Sanish Sathyan

DNA Methyl Transferase (DNMT) Gene Polymorphisms Could Be a Primary Event in Epigenetic Susceptibility to Schizophrenia

DNA methylation has been implicated in the etiopathology of various complex disorders. DNA methyltransferases are involved in maintaining and establishing new methylation patterns. The aim of the present study was to investigate the inherent genetic variations within DNA methyltransferase genes in predisposing to susceptibility to schizophrenia. We screened for polymorphisms in DNA methyltransferases, DNMT1, DNMT3A, DNMT3B and DNMT3L in 330 schizophrenia patients and 302 healthy controls for association with Schizophrenia in south Indian population. These polymorphisms were also tested for subgroup analysis with patients gender, age of onset and family history. DNMT1 rs2114724 (genotype P = .004, allele P = 0.022) and rs2228611 (genotype P = 0.004, allele P = 0.022) were found to be significantly associated at genotypic and allelic level with Schizophrenia in South Indian population. DNMT3B rs2424932 genotype (P = 0.023) and allele (P = 0.0063) increased the risk of developing schizophrenia in males but not in females. DNMT3B rs1569686 (genotype P = 0.027, allele P = 0.033) was found to be associated with early onset of schizophrenia and also with family history and early onset (genotype P = 0.009). DNMT3L rs2070565 (genotype P = 0.007, allele P = 0.0026) confers an increased risk of developing schizophrenia at an early age in individuals with family history. In-silico prediction indicated functional relevance of these SNPs in regulating the gene. These observations might be crucial in addressing and understanding the genetic control of methylation level differences from ethnic viewpoint. Functional significance of genotype variations within the DNMTs indeed suggest that the genetic nature of methyltransferases should be considered while addressing epigenetic events mediated by methylation in Schizophrenia.

Major vault protein (MVP) gene polymorphisms and drug resistance in mesial temporal lobe epilepsy with hippocampal sclerosis.

The human major vault protein (MVP) has been implicated in the development of drug resistance in cancer cells. Over expression of MVP has also been reported in brain tissue samples from antiepileptic drug (AED)-resistant human focal epilepsies. To investigate the relationship between single nucleotide polymorphisms (SNPs) involving the MVP gene and AED-resistance, we compared the distribution of three SNPs in the MVP gene, rs4788187, rs3815824 and rs3815823, among 220 patients with mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS) (prototype of AED-resistant epilepsy syndrome), 201 patients with juvenile myoclonic epilepsy (JME) (prototype of AED-responsive epilepsy syndrome) and 213 ethnically matched non-epilepsy controls. All the patients and controls were residents of the South Indian state of Kerala for more than three generations. We did not find any significant difference in allele and genotypic frequencies of the studied SNPs between AED-resistant and AED-responsive cohorts, and between AED-resistant and AED-responsive cohorts independently and pooled together when compared with the controls. We conclude that rs4788187, rs3815824, rs3815823 variants of the MVP gene are associated neither with predisposition for epilepsy nor with AED-resistance in the population that we have studied. Our results suggest the need for further research into the link between MVP and AED-resistance.

Pathogenesis of intracranial aneurysm is mediated by proinflammatory cytokine TNFA and IFNG and through stochastic regulation of IL10 and TGFB1 by comorbid factors

