Academic Journal
A rat liver cell atlas reveals intrahepatic myeloid heterogeneity.
| Title: | A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. |
|---|---|
| Authors: | Pouyabahar D; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada., Chung SW; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.; Department of Immunology, University of Toronto, Toronto, ON, Canada., Pezzutti OI; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., Perciani CT; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., Wang X; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., Ma XZ; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., Jiang C; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., Camat D; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.; Department of Immunology, University of Toronto, Toronto, ON, Canada., Chung T; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., Sekhon M; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada., Manuel J; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., Chen XC; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., McGilvray ID; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada., MacParland SA; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.; Department of Immunology, University of Toronto, Toronto, ON, Canada.; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada., Bader GD; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada.; Department of Computer Science, University of Toronto, Toronto, ON, Canada.; Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada.; Princess Margaret Research Institute, University Health Network, Toronto, ON, Canada.; The Multiscale Human Program, Canadian Institute for Advanced Research, Toronto, ON, Canada. |
| Source: | IScience [iScience] 2023 Oct 14; Vol. 26 (11), pp. 108213. Date of Electronic Publication: 2023 Oct 14 (Print Publication: 2023). |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Cell Press Country of Publication: United States NLM ID: 101724038 Publication Model: eCollection Cited Medium: Internet ISSN: 2589-0042 (Electronic) Linking ISSN: 25890042 NLM ISO Abbreviation: iScience Subsets: PubMed not MEDLINE |
| Imprint Name(s): | Original Publication: [Cambridge, MA] : Cell Press, [2018]- |
| Abstract: | The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) make it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single-cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single-cell and single-nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models. (© 2023 The Author(s).) |
| Competing Interests: | G.D.B. is an advisor for Deep Genomics and is on the Scientific Advisory Board of Adela Bio. |
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| Grant Information: | P41 GM103504 United States GM NIGMS NIH HHS |
| Contributed Indexing: | Keywords: Components of the immune system; Model organism; Transcriptomics |
| Entry Date(s): | Date Created: 20231129 Latest Revision: 20240130 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC10651689 |
| DOI: | 10.1016/j.isci.2023.108213 |
| PMID: | 38026201 |
| Database: | MEDLINE |
| FullText | Links: – Type: other Url: https://resolver.ebsco.com:443/public/rma-ftfapi/ejs/direct?AccessToken=4681B99BB9336D7013E9&Show=Object Text: Availability: 0 CustomLinks: – Url: https://www.doi.org/10.1016/j.isci.2023.108213? Name: ScienceDirect (all content) (s7799221) Category: fullText Text: View record from ScienceDirect MouseOverText: View record from ScienceDirect |
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| Header | DbId: cmedm DbLabel: MEDLINE An: 38026201 AccessLevel: 3 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
| IllustrationInfo | |
| Items | – Name: Title Label: Title Group: Ti Data: A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AU" term="%22Pouyabahar+D%22">Pouyabahar D</searchLink>; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Chung+SW%22">Chung SW</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.; Department of Immunology, University of Toronto, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Pezzutti+OI%22">Pezzutti OI</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Perciani+CT%22">Perciani CT</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Wang+X%22">Wang X</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Ma+XZ%22">Ma XZ</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Jiang+C%22">Jiang C</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Camat+D%22">Camat D</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.; Department of Immunology, University of Toronto, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Chung+T%22">Chung T</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Sekhon+M%22">Sekhon M</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Manuel+J%22">Manuel J</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Chen+XC%22">Chen XC</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22McGilvray+ID%22">McGilvray ID</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22MacParland+SA%22">MacParland SA</searchLink>; Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada.; Department of Immunology, University of Toronto, Toronto, ON, Canada.; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.<br /><searchLink fieldCode="AU" term="%22Bader+GD%22">Bader GD</searchLink>; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.; The Donnelly Centre, University of Toronto, Toronto, ON, Canada.; Department of Computer Science, University of Toronto, Toronto, ON, Canada.; Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada.; Princess Margaret Research Institute, University Health Network, Toronto, ON, Canada.; The Multiscale Human Program, Canadian Institute for Advanced Research, Toronto, ON, Canada. – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22101724038%22">IScience</searchLink> [iScience] 2023 Oct 14; Vol. 26 (11), pp. 108213. <i>Date of Electronic Publication: </i>2023 Oct 14 (<i>Print Publication: </i>2023). – Name: TypePub Label: Publication Type Group: TypPub Data: Journal Article – Name: Language Label: Language Group: Lang Data: English – Name: TitleSource Label: Journal Info Group: Src Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22Cell+Press%22">Cell Press </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>101724038 <i>Publication Model: </i>eCollection <i>Cited Medium: </i>Internet <i>ISSN: </i>2589-0042 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2225890042%22">25890042 </searchLink><i>NLM ISO Abbreviation: </i>iScience <i>Subsets: </i>PubMed not MEDLINE – Name: PublisherInfo Label: Imprint Name(s) Group: PubInfo Data: <i>Original Publication</i>: [Cambridge, MA] : Cell Press, [2018]- – Name: Abstract Label: Abstract Group: Ab Data: The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) make it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single-cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single-cell and single-nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models.<br /> (© 2023 The Author(s).) – Name: Abstract Label: Competing Interests Group: Ab Data: G.D.B. is an advisor for Deep Genomics and is on the Scientific Advisory Board of Adela Bio. – Name: Ref Label: References Group: RefInfo Data: Nat Commun. 2016 Jan 27;7:10321. (PMID: <searchLink fieldCode="PM" term="%2226813785%22">26813785)</searchLink><br />Nat Immunol. 2019 Dec;20(12):1558. (PMID: <searchLink fieldCode="PM" term="%2231745342%22">31745342)</searchLink><br />Cell Rep. 2015 Dec 1;13(9):1757-64. (PMID: <searchLink fieldCode="PM" term="%2226655896%22">26655896)</searchLink><br />Front Cell Infect Microbiol. 2012 Aug 02;2:105. (PMID: <searchLink fieldCode="PM" term="%2222919694%22">22919694)</searchLink><br />Korean J Hepatobiliary Pancreat Surg. 2011 May;15(2):67-77. 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(PMID: <searchLink fieldCode="PM" term="%2220800674%22">20800674)</searchLink> – Name: GrantInfo Label: Grant Information Group: Grant Data: P41 GM103504 United States GM NIGMS NIH HHS – Name: SubjectMinor Label: Contributed Indexing Group: Data: <i>Keywords: </i>Components of the immune system; Model organism; Transcriptomics – Name: DateEntry Label: Entry Date(s) Group: Date Data: <i>Date Created: </i>20231129 <i>Latest Revision: </i>20240130 – Name: DateUpdate Label: Update Code Group: Date Data: 20260130 – Name: PubmedCentralID Label: PubMed Central ID Group: ID Data: PMC10651689 – Name: DOI Label: DOI Group: ID Data: 10.1016/j.isci.2023.108213 – Name: AN Label: PMID Group: ID Data: 38026201 |
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