Identifying miRNA-mRNA Pairs and Novel miRNAs from Hepatocelluar Carcinoma miRNomes and TCGA Database

The Computational Analysis of Single Nucleotide Associated with MicroRNA Affecting Hepatitis B Infection

BACKGROUND

MicroRNAs (miRNAs) have a pivotal role in Hepatitis B Virus (HBV) infection and its complications by targeting the cellular transcription factors required for gene expression or directly binding to HBV transcripts. Single Nucleotide Polymorphisms (SNPs) in miRNA genes affect their expression and the regulation of target genes, clinical course, diagnosis, and therapeutic interventions of HBV infection.

METHODS

Computational assessment and cataloging of miRNA gene polymorphisms targeting mRNA transcripts straightly or indirectly through the regulation of hepatitis B infection by annotating the functional impact of SNPs on mRNA-miRNA and miRNA-RBS (miRNA binding sites) interaction were screened by applying various universally available datasets such as the miRNA SNP3.0 software.

RESULTS

2987 SNPs were detected in 139 miRNAs affecting hepatitis B infection. Among them, 313 SNPs were predicted to have a significant role in the progression of hepatitis B infection. The computational analysis also revealed that 45 out of the 313 SNPs were located in the seed region and were more important than others. Has-miR-139-3p had the largest number of SNPs in the seed region (n=6). On the other hand, proteoglycans in cancer, adherens junction, lysine degradation, NFkappa B signaling cascade, ECM-receptor binding, viral carcinogenesis, fatty acid metabolism, TGF-beta signaling pathway, p53 signaling pathway, immune evasion related pathways, and fatty acid biosynthesis were the most important pathways affected by these 139 miRNAs.

CONCLUSION

The results revealed 45 SNPs in the seed region of 25 miRNAs as the catalog in miRNA genes that regulated the hepatitis B infection. The results also showed the most important pathways regulated by these miRNAs that can be targeted for therapeutic purposes.

Autophagy-Related Signatures as Prognostic Indicators for Hepatocellular Carcinoma

Background

Hepatocellular carcinoma (HCC) is the most common and deadly type of liver cancer. Autophagy is the process of transporting damaged or aging cellular components into lysosomes for digestion and degradation. Accumulating evidence implies that autophagy is a key factor in tumor progression. The aim of this study was to determine a panel of novel autophagy-related prognostic markers for liver cancer.

Methods

We conducted a comprehensive analysis of autophagy-related gene (ARG) expression profiles and corresponding clinical information based on The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. The univariate Cox proportional regression model was used to screen candidate autophagy-related prognostic genes. In addition, a multivariate Cox proportional regression model was used to identify five key prognostic autophagy-related genes (ATIC, BAX, BIRC5, CAPNS1, and FKBP1A), which were used to construct a prognostic signature. Real-time qPCR analysis was used to evaluate the expression levels of ARGs in 20 surgically resected HCC samples and matched tumor-adjacent normal tissue samples. In addition, the effect of FKBP1A on autophagy and tumor progression was determined by performing in vitro and in vivo experiments.

Results

Based on the prognostic signature, patients with liver cancer were significantly divided into high-risk and low-risk groups in terms of overall survival (OS). A subsequent multivariate Cox regression analysis indicated that the prognostic signature remained an independent prognostic factor for OS. The prognostic signature possessing a better area under the curve (AUC) displayed better performance in predicting the survival of patients with HCC than other clinical parameters. Furthermore, FKBP1A was overexpressed in HCC tissues, and knockdown of FKBP1A impaired cell proliferation, migration, and invasion through the PI3K/AKT/mTOR signaling pathway.

Conclusion

This study provides a prospective biomarker for monitoring outcomes of patients with HCC.

Recent development of bioinformatics tools for microRNA target prediction

MicroRNAs (miRNAs) are central players that regulate the post-transcriptional processes of gene expression. Binding of miRNAs to target mRNAs can repress their translation by inducing the degradation or by inhibiting the translation of the target mRNAs. High-throughput experimental approaches for miRNA target identification are costly and time-consuming, depending on various factors. It is vitally important to develop the bioinformatics methods for accurately predicting miRNA targets. With the increase of RNA sequences in the post-genomic era, bioinformatics methods are being developed for miRNA studies specially for miRNA target prediction. This review summarizes the current development of state-of-the-art bioinformatics tools for miRNA target prediction, points out the progress and limitations of the available miRNA databases, and their working principles. Finally, we discuss the caveat and perspectives of the next-generation algorithms for the prediction of miRNA targets.

Genetic expression and mutational profile analysis in different pathologic stages of hepatocellular carcinoma patients

BACKGROUND

The clinical pathologic stages (stage I, II, III-IV) of hepatocellular carcinoma (HCC) are closely linked to the clinical prognosis of patients. This study aims at investigating the gene expression and mutational profile in different clinical pathologic stages of HCC.

