTORC1 (mechanistic target of rapamycin complex 1) that drives enhanced cytokine production, induction of senescence-related genes, and increased activation of caspase-3/7, which are restored by inhibition of mTORC1. Critically, normal aged T cells exhibit similar phenotypes and responses. Mechanistically, a combined deficiency of RIPK3 and caspase-8 inhibition restores the impaired proliferative responses; the elevated activation of Akt, mTORC1, extracellular signal-regulated kinase, and caspase-3/7; and the increased expression of senescence-related genes in RIPK1-deficient CD4 T cells. Last, we revealed that the senescent phenotype of RIPK1-deficient and aged CD4 T cells is restored in the normal tissue environment. Thus, we have clarified the function of RIPK3 and caspase-8 in inducing CD4 T cell senescence, which is modulated by environmental signals.
    DOI:  https://doi.org/10.1126/sciadv.add6097
  4. Mol Syst Biol. 2023 Jan 23. e10631
    Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival.
    Abel Sousa, Aurelien Dugourd, Danish Memon, Borgthor Petursson, Evangelia Petsalaki, Julio Saez-Rodriguez, Pedro Beltrao.
      Genetic alterations in cancer cells trigger oncogenic transformation, a process largely mediated by the dysregulation of kinase and transcription factor (TF) activities. While the mutational profiles of thousands of tumours have been extensively characterised, the measurements of protein activities have been technically limited until recently. We compiled public data of matched genomics and (phospho)proteomics measurements for 1,110 tumours and 77 cell lines that we used to estimate activity changes in 218 kinases and 292 TFs. Co-regulation of kinase and TF activities reflects previously known regulatory relationships and allows us to dissect genetic drivers of signalling changes in cancer. We find that loss-of-function mutations are not often associated with the dysregulation of downstream targets, suggesting frequent compensatory mechanisms. Finally, we identified the activities most differentially regulated in cancer subtypes and showed how these can be linked to differences in patient survival. Our results provide broad insights into the dysregulation of protein activities in cancer and their contribution to disease severity.
    Keywords:  adaptation; cancer genomics; cell signalling; phosphoproteomics; protein activities
    DOI:  https://doi.org/10.15252/msb.202110631
  5. Curr Biol. 2023 Jan 20. pii: S0960-9822(23)00008-8. [Epub ahead of print]
    Stochastic phenotypes in RAS-dependent developmental diseases.
    Robert A Marmion, Alison G Simpkins, Lena A Barrett, David W Denberg, Susan Zusman, Jodi Schottenfeld-Roames, Trudi Schüpbach, Stanislav Y Shvartsman.
      Germline mutations upregulating RAS signaling are associated with multiple developmental disorders. A hallmark of these conditions is that the same mutation may present vastly different phenotypes in different individuals, even in monozygotic twins. Here, we demonstrate how the origins of such largely unexplained phenotypic variations may be dissected using highly controlled studies in Drosophila that have been gene edited to carry activating variants of MEK, a core enzyme in the RAS pathway. This allowed us to measure the small but consistent increase in signaling output of such alleles in vivo. The fraction of mutation carriers reaching adulthood was strongly reduced, but most surviving animals had normal RAS-dependent structures. We rationalize these results using a stochastic signaling model and support it by quantifying cell fate specification errors in bilaterally symmetric larval trachea, a RAS-dependent structure that allows us to isolate the effects of mutations from potential contributions of genetic modifiers and environmental differences. We propose that the small increase in signaling output shifts the distribution of phenotypes into a regime, where stochastic variation causes defects in some individuals, but not in others. Our findings shed light on phenotypic heterogeneity of developmental disorders caused by deregulated RAS signaling and offer a framework for investigating causal effects of other pathogenic alleles and mild mutations in general.
    DOI:  https://doi.org/10.1016/j.cub.2023.01.008
  6. Front Aging. 2022 ;3 1115408
    Editorial: Somatic mutations, genome mosaicism and aging.
    Michael A Lodato, Jan Vijg.
      
    Keywords:  DNA damage; aging; genome mosaicism; oxidative stress; somatic mutation
    DOI:  https://doi.org/10.3389/fragi.2022.1115408
  7. Dev Cell. 2023 Jan 23. pii: S1534-5807(22)00872-3. [Epub ahead of print]58(2): 139-154.e8
    Primary cilia are WNT-transducing organelles whose biogenesis is controlled by a WNT-PP1 axis.
    Kaiqing Zhang, Fabio Da Silva, Carina Seidl, Michaela Wilsch-Bräuninger, Jessica Herbst, Wieland B Huttner, Christof Niehrs.
