Deep sequencing reveals recurrent somatic mutations and distinct molecular subgroups in gastric cancer in Mizo population, North East India.

In India, Mizoram has the highest incidence of gastric cancer (GC) which might be associated with environmental factors such as diet, Helicobacter pylori (H.pylori) and Epstein-Barr virus (EBV) infections, and somatic genomic alterations. We performed PCR cum sequencing and fragment analysis for detection of H. pylori/EBV infection and microsatellite Instability (MSI) in GC patients (N = 68). Somatic mutations were identified by targeted and exome sequencing. We found 87% of GC patients infected with H. pylori and or EBV. Pathogenic infections were mostly mutually exclusive with only 16% of coinfection. TP53, MUC6, and ARID1A were significantly mutated. Two molecular subgroups with distinctive mutational profiles were identified: (1) patients harboring mutations in TP53 and (2) patients harboring mutations in RTK/RAS/PI3-K signaling pathway and chromatin-remodeling genes. Therefore, EBV and H. pylori infections and somatic mutations in the genes involved in RTK/RAS/PI3K signaling pathway, chromatin-remodeling, and TP53 might drive GC development and progression in Mizo patients.

Transcriptome analysis reveals SALL4 as a prognostic key gene in gastric adenocarcinoma.

BACKGROUND: Stomach adenocarcinoma (STAD) dominates 80-90% of gastric cancer (GC). Over the years, it has been realized that the identification of the genes responsible for gastric carcinogenesis is essential to understand the biomarker discovery. METHODS: This study aims to identify candidate genes for biomarker discovery in STAD. RNA-Seq was performed on three paired tumor-normal and one unpaired tumor samples from four GC patients and investigated for differentially expressed genes (DEGs) using DESeq2. Gene set enrichment analysis were performed. The DEGs were compared with two STAD microarray datasets available on Gene Expression Omnibus (GEO) database. Survival study (OS) were performed using KM-Plotter on the common genes between all the datasets. RESULTS: Totally, 148 DEGs were identified, wherein 55 genes were upregulated and 93 genes were downregulated with |log2foldchange| > 1 and Benjamini-Hochberg (BH) Adjusted P value < 0.01. Cell adhesion molecule (CAM) Pathway was found to be the most significant among the upregulated genes. Gastric acid secretion and mineral absorption pathways were the most significant pathways among the downregulated genes. Comparison with two GEO datasets followed by OS analysis revealed two upregulating genes, APOC1 and SALL4 with prognostic significance. CONCLUSION: Upregulation of APOC1 is associated with marginal overall survival (OS) and SALL4 over-expression was associated with the poor OS using KM-Plotter during 5 years data period. Our study suggests that SALL4 could be a promising biomarker candidate in STAD.

Fermented pork fat (Sa-um) and lifestyle risk factors as potential indicators for type 2 diabetes among the Mizo population, Northeast India.

Over the last few decades, Mizoram has shown an increase in cases of type 2 diabetes mellitus; however, no in-depth scientific records are available to understand the occurrence of the disease. In this study, 500 patients and 500 healthy controls were recruited to understand the possible influence of their dietary and lifestyle habits in relation with type 2 diabetes mellitus. A multivariate analysis using Cox regression was carried out to find the influence of dietary and lifestyle factors, and an unpaired t test was performed to find the difference in the levels of biochemical tests. Out of 500 diabetic patients, 261 (52.3%) were males and 239 (47.7%) were females, and among the control group, 238 (47.7%) were males and 262 (52.3%) were females. Fermented pork fat, Sa-um (odds ratio (OR) 18.98), was observed to be a potential risk factor along with tuibur (OR 0.1243) for both males and females. Creatinine level was found to be differentially regulated between the male and female diabetic patients. This is the first report of fermented pork fat and tobacco (in a water form) to be the risk factors for diabetes. The unique traditional foods like Sa-um and local lifestyle habits like tuibur of the Mizo population may trigger the risk for the prevalence of the disease, and this may serve as a model to study other populations with similar traditional practices.

Panel of significant risk factors predicts early stage gastric cancer and indication of poor prognostic association with pathogens and microsatellite stability.

BACKGROUND: There are very few studies covering the epidemiological risk factors associated with Epstein Barr Virus (EBV) and Microsatellite stability for Gastric Cancer (GC) cases. Early diagnosis of GC through epidemiological risk factors is very necessary for the clinical assessment of GC. The aim of this study was to find out the major risk factors to predict GC in early stage and the impact of pathogen infection and MSI on survival rate of patients. GC samples were screened for Helicobacter pylori, Epstein Barr Virus, and Mismatch repair (MMR) gene status (microsatellite stable or instable). Chi-square and logistic regression analysis of Odd ratio and 95% confidence interval (OR, 95% CI) were performed to find out the association between epidemiological factors and the risk of gastric cancer. The pathogen and MMR gene status were analysed to predict their effect on overall survival and the risk score and hazard ratio was calculated for prognostic assessment. RESULTS: Excess body weight, consumption of extra salt, smoked food, alcohol, and smoking were the major risk factors for GC development. This study achieved a high area under the curve (AUC 0.94) for the probable GC patients in early-stage using the five-panel epidemiological risk factors. H. pylori infected cases were significant with smoked food, while EBV was found to be associated with tuibur intake and smoked food. In overall survival analysis EBV infected and microsatellite stable (HR: 1.32 and 1.34 respectively) GC cases were showing poor prognosis. CONCLUSION: This study might provide new opportunities for personalized treatment options using this epidemiological factor risk score and clinicopathological factors assessment for early detection and prognosis in high-risk GC populations.