METHODS

Based on the TCGA-LIHC cohort, we utilized a series of analytical approaches, such as statistical analysis, random forest, decision tree, principal component analysis (PCA), to identify the differential gene expression and mutational profiles. The expression patterns of several targeting genes were also verified by analyzing the Chinese HLivH060PG02 HCC cohort, several GEO datasets, HPA database, and diethylnitrosamine-induced HCC mouse model.

RESULTS

We identified a series of targeting genes with copy number variation, which is statistically associated with gene expression. Non-synonymous mutations mainly existed in some genes (e.g.,TTN, TP53, CTNNB1). Nevertheless, no association between gene mutation frequency and pathologic stage distribution was detected. The random forest and decision tree modeling analysis data showed a group of genes related to different HCC pathologic stages, including GAS2L3 and SEMA3F. Additionally, our PCA data indicated several genes associated with different pathologic stages, including SNRPA and SNRPD2. Compared with adjacent normal tissues, we observed a highly expressed level of GAS2L3, SNRPA, and SNRPD2 (P = 0.002) genes in HCC tissues of our HLivH060PG02 cohort. We also detected the high expression pattern of GAS2L3, SEMA3F, SNRPA, and SNRPD2 in the datasets of GSE102079, GSE76427, GSE64041, GSE121248, GSE84005, and the qPCR assay using diethylnitrosamine-induced HCC mouse model. Moreover, SEMA3F and SNRPD2 protein were highly stained in the HCC tissues of the HPA database. The high expression level of these four genes was associated with the poor survival prognosis of HCC cases.

CONCLUSIONS

Our study provides evidence regarding the gene expression and mutational profile in different clinical pathologic stages of TCGA HCC cases. Identifying four targeting genes, including GAS2L3, SNRPA, SNRPD2, and SEMA3F, offers insight into the molecular mechanisms associated with different prognoses of HCC.

Bioinformatics Analyses of Potential miRNA-mRNA Regulatory Axis in HBV-related Hepatocellular Carcinoma

Aims: We aimed to explore the crucial miRNA-mRNA axis through bioinformatics analysis and provide evidences for the development of pathophysiological mechanisms and new therapies for HBV-related HCC. Methods: MiRNA (GSE76903) and mRNA (GSE77509) dataset were used to screen differentially expressed miRNAs (DE-miRNAs) and differentially expressed mRNAs (DE-mRNAs) using R software. Overlapping genes between DE-mRNAs and target genes of DE-miRNAs were identified as candidate genes. Hub genes were obtained via cytohubba analysis. The expression at protein and mRNA levels and prognostic value of hub genes were evaluated based on The Cancer Genome Atlas (TCGA) data. Key miRNA-mRNA axes were constructed according to predicted miRNA-mRNA pairs. MiRNA expression and prognostic role were respectively identified using starBase v3.0 and Kaplan-Meier plotter database. Real-time PCR was performed to verify the expression of crucial miRNAs and mRNAs. Coexpression of crucial miRNA and mRNA were analyzed using starBase v3.0. Results: CDK1, CCNB1, CKS2 and CCNE1 were screened as hub genes, which were significantly upregulated at protein and mRNA levels. These up-regulated hub genes were also significantly associated with poor prognosis. Hsa-mir-195-5p/CDK1, hsa-mir-5589-3p/CCNB1 and hsa-let-7c-3p/CKS2 were screened as critical miRNA-mRNA axes. Critical miRNAs were decreased in HCC, which indicates unfavourable prognosis. QPCR results showed that crucial miRNAs were decreased, whereas critical mRNAs were increased in HBV-related HCC. A reverse relationship between miRNA and mRNA in crucial axis was further verified. Conclusion: This study identified several miRNA-mRNA axes in HBV-related HCC. Hsa-mir-195-5p/CDK1, hsa-mir-5589-3p/CCNB1 and hsa-let-7c-3p/CKS2 might serve as potential prognostic biomarkers and therapeutic targets for HBV-related HCC.

miR-490: A potential biomarker and therapeutic target in cancer and other diseases

