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Zhang HY, Zhu JJ, Liu ZM, Zhang YX, Chen JJ, Chen KD. A prognostic four-gene signature and a therapeutic strategy for hepatocellular carcinoma: Construction and analysis of a circRNA-mediated competing endogenous RNA network. Hepatobiliary Pancreat Dis Int 2024; 23:272-287. [PMID: 37407412 DOI: 10.1016/j.hbpd.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 06/13/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) has a poor long-term prognosis. The competition of circular RNAs (circRNAs) with endogenous RNA is a novel tool for predicting HCC prognosis. Based on the alterations of circRNA regulatory networks, the analysis of gene modules related to HCC is feasible. METHODS Multiple expression datasets and RNA element targeting prediction tools were used to construct a circRNA-microRNA-mRNA network in HCC. Gene function, pathway, and protein interaction analyses were performed for the differentially expressed genes (DEGs) in this regulatory network. In the protein-protein interaction network, hub genes were identified and subjected to regression analysis, producing an optimized four-gene signature for prognostic risk stratification in HCC patients. Anti-HCC drugs were excavated by assessing the DEGs between the low- and high-risk groups. A circRNA-microRNA-hub gene subnetwork was constructed, in which three hallmark genes, KIF4A, CCNA2, and PBK, were subjected to functional enrichment analysis. RESULTS A four-gene signature (KIF4A, CCNA2, PBK, and ZWINT) that effectively estimated the overall survival and aided in prognostic risk assessment in the The Cancer Genome Atlas (TCGA) cohort and International Cancer Genome Consortium (ICGC) cohort was developed. CDK inhibitors, PI3K inhibitors, HDAC inhibitors, and EGFR inhibitors were predicted as four potential mechanisms of drug action (MOA) in high-risk HCC patients. Subsequent analysis has revealed that PBK, CCNA2, and KIF4A play a crucial role in regulating the tumor microenvironment by promoting immune cell invasion, regulating microsatellite instability (MSI), and exerting an impact on HCC progression. CONCLUSIONS The present study highlights the role of the circRNA-related regulatory network, identifies a four-gene prognostic signature and biomarkers, and further identifies novel therapy for HCC.
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Affiliation(s)
- Hai-Yan Zhang
- Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jia-Jie Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Zong-Ming Liu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Yu-Xuan Zhang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Jia-Jia Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Ke-Da Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China.
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Ran XM, Yang J, Wang ZY, Xiao LZ, Deng YP, Zhang KQ. M2 macrophage-derived exosomal circTMCO3 acts through miR-515-5p and ITGA8 to enhance malignancy in ovarian cancer. Commun Biol 2024; 7:583. [PMID: 38755265 PMCID: PMC11098810 DOI: 10.1038/s42003-024-06095-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 03/22/2024] [Indexed: 05/18/2024] Open
Abstract
Tumor-associated macrophages of the M2 phenotype promote cancer initiation and progression. Importantly, M2 macrophage-derived exosomes play key roles in the malignancy of cancer cells. Here, we report that circTMCO3 is upregulated in ovarian cancer patients, and its high expression indicates poor survival. M2-derived exosomes promote proliferation, migration, and invasion in ovarian cancer, but these effects are abolished by knockdown of circTMCO3. Furthermore, circTMCO3 functions as a competing endogenous RNA for miR-515-5p to reduce its abundance, thus upregulating ITGA8 in ovarian cancer. miR-515-5p inhibits ovarian cancer malignancy via directly downregulating ITGA8. The decreased oncogenic activity of circTMCO3-silencing exosomes is reversed by miR-515-5p knockdown or ITGA8 overexpression. Exosomal circTMCO3 promotes ovarian cancer progression in nude mice. Thus, M2 macrophage-derived exosomes promote malignancy by delivering circTMCO3 and targeting the miR-515-5p/ITGA8 axis in ovarian cancer. Our findings not only provide mechanistic insights into ovarian cancer progression, but also suggest potential therapeutic targets.
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Affiliation(s)
- Xiao-Min Ran
- Department of Gynecologic Oncology Ward 5, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Juan Yang
- Department of Gynecologic Oncology Ward 5, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Zi-Yi Wang
- Department of Gynecologic Oncology Ward 5, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Ling-Zhi Xiao
- Department of Gynecologic Oncology Ward 5, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yu-Ping Deng
- Department of Gynecologic Oncology Ward 5, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Ke-Qiang Zhang
- Department of Gynecologic Oncology Ward 5, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan Province, PR China.
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Tian Y, Han W, Lv K, Fu L, Zhou X. CircSNX6 promotes proliferation, metastasis, and angiogenesis in hepatocellular carcinoma via miR-383-5p/VEGFA signaling pathway. Sci Rep 2024; 14:8243. [PMID: 38589413 PMCID: PMC11001896 DOI: 10.1038/s41598-024-58708-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/02/2024] [Indexed: 04/10/2024] Open
Abstract
The role of circular RNA (circRNAs) in hepatocellular carcinoma (HCC) has been extensively studied. Previous research has highlighted the regulatory role of circSNX6 in HCC cells and tissues. However, the precise mechanism underlying HCC progression still requires comprehensive investigation. The study initially utilized quantitative reverse transcription-polymerase chain reaction (qRT-PCR) to assess circSNX6 expression levels in HCC cell lines and tissues. Subsequently, the stability of circRNA was evaluated through Ribonuclease R and actinomycin D treatment assays. The impact of circSNX6 knockdown on proliferation, migration, invasion, and angiogenesis abilities was determined using various assays including colony formation, Transwell culture system, tube formation assay, and cell counting kit (CCK)-8 assays. Additionally, RNA immunoprecipitation chip and dual-luciferase reporter assays were employed to investigate the interactions between circSNX6 and miR-383-5p. Finally, an HCC xenograft tumor model in mice was established to assess the in vivo expression of circSNX6 and its functional role in HCC. Our findings revealed an elevated circSNX6 expression in HCC tissues, which was correlated with poor patient prognosis. Knockdown of circSNX6 suppressed HCC cell growth, invasion, metastasis, and angiogenesis. The downregulation of miR-383-5p, a target of circSNX6, significantly attenuated the tumor-suppressive effects induced by circSNX6 knockdown. Moreover, circSNX6 was found to modulate VEGFA expression by targeting miR-383-5p. The inhibition of HCC cell proliferation by miR-383-5p could be partially reversed by overexpressing VEGFA. Silencing circSNX6 also suppressed tumor formation and the metastasis of HCC cells in a mouse model. In summary, our findings suggest that circSNX6 promotes cell proliferation, metastasis, and angiogenesis in HCC by regulating the miR-383-5p/VEGFA pathway.