Whole exome sequencing identifies the novel putative gene variants related with type 2 diabetes in Mizo population, northeast India.

The contribution of genes towards T2D development varies among different population groups across the world. It has been reported that a number of loci involved in T2D susceptibility are common across certain population groups, but ethnicity specific variants are also observed. The population of Mizoram has an independent ethnic identity and there are no scientific records about the history of the Mizo people; which makes this ethnic group unique and interesting to study. The aim of the study focuses on the identification of the gene variants which may contribute to T2D susceptibility in Mizo-Mongloid ethnic tribe of North east India through whole exome sequencing. The variants like 328G > C (KRT18), 997G > T (CYP4A11), 2368 T > C (SLC4A3), 508G > A (SLC26A5), 1659C > T (KCNS1), 650C > A (ABCD1) 821A > T (YTHDC2), 931G > T (PINX1), 3280C > A (TNRC6A), 48C > A(TACO1), 6035A > T(LAMA1), 805C > A(ACP7) and 806A > G(ACP7) variants were not reported for any disease in the database and were found to be pathogenic in different insilico analysis softwares. The changes in protein stability upon mutation has been predicted where 35.71% increases the stability of the protein, while 64.28% of the variants decrease the stability of the protein. These findings present the population specific variants which might involve in the susceptibility to T2D in Mizo population. Further, in this study some gene variants have contribution as a possible diagnostic or prognostic marker for other diseases as well, which suggests the need for performing association analysis for different disease manifestations in Mizo population in the near future.

Association of tobacco smoke-infused water (tuibur) use by Mizo people and risk of Helicobacter pylori infection.

The study aims to understand the influence of environmental and lifestyle factors and more specifically the role of tobacco smoke-infused water (tuibur) on Helicobacter pylori infection. It was a cross-sectional study to measure the epidemiological risk factors associated with H. pylori infection among the tribal population in Northeast India. Endoscopic samples were collected from the antrum region of the stomach from 863 participants with gastritis. H. pylori infection was confirmed in 475 samples by the rapid urease test and PCR-based methods. Information on demographic and lifestyle factors was collected using a validated and standardized questionnaire. Logistic regression was used to estimate odds ratio (OR) and 95% confidence interval (CI) for the association between the various factors and H. pylori. The use of tuibur was associated with an increased OR of H. pylori infection (OR = 3.32, 95% Cl = 1.95-5.83). Tobacco chewers (OR = 1.49, 95% Cl = 1.06-2.09), smokers (OR = 1.81, 95% Cl = 1.26-2.61), and alcohol consumers (OR = 1.81, 95% Cl = 1.19-2.76) were also infected with H. pylori. The results were not attenuated after adjusting for major well-known risk factors of H. pylori infection. The habit of tuibur consumption may be a contributing factor to the high prevalence of H. pylori infection and in turn, may contribute to the high prevalence of gastritis among the Mizo population.

Genomic profiling of mitochondrial DNA reveals novel complex gene mutations in familial type 2 diabetes mellitus individuals from Mizo ethnic population, Northeast India.

The variants reported for mitochondrial DNA (mtDNA) and type 2 diabetes (T2D) may not be accountable for the disease in certain other populations and the risk depends upon numerous factors which may include genetics, environment as well as ethnicity. This leads to a challenge in identifying, exploring and comparing the variants between diabetic cases and healthy controls in a remote unexplored tribal population. To study the possible contribution of mtDNA variants, we sequenced the entire mitochondrial genomes and the frequencies of mtSNPs, their association with familial T2D and the potential impact of non-synonymous substitutions on protein functions were determined. The mtSNP 8584 G > A (ATP6: A20T) was detected in 14.28% of the diabetic patients and none in the control groups. The mitochondrial ND3 variant 10398A > G was found to be significantly associated with the risk of T2D (OR = 9.489, 95% CI = 1.161-77.54, P value = 0.036). A novel Frame-shift substitution ND5: 81_81ins A at position 12,417 was observed in 53.57% of diabetic individuals. Majority of the variants lie in tRNA-Phe in the non-protein coding region of mtDNA for both diabetic cases and common cases. We concluded that mutations in the coding (synonymous or non-synonymous) and noncoding regions of the mitochondria might have contribution towards the development of T2D. Our study is the first to report the distinct mitochondrial variants which may be attributed to the susceptibility as well as development of type 2 diabetes in an ethnic tribe from northeast India.

