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Wang Y, Chen X, Zheng Z, Huang L, Xie W, Wang F, Zhang Z, Wong KC. scGREAT: Transformer-based deep-language model for gene regulatory network inference from single-cell transcriptomics. iScience 2024; 27:109352. [PMID: 38510148 PMCID: PMC10951644 DOI: 10.1016/j.isci.2024.109352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/29/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
Gene regulatory networks (GRNs) involve complex and multi-layer regulatory interactions between regulators and their target genes. Precise knowledge of GRNs is important in understanding cellular processes and molecular functions. Recent breakthroughs in single-cell sequencing technology made it possible to infer GRNs at single-cell level. Existing methods, however, are limited by expensive computations, and sometimes simplistic assumptions. To overcome these obstacles, we propose scGREAT, a framework to infer GRN using gene embeddings and transformer from single-cell transcriptomics. scGREAT starts by constructing gene expression and gene biotext dictionaries from scRNA-seq data and gene text information. The representation of TF gene pairs is learned through optimizing embedding space by transformer-based engine. Results illustrated scGREAT outperformed other contemporary methods on benchmarks. Besides, gene representations from scGREAT provide valuable gene regulation insights, and external validation on spatial transcriptomics illuminated the mechanism behind scGREAT annotation. Moreover, scGREAT identified several TF target regulations corroborated in studies.
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Affiliation(s)
- Yuchen Wang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Xingjian Chen
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zetian Zheng
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Lei Huang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Weidun Xie
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
| | - Zhaolei Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
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Mellough CB, Bauer R, Collin J, Dorgau B, Zerti D, Dolan DWP, Jones CM, Izuogu OG, Yu M, Hallam D, Steyn JS, White K, Steel DH, Santibanez-Koref M, Elliott DJ, Jackson MS, Lindsay S, Grellscheid S, Lako M. An integrated transcriptional analysis of the developing human retina. Development 2019; 146:146/2/dev169474. [PMID: 30696714 PMCID: PMC6361134 DOI: 10.1242/dev.169474] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/24/2018] [Indexed: 12/11/2022]
Abstract
The scarcity of embryonic/foetal material as a resource for direct study means that there is still limited understanding of human retina development. Here, we present an integrated transcriptome analysis combined with immunohistochemistry in human eye and retinal samples from 4 to 19 post-conception weeks. This analysis reveals three developmental windows with specific gene expression patterns that informed the sequential emergence of retinal cell types and enabled identification of stage-specific cellular and biological processes, and transcriptional regulators. Each stage is characterised by a specific set of alternatively spliced transcripts that code for proteins involved in the formation of the photoreceptor connecting cilium, pre-mRNA splicing and epigenetic modifiers. Importantly, our data show that the transition from foetal to adult retina is characterised by a large increase in the percentage of mutually exclusive exons that code for proteins involved in photoreceptor maintenance. The circular RNA population is also defined and shown to increase during retinal development. Collectively, these data increase our understanding of human retinal development and the pre-mRNA splicing process, and help to identify new candidate disease genes.
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Affiliation(s)
- Carla B. Mellough
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK,Lions Eye Institute, 2 Verdun Street, Nedlands, Perth, WA 6009, Australia
| | - Roman Bauer
- School of Computing, Newcastle University, Newcastle NE4 5TG, UK
| | - Joseph Collin
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Birthe Dorgau
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Darin Zerti
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - David W. P. Dolan
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Carl M. Jones
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Osagie G. Izuogu
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Min Yu
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Dean Hallam
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Jannetta S. Steyn
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Kathryn White
- EM Research Services, Newcastle University, Newcastle NE2 4HH, UK
| | - David H. Steel
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | | | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Michael S. Jackson
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
| | - Sushma Grellscheid
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, UK
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Viringipurampeer IA, Ferreira T, DeMaria S, Yoon JJ, Shan X, Moosajee M, Gregory-Evans K, Ngai J, Gregory-Evans CY. Pax2 regulates a fadd-dependent molecular switch that drives tissue fusion during eye development. Hum Mol Genet 2012; 21:2357-69. [PMID: 22357656 DOI: 10.1093/hmg/dds056] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Tissue fusion is an essential morphogenetic mechanism in development, playing a fundamental role in developing neural tube, palate and the optic fissure. Disruption of genes associated with the tissue fusion can lead to congenital malformations, such as spina bifida, cleft lip/palate and ocular coloboma. For instance, the Pax2 transcription factor is required for optic fissure closure, although the mechanism of Pax2 action leading to tissue fusion remains elusive. This lack of information defining how transcription factors drive tissue morphogenesis at the cellular level is hampering new treatments options. Through loss- and gain-of-function analysis, we now establish that pax2 in combination with vax2 directly regulate the fas-associated death domain (fadd) gene. In the presence of fadd, cell proliferation is restricted in the developing eye through a caspase-dependent pathway. However, the loss of fadd results in a proliferation defect and concomitant activation of the necroptosis pathway through RIP1/RIP3 activity, leading to an abnormal open fissure. Inhibition of RIP1 with the small molecule drug necrostatin-1 rescues the pax2 eye fusion defect, thereby overcoming the underlying genetic defect. Thus, fadd has an essential physiological function in protecting the developing optic fissure neuroepithelium from RIP3-dependent necroptosis. This study demonstrates the molecular hierarchies that regulate a cellular switch between proliferation and the apoptotic and necroptotic cell death pathways, which in combination drive tissue morphogenesis. Furthermore, our data suggest that future therapeutic strategies may be based on small molecule drugs that can bypass the gene defects causing common congenital tissue fusion defects.
