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Haldar S, Jadhav SR, Gulati V, Beale DJ, Balkrishna A, Varshney A, Palombo EA, Karpe AV, Shah RM. Unravelling the gut-lung axis: insights into microbiome interactions and Traditional Indian Medicine's perspective on optimal health. FEMS Microbiol Ecol 2023; 99:fiad103. [PMID: 37656879 PMCID: PMC10508358 DOI: 10.1093/femsec/fiad103] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 07/05/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023] Open
Abstract
The microbiome of the human gut is a complex assemblage of microorganisms that are in a symbiotic relationship with one another and profoundly influence every aspect of human health. According to converging evidence, the human gut is a nodal point for the physiological performance matrixes of the vital organs on several axes (i.e. gut-brain, gut-lung, etc). As a result of COVID-19, the importance of gut-lung dysbiosis (balance or imbalance) has been realised. In view of this, it is of utmost importance to develop a comprehensive understanding of the microbiome, as well as its dysbiosis. In this review, we provide an overview of the gut-lung axial microbiome and its importance in maintaining optimal health. Human populations have successfully adapted to geophysical conditions through traditional dietary practices from around the world. In this context, a section has been devoted to the traditional Indian system of medicine and its theories and practices regarding the maintenance of optimally customized gut health.
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Affiliation(s)
- Swati Haldar
- Drug Discovery and Development Division, Patanjali Research Institute, NH-58, Haridwar 249405, Uttarakhand, India
| | - Snehal R Jadhav
- Consumer-Analytical-Safety-Sensory (CASS) Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, Burwood, VIC 3125, Australia
| | - Vandana Gulati
- Biomedical Science, School of Science and Technology Faculty of Science, Agriculture, Business and Law, University of New England, Armidale, NSW 2351, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Acharya Balkrishna
- Drug Discovery and Development Division, Patanjali Research Institute, NH-58, Haridwar 249405, Uttarakhand, India
- Department of Allied and Applied Sciences, University of Patanjali, Patanjali Yog Peeth, Roorkee-Haridwar Road, Haridwar 249405, Uttarakhand, India
| | - Anurag Varshney
- Drug Discovery and Development Division, Patanjali Research Institute, NH-58, Haridwar 249405, Uttarakhand, India
- Department of Allied and Applied Sciences, University of Patanjali, Patanjali Yog Peeth, Roorkee-Haridwar Road, Haridwar 249405, Uttarakhand, India
| | - Enzo A Palombo
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Avinash V Karpe
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- Socio-Eternal Thinking for Unity (SETU), Melbourne, VIC 3805, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Acton, ACT 2601, Australia
| | - Rohan M Shah
- Department of Chemistry and Biotechnology, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
- School of Health and Biomedical Sciences, STEM College, RMIT University, Bundoora West, VIC 3083, Australia
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Mukerji M. Ayurgenomics-based frameworks in precision and integrative medicine: Translational opportunities. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e29. [PMID: 38550940 PMCID: PMC10953754 DOI: 10.1017/pcm.2023.15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/22/2023] [Accepted: 06/11/2023] [Indexed: 11/06/2024]
Abstract
In today's globalized and flat world, a patient can access and seek multiple health and disease management options. A digitally enabled participatory framework that allows an evidence-based informed choice is likely to assume an immense importance in the future. In India, traditional knowledge systems, like Ayurveda, coexist with modern medicine. However, due to limited crosstalk between the clinicians of both disciplines, a patient attempts integrative medicine by seeking both options independently with limited understanding and evidence. There is a need for an integrative medicine platform with a formalized approach, which allows practitioners from the two diverse systems to crosstalk, coexist, and coevolve for an informed cross-referral that benefits the patients. To be successful, this needs frameworks that enable the bridging of disciplines through a common interface with shared ontologies. Ayurgenomics is an emerging discipline that explores the principles and practices of Ayurveda combined with genomics approaches for mainstream integration. The present review highlights how in conjunction with different disciplines and technologies this has provided frameworks for (1) the discovery of molecular correlates to build ontological links between the two systems, (2) the discovery of biomarkers and targets for early actionable interventions, (3) understanding molecular mechanisms of drug action from its usage perspective in Ayurveda with applications in repurposing, (4) understanding the network and P4 medicine perspective of Ayurveda through a common organizing principle, (5) non-invasive stratification of healthy and diseased individuals using a compendium of system-level phenotypes, and (6) developing evidence-based solutions for practice in integrative medicine settings. The concordance between the two contrasting streams has been built through extensive explorations and iterations of the concepts of Ayurveda and genomic observations using state-of-the-art technologies, computational approaches, and model system studies. These highlight the enormous potential of a trans-disciplinary approach in evolving solutions for personalized interventions in integrative medicine settings.
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Affiliation(s)
- Mitali Mukerji
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Karwar, India
- School of Artificial Intelligence and Data Science (AIDE), Indian Institute of Technology Jodhpur, Karwar, India
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Bhat S, Rotti H, Prasad K, Kabekkodu SP, Saadi AV, Shenoy SP, Joshi KS, Nesari TM, Shengule SA, Dedge AP, Gadgil MS, Dhumal VR, Salvi S, Satyamoorthy K. Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function. J Ayurveda Integr Med 2023; 14:100692. [PMID: 37018893 PMCID: PMC10122039 DOI: 10.1016/j.jaim.2023.100692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 10/13/2022] [Accepted: 02/01/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The Indian traditional medicinal system, Ayurveda, describes several lifestyle practices, processes and medicines as an intervention to treat asthma. Rasayana therapy is one of them and although these treatment modules show improvement in bronchial asthma, their mechanism of action, particularly the effect on DNA methylation, is largely understudied. OBJECTIVES Our study aimed at identifying the contribution of DNA methylation changes in modulating bronchial asthma phenotype upon Ayurveda intervention. MATERIALS AND METHODS In this study, genome-wide methylation profiling in peripheral blood DNA of healthy controls and bronchial asthmatics before (BT) and after (AT) Ayurveda treatment was performed using array-based profiling of reference-independent methylation status (aPRIMES) coupled to microarray technique. RESULTS We identified 4820 treatment-associated DNA methylation signatures (TADS) and 11,643 asthma-associated DNA methylation signatures (AADS), differentially methylated [FDR (≤0.1) adjusted p-values] in AT and HC groups respectively, compared to BT group. Neurotrophin TRK receptor signaling pathway was significantly enriched for differentially methylated genes in bronchial asthmatics, compared to AT and HC subjects. Additionally, we identified over 100 differentially methylated immune-related genes located in the promoter/5'-UTR regions of TADS and AADS. Various immediate-early response and immune regulatory genes with functions such as transcription factor activity (FOXD1, FOXD2, GATA6, HOXA3, HOXA5, MZF1, NFATC1, NKX2-2, NKX2-3, RUNX1, KLF11), G-protein coupled receptor activity (CXCR4, PTGER4), G-protein coupled receptor binding (UCN), DNA binding (JARID2, EBF2, SOX9), SNARE binding (CAPN10), transmembrane signaling receptor activity (GP1BB), integrin binding (ITGA6), calcium ion binding (PCDHGA12), actin binding (TRPM7, PANX1, TPM1), receptor tyrosine kinase binding (PIK3R2), receptor activity (GDNF), histone methyltransferase activity (MLL5), and catalytic activity (TSTA3) were found to show consistent methylation status between AT and HC group in microarray data. CONCLUSIONS Our study reports the DNA methylation-regulated genes in bronchial asthmatics showing improvement in symptoms after Ayurveda intervention. DNA methylation regulation in the identified genes and pathways represents the Ayurveda intervention responsive genes and may be further explored as diagnostic, prognostic, and therapeutic biomarkers for bronchial asthma in peripheral blood.
