Container-aided integrative QTL and RNA-seq analysis of Collaborative Cross mice supports distinct sex-oriented molecular modes of response in obesity

Background: The Collaborative Cross (CC) mouse population is a valuable resource to study the genetic basis of complex traits, such as obesity. Although the development of obesity is influenced by environmental factors, underlying genetic mechanisms play a crucial role in the response to these factors. The interplay between the genetic background and the gene expression pattern can provide further insight into this response, but we lack robust and easily reproducible workflows to integrate genomic and transcriptomic information in the CC mouse population. Results: We established an automated and reproducible integrative workflow to analyse complex traits in the CC mouse genetic reference panel at the genomic and transcriptomic levels. We implemented the analytical workflow to assess the underlying genetic mechanisms of host susceptibility to diet induced obesity and integrated these results with diet induced changes in the hepatic gene expression of susceptible and resistant mice. Hepatic gene expression differs significantly between obese and non-obese mice, with a significant sex effect, where male and female mice exhibit different responses and coping mechanisms. Conclusion: Integration of the data showed that different genes but similar pathways are involved in the genetic susceptibility and disturbed in diet induced obesity. Genetic mechanisms underlying susceptibility to high-fat diet induced obesity are different in female and male mice. The clear distinction we observed in the systemic response to the high-fat diet challenge and to obesity between male and female mice points to the need for further research into distinct sex-related mechanisms in metabolic disease.This work was funded by the Operational Program ”Competitiveness, Entrepreneurship and Innovation 2014–2020″ (co-funded by the European Regional Development Fund) and managed by the General Secretariat of Research and Technology, Ministry Of Education, Research & Religious Affairs, under the project” Innovative Nanopharmaceuticals: Targeting Breast CancerStem Cells by a Novel Combination of Epigenetic and Anticancer Drugs with Gene Therapy (INNOCENT)” (7th Joint Translational Call - 2016, European Innovative Research and Technological Development Projects In Nanomedicine) of the ERA-NET EuroNanoMed II and by “BioS: Digital Skills on Computational Biology”, ΕRASMUS+, EACEA/04/2017, “KA2: Cooperation for innovation and the exchange of good practices - Sector Skills Alliances” for the development of the bioinformatic analysis pipeline, Hendrech and Eiran Gotwert Fund for studying diabetes, Wellcome Trust grants 085906/Z/ 08/Z, 075491/Z/04 and 090532/Z/09/Z; for financially supporting the initiation, breeding, genotyping and maintaining the CC mouse colony at TAU, core funding by Tel-Aviv University (TAU) for supporting staff at Iraqi’s lab, Israeli Science foundation (ISF) grants 429/09 and 1085/18, Binational Science Foundation (BSF) grant number 2015077 and German Israeli Science Foundation (GIF) grant I-63-410.20-2017 for performing the mouse assessment for T2D and technical staff, and European Sequencing and Genotyping Infrastructure (ESGI) consortium grant for conducting the RNAseq analysis.Ilona Binenbaum’s PhD thesis was supported by a scholarship from the State Scholarship Foundation in Greece (IKY) (Operational Program “Human Resources Development - Education and Lifelong Learning” Partnership Agreement (PA) 2014–2020