HCMV detection in Asian gastric cancer RNA-seq data sets and clinical validation in Indian GC patients reveals the HCMV-GC specific gene signatures.

Gastric cancer (GC) prevalence is very high in the Asian population. Oncogenic viruses play a crucial role in the progression of different types of cancers. Through reanalysis of clinical RNA-seq data sets derived from Asian GC patients, this study identified the presence of human cytomegalovirus (HCMV) in Asian GC tumors, next to the well-studied association of EBV. Clinical recruitment of the Indian GC cohort and screening for HCMV presence identified a 14.28% occurrence, similar to that observed in the bioinformatics analysis. A combinatorial approach of rank-based meta-analysis and ranking of groups based on an expectation-maximization algorithm identified that the upregulated LINC02864 and MAGEA10 correlated with poor survival of GC patients and downregulated tumor suppressor genes enriching for gastric acid secretion pathway to be associated with HCMV-positive GC patients, revealing the progressive role of HCMV infection in GC. Genes that discriminate between different stages of GC were identified through feature selection implemented in a machine-learning approach. LTF and KLK10 expressions were found to be specifically dysregulated by HCMV and can also indicate the GC stages. The results of this study will guide future studies to identify the functional role of these genes in the HCMV-associated GC.IMPORTANCENearly 75% of gastric cancer (GC) cases reported globally are from the Asian population. Most existing public databases, such as TCGA, comprise only a fractional portion of data derived from Asian ancestry. This study identified EBV and human cytomegalovirus (HCMV)'s higher detection in GC patients. The presence and role of EBV associated with GC are well-known, and the observation of HCMV prompted us to validate the findings in a small cohort of 40 Indian GC patients. We observed a 14.28% occurrence of HCMV in the Indian cohort, similar to that observed from next-generation sequencing. A combinatorial approach of rank-based meta-analysis and ranking of groups based on an expectation-maximization algorithm identified that the upregulated LINC02864 and MAGEA10 correlated with poor survival of GC patients and downregulated tumor suppressor genes enriching for gastric acid secretion pathway to be associated with HCMV-positive GC patients, revealing the progressive role of HCMV infection in GC.

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.

Cancer awareness, diagnosis and treatment needs in Mizoram, India: evidence from 18 years trends (2003-2020).

Background: Despite being the second least populated state, Mizoram exhibits the highest incidence rate of cancer in India. Its inhabitants, constituting an endogamous and isolated population, have embraced their own distinct culture, way of life and dietary preferences, setting them apart from the rest of mainland India. In 2003, the Mizoram Population Based Cancer Registry (PBCR) was established under the auspices of the National Centre for Disease Informatics and Research (NCDIR), a division of the Indian Council of Medical Research (ICMR), in collaboration with the Department of Health & Family Welfare of the Government of Mizoram, India. Methods: Cancer incidence and mortality data were extracted from the Mizoram PBCR spanning the years 2003-2020. The Age Standardized Incidence Rate (ASIR) and Age Standardized Mortality Rate (ASMR) were computed per 100,000 individuals, utilizing Segi's World Standard Population as the benchmark. The trajectory of these changes was analysed employing the Joinpoint Regression Analysis Program, Version 4.9.1.0.13, to unveil the Annual Percent Change (APC) with a 95% Confidence Interval and a Significance test (p < 0.05) using Monte Carlo Permutation. The resulting graphical visualizations were generated using Flourish Studio.15. Findings: The overall ASIR for all cancer sites among men was 197.2 per 100,000, while for women, it was 164.9 per 100,000. Among men, the most prevalent cancer site was the Stomach (ASIR = 41.4), followed by Head & Neck, Lung, Oesophagus, Colorectal, Liver, Urinary, Non-Hodgkin's Lymphoma and Prostate cancers. Conversely, among women, Lung cancer exhibited the highest incidence (ASIR = 26.7), succeeded by Cervical, Breast, Stomach, Head & Neck, Colorectal, Oesophagus, Liver and Ovarian cancers. Stomach cancer emerged as the leading cause of death among men (ASMR = 22.6) and among women, Lung cancer held the highest ASMR (15.9). Joinpoint regression analysis revealed a rising trend in incidence and mortality over time for overall cancer sites. Among the primary cancer sites contributing to incidence and mortality, an increase in APC was observable for all, except Stomach cancer, in both men and women. The diagnostic approach, except for cases of cancer with unknown primary sites, involved a microscopic method. Interpretation: This cross-sectional study examines PBCR reports spanning from 2003 to 2020, shedding light on a consistent uptick in cancer incidence and mortality trends in Mizoram. Stomach cancer emerges as the most prevalent and primary cause of cancer-related deaths among men, while Lung cancer takes a parallel role in women. The elevated cancer incidence and the growing trend among younger generations might stem from the static lifestyle and dietary patterns prevalent within the endogamous tribal population, potentially contributing to a genetic predisposition. The escalation in mortality rates could be attributed to a dearth of specialized diagnostic facilities and skilled human resources, treatment strategies guided by genomic research and transportation challenges. This underscores the urgent requirement for comprehensive scientific exploration across diverse facets. The implementation of easily accessible diagnostic facilities in proximity and genetic testing for pharmacogenomics to enhance prognoses would also aid in mitigating the burden and advancing the healthcare system's effectiveness. Funding: Population Based Cancer Registry (PBCR) was supported by National Centre for Disease Informatics and Research (NCDIR) of the Indian Council of Medical Research (ICMR), India.

