Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues

Bryan B Teefy; Aaron J J Lemus; Ari Adler; Alan Xu; Rajyk Bhala; Katelyn Hsu; Bérénice A Benayoun

doi:10.1016/j.celrep.2023.113237

Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues

Cell Rep. 2023 Oct 31;42(10):113237. doi: 10.1016/j.celrep.2023.113237. Epub 2023 Oct 12.

Authors

Bryan B Teefy¹, Aaron J J Lemus², Ari Adler¹, Alan Xu³, Rajyk Bhala¹, Katelyn Hsu², Bérénice A Benayoun⁴

Affiliations

¹ Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.
² 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.
³ 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.
⁴ 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. Electronic address: berenice.benayoun@usc.edu.

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.

Keywords: African turquoise killifish; CP: Developmental biology; CP: Metabolism; sex-dimorphism; single-cell RNA-seq.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Aging
Animals
Animals, Genetically Modified
Female
Fundulidae*
Male
Sex Characteristics
Transcriptome / genetics

Supplementary concepts

Nothobranchius furzeri

Abstract

Publication types

MeSH terms

Supplementary concepts

Grants and funding