Differentially Expressed Long Noncoding RNAs Involved in FUBP1 Promoting Hepatocellular Carcinoma Cells Proliferation

Background. Far upstream element-binding protein 1 (FUBP1) is reported to be involved in cancer development by regulating the transcription of c-myc gene through binding to far upstream element. Highly expressed FUBP1 was negatively correlated with survival rate of patients with hepatocellular carcinoma (HCC) and could promote the proliferation of HCC cells. However, the downstream mechanism of FUBP1 has not yet been clearly explained. This study is aimed at identifying the expression profiles of long noncoding RNA (lncRNA) in HCC cells in response to FUBP1 overexpression and at investigating the possible lncRNAs that participated in cell proliferation process regulated by FUBP1. Methods. The overexpression of FUBP1 was mediated by lentiviral infection on 3 different types of HCC cell lines (MHCC97-H, MHCC97-L, and Huh-7). The expression of target genes was detected by quantitative reverse transcription-PCR (RT-PCR) and western blotting assays. Microarray and quantitative RT-PCR were applied to screen the differentially expressed lncRNAs in HCC cells after FUBP1 overexpression. The Cell Counting Kit-8 assay was used to confirm the growth vitality of HCC cells. Results. The growth vitality of HCC cells was significantly increased after lentivirus infection. A total of 12 lncRNAs had the same expression trend in the 3 HCC cell lines in response to FUBP1 overexpression, including 3 upregulated lncRNAs and 9 downregulated lncRNAs. Coexpression analysis of dysregulated lncRNAs-mRNAs network showed that lnc-LYZ-2 was the lncRNA most relevant to FUBP1. Inhibition of lnc-LYZ-2 could significantly relieve the proproliferation effect of FUBP1 on HCC cells, suggesting that lnc-LYZ-2 was partially involved in proproliferation regulation of FUBP1. Conclusions. Our results indicated that FUBP1 induced the abnormal expression of lncRNAs and the FUBP1-lncRNAs coexpression network in HCC cells, which could provide theoretical and experimental basis for FUBP1-lncRNAs network involved in HCC development.

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CircRNA profiling identifies circRNF180 as a tumor suppressor in hepatocellular carcinoma

Epigenomics ◽

10.2217/epi-2020-0385 ◽

2021 ◽

Vol 13 (7) ◽

pp. 513-530

Author(s):

Xi Zeng ◽

Chao Tan ◽

Meile Mo ◽

Xiaoling Qin ◽

Xiaoyun Ma ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Tumor Suppressor ◽

Real Time ◽

Real Time Pcr ◽

Expression Profiles ◽

Cell Counting ◽

Migration And Invasion ◽

Quantitative Real Time Pcr ◽

Potential Biomarker ◽

Hcc Cells

Aim: To explore the expression profiles and functions of circRNAs in hepatocellular carcinoma (HCC). Materials & methods: We obtained circRNA expression profiles through RNA sequencing. Expression levels of circRNAs were confirmed by quantitative real-time PCR. The effects on HCC progression were determined using Cell Counting Kit 8, clone formation and transwell assays. Results: We identified 114 upregulated and 144 downregulated circRNAs in HCC tissues. The results of quantitative real-time PCR showed that circGNAO1, circRNF180 and circMERTK were significantly downregulated in HCC tissues, whereas circSNX6 was significantly upregulated. CircRNF180 was associated with microvascular invasion. Overexpression of circRNF180 inhibits the proliferation, colony formation, migration and invasion of HCC cells. Conclusion: CircRNF180 may function as a tumor suppressor and could serve as a potential biomarker and therapeutic target in HCC.

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MiR-486-5p Suppresses Proliferation and Migration of Hepatocellular Carcinoma Cells through Downregulation of the E3 Ubiquitin Ligase CBL

BioMed Research International ◽

10.1155/2019/2732057 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9

Author(s):