An assessment of childhood cancer care services in India - gaps, challenges and the way forward.

Background: Childhood cancers are emerging as an essential concern in India where there is lack of a specific programme component or policy to address childhood cancer control. There is limited information on the status and quality of childhood cancer care services in India. This paper describes the childhood cancer care services available at secondary and tertiary-level hospitals in India through a cross sectional study design. Methods: The survey was conducted in 137 tertiary-level and 92 secondary-level hospitals in 26 states and 4 Union Territories (UTs), ensuring a uniform representation of public and private care hospitals. The study tool collected data on the organisational infrastructure, type of oncology services, health workforce, equipment, treatment and referral protocols, and treatment guidelines. Descriptive statistics was used to primarily present the health service status and data on childhood cancer care services in proportions and mean. Findings: A dedicated pediatric oncology department was available in 41.6% of the public, 48.6% of private, and 64% Non Government Organization (NGO) managed tertiary-level hospitals. In 36 (39%) of the 92 hospitals providing secondary care, childhood cancer care was provided. The availability of bone (41.5%) and positron emission tomography (PET) scans (25.9%) was lower in public tertiary hospitals, whereas histopathology, computerised tomography (CT scan), and magnetic resonance imaging (MRI) were lower in public secondary hospitals than private and NGO managed hospitals for the corresponding level of care. Most tertiary hospitals had the required supportive care facilities except for play therapy and hospice care. Less than 50% of the public tertiary hospitals had stocks of the four categories of cancer-treating drugs and essential infrastructure for radiotherapy and chemotherapy. Most secondary-level hospitals not treating childhood cancer had referral linkages with tertiary hospitals. Interpretation: The situational analysis of childhood cancer care services in India showed the concentration of availability of childhood cancer care services at the tertiary level of health care. There were gaps in the availability of specialised pediatric oncology care in all the tertiary hospitals. The availability of childhood cancer care services was higher in private and NGO-managed hospitals than in public hospitals. Integration of childhood cancer as a part of the national cancer control response should be taken up as a matter of priority. The need of the hour is to formulate a childhood cancer policy that will enable timely access to care universally. Funding: World Health Organization, India provided funding and technical support.

Whole exome sequencing of pediatric leukemia reveals a novel InDel within FLT-3 gene in AML patient from Mizo tribal population, Northeast India.

BACKGROUND: Leukemia is the most common type of cancer in pediatrics. Genomic mutations contribute towards the molecular mechanism of disease progression and also helps in diagnosis and prognosis. This is the first scientific mutational exploration in whole exome of pediatric leukemia patients from a cancer prone endogamous Mizo tribal population, Northeast India. RESULT: Three non-synonymous exonic variants in NOTCH1 (p.V1699E), MUTYH (p.G143E) and PTPN11 (p.S502P) were found to be pathogenic. A novel in-frame insertion-deletion within the juxtamembrane domain of FLT3 (p.Tyr589_Tyr591delinsTrpAlaGlyAsp) was also observed. CONCLUSION: These unique variants could have a potential mutational significance and these could be candidate genes in elucidating the possibility of predisposition to cancers within the population. This study merits further investigation for its role in diagnosis and prognosis and also suggests the need for population wide screening to identify unique mutations that might play a key role towards precision medicine.

