LINC02476 Promotes the Malignant Phenotype of Hepatocellular Carcinoma by Sponging miR-497 and Increasing HMGA2 Expression

Prediction model of clinical prognosis and immunotherapy efficacy of gastric cancer based on level of expression of cuproptosis-related genes

Background

Gastric cancer is one of the most common malignancies in the world and ranks fourth among cancer-related causes of death. Gastric adenocarcinoma is the most common pathological type of gastric cancer; usually, this tumor is associated with distant metastasis upon first diagnosis and has a poor prognosis. Cuproptosis is a novel mechanism of cell death induced by copper, and is closely related to tumor progression, prognosis and immune response. However, the role of cuproptosis-related genes (CRGs) in the tumor microenvironment (TME) of gastric cancer has yet to be elucidated.

Methods

Gastric adenocarcinoma data were downloaded from the Cancer Genome Atlas (TCGA) database. Through bioinformatics analysis, a risk scoring model was constructed from cuproptosis gene-related lncRNA. Then, we investigated the relationship between prognosis and the TIME of gastric cancer according to clinical characteristics and risk score.

Results

Validation of the model showed that the overall survival (OS) of the high-risk group was significantly lower than that of the low-risk group (P < 0.001) and that the risk score was an independent predictor of prognosis (P < 0.001). The new model was significantly correlated with the prognosis and TIME of patients with gastric cancer, including immune cell infiltration, tumor mutation burden (TMB) score, targeted drug sensitivity, and immune checkpoint gene expression. In addition, a prognostic nomogram was established based on the risk score (AC008915.2, AC011005.4, AC023511.1, AC139792.1, AL355312.2, LINC01094 and LINC02476).

Conclusion

Our analysis revealed that the prognostic model of cuproptosis-related genes could effectively predict the prognosis of patients with gastric cancer and comprehensively establish the relationship between cuproptosis genes and tumor immunity. This may provide a new strategy for the precise treatment of gastric cancer.

High-throughput single nucleus total RNA sequencing of formalin-fixed paraffin-embedded tissues by snRandom-seq

Formalin-fixed paraffin-embedded (FFPE) tissues constitute a vast and valuable patient material bank for clinical history and follow-up data. It is still challenging to achieve single cell/nucleus RNA (sc/snRNA) profile in FFPE tissues. Here, we develop a droplet-based snRNA sequencing technology (snRandom-seq) for FFPE tissues by capturing full-length total RNAs with random primers. snRandom-seq shows a minor doublet rate (0.3%), a much higher RNA coverage, and detects more non-coding RNAs and nascent RNAs, compared with state-of-art high-throughput scRNA-seq technologies. snRandom-seq detects a median of >3000 genes per nucleus and identifies 25 typical cell types. Moreover, we apply snRandom-seq on a clinical FFPE human liver cancer specimen and reveal an interesting subpopulation of nuclei with high proliferative activity. Our method provides a powerful snRNA-seq platform for clinical FFPE specimens and promises enormous applications in biomedical research.

HMGA2 regulation by miRNAs in cancer: affecting cancer hallmarks and therapy response

High mobility group A 2 (HMGA2) is a protein that modulates the structure of chromatin in the nucleus. Importantly, aberrant expression of HMGA2 occurs during carcinogenesis, and this protein is an upstream mediator of cancer hallmarks including evasion of apoptosis, proliferation, invasion, metastasis, and therapy resistance. HMGA2 targets critical signaling pathways such as Wnt/β-catenin and mTOR in cancer cells. Therefore, suppression of HMGA2 function notably decreases cancer progression and improves outcome in patients. As HMGA2 is mainly oncogenic, targeting expression by non-coding RNAs (ncRNAs) is crucial to take into consideration since it affects HMGA2 function. MicroRNAs (miRNAs) belong to ncRNAs and are master regulators of vital cell processes, which affect all aspects of cancer hallmarks. Long ncRNAs (lncRNAs) and circular RNAs (circRNAs), other members of ncRNAs, are upstream mediators of miRNAs. The current review intends to discuss the importance of the miRNA/HMGA2 axis in modulation of various types of cancer, and mentions lncRNAs and circRNAs, which regulate this axis as upstream mediators. Finally, we discuss the effect of miRNAs and HMGA2 interactions on the response of cancer cells to therapy. Regarding the critical role of HMGA2 in regulation of critical signaling pathways in cancer cells, and considering the confirmed interaction between HMGA2 and one of the master regulators of cancer, miRNAs, targeting miRNA/HMGA2 axis in cancer therapy is promising and this could be the subject of future clinical trial experiments.