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Affiliation(s)
- Yuan Tian
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315100, Zhejiang, China
| | - Wenwen Han
- Department of Emergency, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315100, Zhejiang, China
| | - Kaiji Lv
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315100, Zhejiang, China
| | - Long Fu
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315100, Zhejiang, China
| | - Xinhua Zhou
- Department of General Surgery, Ningbo Medical Center Lihuili Hospital, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315100, Zhejiang, China.
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Zahir M, Tavakoli B, Zaki-Dizaji M, Hantoushzadeh S, Majidi Zolbin M. Non-coding RNAs in Recurrent implantation failure. Clin Chim Acta 2024; 553:117731. [PMID: 38128815 DOI: 10.1016/j.cca.2023.117731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Recurrent implantation failure (RIF), defined as the inability to achieve conception following multiple consecutive in-vitro fertilization (IVF) attempts, represents a complex and multifaceted challenge in reproductive medicine. The emerging role of non-coding RNAs in RIF etiopathogenesis has only gained prominence over the last decade, illustrating a new dimension to our understanding of the intricate network underlying RIF. Successful embryo implantation demands a harmonious synchronization between an adequately decidualized endometrium, a competent blastocyst, and effective maternal-embryonic interactions. Emerging evidence has clarified the involvement of a sophisticated network of non-coding RNAs, including microRNAs, circular RNAs, and long non-coding RNAs, in orchestrating these pivotal processes. Disconcerted expression of these molecules can disrupt the delicate equilibrium required for implantation, amplifying the risk of RIF. This comprehensive review presents an in-depth investigation of the complex role played by non-coding RNAs in the pathogenesis of RIF. Furthermore, it underscores the vast potential of non-coding RNAs as diagnostic biomarkers and therapeutic targets, with the ultimate goal of enhancing implantation success rates in IVF cycles. As ongoing research continues to unravel the intercalated web of molecular interactions, exploiting the power of non-coding RNAs may offer promising avenues for mitigating the challenges posed by RIF and improving the outcomes of assisted reproduction.
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Affiliation(s)
- Mazyar Zahir
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahareh Tavakoli
- Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Biology, Maragheh University, Maragheh, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Sedigheh Hantoushzadeh
- Vali-E-Asr Reproductive Health Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Masoumeh Majidi Zolbin
- Pediatric Urology and Regenerative Medicine Research Center, Gene, Cell and Tissue Research Institute, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
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Yuan Q, Zhang Y, Li J, Zhang D, Yang W. Circ_TEX2 Functions as a Tumor Suppressor in Hepatoma via miR-96-5p/SPRED1 Axis. Mol Biotechnol 2023; 65:1679-1692. [PMID: 36745282 DOI: 10.1007/s12033-023-00669-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/14/2023] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) have been shown to have a vital effect on hepatoma progression. The purpose of this study was to explore the function and mechanism of circRNA testis expressed 2 (circ_TEX2, circ_0004913) in hepatoma pathogenesis. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to detect circ_TEX2, miR-96-5p, and sprouty-related EVH1 domain containing 1 (SPRED1) expression. Western blot analyzed the proliferating cell nuclear antigen (PCNA), SPRED1, and the apoptosis-related protein levels. 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), and colony formation assays were used to test cell proliferation. Cell migration and invasion were analyzed by transwell assay, and cell apoptosis was detected by flow cytometry. Dual-luciferase reporter assay was done to analyze the target relationship between miR-96-5p and circ_TEX2 or SPRED1. The effects of circ_TEX2 on tumor growth in vivo were verified by xenograft model experiment and immunohistochemistry assay. The levels of circ_TEX2 and SPRED1 were down-regulated in hepatoma tissues and cells, and miR-96-5p expression was up-regulated. Overexpression of circ_TEX2 could inhibit the proliferation, migration, and invasion and boost cell apoptosis of hepatoma cells. Circ_TEX2 affected SPRED1 expression by sponging miR-96-5p. The overexpression of miR-96-5p could overturn the influence of circ_TEX2 up-regulation on malignant behaviors of hepatoma cells, and reduced SPRED1 expression could reverse the function of miR-96-5p knockdown on hepatoma cell malignant behaviors. Circ_TEX2 could suppress the growth of xenograft tumors in vivo. Our study demonstrates the tumor-suppressive role of circ_TEX2 in hepatoma through miR-96-5p/SPRED1 axis, suggesting that strategies directed toward restoring the production of circ_TEX2 might have a therapeutic value for hepatoma treatment.
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Affiliation(s)
- Qinggong Yuan
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an, 710004, Shaanxi, China
| | - Yan Zhang
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an, 710004, Shaanxi, China
| | - Junhui Li
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an, 710004, Shaanxi, China
| | - Di Zhang
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an, 710004, Shaanxi, China
| | - Wenbin Yang
- Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an, 710004, Shaanxi, China.
