DNA methylation analysis of phenotype specific stratified Indian population

Abstract

BackgroundDNA methylation and its perturbations are an established attribute to a wide spectrum of phenotypic variations and disease conditions. Indian traditional system practices personalized medicine through indigenous concept of distinctly descriptive physiological, psychological and anatomical features known as prakriti. Here we attempted to establish DNA methylation differences in these three prakriti phenotypes.MethodsFollowing structured and objective measurement of 3416 subjects, whole blood DNA of 147 healthy male individuals belonging to defined prakriti (Vata, Pitta and Kapha) between the age group of 20-30years were subjected to methylated DNA immunoprecipitation (MeDIP) and microarray analysis. After data analysis, prakriti specific signatures were validated through bisulfite DNA sequencing.ResultsDifferentially methylated regions in CpG islands and shores were significantly enriched in promoters/UTRs and gene body regions. Phenotypes characterized by higher metabolism (Pitta prakriti) in individuals showed distinct promoter (34) and gene body methylation (204), followed by Vata prakriti which correlates to motion showed DNA methylation in 52 promoters and 139 CpG islands and finally individuals with structural attributes (Kapha prakriti) with 23 and 19 promoters and CpG islands respectively. Bisulfite DNA sequencing of prakriti specific multiple CpG sites in promoters and 5′-UTR such as; LHX1 (Vata prakriti), SOX11 (Pitta prakriti) and CDH22 (Kapha prakriti) were validated. Kapha prakriti specific CDH22 5′-UTR CpG methylation was also found to be associated with higher body mass index (BMI).ConclusionDifferential DNA methylation signatures in three distinct prakriti phenotypes demonstrate the epigenetic basis of Indian traditional human classification which may have relevance to personalized medicine.Electronic supplementary materialThe online version of this article (doi:10.1186/s12967-015-0506-0) contains supplementary material, which is available to authorized users.

Epigenetic Mechanisms of Integrative Medicine

“…This confirms an epigenetic basis for the underlying prakriti classification [134]. Such epigenetic signatures corresponding to individual prakritis may be crucial in understanding and harnessing the power of Ayurvedic medicine and ascertaining its mechanism for delivering beneficial results in health and wellness.…”

A glimpse of Ayurveda – The forgotten history and principles of Indian traditional medicine

“…Vata, Pitta and Kapha, were carried out to identify molecular differences that affect susceptibility and responses of individuals to various environmental or disease conditions. A classification method for human population, with respect to DNA methylation signatures is reported based upon traditional Ayurveda concept of prakriti 32 . In a study involving genome-wide SNP (single nucleotide polymorphism) in 262 male individuals from three different prakritis , it was found that PGM1 gene is associated with energy production.…”

Traditional Medicine:A Review of Work in India (2012-2017)

“…One study conducted in a total of 3416 healthy male, non-smoking, non-alcoholic participants between the age group of 20 and 30 found significant correlations of the dominant prakriti to place of birth and BMI (p < 0.01) (Rotti et al, 2014). A genomewide single nucleotide polymorphism analysis of 262 well-classified male individuals found 52 SNPs (p < 1 x 10 -5 ) were significantly different between Prakritis, without any confounding effect of stratification, after 10 6 permutations) (Govindaraj et al, 2015).…”

“…The main objective of these projects was to apply scientific methods in the study of Ayurvedic concepts, procedures and mechanistic basis of therapeutic effects. The work on the genomics correlates of the prakriti concept has already been alluded to (Govindaraj et al, 2015).…”