      WNT signaling is important in development, stem cell maintenance, and disease. WNT ligands typically signal via receptor activation across the plasma membrane to induce β-catenin-dependent gene activation. Here, we show that in mammalian primary cilia, WNT receptors relay a WNT/GSK3 signal that β-catenin-independently promotes ciliogenesis. Characterization of a LRP6 ciliary targeting sequence and monitoring of acute WNT co-receptor activation (phospho-LRP6) support this conclusion. Ciliary WNT signaling inhibits protein phosphatase 1 (PP1) activity, a negative regulator of ciliogenesis, by preventing GSK3-mediated phosphorylation of the PP1 regulatory inhibitor subunit PPP1R2. Concordantly, deficiency of WNT/GSK3 signaling by depletion of cyclin Y and cyclin-Y-like protein 1 induces primary cilia defects in mouse embryonic neuronal precursors, kidney proximal tubules, and adult mice preadipocytes.
    Keywords:  GSK3; LRP6; PP1; Wnt; cilia; exencephaly; lipodystrophy
    DOI:  https://doi.org/10.1016/j.devcel.2022.12.006
  8. Am J Med Genet A. 2023 Jan 25.
    Mosaic pathogenic variants in AKT3 cause capillary malformation and undergrowth.
    Amber Bolli, Bede Nriagu, Allison D Britt, Anjali D Toole, James Treat, Abhay Srinivasan, Sarah E Sheppard.
      Capillary malformations are slow-flow vascular malformations that affect the microcirculation including capillaries and post capillary venules and can be associated with growth differences. Specifically, the association of capillary malformations with undergrowth is a vastly understudied vascular syndrome with few reports of genetic causes including PIK3CA, GNAQ, and GNA11. Recently, a somatic pathogenic variant in AKT3 was identified in one child with a cutaneous vascular syndrome similar to cutis marmorata telangiectatica congenita, undergrowth, and no neurodevelopmental features. Here, we present a male patient with a capillary malformation and undergrowth due to a somatic pathogenic variant in AKT3 to confirm this association. It is essential to consider that mosaic pathogenic variants in AKT3 can cause a wide spectrum of disease. There is a need for future studies focusing on capillary malformations with undergrowth to understand the underlying mechanism.
    Keywords:  AKT3; capillary malformation; postzygotic pathogenic variant; somatic mosaicism; undergrowth; vascular malformation
    DOI:  https://doi.org/10.1002/ajmg.a.63121
  9. Dev Cell. 2023 Jan 13. pii: S1534-5807(22)00895-4. [Epub ahead of print]
    Endoderm-derived islet1-expressing cells differentiate into endothelial cells to function as the vascular HSPC niche in zebrafish.
    Hiroyuki Nakajima, Hiroyuki Ishikawa, Takuya Yamamoto, Ayano Chiba, Hajime Fukui, Keisuke Sako, Moe Fukumoto, Kenny Mattonet, Hyouk-Bum Kwon, Subhra P Hui, Gergana D Dobreva, Kazu Kikuchi, Christian S M Helker, Didier Y R Stainier, Naoki Mochizuki.
      Endothelial cells (ECs) line blood vessels and serve as a niche for hematopoietic stem and progenitor cells (HSPCs). Recent data point to tissue-specific EC specialization as well as heterogeneity; however, it remains unclear how ECs acquire these properties. Here, by combining live-imaging-based lineage-tracing and single-cell transcriptomics in zebrafish embryos, we identify an unexpected origin for part of the vascular HSPC niche. We find that islet1 (isl1)-expressing cells are the progenitors of the venous ECs that constitute the majority of the HSPC niche. These isl1-expressing cells surprisingly originate from the endoderm and differentiate into ECs in a process dependent on Bmp-Smad signaling and subsequently requiring npas4l (cloche) function. Single-cell RNA sequencing analyses show that isl1-derived ECs express a set of genes that reflect their distinct origin. This study demonstrates that endothelial specialization in the HSPC niche is determined at least in part by the origin of the ECs.
    Keywords:  endothelial specialization; hematopoietic stem and progenitor cell; imaging-based lineage tracing; vascular niche
    DOI:  https://doi.org/10.1016/j.devcel.2022.12.013
  10. Nat Commun. 2023 Jan 21. 14(1): 349
    Epithelial disruption drives mesendoderm differentiation in human pluripotent stem cells by enabling TGF-β protein sensing.
    Thomas Legier, Diane Rattier, Jack Llewellyn, Thomas Vannier, Benoit Sorre, Flavio Maina, Rosanna Dono.