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Affiliation(s)
- Smitha Bhat
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Harish Rotti
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Keshava Prasad
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushma P Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Kalpana S Joshi
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Tanuja M Nesari
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sushant A Shengule
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Amrish P Dedge
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Maithili S Gadgil
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Vikram R Dhumal
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sundeep Salvi
- Department of Pulmonary Medicine, Chest Research Foundation, Pune, Maharashtra, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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Karmegam D, Prakash M, Karikalan N, Mappillairajan B. Development of database structure and indexing for siddha medicine system - A platform for siddha literature analytics. DIALOGUES IN HEALTH 2022; 1:100008. [PMID: 38515917 PMCID: PMC10953876 DOI: 10.1016/j.dialog.2022.100008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 03/23/2024]
Abstract
Background Siddha Medicine system is one among the oldest traditional systems of medicines in India and has its entire literature in the Tamil language in the form of poems (padal in tamil). Even if the siddha poems are available in public domain, they are not known to other parts of the world because, researchers of other languages are not able to understand the contents of these poems and there exists a language barrier. Hence there is a need to develop a system to extract structured information from these texts to facilitate searching, comparing, analysis and implementing. Objective This study aimed at creating a comprehensive digital database system that systematically stores information from classical Siddha poems and to develop a web portal to facilitate information retrieval for comparative and logical analysis of Siddha content. Methods We developed an expert system for siddha (eSS) that can collect, annotate classical siddha text, and visualizes the pattern in siddha medical prescriptions (Siddha Formulations) that can be useful for exploration in this system using modern techniques like machine learning and artificial learning. eSS has the following three aspects: (1) extracting data from Siddha classical text (2) defining the annotation method and (3) visualizing the patterns in the medical prescriptions based on multiple factors mentioned in the Siddha system of medicine. The data from three books were extracted, annotated and integrated into the developed eSS database. The annotations were used for analyzing the pattern in the drug prescriptions as a pilot work. Results Overall, 110 medicinal preparations from 2 Siddhars (Agathiyar and Theran) were extracted and annotated. The generated annotations were indexed into the data repository created in eSS. The system can compare and visualize individual and multiple prescriptions to generate a hypothesis for siddha practitioners and researchers. Conclusions We propose an eSS framework using standard siddha terminologies created by WHO to have a standard expert system for siddha. This proof-of-concept work demonstrated that the database can effectively process and visualize data from siddha formulations which can help students, researchers from siddha and other various fields to expand their research in herbal medicines.
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Affiliation(s)
- Dhivya Karmegam
- School of Public Health, SRM University, Kattankulathur 603 203, Kancheepuram District, Tamil Nadu, India
| | - Muthuperumal Prakash
- School of Public Health, SRM University, Kattankulathur 603 203, Kancheepuram District, Tamil Nadu, India
| | - N. Karikalan
- National Institute for Research in Tuberculosis, Chetpet, Chennai 600 031, Tamil Nadu, India
| | - Bagavandas Mappillairajan
- Centre for statistics, SRM University, Kattankulathur 603 203, Kancheepuram District, Tamil Nadu, India
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Arnold JT. Integrating ayurvedic medicine into cancer research programs part 1: Ayurveda background and applications. J Ayurveda Integr Med 2022:100676. [DOI: 10.1016/j.jaim.2022.100676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
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Joshi K, Patwardhan B, Valiathan MS. Ayurvedic Biology and road ahead: The first decade. J Ayurveda Integr Med 2022:100588. [PMID: 35710895 DOI: 10.1016/j.jaim.2022.100588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 05/10/2022] [Indexed: 11/26/2022] Open
Affiliation(s)
- Kalpana Joshi
- Sinhgad College of Engineering Affiliated to Savitribai Phule Pune University (SPPU), Pune, India.
| | - Bhushan Patwardhan
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | - M S Valiathan
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Gupta A, Garg R, Singh V. Using Traditional Typologies to Understand Posture Movement and Cognitive Performance - A cross sectional study. Int J Yoga 2022; 15:106-113. [PMID: 36329775 PMCID: PMC9623887 DOI: 10.4103/ijoy.ijoy_12_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/26/2022] [Accepted: 06/10/2022] [Indexed: 06/16/2023] Open
Abstract
CONTEXT We employed two classification methods that characterize psycho-somatotype categorization to understand motor and cognitive performance. The Trunk Index produces three somatotypes/body type categories: ectomorphs, mesomorphs, and endomorphs, and Prakriti classifications categorizes people into three categories: Vata, Pitta, and Kapha. Comparing these two categorization methods offers insights into anthropometric measures that combine psychological and physical characteristics to account for motor and cognitive behavior. AIMS The present study examined variations in cognitive and motor performances using the two typologies - prakriti and somato body types using cross-sectional study design. SUBJECTS AND METHODS The study employed fifty-eight healthy young adults, classified into prakriti (vata, pitta, kapha) and ecto-, meso-, endo-morph body types, to examine their cognitive performance (reaction time [RT] and accuracy), and motor performance (posture stability and posture accuracy) in standing yoga postures. STATISTICAL ANALYSIS USED Analysis of covariance was performed to compare the cognitive and postural performance across the three somato and prakriti types after adjusting for age and gender as covariates. Post-hoc analysis of Bonferroni was performed with the consideration of Levene's test. Partial correlations were employed to investigate the correlation between postural stability and cognitive performance measures for each of the prakriti- and somato-body types as well as between the prakriti typology (scores) and trunk index values (adjusting the effects of age and gender as control variables). A P < 0.05 was selected at the statistical significance level. SPSS 26.0 version was used for the analysis. RESULTS Cognitive performance was observed to vary in terms of RT across somato- and prakriti body types (P < 0.05). Postural stability and cognitive performance are positively connected only for ectomorph body types (P < 0.05). Variations in motor performance were not significant. Barring ectomorph type, no other somato- and prakriti body types showed significant relationships between postural stability and cognitive performance. Likewise, the association between the features used for prakriti classification, and the trunk index scores showed marginal significance, only for a small subset of physical features of prakriti assessment (P = 0.055) (P1). CONCLUSIONS Comparing classifications that use psychophysical attributes might offer insights into understanding variations in measures of motor and cognitive performance in a sample of healthy individuals.
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Affiliation(s)
- Ankit Gupta
- National Resource Centre for Value Education in Engineering, Indian Institute of Technology, Delhi, India
| | - Rahul Garg
- National Resource Centre for Value Education in Engineering, Indian Institute of Technology, Delhi, India
- Department of Computer Science and Engineering, Indian Institute of Technology Delhi, India
- Amar Nath and Shashi Khosla School of Information Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Varsha Singh
- Department of Humanities and Social Sciences, Indian Institute of Technology, New Delhi, India
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Huang Z, Chavda VP, Bezbaruah R, Uversky VN, P. S, Patel AB, Chen ZS. An Ayurgenomics Approach: Prakriti-Based Drug Discovery and Development for Personalized Care. Front Pharmacol 2022; 13:866827. [PMID: 35431922 PMCID: PMC9011054 DOI: 10.3389/fphar.2022.866827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Originating in ancient India, Ayurveda is an alternative medicinal approach that provides substantial evidence for a theoretical-level analysis of all aspects of life. Unlike modern medicine, Ayurveda is based upon tridoshas (Vata, pitta, and Kapha) and Prakriti. On the other hand, the research of all the genes involved at the proteomics, metabolomics, and transcriptome levels are referred to as genomics. Geoclimatic regions (deshanupatini), familial characteristics (kulanupatini), and ethnicity (jatiprasakta) have all been shown to affect phenotypic variability. The combination of genomics with Ayurveda known as ayurgenomics provided new insights into tridosha that may pave the way for precision medicine (personalized medicine). Through successful coordination of “omics,” Prakriti-based treatments can help change the existing situation in health care. Prakriti refers to an individual’s behavioral trait, which is established at the moment of birth and cannot be fully altered during one’s existence. Ayurvedic methodologies are based on three Prakriti aspects: aushadhi (medication), vihara (lifestyle), and ahara (diet). A foundation of Prakriti-based medicine, preventative medicine, and improvement of life quality with longevity can be accomplished through these ayurvedic characteristics. In this perspective, we try to understand prakriti’s use in personalized medicine, and how to integrate it with programs for drug development and discovery.
