Genomic determinants of antibody response to a typhoid vaccine in Indian recipients.

Typhoid is endemic in India and has high global incidence. There were large outbreaks of typhoid in India between 1990 and 2018. Available typhoid vaccines induce variable levels of protective antibodies among recipients; thus, there is variability in response to the vaccine. Interindividual genomic differences is hypothesized to be a determinant of the variability in response. We studied the antibody response of ~1000 recipients of the Vi-polysaccharide typhoid vaccine from Kolkata, India, who showed considerable variability of antibody response, i.e., anti-Vi-polysaccharide antibody level 28 days postvaccination relative to prevaccination. For each vaccinee, wholegenome genotyping was performed using the Infinium Global Screening Array (Illumina). We identified 39 SNPs that mapped to 13 chromosomal regions to be associated with antibody response to the vaccine; these included SNPs on genes LRRC28 (15q26.3), RGS7 (1q43), PTPRD (9p23), CERKL (2q31.3), DGKB (7p21.2), and TCF4 (18q21.2). Many of these loci are known to be associated with various blood cell traits, autoimmune traits and responses to other vaccines; these genes are involved in immune related functions, including TLR response, JAK-STAT signalling, phagocytosis and immune homeostasis.

Genetic variants associated with spontaneous preterm birth in women from India: a prospective cohort study.

Background: Despite having the highest number of preterm births globally, no genomic study on preterm birth was previously published from India or other South-Asian countries. Methods: We conducted a genome-wide association (GWA) study of spontaneous preterm birth (sPTB) on 6211 women from India. We used a novel resampling procedure to identify the associated single nucleotide polymorphisms (SNPs) followed by haplotype association analysis and imputation. Findings: We found that 512 maternal SNPs were associated with sPTB (p < 2.51e-3), of which minor allele at 19 SNPs (after Bonferroni correction) had increased genotype relative risk. Haplotypes containing six of the 19 SNPs (rs13011430, rs8179838, rs2327290, rs4798499, rs7629800, and rs13180906) were associated with sPTB (p < 9.9e-4; Bonferroni adjusted p-value <0.05). After imputation in regions around the 19 SNPs, 15 imputed SNPs were found to be associated with sPTB (Bonferroni adjusted p-value <0.05). One of these imputed SNPs, rs35760881, and three other SNPs (rs17307697, rs4308815, and rs10983507) were also reported to be associated with sPTB in women belonging to European ancestry. Moreover, we found that GG genotype at rs1152954, one of the associated SNPs, enhanced risk of sPTB and reduced telomere length. Interpretation: This is the first study from South Asia on the genome-wide identification of maternal SNPs associated with sPTB. These SNPs are known to alter the expression of genes associated with major pathways in sPTB viz. inflammation, apoptosis, cervical ripening, telomere maintenance, selenocysteine biosynthesis, myometrial contraction, and innate immunity. From a public health perspective, the trans-ethnic association of four SNPs identified in our study may help to stratify women with risk of sPTB in most populations. Funding: Department of Biotechnology (India), Grand Challenges India - All Children Thriving Program and Biotechnology Industry Research Assistance Council (BIRAC).

Density of CD3+ and CD8+ cells in gingivo-buccal oral squamous cell carcinoma is associated with lymph node metastases and survival.

The tumor immune microenvironment is emerging as a critical player in predicting cancer prognosis and response to therapies. However, the prognostic value of tumor-infiltrating immune cells in Gingivo-Buccal Oral Squamous Cell Carcinoma (GBOSCC) and their association with tumor size or lymph node metastases status require further elucidation. To study the relationship of tumor-infiltrating immune cells with tumor size (T stage) and lymph node metastases (N stages), we analyzed the density of tumor-infiltrating immune cells in archived, whole tumor resections from 94 patients. We characterized these sections by immune-histochemistry using 12 markers and enumerated tumor-infiltrating immune cells at the invasive margins (IM) and centers of tumors (CT). We observed that a higher density of CD3+ cells in the IM and CT was associated with smaller tumor size (T1-T2 stage). Fewer CD3+ cells was associated with larger tumor size (T3-T4 stage). High infiltration of CD3+and CD8+ cells in IM and CT as well as high CD4+ cell infiltrates in the IM was significantly associated with the absence of lymph node metastases. High infiltrates of CD3+ and CD8+ cells in CT was associated with significantly improved survival. Our results illustrate that the densities and spatial distribution of CD3+ and CD8+ cell infiltrates in primary GBOSCC tumors is predictive of disease progression and survival. Based on our findings, we recommend incorporating immune cell quantification in the TNM classification and routine histopathology reporting of GBOSCC. Immune cell quantification in CT and IM may help predict the efficacy of future therapies.

An exome wide association study of pulmonary tuberculosis patients and their asymptomatic household contacts.

