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Abstract
Coronary artery disease (CAD) has emerged as a major cause of morbidity and mortality worldwide. Recent findings on the role of genetic factors in the aetiopathology of CAD have implicated novel genes and variants in addition to those involved in lipid and lipoprotein metabolism. However, our present knowledge is limited due to lack of clarity on their exact identity and the quantum of impact on disease susceptibility, and incident risk. It is a matter of great interest to understand the role of genetic factors in ethnic populations that have a strong underlying predisposition to CAD such as the South Asian populations, particularly among Asian Indians living in India and abroad. Although, a number of isolated studies do implicate certain gene polymorphisms towards enhanced disease susceptibility, the available data remains scanty and inconclusive as they have not been validated in large, prospective cohorts. The present review aims to consolidate the available literature on the genetics of CAD in Asian Indians and seeks to provide insights on the concerns that need to be addressed in future studies to generate information having clinical value.
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Chattopadhyay E, De Sarkar N, Singh R, Ray A, Roy R, Paul RR, Pal M, Ghose S, Ghosh S, Kabiraj D, Banerjee R, Roy B. Genome-wide mitochondrial DNA sequence variations and lower expression of OXPHOS genes predict mitochondrial dysfunction in oral cancer tissue. Tumour Biol 2016; 37:11861-11871. [PMID: 27055661 DOI: 10.1007/s13277-016-5026-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/18/2016] [Indexed: 12/17/2022] Open
Abstract
Several studies reported that mtDNA mutations may play important roles in carcinogenesis although the mechanism is not clear yet. Most of the studies compared mtDNA sequences in a tumor with those in normal tissues from different individuals ignoring inter-individual variations. In this study, 271 SNPs, 7 novel SNPs (or SNVs), and 15 somatic mutations were detected in mtDNA of 8 oral cancer tissues with respect to reference (rCRS) and adjacent normal tissues, respectively, using Ion PGM next generation sequencing method. Most of the sequence variations (76 SNPs and 1 somatic) are present in D-loop region followed by CyB (36 SNPs), ATP6 (24 SNPs), ND5 (17 SNPs and 5 somatic), ND4 (18 coding and 2 somatic) and other non-coding and coding DNA sequences. A total of 53 and 8 non-synonymous SNPs and somatic mutations, respectively, were detected in tumor tissues and some of these variations may have deleterious effects on the protein function as predicted by bioinformatic analysis. Moreover, significantly low mtDNA contents and expression of several mitochondrial genes in tumor compared to adjacent normal tissues may have also affected mitochondrial functions. Taken together, this study suggests that mtDNA mutations as well as low expression of mtDNA coded genes may play important roles in tumor growth. Although the sample size is low, an important aspect of the study is the use of adjacent control tissues to find out somatic mutations and a change in the expression of mitochondrial genes, to rule out inter-individual and inter-tissue variations which are important issues in the study of mitochondrial genomics.
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Affiliation(s)
- Esita Chattopadhyay
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Navonil De Sarkar
- Fred Hutchinson Cancer Research center, University of Washington, Seattle, WA, USA
| | - Richa Singh
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Anindita Ray
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Roshni Roy
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Ranjan Rashmi Paul
- Department of Oral Pathology, Guru Nanak Institute of Dental Science & Research, 157/F Nilganj Road, Kolkata, 700114, India
| | - Mousumi Pal
- Department of Oral Pathology, Guru Nanak Institute of Dental Science & Research, 157/F Nilganj Road, Kolkata, 700114, India
| | - Sandip Ghose
- Department of Oral Pathology, Dr. R Ahmed Dental College and Hospital, 114- AJC Bose Road, Kolkata, 700014, India
| | - Subhrendu Ghosh
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (formerly known as WBUT), BF-142, Sector 1, Salt Lake City, Kolkata, 700064, India
| | - Debajyoti Kabiraj
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (formerly known as WBUT), BF-142, Sector 1, Salt Lake City, Kolkata, 700064, India
| | - Raja Banerjee
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (formerly known as WBUT), BF-142, Sector 1, Salt Lake City, Kolkata, 700064, India
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology West Bengal (formerly known as WBUT), BF-142, Sector 1, Salt Lake City, Kolkata, 700064, India
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India.
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The challenges for molecular nutrition research 1: linking genotype to healthy nutrition. GENES AND NUTRITION 2011; 3:41-9. [PMID: 18850186 DOI: 10.1007/s12263-008-0086-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nutrition science finds itself at a major crossroad. On the one hand we can continue the current path, which has resulted in some substantial advances, but also many conflicting messages which impair the trust of the general population, especially those who are motivated to improve their health through diet. The other road is uncharted and is being built over the many exciting new developments in life sciences. This new era of nutrition recognizes the complex relation between the health of the individual, its genome, and the life-long dietary exposure, and has lead to the realisation that nutrition is essentially a gene-environment interaction science. This review on the relation between genotype, diet and health is the first of a series dealing with the major challenges in molecular nutrition, analyzing the foundations of nutrition research. With the unravelling of the human genome and the linking of its variability to a multitude of phenotypes from "healthy" to an enormously complex range of predispositions, the dietary modulation of these propensities has become an area of active research. Classical genetic approaches applied so far in medical genetics have steered away from incorporating dietary effects in their models and paradoxically, most genetic studies analyzing diet-associated phenotypes and diseases simply ignore diet. Yet, a modest but increasing number of studies are accounting for diet as a modulator of genetic associations. These range from observational cohorts to intervention studies with prospectively selected genotypes. New statistical and bioinformatics approaches are becoming available to aid in design and evaluation of these studies. This review discusses the various approaches used and provides concrete recommendations for future research.
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Abstract
The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time.
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