Hyaluronan-mediated motility receptor antisense RNA 1 promotes hepatitis B virus-related hepatocellular carcinoma progression by regulating miR-627-3p/High Mobility Group AT-hook 2 axis

Hepatocellular carcinoma (HCC) is a common malignancy in the world, with high mortality and poor prognosis. Hepatitis B virus (HBV) is one of the key factors implicated in the occurrence of HCC. Increasing evidence suggests that miRNAs play important roles in the development and metastasis of HBV-associated HCC (HBV-HCC). Here, we performed CCK8 (Cell count kit-8), EdU (5-ethynyl-2’-deoxyuridine) incorporation assay, wound-healing assay, transwell assay to study the changes in the cellular phenotype. Luciferase reporter assay, RNA pull-down experiment, RT-qPCR and western blotting were employed to study molecular mechanism. In addition, we also constructed a mouse HCC xenograft model to verify the functional role of HMMR-AS1/miR-627-3p/HMGA2 signal axis in vivo. Our study demonstrated that HMMR-AS1 was highly expressed in HCC tissues and cell lines, suggesting its implication in the progression of HCC. In addition, in vitro experiments showed that high HMMR-AS1 expression facilitated the migration, invasion, and proliferation of HCC cells. We further revealed that HMMR-AS1 promoted the malignant phenotype of HCC cells by regulating miR-627-3p/HMGA2 axis. Together, our data suggest that HMMR-AS1 regulates HBV-HCC progression via miR-627-3p/HMGA2 axis.

CircRNA Circ-CCND1 Aggravates Hepatocellular Carcinoma Tumorigenesis by Regulating the miR-497-5p/HMGA2 Axis

Circular RNAs (circRNAs) are key regulators in hepatocellular carcinoma (HCC) tumorigenesis and development, yet it is unclear whether circ-CCND1 participates in regulating HCC progression. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed for detecting the expressions of circ-CCND1, microRNA (miR) -497-5p, and high mobility group AT-hook 2 (HMGA2) mRNA in HCC tissues and cell lines. Subcellular fractionation assay was used to analyze the localization of circ-CCND1 in HCC cell lines. Loss-of-function experiments were conducted to examine the effects of circ-CCND1 on HCC cell proliferation, migration, and invasion. Dual-luciferase reporter gene assay was employed for detecting the targeting relationships of circ-CCND1 and miR-497-5p, as well as miR-497-5p and HMGA2, respectively. Western blot was used to detect the regulatory functions of circ-CCND1 and miR-497-5p on HMGA1 expression at protein level. Circ-CCND1 and HMGA2 expressions in HCC were significantly up-regulated and miR-497-5p expression was markedly decreased. High circ-CCND1 expression was associated with relatively large tumor size and lymph node metastasis in HCC patients. In addition, circ-CCND1 was mainly distributed in the cytoplasm of HCC cells. Functionally, knockdown of circ-CCND1 remarkably suppressed HCC cell proliferation, migration, and invasion. Mechanistically, miR-497-5p was a direct target of circ-CCND1 and miR-497-5p specifically modulated HMGA2 expression. Furthermore, miR-497-5p inhibitors and or HMGA2 overexpression partially counteracted the suppressing effect induced by si-circ-CCND1 on the malignant phenotype of HCC cells. Circ-CCND1 plays a cancer-promoting role in HCC by modulating the miR-497-5p/HMGA2 axis. Therefore, targeting circ-CCND1 is likely to be a promising therapeutic strategy for HCC.

Expression and Diagnostic Value of miR-497 and miR-1246 in Hepatocellular Carcinoma

OBJECTIVE

Serum microRNAs (miRNAs) may serve as biomarkers in various cancers. Our study aims to explore the roles of miR-497 and miR-1246 in hepatocellular carcinoma (HCC).

METHODS

The expression levels of miR-497 and miR-1246 were measured by RT-PCR. A correlation analysis was conducted between the expression levels of miR-497 and miR-1246 and clinicopathological characteristics of patients. The receiver operating characteristic (ROC) curve was applied to evaluate the diagnostic efficacy in HCC. In addition, bioinformatics tools were also utilized to predict the potential targets of miR-497 and miR-1246.

RESULTS

The expression level of miR-497 in HCC was significantly down-regulated compared with the control group while the miR-1246 revealed a significantly higher expression level in HCC. There was a significant correlation demonstrated between the expression levels of miR-497 and miR-1246 in preoperative serum of HCC and the differentiation degree, Tumor Node Metastasis (TNM) classification, and metastasis. The expression levels of serum miR-497 and miR-1246 were significantly associated with the diagnosis, prognosis, and overall survival rate of patients with HCC. Moreover, the potential target genes of miR-497 in HCC include ARL2, UBE2Q1, PHF19, APLN, CHEK1, CASK, SUCO, CCNE1, and KIF23. The low expression of these nine genes is associated with a better prognosis of HCC patients. AUTS2 is a novel target gene of miR-1246, and its low expression is significantly related to the low overall survival rate of HCC patients.