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.

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.

Pediatric leukemia could be driven predominantly by non-synonymous variants in mitochondrial complex V in Mizo population from Northeast India.

Leukemia is the most common childhood malignancy and studies had been carried out with promising revelations in its diagnosis and prognosis. However, majority of the studies are focused on nuclear alterations, while mitochondrial mutations are not well studied. Although there are studies of mitochondrial mutations in the adult leukemias, it does not represent the same for childhood malignancy. This is the first scientific report on the mtDNA mutational pattern of pediatric leukemic cases from a endogamous tribal population in Northeast India. ATP6 involved in the Complex V was found to be more altered with respect to the Non-synonymous variants. mtDNA variations in the non-coding region (D-Loop - g.152 T>C) and in the coding region (MT-ND2, g.4824 A>G, p.T119A) showed a maternal inheritance which could reveal a genetic predisposition with lower penetrance. D-Loop variant (g.152 T>C) could be a diagnostic marker in accordance with previous report but is in contrast to pertaining only in AML - M3 subtype rather was found across in myeloid malignancies.

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.

Lifestyle chemical carcinogens associated with mutations in cell cycle regulatory genes increases the susceptibility to gastric cancer risk.

In the present study, we correlated the various lifestyle habits and their associated mutations in cell cycle (P21 and MDM2) and DNA damage repair (MLH1) genes to investigate their role in gastric cancer (GC). Multifactor dimensionality reduction (MDR) analysis revealed the two-factor model of oral snuff and smoked meat as the significant model for GC risk. The interaction analysis between identified mutations and the significant demographic factors predicted that oral snuff is significantly associated with P21 3'UTR mutations. A total of five mutations in P21 gene, including three novel mutations in intron 2 (36651738G > A, 36651804A > T, 36651825G > T), were identified. In MLH1 gene, two variants were identified viz. one in exon 8 (37053568A > G; 219I > V) and a novel 37088831C > G in intron 16. Flow cytometric analysis predicted DNA aneuploidy in 07 (17.5%) and diploidy in 33 (82.5%) tumor samples. The G2/M phase was significantly arrested in aneuploid gastric tumor samples whereas high S-phase fraction was observed in all the gastric tumor samples. This study demonstrated that environmental chemical carcinogens along with alteration in cell cycle regulatory (P21) and mismatch repair (MLH1) genes may be stimulating the susceptibility of GC by altering the DNA content level abnormally in tumors in the Mizo ethic population.

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.

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.

Relevance of GSTM1, GSTT1 and GSTP1 Gene Polymorphism to Breast Cancer Susceptibility in Mizoram Population, Northeast India.

The enzymes encoded by glutathione S-transferase mu 1 (GSTM1) and theta 1 (GSTT1) genes are involved in the metabolism of wide range of carcinogens that are ubiquitous in the environment. Homozygous deletions of the GSTM1 and GSTT1 genes are commonly found and result in lack of enzyme activity. This study was undertaken to evaluate the association between GSTM1, GSTT1 and GSTP1 gene polymorphism and breast cancer risk in Mizoram population. Odd ratio (OR) and 95% confidence interval (CI) from conditional logistic regression model were used to estimate the association between genetic polymorphism and breast cancer risk. The GSTM1 and GSTT1 null genotypes were associated with an increased risk of breast cancer [OR = 10.80 (95% CI 1.16-100.43)]. The risk of breast cancer associated with the GSTT1 null genotype was observed to be low among postmenopausal women. When considered together, GSTM1 and GSTT1 genotypes were found to be associated with an increased risk of breast cancer. The relationship between GSTM1 and GSTT1 gene deletions and breast cancer risk was substantially altered by consumption of Smoked Meat/Vegetable. In the present study, GSTP1Ile105Val (rs1695) polymorphism was related to breast cancer susceptibility or phenotype. Our data provides evidence for substantially increased risk of breast cancer associated with GSTM1 and/or GSTT1 homozygous gene deletions in Mizoram population.

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.

Polymorphism in mtDNA control region of Mizo-Mongloid Breast Cancer samples as revealed by PCR-RFLP analysis.

