Identification and characterization of a potential Biomarker and Modulator for HCC development derived from cancer type-specific long noncoding (Lnc) RNAs.

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Cancer research has entered a new phase in which information from genomics, bioinformatics and modern genetics are beginning to provide new indications of potential cancer type-specific biomarkers. Recent Ribo-seq data revealed that 40% of all long noncoding (lnc) RNAs expressed in human cells are translated as “hidden peptides.”. Since lncRNAs express human cell- specific, cell type-specific and cancer- specific properties, these hidden peptides may be cancer type-specific antigens and may also be associated with biological functions. Unraveling the patterns of genomic alterations in heterogeneous tumors such as Hepatocellular carcinoma (HCC) is pivotal for identifying biomarkers in risk groups, and for targeted therapies that could improve patient care. Indeed, we recently found that Linc00176 is spliced within Exon 2 in an HCC specific manner and is translated into a polypeptide 189 amino acids long. In addition, we detected 30 HepG2 specific potential “hidden peptides” by analyzing Ribo-seq data. This application is to undertake the following: Firstly, novel lncRNAs and splice variants of lncRNAs will be identified using nanopore technology that has recently been established in our laboratory. Secondly, to examine whether these peptides are endogenously synthesized and are stable in cells, we will generate synthetic peptide specific antibodies against potential “hidden peptides.”. Thirdly, we will isolate and sequence small peptides from HepG2 cells. Furthermore, to examine their biological functions, the first methionine residue will be replaced by a stop codon using CRISPER and the phenotype will be examined. Finally, using antibodies against these peptides we will examine whether they are expressed in primary HCC, hepatocellular adenoma, liver cirrhosis, and normal liver to determine whether these are useful as biomarkers for pre-HCCs and HCCs. In the future, antigen presentation of these peptides will be examined.