Tissue-specific pathways and networks underlying sexual dimorphism in non-alcoholic fatty liver disease

Kurt et al. Biology of Sex Differences (2018) 9:46 https://doi.org/10.1186/s13293-018-0205-7 RESEARCH Open Access Tissue-specific pathways and networks underlying sexual dimorphism in nonalcoholic fatty liver disease Zeyneb Kurt1, Rio Barrere-Cain1, Jonnby LaGuardia1, Margarete Mehrabian2, Calvin Pan2, Simon T Hui2, Frode Norheim2, Zhiqiang Zhou2, Yehudit Hasin2, Aldons J Lusis2* and Xia Yang1* Abstract Background: Non-alcoholic fatty liver disease (NAFLD) encompasses benign steatosis and more severe conditions such as non-alcoholic steatohepatitis (NASH), cirrhosis, and liver cancer. This chronic liver disease has a poorly understood etiology and demonstrates sexual dimorphisms. We aim to examine the molecular mechanisms underlying sexual dimorphisms in NAFLD pathogenesis through a comprehensive multi-omics study. We integrated genomics (DNA variations), transcriptomics of liver and adipose tissue, and phenotypic data of NAFLD derived from female mice of ~ 100 strains included in the hybrid mouse diversity panel (HMDP) and compared the NAFLD molecular pathways and gene networks between sexes. Results: We identified both shared and sex-specific biological processes for NAFLD. Adaptive immunity, branched chain amino acid metabolism, oxidative phosphorylation, and cell cycle/apoptosis were shared between sexes. Among the sex-specific pathways were vitamins and cofactors metabolism and ion channel transport for females, and phospholipid, lysophospholipid, and phosphatidylinositol metabolism and insulin signaling for males. Additionally, numerous lipid and insulin-related pathways and inflammatory processes in the adipose and liver tissue appeared to show more prominent association with NAFLD in male HMDP. Using data-driven network modeling, we identified plausible sex-specific and tissue-specific regulatory genes as well as those that are shared between sexes. These key regulators orchestrate the NAFLD pathways in a sex- and tissue-specific manner. Gonadectomy experiments support that sex hormones may partially underlie the sexually dimorphic genes and pathways involved in NAFLD. Conclusions: Our multi-omics integrative study reveals sex- and tissue-specific genes, processes, and networks underlying sexual dimorphism in NAFLD and may facilitate sex-specific precision medicine. Keywords: Non-alcoholic fatty liver disease (NAFLD), Sexual dimorphism, Multi-omics integration, Key regulator genes, Bayesian networks, Coexpression networks, Hybrid mouse diversity panel Background Nonalcoholic fatty liver disease (NAFLD) covers a wide spectrum of disorders spanning simple liver steatosis, nonalcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma [1–3]. NAFLD has rapidly become a significant health threat globally, affecting 25% of the world population on average, and is strongly associated with * Correspondence: ; 2 Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 1 Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA insulin resistance, type II diabetes, and obesity [1, 4–6]. Due to the lack of mechanistic understanding of NAFLD, there are no existing therapies directly targeting NAFLD. Moreover, significant unexplained age-dependent sexual dimorphisms have been observed in NAFLD. At younger ages, NAFLD has a higher prevalence in males than females, whereas at older ages, especially after menopause, the prevalence in females increases [7–10]. Males with NAFLD have more severe metabolic phenotypes than females, including higher glucose levels, higher systolic blood pressure, greater visceral adiposity, lower adiponectin levels, © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Kurt et al. Biology of Sex Differences (2018) 9:46 lower high-density lipoprotein cholesterol levels, and greater liver injury as measured by alanine aminotransferase levels and aspartate aminotransferase levels [11]. Although endogenous estrogens, adipose distribution, and other lifestyle factors have all been proposed as possible contributors to sex differences in NAFLD [10–13], the molecular mechanisms are unclear. Revealing the underlying biological mechanisms driving the sex differences in NAFLD can enable the identification of novel therapies and preventive strategies to ameliorate the heightening global health threat from NAFLD in a sex-specific and personalized manner. Recently, human genome-wide association studies (GWAS) have revealed a handful of candidate causal genes such as PNPLA3, SAMM50, PARVB, GCKR, LCP1, LYPLAL1, PPP1R3B, TM6SF2, and TRIB1 for NAFLD [14–16]. However, sex differences in genetic risks have not been investigated in these studies. In addition, NAFLD is strongly influenced by environmental factors such as diet, which are difficult to control in human studies. Rodent models, on the other hand, allow for control of environmental factors and collection of molecular traits from the relevant tissues when examining a complex disease. To enable the study of sex-specific mechanisms of NAFLD, hepatic steatosis and its relevant clinical and molecular traits were recently examined in both male and female mice of more than 100 distinct inbred and recombinant inbred strains from the hybrid mouse diversity panel (HMDP) [17]. These mice were treated with a high fat and high sucrose diet to generate hepatic triglyceride accumulation or steatosis, a hallmark of NAFLD. A comprehensive NAFLD-associated and sex-specific multiomics data resource has also been generated, encompassing genotyping of common genetic variants, transcriptome data from liver and adipose tissue, and tissue-specific expression quantitative trait loci (eQTLs, reflecting the genetic regulation of gene expression in individual tissues). These data sets enable tissue-specific and sex-specific investigations of NAFLD mechanisms. To fully leverage the multi-omic datasets from HMDP mice and incorporate disease-associated molecular signals with strong, moderate, and subtle effects, we have recently deployed an integrative approach to identify potential causal pathways, gene networks, and key regulators of NAFLD in males in a tissue-specific fashion, followed by experimental validation of the novel predictions [18]. In the current study, we apply this validated approach to compare the NAFLD biology between se (...truncated)