Tuberculosis is a leading cause of death in India. To identify genetic variants associated with susceptibility or resistance to Mycobacterium tuberculosis infection, we have performed an exome-wide association study with 0.2 million exonic variants among 119 pairs of tuberculosis patients and their clinically asymptomatic household contacts. The strongest association was identified for rs61104666[A], a synonymous variant (p.E292E) of exon 5 of the gene SIGLEC15 (OR = 2.4, p = 1.49 × 10-5). We also found association of non-coding variants in the 3'UTR region of a gene encoding the class II human leukocyte antigens (HLAs), HLA-DRA. rs13209234[A] (minor allele frequency (MAF) = 13.8%) (OR = 0.35, P = 2.5 × 10-4) and rs3177928[A] (minor allele frequency (MAF) = 13.7%) (OR = 0.35, P = 3.3 × 10-4) were associated with protection from tuberculosis. These two SNPs, rs13209234 and rs3177928, are in complete linkage disequilibrium. These associations remained valid when additional data on freshly recruited individuals were jointly analyzed on 250 patient-control pairs. The identified gene, HLA-DRA, suggest involvement of immune regulation, indicating pathways associated with antigen presentation in tuberculosis infection.

Profiling of genomic alterations of mitochondrial DNA in gingivobuccal oral squamous cell carcinoma: Implications for disease progress.

We have identified 164 somatic mutations in mitochondrial DNA in gingivobuccal oral cancer by deep sequencing the mitochondrial genome from paired tumor and blood DNA samples from 89 patients. We have found evidence of positive selection of somatic nonsynonymous mutations. Non-synonymous mutations in mitochondrial respiratory genes were found to increase the risk of lymph node metastasis (P = 0.0028). We have observed a significant reduction in mitochondrial DNA copy number in tumor DNA of these patients compared to the DNA from adjacent normal tissue samples (P < 1 × 10-6). Analysis of transcriptome data of tumor and adjacent normal tissue revealed patients harboring mutations in mitochondrial protein-coding genes exhibited reduced expression of mitochondrial transcripts.

A powerful method to integrate genotype and gene expression data for dissecting the genetic architecture of a disease.

To decipher the genetic architecture of human disease, various types of omics data are generated. Two common omics data are genotypes and gene expression. Often genotype data for a large number of individuals and gene expression data for a few individuals are generated due to biological and technical reasons, leading to unequal sample sizes for different omics data. Unavailability of standard statistical procedure for integrating such datasets motivates us to propose a two-step multi-locus association method using latent variables. Our method is powerful than single/separate omics data analysis and it unravels comprehensively deep-seated signals through a single statistical model. Extensive simulation confirms that it is robust to various genetic models as its power increases with sample size and number of associated loci. It provides p-values very fast. Application to real dataset on psoriasis identifies 17 novel SNPs, functionally related to psoriasis-associated genes, at much smaller sample size than standard GWAS.

CXCL10 is overexpressed in active tuberculosis patients compared to M. tuberculosis-exposed household contacts.

INTRODUCTION: Variability in clinical outcome of tuberculosis infection is dependent, among other factors, on variation in host immunological response to the infection, which is modulated, in part by genetic variations present in the host. We undertook a study to identify host factors associated with such clinical variability. STUDY DESIGN AND METHODS: A comparative study between groups of active TB patients vs. clinically normal household contacts, family members living under the same roof with the patients for a long period of time, was carried out. We screened 22 candidate cytokines and chemokines in the plasma of 119 pairs ("discovery set") of TB patients and their asymptomatic household contacts. Identified associations were validated in an independent cohort of 78 patient-household contact pairs ("validation set"). Validated associations were further cross-validated by gene expression assays using RT-PCR and in-vitro whole blood stimulation by mycobacterial antigens ESAT6 and Rv2031c, two well-characterized antigens that are expressed in active and latent phases of disease, respectively. In a concomitant SNP association study, we have sequenced the validated gene in these patients and household contacts. RESULT: CXCL10 was found to be the most significantly (p = 0.0002) elevated chemokine - discovered and validated -- in patients' plasma compared to their household contacts. We found that CXCL10 was overexpressed by 5-fold at the RNA level in patients compared to asymptomatic household contacts (p = 0.004). On stimulation of whole blood collected from normal healthy volunteers with mycobacterial antigens ESAT6 and Rv2031c, we found that production of CXCL10 by ESAT6 was significantly higher (p = 2.8 × 10-12) than Rv2031c. The production of CXCL10 was 20-fold more than IFN-γ, the most widely validated cytokine, by ESAT6 stimulation (p = 4.6 × 10-8). One of the polymorphisms in promoter of CXCL10, rs4508917 (-1447 A > G), was identified as a proteinQTL (pQTL). Reduced expression of CXCL10 was observed among individuals with GG genotype, but the reduction was statistically significant only among controls, but not among patients. Among patients, the expression level was very high compared to the controls irrespective of the genotypes at this locus. CONCLUSION: Plasma level of CXCL10 is predictive of the active phase of TB infection.