Whole exome sequencing identifies novel variants of PIK3CA and validation of hotspot mutation by droplet digital PCR in breast cancer among Indian population.

BACKGROUND: Breast cancer (BC) is the most common malignancy with very high incidence and relatively high mortality in women. The PIK3CA gene plays a pivotal role in the pathogenicity of breast cancer. Despite this, the mutational status of all exons except exons 9 and 20 still remains unknown. METHODS: This study uses the whole exome sequencing (WES) based approach to identify somatic PIK3CA mutations in Indian BC cohorts. The resultant hotspot mutations were validated by droplet digital PCR (ddPCR). Further, molecular dynamics (MD) simulation was applied to elucidate the conformational and functional effects of hotspot position on PIK3CA protein. RESULTS: In our cohort, PIK3CA showed a 44.4% somatic mutation rate and was among the top mutated genes. The mutations of PIK3CA were confined in Exons 5, 9, 11, 18, and 20, whereas the maximum number of mutations lies within exons 9 and 20. A total of 9 variants were found in our study, of which 2 were novel mutations observed on exons 9 (p.H554L) and 11 (p.S629P). However, H1047R was the hotspot mutation at exon 20 (20%). In tumor tissues, there was a considerable difference between copy number of wild-type and H1047R mutant was detected by ddPCR. Significant structural and conformational changes were observed during MD simulation, induced due to point mutation at H1047R/L position. CONCLUSIONS: The current study provides a comprehensive view of novel as well as reported single nucleotide variants (SNVs) in PIK3CA gene associated with Indian breast cancer cases. The mutation status of H1047R/L could serve as a prognostic value in terms of selecting targeted therapy in BC.

Comprehensive mutations analyses of FTO (fat mass and obesity-associated gene) and their effects on FTO's substrate binding implicated in obesity.

An excessive amount of fat deposition in the body leads to obesity which is a complex disease and poses a generic threat to human health. It increases the risk of various other diseases like diabetes, cardiovascular disease, and multiple types of cancer. Genomic studies have shown that the expression of the fat mass obesity (FTO) gene was highly altered and identified as one of the key biomarkers for obesity. This study has been undertaken to investigate the mutational profile of the FTO gene and elucidates its effect on the protein structure and function. Harmful effects of various missense mutations were predicted using different independent tools and it was observed that all mutations were highly pathogenic. Molecular dynamics (MD) simulations were performed to study the structure and function of FTO protein upon different mutations and it was found that mutations decreased the structure stability and affected protein conformation. Furthermore, a protein residue network analysis suggested that the mutations affected the overall residues bonding and topology. Finally, molecular docking coupled with MD simulation suggested that mutations affected FTO substrate binding by changing the protein-ligand affinity. Hence, the results of this finding would help in an in-depth understanding of the molecular biology of the FTO gene and its variants and lead to the development of effective therapeutics against associated diseases and disorders.

Association of ACE I/D gene polymorphism and related risk factors in impaired fasting glucose and type 2 diabetes: a study among two tribal populations of North-East India.

BACKGROUND: Type 2 diabetes is a serious public health concern in India, even the indigenous tribal populations are not left unaffected. The present study aims to understand the association of major risk factors i.e. obesity, hypertension, dyslipidemia, ACE I/D polymorphism with impaired fasting glucose (IFG) and type 2 diabetes (T2D) among two different Mendelian populations of North East India. METHODS: Demographic, somatometric, physiological variables along with fasting blood samples were collected from 609 individuals. The participants were screened for ACE I/D polymorphism. RESULTS: ACE I/D polymorphism was found to follow HWE among Liangmai tribe but not among Mizo tribe. Distribution of DD genotype/D allele was found to be significantly higher for T2D among Mizo tribe. Significant association were observed between DD genotype/D allele of ACE I/D polymorphism and TC as well as LDL with both IFG and T2D only in Mizo tribe. CONCLUSIONS: The present study is an example of gene-environment interaction where DD genotype or D allele and dyslipidemia (high TC and high LDL) are posing risk for IFG and T2D both independently and in combination only among Mizo tribe with relatively less physical activity attributed to their residence in less hilly terrain however Liangmai tribe which resides in high hilly terrain shows no such association.