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Affiliation(s)
- Zoufang Huang
- Ganzhou Key Laboratory of Hematology, Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad, India
- *Correspondence: Vivek P. Chavda, ; Zhe-Sheng Chen,
| | - Rajashri Bezbaruah
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Sucharitha P.
- Department of Pharmaceutics, Seven Hills College of Pharmacy, Tirupati, India
| | | | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY, United States
- *Correspondence: Vivek P. Chavda, ; Zhe-Sheng Chen,
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Abbas T, Chaturvedi G, Prakrithi P, Pathak AK, Kutum R, Dakle P, Narang A, Manchanda V, Patil R, Aggarwal D, Girase B, Srivastava A, Kapoor M, Gupta I, Pandey R, Juvekar S, Dash D, Mukerji M, Prasher B. Whole Exome Sequencing in Healthy Individuals of Extreme Constitution Types Reveals Differential Disease Risk: A Novel Approach towards Predictive Medicine. J Pers Med 2022; 12:jpm12030489. [PMID: 35330488 PMCID: PMC8952204 DOI: 10.3390/jpm12030489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
Precision medicine aims to move from traditional reactive medicine to a system where risk groups can be identified before the disease occurs. However, phenotypic heterogeneity amongst the diseased and healthy poses a major challenge for identification markers for risk stratification and early actionable interventions. In Ayurveda, individuals are phenotypically stratified into seven constitution types based on multisystem phenotypes termed “Prakriti”. It enables the prediction of health and disease trajectories and the selection of health interventions. We hypothesize that exome sequencing in healthy individuals of phenotypically homogeneous Prakriti types might enable the identification of functional variations associated with the constitution types. Exomes of 144 healthy Prakriti stratified individuals and controls from two genetically homogeneous cohorts (north and western India) revealed differential risk for diseases/traits like metabolic disorders, liver diseases, and body and hematological measurements amongst healthy individuals. These SNPs differ significantly from the Indo-European background control as well. Amongst these we highlight novel SNPs rs304447 (IFIT5) and rs941590 (SERPINA10) that could explain differential trajectories for immune response, bleeding or thrombosis. Our method demonstrates the requirement of a relatively smaller sample size for a well powered study. This study highlights the potential of integrating a unique phenotyping approach for the identification of predictive markers and the at-risk population amongst the healthy.
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Affiliation(s)
- Tahseen Abbas
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Gaura Chaturvedi
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - P. Prakrithi
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - Ankit Kumar Pathak
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
| | - Rintu Kutum
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Pushkar Dakle
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
| | - Ankita Narang
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
| | - Vijeta Manchanda
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
| | - Rutuja Patil
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Dhiraj Aggarwal
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Bhushan Girase
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Ankita Srivastava
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Manav Kapoor
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA;
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India;
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi 110007, India;
| | - Sanjay Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune 412216, India; (R.P.); (D.A.); (B.G.); (A.S.); (S.J.)
| | - Debasis Dash
- Informatics and Big Data Unit, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Correspondence: (D.D.); (M.M.); (B.P.)
| | - Mitali Mukerji
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Jodhpur 342037, India
- Correspondence: (D.D.); (M.M.); (B.P.)
| | - Bhavana Prasher
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi 110020, India; (T.A.); (G.C.); (R.K.); (P.D.); (A.N.); (V.M.)
- Academy of Scientific and Innovative Research, Ghaziabad 201002, India
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110020, India; (P.P.); (A.K.P.)
- Correspondence: (D.D.); (M.M.); (B.P.)
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10
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Exploring the signature gut and oral microbiome in individuals of specific Ayurveda prakriti. J Biosci 2021. [DOI: 10.1007/s12038-021-00182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Chakraborty S, Singhmar S, Singh D, Maulik M, Patil R, Agrawal SK, Mishra A, Ghazi M, Vats A, Natarajan VT, Juvekar S, Prasher B, Mukerji M. Baseline cell proliferation rates and response to UV differ in lymphoblastoid cell lines derived from healthy individuals of extreme constitution types. Cell Cycle 2021; 20:903-913. [PMID: 33870855 DOI: 10.1080/15384101.2021.1909884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Differences in human phenotypes and susceptibility to complex diseases are an outcome of genetic and environmental interactions. This is evident in diseases that progress through a common set of intermediate patho-endophenotypes. Precision medicine aims to delineate molecular players for individualized and early interventions. Functional studies of lymphoblastoid cell line (LCL) model of phenotypically well-characterized healthy individuals can help deconvolute and validate these molecular mechanisms. In this study, LCLs are developed from eight healthy individuals belonging to three extreme constitution types, deep phenotyped on the basis of Ayurveda. LCLs were characterized by karyotyping and immunophenotyping. Growth characteristics and response to UV were studied in these LCLs. Significant differences in cell proliferation rates were observed between the contrasting groups such that one type (Kapha) proliferates significantly slower than the other two (Vata, Pitta). In response to UV, one of the fast growing groups (Vata) shows higher cell death but recovers its numbers due to an inherent higher rates of proliferation. This study reveals that baseline differences in cell proliferation could be a key to understanding the survivability of cells under UV stress. Variability in baseline cellular phenotypes not only explains the cellular basis of different constitution types but can also help set priors during the design of an individualized therapy with DNA damaging agents. This is the first study of its kind that shows variability of intermediate patho-phenotypes among healthy individuals with potential implications in precision medicine.
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Affiliation(s)
- Sumita Chakraborty
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sunanda Singhmar
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dayanidhi Singh
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mahua Maulik
- CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Department of Biological Sciences, Indian Institute of Science Education & Research, IISER Kolkata, Mohanpur, Nadia, West Bengal, India
| | - Rutuja Patil
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, Maharashtra, India
| | - Satyam Kumar Agrawal
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,School of Pharmacy and Emerging Sciences (SPES), Baddi University of Emerging Science and Technology (BUEST), Baddi, Himachal Pradesh, India
| | - Anushree Mishra
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Madeeha Ghazi
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Archana Vats
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India
| | - Vivek T Natarajan
- Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Juvekar
- Vadu Rural Health Program, KEM Hospital Research Centre, Pune, Maharashtra, India
| | - Bhavana Prasher
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mitali Mukerji
- Centre of Excellence for Applied Development of Ayurveda Prakriti and Genomics, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,CSIR Ayurgenomics Unit-TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Genomics and Molecular Medicine, CSIR-Institute of Genomics & Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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12
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Bhargav H, Jasti N, More P, Kumar V, Chikkanna U, Kishore Kumar R, Varambally S. Correlation of prakriti diagnosis using AyuSoft prakriti diagnostic tool with clinician rating in patients with psychiatric disorders. J Ayurveda Integr Med 2021; 12:365-368. [PMID: 33750638 PMCID: PMC8185963 DOI: 10.1016/j.jaim.2021.01.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/21/2021] [Accepted: 01/29/2021] [Indexed: 11/29/2022] Open
Abstract
Assessment of individual constitution (prakriti) has been an important basic construct of the Ayurveda system of medicine. The AyuSoft prakriti diagnostic tool has been extensively used in Ayurveda research. However, we could not find any literature regarding reliability of a prakriti diagnostic tool in patients with psychiatric conditions. One hundred and twelve patients (M = 70) suffering from various psychiatric disorders as per ICD-10 criteria were recruited (Depression = 31; Schizophrenia = 30, Anxiety disorders = 27; OCD = 9; BPAD = 15). The AyuSoft tool (developed by C-DAC, Pune, India) was applied to determine their prakriti after obtaining written informed consent. Two Ayurveda physicians independently assessed prakriti of the same patients through clinical examination. Inter-rater reliability was assessed between prakriti scores obtained from AyuSoft and those from the Ayurveda physicians by determining Cohen’s Kappa intra-class correlation coefficient (ICC). ICC estimates and their 95% confidence intervals were calculated using SPSS statistical package (version 24.0) based on a mean-rating (k = 2), consistency and two-way mixed-effects model. We observed that there was a significant correlation between dosha scores obtained through AyuSoft and those from the two Ayurveda physicians (for all three doshas: p < 0.01). Inter-rater reliability was moderately strong for vata (ICC = 0.72; Cronbach’s alpha = 0.83), good for pitta (ICC = 0.58; Cronbach’s alpha = 0.62) and comparatively weak for kaphadosha (ICC = 0.44; Cronbach’s alpha = 0.51) respectively. Prakriti diagnosis by AyuSoft was feasible in stabilized psychiatric patients and was found comparable to clinical diagnosis of prakriti by Ayurveda physicians in patients with psychiatric disorders.
