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Li J, Zhang Y, Sun F, Zhang G, Pan XA, Zhou Q. Long Noncoding RNA PCGEM1 Facilitates Tumor Growth and Metastasis of Osteosarcoma by Sponging miR-433-3p and Targeting OMA1. Orthop Surg 2023; 15:1060-1071. [PMID: 36782343 PMCID: PMC10102293 DOI: 10.1111/os.13648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 02/15/2023] Open
Abstract
OBJECTIVE Osteosarcoma (OS) is regarded as one of the most common malignant bone tumors, mainly occurring in children and adolescents with high mortality. The dysregulation of lncRNAs is reported to regulate tumor development and be closely related to patient prognosis. Nevertheless, the role of long noncoding RNAs (lncRNAs) prostate-specific transcript 1 (PCGEM1) in OS remains uncharacterized. The current study aimed to explore the role of PCGEM1 in OS. METHODS Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to examine the expression of PCGEM1 in OS cell lines. CCK-8, colony formation, Transwell, and western blotting analyses were applied to measure OS cell viability, proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) after PCGEM1 downregulation. Nuclear-cytoplasmic fractionation, RNA pulldown, RNA immunoprecipitation (RIP), luciferase reporter assays were performed to verify the relationship among PCGEM1, miR-433-3p. and OMA1 in OS. The xenograft tumor models were established to evaluate the effect of PCGEM1 on tumor growth of OS. RESULTS In this study, we discovered that PCGEM1 knockdown inhibited cell proliferation, migration, invasion and EMT in OS (P < 0.05). Additionally, PCGEM1 directly bound to miR-433-3p (P < 0.01). OMA1 was confirmed to be a target gene of miR-433-3p (P < 0.05), positively regulated by PCGEM1 but negatively regulated by miR-433-3p. Rescue assays further verified that overexpression of OMA1 reversed the PCGEM1 knockdown-mediated inhibitory effect on the malignant phenotype in OS cells (P < 0.05). Moreover, knockdown of PCGEM1 inhibited tumor growth and metastasis in vivo (P < 0.05). CONCLUSIONS Overall, PCGEM1 mediated tumor growth and metastasis of OS by sponging miR-433-3p and regulating OMA1, which might provide an innovative strategy for OS diagnosis or treatment.
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Affiliation(s)
- Jun Li
- Department of Orthopedics, Huangshi Central Hospital, Huangshi, China
| | - Yuanjin Zhang
- Department of Orthopedics, Huangshi Central Hospital, Huangshi, China
| | - Farui Sun
- Department of Orthopedics, Huangshi Central Hospital, Huangshi, China
| | - Guofu Zhang
- Department of Orthopedics, Huangshi Central Hospital, Huangshi, China
| | - Xi-An Pan
- Department of Orthopedics, Huangshi Central Hospital, Huangshi, China
| | - Qian Zhou
- Department of Geriatrics, Huangshi Central Hospital, Huangshi, China
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Habashy DA, Hamad MHM, Ragheb M, Khalil ZA, El Sobky SA, Hosny KA, Esmat G, El-Ekiaby N, Fawzy IO, Abdelaziz AI. Regulation of IGF2BP1 by miR-186 and its impact on downstream lncRNAs H19, FOXD2-AS1, and SNHG3 in HCC. Life Sci 2022; 310:121075. [DOI: 10.1016/j.lfs.2022.121075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
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Zhang R, Zhang G, Li B, Wang J, Wang J, Che J, Wang X, Zhang Z. Analysis of LINC01314 and miR-96 Expression in Colorectal Cancer Patients via Tissue Microarray-Based Fluorescence In Situ Hybridization. DISEASE MARKERS 2022; 2022:5378963. [PMID: 36246563 PMCID: PMC9568347 DOI: 10.1155/2022/5378963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]
Abstract
Methods A tissue microarray (TMA) containing 76 individual colorectal tumor samples and 28 adjacent normal samples was constructed, and the expression levels of LINC01314 and miR-96 were detected by fluorescence in situ hybridization. Results The expression levels of both LINC01314 and miR-96 were upregulated in CRC tissues and were associated with vascular metastasis (p < 0.05). A significantly positive correlation was observed between LINC01314 and miR-96 expression in tumor tissues (p < 0.001, r = 0.870). Dominant expression of LINC01314 was a risk factor for both blood vessel invasion (p < 0.05) and poor 5-year survival (p = 0.001, hazard ratio = 4.144). The Kaplan-Meier analysis indicated that patients with LINC01314-dominant expression exhibited worse 5-year survival rates than those with miR-96-dominant expression (p < 0.05). Conclusion The expression patterns of both LINC01314 and miR-96 may be diagnostic of, and prognostic for, CRC. These findings will facilitate further exploration of the molecular mechanism of lncRNAs in CRC.