      The processes of primitive streak formation and fate specification in the mammalian epiblast rely on complex interactions between morphogens and tissue organization. Little is known about how these instructive cues functionally interact to regulate gastrulation. We interrogated the interplay between tissue organization and morphogens by using human induced pluripotent stem cells (hiPSCs) downregulated for the morphogen regulator GLYPICAN-4, in which defects in tight junctions result in areas of disrupted epithelial integrity. Remarkably, this phenotype does not affect hiPSC stemness, but impacts on cell fate acquisition. Strikingly, cells within disrupted areas become competent to perceive the gastrulation signals BMP4 and ACTIVIN A, an in vitro surrogate for NODAL, and thus differentiate into mesendoderm. Yet, disruption of epithelial integrity sustains activation of BMP4 and ACTIVIN A downstream effectors and correlates with enhanced hiPSC endoderm/mesoderm differentiation. Altogether, our results disclose epithelial integrity as a key determinant of TGF-β activity and highlight an additional mechanism guiding morphogen sensing and spatial cell fate change within an epithelium.
    DOI:  https://doi.org/10.1038/s41467-023-35965-8
  11. Gigascience. 2022 Dec 28. pii: giac126. [Epub ahead of print]12
    scShapes: a statistical framework for identifying distribution shapes in single-cell RNA-sequencing data.
    Malindrie Dharmaratne, Ameya S Kulkarni, Atefeh Taherian Fard, Jessica C Mar.
       BACKGROUND: Single-cell RNA sequencing (scRNA-seq) methods have been advantageous for quantifying cell-to-cell variation by profiling the transcriptomes of individual cells. For scRNA-seq data, variability in gene expression reflects the degree of variation in gene expression from one cell to another. Analyses that focus on cell-cell variability therefore are useful for going beyond changes based on average expression and, instead, identifying genes with homogeneous expression versus those that vary widely from cell to cell.
    RESULTS: We present a novel statistical framework, scShapes, for identifying differential distributions in single-cell RNA-sequencing data using generalized linear models. Most approaches for differential gene expression detect shifts in the mean value. However, as single-cell data are driven by overdispersion and dropouts, moving beyond means and using distributions that can handle excess zeros is critical. scShapes quantifies gene-specific cell-to-cell variability by testing for differences in the expression distribution while flexibly adjusting for covariates if required. We demonstrate that scShapes identifies subtle variations that are independent of altered mean expression and detects biologically relevant genes that were not discovered through standard approaches.
    CONCLUSIONS: This analysis also draws attention to genes that switch distribution shapes from a unimodal distribution to a zero-inflated distribution and raises open questions about the plausible biological mechanisms that may give rise to this, such as transcriptional bursting. Overall, the results from scShapes help to expand our understanding of the role that gene expression plays in the transcriptional regulation of a specific perturbation or cellular phenotype. Our framework scShapes is incorporated into a Bioconductor R package (https://www.bioconductor.org/packages/release/bioc/html/scShapes.html).
    Keywords:  distribution shapes; single-cell RNA-sequencing; zero inflation
    DOI:  https://doi.org/10.1093/gigascience/giac126
  12. Nature. 2023 Jan;613(7945): 629
    Early insight into spontaneous mutations.
    Richard P Novick.
      
    Keywords:  Evolution; Genetics; History
    DOI:  https://doi.org/10.1038/d41586-023-00141-x
  13. Nat Commun. 2023 Jan 24. 14(1): 384
    scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection.
    Ziqi Zhang, Haoran Sun, Ragunathan Mariappan, Xi Chen, Xinyu Chen, Mika S Jain, Mirjana Efremova, Sarah A Teichmann, Vaibhav Rajan, Xiuwei Zhang.
      Single cell data integration methods aim to integrate cells across data batches and modalities, and data integration tasks can be categorized into horizontal, vertical, diagonal, and mosaic integration, where mosaic integration is the most general and challenging case with few methods developed. We propose scMoMaT, a method that is able to integrate single cell multi-omics data under the mosaic integration scenario using matrix tri-factorization. During integration, scMoMaT is also able to uncover the cluster specific bio-markers across modalities. These multi-modal bio-markers are used to interpret and annotate the clusters to cell types. Moreover, scMoMaT can integrate cell batches with unequal cell type compositions. Applying scMoMaT to multiple real and simulated datasets demonstrated these features of scMoMaT and showed that scMoMaT has superior performance compared to existing methods. Specifically, we show that integrated cell embedding combined with learned bio-markers lead to cell type annotations of higher quality or resolution compared to their original annotations.
    DOI:  https://doi.org/10.1038/s41467-023-36066-2
  14. Proc Natl Acad Sci U S A. 2023 Jan 31. 120(5): e2210038120
    The fidelity of transcription in human cells.
    Claire Chung, Bert M Verheijen, Xinmin Zhang, Biao Huang, Aeowynn Coakley, Eric McGann, Emily Wade, Olivia Dinep-Schneider, Jessica LaGosh, Maria-Eleni Anagnostou, Stephen Simpson, Kelly Thomas, Mimi Ernst, Allison Rattray, Michael Lynch, Mikhail Kashlev, Berenice A Benayoun, Zhongwei Li, Jeffrey Strathern, Jean-Francois Gout, Marc Vermulst.