CONCLUSIONS

miR-497 and miR-1246 are possibly involved in the progression of HCC by regulating target genes, respectively, and could serve as biomarkers in HCC.

miR-497 inhibits proliferation and invasion in triple-negative breast cancer cells via YAP1

MicroRNA (miR)-497 has been reported as a tumor suppressor in various cancer types. Nonetheless, the regulation of triple-negative breast cancer (TNBC) by miR-497 remains poorly understood. The present study aimed to investigate the potential function and mechanism of miR-497 in TNBC. A total of 36 TNBC and matched non-cancerous tissue samples were collected for analysis. Reverse transcription-quantitative PCR was performed to detect the miR-497 levels in TNBC tissue. The association between miR-497 expression, clinical characteristics and survival was then analyzed. To investigate the role of miR-497 in TNBC, MTT, colony formation, Transwell invasion, cell cycle and cell apoptosis assays were conducted following transfection of miR-497 mimics into the MDA-MB-231 and MDA-MB-468 cell lines. Luciferase reporter assays and western blot analysis were used to confirm the regulation of a putative target of miR-497. The results indicated that the expression of miR-497 was downregulated in the TNBC specimens. Further analysis demonstrated that the expression of miR-497 was downregulated in patients with advanced TNBC stages and that low miR-497 was associated with poor prognosis in patients with TNBC. Transfection of miR-497 mimics inhibited TNBC cell proliferation and increased cell apoptosis in MDA-MB-231 and MDA-MB-468 cells. Moreover, cell migration was inhibited following overexpression of miR-497, which also led to the arrest of the breast cancer cells in the G₀/G₁ phase of the cell cycle. Yes-associated protein 1 (YAP1), a critical molecule in the Hippo pathway, was identified as a target of miR-497. Notably, the protein and mRNA expression levels of YAP1 in MDA-MB-231 and MDA-MB-468 cells were downregulated following overexpression of miR-497. Overall, the findings of the present study indicated that miR-497 inhibited TNBC cell proliferation and migration and induced cell apoptosis by negatively regulating YAP1 expression. Thus, targeting miR-497 may represent a potential strategy for the treatment of TNBC.

LncRNA SNHG6 promotes G1/S-phase transition in hepatocellular carcinoma by impairing miR-204-5p-mediated inhibition of E2F1

Emerging evidence suggests that long noncoding RNAs (lncRNAs) function as competitive endogenous RNA (ceRNA) targeting proteins and genes; however, the role of lncRNAs in hepatocellular carcinoma (HCC) is not well understood. We investigated the mechanism by which lncRNA SNHG6 promotes the development of HCC. RT-qPCR revealed upregulated lncRNA SNHG6 in the HCC setting. Elevated SNHG6 expression was indicative of poor prognosis in patients with HCC. SNHG6 overexpression resulted in increased cyclin D1, cyclin E1, and E2F1 expression both in vitro and in vivo. SNHG6 also promoted HCC cell proliferation by enhancing G1-S phase transition in vitro. Dual luciferase reporter assays, RIP, and RNA pull-down assays demonstrated SNHG6 competitively bound to miR-204-5p and inhibited its expression preventing miR-204-5p from targeting E2F1. Overexpression of miR-204-5p abolished the effect of SNHG6. Our data suggest that SNHG6 functions as a ceRNA that targets miR-204-5p resulting in an increased E2F1 expression and enhanced G1-S phase transition, thereby promoting the tumorigenesis of HCC.

Crosstalk between lncRNA DANCR and miR-125b-5p in HCC cell progression

Objective:

To investigate the mechanism of long noncoding RNA (lncRNA) DANCR on the progression of hepatocellular carcinoma (HCC) cells.

Methods:

The expression levels of DANCR and miR-125b-5p were measured in normal hepatocytes (LO2) and HCC cell lines by quantitative reverse transcription polymerase chain reaction. HepG2 and Huh-7 cells were transfected with sh-DANCR, the negative control (sh-NC), miR-125b-5p mimic, or mimic NC or cotransfected with sh-DANCR and miR-125b-5p inhibitor. HCC cell proliferation was assessed through CCK8 and plate colony formation assay. Western blot quantified the expression levels of Bcl-2, Bax, caspase-3, and cleaved-caspase-3. Apoptotic rate was detected as well as migratory and invasive capacities. The implication of the MAPK signal pathway was assessed by detecting the expression levels of p38, ERK1/2, JNK, p-p38, p-ERK1/2, and p-JNK. Interactions between DANCR and miR-125b-5p were detected by dual luciferase reporter assay.

Results:

In HCC cells, DANCR was highly expressed and miR-125b-5p was decreased. sh-DANCR or miR-125b-5p mimic stimulation reduced HepG2 or Huh-7 cell progression while promoted cell apoptosis evidenced by increased apoptotic rate, elevated levels of Bax and cleaved-caspase-3, and decreased Bcl-2. Moreover, the migration rate and invasiveness of HCC cells were also inhibited by sh-DANCR and miR-125b-5p mimic. Levels of p-p38/p38, p-ERK1/2/ERK1/2, and p-JNK/JNK were suppressed by sh-DANCR and miR-125b-5p mimic. LncRNA DANCR negatively targeted and directly bound to miR-125b-5p. Knockdown of miR-125b-5p could reverse the inhibitory effects of sh-DANCR on HCC cells.

Conclusion:

In HCC cells, lncRNA DANCR sponges miR-125b-5p and activates MAPK pathway, thus facilitating HCC cell progression.