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Affiliation(s)
- Runan Zhang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Genhua Zhang
- Department of Pathology, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Baohua Li
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Juan Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jvfang Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jia Che
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xiaojun Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Zhen Zhang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
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Yuan Z, Zhao H, Zhi Q, Wang S, Liu C, Han Y, Xu Z, Liu F, Liu X, Zan X, Wang Q, Wan D. Long non-coding RNA H19X promotes tumorigenesis and metastasis of colorectal cancer through regulating the miR-503-5p/KANK1 axis. Genes Genomics 2022; 44:1577-1591. [PMID: 35567714 DOI: 10.1007/s13258-022-01259-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/12/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND It has been well established that the long non-coding RNAs (lncRNAs) plays a critical role in tumor progression. However, the function of these transcripts and mechanisms responsible for their deregulation in colorectal cancer (CRC) remain to be investigated. OBJECTIVE To explore the potential effect and regulation mechanism of lncRNA H19X in colorectal cancer. METHODS We predicted and validated long non-coding RNA H19X from microarray data of colorectal cancer tissues. In addition, the biological behaviors of H19X and miR-503-5p on CRC were examined in vitro and in vivo, including MTT, colony formation assay, Hoechst33342 and transwell assay. The mRNA and protein levels of KN Motif and Ankyrin Repeat Domains 1 (KANK1) were analyzed by Quantitative real-time PCR (qRT-PCR), western blotting (WB) assay. Moreover, bioinformatics tools and dual-luciferase reporter assay were applied to demonstrate the relationship between KANK1 and miR-503-5p. RESULTS H19X was remarkably up-regulated in CRC tissues. Its expression related to tumor size (p = 0.041), lymph node metastasis (p = 0.037), distal metastasis (p = 0.028), advanced TNM stage (p = 0.034) and poor survival in CRC. H19X acted as an oncogenic lncRNA that induced CRC cell proliferation, invasion and metastasis. Through a number of functional studies, we found that H19X silencing inhibited the malignance phenotype of cancer cells through loss of miR-503-5p. Further studies demonstrated that miR-503-5p was involved in the progression of CRC by directly regulating the downstream target KANK1. CONCLUSION Collectively, the findings of the present study indicate H19X/miR-503-5p/KANK1 axis has critical role in the progression of colorectal cancer, providing an effective prognostic indicator and promising target in treatment of colorectal cancer.
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Affiliation(s)
- Zihan Yuan
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China
| | - Haizhou Zhao
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China
| | - Qiaoming Zhi
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China
| | - Sentai Wang
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China
| | - Chao Liu
- Liver Disease Center, The Affiliated Hospital of Qingdao University, No. 59 Haier Rd, Qingdao, 266003, Shandong Province, People's Republic of China
| | - Ye Han
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China
| | - Zhihua Xu
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China
| | - Fei Liu
- Department of Gastroenterology, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China
| | - Xingyi Liu
- Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, Jiangsu Province, People's Republic of China
| | - Xinquan Zan
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China
| | - Qiang Wang
- Department of General Surgery, Jiangsu Shengze Hospital, Wujiang, 215228, Jiangsu Province, People's Republic of China.
| | - Daiwei Wan
- Department of General Surgery, First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu Province, People's Republic of China.
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Dong Y, Wang Q, Sun J, Liu H, Wang H. Long non-coding RNA TPTEP1 exerts inhibitory effects on hepatocellular carcinoma by impairing microRNA-454-3p-mediated DLG5 downregulation. Dig Liver Dis 2022; 54:268-279. [PMID: 34238665 DOI: 10.1016/j.dld.2021.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/07/2021] [Accepted: 04/13/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is usually diagnosed at late stages, making it the second cause of malignancy-related death across the world. Long noncoding RNAs (lncRNAs) are of significance to tumorigenesis, highly suggestive of their functional roles as novel biomarkers for cancer therapy. The current study investigated the specific role of lncRNA TPTE pseudogene 1 (TPTEP1) in HCC. METHODS Expression of lncRNA TPTEP1, microRNA-454-3p (miR-454-3p) and discs large homolog 5 (DLG5) was determined in tissues samples from the recruited patients with HCC. Cell proliferation, migration and invasion assays were performed to determine effects of lncRNA TPTEP1, miR-454-3p and DLG5 on the malignant phenotype of tumor cells. Finally, the mouse HCC model was also established to disclose the tumor suppressor effects of lncRNA TPTEP1 in vivo. RESULTS LncRNA TPTEP1 was downregulated both in HCC cells and tissues, and played a negative regulatory role in HCC cell proliferation, migration and invasion. Mechanistically, lncRNA TPTEP1 competitively bound to miR-454-3p, thereby upregulating its endogenous target DLG5. Moreover, lncRNA TPTEP1 hindered activation of the protein kinase B signaling pathway, causing inhibited malignant phenotypes of HCC cells. Also, lncRNA TPTEP1 suppressed tumor growth and extrahepatic metastasis (lung) via miR-454-3p/DLG5 axis. CONCLUSION Taken together, this research revealed a concrete mechanism of lncRNA TPTEP1 in HCC.
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Affiliation(s)
- Yuandi Dong
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150000, PR China; Department of Interventional Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, Heilongjiang Province 150000, PR China
| | - Qingshan Wang
- Department of Interventional Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, Heilongjiang Province 150000, PR China; Department of Vascular Surgery, Heilongjiang Provincial Hospital, Harbin 150000, PR China
| | - Jianmin Sun
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150000, PR China
| | - Haishi Liu
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Tumor Hospital of Harbin Medical University, Harbin 150000, PR China
| | - Haiyang Wang
- Department of Interventional Vascular Surgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, Heilongjiang Province 150000, PR China.
