A nomogram based on 4-lncRNAs signature for improving prognostic prediction of hepatocellular carcinoma

Purpose Long noncoding RNAs (lncRNAs) with abnormal expression are frequently seen in hepatocellular cancer patients (HCC). Previous studies have reported the correlation between lncRNA and prognosis processes of HCC patients. In this research, a graphical nomogram with lncRNAs signatures, T, M phases was developed using the rms R package to estimate the survival rates of HCC patients in year 1, 3, and 5. Methods To find the prognostic lncRNA and create the lncRNA signatures, univariate Cox survival analysis and multivariate Cox regression analysis were chosen. The rms R software package was used to build a graphical nomogram based on lncRNAs signatures to predict the survival rates in of HCC patients in 1, 3, and 5 years. Using “edgeR”, “DEseq” R packages to find the differentially expressed genes (DEGs). Results Firstly, a total of 5581 DEGs including 1526 lncRNAs and 3109 mRNAs were identified through bioinformatic analysis, of which 4 lncRNAs (LINC00578, RP11-298O21.2, RP11-383H13.1, RP11-440G9.1) were identified to be strongly related to the prognosis of liver cancer (P < 0.05). Moreover, we constructed a 4-lncRNAs signature by using the calculated regression coefficient. 4-lncRNAs signature is identified to significantly correlated with clinical and pathological characteristics (such as T stage, and death status of HCC patients). Conclusions A prognostic nomogram on the base of 4-lncRNAs markers was built, which is capable to accurately predict the 1-year, 3-year, and 5-year survival of HCC patients after the construction of the 4-lncRNAs signature linked with prognosis of HCC (AU)

A nomogram based on 4-lncRNAs signature for improving prognostic prediction of hepatocellular carcinoma.

PURPOSE: Long noncoding RNAs (lncRNAs) with abnormal expression are frequently seen in hepatocellular cancer patients (HCC). Previous studies have reported the correlation between lncRNA and prognosis processes of HCC patients. In this research, a graphical nomogram with lncRNAs signatures, T, M phases was developed using the rms R package to estimate the survival rates of HCC patients in year 1, 3, and 5. METHODS: To find the prognostic lncRNA and create the lncRNA signatures, univariate Cox survival analysis and multivariate Cox regression analysis were chosen. The rms R software package was used to build a graphical nomogram based on lncRNAs signatures to predict the survival rates in of HCC patients in 1, 3, and 5 years. Using "edgeR", "DEseq" R packages to find the differentially expressed genes (DEGs). RESULTS: Firstly, a total of 5581 DEGs including 1526 lncRNAs and 3109 mRNAs were identified through bioinformatic analysis, of which 4 lncRNAs (LINC00578, RP11-298O21.2, RP11-383H13.1, RP11-440G9.1) were identified to be strongly related to the prognosis of liver cancer (P < 0.05). Moreover, we constructed a 4-lncRNAs signature by using the calculated regression coefficient. 4-lncRNAs signature is identified to significantly correlated with clinical and pathological characteristics (such as T stage, and death status of HCC patients). CONCLUSIONS: A prognostic nomogram on the base of 4-lncRNAs markers was built, which is capable to accurately predict the 1-year, 3-year, and 5-year survival of HCC patients after the construction of the 4-lncRNAs signature linked with prognosis of HCC.

PTBP1 promotes hepatocellular carcinoma progression by regulating the skipping of exon 9 in NUMB pre-mRNA.

Aberrant alternative splicing is one of the important causes of cancer. Polypyrimidine tract binding protein 1 (PTBP1) has been found to be involved in splicing regulation in a variety of tumors. Here, we observed significant up-regulation of PTBP1 in primary hepatocellular carcinoma (HCC) tissues. High levels of PTBP1 expression were associated with poor prognosis and increased metastatic potential in HCC. In vitro studies demonstrated that elevated PTBP1 promoted both migration and invasion by HCC cells. In contrast, knockdown of PTBP1 significantly inhibited the migration and invasion of HCC cells in vitro. Further, up-regulation of PTBP1 markedly accumulated the expression of oncogenic isoform of NUMB, NUMB-PRRL. We observed two isoforms of NUMB, NUMB-PRRL and NUMB-PRRS exhibit opposite function in HCC cells, which partially explain PTBP1 plays the tumor promoting roles in a NUMB splicing-dependent manner. In summary, our study indicates that PTBP1 may serve as an oncogene in HCC patients by regulating the alternative splicing of NUMB exon 9 and could potentially serve as a prognostic indicator.

Effects of melanoma differentiation associated gene-7 (MDA-7/IL-24) on apoptosis of liver cancer cells via regulating the expression of B-cell lymphoma-2.

The present study investigated the mechanism of selective killing of liver cancer cells of melanoma differentiation associated gene-7 (MDA-7, also called IL-24α) in order to provide a theoretical basis for gene therapy of liver cancer. A recombinant eukaryotic expression vector (pcDNA3-MDA-7) containing human MDA-7 gene was constructed, which was then delivered to liver cancer cell line HepG2 and normal liver cell line L02. The positive cell clone was screened by G418. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was performed to confirm the occurrence of MDA-7 transcription in the transfected cells. The protein expression of MDA-7 was determined by western blot analysis. The effects of MDA-7 on liver cancer cell proliferation and apoptosis were investigated through MTT assay and flow cytometry by Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) double-staining. The mitochondrial protein was extracted from the normal liver cell line L02 and liver cancer cell line HepG2 at 3 day post-culture, in which the alterations of anti-apoptotic B-cell lymphoma-2 (Bcl-2), pro-apoptotic Bcl-2 associated X protein (Bax), mitochondria-released cytochrome c and caspase 9 were determined by western blot analysis. pcDNA3-MDA-7 mediated the expression of foreign gene MDA-7 in HepG2 and L02 cells. MDA-7 promoted liver cancer cell apoptosis and inhibited cell proliferation; while no effect was exerted on normal liver cells, as determined by the MTT assay and flow cytometry. Relative to the L02 cells, the protein expression of Bcl-2 was downregulated in the HepG2 cells, while that of Bax, cytochrome c and caspase 9 were upregulated. In the study, the eukaryotic expression vector pcDNA3-MDA-7 was successfully constructed, it can mediate the expression of MDA-7 in human liver cancer cells and normal liver cells and inhibits the proliferation of human liver cancer cells through the restored expression of mitochondrial pro-apoptotic Bcl-2.