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Affiliation(s)
- Ishaq A Viringipurampeer
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, Canada
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Samson M, Emerson MM, Cepko CL. Robust marking of photoreceptor cells and pinealocytes with several reporters under control of the Crx gene. Dev Dyn 2010; 238:3218-25. [PMID: 19882727 DOI: 10.1002/dvdy.22138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Crx is a member of the Otx family of homeobox genes with expression restricted to vertebrate retinal photoreceptor and bipolar cells as well as the pinealocytes of the pineal organ. To facilitate the visualization of Crx-expressing cells, we generated transgenic mice expressing several reporters under the control of the Crx regulatory sequences present within a bacterial artificial chromosome (BAC). These mice expand the transgenic mouse collection, which uses photoreceptor regulatory elements for reporter gene expression by providing a broader repertoire of reporter genes. In addition, because Crx is expressed very soon after a cell fated to be a photoreceptor cell becomes postmitotic, they provide a means for early identification of immature photoreceptor cells.
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Affiliation(s)
- Maria Samson
- Department of Genetics and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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Moosajee M, Gregory-Evans K, Ellis CD, Seabra MC, Gregory-Evans CY. Translational bypass of nonsense mutations in zebrafish rep1, pax2.1 and lamb1 highlights a viable therapeutic option for untreatable genetic eye disease. Hum Mol Genet 2008; 17:3987-4000. [PMID: 18809619 DOI: 10.1093/hmg/ddn302] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The extensive molecular genetic heterogeneity seen with inherited eye disease is a major barrier to the development of gene-based therapeutics. The underlying molecular pathology in a considerable proportion of these diseases however are nonsense mutations leading to premature termination codons. A therapeutic intervention targeted at this abnormality would therefore potentially be relevant to a wide range of inherited eye diseases. We have taken advantage of the ability of aminoglycoside drugs to suppress such nonsense mutations and partially restore full-length, functional protein in a zebrafish model of choroideraemia (chm(ru848); juvenile chorio-retinal degeneration) and in two models of ocular coloboma (noi(tu29a) and gup(m189); congenital optic fissure closure defects). In vitro cell-based assays showed significant readthrough with two drugs, gentamicin and paromomycin, which was confirmed by western blot and in vitro prenylation assays. The presence of either aminoglycoside during zebrafish development in vivo showed remarkable prevention of mutant ocular phenotypes in each model and a reduction in multisystemic defects leading to a 1.5-1.7-fold increase in survival. We also identified a significant reduction in abnormal cell death shown by TUNEL assay. To test the hypothesis that optic fissure closure was apoptosis-dependent, the anti-apoptotic agents, curcumin and zVAD-fmk, were tested in gup(m189) embryos. Both drugs were found to reduce the size of the coloboma, providing molecular evidence that cell death is required for optic fissure remodelling. These findings draw attention to the value of zebrafish models of eye disease as useful preclinical drug screening tools in studies to identify molecular mechanisms amenable to therapeutic intervention.
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Affiliation(s)
- Mariya Moosajee
- Department of Clinical Neuroscience, Imperial College London, London SW7 2AZ, UK
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