bioRxiv preprint doi: https://doi.org/10.1101/2020.03.16.993824; this version posted March 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A tissue- and organ-based cell biological atlas of obesity-related human genes and cellular pathways 1* 1* 1,2 1 1 Iman Tavassoly , Valentina Barbieri , Coen van Hasselt Pedro Martinez , Eric A. Sobie , Jens Hansen1, Evren Azeloglu3, Joseph Goldfarb1, Philippe Sanseau4, Deepak K Rajpal5,6 and Ravi Iyengar1** 1. Department of Pharmacological Sciences and Systems Biology Center New York, Icahn School of Medicine at Mount Sinai, New York NY 10029, USA 2. Leiden Academic Centre for Drug Research, LACDR/Pharmacology, Einsteinweg 55, 2333 CC Leiden, The Netherlands 3. Department of Medicine – Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York NY 10029, USA 4. GSK, Medicines Research Center, Gunnels Wood Road, Stevenage SG1 2NY, UK 5. GSK,1250 South Collegeville Road, Collegeville, PA 19426, USA 6. Current Affiliation: Bioinformatics, Translational Sciences, Sanofi, Cambridge, MA 02139, USA *Equal contributions as first authors. **Corresponding author: Dr. Ravi Iyengar, Department of Pharmacological Sciences, Box 1215 Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 12-70, New York, 10029, NY, USA; [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.16.993824; this version posted March 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Over the last decades, several features of obesity have been identified at behavioral, physiological, endocrine and genomic levels, and they have revealed the complexity of the disease; obesity results from a combination of genetic predisposition, endocrine disorders, and dysregulation of both food intake and energy expenditure. This complexity makes the development of new therapeutic regimens challenging and bariatric surgery is still the treatment of choice for many obese patients. Given the need for noninvasive therapeutic intervention strategies, we sought to systematically study the biological manifestations of obesity in peripheral organs. We analyzed publicly available datasets of genes, genomic determinants, and levels of obesity-related hormones in the blood, using a combination of methodologies, including graph theory and dynamical modeling, that allow for the integration of different types of datasets. The analysis revealed tissue- and organ-specific metabolic impairments and potential new drug targets. All the data are organized into a tissue/organ-based subcellular-function atlas for human obesity. The data show that the complexity of the obesity arises due to the multiplicity of subcellular processes in different peripheral organs. 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.16.993824; this version posted March 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Introduction Over the past decade, the prevalence of obesity and severe obesity among adults has risen to almost 40% of the world population [1]. According to the World Health Organization (WHO), obesity is a health issue not only in high income, but also in low- and mid-income countries, and is a risk factor for many chronic diseases including diabetes, cardiovascular diseases and cancer [2]. Obesity has been extensively studied at the behavioral, physiological, endocrine, and, more recently, the genomic level [3-6]. All these different biological levels and the interactions among them play a role in both the etiology and the pathophysiology of obesity and contribute to its complexity. Obesity is physiologically defined as a body mass index (BMI) of over 30kg/m2; it manifests itself as a combination of genetic predisposition, dysregulation of food intake and energy expenditure, and as an endocrine disorder making it challenging to develop therapeutic approaches to maintain body weight in a healthy range [3, 4]. After many years of trying, several large pharmaceutical companies have discontinued programs for the development of anti-obesity drugs [7]. Although there have been recent studies of peripheral drug targets for the treatment of obesity (incidental data have shown that GLP-1 agonists can be effective in moderate weight loss [8]), most FDA-approved drugs have primary targets in the Central Nervous System (CNS) [7]. Currently, the most effective treatment for obesity is bariatric surgery [9]. Given the need for new therapeutics that can control obesity without surgery, we hypothesized that we could identify potential novel therapeutic targets by systematically studying biological expressions of obesity in peripheral organs. We decided to utilize publicly available data because an enormous amount of information exists that can be analyzed using multiple computational systems biology approaches allowing for the integration of diverse types of datasets and models. 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.16.993824; this version posted March 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. In principle, it is straightforward to argue that changes in genes and genomic determinants lead to alterations in cell biological pathways, and these, in turn, affect tissue and organ function, and finally whole-body physiology. However, it has been difficult, in practice, to connect the genomic information to the dynamics of physiological functions [10]. A recent review demonstrates the utility of integrated analyses of genomic determinants such as Single Nucleotide Polymorphisms (SNPs) with biological and behavioral determinants in obesity [11]. We sought to determine the relationships between genomic and molecular determinants and the dynamics associated with lean and obese physiological states. Data from patients after bariatric surgery provided a sample of subjects who had been obese but who had reduced their weight and BMI toward normal levels. As a measure of the physiological states, we used orexigenic and anorexigenic hormone levels in the blood and their changes after feeding. We hypothesized a) that genetic predisposition could be linked to endocrine impairment in energy homeostasis; b) that different tissues and organs could respond differently to genetic predisposition and endocrine impairment at the level of gene expression; c) that this variability could produce differences in catabolism and anabolism and confer distinct physiological profiles in lean, obese, and post-bariatric-surgery individuals. Because the effects of the same genetic and genomic determinants on cellular pathways may vary among different tissues and organs, we decided to map the genes and their associated cell biological processes to six peripheral tissues/organs that are known to be involved in nutrient processing and energy storage: stomach, intestine, pancreas, liver, adipose tissue, and skeletal muscle [12]. Upon performing this analysis, we organized the information as an atlas for human obesity, containing data from multiple biological levels. 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.16.993824; this version posted March 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The basic framework for the construction of the atlas is shown in Figure 1. The flow chart used for the analyses is shown in Supplementary Figure S1, and the databases used in the study are listed in Supplementary Table S1. The major goal of our mapping was to identify key genes and subcellular pathways by integrating the genomic and endocrine information using several computational methods. Genomic and genetic data were obtained from public databases [13-16] and then expanded utilizing the human interactome to take into consideration the role of possible intermediate genes. Because differences in endocrine regulation following food intake have been shown in lean, obese and post-bariatric surgery individuals [12], we determined whether such differences could be linked to genetic predisposition and how they would affect the genomic and genetic data. We used published data on changes in plasma levels of orexigenic and anorexigenic hormones to analyze physiological differences between lean and obese individuals and the effects of bariatric surgery on the plasma levels of hormones related to the regulation of food intake and obesity. We then developed a dynamical model that allowed us to identify those kinetic parameters that regulate the hormone levels in the systemic circulation and are more likely to be different in lean, obese, and post-bariatric surgery subjects. These findings allowed us to rank these kinetic parameters and the genes that are associated to them; the genes were then mapped onto the genomic and genetic network and weighted according to their significance in physiological functions; because we had three different physiological profiles, three endocrine- weighted genetic and genomic networks were obtained. To organize the information in terms of anatomy and biological functions, we filtered the ranked networks according to