Cross-tissue omics analysis discovers ten adipose genes encoding secreted proteins in obesity-related non-alcoholic fatty liver disease

• Published in: EBioMedicine 2023-06, Vol.92, p.104620, Article 104620
• Main Authors: Darci-Maher, Nicholas, Alvarez, Marcus, Arasu, Uma Thanigai, Selvarajan, Ilakya, Lee, Seung Hyuk T., Pan, David Z., Miao, Zong, Das, Sankha Subhra, Kaminska, Dorota, Örd, Tiit, Benhammou, Jihane N., Wabitsch, Martin, Pisegna, Joseph R., Männistö, Ville, Pietiläinen, Kirsi H., Laakso, Markku, Sinsheimer, Janet S., Kaikkonen, Minna U., Pihlajamäki, Jussi, Pajukanta, Päivi
• Format: Article
• Language: English
• Subjects: Adipogenesis; Biomarkers - metabolism; cis regulatory variants; Dual-tissue transcriptomics screening; Genome-Wide Association Study; Humans; Liver - metabolism; Liver histology; Non-alcoholic fatty liver disease; Non-alcoholic Fatty Liver Disease - complications; Non-alcoholic Fatty Liver Disease - genetics; Obesity; Obesity - complications; Obesity - genetics; Obesity - metabolism; Serum biomarkers
• ISSN: 2352-3964; 2352-3964
• DOI: 10.1016/j.ebiom.2023.104620

Non-alcoholic fatty liver disease (NAFLD) is a fast-growing, underdiagnosed, epidemic. We hypothesise that obesity-related inflammation compromises adipose tissue functions, preventing efficient fat storage, and thus driving ectopic fat accumulation into the liver. To identify adipose-based mechanisms and potential serum biomarker candidates (SBCs) for NAFLD, we utilise dual-tissue RNA-sequencing (RNA-seq) data in adipose tissue and liver, paired with histology-based NAFLD diagnosis, from the same individuals in a cohort of obese individuals. We first scan for genes that are differentially expressed (DE) for NAFLD in obese individuals’ subcutaneous adipose tissue but not in their liver; encode proteins secreted to serum; and show preferential adipose expression. Then the identified genes are filtered to key adipose-origin NAFLD genes by best subset analysis, knockdown experiments during human preadipocyte differentiation, recombinant protein treatment experiments in human liver HepG2 cells, and genetic analysis. We discover a set of genes, including 10 SBCs, that may modulate NAFLD pathogenesis by impacting adipose tissue function. Based on best subset analysis, we further follow-up on two SBCs CCDC80 and SOD3 by knockdown in human preadipocytes and subsequent differentiation experiments, which show that they modulate crucial adipogenesis genes, LPL, SREBPF1, and LEP. We also show that treatment of the liver HepG2 cells with the CCDC80 and SOD3 recombinant proteins impacts genes related to steatosis and lipid processing, including PPARA, NFE2L2, and RNF128. Finally, utilizing the adipose NAFLD DE gene cis-regulatory variants associated with serum triglycerides (TGs) in extensive genome-wide association studies (GWASs), we demonstrate a unidirectional effect of serum TGs on NAFLD with Mendelian Randomization (MR) analysis. We also demonstrate that a single SNP regulating one of the SBC genes, rs2845885, produces a significant MR result by itself. This supports the conclusion that genetically regulated adipose expression of the NAFLD DE genes may contribute to NAFLD through changes in serum TG levels. Our results from the dual-tissue transcriptomics screening improve the understanding of obesity-related NAFLD by providing a targeted set of 10 adipose tissue-active genes as new serum biomarker candidates for the currently grossly underdiagnosed fatty liver disease. The work was supported by NIH grants R01HG010505 and R01DK132775. The Genotype-Tissue Expressio