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6
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Chen W, Xu J, Wu Y, Liang B, Yan M, Sun C, Wang D, Hu X, Liu L, Hu W, Shao Y, Xing D. The potential role and mechanism of circRNA/miRNA axis in cholesterol synthesis. Int J Biol Sci 2023; 19:2879-2896. [PMID: 37324939 PMCID: PMC10266072 DOI: 10.7150/ijbs.84994] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
Cholesterol levels are an initiating risk factor for atherosclerosis. Many genes play a central role in cholesterol synthesis, including HMGCR, SQLE, HMGCS1, FDFT1, LSS, MVK, PMK, MVD, FDPS, CYP51, TM7SF2, LBR, MSMO1, NSDHL, HSD17B7, DHCR24, EBP, SC5D, DHCR7, IDI1/2. Especially, HMGCR, SQLE, FDFT1, LSS, FDPS, CYP51, and EBP are promising therapeutic targets for drug development due to many drugs have been approved and entered into clinical research by targeting these genes. However, new targets and drugs still need to be discovered. Interestingly, many small nucleic acid drugs and vaccines were approved for the market, including Inclisiran, Patisiran, Inotersen, Givosiran, Lumasiran, Nusinersen, Volanesorsen, Eteplirsen, Golodirsen, Viltolarsen, Casimersen, Elasomeran, Tozinameran. However, these agents are all linear RNA agents. Circular RNAs (circRNAs) may have longer half-lives, higher stability, lower immunogenicity, lower production costs, and higher delivery efficiency than these agents due to their covalently closed structures. CircRNA agents are developed by several companies, including Orna Therapeutics, Laronde, and CirCode, Therorna. Many studies have shown that circRNAs regulate cholesterol synthesis by regulating HMGCR, SQLE, HMGCS1, ACS, YWHAG, PTEN, DHCR24, SREBP-2, and PMK expression. MiRNAs are essential for circRNA-mediated cholesterol biosynthesis. Notable, the phase II trial for inhibiting miR-122 with nucleic acid drugs has been completed. Suppressing HMGCR, SQLE, and miR-122 with circRNA_ABCA1, circ-PRKCH, circEZH2, circRNA-SCAP, and circFOXO3 are the promising therapeutic target for drug development, specifically the circFOXO3. This review focuses on the role and mechanism of the circRNA/miRNA axis in cholesterol synthesis in the hope of providing knowledge to identify new targets.
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Affiliation(s)
- Wujun Chen
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
| | - Jiazhen Xu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
| | - Yudong Wu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
| | - Bing Liang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
| | - Mingzhe Yan
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
| | - Chuandong Sun
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
- Department of Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266000, China
| | - Dong Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
- Department of Liver Disease Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266000, China
| | - Xiaokun Hu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
- Interventional Medicine Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266000, China
| | - Li Liu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
- Department of Community Health Promotion, Qingdao Municipal Center for Disease Control & Prevention, Qingdao Institute of Preventive Medicine, Qingdao, Shandong, 266033, China
| | - Wenchao Hu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
- Department of Endocrinology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, Shandong, 266000, China
| | - Yingchun Shao
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
| | - Dongming Xing
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao Cancer Institute, Qingdao, Shandong, 266000, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
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Lin J, Lin Z, Hua Y, Chen Y. Circ_0031242 regulates the functional properties of hepatocellular carcinoma cells through the miR-944/MAD2L1 axis. Histol Histopathol 2023; 38:303-316. [PMID: 36125054 DOI: 10.14670/hh-18-519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND Circular RNAs (circRNAs) possess key functions in the pathogenesis of hepatocellular carcinoma (HCC). Nonetheless, the actions of individual circRNAs in HCC remain undefined. METHODS circ_0031242, miR-944, and MAD2L1 expression were quantified by qRT-PCR. Transwell assay was utilized to examine cell invasion and migration. Glucose consumption and lactate production were measured to assess the impact on glycolysis. The relationships among circ_0031242, MAD2L1, and miR-944 were examined via luciferase reporter assay. RESULTS circ_0031242 was notably augmented in HCC. Loss of function of circ_0031242 hindered cell proliferation, invasion, migration, glycolysis, and promoted apoptosis, as well as impeding HCC tumor growth. circ_0031242 directly targeted miR-944. Inhibition of miR-944 counteracted the effects of si-circ_0031242 on HCC cells. Additionally, miR-944 was proved to directly target MAD2L1 in HCC cells. Moreover, the promotion of MAD2L1 was able to rescue the inhibition of high miR-944 expression on HCC cell progression. Meanwhile, circ_0031242 involved the post-transcriptional modulation of MAD2L1 through miR-944. CONCLUSION This study suggested that circ_0031242 regulated tumor cell progression and tumor growth through the miR-944/MAD2L1 axis in HCC.
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Affiliation(s)
- Jianwei Lin
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zenghai Lin
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Yaqiong Hua
- Department of Medicine, Shenzhen Letu Biotechnology Co., Ltd., Guangdong, China
| | - Yan Chen
- Department of Medicine, Shenzhen Letu Biotechnology Co., Ltd., Guangdong, China
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Zhang Y, Shi J, Luo J, Liu C, Zhu L. Metabolic heterogeneity in early-stage lung adenocarcinoma revealed by RNA-seq and scRNA-seq. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:1844-1855. [PMID: 36692643 DOI: 10.1007/s12094-023-03082-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023]
Abstract
PURPOSE Cancer cells maintain cell growth, division, and survival through altered energy metabolism. However, research on metabolic reprogramming in lung adenocarcinoma (LUAD) is limited METHODS: We downloaded TCGA and GEO sequencing data. Consistent clustering with the ConsensusClusterPlus package was employed to detect the scores for four metabolism-related pathways. The LUAD samples in the TCGA dataset were clustered with ConsensusClusterPlus, and the optimal number of clusters was determined according to the cumulative distribution function (CDF). The cell score for each sample in the TCGA dataset was calculated using the MCPcounter estimate function of the MCPcounter package. RESULTS We identified two subtypes by scoring the samples based on the 4 metabolism-related pathways and cluster dimensionality reduction. The prognosis of cluster B was obviously poorer than that of cluster A in patients with LUAD. The analysis of single-nucleotide variation (SNV) data showed that the top 15 genes in the four metabolic pathways with the most mutations were TKTL2, PGK2, HK3, EHHADH, GLUD2, PKLR, TKTL1, HADHB, CPT1C, HK1, HK2, PFKL, SLC2A3, PFKFB1, and CPT1A. The IFNγ score of cluster B was significantly higher than that of cluster A. The immune T-cell lytic activity score of cluster B was significantly higher than that of cluster A. We further identified 5 immune cell subsets from single-cell sequencing data. The top 5 marker genes of B cells were IGHM, JCHAIN, IGLC3, IGHA1, and IGKC. The C0 subgroup of monocytes had a higher pentose phosphate pathway (PPP) score than the C6 subgroup. CONCLUSIONS Metabolism-related subtypes could be potential biomarkers in the prognosis prediction and treatment of LUAD.
