In silico analysis of the association between long non‐coding RNA family with sequence similarity 99 member A (FAM99A) and hepatic cancer

Abstract

The link between family with sequence similarity 99 member A ( FAM99A ), a type of long non‐coding RNA, and tumourigenesis remains ambiguous. Therefore, in this study, the authors conducted an expression profile analysis of FAM99A based on 33 types of cancer within The Cancer Genome Atlas project. The expression profile data revealed low expression levels of FAM99A in hepatocellular carcinoma, cholangiocarcinoma, and testicular germ cell tumour tissues than in the normal control tissues. Survival analysis indicated a correlation between low FAM99A expression and worse survival outcome in patients with hepatic cancer. Further investigation revealed the possible implication of DNA methylation, but not copy number variation, in FAM99A ‐associated hepatic tumourigenesis. The authors also identified a set of differentially expressed genes between patients with hepatic cancer and negative controls, which were found to be related to biochemical metabolism or the cell cycle. Additionally, FAM99A expression may be associated with the infiltration status of several immune cells, such as dendritic cells, natural killer cells, and neutrophils. Overall, FAM99A may function as a prognostic marker that is potentially associated with DNA methylation, immune cell infiltration, and biochemical metabolism in hepatic cancer.

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“…It included methylation-based stemness scores, but no significant association was found in TGCT [73]. FAM99A gene, which codes for an lncRNA, had a lower expression in TGCT compared with normal tissue of the GTEx database; however, further investigations found a positive correlation with four methylation probe sites, and no prognostic value was considered for this cancer type, given the limitations of the study [62]. Interesting results were also obtained in a study on SMARCA1, a gene that encodes for a chromatin remodeling protein, which only evaluated its expression and DNA methylation due to limited data [74].…”