Effect of internal migration on diabetes and metabolic abnormalities in India - The ICMR-INDIAB study.

AIMS: To assess the effect of migration (rural-to-urban and vice versa) on prevalence of diabetes and metabolic disorders in Asian Indians participating in the Indian Council of Medical Research-India Diabetes (ICMR-INDIAB) study. MATERIALS AND METHODS: The ICMR-INDIAB study is a national study on diabetes and associated cardiometabolic disorders in individuals aged ≥20 years from 28 states and 2 union territories of India. Individuals who moved to a different place from their place of birth and had resided in the new location for at least one year were considered as migrants. Anthropometric measurements, blood pressure estimation and a capillary oral glucose tolerance test were performed. RESULTS: Of the 113,043 participants, 66.4% were non-migrant rural dwellers, 19.4% non-migrant urban dwellers, 8.4% rural-urban migrants, 3.8% multiple migrants and 2.0% urban-rural migrants. Weighted prevalence of diabetes was highest in rural-urban migrants followed by urban dwellers, urban-rural migrants and rural dwellers [14.7%, 13.2%, 12.7% and 7.7% respectively (p < 0.001)]. Rural-urban migrants had highest prevalence of abdominal obesity (50.5%) compared to the other three groups. The risk for diabetes was 1.9 times higher in rural-urban migrants than among rural dwellers. Five risk factors [hypertension, abdominal and generalized obesity, physical inactivity and low fruit and vegetable intake] together explained 69.8% (partial population attributable risk) of diabetes among rural-urban migrants and 66.4% among non-migrant urban dwellers. CONCLUSIONS: Rural-to-urban migration is associated with increased risk of developing diabetes and other cardiometabolic abnormalities. Adoption of healthier lifestyle patterns among migrants could help prevent/delay onset of these abnormalities in this population.

Obesity, dyslipidaemia and candidate gene polymorphisms: a cross-sectional study among the Liangmai and Mizo tribes of Manipur, India.

BACKGROUND: The prevalence of obesity and dyslipidaemia was observed to be increased among the tribal populations, due to globalization. MATERIALS AND METHODS: In the present study, data on demographic, somatometric and blood samples were collected from 613 participants of both sex, age 18-60 years, further lipid profiling and genotyping was executed. Multifactor dimensionality reduction (MDR) software was used for gene-gene interactions analysis. RESULTS: Significantly differences were observed with respect to the general characteristic and selected gene polymorphisms in both the tribes. Among the Liangmai tribe, MC4R gene was found to pose significant decreased risk for waist-height ratio (WHtR) (OR = 0.56; 95% confidence interval (CI)= 0.32-0.99; p value = .04) and HDL (OR = 0.58; 95% CI = 0.36-0.92; p value = .02). Similar trends of significant decreased risk (OR = 0.39; 95% CI = 0.20-0.76; p value=.006) for BMI were observed among the Mizo tribe. The gene-gene interaction revealed the combined model of FTO+MC4R genes shows an increased risk for BMI in both the tribes. The independent significant increased risk posed by FTO gene was moderated by interaction with MC4R gene. CONCLUSIONS: The observed differences can possibly attribute to both their respective ancestries resulting in different gene pools and the physical environment. The results of the study highlight the importance of gene-gene and gene-environment interactions in adverse phenotype groups.KEY MESSAGEAmong the tribal population, the prevalence of obesity and dyslipidaemia has been increased.Differential distribution and associations of selected markers hint towards differential genetic architecture in these populations.MC4R rs17782313 polymorphism was found to show a significantly decreased risk for WHtR and low HDL among the Liangmai tribe and BMI among the Mizo tribe.Significant increased risk posed by FTO rs9939609 gene polymorphism was moderated by the interaction with MC4R rs17782313.

Mutant strains of SARS-CoV-2 are more prone to infect obese patient: a review.

