Background: Obesity is a leading cause of death worldwide. Although the disease significantly increases the likelihood of type 2 diabetes (T2D) it remains unclear why not all obese patients develop T2D. Genetic factors are important but confer only a modest risk. Likewise, no clear mechanistic model exists that can explain bariatric surgery-induced T2D remission, nor the substantial interindividual variation in patient response. Epigenomic aberrations may be key underlying factors but the specific regulatory pathways remains poorly understood. Objectives: Here, we aim to generate novel insight into metabolic disease etiology by unraveling epigenetic signatures and mechanisms underlying risk of obesity and T2D. A state of the art, multidimensional epigenetic approach will be applied intersecting unique clinical cohorts and pre-clinical models with in depth cellular analyses of obesity and T2D, with a focus on adipose (AT) and liver as well as multiple related pure cellular subpopulations. Translation and validation of these findings will be performed in one of the largest longitudinal cohort of patients undergoing bariatric surgery allowing identification of epigenetic mechanisms and associated biomarkers predicting surgery-induced T2D remission. Methods: Applying pipelines and standards established within IHEC, we will generate high-quality epigenomes comprising next-generation sequencing assays that are established (“core” ChIP-Seq, RNA-Seq), newly implemented (ATAC-Seq) or program-developed (ChiP-Seq of novel enhancers and capture-based functional methylome - MCC-Seq) in 1) hepatocytes, adipocytes, AT macrophages and mast cells from lean, non-T2D and T2D obese subjects undergoing bariatric surgery; and 2) hepatocytes and adipocytes from two highly complementary mouse and rat models of spontaneous and diet-induced obesity and T2D, as well as T2D remission through bariatric surgery. Key findings from these discovery phase mapping efforts will be translated in large clinical cohorts using the innovative and cost-effective MCC-Seq method for metabolic disease and tissue-targeted profiling of the methylation landscape in: 1) 350 AT and 200 liver samples from non-T2D and T2D obese subjects undergoing bariatric surgery with the larger cohort possessing detailed phenotyping 1 year post surgery and 2) 2000 blood samples from a population-based cohort of unrelated individuals deeply phenotyped for metabolic traits. Expected Results and Potential Impact: This program has the potential to identify both tissue specific and conserved epigenetic signatures and cellular pathways for the development of disease biomarkers, and, to offer new avenues for dissecting mechanisms underlying obesity-induced T2D, respectively. Unique access to longitudinal cohorts will aid in the development of statistical models for the prediction of obesity-induced T2D remission following surgery, which may have strong impact in patient care and disease management.