Biology subjects

Siddappa, G.

Publications and source records attributed to Siddappa, G..

2 recordsLinked to original sources

bioRxiv2017

A minimal set of internal control genes for gene expression studies in head and neck squamous cell carcinoma

BackgroundSelection of the right reference gene(s) is crucial in the analysis and interpretation of gene expression data. In head and neck cancer, studies evaluating the efficacy of internal reference genes are rare. Here, we present data for a minimal set of candidates as internal control genes for gene expression studies in head and neck cancer.\n\nMethodsWe analyzed data from multiple sources (in house whole-genome gene expression microarrays, n=21; TCGA RNA-seq, n=42, and published gene expression studies in head and neck tumors from literature) to come up with a set of genes (discovery set) for their stable expression across tumor and normal tissues. We then performed independent validation of their expression using qPCR in 14 tumor:normal pairs. Genes in the discovery set were ranked using four different algorithms (BestKeeper, geNorm, NormFinder, and comparative delta Ct) and a web-based comparative tool, RefFinder, for their stability and variance in expression across tissues.\n\nResultsOur analyses resulted in 18 genes (discovery set) that had lowest variance and high level of expression across tumor and normal samples. Independent experimental validation and analyses with multiple tools resulted in top ranked five genes (RPL30, RPL27, PSMC5, OAZ1 and MTCH1) out of which, RPL30 (60S ribosomal protein L30) and RPL27 (60S ribosomal protein L27), performed best and were abundantly expressed across tumor and normal tissues.\n\nConclusionsRPL30 and RPL27 are stably expressed in HNSCC and should be used as internal control genes in gene expression in head and neck tumors studies.

cancer biology↗

bioRxiv2016

High-risk human papillomavirus in oral cavity squamous cell carcinoma

PurposeThe prevalence of human papillomavirus (HPV) in oral cavity squamous cell carcinoma (OSCC) varies significantly based on assay sensitivity and patient geography. Accurate detection is essential to understand the role of HPV in disease prognosis and management of patients with OSCC.\n\nMethodsWe generated and integrated data from multiple analytes (HPV DNA, HPV RNA, and p16), assays (immunohistochemistry, PCR, qPCR and digital PCR) and molecular changes (somatic mutations and DNA methylation) from 153 OSCC patients to correlate p16 expression, HPV DNA, and HPV RNA with HPV incidence and patient survival.\n\nResultsHigh prevalence (33-58%) of HPV16/18 DNA did not correlate with the presence of transcriptionally active viral genomes (15%) in tumors. Eighteen percent of the tumors were p16 positive. and only 6% were both HPV DNA and RNA positive. Most tumors with relatively high-copy HPV DNA, and/or HPV RNA, but not with HPV DNA alone (irrespective of copy number), were wild-type for TP53 and CASP8 genes. In our study, p16 protein, HPV DNA and HPV RNA, either alone or in combinations, did not correlate with patient survival. Nine HPV-associated genes stratified the virus +ve from the -ve tumor group with high confidence (p<0.008) when HPV DNA copy number and/or HPV RNA were considered to define HPV positivity and not HPV DNA alone irrespective of their copy number (p < 0.2).\n\nConclusionsIn OSCC, the presence of both HPV RNA and p16 are rare. HPV DNA alone is not an accurate measure of HPV positivity and therefore not informative. Moreover, HPV DNA, RNA or p16 dont correlate with outcome.

cancer biology↗