PROJECT SUMMARY/ABSTRACT Non-alcoholic fatty liver disease (NAFLD) is increasingly being recognized as the hepatic manifestation of metabolic syndrome that can lead to cardiovascular diseases. Currently, very little is known about the genetic and molecular factors underlying NAFLD. Besides, no known therapeutic strategies are available to prevent or treat the condition. To address this problem, we applied an integrative multi-omics approach using an extensively phenotyped mouse cohort, Hybrid Mouse Diversity Panel (HMDP) and identified many known and several novel candidate genes regulating NAFLD. We further validated two novel candidates, pyruvate kinase, liver isoform (PKLR) and coiled-coil-helix-coiled-coil-helix domain containing 6 (CHCHD6). When these two genes were knockdown in male mouse models of steatosis, both NAFLD and insulin sensitivity improved as measured by intrahepatic triglyceride accumulation levels, glucose- and insulin- tolerance tests, and fasting glucose and insulin levels. Follow-up bioenergetic analyses revealed these two genes regulated mitochondrial metabolism in developing steatosis and insulin resistance. When we further expanded this to include the female HMDP strains, we found that these two genes have no effect. Specifically, correlation analyses revealed PKLR and CHCHD6 do not develop NAFLD and insulin resistance in female strains, respectively. To further our understanding on the gene-by-sex interactions mediated by these two genes in regulating mitochondrial metabolism and in developing NAFLD and insulin resistance, I have proposed three interrelated aims to examine 1) mechanisms underlying PKLR- and CHCHD6- mediated lipid metabolism, 2) metabolic consequences of liver-specific overexpression or knockdown in female mouse models of steatosis, 3) gene networks and cellular heterogeneity altered by liver-specific overexpression or knockdown in mouse models of advanced NASH and fibrosis. Furthermore, I have developed a detailed five-year career development plan that includes two-year mentored phase (K99 phase) followed by three-year independent phase (R00 phase) for my transition into an independent academic career. I have included a highly talented and distinguished panel of advisors including Drs. Aldons J. Lusis, Orian Shirihai, Neil Kaplowitz, Andrea Hevener, Peter Tontonoz, and Steven Bensinger, to assist in my transition to independence. I have significant experience in studying how host genetics and sex differences dictate the outcomes of complex disease traits using systems genetics analyses. I now plan to expand my training in liver and mitochondrial physiology, lipid metabolism, metabolic phenotyping and single cell sequencing. Overall, the goal is to advance my training to become an independent investigator and perform research bridging systems genetics, mitochondria and liver metabolism.