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Lou W, Xiao S, Lin K. Identification of a hypoxia-suppressed lncRNA RAMP2-AS1 in breast cancer. Noncoding RNA Res 2024; 9:782-795. [PMID: 38590436 PMCID: PMC10999373 DOI: 10.1016/j.ncrna.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/08/2024] [Accepted: 02/06/2024] [Indexed: 04/10/2024] Open
Abstract
Hypoxia is a critical feature of solid tumors and exerts crucial roles in cancers, including breast cancer. However, the detailed relationship between lncRNA-miRNA-mRNA triple network and hypoxia in breast cancer is still indistinct. In this study, a series of in silico analyses and online databases or tools were employed to establish a hypoxia-related lncRNA-miRNA-mRNA network in breast cancer based on competing endogenous RNA mechanism at single-cell resolution. RAMP2-AS1 was, eventually, identified as the most potential lncRNA, which was significantly negatively associated with hypoxia in breast cancer. Compared with normal controls, RAMP2-AS1 was markedly downregulated in breast cancer. Moreover, survival analysis revealed favorable prognostic values of RAMP2-AS1 in total or in specific clinicopathological breast cancer patients. Next, miR-660-5p, miR-2277-5p and miR-1301-3p, upregulated and possessed poor prognostic values in breast cancer, were identified as three potential downstream miRNAs of RAMP2-AS1. Then, the most potential downstream hypoxia-related genes (ATM and MYH11) of RAMP2-AS1/miRNA axis in breast cancer were screened out. Intriguingly, in vitro experiments confirmed that RAMP2-AS1 was a hypoxia-suppressed lncRNA and miR-660-5p/ATM was a potential downstream axis of RAMP2-AS1 in breast cancer. Collectively, our current data elucidated a key hypoxia-suppressed lncRNA RAMP2-AS1 and its possible miRNA-mRNA regulatory mechanism in breast cancer.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Shuyuan Xiao
- Department of Anesthesiology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Kuailu Lin
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325015, China
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2
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Liu J, Wang M, Wang M, Wang F, Zhang B. LncRNAs-Regulated High Expression of LAMC2 Reveals a Prognostic and Immunological Value in Pancreatic Adenocarcinoma. Biochem Genet 2024; 62:485-503. [PMID: 37382751 DOI: 10.1007/s10528-023-10435-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/18/2023] [Indexed: 06/30/2023]
Abstract
Pancreatic adenocarcinoma (PAAD) is one of the most hazardous cancers in digestive system, and the prognosis is notoriously bad. Increasing evidences indicate that Laminin Subunit Gamma 2 (LAMC2) is critical for the initiation and the growth of various sorts of human cancers. However, the involved molecular pathways of LAMC2 in PAAD are still poorly understood. In this study, prediction programs and databases were employed to conduct pan-cancer analysis. Multiple variations of human malignancies showed increased LAMC2 expression, which was positively correlated to a poor prognosis in PAAD. Moreover, LAMC2 was positively correlated with the biomarkers of immune cells including CD19, CD163, and NOS2 in PAAD. The lncRNA C5orf66 /PTPRG-AS1- miR-128-3p -LAMC2 axis was identified to be a potential upstream regulatory pathway of LAMC2 in PAAD. Furthermore, LAMC2 upregulation in PAAD was associated with PD-L1 expression, indicating promoting carcinoma immune cell infiltration. Our study elucidated prognostic and immunological values of LAMC2 in PAAD, providing a promise target for PAAD treatment.
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Affiliation(s)
- Jingyun Liu
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Mengyue Wang
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Miaowen Wang
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Fu Wang
- School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Xianyang Key Laboratory of Molecular Imaging and Drug Synthesis, School of Pharmacy, Shaanxi Institute of International Trade and Commerce, Xianyang, 712046, China.
| | - Beilei Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Department of Obstetrics and Gynecology, Tangdu Hospital, Air Force Medical University, Xi'an, 710038, Shaanxi, China.