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Affiliation(s)
- Yang Zhang
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Jiang Shi
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Junfang Luo
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Cong Liu
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Lixu Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Integrated Tissue and Blood miRNA Expression Profiles Identify Novel Biomarkers for Accurate Non-Invasive Diagnosis of Breast Cancer: Preliminary Results and Future Clinical Implications. Genes (Basel) 2022; 13:genes13111931. [DOI: 10.3390/genes13111931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
We aimed to identify miRNAs that were closely related to breast cancer (BRCA). By integrating several methods including significance analysis of microarrays, fold change, Pearson’s correlation analysis, t test, and receiver operating characteristic analysis, we developed a decision-tree-based scoring algorithm, called Optimized Scoring Mechanism for Primary Synergy MicroRNAs (O-PSM). Five synergy miRNAs (hsa-miR-139-5p, hsa-miR-331-3p, hsa-miR-342-5p, hsa-miR-486-5p, and hsa-miR-654-3p) were identified using O-PSM, which were used to distinguish normal samples from pathological ones, and showed good results in blood data and in multiple sets of tissue data. These five miRNAs showed accurate categorization efficiency in BRCA typing and staging and had better categorization efficiency than experimentally verified miRNAs. In the Protein-Protein Interaction (PPI) network, the target genes of hsa-miR-342-5p have the most regulatory relationships, which regulate carcinogenesis proliferation and metastasis by regulating Glycosaminoglycan biosynthesis and the Rap1 signaling pathway. Moreover, hsa-miR-342-5p showed potential clinical application in survival analysis. We also used O-PSM to generate an R package uploaded on github (SuFei-lab/OPSM accessed on 22 October 2021). We believe that miRNAs included in O-PSM could have clinical implications for diagnosis, prognostic stratification and treatment of BRCA, proposing potential significant biomarkers that could be utilized to design personalized treatment plans in BRCA patients in the future.
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Zhang X, Chen W, Guo D, Li Y, Zhao Y, Ren M, Lu G, Lu X, He S. Circ_0003570 Suppresses the progression of hepatocellular carcinoma through miR-182-5p/STARD13 regulatory axis. Biol Proced Online 2022; 24:14. [PMID: 36241975 PMCID: PMC9563790 DOI: 10.1186/s12575-022-00176-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022] Open
Abstract
Background Emerging evidence have revealed that circRNAs exert important biological effects in the development and progression of various diseases, including cancer. Our study aimed to elaborated the biological effects of hsa-circ_0003570 in hepatocellular carcinoma (HCC) development at the molecular level. Results The results of functional experiments showed that knockdown of circ_0003570 induced HCC cell growth, migration and invasion, whereas overexpression of circ_0003570 presented the opposite effects. In vivo experiments, xenograft tumors grown from circ-overexpressed cells had smaller tumor volume and weight than the control group. Further investigations suggested that circ_0003570 may function as a competing endogenous RNA via competitively binding miR-182-5p and thereby regulating the repression of downstream target gene STARD13, which were demonstrated by dual luciferase reporter assay and functional rescued experiments. Conclusions Taken together, circ_0003570 suppresses the development of HCC by modulating miR-182-5p/STARD13 axis. Supplementary Information The online version contains supplementary material available at 10.1186/s12575-022-00176-w.
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Affiliation(s)
- Xu Zhang
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Wenwen Chen
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Dan Guo
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Yarui Li
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Yan Zhao
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Mudan Ren
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Guifang Lu
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Xinlan Lu
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China.
| | - Shuixiang He
- Department of Gastroenterology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, People's Republic of China.
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11
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Liu Q, Xu X, Sun W. Down-regulated HSA_circ_0003528 inhibits hepatocellular carcinoma aggressiveness via the miR-212-3p/ XIAP axis. Bioengineered 2022; 13:11269-11280. [PMID: 35484994 PMCID: PMC9208529 DOI: 10.1080/21655979.2022.2066046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is characterized by a high mortality rate. Dysregulated circular RNAs (circRNAs) play a vital role in HCC. We aimed to study the role of circ_0003528 in HCC and its fundamental molecular mechanisms. HSA_circ_0003528 was identified through bioinformatics dataset analysis. The binding sites between mRNA and miRNA were predicted using online bioinformatics tools. The interaction between miR-212-3p and X-linked inhibitor of apoptosis protein (XIAP) or circ_0003528 was confirmed through the luciferase reporter assay. RT-qPCR and western blot assays were used to analyze the expression of all miRNAs/mRNAs and proteins. Cellular functions were evaluated using the MTT and TUNEL assays. A xenograft model was established to evaluate the function of circ_0003528 in vivo. Circ_0003528 was dramatically overexpressed in HepG2 and HUH7 cells. However, knockdown of circ_0003528 suppressed the aggressiveness of HCC cells and tumor growth both in vitro and in vivo. Furthermore, binding of miR-212-3p to circ_0003528 and XIAP was verified. Downregulation of miR-212-3p abrogated the effects of si-circ_0003528 on cell viability and apoptosis, and upregulation of XIAP antagonized the functions of the miR-212-3p mimic in HCC cells. circ_0003528 contributes to the development of HCC in vitro and in vivo via the miR-212-3p/XIAP axis. Hence, circ_0003528 knockdown may be a potential therapeutic strategy for HCC treatment.
