Detection of viral induced double-stranded RNA intermediates in archival paraffin blocks

Double strand RNA (dsRNA) species were previously thought to be a ‘junk DNA’ equivalent are related to endogenous retroviral elements (ERV) inserted into the human genome. Genomic integration sites and blocking of these processes have been well documented in HIV and Hepatitis C related diseases. Viral integration into human genome has been shown in a range of solid tumors, but mechanisms less understood. The detection of dsRNA in the research setting has been largely limited to cell line models and controlled transfections. To better characterize function significance of ERV and interactions at the cellular level, we outline efforts to detect and quantify such viral genomic elements with a focus on archival clinical samples in the commonly stored paraffin block. Tissue blocks issues with clinical and biochemical documented viral infection and associated viral cytopathic changes were selected from the Department of Pathology and Biorepository and standard 4 micron sections were prepared. Two (2) commercially available antibodies raised to dsRNA fragments (J2 and K1 antibodies) were directly compared by chromogenic and immunofluorescent methods. In addition, downstream biomarkers as identified by literature searches include RIG-1 and IRF 7 as moderate probable success and MDA-5 and STAT 1 as higher level success. Correlative analysis of downstream pathway markers with labeling results of dsRNA antibodies suffers from lack of sensitive measures of dsRNA fragments as opposed to the downstream cellular pathway markers. This lack of concordance likely reflects the short nature of dsRNAs in decade old paraffin tissue and/or differences in abundance. Future work will focus on developing more sensitive probes or IF probe signal amplification. Prediction of distant recurrence-free survival in resectable lung adenocarcinoma