Identification of long non-coding RNA-related and -coexpressed mRNA biomarkers for hepatocellular carcinoma

Construction of a genome instability-derived lncRNA-based risk scoring system for the prognosis of hepatocellular carcinoma

Emerging evidence revealed the critical roles of long non-coding RNAs (lncRNAs) in maintaining genomic instability. However, genome instability-associated lncRNAs (GILncRNAs) and their performance in clinical prognostic significance in hepatocellular carcinoma (HCC) are rarely reported. Our study constructed a computational framework integrating somatic mutation information and lncRNA expression profiles of HCC genome and we identified 88 GILncRNAs of HCC. Function enrichment analysis revealed that GILncRNAs were involved in various metabolism processes and genome instability of cancer. A genome instability-derived lncRNA-based gene signature (GILncSig) was constructed using training set data. The performance of GILncSig for outcome prediction was validated in testing set and The Cancer Genome Atlas (TCGA) set. The multivariate cox regression analysis and stratification analysis demonstrated GILncSig could serve as an independent prognostic factor for the overall survival of HCC patients. The time-dependent Receiver Operating Characteristic (ROC) curve illustrated GILncSig outperformed two recently published lncRNA signatures for overall survival prediction. The combination of GILncSig and tumor protein p53 (TP53) mutation status exhibited better prognostic performance in survival evaluation compared to TP53 mutation status alone. AC145343.1 was further validated to be a risk factor for HCC in vitro among GILncSig. Overall, our study provided a novel approach for identification of genome instability-associated lncRNAs and established an independent risk score system for outcome prediction of HCC patients, which provided a new insight for exploring in-depth mechanism and potential therapy strategy.

Construction of a genome instability-derived lncRNA-based risk scoring system for the prognosis of hepatocellular carcinoma

Emerging evidence revealed the critical roles of long non-coding RNAs (lncRNAs) in maintaining genomic instability. However, genome instability-associated lncRNAs (GILncRNAs) and their performance in clinical prognostic significance in hepatocellular carcinoma (HCC) are rarely reported. Our study constructed a computational framework integrating somatic mutation information and lncRNA expression profiles of HCC genome and we identified 88 GILncRNAs of HCC. Function enrichment analysis revealed that GILncRNAs were involved in various metabolism processes and genome instability of cancer. A genome instability-derived lncRNA-based gene signature (GILncSig) was constructed using training set data. The performance of GILncSig for outcome prediction was validated in testing set and The Cancer Genome Atlas (TCGA) set. The multivariate cox regression analysis and stratification analysis demonstrated GILncSig could serve as an independent prognostic factor for the overall survival of HCC patients. The time-dependent Receiver Operating Characteristic (ROC) curve illustrated GILncSig outperformed two recently published lncRNA signatures for overall survival prediction. The combination of GILncSig and tumor protein p53 (TP53) mutation status exhibited better prognostic performance in survival evaluation compared to TP53 mutation status alone. AC145343.1 was further validated to be a risk factor for HCC in vitro among GILncSig. Overall, our study provided a novel approach for identification of genome instability-associated lncRNAs and established an independent risk score system for outcome prediction of HCC patients, which provided a new insight for exploring in-depth mechanism and potential therapy strategy.

Regulation of Tumorigenesis in Hepatocellular Carcinoma via the AKT3 Pathway in Cell Lines

BACKGROUND

The estimation of hepatocellular carcinoma (HCC) is tremendously inferior because of the formation of chemoresistance, integrated with essentially increased stemness belongings. At present, the relevance between miR-122 and cancer development was mostly undisclosed with single study reflecting its importance in glioblastoma. Material and Methods. The research here was focused to investigate the task of miR-122 to modulate tumorigenesis in hepatocellular carcinoma by aiming AKT3 in the management of hepatocellular carcinoma stemness and chemosensitivity. The method of QRT-PCR was performed to investigate the aspect of miR-122 and AKT3 in tissue sample and cell lines. The evaluation was done using gain- or loss-of-function in order to retrieve the function of miR-122 in the hepatocellular carcinoma cells, including cell multiplication and stemness effects. The properties of hepatocellular carcinoma were discovered by the development of sphere development, cell feasibility, and the emergence of colony. RNA immunoprecipitation (RIP), luciferase reporter, and the RNA pull down evaluation were conducted to investigate the communication between the miR-122 and AKT3. Therefore, a naked mouse xenograft specimen was set up for the in vivo analysis.