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叶 静, 徐 文, 陈 天. [Identification of onco-miRNAs in hepatocellular carcinoma and analysis of their regulatory network]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:45-54. [PMID: 35249869 PMCID: PMC8901393 DOI: 10.12122/j.issn.1673-4254.2022.01.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To construct the regulatory network of survival-related onco-miRNAs and their target genes in hepatocellular carcinoma (HCC) and verify the interactions between the key miRNAs and their targets. METHODS We screened survival-related miRNAs in HCC in OncomiR and Oncolnc databases, predicted their target genes using miRNet, and conducted survival and expression analysis using GEPIA2 and Ualcan, respectively. The miRNA-target gene co-expression analysis was performed and the miRNA-target network was constructed. Enrichment analysis was performed in Enrichr and protein-protein interaction analysis in STRING database. We tested the effects of transfection with the mimic or inhibitor of hsa-miR-1226-3p or hsa-miR-221-5p on proliferation of HepG2 cells using CCK8 assay and examined the changes in the expressions of the target genes using RT-qPCR. The effect of transfection with hsa-miR-221-5p mimic or inhibitor on protein expressions of the target genes was examined using Western blotting in. A dual luciferase reporter assay was used to test the interaction between hsa-miR-221-5p and its potential target gene GCDH. We further examined the effect of transfection with hsa-miR-221-5p mimic and pEGFP N1-GCDH, alone or in combination, on proliferation, migration and invasion of HepG2 cells. RESULTS We identified 223 survival-related miRNAs in HCC from OncomiR and 146 miRNAs from Oncolnc with an intersection of 131 miRNAs, and 48 miRNAs were identified as onco-miRNAs in HCC after survival and expression analysis. Twenty-seven eligible target genes were identified after miRNA-mRNA co-expression analysis. The constructed miRNA-target gene network consisted of 25 miRNAs and 27 target genes. The most enriched term was fatty acid metabolism for the target genes. In HepG2 cells, transfection with the mimic or inhibitor of hsa-miR-1226-3p or hsa-miR-221-5p caused significant changes of the mRNA and protein levels of their respective target genes (P < 0.05). The results of dual luciferase reporter assay confirmed the targeting relationship between hsa-miR-221-5p and GCDH gene (P < 0.05). Transfection with hsa-miR-221-5p mimic significantly suppressed the proliferation, migration and invasion of HepG2 cells, but this effect was obviously relieved by co-transformation with pEGFP N1-GCDH (P < 0.05). CONCLUSION Fatty acid metabolism might be one of the most crucial pathways that mediate the effect of the oncomiRNAs in HCC, and the hsa-miR-221-5p/GCDH axis is an important molecular mechanism for HCC progression.
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Affiliation(s)
- 静静 叶
- 皖南医学院弋矶山医院中心实验室,安徽 芜湖 241001Central Laboratory, Yijishan Hospital, Wannan Medical College, Wuhu 241001, China
- 皖南医学院重大疾病非编码 RNA 转化研究安徽普通高校重点实验室,安徽 芜湖 241001Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - 文琴 徐
- 皖南医学院弋矶山医院中心实验室,安徽 芜湖 241001Central Laboratory, Yijishan Hospital, Wannan Medical College, Wuhu 241001, China
- 皖南医学院重大疾病非编码 RNA 转化研究安徽普通高校重点实验室,安徽 芜湖 241001Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
| | - 天兵 陈
- 皖南医学院弋矶山医院中心实验室,安徽 芜湖 241001Central Laboratory, Yijishan Hospital, Wannan Medical College, Wuhu 241001, China
- 皖南医学院重大疾病非编码 RNA 转化研究安徽普通高校重点实验室,安徽 芜湖 241001Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Wannan Medical College, Wuhu 241001, China
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Shan G, Huang T, Tang T. Long non-coding RNA MEG8 induced by PLAG1 promotes clear cell renal cell carcinoma through the miR-495-3p/G3BP1 axis. Pathol Res Pract 2022; 229:153734. [PMID: 35030351 DOI: 10.1016/j.prp.2021.153734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 01/05/2023]
Abstract
Clear cell renal cell carcinoma (ccRCC) is recognized as one of the most lethal malignancies among the urological system, with constantly increasing mortality. While the molecular mechanisms underlying ccRCC progression are still poorly understood, the molecular and functional role of lncRNA in multiple diseases has been well demonstrated. In this study, we hypothesized that lncRNA MEG8 might participate in ccRCC development. At first, we found that MEG8 expression was increased in ccRCC tumor tissues and cells. Next, we demonstrated that MEG8 knockdown suppressed cell viability, migration, and invasion in vitro and inhibited tumor growth in vivo. Subsequently, we utilized bioinformatics analysis, ChIP, and luciferase assays, and we found that PLAG1 could transcriptionally regulate MEG8 in ccRCC cells. Furthermore, MEG8 promoted G3BP1 expression to aggravate ccRCC tumorigenic properties through sponging miR-495-3p. Our study identified a novel PLAG1/MEG8/miR-495-3p/G3BP1 network in ccRCC development, which might be a promising direction for developing new diagnoses or therapeutic agents for ccRCC.