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Affiliation(s)
- Hemant Bhargav
- Department of Integrative Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Nishitha Jasti
- Department of Integrative Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Pooja More
- Department of Integrative Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Vinod Kumar
- Central Council for Research in Yoga and Naturopathic Medicine (CCRYN), Department of Integrative Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Umesh Chikkanna
- Department of Integrative Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Ramakrishna Kishore Kumar
- Department of Integrative Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India.
| | - Shivarama Varambally
- Department of Integrative Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
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13
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Gheware A, Panda L, Khanna K, Bhatraju NK, Jain V, Sagar S, Kumar M, Singh VP, Kannan S, Subramanian V, Mukerji M, Agrawal A, Prasher B. Adhatoda vasica rescues the hypoxia-dependent severe asthma symptoms and mitochondrial dysfunction. Am J Physiol Lung Cell Mol Physiol 2021; 320:L757-L769. [PMID: 33565386 DOI: 10.1152/ajplung.00511.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Severe asthma is a chronic airway disease that exhibits poor response to conventional asthma therapies. Growing evidence suggests that elevated hypoxia increases the severity of asthmatic inflammation among patients and in model systems. In this study, we elucidate the therapeutic effects and mechanistic basis of Adhatoda vasica (AV) aqueous extract on mouse models of acute allergic as well as severe asthma subtypes at physiological, histopathological, and molecular levels. Oral administration of AV extract attenuates the increased airway resistance and inflammation in acute allergic asthmatic mice and alleviates the molecular signatures of steroid (dexamethasone) resistance like IL-17A, KC (murine IL-8 homologue), and HIF-1α (hypoxia-inducible factor-1α) in severe asthmatic mice. AV inhibits HIF-1α levels through restoration of expression of its negative regulator-PHD2 (prolyl hydroxylase domain-2). Alleviation of hypoxic response mediated by AV is further confirmed in the acute and severe asthma model. AV reverses cellular hypoxia-induced mitochondrial dysfunction in human bronchial epithelial cells-evident from bioenergetic profiles and morphological analysis of mitochondria. In silico docking of AV constituents reveal higher negative binding affinity for C and O-glycosides for HIF-1α, IL-6, Janus kinase 1/3, TNF-α, and TGF-β-key players of hypoxia inflammation. This study for the first time provides a molecular basis of action and effect of AV whole extract that is widely used in Ayurveda practice for diverse respiratory ailments. Further, through its effect on hypoxia-induced mitochondrial dysfunction, the study highlights its potential to treat severe steroid-resistant asthma.
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Affiliation(s)
- Atish Gheware
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,CSIR's Ayurgenomics Unit, TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-IGIB, Delhi, India.,Centre of Excellence for Applied Development of Ayurveda, Prakriti and Genomics, CSIR-IGIB, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Lipsa Panda
- Centre of Excellence for Translational Research in Asthma & Lung disease, CSIR-IGIB, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kritika Khanna
- Centre of Excellence for Translational Research in Asthma & Lung disease, CSIR-IGIB, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Naveen Kumar Bhatraju
- Centre of Excellence for Translational Research in Asthma & Lung disease, CSIR-IGIB, Delhi, India
| | - Vaibhav Jain
- Centre of Excellence for Translational Research in Asthma & Lung disease, CSIR-IGIB, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shakti Sagar
- Centre of Excellence for Translational Research in Asthma & Lung disease, CSIR-IGIB, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Manish Kumar
- Centre of Excellence for Translational Research in Asthma & Lung disease, CSIR-IGIB, Delhi, India
| | - Vijay Pal Singh
- Centre of Excellence for Translational Research in Asthma & Lung disease, CSIR-IGIB, Delhi, India
| | - Sadasivam Kannan
- Center for High Computing, CSIR-Central Leather Research Institute (CLRI), Chennai, India
| | - Venkatesan Subramanian
- Center for High Computing, CSIR-Central Leather Research Institute (CLRI), Chennai, India
| | - Mitali Mukerji
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,CSIR's Ayurgenomics Unit, TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-IGIB, Delhi, India.,Centre of Excellence for Applied Development of Ayurveda, Prakriti and Genomics, CSIR-IGIB, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anurag Agrawal
- Centre of Excellence for Translational Research in Asthma & Lung disease, CSIR-IGIB, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Bhavana Prasher
- Genomics and Molecular Medicine, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.,CSIR's Ayurgenomics Unit, TRISUTRA (Translational Research and Innovative Science ThRough Ayurgenomics), CSIR-IGIB, Delhi, India.,Centre of Excellence for Applied Development of Ayurveda, Prakriti and Genomics, CSIR-IGIB, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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14
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Ayurgenomics and Modern Medicine. ACTA ACUST UNITED AC 2020; 56:medicina56120661. [PMID: 33265906 PMCID: PMC7760374 DOI: 10.3390/medicina56120661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
Within the disciplines of modern medicine, P4 medicine is emerging as a new field which focuses on the whole patient. The development of Ayurgenomics could greatly enrich P4 medicine by providing a clear theoretical understanding of the whole patient and a practical application of ancient and modern preventative and therapeutic practices to improve mental and physical health. One of the most difficult challenges today is understanding the ancient concepts of Ayurveda in terms of modern science. To date, a number of researchers have attempted this task, of which one of the most successful outcomes is the creation of the new field of Ayurgenomics. Ayurgenomics integrates concepts in Ayurveda, such as Prakriti, with modern genetics research. It correlates the combination of three doshas, Vata, Pitta and Kapha, with the expression of specific genes and physiological characteristics. It also helps to interpret Ayurveda as an ancient science of epigenetics which assesses the current state of the doshas, and uses specific personalized diet and lifestyle recommendations to improve a patient’s health. This review provides a current update of this emerging field.
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15
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Sharma R, Prajapati PK. Predictive, Preventive and Personalized Medicine: Leads From Ayurvedic Concept of Prakriti (Human Constitution). ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s40495-020-00244-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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16
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Mobeen F, Sharma V, Prakash T. Comparative gut microbiome analysis of the Prakriti and Sasang systems reveals functional level similarities in constitutionally similar classes. 3 Biotech 2020; 10:379. [PMID: 32802721 PMCID: PMC7413973 DOI: 10.1007/s13205-020-02376-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/31/2020] [Indexed: 12/12/2022] Open
Abstract
The traditional medicinal systems (TMS) of India (Prakriti) and Korea (Sasang) classify human individuals based on their constitution determined by the physiological and psychological traits of individuals. Similarities in the constitutions are already found between the classes of Prakriti (Vata, Pitta, and Kapha) and Sasang (TE: Taeeumin, SE: Soeumin, and SY: Soyangin) systems. Gut health is an important aspect of this constitution based classification in TMS. To determine the role of gut microbes in such classifications, we have analyzed the gut microbiome (taxa and imputed functions) in the constitutionally similar Prakriti and Sasang classes. An enrichment of Bacteroides and Prevotella enterotypes is observed in the Sasang and Prakriti samples, respectively. The impact of the constitution is found to be more prominent with respect to the taxa and predicted-functions within the Prakriti classes. Gut microbiome functional-level similarities are found to correlate well with the host phenotypes of the constitutionally similar Prakriti and Sasang classes. An enrichment of carbohydrate and amino-acid metabolism is observed in the Vata and SE classes which may be responsible for meeting with their high energy demands and lean phenotype. The Pitta and SY classes exhibit the high capacity to metabolize toxins. An enrichment of functions responsible for predisposition to obesity and high drug metabolism is observed in the Kapha and TE classes. The contribution of gut adaptive functions is found to correlate with the constitution-based classification in both Prakriti and Sasang systems. The TE class harboured the highest number of biofilm-forming and stress-tolerant microbes thus exhibiting the maximum tolerance of environmental stress. Similarities in the gut microbiota and the resulting disease predisposition patterns are found to exist between the constitutionally matching Prakriti and Sasang classes.
