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ACSS2 gene variants determine kidney disease risk by controlling de novo lipogenesis in kidney tubules
Dhanunjay Mukhi, Lingzhi Li, Hongbo Liu, Tomohito Doke, Lakshmi P. Kolligundla, Eunji Ha, Konstantin Kloetzer, Amin Abedini, Sarmistha Mukherjee, Junnan Wu, Poonam Dhillon, Hailong Hu, Dongyin Guan, Katsuhiko Funai, Kahealani Uehara, Paul M. Titchenell, Joseph A. Baur, Kathryn E. Wellen, Katalin Susztak
Dhanunjay Mukhi, Lingzhi Li, Hongbo Liu, Tomohito Doke, Lakshmi P. Kolligundla, Eunji Ha, Konstantin Kloetzer, Amin Abedini, Sarmistha Mukherjee, Junnan Wu, Poonam Dhillon, Hailong Hu, Dongyin Guan, Katsuhiko Funai, Kahealani Uehara, Paul M. Titchenell, Joseph A. Baur, Kathryn E. Wellen, Katalin Susztak
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Research Article Genetics Nephrology

ACSS2 gene variants determine kidney disease risk by controlling de novo lipogenesis in kidney tubules

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Abstract

Worldwide, over 800 million people are affected by kidney disease, yet its pathogenesis remains elusive, hindering the development of novel therapeutics. In this study, we used kidney-specific expression of quantitative traits and single-nucleus open chromatin analysis to show that genetic variants linked to kidney dysfunction on chromosome 20 target the acyl-CoA synthetase short-chain family 2 (ACSS2). By generating ACSS2-KO mice, we demonstrated their protection from kidney fibrosis in multiple disease models. Our analysis of primary tubular cells revealed that ACSS2 regulated de novo lipogenesis (DNL), causing NADPH depletion and increasing ROS levels, ultimately leading to NLRP3-dependent pyroptosis. Additionally, we discovered that pharmacological inhibition or genetic ablation of fatty acid synthase safeguarded kidney cells against profibrotic gene expression and prevented kidney disease in mice. Lipid accumulation and the expression of genes related to DNL were elevated in the kidneys of patients with fibrosis. Our findings pinpoint ACSS2 as a critical kidney disease gene and reveal the role of DNL in kidney disease.

Authors

Dhanunjay Mukhi, Lingzhi Li, Hongbo Liu, Tomohito Doke, Lakshmi P. Kolligundla, Eunji Ha, Konstantin Kloetzer, Amin Abedini, Sarmistha Mukherjee, Junnan Wu, Poonam Dhillon, Hailong Hu, Dongyin Guan, Katsuhiko Funai, Kahealani Uehara, Paul M. Titchenell, Joseph A. Baur, Kathryn E. Wellen, Katalin Susztak

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Figure 1

Prioritization of ACSS2 as a kidney disease gene from GWAS.

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Prioritization of ACSS2 as a kidney disease gene from GWAS.
(A) Regional...
(A) Regional plot showing SNPs associated with kidney eGFR GWAS (n = 1,508,569 individuals). The x axis shows the chromosomal location, and the y axis shows the strength of association [–log(P)] on chromosome 20. The locus top variants (rs11698977) tagging the independent signal closest to ACSS2 gene was selected as the index variant to calculate the linkage disequilibrium (LD) correlation coefficient (r2), with other variants in the locus shown by blue dots (lower r2) and red dots (higher r2). (B) Gene prioritization strategy (top left). Genes with gene priority scores higher than 3 at the chromosome 20 eGFR GWAS locus (right). The color indicates the priority score. Coloc, colocalization. (C) Regional plot of SNPs associated with kidney tubule cytosine methylation levels (mQTL) (n = 443). The x axis shows chromosomal location, and the y axis shows the strength of association [–log(P)]. (D) Regional plot for SNPs associated with ACSS2 expression in kidney glomeruli (n = 303). The x axis shows the chromosomal location, and the y axis shows the strength of association [–log(P)]. (E) Regional plot for SNPs associated with kidney tubule ACSS2 expression (n = 356). The x axis shows the chromosomal (chr) location, and the y axis shows the strength of association [–log(P)]. (F) Human kidney ACSS2 gene expression in tubules (n = 356) in microdissected samples. The y axis shows normalized ACSS2 expression, and the x axis shows genotype information. (G) Upper panel: Locus zoom plot of eGFRcrea GWAS associations (n = 1,508,659 individuals; the same is shown in A) in the ACSS2 locus. Lower panel: Epigenetic information on the ACSS2 locus in human kidney samples including mQTL SNPs; all eGFR GWAS SNPs (blue) followed by eGFR GWAS SNPs with a priority score of greater than 2 (dark green); eGFRcrea GWAS SNPs with a priority score of greater than 4 (magenta); adult human kidney open chromatin information for each cell type; and histone modifications (H34me3, H3K27ac, and H3K4me1) from human kidney ChIP-Seq and chromatin states predicted by ChromHMM. PT-S1, PT segment S1; LOH, loop of Henle; DCT, distal convoluted tubule; PC, collecting duct principal cells; IC, collecting duct intercalated cells; Podo, podocytes; Endo, endothelial cells; Immune, immune cells; Stroma, stromal fraction. (H) Scheme of CRISPR-mediated genomic region deletion. (I) Transcript levels of ACSS2 following deletion of the genetic risk locus containing SNPs 1, 3, 4, 5, and 6. Int, intron; Prm, promoter. Data are presented as the mean ± SEM. ****P < 0.0001, by 1-way ANOVA after Tukey’s multiple-comparison test.

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ISSN: 0021-9738 (print), 1558-8238 (online)

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