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Affiliation(s)
- Guang Shan
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| | - Ting Huang
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Tian Tang
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
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Xiao M, You Z, Zeng C, Huang Z, Dong L. Update on neurological symptoms in patients infected with severe acute respiratory syndrome coronavirus-2. IBRAIN 2021; 7:351-361. [PMID: 37786557 PMCID: PMC10528815 DOI: 10.1002/ibra.12008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 10/04/2023]
Abstract
Novel coronavirus 19 (COVID-19) is the latest and most intense epidemic, which is caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). In addition to causing respiratory symptoms, SARS-CoV-2 can have severe effects on the nervous system. Clinically, COVID-19 patients have been reported ranging from mild hypogeusia and hyposmia to severe neurological disorders, such as encephalopathy, encephalitis, strokes, and seizures syndrome. However, the pathological mechanisms of this SARS-CoV-2 neuro aggressiveness remain unclear, so it is of great significance to explore the neurological effects of SARS-CoV-2 infection. To facilitate clinicians to timely recognize the manifestations of COVID-19 patients with neurological injury and timely treatment, the author hereby reviews the latest research progress in the possible pathways, clinical manifestations, and pathogenesis of COVID-19 patients with nerve injury.
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Affiliation(s)
- Mei‐Fang Xiao
- Health Management Center, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Zhi‐Jian You
- Department of AnesthesiologyLiuzhou People's Hospital Affiliated to Guangxi Medical UniversityLiuzhouGuangxiChina
| | - Chang Zeng
- Health Management Center, Xiangya HospitalCentral South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric Disorders, Xiangya HospitalCentral South UniversityChangshaChina
| | - Ze‐Bing Huang
- Department of Infectious Diseases, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Viral HepatitisChangshaHunanChina
| | - Liang Dong
- Department of AnesthesiologyLiuzhou People's Hospital Affiliated to Guangxi Medical UniversityLiuzhouGuangxiChina
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Qi F, Du X, Zhao Z, Zhang D, Huang M, Bai Y, Yang B, Qin W, Xia J. Tumor Mutation Burden-Associated LINC00638/miR-4732-3p/ULBP1 Axis Promotes Immune Escape via PD-L1 in Hepatocellular Carcinoma. Front Oncol 2021; 11:729340. [PMID: 34568062 PMCID: PMC8456090 DOI: 10.3389/fonc.2021.729340] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Tumor mutation burden (TMB) is associated with immune infiltration, while its underlying mechanism in hepatocellular carcinoma (HCC) remains unclear. A long noncoding RNA (lncRNA)-related competitive endogenous RNA (ceRNA) network can regulate various tumor behaviors, and research about its correlation with TMB and immune infiltration is warranted. Data were downloaded from TCGA and ArrayExpress databases. Cox analysis and machine learning algorithms were employed to establish a lncRNA-based prognostic model for HCC. We then developed a nomogram model to predict overall survival and odds of death for HCC patients. The association of this prognostic model with TMB and immune infiltration was also analyzed. In addition, a ceRNA network was constructed by using DIANA-LncBasev2 and the starBase database and verified by luciferase reporter and colocalization analysis. Multiplex immunofluorescence was applied to determine the correlation between ULBP1 and PD-L1. An eight-lncRNA (SLC25A30-AS1, HPN-AS1, LINC00607, USP2-AS1, HCG20, LINC00638, MKLN1-AS and LINC00652) prognostic score model was constructed for HCC, which was highly associated with TMB and immune infiltration. Next, we constructed a ceRNA network, LINC00638/miR-4732-3p/ULBP1, that may be responsible for NK cell infiltration in HCC with high TMB. However, patients with high ULBP1 possessed a poorer prognosis. Using multiplex immunofluorescence, we found a significant correlation between ULBP1 and PD-L1 in HCC, and patients with high ULBP1 and PD-L1 had the worst prognosis. In brief, the eight-lncRNA model is a reliable tool to predict the prognosis of HCC patients. The LINC00638/miR-4732-3p/ULBP1 axis may regulate immune escape via PD-L1 in HCC with high TMB.
