Genetic differences between extreme and composite constitution types from whole exome sequences reveal actionable variations

Abstract

Personalized medicine relies on successful identification of genome-wide variations that governs inter-individual differences in phenotypes and system level outcomes. In Ayurveda, assessment of composite constitution types "Prakriti" forms the basis for risk stratification, predicting health and disease trajectories and personalized recommendations. Here, we report a novel method for identifying pleiotropic genes and variants that associate with healthy individuals of three extreme and contrasting "Prakriti" constitutions through exome sequencing and state-of-the-art computational methods. Exome Seq of three extreme Prakriti types from 108 healthy individuals 54 each from genetically homogeneous populations of North India (NI, Discovery cohort) and Western India (VADU, Replication cohort) were evaluated. Fisher's Exact Test was applied between Prakriti types in both cohorts and further permutation based p-value was used for selection of exonic variants. To investigate the effect of sample size per genetic association test, we performed power analysis. Functional impact of differentiating genes and variations were inferred using diverse resources -Toppfun, GTEx, GWAS, PheWAS, UK Biobank and mouse knockdown/knockout phenotype (MGI). We also applied supervised machine learning approach to evaluate the association of exonic variants with multisystem phenotypes of Prakriti. Our targeted investigation into exome sequencing from NI (discovery) and VADU (validation) cohorts datasets provide ~7,000 differentiating SNPs. Closer inspection further identified a subset of SNPs (2407 (NI) and 2393 (VADU)), that mapped to an overlapping set of 1181 genes. This set can robustly stratify the Prakriti groups into three distinct clusters with distinct gene ontological (GO) enrichments. Functional analysis further strengthens the potential pleiotropic effects of these differentiating genes/variants and multisystem phenotypic consequences. Replicated SNPs map to some very prominent genes like FIG4, EDNRA, ANKLE1, BCKDHA, ATP5SL, EXOCS5, IFIT5, ZNF502, PNPLA3 and IL6R. Lastly, multivariate analysis using random forest uncovered rs7244213 within urea transporter SLC14A2, that associate with an ensemble of features linked to distinct constitutions. Our results reinforce the concept of integration of Prakriti based deep phenotypes for risk stratification of healthy individuals and provides markers for early actionable interventions.

Baseline cell proliferation rates and response to UV differ in Lymphoblastoid Cell Lines derived from healthy individuals of extreme constitution types

“…Processes such as cell proliferation are thought to be homeostatic and not expected to vary systematically across individuals, our data suggests otherwise. The LCLs studied here were derived from individuals of extreme and contrasting constitutions who differ with respect to multisystem and molecular attributes [16][17][18][19]24 . We show a core cellular phenotype differentiating between these groups where Vata and Pitta have higher rates of cell proliferation compared to Kapha.…”

“…The Prakriti types are an outcome of relative proportions of the three groups of physiological entities "Tridosha", that govern the kinetic "Vata", metabolic "Pitta" and "Kapha" structural components of the body. These proportions in Prakriti types, is established at the time of embryonic development, and remains invariant throughout lifetime 14,24 . Our previous report on the blood transcriptome from another cohort shows differential enrichment of molecular pathways between the Prakriti types 16 .…”

Ayurgenomics-based frameworks in precision and integrative medicine: Translational opportunities

“…Prakriti of individuals is assessed using a compendium of composite phenotypes that encompass anatomical, physiological, response, and activity-associated attributes. Nearly two decades of exploratory research carried out by different groups have provided molecular correlates of Prakriti from different functional hierarchiesphenomic, genetic, genomic, epigenomic, transcriptomic, metagenomic as well as at biochemical, immunological, and cellular levels, and most recently, at the physiological level (Bhushan et al, 2005;Prasher et al, 2008;Aggarwal et al, 2010Aggarwal et al, , 2015Joshi et al, 2011;Rotti et al, 2014Rotti et al, , 2015Satyamoorthy et al, 2014;Govindaraj et al, 2015;Tiwari et al, 2017;Chauhan et al, 2018;Chaudhari et al, 2019;Abbas et al, 2020Abbas et al, , 2022Mobeen et al, 2020;Chakraborty et al, 2021;Shalini et al, 2021;Rani et al, 2022). These studies have been primarily conducted on healthy individuals of extreme and contrasting constitution types that are most easily discernible at the level of composite phenotypes, and who also have contrasting responses and vulnerability (Prasher et al, 2017).…”

“…Genome-wide expression, genetic variation (microarray based as well as exome), and epigenome (global methylation and array based) studies on extreme Prakriti healthy individuals that have predominance of one of the doshas, have provided molecular correlates of tridosha (Prasher et al, 2008;Govindaraj et al, 2015;Rotti et al, 2015;Abbas et al, 2020Abbas et al, , 2022. Some of the highlights of these studies have been provided in Table 1.…”

“…Corroborating observations of differences in ontological enrichments between different constitution types have been reported from multiple studies that have been carried out at different functional hierarchies and in different population cohorts. For instance cell proliferation and DNA damage response differentiates Vata Prakriti, T-cell mediated immunity, elevated metabolism and inflammation in Pitta Prakriti, and lipid profiles and BMI-associated correlates differentiate Kapha have been observed from expression, epigenetic as well as genetic studies (Prasher et al, 2008;Rotti et al, 2015;Abbas et al, 2020Abbas et al, , 2022. Besides these, there are differences in different cellular and physiological axes that are associated with development, cell adhesion, signaling, and transport functions as well as processes that govern circadian rhythm, olfaction, and so on.…”