The current review critically analyzes obesity as an important risk factor for increased predisposition towards coronavirus disease 2019 (COVID-19), its severity and causal death in current pandemic. Countries with higher prevalence of exposed obese individuals experienced the highest number of mortalities. The analysis also proved that individuals having more adipose tissue in body have a higher level of angiotensin-converting enzyme 2 (ACE2), which is identified as functional receptor for COVID-19. Therefore, obese individuals are worse in condition because of a higher presence of adiposity increases the number of ACE2 expressing cells. Furthermore, in silico interactions of ACE2 and different variants of coronavirus 2 (CoV-2) spike S1 protein suggest that mutant strains are more infectious than wildtype as they bind to host ACE2 protein with high binding affinities. Certain specific cancers including cervical cancer, pancreatic and rectal adenocarcinomas have more expression of such receptors and pose additional risk to already immunocompromised cancer patients. This review emphasizes obesity, as the covert risk factor of COVID-19 infection and sensitizes about of calorie restrictions, immunity building and preventive measures.

Genomic Heterogeneity of the Naga and Kuki Tribal Populations of Manipur, Northeast India.

Manipur, one of the northeastern states of India, lies on the ancient silk route and serves as a meeting point between Southeast Asia and South Asia. The origin and migration histories of Naga and Kuki tribal populations are not clearly understood. Moreover, Kukis have been traced to two different ancestries, which has created confusion among the people. The present study examined genomic affinities and differentiation of the Naga and Kuki tribal populations of Manipur, Northeast India. Twenty autosomal markers (8 Alu insertion-deletions, 12 restriction-fragment-length polymorphisms) were analyzed. Findings show genetic differences between Naga and Kuki tribal populations with respect to the allele distribution pattern, which was substantiated by genetic differentiation (GST = 5.2%) and molecular variance (AMOVA), where the highest percentage of among-group variances was observed between Naga and Kuki tribal groups (7.09%). However, genetic similarities with respect to allele distribution patterns in most of the loci were seen among their respective groups (Rongmei and Inpui, Thadou and Vaiphei). Rongmei and Inpui tribal populations (Naga group) belong to the Naga-Bodo linguistic group, and Thadou and Vaiphei (Kuki group) belong to the Northern Kuki-Chin linguistic group, suggesting that genetic similarities may not be independent of linguistic affinities. Despite differential genetic affinities, both Naga and Kuki tribal populations in Manipur show more proximity with Southeast Asian populations and Northeast Indian populations than with other Indian populations and global populations taken for comparison.

Prevalence of cardiovascular risk factors among tribal and non-tribal populations with East Asian Ancestry from North East India.

OBJECTIVES: The distribution of hypertension, type 2 diabetes, dyslipidemia, and obesity variables were studied among tribal and non-tribal populations with East Asian ancestry from northeast India. METHODS: Data pertaining to somatometric measurements, blood pressure, lipid profile, and fasting blood glucose were collected from 1916 participants (Mizo-422, Liangmai-352, and Meitei-1142) of both sexes older than 18 years. Two-way ANOVA and chi square analysis were done to understand the inter-population prevalence differences. RESULTS: Differential distribution of obesity variables, hypertension, type 2 diabetes, and dyslipidemia was observed among the three populations. CONCLUSIONS: Population-specific prevalence studies need to be conducted to develop population-specific health strategies, specifically in countries like India with huge diversity.

Differential distribution and association of FTO rs9939609 gene polymorphism with obesity: A cross-sectional study among two tribal populations of India with East-Asian ancestry.