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Affiliation(s)
- Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005 India
| | - Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005 India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, Himachal Pradesh 175005 India
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17
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Jnana A, Murali TS, Guruprasad KP, Satyamoorthy K. Prakriti phenotypes as a stratifier of gut microbiome: A new frontier in personalized medicine? J Ayurveda Integr Med 2020; 11:360-365. [PMID: 32718805 PMCID: PMC7527847 DOI: 10.1016/j.jaim.2020.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/13/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
Ayurveda has a rich history and its significance woven deeply in the Indian culture. The concept of prakriti (a person’s “nature” or constitutional type determined by the proportion of three doshas, namely - vata, pitta and kapha) in Ayurveda is deeply rooted in personalized health management. While the attributes of prakriti has been established to have a genomic basis, there is dearth of elaborate evidences linking prakriti with manifestation of diseases. Next generation sequencing studies have provided a causal link between variation in the gut microbiome and its effect on an individual’s fitness. Separately, reports have identified gut microbial patterns associated with several host variables such as geography, age, diet and extreme prakriti phenotypes. Recently, few reports have identified a “core gut microbiome” consisting of Bacteroides, Faecalibacterium, Prevotella and Ruminococcus prevalent across the Indian population; however, a few bacterial genera were specifically enriched in certain prakritis. Hence, in this review we aim to analyse the role of prakriti variations on dysbiosis of the gut microbiome and concomitantly its effect on human health. We suggest that prakriti phenotyping can function as a potential stratifier of the gut microbiome in a given population and may provide evidence for the conceptual framework of personalized medicine in Ayurvedic system of medicine.
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Affiliation(s)
- Apoorva Jnana
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Thokur Sreepathy Murali
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Kanive Parashiva Guruprasad
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India; Centre for Ayurvedic Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India; Centre for Ayurvedic Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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18
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Kougioumtsidou N, Vavoulidis E, Nasioutziki M, Symeonidou M, Pratilas GC, Mareti E, Petousis S, Chatzikyriakidou A, Grimbizis G, Theodoridis T, Miliaras D, Dinas K, Zepiridis L. DNA methylation patterns of RAR-β2 and RASSF1A gene promoters in FNAB samples from Greek population with benign or malignant breast lesions. Diagn Cytopathol 2020; 49:153-164. [PMID: 32530576 DOI: 10.1002/dc.24513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/27/2020] [Accepted: 05/19/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Promoter hypermethylation is common in Breast Cancer (BC) with studies mainly in histological specimens showing frequent methylation of tumor suppressor genes (TSGs) compared with normal tissues. The aim of this study was to estimate the frequency of promoter methylation of RAR-β2 and RASSF1A genes in breast FNAB material aiming to evaluate the methylation status of these two genes as biomarker for detecting BC in Greek population. METHODS FNAB material from 104 patients was collected for cytological evaluation and epigenetic analysis. DNA was extracted and subjected to bisulfite conversion. A methylation-specific PCR was carried out and the final products were separated with electrophoresis in 2% agarose gels. RESULTS From 104 samples, RASSF1A hypermethylation was observed in 78 (75%) and RAR-β2 hypermethylation in 64 (61.6%). 84% and 78% of the cases diagnosed with breast malignancy (n = 50) were methylated for RASSF1A and RAR-β2, respectively. Methylated RASSF1A and RAR-β2 were also detected in 88.3% and 76.5% in samples diagnosed as suspicious for malignancy (n = 17) and in 57.2% of samples diagnosed with atypia (n = 14). The Odds Ratio for breast malignancy was 4.545 in patients with RASSF1A hypermethylation and 9.167 in patients with RAR-β2 hypermethylation underlying their promoter's methylation positive correlation with breast malignancy. CONCLUSION To optimize the sensitivity and specificity of this epigenetic setting, more TSGs related to BC should be gradually imported in our evaluated methylation panel and be validated in a larger study sample with the aim that the obtained epigenetic profiles will provide clinicians with valuable tools for management of BC patients in Greece.
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Affiliation(s)
- Niki Kougioumtsidou
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Eleftherios Vavoulidis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Maria Nasioutziki
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Marianthi Symeonidou
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Georgios Chrysostomos Pratilas
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Mareti
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Stamatios Petousis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Anthoula Chatzikyriakidou
- Faculty of Medicine, Laboratory of Medical Biology-Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Gregorios Grimbizis
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Theodoros Theodoridis
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Dimosthenis Miliaras
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Dinas
- Faculty of Medicine, First Department of Obstetrics and Gynaecology, Aristotle University of Thessaloniki, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Leonidas Zepiridis
- Faculty of Medicine, Second Department of Obstetrics and Gynaecology and Molecular Cytopathology Laboratory, Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece
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19
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Mobeen F, Sharma V, Prakash T. Functional signature analysis of extreme Prakriti endophenotypes in gut microbiome of western Indian rural population. Bioinformation 2019; 15:490-505. [PMID: 31485135 PMCID: PMC6704335 DOI: 10.6026/97320630015490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/30/2019] [Indexed: 12/27/2022] Open
Abstract
Ayurveda is practiced in India from ancient times and stratifies the individuals based on their Prakriti constitution. Advancements in modern science have led to the association of Prakriti with molecular, biochemical, genomic and other entities. We have recently explored the gut microbiome composition and microbial signatures in healthy extreme Prakriti endo-phenotypes. However, their functional potentials are still lacking. The present study includes 63 females (29 Vata, 11 Pitta, and 23 Kapha) and 50 males (13 Vata, 18 Pitta, and 19 Kapha) samples. The predictive functional profiling and organism level functional traits of the human gut microbiome have been carried out in Prakriti groups using imputed metagenomic approach. A higher functional level redundancy is found than the taxonomy across the Prakriti groups, however the dominant taxa contributing to the functional profiles are found to be different. A high number of functional signatures specific to the Prakriti groups were identified in female datasets. Some of the functional signatures were found to be gender specific. For example, a higher abundance of microbes contributing potential pathogenic and stress tolerance related functions was found in Kapha in female and Pitta in male. The functional signatures correlated well with phenotypes and disease predisposition of Prakriti groups.
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Affiliation(s)
- Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| | - Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand 175005, Mandi, Himachal Pradesh, India
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Big Data Analysis of Traditional Knowledge-based Ayurveda Medicine. PROGRESS IN PREVENTIVE MEDICINE 2018. [DOI: 10.1097/pp9.0000000000000020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Varghese VK, Shukla V, Kabekkodu SP, Pandey D, Satyamoorthy K. DNA methylation regulated microRNAs in human cervical cancer. Mol Carcinog 2018; 57:370-382. [PMID: 29077234 DOI: 10.1002/mc.22761] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 01/19/2023]
Abstract
Regulation of miRNA gene expression by DNA promoter methylation may represent a key mechanism to drive cervical cancer progression. In order to understand the impact of DNA promoter methylation on miRNAs at various stages of cervical carcinogenesis, we performed DNA methylation microarray on Normal Cervical Epithelium (NCE), Cervical Intraepithelial Neoplasia (CIN I-III) and Squamous Cell Carcinoma (SCC) tissues to identify differentially methylated miRNAs followed by validation by bisulfite sequencing. Further, expression of miRNAs was analyzed by qRT-PCR in clinical tissues and cervical cancer cell lines. Transcriptional activity was determined by luciferase assay. We identified a total of 69 hypermethylated and hypomethylated miRNA promoters encompassing 78 CpG islands in all except Y chromosome, among the three groups. The candidate DNA promoters of miR-424 were significantly hypermethylated and miR-200b and miR-34c were significantly hypomethylated in SCC compared to NCE (P < 0.05). Expression of miR-424, miR-200b, and miR-34c were inversely correlated with promoter DNA methylation in tissue samples. Treatment of cell lines with 5-aza-2'-deoxycytidine showed differential expression in all three miRNAs. We observed a decrease in miRNA promoter activity following in vitro SssI methylase treatment of miR-424, miR-200b, and miR-34c. Luciferase assay demonstrated that miR-200b and miR-424 functionally interacts with 3'-UTR of HIPK3 and RBBP6 respectively and decreased their activity in presence of miR-200b and miR-424 mimics transfected in SiHa cells. Taken together, we have identified deregulation of miRNAs by aberrant DNA promoter methylation, leading to its transcriptional silencing during cervical carcinogenesis, which can be potential targets for diagnosis and therapy.
