Decreased expression of long non-coding LOC285194 predicts tumour progression and poor prognosis of hepatocellular carcinoma after curative hepatectomy

The potential, analysis and prospect of ctDNA sequencing in hepatocellular carcinoma

Background

The genome map of hepatocellular carcinoma (HCC) is complex. In order to explore whether circulating tumor cell DNA (ctDNA) can be used as the basis for sequencing and use ctDNA to find tumor related biomarkers, we analyzed the mutant genes of ctDNA in patients with liver cancer by sequencing.

Methods

We used next-generation targeted sequencing technology to identify mutations in patients with liver cancer. The ctDNA from 10 patients with hepatocellular carcinoma (including eight cases of primary hepatocellular carcinoma and two cases of secondary hepatocellular carcinoma) was sequenced. We used SAMtools to detect and screen single nucleotide polymorphisms (SNPs) and insertion deletion mutations (INDELs) and ANNOVAR to annotate the structure and function of the detected mutations. Screening of pathogenic and possible pathogenic genes was performed using American College of Medical Genetics and Genomics (ACMG) guidelines. GO analysis and KEGG analysis of pathogenic and possible pathogenic genes were performed using the DAVID database, and protein-protein interaction network analysis of pathogenic and possible pathogenic genes was performed using the STRING database. Then, the Kaplan-Meier plotter database, GEPIA database and HPA database were used to analyse the relationship between pathogenic and possible pathogenic genes and patients with liver cancer.

Results

Targeted capture and deep sequencing of 560 cancer-related genes in 10 liver cancer ctDNA samples revealed 8,950 single nucleotide variation (SNV) mutations and 70 INDELS. The most commonly mutated gene was PDE4DIP, followed by SYNE1, KMT2C, PKHD1 and FN1. We compared these results to the COSMIC database and determined that ctDNA could be used for sequencing. According to the ACMG guidelines, we identified 54 pathogenic and possible pathogenic mutations in 39 genes in exons and splice regions of 10 HCC patients and performed GO analysis, KEGG analysis, and PPI network analysis. Through further analysis, four genes significantly related to the prognosis of liver cancer were identified.

Conclusion

In this study, our findings indicate that ctDNA can be used for sequencing. Our results provide some molecular data for the mapping of genetic variation in Chinese patients with liver cancer, which enriches the understanding of HCC pathogenesis and provides new ideas for the diagnosis and prognosis of HCC patients.

LOC285194 inhibits proliferation of human keratinocytes through regulating miR-616/GATA3 pathway

LncRNA LOC285194 has been associated with the occurrence of psoriasis. However, the underlying mechanisms that lead to psoriasis remain unclear. In this study, the expression of LOC285194, miR-616, and GATA3 was determined by western blotting and quantitative real-time PCR, and their relationships were assessed using dual-luciferase reporter assays. The effects of LOC285194 on the proliferation and apoptosis of keratinocytes were investigated using cell counting kit-8 assays and flow cytometry, respectively. Reduced expression of LOC285194 was detected in the skin lesion samples from patients with psoriasis. Overexpression of LOC285194 led to reduced cell viability, cell cycle arrest, and increased cell apoptosis in keratinocytes, whereas LOC285194 silencing resulted in opposite effects. In addition, LOC285194 was found to negatively regulate miR-616, which modulated GATA3 expression through its direct binding to the 3'-untranslated region of GATA3. Knockdown of GATA3 rescued LOC285194 overexpression-mediated cell viability reduction, cell cycle arrest and apoptosis induction in keratinocytes. Taken together, LOC285194 was found to inhibit keratinocyte growth by sponging miR-616 that regulates GATA3.