BackgroundIntracranial aneurysm (IA) is often asymptomatic until the time of rupture resulting in subarachnoid hemorrhage (SAH).There is no precise biochemical or phenotype marker for diagnosis of aneurysm. Environmental risk factors that associate with IA can result in modifying the effect of inherited genetic factors and thereby increase the susceptibility to SAH. In addition subsequent to aneurismal rupture, the nature and quantum of inflammatory response might be critical for repair. Therefore, genetic liability to inflammatory response caused by polymorphisms in cytokine genes might be the common denominator for gene and environment in the development of aneurysm and complications associated with rupture.MethodsFunctionally relevant polymorphisms in the pro- and anti-inflammatory cytokine genes IL-1 complex (IL1A, IL1B, and IL1RN), TNFA, IFNG, IL3, IL6, IL12B, IL1RN, TGFB1, IL4, and IL10] were screened in radiologically confirmed 220 IA patients and 250 controls from genetically stratified Malayalam-speaking Dravidian ethnic population of south India. Subgroup analyses with genetic and environmental variables were also carried out.ResultsPro-inflammatory cytokines TNFA rs361525, IFNG rs2069718, and anti-inflammatory cytokine IL10 rs1800871 and rs1800872 were found to be significantly associated with IA, independent of epidemiological factors. TGFB1 rs1800469 polymorphism was observed to be associated with IA through co-modifying factors such as hypertension and gender. Functional prediction of all the associated SNPs of TNFA, IL10, and TGFB1 indicates their potential role in transcriptional regulation. Meta-analysis further reiterates that IL1 gene cluster and IL6 were not associated with IA.ConclusionsThe study suggests that chronic exposure to inflammatory response mediated by genetic variants in pro-inflammatory cytokines TNFA and IFNG could be a primary event, while stochastic regulation of IL10 and TGFB1 response mediated by comorbid factors such as hypertension may augment the pathogenesis of IA through vascular matrix degradation. The implication and interaction of these genetic variants under a specific environmental background will help us identify the resultant phenotypic variation in the pathogenesis of intracranial aneurysm. Identifying genetic risk factors for inflammation might also help in understanding and addressing the posttraumatic complications following the aneurismal rupture.

Genetic association analysis of ATP binding cassette protein family reveals a novel association of ABCB1 genetic variants with epilepsy risk, but not with drug-resistance.

Epilepsy constitutes a heterogeneous group of disorders that is characterized by recurrent unprovoked seizures due to widely different etiologies. Multidrug resistance remains a major issue in clinical epileptology, where one third of patients with epilepsy continue to have seizures. Role of efflux transporters in multidrug resistant epilepsy has been attributed to drug-resistant epilepsy although, with discrepant observation in genetic studies. These discrepancies could be attributed to variety of factors such as variable definition of the anti-epileptic drug (AED)-resistance, variable epilepsy phenotypes and ethnicities among the studies. In the present study we inquired the role of multidrug transporters ABCB1 and ABCG2 variants in determining AED-resistance and susceptibility to epilepsy in three well-characterized cohorts comprising of mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS) (prototype for AED-resistant epilepsy); juvenile myoclonic epilepsy (JME) (prototype for AED-responsive epilepsy); and healthy non-epileptic controls, in 738 subjects of Malayalam speaking south Indian ancestry. ABCB1 and ABCG2 variants were not found to be associated with drug resistance when AED-resistant and AED-responsive cohorts were compared. However, a significant association was observed between ABCB1 (C3435T) rs1045642 and risk of having epilepsy (MTLE-HS and JME pooled cohort; genotypic p-value = 0.0002; allelic p-value = 0.004). This association was seen persistent with MTLE-HS (genotypic p-value = 0.0008; allelic p-value = 0.004) and also with JME (genotypic p-value = 0.01; allelic p-value = 0.05) cohort individually. In-silico functional prediction indicated that ABCB1 rs1045642 has a deleterious impact on protein coding function and in splicing regulation. We conclude that the ABCB1 and ABCG2 variants do not confer to AED-resistance in the study population. However, ABCB1 rs1045642 increases vulnerability to epilepsy with greater tendency for MTLE-HS in south Indian ancestry from Kerala.

Association of Cytokine Gene Polymorphisms with Oral Lichen Planus in Malayalam-Speaking Ethnicity from South India (Kerala)

Oral lichen planus (OLP) is a chronic mucocutaneous condition that affects the oral mucous membrane as well as skin. It is a chronic cell-mediated autoimmune condition where the T-cell-mediated immune response plays an important part in the pathogenesis by causing damage to basal keratinocytes in oral mucosa. Cytokine gene polymorphisms have an unquestionable role in the orchestration of the immune response, leading to different functional scenarios, which in turn influence the outcome of the disease establishment and evolution. The purpose of this study was to understand the role of these cytokine gene polymorphisms in the tumor necrosis factor-alpha (TNF-α), interleukin-1β (IL-1β), and IL-6 genes with OLP in 101 individuals of Malayalam-speaking ethnicity from South India (Kerala). We further investigated the role of these polymorphisms in patients suffering from OLP with other comorbid factors. Genotyping was carried out by polymerase chain reaction-restriction fragment length polymorphism. The results demonstrate that the A allele in the TNF-α -308 polymorphism could play an important role in the susceptibility to OLP. IL-1β +3954 in OLP was associated with other comorbid factors in both allelic and genotypic combinations. However, when patients suffering from OLP were stratified to understand the involvement of other comorbid factors, we observed that the T and C alleles were independent risk factors for chronic periodontitits and diabetes mellitus. On the other hand, IL-6 -597 did not show any disease association with OLP in the study population. This study indicates that proinflammatory cytokines are an important factor in understanding the disease burden of OLP and their comorbid factors.