MicroRNAs (miRNAs) are small non-coding RNAs that function as posttranscriptional gene regulators. Among a pool of >2600 known human mature miRNAs, only a small subset have been functionally interrogated and a further smaller pool shown to be associated with the pathogenesis of a variety of diseases suggesting their critical role in maintaining homeostasis. Here, we draw your attention to one such miRNA, miR-490, that has been reported to be deregulated in a myriad of diseases (23 diseases) ranging from cardiomyopathy, depression, and developmental disorders to many cancer types (28 cancer types), such as hepatocellular carcinoma, gastric cancer, cancers of the reproductive and central nervous system among others. The prognostic and diagnostic potential of miR-490 has been reported in many diseases including cancer underlining its clinical relevance. We also collate a complex plethora of epigenetic (histone and DNA methylation), transcriptional (TF), and posttranscriptional (lncRNA and circRNA) mechanisms that have been shown to tightly regulate miR-490 levels. The targets of miR-490 involve a range of cancer-related genes involved in the regulation of various cancer hallmarks like cell proliferation, migration, and invasion, apoptotic cell death, angiogenesis, and so forth. Overall, our in-depth review highlights for the first time the emerging role of miR-490 in disease pathology, diagnosis, and prognosis that assigns a unique therapeutic potential to miR-490 in the era of precision medicine.

Construction of a potential microRNA, transcription factor and mRNA regulatory network in hepatocellular carcinoma

Background

Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and the third leading cause of cancer-related death. MicroRNAs and transcription factors (TFs) cooperate to regulate the same target gene, thus affecting the progression of HCC.

Methods

Differentially expressed miRNAs and mRNAs were screened. Functional enrichment analysis of these HCC-related mRNAs was performed, and a protein-protein interaction network was constructed. TFs that regulate these miRNAs and hub genes were also screened.

Results

Ten differentially upregulated miRNAs and 5 differentially downregulated miRNAs were screened. Additionally, 183 downregulated mRNAs and 303 upregulated mRNAs that are potentially bound to these differentially expressed miRNAs were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the differentially expressed mRNAs were significantly enriched in pathways in cancer, the Wnt signaling pathway, and the Rap1 signaling pathway. Then, 220 TFs were identified for 5 candidate genes of the downregulated mRNAs, and 258 TFs were identified for 9 candidate genes of the upregulated mRNAs. Finally, the 9 upregulated hub genes were related to higher overall survival (OS) in the low-expression group, and 4/5 downregulated hub genes were related to higher OS in the high-expression group.

Conclusions

This study constructed a potential regulatory network between candidate molecules and that need to be further verified. These regulatory relationships are expected to clarify the new molecular mechanisms of the occurrence and development of HCC.

Value of miR-1271 and glypican-3 in evaluating the prognosis of patients with hepatocellular carcinoma after transcatheter arterial chemoembolization

BACKGROUND

Hepatocellular carcinoma (HCC) is the third leading cause of cancer death, causing about 750000 deaths worldwide every year. Patients with advanced hepatocellular carcinoma will often only receive transcatheter arterial chemoembolization (TACE). Glypican-3 (GPC3) is one of the most promising serum markers for HCC. Abnormal expression of miRNAs may be involved in the occurrence and development of tumor.

AIM

To explore the value of miR-1271 and GPC3 in evaluating the prognosis of patients with HCC after TACE.

METHODS

From January 2016 to December 2018, 162 patients with advanced HCC who received TACE in our hospital were selected into the cancer group, and 162 patients who underwent physical examination during the same period were selected into the health group. The patients in the HCC group were treated with TACE. The changes of serum GPC3 and circulating miR-1271 in the HCC before and after TACE were analyzed. The expression of serum GPC3 was detected by enzyme-linked immunosorbent assay, and the expression of circulating miR-1271 was detected by real-time quantitative polymerase chain reaction. The methodological results of sensitivity, specificity, and accuracy of miR-1271 and GPC3 alone and joint detection of HCC were also evaluated.

RESULTS

The level of serum GPC3 in patients with HCC was significantly higher than that in healthy controls. GPC3 levels were increased in both HCC patients and those treated with TACE compared with healthy controls. After TACE, the level of serum GPC3 was significantly lower than that before treatment (P < 0.05), and the level of circulating miR-1271 was significantly higher than that before treatment (P < 0.05). There were 112 cases (69.14%) with remission (complete remission + complete remission + stable disease) and 50 cases (30.86%) with relapse disease progression in HCC patients. After TACE, the miR-1271 level in patients with remission and relapse was lower than that in the healthy group, and the GPC3 level was higher than that in the healthy group, the differences were statistically significant (P < 0.05). The miR-1271 of relapsed patients was lower than that of remission patients, and the level of GPC3 was higher than that of remission patients, and the difference was statistically significant (P < 0.05). The sensitivity of combined detection of miR-1271 and GPC3 was significantly higher than that of single detection, and the difference was statistically significant (P < 0.05); while the specificity of the two combined detections was lower than that of the single detection; and the accuracy was slightly higher than that of single detection, but the difference was not statistically significant.

CONCLUSION

The level of miR-1271 in patients with HCC was significantly increased and the level of GPC3 was decreased after TACE. Monitoring the levels of serum GPC3 and circulating miR-1271 has important clinical reference value for evaluating the prognosis of patients with HCC. The levels of serum GPC3 and circulating miR-1271 may help to determine tumor recurrence, evaluate survival status, and guide the next step of treatment.

