MiRNAs as non-invasive biomarkers in the serum of Oral Squamous Cell Carcinoma (OSCC) and Oral Potentially Malignant Disorder (OPMD) patients.

OBJECTIVE: Cell-free microRNAs have shown differential levels in the serum of individuals under disease conditions suggesting its potential to act as biomarkers. A population specific miRNA signature in oral cancer is reported in different studies. We aim to identify a set of serum specific miRNAs that may differentiate oral cancer, oral pre-malignant conditions from the healthy individuals. DESIGN: We investigated the levels of 24 miRNAs in the serum of 47 Oral squamous cell carcinoma (OSCC) patients, 20 patients with Oral potentially malignant disorders (OPMD) and 42 healthy controls from Eastern India. Small RNAs were isolated from serum samples followed by cDNA synthesis. Levels of miRNAs were determined using qRT-PCR. The sources of serum specific miRNAs were evaluated using GTEx-RNAseq and TCGA-HNSCC database. RESULTS: Five miRNAs, miR-483-5p, miR-31-5p, Let-7b-5p, miR-486-5p and miR-30e-5p showed significant elevation in OSCC patients. An Elastic-Net model with 4 miRNAs classified OSCC from healthy controls with 80 % sensitivity, 64.3 % specificity, and 72.4 % accuracy. Mir-483-5p and miR-31-5p was significantly overexpressed in OSCC tissues as well as significantly higher in the serum of Leukoplakia and Verrucous carcinoma patients suggesting their potential as early disease markers. MiR-483-5p showed a consistent elevated level in the serum/plasma of oral cancer patients across different population and was found to be tumour specific while, the rest of the miRNAs showed variable results across different studies. CONCLUSIONS: Our study suggested that the serum miRNAs in oral cancer and pre-malignant disorder conditions can be used as a non-invasive marker for screening of these oral conditions.

Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India.

BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the varied environmental and genotoxic exposures among the Indian population, we conducted a genome-wide DNA methylation study on paired tumor and adjacent normal tissues of ten well-differentiated OSCC patients and validated in an additional 53 well-differentiated OSCC and adjacent normal samples. RESULTS: Genome-wide DNA methylation analysis identified several novel differentially methylated regions associated with OSCC. Hypermethylation is primarily enriched in the CpG-rich regions, while hypomethylation is mainly in the open sea. Distinct epigenetic drifts for hypo- and hypermethylation across CpG islands suggested independent mechanisms of hypo- and hypermethylation in OSCC development. Aberrant DNA methylation in the promoter regions are concomitant with gene expression. Hypomethylation of immune genes reflect the lymphocyte infiltration into the tumor microenvironment. Comparison of methylome data with 312 TCGA HNSCC samples identified a unique set of hypomethylated promoters among the OSCC patients in India. Pathway analysis of unique hypomethylated promoters indicated that the OSCC patients in India induce an anti-tumor T cell response, with mobilization of T lymphocytes in the neoplastic environment. Survival analysis of these epigenetically regulated immune genes suggested their prominent role in OSCC progression. CONCLUSIONS: Our study identified a unique set of hypomethylated regions, enriched in the promoters of immune response genes, and indicated the presence of a strong immune component in the tumor microenvironment. These methylation changes may serve as potential molecular markers to define risk and to monitor the prognosis of OSCC patients in India.

Increased Risk of Psoriasis due to combined effect of HLA-Cw6 and LCE3 risk alleles in Indian population.

HLA-Cw6 is one of the most associated alleles in psoriasis. Recently, Late Cornified Envelop 3 (LCE3) genes were identified as a susceptibility factor for psoriasis. Some population showed epistatic interaction of LCE3 risk variants with HLA-Cw6, while some population failed to show any association. We determined the associations of a 32.2 kb deletion comprising LCE3C-3B genes and three SNPs (rs1886734, rs4112788; rs7516108) at the LCE3 gene cluster among the psoriasis patients in India. All three SNPs at the LCE3 gene cluster failed to show any association. In contrary, for patients with HLA-Cw6 allele, all three SNPs and the LCE3C-3B deletion showed significant associations. While, all five LCE3 genes were upregulated in psoriatic skin, only LCE3A showed significant overexpression with homozygous risk genotype compared to the non-risk genotype. LCE3B also showed significant overexpression in patients with HLA-Cw6 allele. Moreover, LCE3A showed significantly higher expression in patients bearing homozygous risk genotype in presence of HLA-Cw6 allele but not in those having non-risk genotype, demonstrating the combined effect of HLA-Cw6 allele and risk associated genotype near LCE3A gene. Integration of genetic and gene expression data thus allowed us to identify the actual disease variants at the LCE3 cluster among the psoriasis patients in India.