Jia He ◽

Bin Xiao ◽

Xiaoyan Li ◽

Yongyin He ◽

Linhai Li ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Lines ◽

Ubiquitin Ligase ◽

Target Genes ◽

E3 Ubiquitin Ligase ◽

Tumor Stage ◽

Suppressor Gene ◽

Cell Counting ◽

And Migration ◽

Proliferation And Migration

MicroRNAs have been broadly implicated in cancer, but precise functions and mechanisms in carcinogenesis vary among cancer types and in many cases remain poorly understood. Hepatocellular carcinoma (HCC) is among the most frequent and lethal cancers. The aim of the present study was to investigate the role of miR-486-5p in HCC and identify its specific target. MiR-486-5p was significantly downregulated in HCC tissues and cell lines compared with noncancerous tissues and, respectively, although expression level was not correlated with the degree of infiltration or tumor stage. However, miR-486-5p overexpression in HCC cells inhibited proliferation and migration as evidenced by CCK-8 cell counting, wound healing, and transwell assays, indicating that miR-486-5p is an HCC suppressor. We employed four miRNA databases to predict the target genes of miR-486-5p and verified retrieved genes using qPCR and western blotting. The E3 ubiquitin ligase CBL was significantly downregulated by miR-486-5p overexpression in HCC cell lines at both mRNA and protein level, and overexpression of CBL counteracted the inhibitory effects of miR-486-5p on HCC cell proliferation and migration. Moreover, CBL expression was negatively correlated with miR-486-5p expression in HCC tissues. Collectively, our results suggest that miR-486-5p may act as a tumor suppressor gene in HCC by downregulating CBL expression.

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Hsa_circ_0013290 Acts as Cancer-Promoting Gene in Hepatocellular Carcinoma

Cancer Control ◽

10.1177/10732748211055681 ◽

2021 ◽

Vol 28 ◽

pp. 107327482110556

Author(s):

Xi Luo ◽

Yicun Liu ◽

Han Li ◽

Tiaochun Cheng ◽

Jianjun Wu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Lines ◽

Cell Invasion ◽

Cell Apoptosis ◽

Subcellular Location ◽

Cell Counting ◽

Cell Cycle Distribution ◽

Invasion And Migration ◽

And Migration ◽

Hcc Cells

Background As a new class of non-coding RNAs, circRNAs have been recently reported to be involved in the tumorigenesis and progression of human cancers. In the current study, we attempted to explore the potential function of a novel circRNA (hsa_circ_0013290) in hepatocellular carcinoma (HCC). Methods Relative hsa_circ_0013290 expression was analyzed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The subcellular location of hsa_circ_0013290 was performed by RNA subcellular isolation and fluorescence in situ hybridization (FISH) assays. The effect of hsa_circ_0013290 on proliferation was detected by Cell Counting Kit-8 (CCK-8) assays. The effect of hsa_circ_0013290 on cell cycle distribution and apoptosis was detected by flow cytometry. The invasion and migration abilities of hsa_circ_0013290 were detected by transwell assays. Results Hsa_circ_0013290 is significantly upregulated in HCC cell lines and mainly located in cytoplasm of HCC cells. Hsa_circ_0013290 overexpression promotes cell invasion and migration and inhibits cell apoptosis. In contrast, hsa_circ_0013290 knockdown impedes cell invasion and migration and accelerates cell apoptosis. However, hsa_circ_0013290 did not affect cell proliferation. Conclusions Hsa_circ_0013290 is overexpressed in HCC cell lines and is mainly located in the cytoplasm of HCC cells. Hsa_circ_0013290 promotes cell invasion and migration, and inhibits cell apoptosis.

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Inhibition of HIF1A-AS1 promoted starvation-induced hepatocellular carcinoma cells apoptosis by reducing HIF-1α/mTOR mediated autophagy

10.21203/rs.2.23954/v2 ◽

2020 ◽

Author(s):

