Mitochondrial GWAS and association of nuclear - mitochondrial epistasis with BMI in T1DM patients

• Published in: BMC medical genomics 2020-07, Vol.13 (1), p.97-11, Article 97
• Main Authors: Ludwig-Słomczyńska, Agnieszka H, Seweryn, Michał T, Kapusta, Przemysław, Pitera, Ewelina, Handelman, Samuel K, Mantaj, Urszula, Cyganek, Katarzyna, Gutaj, Paweł, Dobrucka, Łucja, Wender-Ożegowska, Ewa, Małecki, Maciej T, Wołkow, Paweł P
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Analysis; Body Mass Index; Cell Nucleus - genetics; Cohort Studies; Diabetes mellitus; Diabetes Mellitus, Type 1 - genetics; Diabetes Mellitus, Type 1 - pathology; Diabetics; DNA, Mitochondrial - analysis; DNA, Mitochondrial - genetics; Epistasis; Epistasis, Genetic; Female; Gene Expression Regulation; Generalized linear models; Genes; Genetic aspects; Genome-Wide Association Study; Genomes; Genomics; Genotype & phenotype; GWAS; Humans; Male; Metabolism; Mitochondria; Mitochondria - genetics; Mitochondrial-nuclear interactions; Obesity; Population; Single-nucleotide polymorphism; Transcription (Genetics); Type 1 diabetes; Young Adult
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/s12920-020-00752-7

BMI is a strong indicator of complications from type I diabetes, especially under intensive treatment. We have genotyped 435 type 1 diabetics using Illumina Infinium Omni Express Exome-8 v1.4 arrays and performed mitoGWAS on BMI. We identified additive interactions between mitochondrial and nuclear variants in genes associated with mitochondrial functioning MitoCarta2.0 and confirmed and refined the results on external cohorts: the Framingham Heart Study (FHS) and GTEx data. Linear mixed model analysis was performed using the GENESIS package in R/Bioconductor. We find a borderline significant association between the mitochondrial variant rs28357980, localized to MT-ND2, and BMI (β = - 0.69, p = 0.056). This BMI association was confirmed on 1889 patients from FHS cohort (β = - 0.312, p = 0.047). Next, we searched for additive interactions between mitochondrial and nuclear variants. MT-ND2 variants interacted with variants in the genes SIRT3, ATP5B, CYCS, TFB2M and POLRMT. TFB2M is a mitochondrial transcription factor and together with TFAM creates a transcription promoter complex for the mitochondrial polymerase POLRMT. We have found an interaction between rs3021088 in MT-ND2 and rs6701836 in TFB2M leading to BMI decrease (inter_pval = 0.0241), while interaction of rs3021088 in MT-ND2 and rs41542013 in POLRMT led to BMI increase (inter_pval = 0.0004). The influence of these interactions on BMI was confirmed in external cohorts. Here, we have shown that variants in the mitochondrial genome as well as additive interactions between mitochondrial and nuclear SNPs influence BMI in T1DM and general cohorts.