Variants in Long non-Coding RNAs (lncRNAs)-Genomic Regions may Contribute to Nonalcoholic Fatty Liver Disease Severity

CARLOS J. PIROLA, TOMAS FERNÁNDEZ GIANOTTI, HERNÁN DOPAZO, CRISTIAN ROHR, GUSTAVO O. CASTAÑO, SILVIA SOOKOIAN.

Boston

Congreso; Annual Meeting of the American Association for the Study of Liver Diseases; 2014

aASLD. American Association for the Study of Liver Diseases

Background: The human transcriptome is composed by a myriad of non-protein-coding RNA species, including lncRNAs, which are located at intergenic and intronic regions and even in the antisense strand of protein-coding genes. LncRNAs have a remarkable role in transcriptional and epigenetic regulation, and disease. Notably, a large number (>90%) of genetic variants related to diseases/traits from genome-wide association studies map to intergenic or intronic regions and reside in non-coding protein genes. Hence, we hypothesized that variants in lncRNAs can affect the NAFLD phenotype and disease susceptibility. We took advantage of deep-sequencing techniques to comprehensively characterize human lncRNA genomic regions in 96 subjects, including 64 patients with NAFLD confirmed by liver biopsy (32 simple steatosis and 32 NASH), and 32 matched healthy controls. Methods: As a proof of principle, we performed a global survey of genetic variation associated with randomly selected lncRNA-genomic regions by next generation sequencing technology undertaken by a Ion Torrent Personal Genome Machine using 316 chips and barcoding (>50 x coverage). Results: We sequenced >240 Mb at >Q20, in a total of 2,027,565 reads of 140 bp fragments on average, including >60 lncRNAs encompassing 50 kb. Based on the analysis of single nucleotide polymorphisms (SNPs), we identified the rs11171490 located at the ENST00000554049 gene -a lncRNA (transcript ID: NONHSAT028661) spanning 555 kb (Chr12:55,828,539-55,979,255), reverse strand. This SNP, which also localizes to an intron of OR6C2 locus, was significantly associated with the histological progression of NAFLD (chi2 test 10.8, regression analysis for an ordinal multinomial distribution p