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Affiliation(s)
- Feng Qi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Oncology, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Xiaojing Du
- Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China.,The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhiying Zhao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ding Zhang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Mengli Huang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yuezong Bai
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Biwei Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenxing Qin
- Department of Oncology, Second Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Jinglin Xia
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Chang PY, Cheng CY, Hon JS, Kuo CD, Yen CL, Chai JW. Traditional versus Microsphere Embolization for Hepatocellular Carcinoma: An Effectiveness Evaluation Using Data Mining. Healthcare (Basel) 2021; 9:healthcare9080929. [PMID: 34442066 PMCID: PMC8392597 DOI: 10.3390/healthcare9080929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/07/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background: For hepatocellular carcinoma (“HCC”), the current standard of treatment is hepatic artery embolization, generally through trans-catheter arterial chemoembolization (“TACE”). There are two types: traditional (“conventional” or “cTACE”) and microsphere (“DC bead TACE”). Unfortunately, the literature comparing the relative effectiveness of cTACE versus DC bead TACE is inconclusive, partially due to the complexity of HCC and its response to treatment. Data mining is an excellent method to extract meaning from complex data sets. Purpose: Through the application of data mining techniques, to compare the relative effectiveness of cTACE and DC bead TACE using a large patient database and to use said comparison to establish usable guidelines for developing treatment plans for HCC patients. Materials and Methods: The data of 372 HCC patients who underwent TACE in Taichung Veterans General Hospital were analyzed. The chi-square test was used to compare the difference in the effectiveness of the two therapies was compared. Logistic regression was used to calculate the odds ratios. Furthermore, using the C4.5 decision tree, the two therapies were classified into applicable fields. Chi-square test, the t-test, and logistic regression were used to verify the classification results. Results: In Barcelona Clinic Stages A and B cancers, cTACE was found to be 22.7% more effective than DC bead TACE. By using the decision tree C4.5 as a classifier, the effectiveness of either treatment for small tumors was 8.475 times than that for large tumors. DC bead TACE was 3.39 times more successful in treating patients with a single tumor than with multiple tumors. For patients with a single tumor, the chi-square test showed that 100–300 μm microspheres were significantly more effective than 300–500 μm. While these findings provide a reference for the selection of an appropriate TACE approach, we noted that overall accuracy was somewhat low, possibly due to the limited population. Conclusions: We found that data mining could be applied to develop clear guidelines for physician and researcher use in the case of complex pathologies such as HCC. However, some of our results contradicted those elsewhere in the literature, possibly due to a relatively small sample size. Significantly larger data sets with appropriate levels of granularity could produce more accurate results.
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Affiliation(s)
- Pi-Yi Chang
- Radiology Department, Taichung Veterans General Hospital, Taichung 40705, Taiwan; (P.-Y.C.); (J.-W.C.)
| | - Chen-Yang Cheng
- Department of Industrial Engineering & Management, National Taipei University of Technology, Taipei 10608, Taiwan;
| | - Jau-Shin Hon
- Department of Industrial Engineering & Enterprise Information, Tunghai University, Taichung 40704, Taiwan;
- Correspondence:
| | - Cheng-Ding Kuo
- Department of Industrial Engineering & Enterprise Information, Tunghai University, Taichung 40704, Taiwan;
| | - Chieh-Ling Yen
- Gastrointestinal Department, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
| | - Jyh-Wen Chai
- Radiology Department, Taichung Veterans General Hospital, Taichung 40705, Taiwan; (P.-Y.C.); (J.-W.C.)
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Lin L, Zhao H, Zhai L, Xu B, Xiao L, Chen Z. Downregulation of microRNA-3646 Through Direct Targeting of F-Box Protein 4 on Interleukin-17-Induced Lung Cancer Cell Migration and Invasion. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
IL-17 participates in the initiation and growth of malignant cancers, including lung cancer. The aberrant expression of miRNA is also related to tumor growth and metastasis. Studies have confirmed that high expression of miRNA-3646 can boost breast cancer cell invasion and migration,
suggesting that miRNA-3646 is a tumor-promoting factor. However, the role of miRNA-3646 in the migration and invasion of IL-17-induced lung cancer cells is unclear. In this study, qRT-PCR was used to determine the level of miRNA-3646. We found that in lung cancer cells, miRNA-3646 levels exceeded
those of normal bronchial epithelial 16HBE cells (P < 0.05). The level of miRNA-3646 in NCI-H1299 cells was higher than that in A549, NCI-H446, and SK-MES-1 cells (P < 0.05). After IL-17 treatment, the number of proliferating and migrating lung carcinoma NCI-H1299 cells
increased, transport of vimentin increased, and transport of E-cadherin decreased (P < 0.05). After IL-17 treatment, the number of proliferating and migrating lung carcinoma NCI-H1299 cells transfected with miRNA-3646 inhibitor decreased, transport of vimentin decreased, and transport
of E-cadherin increased (P < 0.05). FBXO4 siRNA reversed the inhibition of miRNA-3646 on the proliferation and migration of IL-17-induced lung carcinoma NCI-H1299 cells and the transport of E-cadherin and vimentin. Thus, downregulation of miRNA-3646 inhibited IL-17-induced lung carcinoma
cell migration and proliferation by directly targeting FBXO4.