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Affiliation(s)
- Vinay K Varghese
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Shama P Kabekkodu
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
| | - Deeksha Pandey
- Department of Obstetrics and Gynecology, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, India
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Recapitulation of Ayurveda constitution types by machine learning of phenotypic traits. PLoS One 2017; 12:e0185380. [PMID: 28981546 PMCID: PMC5628820 DOI: 10.1371/journal.pone.0185380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 09/10/2017] [Indexed: 01/19/2023] Open
Abstract
In Ayurveda system of medicine individuals are classified into seven constitution types, “Prakriti”, for assessing disease susceptibility and drug responsiveness. Prakriti evaluation involves clinical examination including questions about physiological and behavioural traits. A need was felt to develop models for accurately predicting Prakriti classes that have been shown to exhibit molecular differences. The present study was carried out on data of phenotypic attributes in 147 healthy individuals of three extreme Prakriti types, from a genetically homogeneous population of Western India. Unsupervised and supervised machine learning approaches were used to infer inherent structure of the data, and for feature selection and building classification models for Prakriti respectively. These models were validated in a North Indian population. Unsupervised clustering led to emergence of three natural clusters corresponding to three extreme Prakriti classes. The supervised modelling approaches could classify individuals, with distinct Prakriti types, in the training and validation sets. This study is the first to demonstrate that Prakriti types are distinct verifiable clusters within a multidimensional space of multiple interrelated phenotypic traits. It also provides a computational framework for predicting Prakriti classes from phenotypic attributes. This approach may be useful in precision medicine for stratification of endophenotypes in healthy and diseased populations.
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Genetic and epigenetic changes in host ABCB1 influences malaria susceptibility to Plasmodium falciparum. PLoS One 2017; 12:e0175702. [PMID: 28422980 PMCID: PMC5397027 DOI: 10.1371/journal.pone.0175702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/30/2017] [Indexed: 01/20/2023] Open
Abstract
Multiple mechanisms such as genetic and epigenetic variations within a key gene may play a role in malarial susceptibility and response to anti-malarial drugs in the population. ABCB1 is one of the well-studied membrane transporter genes that code for the P-glycoprotein (an efflux protein) and whose effect on malaria disease predisposition and susceptibility to drugs remains to be understood. We studied the association of single nucleotide variations in human ABCB1 that influences its function in subjects with uncomplicated and complicated malaria caused by Plasmodium falciparum (Pf). Global DNA methylation and ABCB1 DNA promoter methylation levels were performed along with transcriptional response and protein expression in subjects with malaria and healthy controls. The rs2032582 locus was significantly associated with complicated and combined malaria groups when compared to controls (p < 0.05). Significant DNA methylation difference was noticed between case and control (p < 0.05). In addition, global DNA methylation levels of the host DNA were inversely proportional to parasitemia in individuals with Pf infection. Our study also revealed the correlation between ABCB1 DNA promoter methylation with rs1128503 and rs2032582 polymorphisms in malaria and was related to increased expression of ABCB1 protein levels in complicated malaria group (p < 0.05) when compared to uncomplicated malaria and control groups. The study provides evidence for multiple mechanisms that may regulate the role of host ABCB1 function to mediate aetiology of malaria susceptibility, prognosis and drug response. These may have clinical implications and therapeutic application for various malarial conditions.
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Bhat S, Kabekkodu SP, Jayaprakash C, Radhakrishnan R, Ray S, Satyamoorthy K. Gene promoter-associated CpG island hypermethylation in squamous cell carcinoma of the tongue. Virchows Arch 2017; 470:445-454. [PMID: 28255813 DOI: 10.1007/s00428-017-2094-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/28/2016] [Accepted: 02/15/2017] [Indexed: 01/10/2023]
Abstract
The present study was undertaken to explore and validate novel hypermethylated DNA regions in squamous cell carcinoma of the tongue (SCCT). Genome-wide methylation changes were identified by differential methylation hybridization (DMH) microarray and validated by bisulfite genome sequencing (BGS). The results were compared against datasets from The Cancer Genome Atlas head and neck squamous cell carcinoma (TCGA-HNSCC), Gene Expression Omnibus (GSE26549), and ArrayExpress (E-MTAB-1328). DMH identified 116 hypomethylated and 241 hypermethylated regions. Of the latter, 24 were localized to promoter or 5'-UTR regions. By BGS, promoter sequences of DAPK1, LRPPRC, RAB6C, and ZNF471 were significantly hypermethylated in tumors when compared with matched normal tissues (P < 0.0001). A TCGA-HNSCC dataset (516 cases of cancer and 50 normal tissue samples) further confirmed hypermethylation of DAPK1, RAB6C, and ZNF471. Sensitivity and specificity of methylation markers for a diagnosis of cancer were in the range of 70-100% in our study and from TCGA-HNSCC datasets, with an area under curve (AUC) of 0.83 and above. Kaplan-Meier survival analysis of TCGA-HNSCC expression data revealed that patients with low expressions of DAPK1, RAB6C, and ZNF471 showed poorer survival than patients with high expression (P = 0.02). Human papillomavirus (HPV) was found in 55% of cases, HPV16 being the predominant genotype. DAPK1 immunohistochemical staining was lower in SCCT than in normal buccal epithelial cells. This is the first study to report hypermethylation of LRPPRC, RAB6C, and ZNF471 in SCCT and its diagnostic and prognostic potentials in a specific head and neck squamous cell carcinoma.
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Affiliation(s)
- Samatha Bhat
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Chinchu Jayaprakash
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal University, Manipal, 576104, India
| | - Satadru Ray
- Department of Surgical Oncology, Kasturba Medical College, Manipal University, Manipal, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, Karnataka, 576104, India.
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Bhat S, Kabekkodu SP, Varghese VK, Chakrabarty S, Mallya SP, Rotti H, Pandey D, Kushtagi P, Satyamoorthy K. Aberrant gene-specific DNA methylation signature analysis in cervical cancer. Tumour Biol 2017; 39:1010428317694573. [PMID: 28351298 DOI: 10.1177/1010428317694573] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Abstract
Multicomponent molecular modifications such as DNA methylation may offer sensitive and specific cervical intraepithelial neoplasia and cervical cancer biomarkers. In this study, we tested cervical tissues at various stages of tumor progression for 5-methylcytosine and 5-hydroxymethylcytosine levels and also DNA promoter methylation profile of a panel of genes for its diagnostic potential. In total, 5-methylcytosine, 5-hydroxymethylcytosine, and promoter methylation of 33 genes were evaluated by reversed-phase high-performance liquid chromatography, enzyme-linked immunosorbent assay based technique, and bisulfate-based next generation sequencing. The 5-methylcytosine and 5-hydroxymethylcytosine contents were significantly reduced in squamous cell carcinoma and receiver operating characteristic curve analysis showed a significant difference in (1) 5-methylcytosine between normal and squamous cell carcinoma tissues (area under the curve = 0.946) and (2) 5-hydroxymethylcytosine levels among normal, squamous intraepithelial lesions and squamous cell carcinoma. Analyses of our next generation sequencing results and data from five independent published studies consisting of 191 normal, 10 low-grade squamous intraepithelial lesions, 21 high-grade squamous intraepithelial lesions, and 335 malignant tissues identified a panel of nine genes ( ARHGAP6, DAPK1, HAND2, NKX2-2, NNAT, PCDH10, PROX1, PITX2, and RAB6C) which could effectively discriminate among the various groups with sensitivity and specificity of 80%-100% (p < 0.05). Furthermore, 12 gene promoters (ARHGAP6, HAND2, LHX9, HEY2, NKX2-2, PCDH10, PITX2, PROX1, TBX3, IKBKG, RAB6C, and DAPK1) were also methylated in one or more of the cervical cancer cell lines tested. The global and gene-specific methylation of the panel of genes identified in our study may serve as useful biomarkers for the early detection and clinical management of cervical cancer.