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Affiliation(s)
- Qi Liu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Xin Xu
- Department of Blood Transfusion, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Wei Sun
- Department of Gastroenterology, The Fourth Affiliated Hospital of Inner Mongolia Medical University, Baotou, Qingshan, China
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12
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Mo M, Liu B, Luo Y, Tan JHJ, Zeng X, Zeng X, Huang D, Li C, Liu S, Qiu X. Construction and Comprehensive Analysis of a circRNA-miRNA-mRNA Regulatory Network to Reveal the Pathogenesis of Hepatocellular Carcinoma. Front Mol Biosci 2022; 9:801478. [PMID: 35141281 PMCID: PMC8819184 DOI: 10.3389/fmolb.2022.801478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Circular RNAs (circRNAs) have been demonstrated to be closely related to the carcinogenesis of human cancer in recent years. However, the molecular mechanism of circRNAs in the pathogenesis of hepatocellular carcinoma (HCC) has not been fully elucidated. We aimed to identify critical circRNAs and explore their potential regulatory network in HCC.Methods: The robust rank aggregation (RRA) algorithm and weighted gene co-expression network analysis (WGCNA) were conducted to unearth the differentially expressed circRNAs (DEcircRNAs) in HCC. The expression levels of DEcircRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). A circRNA-miRNA-mRNA regulatory network was constructed by computational biology, and protein-protein interaction (PPI) network, functional enrichment analysis, survival analysis, and infiltrating immune cells analysis were performed to uncover the potential regulatory mechanisms of the network.Results: A total of 22 DEcircRNAs were screened out from four microarray datasets (GSE94508, GSE97332, GSE155949, and GSE164803) utilizing the RRA algorithm. Meanwhile, an HCC-related module containing 404 circRNAs was identified by WGCNA analysis. After intersection, only four circRNAs were recognized in both algorithms. Following qRT-PCR validation, three circRNAs (hsa_circRNA_091581, hsa_circRNA_066568, and hsa_circRNA_105031) were chosen for further analysis. As a result, a circRNA-miRNA-mRNA network containing three circRNAs, 17 miRNAs, and 222 mRNAs was established. Seven core genes (ESR1, BUB1, PRC1, LOX, CCT5, YWHAZ, and DDX39B) were determined from the PPI network of 222 mRNAs, and a circRNA-miRNA-hubgene network was also constructed. Functional enrichment analysis suggested that these seven hub genes were closely correlated with several cancer related pathways. Survival analysis revealed that the expression levels of the seven core genes were significantly associated with the prognosis of HCC patients. In addition, we also found that these seven hub genes were remarkably related to the infiltrating levels of immune cells.Conclusion: Our research identified three pivotal HCC-related circRNAs and provided novel insights into the underlying mechanisms of the circRNA-miRNA-mRNA regulatory network in HCC.
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Affiliation(s)
- Meile Mo
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Bihu Liu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Yihuan Luo
- Department of Acute Care Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jennifer Hui Juan Tan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xi Zeng
- Department of Occupational and Environmental Health, School of Public Health, Guilin Medical University, Guilin, China
| | - Xiaoyun Zeng
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Dongping Huang
- Department of Sanitary Chemistry, School of Public Health, Guangxi Medical University, Nanning, China
| | - Changhua Li
- Department of Acute Care Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shun Liu
- Department of Maternal, Child and Adolescent Health, School of Public Health, Guangxi Medical University, Nanning, China
- *Correspondence: Xiaoqiang Qiu, ; Shun Liu,
| | - Xiaoqiang Qiu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
- *Correspondence: Xiaoqiang Qiu, ; Shun Liu,
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13
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Wang Y, Yang F, Shang J, He H, Yang Q. Integrative analysis reveals the prognostic value and functions of splicing factors implicated in hepatocellular carcinoma. Sci Rep 2021; 11:15175. [PMID: 34312475 PMCID: PMC8313569 DOI: 10.1038/s41598-021-94701-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/15/2021] [Indexed: 02/08/2023] Open
Abstract
Splicing factors (SFs) play critical roles in the pathogenesis of various cancers through regulating tumor-associated alternative splicing (AS) events. However, the clinical value and biological functions of SFs in hepatocellular carcinoma (HCC) remain obscure. In this study, we identified 40 dysregulated SFs in HCC and established a prognostic model composed of four SFs (DNAJC6, ZC3H13, IGF2BP3, DDX19B). The predictive efficiency and independence of the prognostic model were confirmed to be satisfactory. Gene Set Enrichment Analysis (GSEA) illustrated the risk score calculated by our prognostic model was significantly associated with multiple cancer-related pathways and metabolic processes. Furthermore, we constructed the SFs-AS events regulatory network and extracted 108 protein-coding genes from the network for following functional explorations. Protein–protein interaction (PPI) network delineated the potential interactions among these 108 protein-coding genes. GO and KEGG pathway analyses investigated ontology gene sets and canonical pathways enriched by these 108 protein-coding genes. Overlapping the results of GSEA and KEGG, seven pathways were identified to be potential pathways regulated by our prognostic model through triggering aberrant AS events in HCC. In conclusion, the present study established an effective prognostic model based on SFs for HCC patients. Functional explorations of SFs and SFs-associated AS events provided directions to explore biological functions and mechanisms of SFs in HCC tumorigenesis.