The fat mass and obesity associated (FTO) rs9939609 gene polymorphism is most widely studied in terms of obesity in various populations. Recently, the prevalence of obesity has been reported to be very high among the North-Eastern State of India. The major aim of the present study is to understand the extent of FTO rs9939609 gene polymorphism and its association with obesity among the two North-East Indian tribal populations with similar East Asian ancestry. Somatometric data and fasting blood sample were collected from 521 tribal individuals (258 Liangmai and 263 Mizo) of Manipur after obtaining written informed consent. Genotyping of FTO rs9939609 single nucleotide polymorphism (SNP) was done using restriction fragment length polymorphism method for PCR-amplified fragments. Both the presently studied populations were not following Hardy-Weinberg law. The prevalence of obesity and minor allele frequency of FTO rs9939609 polymorphism was found to be significantly higher among the Mizo tribe compared to that of Liangmai. The selected polymorphism was found to be significantly associated with obesity (BMI) only among the Liangmai tribe (Odds ratio-3.0; 95% CI-1.4, 6.4; p-0.003), after adjusting for age and occupation. Age-cohort wise distribution and absolute fitness analysis indicated the lower fitness of minor allele in the higher age group among the Liangmai tribe. To the best of the author's knowledge this is the first study, associating FTO rs9939609 gene polymorphism and obesity in the North-eastern Indian tribal populations with East-Asian ancestry. This study revealed the FTO rs9939609 polymorphism is observed to be associated with obesity only among the Liangmai tribe not among the Mizo tribe. The differential distribution and association observed in the two selected tribes, inhabited in a similar geographical region, could be attributed to differences in their migratory histories in terms of both route and time of settlement.

Prevalence of diabetes and prediabetes in 15 states of India: results from the ICMR-INDIAB population-based cross-sectional study.

BACKGROUND: Previous studies have not adequately captured the heterogeneous nature of the diabetes epidemic in India. The aim of the ongoing national Indian Council of Medical Research-INdia DIABetes study is to estimate the national prevalence of diabetes and prediabetes in India by estimating the prevalence by state. METHODS: We used a stratified multistage design to obtain a community-based sample of 57 117 individuals aged 20 years or older. The sample population represented 14 of India's 28 states (eight from the mainland and six from the northeast of the country) and one union territory. States were sampled in a phased manner: phase I included Tamil Nadu, Chandigarh, Jharkhand, and Maharashtra, sampled between Nov 17, 2008, and April 16, 2010; phase II included Andhra Pradesh, Bihar, Gujarat, Karnataka, and Punjab, sampled between Sept 24, 2012, and July 26, 2013; and the northeastern phase included Assam, Mizoram, Arunachal Pradesh, Tripura, Manipur, and Meghalaya, with sampling done between Jan 5, 2012, and July 3, 2015. Capillary oral glucose tolerance tests were used to diagnose diabetes and prediabetes in accordance with WHO criteria. Our methods did not allow us to differentiate between type 1 and type 2 diabetes. The prevalence of diabetes in different states was assessed in relation to socioeconomic status (SES) of individuals and the per-capita gross domestic product (GDP) of each state. We used multiple logistic regression analysis to examine the association of various factors with the prevalence of diabetes and prediabetes. FINDINGS: The overall prevalence of diabetes in all 15 states of India was 7·3% (95% CI 7·0-7·5). The prevalence of diabetes varied from 4·3% in Bihar (95% CI 3·7-5·0) to 10·0% (8·7-11·2) in Punjab and was higher in urban areas (11·2%, 10·6-11·8) than in rural areas (5·2%, 4·9-5·4; p<0·0001) and higher in mainland states (8·3%, 7·9-8·7) than in the northeast (5·9%, 5·5-6·2; p<0·0001). Overall, 1862 (47·3%) of 3938 individuals identified as having diabetes had not been diagnosed previously. States with higher per-capita GDP seemed to have a higher prevalence of diabetes (eg, Chandigarh, which had the highest GDP of US$ 3433, had the highest prevalence of 13·6%, 12.8-15·2). In rural areas of all states, diabetes was more prevalent in individuals of higher SES. However, in urban areas of some of the more affluent states (Chandigarh, Maharashtra, and Tamil Nadu), diabetes prevalence was higher in people with lower SES. The overall prevalence of prediabetes in all 15 states was 10·3% (10·0-10·6). The prevalence of prediabetes varied from 6·0% (5·1-6·8) in Mizoram to 14·7% (13·6-15·9) in Tripura, and the prevalence of impaired fasting glucose was generally higher than the prevalence of impaired glucose tolerance. Age, male sex, obesity, hypertension, and family history of diabetes were independent risk factors for diabetes in both urban and rural areas. INTERPRETATION: There are large differences in diabetes prevalence between states in India. Our results show evidence of an epidemiological transition, with a higher prevalence of diabetes in low SES groups in the urban areas of the more economically developed states. The spread of diabetes to economically disadvantaged sections of society is a matter of great concern, warranting urgent preventive measures. FUNDING: Indian Council of Medical Research and Department of Health Research, Ministry of Health and Family Welfare, Government of India.