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Affiliation(s)
- Ling Lin
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin 301800, PR China
| | - Hongjie Zhao
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin 301800, PR China
| | - Liqiang Zhai
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin 301800, PR China
| | - Baoxin Xu
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin 301800, PR China
| | - Ling Xiao
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin 301800, PR China
| | - Zhengang Chen
- Department of Oncology, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin 301800, PR China
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12
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Tan Z, Li L. Expression of LncRNA DLGAP1-AS1 in a Mouse Model of Atherosclerosis and Its Effect on Oxidized Low-Density Lipoprotein-Induced Vascular Endothelial Cell Injury. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The occurrence of vascular endothelial injury is key to the progression of atherosclerosis (AS). This research explores the expression of lncRNA DLGAP1-AS1 in a mouse model of atherosclerosis and its effect on ox-LDL-induced vascular endothelial cell injury. A mouse model of AS was
constructed, and DLGAP1-AS1 expression was detected using the nano real-time PCR method. Vascular endothelial cells (VEC) are categorized into four groups. Flow cytometry detects cell apoptosis, and Western blot detects Bax and Bcl-2 expressions; WST-8 method detects level of SOD. Thiobarbituric
acid method, Ammonium molybdate colorimetric method, DCFH-DA method were used to detect MDA, CAT, and reactive oxygen species (ROS) levels, respectively. Bioinformatics software predicted the target genes of DLGAP1-AS1. DLGAP1-AS1 expression was raised in AS mice, apoptotic rate and Bax expression
in the ox-LDL group were raised, Bcl-2 expression was abated, MDA and ROS levels were raised, SOD and CAT levels were abated than in control. The si-DLGAP1-AS1+ox-LDL group decreased cell death and Bax expression, increased Bcl-2 expression, decreased MDA and ROS levels, and increased SOD
and CAT levels than in the si-NC+ox-LDL group. Down-regulation of DLGAP1-AS1 was targeted in order to promote miR-26a-5p expression. Compared with co-transfection with DLGAP1-AS1 siRNA and inhibitor control, the apoptosis rate and Bax expression were increased after co-transfection with DLGAP1-AS1
siRNA and miR-26a-5p inhibitor, Bcl-2 expression was decreased, and MDA and ROS levels were increased, the level of SOD and CAT were decreased. DLGAP1-AS1 was up-regulated in AS mice and downregulated to promote miR-26a-5p to inhibit ox-LDL-induced vascular endothelial cell death and oxidative
damage.
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Affiliation(s)
- Zhengli Tan
- Department of Vascular Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, PR China
| | - Lei Li
- Department of Emergency, Beijing First Integrated Hospital of Traditional Chinese and Western Medicine, Beijing 100026, PR China
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13
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Pu Z, Zhu Y, Wang X, Zhong Y, Peng F, Zhang Y. Identification of Prognostic Biomarkers and Correlation With Immune Infiltrates in Hepatocellular Carcinoma Based on a Competing Endogenous RNA Network. Front Genet 2021; 12:591623. [PMID: 34093635 PMCID: PMC8173128 DOI: 10.3389/fgene.2021.591623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 04/22/2021] [Indexed: 12/15/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Recently, competing endogenous RNAs (ceRNA) have revealed a significant role in the progression of HCC. Herein, we aimed to construct a ceRNA network to identify potential biomarkers and illustrate its correlation with immune infiltration in HCC. Methods RNA sequencing data and clinical traits of HCC patients were downloaded from TCGA. The limma R package was used to identify differentially expressed (DE) RNAs. The predicted prognostic model was established using univariate and multivariate Cox regression. A K-M curve, TISIDB and GEPIA website were utilized for survival analysis. Functional annotation was determined using Enrichr and Reactome. Protein-to-protein network analysis was implemented using SRTNG and Cytoscape. Hub gene expression was validated by quantitative polymerase chain reaction, Oncomine and the Hunan Protein Atlas database. Immune infiltration was analyzed by TIMMER, and Drugbank was exploited to identify bioactive compounds. Results The predicted model that was established revealed significant efficacy with 3- and 5-years of the area under ROC at 0.804 and 0.744, respectively. Eleven DEmiRNAs were screened out by a K-M survival analysis. Then, we constructed a ceRNA network, including 56 DElncRNAs, 6 DEmiRNAs, and 28 DEmRNAs. The 28 DEmRNAs were enriched in cancer-related pathways, for example, the TNF signaling pathway. Moreover, six hub genes, CEP55, DEPDC1, KIF23, CLSPN, MYBL2, and RACGAP1, were all overexpressed in HCC tissues and independently correlated with survival rate. Furthermore, expression of hub genes was related to immune cell infiltration in HCC, including B cells, CD8+ T cells, CD4+ T cells, monocytes, macrophages, neutrophils, and dendritic cells. Conclusion The findings from this study demonstrate that CEP55, DEPDC1, KIF23, CLSPN, MYBL2, and RACGAP1 are closely associated with prognosis and immune infiltration, representing potential therapeutic targets or prognostic biomarkers in HCC.