Novel AKT1 mutations associated with cell-cycle abnormalities in gastric carcinoma.

AIM: The aim of this study is to identify the AKT1 gene mutation driven pathogenicity in gastric cancer for Mizo population. METHODS: 50 diffuse-type gastric tumors were analyzed for AKT1 exon 2 and 14 mutations. Cell-cycle aberration was analyzed in the AKT1-mutated samples and the stability of the protein as well as exonic splicing enhancer motifs were examined. RESULTS: The novel mutations, 15553T >A and 25376C >G might affect the exonic splicing enhancers and silencers. Significant decline was observed in the S-phase population in the tumor cells with 15553T >A and 15579G >C mutations suggesting the arrest of G1 phase. CONCLUSION: The present study is a novel finding of the possible role of AKT1 mutations which might help to identify gastric cancer patients.

Mitochondrial complex I and V gene polymorphisms in type II diabetes mellitus among high risk Mizo-Mongoloid population, Northeast India.

INTRODUCTION: The study was carried out to identify the polymorphisms in mitochondrial genes (ATPase and ND1) in type 2 Diabetes Mellitus (T2DM) from Mizo population and to correlate the involvement of demographic factors. FINDINGS: In the present study, 58 patients and 50 healthy volunteers were considered. The mutations observed were mostly base substitutions and were similar as reported for other populations. Three mutations are unreported and were found to be novel polymorphisms for diabetic disease. One heteroplasmic variation (MT3970 C > T) was found in 36.36 % of samples. Subjects with excessive smoked meat consumption and customary habit of smoking (ORs: 4.92; 95 % CI: 0.96-25.21) were found to be more prone to T2DM. Mitochondrial genes sequence analysis revealed the genetic variability between the healthy and diabetic samples. CONCLUSION: Mitochondrial ATPase and ND1 gene polymorphisms may be involved in triggering the risk for T2DM.

Xenobiotic Pathway Gene Polymorphisms Associated with Gastric Cancer in High Risk Mizo-Mongoloid Population, Northeast India.

BACKGROUND: The aim of this study was to evaluate the risk of gastric cancer associated with individual or combined glutathione S-transferases (GSTs) polymorphism and their interaction with environmental factors. MATERIALS AND METHODS: Genotyping by PCR was carried out for 80 cases and controls each for GSTM1, GSTT1, and GSTP1 polymorphism and mapped for gene-environment association studies. The samples were subjected to pathogen detection and GSTP1 expression for analyzing their association with different genotypes. Logistic regression analyses were conducted to compute the influence of both genetic and environmental factors for gastric cancer. MDR analysis was performed to assess the risk of gastric cancer by studying the gene-gene and gene-environment effect on the basis of GST genotyping and GSTP1 gene expression. RESULTS: Infection with Helicobacter pylori and CagA+ strains was more frequent in patients with GSTM1/T1 null genotype. Intake of high fermented fat and smoked meat was found to be significantly associated with gastric cancer. The G/G, A/G (rs1695), and T/T (rs1138272) were found to be significantly associated with low expression of GSTP1 gene in cancer tissue. CONCLUSION: Presence of H. pylori with CagA genotype showed significant individual effect with GSTT1 polymorphism as well as strong synergistic effect in gastric cancer risk. Majority of the gastric cancer samples showed significant negative expression in G/G, A/G (rs1695), and T/T (rs1138272) genotypes. This study shows that GST gene polymorphism was significantly relevant for determining the individual susceptibility to gastric cancer.

Mitochondrial complex I and V gene polymorphisms associated with breast cancer in mizo-mongloid population.

BACKGROUND: Mizoram has the highest incidence of cancer in India. Among women, breast cancer is most prevalent and the state occupies fifth position globally. The reason for high rate of cancer in this region is still not known but it may be related to ethnic/racial variations or lifestyle factors. METHODS: The present study aims to identify the candidate mitochondrial DNA (mtDNA) biomarkers-ND1and ATPase for early breast cancer diagnosis in Mizo population. Genomic DNA was extracted from blood samples of 30 unrelated breast cancer and ten healthy women. The mtNDI and mtATP coding regions were amplified by step-down PCR and were subjected to restriction enzyme digestion and direct sequencing by Sanger method. Subsequently, the results of the DNA sequence analysis were compared with that of the revised Cambridge Reference Sequence (rCRS) using Mutation Surveyor and MITOMAP. RESULTS: Most of the mutations were reported and new mutations that are not reported in relationship with breast cancer were also found. The mutations are mostly base substitutions. The effect of non-synonymous substitutions on the amino acid sequence was determined using the PolyPhen-2 software. Statistical analysis was performed for both cases and controls. Odds ratios (ORs) and 95 % confidence intervals (CIs) were estimated from logistic regression. High intake of animal fat and age at menarche was found to be associated with a higher risk of breast cancer in Mizo population. CONCLUSION: Our results also showed that ATPase6 as compared to ATPase8 gene is far more predisposed to variations in Mizo population with breast cancer and this finding may play an important role in breast cancer prognosis.