Frequent exposure to suboptimal temperatures in vaccine cold-chain system in India: results of temperature monitoring in 10 states.

OBJECTIVE: To estimate the proportion of time the vaccines in the cold-chain system in India are exposed to temperatures of < 0 or > 8 °C. METHODS: In each of 10 states, the largest district and the one most distant from the state capital were selected for study. Four boxes, each containing an electronic temperature recorder and two vials of diphtheria, pertussis and tetanus vaccine, were placed in the state or regional vaccine store for each study state. Two of these boxes were then shipped - one per facility - towards the two most peripheral health facilities where vaccine was stored in each study district. The boxes were shipped, handled and stored as if they were routine vaccine supplies. FINDINGS: In state, regional and district vaccine stores and peripheral health facilities, respectively, the temperatures in the boxes exceeded 8 °C for 14.3%, 13.2%, 8.3% and 14.7% of their combined storage times and fell below 0 °C for 1.5%, 0.2%, 0.6% and 10.5% of these times. The boxes also spent about 18% and 7% of their combined times in transit at < 0 and > 8 °C, respectively. In shake tests conducted at the end of the study, two thirds of the vaccine vials in the boxes showed evidence of freezing. CONCLUSION: While exposure to temperatures above 8 °C occurred at every level of vaccine storage, exposure to subzero temperatures was only frequent during vaccine storage at peripheral facilities and vaccine transportation. Systematic efforts are needed to improve temperature monitoring in the cold-chain system in India.

Prevalence and pattern of substance use among the higher secondary school students of Imphal, Manipur, India.

BACKGROUND: Substance use often begins in adolescence. We did a study to describe substance use and its associated factors among adolescent students in Imphal. METHODS: We defined substance use as the use of licit and illicit substance other than when medically indicated. Using a WHO self-administered questionnaire, we collected Information about substance use from 61 randomly selected students of 1 7 government/private higher secondary schools. We calculated the prevalence of substance use according to selected characteristics. RESULTS: We surveyed 1020 students, 551 of whom reported prior substance use (prevalence of ever use: 54%, 95% confidence interval [CI] 42%-67%). Prevalence of recent and current user was 35% (95% CI 28%-43%) and 22% (95% CI 17%-28%), respectively. Among ever users, tobacco (46%) was used most commonly, followed by alcohol (29%), cannabis (14%) and opiates (12%). On multivariate analysis, substance use was significantly higher among boys (adjusted odds ratio [AOR] 2.6, 95% CI [2.0-3.4]), whose father (AOR 2.0, 95% CI 1.6-2.7) or sibling (AOR 2.1, 95% CI 1.5-3.0) used substance. It was significantly lower among children of Hindu/Jain religion (AOR 0.5, 95% CI 0.4-0.7). CONCLUSION: Prevalence of tobacco and alcohol use was high among students. Familial use of substances was associated with the behaviour of adolescents. Friends were the key proximal determinant. We recommend Introducing a substance use prevention policy in schools to educate students about various adverse effects and to impart refusal skills.

An outbreak of scrub typhus in Bishnupur district of Manipur, India, 2007.

Seasonal outbreaks of febrile illness with eschar have been occurring in Bishnupur district of Manipur since 2001. The aetiology of these outbreaks was unknown. We investigated a similar outbreak in 2007 in order to confirm the aetiology and identify its risk factors. We identified 38 patients who met the case definition (attack rate: 3.4/1000), including two deaths (case fatality ratio = 5.3%). Half of the female patients had eschar on the perineal area. The clinical picture and Weil-Felix positivity suggested that the outbreak was due to scrub typhus. The disease was more common among individuals who defecated or urinated in the jungle or bushy areas from a squatting position. We recommended educating the community about the common symptoms of the disease, encouraging them to seek early treatment from public health facilities and suggested that they be taught to avoid defecating/urinating from a squatting position in the jungle.