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Affiliation(s)
- Samatha Bhat
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Shama Prasada Kabekkodu
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Vinay Koshy Varghese
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Sanjiban Chakrabarty
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Sandeep P Mallya
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Harish Rotti
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
| | - Deeksha Pandey
- 2 Department of Obstetrics & Gynaecology, Kasturba Medical College, Manipal University, Manipal, India
| | - Pralhad Kushtagi
- 3 Department of Obstetrics & Gynaecology, Kasturba Medical College, Manipal University, Mangalore, India
| | - Kapaettu Satyamoorthy
- 1 Department of Cell and Molecular Biology, School of Life Sciences, Manipal University, Manipal, India
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Epigenetic Mechanisms of Integrative Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:4365429. [PMID: 28316635 PMCID: PMC5339524 DOI: 10.1155/2017/4365429] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/13/2016] [Accepted: 01/15/2017] [Indexed: 12/20/2022]
Abstract
Since time immemorial humans have utilized natural products and therapies for their healing properties. Even now, in the age of genomics and on the cusp of regenerative medicine, the use of complementary and alternative medicine (CAM) approaches represents a popular branch of health care. Furthermore, there is a trend towards a unified medical philosophy referred to as Integrative Medicine (IM) that represents the convergence of CAM and conventional medicine. The IM model not only considers the holistic perspective of the physiological components of the individual, but also includes psychological and mind-body aspects. Justification for and validation of such a whole-systems approach is in part dependent upon identification of the functional pathways governing healing, and new data is revealing relationships between therapies and biochemical effects that have long defied explanation. We review this data and propose a unifying theme: IM's ability to affect healing is due at least in part to epigenetic mechanisms. This hypothesis is based on a mounting body of evidence that demonstrates a correlation between the physical and mental effects of IM and modulation of gene expression and epigenetic state. Emphasis on mapping, deciphering, and optimizing these effects will facilitate therapeutic delivery and create further benefits.
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Joshi KS, Nesari TM, Dedge AP, Dhumal VR, Shengule SA, Gadgil MS, Salvi S, Valiathan MVS. Dosha phenotype specific Ayurveda intervention ameliorates asthma symptoms through cytokine modulations: Results of whole system clinical trial. JOURNAL OF ETHNOPHARMACOLOGY 2017; 197:110-117. [PMID: 27473604 DOI: 10.1016/j.jep.2016.07.071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Over the past few decades, there have been significant scientific advances leading to improved understanding of asthma as a disease and treatment providing immediate relief. However, prevention of recurrent attacks, exacerbations and disease cure remains a challenge. Ayurveda refers to bronchial asthma as Tamaka Swasa and it is well explained in Charaka Samhita. Management of asthma in Ayurveda includes removal of vitiated Kapha through Shodhana, Shamana procedures, herbal and herbomineral formulations in addition to advising a healthy lifestyle and diet. Several clinical trials on Ayurvedic formulations for treatment of asthma are reported, however, whole system management of asthma has rarely been studied in the manner in which it is actually being practiced. Ayurveda therapeutics provides Dosha specific approaches, which needs biological investigation. AIM OF THE STUDY The objective of our study was to investigate lung functions and cytokine changes in Asthmatic individuals in response to Ayurvedic intervention. METHODS The study design was approved by the Institutional Ethics Committee of Tilak Ayurveda Mahavidyalaya (TAMV) & Sheth Tarachand Ramnath Charitable Ayurveda Hospital and followed guidelines of the Declaration of Helsinki and Tokyo for humans. It was conducted as a whole system individualized pragmatic clinical trial and written consent of patients was collected before enrollment. One hundred and fifteen patients with mild-to-moderate asthma were divided into 2 sub-groups depending on their disease subsets and administered phenotype specific ayurvedic interventions. Seventy six asthma patients completed the treatment. Serum IgE levels, blood eosinophil counts, spirometry and blood cytokine levels were measured before the start of treatment and six months at the end of treatment. Age and sex matched healthy participants (n=69) were recruited in the study for comparison of cytokines levels. RESULTS Significant improvements in FEV1(% predicted) (p<0.0001) and FVC (% predicted) (p=0.0001) was observed in asthmatic patients who underwent Ayurvedic treatment. Circulating levels of IgE (p<0.03) and eosinophil numbers (p=0.001) reduced significantly in the asthmatics after Ayurvedic treatment. This was associated with significant reduction in levels of circulating cytokines. Levels of Th2, Th1 and inflammatory cytokines in the peripheral blood were higher than healthy control participants at baseline (p values <0.0001) and reduced significantly after ayurvedic intervention. CONCLUSION This proof of concept study highlights the potential benefits and possible mechanism of Ayurvedic interventions in patients with mild-to-moderate asthma. The interventions significantly reduced IgE and eosinophil count, also improved lung function and reduced levels of circulating Th2 cytokines.
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Affiliation(s)
- Kalpana S Joshi
- Department of Biotechnology, Sinhgad College of Engineering, University of Pune, Pune, Maharashtra, India.
| | - Tanuja M Nesari
- Department of Dravyaguna,Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Amrish P Dedge
- Department of Dravyaguna,Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Vikram R Dhumal
- Department of Dravyaguna,Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sushant A Shengule
- Department of Biotechnology, Sinhgad College of Engineering, University of Pune, Pune, Maharashtra, India
| | - Maithili S Gadgil
- Department of Biotechnology, Sinhgad College of Engineering, University of Pune, Pune, Maharashtra, India
| | - Sundeep Salvi
- Department of Pulmonary Medicine, Chest Research Foundation, Pune, Maharashtra, India
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Prasher B, Varma B, Kumar A, Khuntia BK, Pandey R, Narang A, Tiwari P, Kutum R, Guin D, Kukreti R, Dash D, Mukerji M. Ayurgenomics for stratified medicine: TRISUTRA consortium initiative across ethnically and geographically diverse Indian populations. JOURNAL OF ETHNOPHARMACOLOGY 2017; 197:274-293. [PMID: 27457695 DOI: 10.1016/j.jep.2016.07.063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 07/02/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Genetic differences in the target proteins, metabolizing enzymes and transporters that contribute to inter-individual differences in drug response are not integrated in contemporary drug development programs. Ayurveda, that has propelled many drug discovery programs albeit for the search of new chemical entities incorporates inter-individual variability "Prakriti" in development and administration of drug in an individualized manner. Prakriti of an individual largely determines responsiveness to external environment including drugs as well as susceptibility to diseases. Prakriti has also been shown to have molecular and genomic correlates. We highlight how integration of Prakriti concepts can augment the efficiency of drug discovery and development programs through a unique initiative of Ayurgenomics TRISUTRA consortium. METHODS Five aspects that have been carried out are (1) analysis of variability in FDA approved pharmacogenomics genes/SNPs in exomes of 72 healthy individuals including predominant Prakriti types and matched controls from a North Indian Indo-European cohort (2) establishment of a consortium network and development of five genetically homogeneous cohorts from diverse ethnic and geo-climatic background (3) identification of parameters and development of uniform standard protocols for objective assessment of Prakriti types (4) development of protocols for Prakriti evaluation and its application in more than 7500 individuals in the five cohorts (5) Development of data and sample repository and integrative omics pipelines for identification of genomic correlates. RESULTS Highlight of the study are (1) Exome sequencing revealed significant differences between Prakriti types in 28 SNPs of 11 FDA approved genes of pharmacogenomics relevance viz. CYP2C19, CYP2B6, ESR1, F2, PGR, HLA-B, HLA-DQA1, HLA-DRB1, LDLR, CFTR, CPS1. These variations are polymorphic in diverse Indian and world populations included in 1000 genomes project. (2) Based on the phenotypic attributes of Prakriti we identified anthropometry for anatomical features, biophysical parameters for skin types, HRV for autonomic function tests, spirometry for vital capacity and gustometry for taste thresholds as objective parameters. (3) Comparison of Prakriti phenotypes across different ethnic, age and gender groups led to identification of invariant features as well as some that require weighted considerations across the cohorts. CONCLUSION Considering the molecular and genomics differences underlying Prakriti and relevance in disease pharmacogenomics studies, this novel integrative platform would help in identification of differently susceptible and drug responsive population. Additionally, integrated analysis of phenomic and genomic variations would not only allow identification of clinical and genomic markers of Prakriti for application in personalized medicine but also its integration in drug discovery and development programs.
