Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Ppublish 8 citations
PubMed: 37837621 DOI: 10.1016/j.celrep.2023.113237
Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues.
Cell Rep 42(10):113237
Authors: Bryan B Teefy, Aaron J J Lemus, Ari Adler, Alan Xu, Rajyk Bhala, Katelyn Hsu, Bérénice A Benayoun
Affiliations
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA.
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA; Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA; Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA.
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, and spleen. We annotate 22 cell types, define marker genes, and infer differentiation trajectories. We find pervasive sex-dimorphic gene expression across cell types. Sex-dimorphic genes tend to be linked to lipid metabolism, consistent with clear differences in lipid storage in female vs. male turquoise killifish livers. We use machine learning to predict sex using single-cell gene expression and identify potential markers for molecular sex identity. As a proof of principle, we show that our atlas can be used to deconvolute existing bulk RNA sequencing (RNA-seq) data to obtain accurate estimates of cell type proportions. This atlas can be a resource to the community that could be leveraged to develop cell-type-specific expression in transgenic animals.
MeSH
Cells, Genes, Biological Science Disciplines, Transcriptome, Liver, Sex Characteristics, Sex, Tissues, Gene Expression, Sex Differences