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Affiliation(s)
- Zhangya Pu
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanyuan Zhu
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaofang Wang
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China
| | - Yun Zhong
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China
| | - Fang Peng
- Department of Infectious Diseases, Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, China.,NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, China
| | - Yiya Zhang
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Dermatology, Xiangya Hospital, Changsha, China
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14
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Sun JR, Kong CF, Xiao KM, Yang JL, Qu XK, Sun JH. Integrated Analysis of lncRNA-Mediated ceRNA Network Reveals a Prognostic Signature for Hepatocellular Carcinoma. Front Genet 2021; 11:602542. [PMID: 33381151 PMCID: PMC7767998 DOI: 10.3389/fgene.2020.602542] [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: 09/03/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common types of malignancy and is associated with high mortality. Prior research suggests that long non-coding RNAs (lncRNAs) play a crucial role in the development of HCC. Therefore, it is necessary to identify lncRNA-associated therapeutic biomarkers to improve the accuracy of HCC prognosis. Transcriptomic data of HCC obtained from The Cancer Genome Atlas (TCGA) database were used in the present study. Differentially expressed RNAs (DERNAs), including 74 lncRNAs, 16 miRNAs, and 35 mRNAs, were identified using bioinformatics analysis. The DERNAs were subsequently used to reconstruct a competing endogenous RNA (ceRNA) network. A lncRNA signature was revealed using Cox regression analysis, including LINC00200, MIR137HG, LINC00462, AP002478.1, and HTR2A-AS1. Kaplan-Meier plot demonstrated that the lncRNA signature is highly accurate in discriminating high- and low-risk patients (P < 0.05). The area under curve (AUC) value exceeded 0.7 in both training and validation cohort, suggesting a high prognostic potential of the signature. Furthermore, multivariate Cox regression analysis indicated that both the TNM stage and the lncRNA signature could serve as independent prognostic factors for HCC (P < 0.05). Then, a nomogram comprising the TNM stage and the lncRNA signature was determined to raise the accuracy in predicting the survival of HCC patients. In the present study, we have introduced a ceRNA network that could contribute to provide a new insight into the identification of potential regulation mechanisms for the development of HCC. The five-lncRNA signature could serve as a reliable biosignature for HCC prognosis, while the nomogram possesses strong potential in clinical applications.
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Affiliation(s)
- Jian-Rong Sun
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China.,Oncology Department of Integrated Traditional Chinese and Western Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Chen-Fan Kong
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China.,Gastroenterology Department, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Kun-Min Xiao
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jia-Lu Yang
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China.,Gastroenterology Department, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Xiang-Ke Qu
- Department of Clinical Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jing-Hui Sun
- Gastroenterology Department, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
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15
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Zhang Q, Wang Q, Wu S, Zhang J. Clinical implication and immunological characterisation of the ARF-GEF family member CYTH4 in ovarian cancer. Autoimmunity 2020; 53:434-442. [PMID: 33078956 DOI: 10.1080/08916934.2020.1836487] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND The GTP exchange factors on ADP-ribosylation factor (ARF) mediate the GDP/GTP exchange on ARF, serve as regulators in protein trafficking and membrane dynamics, and play critical roles in various cell processes. However, the relationship between the expression of ARF-GEF family genes and clinical implications in ovarian cancer remains unclear. METHODS We performed a systematic investigation on the role of ARF-GEF family genes in ovarian cancer by using Gene Expression Omnibus (GEO), Kaplan-Meier plotter, Gene set enrichment analysis (GSEA), TIMER and TISIDB database. RESULTS We found that the ARF-GEF family gene CYTH4 exhibited significant expressional upregulation in ovarian cancer compared to normal ovary tissues. The expression of CYTH4 was also higher in metastases from the omentum than in matched primary ovarian tumours. Kaplan-Meier plotter showed that high expression of CYTH4 predicted worse overall survival, progression free survival and post-progression survival of ovarian cancer patients. Notably, from our correlation analysis, CYTH4 expression showed closely association with tumour-infiltrating immune cells. Intriguingly, the expression of CYTH4 was also significantly correlated with a variety of immunomodulators, chemokines and major histocompatibility complex molecules. CONCLUSION Overall, our findings provide a valuable source of data about the clinical significance of CYTH4 in ovarian cancer.
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Affiliation(s)
- Qinyi Zhang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingying Wang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Sufang Wu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiawen Zhang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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16
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Khalili N, Nouri-Vaskeh M, Hasanpour Segherlou Z, Baghbanzadeh A, Halimi M, Rezaee H, Baradaran B. Diagnostic, prognostic, and therapeutic significance of miR-139-5p in cancers. Life Sci 2020; 256:117865. [PMID: 32502540 DOI: 10.1016/j.lfs.2020.117865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/23/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022]
Abstract
miRNAs are a group of non-coding RNAs that have regulatory functions in post-transcriptional gene expression. These molecules play a fundamental role in cellular processes, for instance cell proliferation, apoptosis, migration, and invasion. Scientific investigations have previously established that miRNAs can either promote or suppress tumor development by mediating different signaling pathways. miR-139-5p, located on chromosome 11q13.4, has been examined extensively in cancers. Studies have demonstrated that miR-139-5p might be an attractive cancer biomarker. Herein, we will review how miR-139-5p acts in cancer diagnosis, prognosis, and therapy, as well as elucidating its major target genes and associated signaling pathways.