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Affiliation(s)
- Bhavana Prasher
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Genomics and Molecular Medicine & CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative research, CSIR-IGIB, Delhi, India.
| | - Binuja Varma
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Arvind Kumar
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Bharat Krushna Khuntia
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Ankita Narang
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Pradeep Tiwari
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative research, CSIR-IGIB, Delhi, India
| | - Rintu Kutum
- G.N.Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative research, CSIR-IGIB, Delhi, India
| | - Debleena Guin
- Genomics and Molecular Medicine & CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Ritushree Kukreti
- Genomics and Molecular Medicine & CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India
| | - Debasis Dash
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; G.N.Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative research, CSIR-IGIB, Delhi, India
| | - Mitali Mukerji
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Genomics and Molecular Medicine & CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110020, India; Academy of Scientific & Innovative research, CSIR-IGIB, Delhi, India.
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Sagner M, McNeil A, Puska P, Auffray C, Price ND, Hood L, Lavie CJ, Han ZG, Chen Z, Brahmachari SK, McEwen BS, Soares MB, Balling R, Epel E, Arena R. The P4 Health Spectrum – A Predictive, Preventive, Personalized and Participatory Continuum for Promoting Healthspan. PROGRESS IN PREVENTIVE MEDICINE 2017. [DOI: 10.1097/pp9.0000000000000002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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DNA methylation-based variation between human populations. Mol Genet Genomics 2016; 292:5-35. [PMID: 27815639 DOI: 10.1007/s00438-016-1264-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022]
Abstract
Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.
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Sagner M, McNeil A, Puska P, Auffray C, Price ND, Hood L, Lavie CJ, Han ZG, Chen Z, Brahmachari SK, McEwen BS, Soares MB, Balling R, Epel E, Arena R. The P4 Health Spectrum - A Predictive, Preventive, Personalized and Participatory Continuum for Promoting Healthspan. Prog Cardiovasc Dis 2016; 59:506-521. [PMID: 27546358 DOI: 10.1016/j.pcad.2016.08.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/10/2016] [Indexed: 02/06/2023]
Abstract
Chronic diseases (i.e., noncommunicable diseases), mainly cardiovascular disease, cancer, respiratory diseases and type-2-diabetes, are now the leading cause of death, disability and diminished quality of life on the planet. Moreover, these diseases are also a major financial burden worldwide, significantly impacting the economy of many countries. Healthcare systems and medicine have progressively improved upon the ability to address infectious diseases and react to adverse health events through both surgical interventions and pharmacology; we have become efficient in delivering reactive care (i.e., initiating interventions once an individual is on the verge of or has actually suffered a negative health event). However, with slowly progressing and often 'silent' chronic diseases now being the main cause of illness, healthcare and medicine must evolve into a proactive system, moving away from a merely reactive approach to care. Minimal interactions among the specialists and limited information to the general practitioner and to the individual receiving care lead to a fragmented health approach, non-concerted prescriptions, a scattered follow-up and a suboptimal cost-effectiveness ratio. A new approach in medicine that is predictive, preventive, personalized and participatory, which we label here as "P4" holds great promise to reduce the burden of chronic diseases by harnessing technology and an increasingly better understanding of environment-biology interactions, evidence-based interventions and the underlying mechanisms of chronic diseases. In this concept paper, we propose a 'P4 Health Continuum' model as a framework to promote and facilitate multi-stakeholder collaboration with an orchestrated common language and an integrated care model to increase the healthspan.
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Affiliation(s)
- Michael Sagner
- College of Applied Health Sciences, University of Illinois at Chicago, Chicago, IL, USA; SARENA Clinic, Medical Center and Research Institute.
| | - Amy McNeil
- College of Applied Health Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Pekka Puska
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, Paris and Lyon, France
| | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
| | - Carl J Lavie
- Department of Cardiovascular Diseases, Ochsner Clinical School-the University of Queensland School of Medicine, New Orleans, LA, USA
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhu Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Samir Kumar Brahmachari
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Bruce S McEwen
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | | | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine (LCSB), Esch-sur-Alzette, Luxembourg
| | - Elissa Epel
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA
| | - Ross Arena
- College of Applied Health Sciences, University of Illinois at Chicago, Chicago, IL, USA; SARENA Clinic, Medical Center and Research Institute
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Jaiswal YS, Williams LL. A glimpse of Ayurveda - The forgotten history and principles of Indian traditional medicine. J Tradit Complement Med 2016; 7:50-53. [PMID: 28053888 PMCID: PMC5198827 DOI: 10.1016/j.jtcme.2016.02.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/19/2016] [Accepted: 02/01/2016] [Indexed: 12/13/2022] Open
Abstract
Ayurveda is considered as one of the oldest of the traditional systems of medicine (TSMs) accepted worldwide. The ancient wisdom in this traditional system of medicine is still not exhaustively explored. The junction of the rich knowledge from different traditional systems of medicine can lead to new avenues in herbal drug discovery process. The lack of the understanding of the differences and similarities between the theoretical doctrines of these systems is the major hurdle towards their convergence apart from the other impediments in the discovery of plant based medicines. This review aims to bring into limelight the age old history and the basic principles of Ayurveda. This would help the budding scholars, researchers and practitioners gain deeper perspicuity of traditional systems of medicine, facilitate strengthening of the commonalities and overcome the challenges towards their global acceptance and harmonization of such medicinal systems.
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Affiliation(s)
| | - Leonard L. Williams
- Corresponding author. Center for Excellence in Post-Harvest Technologies, North Carolina Agricultural and Technical State University, North Carolina Research Campus, 500 Laureate Way, Kannapolis, NC 28081, USA. Tel.: +1 704 250 5700x5703; fax: +1 704 250 5709.
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Abstract
The practice of Ayurveda, the traditional medicine of India, is based on the concept of three major constitutional types (Vata, Pitta and Kapha) defined as “Prakriti”. To the best of our knowledge, no study has convincingly correlated genomic variations with the classification of Prakriti. In the present study, we performed genome-wide SNP (single nucleotide polymorphism) analysis (Affymetrix, 6.0) of 262 well-classified male individuals (after screening 3416 subjects) belonging to three Prakritis. We found 52 SNPs (p ≤ 1 × 10−5) were significantly different between Prakritis, without any confounding effect of stratification, after 106 permutations. Principal component analysis (PCA) of these SNPs classified 262 individuals into their respective groups (Vata, Pitta and Kapha) irrespective of their ancestry, which represent its power in categorization. We further validated our finding with 297 Indian population samples with known ancestry. Subsequently, we found that PGM1 correlates with phenotype of Pitta as described in the ancient text of Caraka Samhita, suggesting that the phenotypic classification of India’s traditional medicine has a genetic basis; and its Prakriti-based practice in vogue for many centuries resonates with personalized medicine.
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