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3
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Zhang R, Gao X, Gu X. BBOX1-AS1: A novel oncogenic long non-coding RNA in human cancers. Pathol Res Pract 2023; 250:154810. [PMID: 37696243 DOI: 10.1016/j.prp.2023.154810] [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: 06/15/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts that contain more than 200 nucleotides. Despite the fact that they cannot encode proteins, many studies have identified roles they play in human cancers through diverse mechanisms. BBOX1-AS1, an oncogenic lncRNA, has recently been demonstrated to participate in tumorigenesis and progression of numerous cancers. Experimental evidence has determined that it participates in diverse biological process, including cell proliferation, invasion, migration, and apoptosis. The dysregulation of BBOX1-AS1 exerts its oncogenicity by acting as a competitive endogenous RNA (ceRNA) or by directly impacting downstream molecules and signaling pathways. Here we summarize the current understanding of the biological functions and clinical significance of BBOX1-AS1 for human cancers.
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Affiliation(s)
- Renfang Zhang
- Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Xiaohui Gao
- Department of Oncology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital of Henan University of Science and Technology, Luoyang 471000, Henan, China.
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Moldogazieva NT, Zavadskiy SP, Astakhov DV, Sologova SS, Margaryan AG, Safrygina AA, Smolyarchuk EA. Differentially expressed non-coding RNAs and their regulatory networks in liver cancer. Heliyon 2023; 9:e19223. [PMID: 37662778 PMCID: PMC10474437 DOI: 10.1016/j.heliyon.2023.e19223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
The vast majority of human transcriptome is represented by various types of small RNAs with little or no protein-coding capability referred to as non-coding RNAs (ncRNAs). Functional ncRNAs include microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), which are expressed at very low, but stable and reproducible levels in a variety of cell types. ncRNAs regulate gene expression due to miRNA capability of complementary base pairing with mRNAs, whereas lncRNAs and circRNAs can sponge miRNAs off their target mRNAs to act as competitive endogenous RNAs (ceRNAs). Each miRNA can target multiple mRNAs and a single mRNA can interact with several miRNAs, thereby creating miRNA-mRNA, lncRNA-miRNA-mRNA, and circRNA-miRNA-mRNA regulatory networks. Over the past few years, a variety of differentially expressed miRNAs, lncRNAs, and circRNAs (DEMs, DELs, and DECs, respectively) have been linked to cancer pathogenesis. They can exert both oncogenic and tumor suppressor roles. In this review, we discuss the recent advancements in uncovering the roles of DEMs, DELs, and DECs and their networks in aberrant cell signaling, cell cycle, transcription, angiogenesis, and apoptosis, as well as tumor microenvironment remodeling and metabolic reprogramming during hepatocarcinogenesis. We highlight the potential and challenges in the use of differentially expressed ncRNAs as biomarkers for liver cancer diagnosis and prognosis.