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Affiliation(s)
- Neda Khalili
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Masoud Nouri-Vaskeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | | | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Monireh Halimi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Haleh Rezaee
- Infectious Diseases and Tropical Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Clinical Pharmacy (Pharmacotherapy), Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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17
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Yan L, Yue C, Xu Y, Jiang X, Zhang L, Wu J. Identification of Potential Diagnostic and Prognostic Pseudogenes in Hepatocellular Carcinoma Based on Pseudogene-miRNA-mRNA Competitive Network. Med Sci Monit 2020; 26:e921895. [PMID: 32457285 PMCID: PMC7249743 DOI: 10.12659/msm.921895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background It is widely known that hepatocellular carcinoma (HCC) has high rates of morbidity and mortality. A large number of studies have indicated that pseudogenes have an important effect on the carcinogenesis of HCC. Pseudogenes can play a role through the ceRNA network. There have been numerous studies on lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks. However, the pseudogene-miRNA-mRNA network in HCC has rarely been researched or reported on. Material/Methods The Cancer Genome Atlas (TCGA) database was researched and differences between selected genes were studied. A pseudogene-miRNA-mRNA network was then constructed and clustering of pseudogenes was studied. The diagnostic value of the selected pseudogenes, their functions, and pathways were investigated using available databases to understand their possible pathogenic mechanism in HCC. The protein-protein interaction network of target genes was found and the top 10 hub genes were identified. Expression of hub genes in HCC tissues was then detected by RT-qPCR. Results By analyzing the gene difference and clinical data of HCC, we constructed a ceRNA network composed of 4 pseudogenes, 8 miRNAs, and 30 mRNAs. The pseudogenes AP000769.1, KRT16P1, KRT16P3, and RPLP0P2 were all correlated with the diagnosis and prognosis of HCC. Functional analyses through the Kyoto Encyclopedia of Genes and Genomes and the Gene Ontology databases indicated that pseudogenes can affect the physiological process of HCC through the p53 pathway. The top 10 hub genes identified were all highly expressed in HCC tissues and affected the patient survival rate. Conclusions In this study, 4 pseudogenes related to the diagnosis and prognosis of liver cancer were found through the construction of a ceRNA network. These 4 pseudogenes might constitute new therapeutic targets for liver cancer patients.
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Affiliation(s)
- Lijun Yan
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Chaosen Yue
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Yingchen Xu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Xincen Jiang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Lijun Zhang
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
| | - Jixiang Wu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China (mainland)
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18
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Varghese RS, Zhou Y, Barefoot M, Chen Y, Di Poto C, Balla AK, Oliver E, Sherif ZA, Kumar D, Kroemer AH, Tadesse MG, Ressom HW. Identification of miRNA-mRNA associations in hepatocellular carcinoma using hierarchical integrative model. BMC Med Genomics 2020; 13:56. [PMID: 32228601 PMCID: PMC7106691 DOI: 10.1186/s12920-020-0706-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/19/2020] [Indexed: 02/07/2023] Open
Abstract
Background The established role miRNA-mRNA regulation of gene expression has in oncogenesis highlights the importance of integrating miRNA with downstream mRNA targets. These findings call for investigations aimed at identifying disease-associated miRNA-mRNA pairs. Hierarchical integrative models (HIM) offer the opportunity to uncover the relationships between disease and the levels of different molecules measured in multiple omic studies. Methods The HIM model we formulated for analysis of mRNA-seq and miRNA-seq data can be specified with two levels: (1) a mechanistic submodel relating mRNAs to miRNAs, and (2) a clinical submodel relating disease status to mRNA and miRNA, while accounting for the mechanistic relationships in the first level. Results mRNA-seq and miRNA-seq data were acquired by analysis of tumor and normal liver tissues from 30 patients with hepatocellular carcinoma (HCC). We analyzed the data using HIM and identified 157 significant miRNA-mRNA pairs in HCC. The majority of these molecules have already been independently identified as being either diagnostic, prognostic, or therapeutic biomarker candidates for HCC. These pairs appear to be involved in processes contributing to the pathogenesis of HCC involving inflammation, regulation of cell cycle, apoptosis, and metabolism. For further evaluation of our method, we analyzed miRNA-seq and mRNA-seq data from TCGA network. While some of the miRNA-mRNA pairs we identified by analyzing both our and TCGA data are previously reported in the literature and overlap in regulation and function, new pairs have been identified that may contribute to the discovery of novel targets. Conclusion The results strongly support the hypothesis that miRNAs are important regulators of mRNAs in HCC. Furthermore, these results emphasize the biological relevance of studying miRNA-mRNA pairs.
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Affiliation(s)
- Rency S Varghese
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room 175, Building D, 4000 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Yuan Zhou
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room 175, Building D, 4000 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Megan Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room 175, Building D, 4000 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Yifan Chen
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room 175, Building D, 4000 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Cristina Di Poto
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room 175, Building D, 4000 Reservoir Rd NW, Washington, DC, 20057, USA
| | | | - Everett Oliver
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room 175, Building D, 4000 Reservoir Rd NW, Washington, DC, 20057, USA
| | - Zaki A Sherif
- Department of Biochemistry & Molecular Biology, College of Medicine, Howard University, Washington DC, USA
| | - Deepak Kumar
- Department of Pharmaceutical Sciences, North Carolina Central University, Durham, NC, USA
| | | | - Mahlet G Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington DC, USA
| | - Habtom W Ressom
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Room 175, Building D, 4000 Reservoir Rd NW, Washington, DC, 20057, USA.
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