RESULTS

Here, we determined the new role of AKT3 and unmediated target of miR-122. The reimposition of miR-122 appearance in the hepatocellular carcinoma cell lines reduces the levels of AKT3 and also hinders the relocation and expansion of cells by prompting apoptosis. These phenotypes are antitumor in nature and can be retrieved by the reorganization of the AKT3 expression which signals the crucial role of AKT3 in the miR-122 arbitrated HCC modification. The in vivo analysis demonstrated the reimposition of miR-122 entirely obstructing the xenograft expansion to manage tumorigenesis in hepatocellular carcinoma and a prospective remedial entrant for the liver cancer.

CONCLUSION

In this study, it was observed that miR-122 encourages the stemness role of hepatocellular carcinoma and diminishes the chemosensitivity by cleaning the miR-122 in order to initiate the AKT3. The in vivo study reflected the restoration of miR-122 which completely hinders the xenograft growth to regulate the tumorigenesis in the HCC.

Microtubule-associated protein tau (MAPT) is a promising independent prognostic marker and tumor suppressive protein in clear cell renal cell carcinoma

INTRODUCTION

Microtubule-associated protein tau (MAPT) overexpression has been linked to poor prognosis in several cancers. MAPT-AS1 is a long noncoding RNA existing at the antisense strand of the MAPT promoter region. The clinical significance of MAPT and MAPT-AS-1 in clear cell renal cell carcinoma (ccRCC) is unknown. This study aimed to assess the expression and function of MAPT and MAPT-AS1 in ccRCC.

METHODS

The expression of MAPT was determined using immunohistochemistry in ccRCC. The effects of MAPT knockdown on cell growth and invasion were evaluated and the interaction between MAPT and microtubule-associated protein tau antisense (MAPT-AS1) were analyzed. The expression of MAPT-AS1 was determined using quantitative reverse transcription polymerase chain reaction in ccRCC tissues. We investigated the effect of MAPT-AS1 knockdown on cell growth and invasion. We analyzed the regulation of MAPT and MAPT-AS1.

RESULTS

Immunohistochemistry in 135 ccRCC cases showed that 61% of the cases were positive for MAPT. Kaplan-Meier analysis showed that the low expression of MAPT was associated with poor overall survival after nephrectomy. Knockdown of MAPT enhanced cell growth and invasion. quantitative reverse transcription polymerase chain reaction revealed a positive correlation between MAPT and MAPT-AS1. The expression of MAPT-AS1 was higher in ccRCC tissue than in nonneoplastic kidney tissue. Kaplan-Meier analysis showed that the low expression of MAPT-AS1 was associated with poor overall survival after nephrectomy by in silico analysis. MAPT-AS1 knockdown promoted cell growth and invasion activity. P53 knockout suppressed the expression of MAPT and MAPT-AS1.

CONCLUSION

These results suggest that MAPT and MAPT-AS1 may be promising predictive biomarkers for survival and play a tumor-suppressive role in ccRCC.

Forms of diagnostic material as sources of miRNA biomarkers in hepatocellular carcinoma: a preliminary study

Aim: To assess the diagnostic value of selected miRNAs from various material collected from hepatocellular carcinoma (HCC) patients. Patients & methods: Tissue, serum, urine and fecal samples from HCC patients and healthy individuals were screened for associated miRNAs using microarray analysis; the selected miRNAs were then validated by real time-quantitative PCR on 65 patients. Results: Serum miR-122, a combination of serum miR-155 with miR-885-5p, a combination of urinary miR-532-3p with miR-765, and fecal miR-320a displayed 100% efficiency in discriminating patients from controls. A combination of urinary miR-532-3p and miR-765 allowed patients with neoplastic grade G3 to be distinguished from those with G1 and G2. Conclusion: Additionally to serum, urine and feces also appeared to be valuable source of potential HCC noninvasive miRNA biomarkers.

The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics meets medicine

During June 10–12, 2018, the International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held in Los Angeles, California, USA. The conference included 11 scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics ranging from 3D genome structure analysis and visualization, next generation sequencing analysis, computational drug discovery, medical informatics, cancer genomics to systems biology. While medical genomics has always been a main theme in ICIBM, this year we for the first time organized the BMC Medical Genomics Supplement for ICIBM. Here, we describe 15 ICIBM papers selected for publishing in BMC Medical Genomics.