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Affiliation(s)
- Nurbubu T. Moldogazieva
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Sergey P. Zavadskiy
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Dmitry V. Astakhov
- Department of Biochemistry, Institute of Biodesign and Complex Systems Modelling, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Susanna S. Sologova
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Arus G. Margaryan
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Anastasiya A. Safrygina
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
| | - Elena A. Smolyarchuk
- Department of Pharmacology, Nelyubin Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, 119991, 8 Trubetskaya str., Moscow, Russia
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5
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Li X, Ma Z, Mei L. Comprehensive analysis of UBE2C expression and its potential roles and mechanisms in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:7397-7407. [PMID: 37580802 PMCID: PMC10457065 DOI: 10.18632/aging.204792] [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: 09/01/2022] [Accepted: 05/01/2023] [Indexed: 08/16/2023]
Abstract
Hepatocellular carcinoma (HCC) ranks one of the most common and lethal cancers all over the world. Previous studies suggest that ubiquitin-conjugating enzyme E2C (UBE2C) serves as an oncogene in human cancers. However, its expression, diagnosis, prognosis and potential mechanisms in HCC remain largely unknown. In this study, the expression of UBE2C in HCC was first analyzed by comprehensive bioinformatic analysis. ROC curve analysis and survival analysis were employed to assess the diagnostic and prognostic roles of UBE2C in HCC. UBE2C promoter methylation level and upstream regulatory miRNAs of UBE2C in HCC were explored. The present work demonstrated that UBE2C was significantly upregulated in HCC compared with normal controls. We also found significant diagnostic and prognostic values of UBE2C in HCC. Promoter methylation of UBE2C was obviously decreased in HCC and was negatively correlated with UBE2C mRNA expression. 10 miRNAs were predicted to potentially bind to UBE2C. In vitro assay and bioinformatic correlation analysis together revealed that hsa-miR-193b-3p might be another key upstream regulatory mechanism of UBE2C in HCC. In conclusion, UBE2C is overexpressed in HCC and may serve as a key diagnostic/prognostic biomarker for patients with HCC.
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Affiliation(s)
- Xiao Li
- Department of Emergency, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 317000, China
| | - Zhaosheng Ma
- Department of Oncological Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 317000, China
| | - Linhang Mei
- Department of Oncological Surgery, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 317000, China
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Xiang Q, Tao JS, Li JJ, Tian RB, Li XH. What is the role of Von Willebrand factor in chronic hepatitis B virus infection to hepatocellular carcinoma: a review article. Ther Adv Chronic Dis 2022; 13:20406223221125683. [PMID: 36407018 PMCID: PMC9669690 DOI: 10.1177/20406223221125683] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/25/2022] [Indexed: 11/12/2023] Open
Abstract
Von Willebrand factor (VWF) is a glycoprotein synthesized and secreted by vascular endothelial cells and megakaryocytes, found on plasma surface, endothelial cells, and α-granule of platelets. VWF can be interacted with collagen and platelet membrane glycoproteins GPIb and GPIb-IIa and play an important role in platelet adhesion and aggregation. Growing research evidence suggests that VWF also mediates the prevention or protesting of hepatocellular carcinoma (HCC) in chronic hepatitis B (CHB) patients from several clinical studies. While the mechanism of VWF in HCC protection or protest is still unclear, further study is required. This article aims to rationalize the role of VWF in the development of HCC, and the functional domain of VWF in cancer as well as cross-talking with platelets and miRNAs. This article also looks forward to the future development and challenges of VWF research.
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Affiliation(s)
- Qiong Xiang
- Medical Research Center, Institute of Medicine,
Jishou University, Jishou, China
| | - Jia-Sheng Tao
- Medical Research Center, Institute of Medicine,
Jishou University, Jishou, China
| | - Jing-Jing Li
- Medical Research Center, Institute of Medicine,
Jishou University, Jishou, China
| | - Rong-Bo Tian
- Medical Research Center, Institute of Medicine,
Jishou University, Jishou, China
| | - Xian-Hui Li
- Institute of Pharmaceutical Sciences, Jishou
University, 120 Ren min south road, Jishou 416000, China
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7
