Bioinformatics e Biostatistics applied to research in pediatric genetic disease. Clinical evidence in IFNλ4 polymorphisms associated with HCV infection in patients with beta thalassemia and WGCNA analysis weighted for IFNλ4 genotype rs12979860 to detect RPL9P18 as hub in HCV infected cell.

Genome-wide association studies have identified host genetic variation to be critical for spontaneous clearance and treatment response in patients infected with hepatitis C virus (HCV). We demonstrated the same in patients with thalassemia major infected by genotype 1b of HCV. In the present first part study we retrospectively analyzed 368 anti-HCV positive patients with beta-thalassemia in two Italian major thalassemic centers (Cagliari and Turin). The strongest IFNλ4 SNP found associated with HCV was rs12979860 where C/C genotype was related to response to the interferon treatment and, above all, to spontaneous clearance of the virus. However, the positive predictive power was stronger for viral persistence than spontaneous clearance indeed TT allele was more predictive than CC. Another polymorphism rs4803221 was analyzed because had independent effects respect to rs12979860. The haplotype tagged by SNP rs12979860 and rs4803221 significantly could improve the viral clearance prediction in infected patients. Neither necrotic-inflammation or bilirubin values in the chronic phase of the hepatitis C were related to IFNλ4 polymorphisms. No relation among IFNλ4 polymorphisms and fibrosis stage directly shown by the liver biopsy was found. Second part of our study was to identify hub genes associated in pathways closely related to IFNλ4 variants in HCV response. We used gene expression profile data of GSE54648, downloaded from Gene Expression Omnibus (GEO). We focused our attention on expression genes differential between rs12979860 unfavorable TT genotype and favorable CC genotype, using weighted gene expression network analysis (WGCNA - R package). Significant modules were selected using the clustering analysis. At the final the best significant module was “black” module. Its pathways were involved in translation mechanisms such as translation termination, translation elongation, nuclear-transcribed mRNA catabolic process, cellular protein complex disassembly, therefore biological mechanisms that occur inside ribosome. We discovered RPL9P18 pseudogene as a hub potentially related in inhibition of spontaneous clearance and furthermore likely involved in drug treatment inhibition. Our result suggests an active role for ribosome pseudogene in innate antiviral response probably during ISG (IFN-stimulated genes) translation. Moreover, through co-expression analysis we demonstrate a new possible role of IFNλ4 genotype in HCV infection, associate with expression of ribosomal pathways.