Integrative analysis of breast cancer profiles in TCGA by TNBC subgrouping reveals novel microRNA-specific clusters, including miR-17-92a, distinguishing basal-like 1 and basal-like 2 TNBC subtypes

Background

The term triple-negative breast cancer (TNBC) is used to describe breast cancers without expression of estrogen receptor, progesterone receptor or HER2 amplification. To advance targeted treatment options for TNBC, it is critical that the subtypes within this classification be described in regard to their characteristic biology and gene expression. The Cancer Genome Atlas (TCGA) dataset provides not only clinical and mRNA expression data but also expression data for microRNAs.

Results

In this study, we applied the Lehmann classifier to TCGA-derived TNBC cases which also contained microRNA expression data and derived subtype-specific microRNA expression patterns. Subsequent analyses integrated known and predicted microRNA-mRNA regulatory nodes as well as patient survival data to identify key networks. Notably, basal-like 1 (BL1) TNBCs were distinguished from basal-like 2 TNBCs through up-regulation of members of the miR-17-92 cluster of microRNAs and suppression of several known miR-17-92 targets including inositol polyphosphate 4-phosphatase type II, INPP4B.

Conclusions

These data demonstrate TNBC subtype-specific microRNA and target mRNA expression which may be applied to future biomarker and therapeutic development studies.

Identifying TF-miRNA-mRNA regulatory modules in nitidine chloride treated HCC xenograft of nude mice

Nitidine chloride (NC) has reported tumor suppressive activities for various human cancers, including hepatocellular carcinoma (HCC). Nevertheless, the pharmacological mechanism of NC on HCC has not previously been elucidated. SMMC7721 HCC cell lines, before and after the treatment of NC, were injected into nude mice for a subcutaneous tumor xenograft model. MiRNA and mRNA sequencing were performed for both control and treated xenograft tissues to further analyze differential expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs). The ten most significant DEmiRNAs were selected for prediction of transcription factors (TFs) and target genes. We constructed an interconnected network composed of TFs the ten most significant DEmiRNAs, the 100 most significant DEmRNAs, and selected target genes from online programs. Hub genes chosen from a protein-to-protein interaction network of hub genes were validated by correlation analysis, expression analysis, and Kaplan-Meier survival analysis. The five most up-regulated miRNAs (hsa-miR-628-5p, hsa-miR-767-5p, hsa-miR-767-3p, hsa-miR-1257, and hsa-miR-33b-3p) and the five most down-regulated miRNAs (hsa-miR-378d, hsa-miR-136-5p, hsa-miR-451a, hsa-miR-144-5p, and hsa-miR-378b) were singled out from the DEmiRNAs. Functional annotations indicated that potential target genes of the top five up-regulated miRNAs were mainly clustered in molecular processes concerning epithelial-to-mesenchymal transition. Hub genes, such as ITGA6 and ITGB4, were validated as up-regulated in HCC; both IFIT2 and IFIT3 were revealed by Kaplan-Meier survival curves as good prognostic factors for HCC. In summary, the regulating axes of NC-DEmiRNAs-DEmRNAs and TFs-DEmiRNAs-DEmRNAs in HCC that were discovered in this study may shed light on the possible molecular mechanism of NC in HCC.

Hsa_circ_0035483 sponges hsa-miR-335 to promote the gemcitabine-resistance of human renal cancer cells by autophagy regulation

Renal clear cell carcinoma (RCC) is the most common pathological type of renal carcinoma and drug resistance often occurs. We studied the effect of hsa_circ_0035483 on gemcitabine sensitivity in RCC, and explored its regulatory effect on downstream hsa-miR-335 and Cyclin B1 (CCNB1). High-throughput sequencing was used to analyze the differentially expressed circRNA in RCC. The expressions of hsa_circ_0035483, hsa-miR-335, CCNB1, and autophagy-related proteins were detected by RT-PCR or Western blot. The target relationships were revealed by RNA pulldown assay and dual luciferase report assay. Autophagy marker LC3 was detected by immunofluorescence. Cell viability was detected by MTT assay. Hsa_circ_0035483 can facilitate gemcitabine-induced autophagy, and enhance the resistance of RCC to gemcitabine. Hsa-miR-335 is the target regulatory point of hsa_circ_0035483. In addition, hsa_circ_0035483 promotes autophagy and tumor growth and enhances gemcitabine resistance in RCC by regulating hsa-miR-335/CCNB1, and silenced hsa_circ_0035483 can enhance gemcitabine sensitivity in vivo. Hsa_circ_0035483 may be the target of gemcitabine resistance in the treatment of RCC.