      To determine the error rate of transcription in human cells, we analyzed the transcriptome of H1 human embryonic stem cells with a circle-sequencing approach that allows for high-fidelity sequencing of the transcriptome. These experiments identified approximately 100,000 errors distributed over every major RNA species in human cells. Our results indicate that different RNA species display different error rates, suggesting that human cells prioritize the fidelity of some RNAs over others. Cross-referencing the errors that we detected with various genetic and epigenetic features of the human genome revealed that the in vivo error rate in human cells changes along the length of a transcript and is further modified by genetic context, repetitive elements, epigenetic markers, and the speed of transcription. Our experiments further suggest that BRCA1, a DNA repair protein implicated in breast cancer, has a previously unknown role in the suppression of transcription errors. Finally, we analyzed the distribution of transcription errors in multiple tissues of a new mouse model and found that they occur preferentially in neurons, compared to other cell types. These observations lend additional weight to the idea that transcription errors play a key role in the progression of various neurological disorders, including Alzheimer's disease.
    Keywords:  Alzheimer's disease; human embryonic stem cells; mutagenesis; transcription; transcription errors
    DOI:  https://doi.org/10.1073/pnas.2210038120
  15. Nat Biotechnol. 2023 Jan 26.
    CLASH enables large-scale parallel knock-in for cell engineering.
      
    DOI:  https://doi.org/10.1038/s41587-023-01664-4
  16. Chembiochem. 2023 Jan 26. e202200626
    Proteomics Update and Perspectives from the Proteomics in Cell Biology and Disease Mechanisms Conference.
    Ilana B Kotliar.
      Proteomics, or the large-scale study of proteomes, has benefitted from many recent advances in chemical biology, mass spectrometry, and machine learning. The Proteomics in Cell Biology and Disease Mechanisms conference showcased the synergy between these elements and the vast range of biological questions that proteomics can now help us to answer.
    DOI:  https://doi.org/10.1002/cbic.202200626
  17. Sci Rep. 2023 Jan 27. 13(1): 1520
    Direct lysis of 3D cell cultures for RT-qPCR gene expression quantification.
    Fien Gysens, Lisa Ostyn, Ellen Goeteyn, Eva Blondeel, Justine Nuyttens, Olivier De Wever, Eric de Bony, Aurélie Crabbé, Pieter Mestdagh.
      In vitro cell culture experiments are widely used to study cellular behavior in most biological research fields. Except for suspension cells, most human cell types are cultured as adherent monolayers on a plastic surface. While technically convenient, monolayer cultures can suffer from limitations in terms of physiological relevance, as their resemblance to complex in vivo tissue structures is limited. To address these limitations, three-dimensional (3D) cell culture systems have gained increased interest as they mimic key structural and functional properties of their in vivo tissue counterparts. Nevertheless, protocols established on monolayer cell cultures may require adjustments if they are to be applied to 3D cell cultures. As gene expression quantification is an essential part of many in vitro experiments, we evaluated and optimized a direct cell lysis, reverse transcription and qPCR protocol applicable for 3D cell cultures. The newly developed protocol wherein gene expression is determined directly from crude cell lysates showed improved cell lysis compared to the standard protocol, accurate gene expression quantification, hereby avoiding time-consuming cell harvesting and RNA extraction.
    DOI:  https://doi.org/10.1038/s41598-023-28844-1
  18. Nat Biotechnol. 2023 Jan 23.
    Precise transcript targeting by CRISPR-Csm complexes.
    David Colognori, Marena Trinidad, Jennifer A Doudna.
      Robust and precise transcript targeting in mammalian cells remains a difficult challenge using existing approaches due to inefficiency, imprecision and subcellular compartmentalization. Here we show that the clustered regularly interspaced short palindromic repeats (CRISPR)-Csm complex, a multiprotein effector from type III CRISPR immune systems in prokaryotes, provides surgical RNA ablation of both nuclear and cytoplasmic transcripts. As part of the most widely occurring CRISPR adaptive immune pathway, CRISPR-Csm uses a programmable RNA-guided mechanism to find and degrade target RNA molecules without inducing indiscriminate trans-cleavage of cellular RNAs, giving it an important advantage over the CRISPR-Cas13 family of enzymes. Using single-vector delivery of the Streptococcus thermophilus Csm complex, we observe high-efficiency RNA knockdown (90-99%) and minimal off-target effects in human cells, outperforming existing technologies including short hairpin RNA- and Cas13-mediated knockdown. We also find that catalytically inactivated Csm achieves specific and durable RNA binding, a property we harness for live-cell RNA imaging. These results establish the feasibility and efficacy of multiprotein CRISPR-Cas effector complexes as RNA-targeting tools in eukaryotes.
    DOI:  https://doi.org/10.1038/s41587-022-01649-9
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