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Chen S, Chen X, Zhang P, Chen S, Wang X, Luo Q, Cui Z, Huang Y, Wan L, Hou X, Yao H, Liu X, He A, Jiang Z, Qiu J, Li Y, Yu K, Zhuang J. Bioinformatics Analysis and Experimental Identification of Immune-Related Genes and Immune Cells in the Progression of Retinoblastoma. Invest Ophthalmol Vis Sci 2022; 63:28. [PMID: 36315123 PMCID: PMC9631497 DOI: 10.1167/iovs.63.11.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Purpose Retinoblastoma (RB) is the most common type of aggressive intraocular malignancy in children. The alteration of immunity during RB progression and invasion has not yet been well defined. This study investigated significantly altered immune-associated genes and cells related to RB invasion. Methods The differentially expressed immune-related genes (IRGs) in noninvasive RB and invasive RB were identified by analysis of two microarray datasets (GSE97508 and GSE110811). Hub IRGs were further identified by real time PCR. The single-sample gene set enrichment analysis algorithm and Pearson correlation analysis were used to define immune cell infiltration and the relationships between hub IRGs and immune cells. Cell viability and migration were evaluated by CCK-8 and Transwell assays. A xenograft mouse model was used to verify the relationship between Src homology 3 (SH3) domain GRB2-like 2 (SH3GL2) expression and myeloid-derived suppressor cells (MDSCs). Results Eight upregulated genes and six downregulated IRGs were identified in invasive RB. Seven IRGs were confirmed by real-time PCR. Moreover, the proportions of MDSCs were higher in invasive RB tissues than in noninvasive RB tissues. Furthermore, correlation analysis of altered immune genes and cells suggested that SH3GL2, Langerhans cell protein 1 (LCP1) and transmembrane immune signaling adaptor TYROBP have strong connections with MDSCs. Specifically, decreased SH3GL2 expression promoted the migration of RB cells in vitro, increased the tumor size and weight, and increased the numbers of MDSCs in the tumor and spleen in vivo. Conclusions This study indicated that SH3GL2 and MDSCs play a critical role in RB progression and invasion and provide candidate targets for the treatment of RB.
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Affiliation(s)
- Shuilian Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Xi Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Ping Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Shuxia Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Xiao Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Qian Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Zedu Cui
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Yuke Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Linxi Wan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Xiangtao Hou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Huan Yao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Xuan Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Anqi He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Zihua Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Jin Qiu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Yan Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Keming Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
| | - Jing Zhuang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou City, China
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Cui Y, Wu J, Zhou Z, Ma J, Dong L. Two novel lncRNAs AF111167.2 and AL162377.1 targeting miR-21-5p mediated down expression of SYDE2 correlates with poor prognosis and tumor immune infiltration of ccRCC. Heliyon 2022; 8:e11079. [PMID: 36311369 PMCID: PMC9614862 DOI: 10.1016/j.heliyon.2022.e11079] [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: 05/05/2022] [Revised: 06/16/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Advanced clear cell Renal Cell Carcinoma (ccRCC) is notoriously known for its poor prognosis. Synapse defective protein 1 homolog 2 encoded by the SYDE2 gene is a Rho GTPase-activating protein whose functional tumorigenic significance is still unclear. Recent pan-cancer analysis using the Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) data showed the potential tumor-suppressing effects of SYDE2 in ccRCC. Subsequently, the TCGA, GTEx data, and human protein atlas were employed to assess the correlation between the SYDE2 expression, clinical data, and overall survival (OS) in ccRCC patients. Furthermore, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) contributing to SYDE2 down expression were identified by expression, relationship, and survival analysis. Eventually, two novel lncRNAs, AL162377.1 and AF111167.2, targeting the miR-21-5p axis, were identified in the SYDE2 upstream non-coding RNAs (ncRNAs)-related pathway in ccRCC. The expression level of SYDE2 highly depends on the tumor immune cell infiltration and immune checkpoint expression. In summary, these data demonstrated that lncRNAs/miRNAs-mediated down-regulation of SYDE2 is related to the tumor immune infiltration. Hence, giving an insight into the prognosis of ccRCC.
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Affiliation(s)
- Yuanshan Cui
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Qingdao, China
| | - Jitao Wu
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Qingdao, China
| | - Zhongbao Zhou
- Department of Urology, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Jian Ma
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Qingdao, China
| | - Liying Dong
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Qingdao, China,Corresponding author.