Fenfen Hong ◽

Yu Gao ◽

Yang Li ◽

Linfeng Zheng ◽

Feng Xu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Lines ◽

Disease Free Survival ◽

Cell Counting ◽

Normal Tissues ◽

Rna Transfection ◽

Normal Hepatocyte ◽

Incidence And Mortality ◽

Cell Progression ◽

Hcc Cells

Abstract Background: Hepatocellular carcinoma (HCC) is still a major health burden in China considering its high incidence and mortality. Long non-coding RNAs (lncRNAs) were found playing vital roles in tumor progression, suggesting a new way of diagnosis and prognosis prediction, or treatment of HCC. This study was designed to investigate the role of HIF1A-AS1 during the progression of HCC, and to explore its related mechanisms. Methods: The expression of HIF1A-AS1 was detected in 50 paired carcinoma tissues and adjacent normal tissues by quantitative real-time PCR assay. HCC cells apoptosis was induced by nutrient-deficient culture medium, and detected by Cell Counting Kit‐8 and flow cytometer assays. HIF1A-AS1 inhibition in HCC cells was accomplished by small interfering RNA transfection. Results: HIF1A-AS1 was overexpressed in HCC tissues and was associated with tumor size, TNM stage and lymph node metastasis. Compared with low HIF1A-AS1 group, high HIF1A-AS1 group had a shorter overall survival and a worse disease-free survival. HIF1A-AS1 expression was significantly higher in HCC cell lines (7721 and Huh7) than that in normal hepatocyte cell line L02 under normal culture condition. However, under nutrient-deficient condition, HIF1A-AS1 expression was significantly increased in both HCC and normal hepatocyte cell lines, and was increased with the prolongation of nutrient-free culture. inhibition of HIF1A-AS1 promoted starvation-induced HCC cells apoptosis. Furthermore, inhibition of HIF1A-AS1 could also reduce starvation-induced HCC cells autophagy. The expression of HIF-1α and phosphorylated mTOR was significantly decreased in HCC cells after HIF1A-AS1 inhibition. Conclusions: HIF1A-AS1, overexpressed in HCC and associated with HCC prognosis, could regulate starvation-induced HCC cells apoptosis by reducing HIF-1α/mTOR mediated autophagy, promoting HCC cell progression. Trial registration: This research is retrospectively registered.

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Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep

10.21203/rs.3.rs-131480/v1 ◽

2020 ◽

Author(s):

Xige He ◽

Rihan Wu ◽

Yueying Yun ◽

Xia Qin ◽

Lu Chen ◽

...

Keyword(s):

Long Noncoding Rna ◽

Messenger Rna ◽

Noncoding Rna ◽

Target Genes ◽

Early Stage ◽

Expression Profiles ◽

Theoretical Data ◽

Differentially Expressed ◽

Growth Stages ◽

Complex Biological Process

Abstract Background: Sunite sheep are a fat-tailed sheep species with a low percentage of intramuscular fat and good quality lean meat, and their tail fat can be used as a source of dietary fat by humans. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6 months, 18 months, and 30 months.Results: A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep (false discovery rate < 0.05, |Fold Change| ≥ 2). Based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found that fat-related DEGs were mainly expressed at 6 months of age, and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their trans-regulators (53 mRNAs at most). Further, we obtained several fat-related differentially-expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Conclusions: Finally, we conclude that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process, and our findings will provide some basic theoretical data for future studies on tail fat development of fat-tailed sheep.

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ORC6, Negatively Regulated by miR-1-3p, Promotes Proliferation, Migration, and Invasion of Hepatocellular Carcinoma Cells

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.652292 ◽

2021 ◽

Vol 9 ◽

Author(s):

Hu Chen ◽

Lequn Bao ◽

Jianhua Hu ◽

Dongde Wu ◽

Xianli Tong

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Cycle ◽

Cell Lines ◽

Cell Cycle Progression ◽

Cell Counting ◽

Luciferase Reporter ◽

Regulatory Function ◽

Migration And Invasion ◽

Cycle Progression ◽

Hcc Cells

BackgroundIn recent years, microRNA-1-3p (miR-1-3p) has been linked to the progression of multiple cancers, whereas little is known about its role in hepatocellular carcinoma (HCC). Herein, we investigated the function of miR-1-3p in HCC, and its regulatory function on origin recognition complex subunit 6 (ORC6).MethodsQuantitative real-time polymerase chain reaction (qRT-PCR) was performed for detecting the expression levels of miR-1-3p and ORC6 mRNA in HCC samples and cell lines. ORC6 expression at the protein level was quantified by Western blot. After gain-of-function and loss-of-function models were established, cell counting kit-8 (CCK-8) assays, Transwell assays, flow cytometry, and 5-Ethynyl-2′-deoxyuridine (EdU) assay were performed for examining cell proliferation, migration, invasion, cell cycle, and apoptosis. The targeting relationship between miR-1-3p and ORC6 was confirmed with bioinformatic analysis and dual-luciferase reporter assays.ResultsThe expression of miR-1-3p was reduced in HCC samples and cell lines. Overexpression of miR-1-3p suppressed the proliferation, migration, and invasion, and induced cell-cycle arrest and apoptosis of HCC cells, whereas the opposite effects were induced by miR-1-3p inhibition. ORC6 is identified as a novel target of miR-1-3p, the expression of which is negatively correlated with miR-1-3p expression in HCC tissues. ORC6 overexpression facilitated the proliferation, migration, invasion, and cell cycle progression, and reduced apoptosis of HCC cells, whereas the opposite effects were induced by ORC6 knockdown. What is more, ORC6 overexpression counteracted the biological functions of miR-1-3p in HCC cells.ConclusionMiR-1-3p targets ORC6 to suppress the proliferation, migration, invasion, and cell cycle progression, and promote apoptosis of HCC cells.