Microsatellite instability in D2S123 flanking the hMSH2 gene in oral squamous cell carcinoma in South India

Background: Oral cancer is the third most common cancer in India. It is a multifactorial disease. Cells with defective mismatch repair gene hMSH2 can result in genomic instability in oral squamous cell carcinoma (OSCC) tumors. The objective of this study was to investigate the incidence of microsatellite instability (MSI) flanking the hMSH2 in OSCC tumors and relate the MSI status with the mutation profile of hMSH2 in Malayalam speaking population from Kerala. Materials and Methods: Patients diagnosed with OSCC, without superimposed premalignant and other malignant conditions, were recruited for the study based on strict selection criteria. 37 subjects from Malayalam speaking ethnic background of Kerala in India were selected. Blood and carcinoma tissues from were obtained from each patient diagnosed with OSCC. Big adenine tract 26 (BAT26) and D2S123 microsatellite flanking the hMSH2 gene were assessed for their peak patterns in each patient′s blood and tissue DNA to analyze MSI and loss of heterozygosity (LOH). Results: No MSI was observed in any of the patient at BAT26 loci. Though BAT26 is reported to be quasi monomorphic, but interestingly it was found to be polymorphic in one patient. In D2S123 loci microsatellite alterations (MA) were observed in 50% of the OSCC patients, which comprised of both LOH and MSI. MA was observed to be significantly increased in moderately differentiated OSCC tumors. These MSI and LOH were independent of clinicopathological characteristics and mutation profile of hMSH2. Conclusion: Higher incidence of MSI at D2S123 in OSCC tumors could be indicative of diagnostic significance. However, this needs to be validated further in increased sample size and across different ethnic population.

Polymorphic variants of mismatch repair gene human MutS homologue-2 influence oral squamous cell carcinoma in a South Indian population

Background: Oral cancer is the third most common cancer in India. It is a multifactorial disease. Cells with defective mismatch repair (MMR) mechanisms cannot correct genetic errors that occur during cellular replication, resulting in a reduction in the fidelity of DNA repair. The objective of this study is to investigate the role of polymorphic variants in MMR gene human MutS homolog-2 (hMSH2) in oral squamous cell carcinoma (OSCC) and associated clinicopathological features in Malayalam speaking population from Kerala. Materials and Methods: Patients diagnosed with OSCC, without superimposed premalignant and other malignant conditions were selected for polymorphism screening of hMSH2 gene. Two single nucleotide polymorphisms (SNPs), rs2303428 (hMSH2-6C/T) located at −6 of the 3′ splice acceptor site of exon 13 and rs61756463 (hMSH2 471C/A) located in exon 3 of hMSH2 were selected based on their functional relevance. Results: Polymorphism screening of hMSH2 gene suggests that rs2303428 was associated with both allelic and genotypic combinations with OSCC. In allelic level, the T allele was associated (P = 0.009) with OR of 2.86, whereas in genotypic level the TT genotype was found to be significantly associated (P = 0.012). In silico prediction of functional implication of this SNP indicated altered transcriptional regulation with functional significance score of 0.176. Although assessing the intergroup comparison within OSCC patients for age (≤50 and >50), gender and histo-differentiation grading, we could not find any association with any of these variables. Conclusion: Certain polymorphic variants in the MMR gene hMSH2 can result in OSCC in Malayalam speaking south Indian population and could indicate defective repair mechanism or Microsatellite instability. Distribution of rs2303428 allele had clear ethnic distribution across world population.