Mutations in mitochondrial D-loop region of DNA (mtDNA) may serve as a potential sensor for cellular DNA damage and marker for cancer development. We investigated the restriction fragment length polymorphism (RFLP) pattern of the D-loop region in the blood samples of breast cancer patients among Mizoram population. Significant differences were observed among breast cancer and healthy blood samples in the RFLP pattern using AluI, HaeIII and RsaI enzymes. Polymorphic information content (PIC - 0.258), band informativeness (∑Ib - 3.283) and marker index (MI - 0.006) were highest in the case of RsaI enzyme. Our data suggest that the RsaI polymorphic site in the mitochondrial control region is an informative marker for breast cancer development in Mizo population.

Coextraction and PCR Based Analysis of Nucleic Acids From Formalin-Fixed Paraffin-Embedded Specimens.

BACKGROUND: Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. Our optimized co-extraction approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies because of the high importance and less availability of clinical FFPE specimen. METHODS: Coextraction of DNA and RNA from a single gastric cancer FFPE specimen was optimized by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. The protocol involves modification of incubation period for 30 min with proteinase K in glycin-tris-ethylenediamine tetra acetic acid buffer before adding TRIzol. RESULTS: All samples tested successfully performed semiquantitative gene expression by reverse transcriptase PCR. The quantity and quality of DNA from FFPE samples was high which resulted in successful PCR amplification. The isolated DNA also aided in detection of Helicobacter pylori by amplifying the ribosomal 16S gene in a multiplex PCR reaction along with cagA. CONCLUSION: These results show that the RNA/DNA isolated by this method can be used for easy clinical diagnosis of disease-related gene expression as well as mutation and pathogen detection from a homogenous population of tumor cells.

The growing burden of cancer in India: epidemiology and social context.

Cancer can have profound social and economic consequences for people in India, often leading to family impoverishment and societal inequity. Reported age-adjusted incidence rates for cancer are still quite low in the demographically young country. Slightly more than 1 million new cases of cancer are diagnosed every year in a population of 1.2 billion. In age-adjusted terms this represents a combined male and female incidence of about a quarter of that recorded in western Europe. However, an estimated 600,000-700,000 deaths in India were caused by cancer in 2012. In age-standardised terms this figure is close to the mortality burden seen in high-income countries. Such figures are partly indicative of low rates of early-stage detection and poor treatment outcomes. Many cancer cases in India are associated with tobacco use, infections, and other avoidable causes. Social factors, especially inequalities, are major determinants of India's cancer burden, with poorer people more likely to die from cancer before the age of 70 years than those who are more affluent. In this first of three papers, we examine the complex epidemiology of cancer, the future burden, and the dominant sociopolitical themes relating to cancer in India.

Mitochondrial D-loop and cytochrome oxidase C subunit I polymorphisms among the breast cancer patients of Mizoram, Northeast India.

Mitochondrial DNA (mtDNA) is known for its high frequencies of polymorphisms and mutations as it is prone to oxidative stress. The aim of the present study is to assess the novel mutations in mitochondrial genes from blood samples among the breast cancer patients from a less studied Northeast Indian population. D, B, L haplogroups were observed in the cancer samples and a total of 44 mtDNA D-loop sequence variations at 42 distinct nucleotide positions were found. All the sequence variations were transitional substitutions and 6 were heteroplasmic states, except for a cytosine copy number change (9C/8C) at np 303e309 in three samples examined. A total of 88 Cytochrome Oxidase C subunit I (COXI) sequence differences with respect to the Revised Cambridge Reference Sequence (rCRS) were identified including 20 missense variants with 100 % sample mutation frequency. All 20 missense mutations are highly conserved with a Cumulate Index of 100 %. Among 88 COXI mutations, 24 (13 were Non-Synonymous and 11 were Synonymous) were not previously reported (novel mutation) in the literature or the public mtDNA mutation databases. Analysis of three-dimensional structure of COXI open reading frame (ORF) predicted the effect of one single codon (96R > C, 217T > I, 224-225GG > EE and 227D > T) mutations located in the signal peptide binding position. Analysis of mitochondrial DNA mutations, as a viable alternative, has the advantage of being capable of detecting inherent risk factors for breast cancer development.