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Dysregulation of Pseudogenes/lncRNA-Hsa-miR-1-3p-PAICS Pathway Promotes the Development of NSCLC. JOURNAL OF ONCOLOGY 2022; 2022:4714931. [PMID: 36081668 PMCID: PMC9448537 DOI: 10.1155/2022/4714931] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/06/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Objective Non-small cell lung cancer (NSCLC) explains about 80 percent of whole lung cancers, and its 5-year survival rate is impoverished, as when people are first diagnosed, 68% of whom are identified at a dangerous stage. The molecular mechanisms of NSCLC are still being explored. Methods GSE18842 and GSE19804 were exerted to scan for diversely expressed genes (DEGs) in NSCLC, and then we used GEPIA for the validation of DEGs expression. The prognostic values were determined through Kaplan–Meier analysis. Three target prediction databases indicated potential microRNAs (miRNAs), while miRNet predicted hsa-miR-1-3p′s upstream long non-coding RNAs (lncRNAs) and pseudogenes. UALCAN was utilized to identify the co-expressed genes of PAICS, while enrichment analysis on them was managed with Enrichr. Results We initially found that the gene expression level of cyclin B1 (CCNB1), cyclin-dependent kinases1 (CDK1), and phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS) had a notable increase in NSCLC. We predicted 6, 10, and 7 microRNAs to target CCNB1, CDK1, and PAICS, respectively. Among miRNA-mRNA (microRNA-messenger RNA) pairs, we deduced that the hsa-miR-1-PAICS axis was the most potential one to inhibit the occurrence of NSCLC. We also noted that the hsa-miR-1-3p-PAICS axis participated in regulating the process of mitosis with mechanical functions. Moreover, we identified 5 pseudogenes and 33 long non-coding RNAs (lncRNAs) that might inhibit the hsa-miR-1-3p-PAICS axis in NSCLC. Conclusions The pseudogene/lncRNA-hsa-miR-1-3p-PAICS is very important in NSCLC on the basis of this study, thus providing us with effective treatments and promising biomarkers for the diagnosis of NSCLC.
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10
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Wu X, Wang Y, Yang M, Wang Y, Wang X, Zhang L, Liao L, Li N, Mao M, Guan J, Ye F. Exploring prognostic value and regulation network of PPP1R1A in hepatocellular carcinoma. Hum Cell 2022; 35:1856-1868. [PMID: 36018458 DOI: 10.1007/s13577-022-00771-9] [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: 04/07/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022]
Abstract
Novel and accurate biomarkers are needed for early detection and progression evaluation of hepatocellular carcinoma (HCC). Protein phosphatase 1 regulatory subunit 1A (PPP1R1A) has been studied in cancer biology; however, the expression pattern and biological function of PPP1R1A in HCC are unclear. The differentially expressed genes (DEGs) in HCC were screened by The Cancer Genome Atlas (TCGA) database. Real-time PCR and immunohistochemistry (IHC) assay were used to detect the expression of PPP1R1A in BALB/c mice, human normal tissues and corresponding tumor tissues, especially HCC. Then, Kaplan-Meier analysis of patients with HCC was performed to evaluate the relationship between PPP1R1A expression and prognosis. The transcriptional regulatory network of PPP1R1A was constructed based on the differentially expressed mRNAs, microRNAs and transcription factors (TFs). To explore the downstream regulation of PPP1R1A, the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis and immune infiltration score were performed. A total of 4 DEGs were screened out. PPP1R1A was differentially distributed and expressed in BALB/c mice and human tissues. PPP1R1A expression was higher in normal tissues than that in tumor tissues, and patients with higher PPP1R1A expression had better clinical outcome in HCC. In addition, we constructed miR-21-3p/TAL1/PPP1R1A transcriptional network. Furthermore, PPP1R1A may modulate the activation of PI3K-Akt pathway, cell cycle, glycogen metabolism and the recruitment of M2 macrophage in HCC. This study may help to clarify the function and mechanism of PPP1R1A in HCC and provide a potential biomarker for tumor prevention and treatment.