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Affiliation(s)
- Yue Wang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021 , Jilin Province, China
| | - Fan Yang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021 , Jilin Province, China
| | - Jiaqi Shang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021 , Jilin Province, China
| | - Haitao He
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021 , Jilin Province, China
| | - Qing Yang
- Department of Pathogenobiology, College of Basic Medical Sciences, Jilin University, 126 Xinmin Street, Changchun, 130021 , Jilin Province, China.
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14
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Wang S, Song Z, Tan B, Zhang J, Zhang J, Liu S. Identification and Validation of Hub Genes Associated With Hepatocellular Carcinoma Via Integrated Bioinformatics Analysis. Front Oncol 2021; 11:614531. [PMID: 34277395 PMCID: PMC8278315 DOI: 10.3389/fonc.2021.614531] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 06/15/2021] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common malignant tumor of the liver, with high morbidity and mortality, yet its molecular mechanisms of tumorigenesis are still unclear. In this study, gene expression profile of GSE62232 was downloaded from the Gene Expression Omnibus (GEO). The RNA-seq expression data and relative clinical information were retrieved from the Cancer Genome Atlas (TCGA) database. The datasets were analyzed by differential gene expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA) to obtain the overlapping genes. Then, we performed a functional enrichment analysis to understand the potential biological functions of these co-expression genes. Finally, we constructed the protein-protein interaction (PPI) analysis combined with survival analysis. MARCO, CLEC4M, FCGR2B, LYVE1, TIMD4, STAB2, CFP, CLEC4G, CLEC1B, FCN2, FCN3 and FOXO1 were identified as the candidate hub genes using the CytoHubba plugin of Cytoscape. Based on survival analysis, the lower expression of FCN3 and FOXO1 were associated with worse overall survival (OS) in HCC patients. Furthermore, the expression levels of FCN3 and FOXO1 were validated by the Human Protein Atlas (HPA) database and the qRT-PCR. In summary, our findings contribute new ideas for the precise early diagnosis, clinical treatment and prognosis of HCC in the future.
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Affiliation(s)
- Sumei Wang
- Department of Clinical Laboratory, The Third Central Hospital of Tianjin, Tianjin, China.,Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.,Artificial Cell Engineering Technology Research Center, Tianjin, China.,Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Zuoli Song
- Department of Clinical Laboratory, The Third Central Hospital of Tianjin, Tianjin, China.,Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.,Artificial Cell Engineering Technology Research Center, Tianjin, China.,Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Bing Tan
- Department of Clinical Laboratory, The Third Central Hospital of Tianjin, Tianjin, China.,Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.,Artificial Cell Engineering Technology Research Center, Tianjin, China.,Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Jinjuan Zhang
- Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.,Artificial Cell Engineering Technology Research Center, Tianjin, China.,Tianjin Institute of Hepatobiliary Disease, Tianjin, China.,Department of Surgery, Third Central Hospital of Tianjin, Tianjin, China
| | - Jiandong Zhang
- Department of Clinical Laboratory, The Third Central Hospital of Tianjin, Tianjin, China.,Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.,Artificial Cell Engineering Technology Research Center, Tianjin, China.,Tianjin Institute of Hepatobiliary Disease, Tianjin, China
| | - Shuye Liu
- Department of Clinical Laboratory, The Third Central Hospital of Tianjin, Tianjin, China.,Tianjin Key Laboratory of Extracorporeal Life Support for Critical Diseases, Tianjin, China.,Artificial Cell Engineering Technology Research Center, Tianjin, China.,Tianjin Institute of Hepatobiliary Disease, Tianjin, China
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15
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Han J, Thurnherr T, Chung AYF, Goh BKP, Chow PKH, Chan CY, Cheow PC, Lee SY, Lim TKH, Chong SS, Ooi LLPJ, Lee CG. Clinicopathological-Associated Regulatory Network of Deregulated circRNAs in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13112772. [PMID: 34199580 PMCID: PMC8199648 DOI: 10.3390/cancers13112772] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/01/2023] Open
Abstract
Simple Summary Here, we present a novel strategy to identify key signatures of clinically-relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate the prognosis of HCC patients, by integrating clinicopathological features, circRNA and mRNA expression profiles. Five master circRNAs were identified and experimentally demonstrated to upregulate proliferate and promote transformation. Through further integration with miRNA-expression profiles, clinically-relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. The most up-regulated nodal-circRNA, circGPC3 was experimentally demonstrated to up-regulate cell-cycle, migration and invasion. circGPC3 was found to act as a sponge of miR-378a-3p to regulate ASPM expression and modulate cell transformation. These 5 nodal circRNAs has potential to be good prognostic biomarkers with good prognostic performance. circGPC3 has great potential to be a promising non-invasive prognostic biomarker for early HCC. We have thus demonstrated the robustness of bioinformatically-predicted master circRNAs in clinically-relevant, circRNA-mRNA networks, underscoring the important roles that these identified deregulated key/master circRNAs play in HCC. Abstract Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. Here, we present a novel strategy to identify key circRNA signatures of clinically relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate prognosis of HCC patients, by integrating clinic-pathological features, circRNA and mRNA expression profiles. Through further integration with miRNA expression profiles, clinically relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. At least five clinically relevant nodal-circRNAs, co-expressed with numerous genes, were identified from the circRNA-mRNA networks. These nodal circRNAs upregulated proliferation (except circRaly) and transformation in cells. The most upregulated nodal-circRNA, circGPC3, associated with higher-grade tumors and co-expressed with 33 genes, competes with 11 mRNAs for two shared miRNAs. circGPC3 was experimentally demonstrated to upregulate cell-cycle and migration/invasion in both transformed and non-transformed liver cell-lines. circGPC3 was further shown to act as a sponge of miR-378a-3p to regulate APSM (Abnormal spindle-like microcephaly associated) expression and modulate cell transformation. This study identifies 5 key nodal master circRNAs in a clinically relevant circRNA-centric network that are significantly associated with poorer prognosis of HCC patients and promotes tumorigenesis in cell-lines. The identification and characterization of these key circRNAs in clinically relevant circRNA-mRNA and ceRNA networks may facilitate the design of novel strategies targeting these important regulators for better HCC prognosis.