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Inhibition of HIF1A-AS1 promoted starvation-induced hepatocellular carcinoma cells apoptosis by reducing HIF-1α/mTOR mediated autophagy

10.21203/rs.2.23954/v1 ◽

2020 ◽

Author(s):

Fenfen Hong ◽

Yang Li ◽

Yu Gao ◽

Linfeng Zheng ◽

Xianpeng Li ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Lines ◽

Disease Free Survival ◽

Cell Counting ◽

Normal Tissues ◽

Rna Transfection ◽

Normal Hepatocyte ◽

Incidence And Mortality ◽

Cell Progression ◽

Hcc Cells

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Potential Diagnostic and Therapeutic Targets for Hepatocellular Carcinoma Based on Exosome-Derived Competitive Endogenous RNA Network

10.21203/rs.3.rs-487982/v1 ◽

2021 ◽

Author(s):

Yuan Tian ◽

Dongliang Yang ◽

Tieshan Wang ◽

He Bu ◽

JinBao Wu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Target Genes ◽

Immune Escape ◽

Malignant Tumors ◽

Expression Profiles ◽

Therapeutic Targets ◽

Differentially Expressed ◽

Cerna Network ◽

Differentially Expressed Mirnas ◽

Competitive Endogenous Rna

Abstract Background: Hepatocellular carcinoma (HCC) is one of the most malignant tumors in the world. The pathogenesis of HCC is complex and closely related to chronic uncontrollable inflammation. As a bridge between inflammation and cancer, circulating exosomes play a vital role in early tumorigenesis, metastasis, and immune escape. Studies have shown that exosomes containing specific RNAs may be potential diagnostic and therapeutic targets for HCC. Purpose The current research investigated key circRNA through exosome-derived competitive endogenous RNA network based on the ExoRBase database. Methods: The circRNA, lncRNA, and mRNA expression profiles of human blood samples were downloaded from the ExoRBase database. At the standard of P<0.05 and log FC>0, differentially expressed genes (DEGs) were further identified between normal human and HCC patients. The co-expressed pairs of DEGs were predicted by TargetScan, miRcode, and StarBase databases. The ceRNA network was constructed by Cytoscape software. Subsequently, target genes corresponding to circRNA in the ceRNA network were annotated and analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG). The potential transcription factors were screened by FunRich database. Results: At the criterion of P<0.05 and log FC>0, 13 differentially expressed circRNAs(DECs) were identified with 9 up-regulated and 4 down-regulated. The co-expressed differentially expressed miRNAs-mRNAs (DEMis-DEMs) (620 pairs), differentially expressed miRNAs- LncRNAs (DEMis-DElncRNA) (684 pairs) and DEMis-DECs (53 pairs) were finally predicted to construct the ceRNA network. The GO analysis indicated that target genes in the ceRNA network were mainly enriched in the molecular function of protein serine/threonine kinase activity. KEGG pathway analysis suggested target genes were enriched in two pathways of MAPK and central carbon metabolism. Conclusion: The study provides a valuable reference for HCC through the ceRNA network in exosomes. Besides, hsa_circ_0000284 may be potential diagnostic markers of HCC.