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Affiliation(s)
- Jian Han
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore;
| | - Alexander Y. F. Chung
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Brian K. P. Goh
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Pierce K. H. Chow
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Chung Yip Chan
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Peng Chung Cheow
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Ser Yee Lee
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Tony K. H. Lim
- Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore;
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - London L. P. J. Ooi
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Caroline G. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore;
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Level 6, Lab 5, 11 Hospital Drive, Singapore 169610, Singapore
- Correspondence: ; Tel.: +65-65163251
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16
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Zhang L, Tao H, Li J, Zhang E, Liang H, Zhang B. Comprehensive analysis of the competing endogenous circRNA-lncRNA-miRNA-mRNA network and identification of a novel potential biomarker for hepatocellular carcinoma. Aging (Albany NY) 2021; 13:15990-16008. [PMID: 34049287 PMCID: PMC8266324 DOI: 10.18632/aging.203056] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/09/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The competing endogenous RNAs (ceRNAs) hypothesis has received increasing attention as a novel explanation for tumorigenesis and cancer progression. However, there is still a lack of comprehensive analysis of the circular RNA (circRNA)-long non-coding RNA (lncRNA)-miRNA-mRNA ceRNA network in hepatocellular carcinoma (HCC). METHODS RNA sequencing data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were employed to identify Differentially Expressed mRNAs (DEmRNAs), DElncRNAs, and DEcircRNAs between HCC and normal tissues. Candidates were identified to construct networks through a comprehensive bioinformatics strategy. A prognostic mRNA signature was established based on data from TCGA database and validated using data from the GEO database. Then, the HCC prognostic circRNA-lncRNA-miRNA-mRNA ceRNA network was established. Finally, the expression and function of an unexplored hub gene, deoxythymidylate kinase (DTYMK), was explored through data mining. The results were examined using clinical samples and in vitro experiments. RESULTS We constructed a prognostic signature with seven target mRNAs by univariate, lasso and multivariate Cox regression analyses, which yielded 1, 3 and 5-year AUC values of 0.797, 0.733 and 0.721, respectively, indicating its sensitivity and specificity in the prognosis of HCC. Moreover, the prognostic signature could be validated in GSE14520. The prognostic ceRNA network of 21 circRNAs, 15 lncRNAs, 5 miRNAs, and 7 mRNAs was established according to the targeting relationship between 7 hub mRNAs and other RNAs. Our experiment results indicated that the depletion of DTYMK inhibited liver cancer cell proliferation and invasion. CONCLUSIONS The network revealed in this study may help comprehensively elucidate the ceRNA mechanisms driving HCC, and provide novel candidate biomarkers for evaluating the prognosis of HCC.
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Affiliation(s)
- Lu Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, Hubei, China
| | - Haisu Tao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, Hubei, China
| | - Jiang Li
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, Hubei, China
| | - Erlei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, Hubei, China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, Hubei, China
| | - Bixiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan 430030, Hubei, China
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17
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Li X, Yang J, Yang X, Cao T. Dysregulated circ_0004913, circ_0008160, circ_0000517, and their potential as biomarkers for disease monitoring and prognosis in hepatocellular carcinoma. J Clin Lab Anal 2021; 35:e23785. [PMID: 34018640 DOI: 10.1002/jcla.23785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE Circular RNA_0004913 (circ_0004913), circular RNA_0008160 (circ_0008160), and circular RNA_0000517 (circ_0000517) are shown to be dysregulated in HCC tissues and cell lines, and also show potential in regulating hepatocellular carcinoma (HCC) pathogenesis. This current study attempted to find possible associations of circ_0004913, circ_0008160, and circ_0000517 with clinical features and prognosis of HCC patients. METHODS A hundred and fifty HCC patients who received hepatectomy were retrospectively reviewed, and their resected specimens including tumor tissues and paired adjacent tissues were obtained, in which the circ_0004913, circ_0008160, and circ_0000517 expressions were detected. Overall survival (OS) data were collected according to the clinical visit records. RESULTS Circ_0004913 (p < 0.001) and circ_0008160 (p < 0.001) were downregulated, while circ_0000517 (p < 0.001) was upregulated in tumor tissue compared with paired adjacent tissue. Additionally, tumor circ_0004913 was negatively associated with largest tumor size (p = 0.009) and Barcelona clinic liver cancer (BCLC) stage (p = 0.020), while tumor circ_0008160 and circ_0000517 were not correlated with any clinicopathological features of HCC patients (all p > 0.05). Tumor circ_0004913 high expression was associated with prolonged OS in total HCC patients (p = 0.008) and in subgroup of patients with largest tumor size <5 cm (p = 0.008). Tumor circ_0008160 high expression was correlated with longer OS in patients with BCLC stage B (p = 0.026). Univariate Cox's analysis disclosed that tumor circ_0004913 high expression was correlated with longer OS; while after adjustment by multivariate Cox's analysis, it failed to predict OS independently. CONCLUSION Circ_0004913 was downregulated in tumor tissue and may serve as a biomarker for evaluating disease severity and prognosis in HCC patients.
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Affiliation(s)
- Xiaoqian Li
- Department of Digestive Medical, Affiliated Nanhua Hospital, University of South China, Hengyang, China
| | - Jun Yang
- Department of Emergency, Affiliated Nanhua Hospital, University of South China, Hengyang, China
| | - Xuefeng Yang
- Department of Digestive Medical, Affiliated Nanhua Hospital, University of South China, Hengyang, China
| | - Ting Cao
- Department of Digestive Medical, Affiliated Nanhua Hospital, University of South China, Hengyang, China
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18
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Ahmadi M, Pashangzadeh S, Moraghebi M, Sabetian S, Shekari M, Eini F, Salehi E, Mousavi P. Construction of circRNA-miRNA-mRNA network in the pathogenesis of recurrent implantation failure using integrated bioinformatics study. J Cell Mol Med 2021; 26:1853-1864. [PMID: 33960101 PMCID: PMC8918409 DOI: 10.1111/jcmm.16586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022] Open
Abstract
This research attempted to elucidate the molecular components are involved in the pathogenesis of recurrent implantation failure (RIF). We initially identified that 386 mRNAs, 144 miRNAs and 2548 circRNAs were differentially expressed (DE) in RIF and then investigated the genetic cause of the observed abnormal expression by constructing a circRNA‐miRNA‐mRNA network considering the competing endogenous RNA theory. We further analysed the upstream transcription factors and related kinases of DEmRNAs (DEMs) and demonstrated that SUZ12, AR, TP63, NANOG, and TCF3 were the top five TFs binding to these DEMs. Besides, protein‐protein interaction analysis disclosed that ACTB, CXCL10, PTGS2, CXCL12, GNG4, AGT, CXCL11, SST, PENK, and FOXM1 were the top 10 hub genes in the acquired network. Finally, we performed the functional enrichment analysis and found that arrhythmogenic right ventricular cardiomyopathy (ARVC), hypertrophic cardiomyopathy (HCM), pathways in cancer, TNF signalling pathway and steroid hormone biosynthesis were the potentially disrupted pathways in RIF patients. Optimistically, our findings may deepen our apprehensions about the underlying molecular and biological causes of RIF and provide vital clues for future laboratory and clinical experiments that will ultimately bring a better outcome for patients with RIF.
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Affiliation(s)
- Mohsen Ahmadi
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.,Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.,Division of Medical Genetics, Booali Medical Diagnostic Laboratory, Qom, Iran
| | - Salar Pashangzadeh
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahta Moraghebi
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Soudabeh Sabetian
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Shekari
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Fatemeh Eini
- Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ensieh Salehi
- Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Pegah Mousavi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.,Fertility and Infertility Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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19
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Qiao Y, Pei Y, Luo M, Rajasekaran M, Hui KM, Chen J. Cytokinesis regulators as potential diagnostic and therapeutic biomarkers for human hepatocellular carcinoma. Exp Biol Med (Maywood) 2021; 246:1343-1354. [PMID: 33899543 DOI: 10.1177/15353702211008380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cytokinesis, the final step of mitosis, is critical for maintaining the ploidy level of cells. Cytokinesis is a complex, highly regulated process and its failure can lead to genetic instability and apoptosis, contributing to the development of cancer. Human hepatocellular carcinoma is often accompanied by a high frequency of aneuploidy and the DNA ploidy pattern observed in human hepatocellular carcinoma results mostly from impairments in cytokinesis. Many key regulators of cytokinesis are abnormally expressed in human hepatocellular carcinoma, and their expression levels are often correlated with patient prognosis. Moreover, preclinical studies have demonstrated that the inhibition of key cytokinesis regulators can suppress the growth of human hepatocellular carcinoma. Here, we provide an overview of the current understanding of the signaling networks regulating cytokinesis, the key cytokinesis regulators involved in the initiation and development of human hepatocellular carcinoma, and their applications as potential diagnostic and therapeutic biomarkers.
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Affiliation(s)
- Yiting Qiao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, P. R. China
| | - Yunxin Pei
- Pharmacy Institute and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
| | - Miao Luo
- Pharmacy Institute and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China
| | - Muthukumar Rajasekaran
- Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore
| | - Kam M Hui
- Pharmacy Institute and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore.,Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.,Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jianxiang Chen
- Pharmacy Institute and Department of Hepatology, Institute of Hepatology and Metabolic Diseases, Institute of Integrated Chinese and Western Medicine for Oncology, The affiliated Hospital of Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province and Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Collaborative Innovation Center of Traditional Chinese Medicines from Zhejiang Province, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 311121, P. R. China.,Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore
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20
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Ely A, Bloom K, Maepa MB, Arbuthnot P. Recent Update on the Role of Circular RNAs in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2021; 8:1-17. [PMID: 33542907 PMCID: PMC7851377 DOI: 10.2147/jhc.s268291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
After being overlooked for decades, circular RNAs (circRNAs) have recently generated considerable interest. circRNAs play a role in a variety of normal and pathological biological processes, including hepatocarcinogenesis. Many circRNAs contribute to hepatocarcinogenesis through sponging of microRNAs (miRs) and disruption of cellular signaling pathways that play a part in control of cell proliferation, metastasis and apoptosis. In most cases, overexpressed circRNAs sequester miRs to cause de-repressed translation of mRNAs that encode oncogenic proteins. Conversely, low expression of circRNAs has also been described in hepatocellular carcinoma (HCC) and is associated with inhibited production of tumor suppressor proteins. Other functions of circRNAs that contribute to hepatocarcinogenesis include translation of truncated proteins and acting as adapters to regulate influence of transcription factors on target gene expression. circRNAs also affect hepatocyte transformation indirectly. For example, the molecules regulate immune surveillance of cancerous cells and influence the liver fibrosis that commonly precedes HCC. Marked over- or under-expression of circRNA expression in HCC, with correlating plasma concentrations, has diagnostic utility and assays of these RNAs are being developed as biomarkers of HCC. Although knowledge in the field has recently surged, the myriad of described effects suggests that not all may be vital to hepatocarcinogenesis. Nevertheless, investigation of the role of circRNAs is providing valuable insights that are likely to contribute to improved management of a serious and highly aggressive cancer.
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Affiliation(s)
- Abdullah Ely
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohube Betty Maepa
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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