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Long Noncoding RNA SNHG16 Promotes Cell Proliferation by Sponging MicroRNA-205 and Upregulating ZEB1 Expression in Osteosarcoma

Cellular Physiology and Biochemistry ◽

10.1159/000495239 ◽

2018 ◽

Vol 51 (1) ◽

pp. 429-440 ◽

Cited By ~ 33

Author(s):

Chenlei Zhu ◽

Dong Cheng ◽

Xubin Qiu ◽

Ming Zhuang ◽

Zhiwei Liu

Keyword(s):

Noncoding Rna ◽

Target Genes ◽

Tumor Development ◽

Differentially Expressed ◽

Cell Counting ◽

Osteosarcoma Cell ◽

Osteosarcoma Cells ◽

Microarray Screening ◽

Biological Methods ◽

Zeb1 Expression

Background/Aims: Long noncoding RNAs (lncRNAs) have been a research hotspot, as they play important roles in tumor development. However, their expression pattern and biological function in osteosarcoma have not yet been clarified. Methods: Differentially expressed lncRNAs in osteosarcoma and paracarcinoma tissues were identified by screening an lncRNA microarray, and candidate lncRNAs were verified by quantitative real-time PCR (qRT-PCR). A series of bioinformatics and molecular biological methods were adopted to investigate the interaction among lncRNA, microRNA (miRNA), and miRNA target genes during the development and occurrence of osteosarcoma. Cell viability was measured using a Cell Counting Kit-8 assay. Results: Chip microarray screening combined with the validation of differentially expressed candidate lncRNAs showed that the lncRNA small nucleolar RNA host gene 16 (SNHG16) had the largest fold change. SNHG16 was highly expressed in osteosarcoma tissues and cell lines, and its downregulation led to the suppressed proliferation of osteosarcoma cells. Further investigations revealed that SNHG16 could upregulate zinc finger E-box-binding homeobox 1 (ZEB1) expression by acting as an endogenous sponge of miR-205. Moreover, rescue assays proved that the effects of SNHG16 on the proliferation of osteosarcoma cells were dependent on miR-205. Conclusion: SNHG16 can significantly enhance the proliferation of osteosarcoma cells. In addition, SNHG16, miR-205, and ZEB1 interact in a common pathway during the development and occurrence of osteosarcoma, providing novel targets for intervention in the treatment of osteosarcoma.

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Clinically Relevant Biomarker Discovery in High-Risk Recurrent Neuroblastoma

Cancer Informatics ◽

10.1177/1176935119832910 ◽

2019 ◽

Vol 18 ◽

pp. 117693511983291 ◽

Cited By ~ 8

Author(s):

Peter Utnes ◽

Cecilie Løkke ◽

Trond Flægstad ◽

Christer Einvik

Keyword(s):

High Risk ◽

Cell Lines ◽

Target Genes ◽

Biomarker Discovery ◽

Expression Profiles ◽

Response To Therapy ◽

Gene Set Enrichment Analysis ◽

Favorable Outcome ◽

Differentially Expressed ◽

Response To Treatment

Neuroblastoma is a pediatric cancer of the developing sympathetic nervous system. High-risk neuroblastoma patients typically undergo an initial remission in response to treatment, followed by recurrence of aggressive tumors that have become refractory to further treatment. The need for biomarkers that can select patients not responding well to therapy in an early phase is therefore needed. In this study, we used next generation sequencing technology to determine the expression profiles in high-risk neuroblastoma cell lines established before and after therapy. Using partial least squares-discriminant analysis (PLS-DA) with least absolute shrinkage and selection operator (LASSO) and leave-one-out cross-validation, we identified a panel of 55 messenger RNAs and 17 long non-coding RNAs (lncRNAs) which were significantly altered in the expression between cell lines isolated from primary and recurrent tumors. From a neuroblastoma patient cohort, we found 20 of the 55 protein-coding genes to be differentially expressed in patients with unfavorable compared with favorable outcome. We further found a twofold increase or decrease in hazard ratios in these genes when comparing patients with unfavorable and favorable outcome. Gene set enrichment analysis (GSEA) revealed that these genes were involved in proliferation, differentiation and regulated by Polycomb group (PcG) proteins. Of the 17 lncRNAs, 3 upregulated ( NEAT1, SH3BP5-AS1, NORAD) and 3 downregulated lncRNAs ( DUBR, MEG3, DHRS4-AS1) were also found to be differentially expressed in favorable compared with unfavorable outcome. Moreover, using expression profiles on both miRNAs and mRNAs in the same cohort of cell lines, we found 13 downregulated and 18 upregulated experimentally observed miRNA target genes targeted by miR-21, -424 and -30e, -29b, -138, -494, - 181a, -34a, -29b, respectively. The advantage of analyzing biomarkers in a clinically relevant neuroblastoma model system enables further studies on the effect of individual genes upon gene perturbation. In summary, this study identified several genes, which may aid in the prediction of response to therapy and tumor recurrence.

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