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Affiliation(s)
- Xixi Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Department of Radiation Oncology, Guangxi Zhuang Autonomous Region People's Hospital, Nanning, Guangxi, China
| | - Yin Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Mi Yang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yingqiao Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoqing Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Longshan Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Liwei Liao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Nan Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Mengyuan Mao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
| | - Feng Ye
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
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11
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Hu X, Zhou J, Zhang Y, Zeng Y, Jie G, Wang S, Yang A, Zhang M. Identifying potential prognosis markers in hepatocellular carcinoma via integrated bioinformatics analysis and biological experiments. Front Genet 2022; 13:942454. [PMID: 35928445 PMCID: PMC9343963 DOI: 10.3389/fgene.2022.942454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/29/2022] [Indexed: 12/18/2022] Open
Abstract
Background: Hepatocellular carcinoma is one kind of clinical common malignant tumor with a poor prognosis, and its pathogenesis remains to be clarified urgently. This study was performed to elucidate key genes involving HCC by bioinformatics analysis and experimental evaluation. Methods: We identified common differentially expressed genes (DEGs) based on gene expression profile data of GSE60502 and GSE84402 from the Gene Expression Omnibus (GEO) database. Gene Ontology enrichment analysis (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, REACTOME pathway enrichment analysis, and Gene Set Enrichment Analysis (GSEA) were used to analyze functions of these genes. The protein-protein interaction (PPI) network was constructed using Cytoscape software based on the STRING database, and Molecular Complex Detection (MCODE) was used to pick out two significant modules. Hub genes, screened by the CytoHubba plug-in, were validated by Gene Expression Profiling Interactive Analysis (GEPIA) and the Human Protein Atlas (HPA) database. Then, the correlation between hub genes expression and immune cell infiltration was evaluated by Tumor IMmune Estimation Resource (TIMER) database, and the prognostic values were analyzed by Kaplan-Meier plotter. Finally, biological experiments were performed to illustrate the functions of RRM2. Results: Through integrated bioinformatics analysis, we found that the upregulated DEGs were related to cell cycle and cell division, while the downregulated DEGs were associated with various metabolic processes and complement cascade. RRM2, MAD2L1, MELK, NCAPG, and ASPM, selected as hub genes, were all correlated with poor overall prognosis in HCC. The novel RRM2 inhibitor osalmid had anti-tumor activity, including inhibiting proliferation and migration, promoting cell apoptosis, blocking cell cycle, and inducing DNA damage of HCC cells. Conclusion: The critical pathways and hub genes in HCC progression were screened out, and targeting RRM2 contributed to developing new therapeutic strategies for HCC.
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Affiliation(s)
- Xueting Hu
- Department of Intensive Care Unit, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Jian Zhou
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yan Zhang
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yindi Zeng
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Guitao Jie
- Department of Hematology, Linyi Central Hospital, Yishui, Shandong, China
| | - Sheng Wang
- Department of Hematology, Linyi Central Hospital, Yishui, Shandong, China
| | - Aixiang Yang
- Department of Intensive Care Unit, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
- *Correspondence: Aixiang Yang, ; Menghui Zhang,
| | - Menghui Zhang
- Department of Hematology, Linyi Central Hospital, Yishui, Shandong, China
- *Correspondence: Aixiang Yang, ; Menghui Zhang,
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12
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Yun JH, Baek MJ, Jung HI. Expression of miR-221 and miR-18a in patients with hepatocellular carcinoma and its clinical significance. KOREAN JOURNAL OF CLINICAL ONCOLOGY 2022; 18:17-26. [PMID: 36945332 PMCID: PMC9942768 DOI: 10.14216/kjco.22003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 11/07/2022]
Abstract
Purpose Recently, microRNA (miRNA) has been evaluated to provide a new diagnostic and therapeutic modality hepatocellular carcinoma (HCC) and other tumors. They are small non-coding RNA molecules that function as transcriptional and post-transcriptional regulators of gene expression by silencing target genes. The aim of this study was to evaluate the clinical significance of microRNA-18a, 221 (miR-18a, miR-221) expression in HCC formalin-fixed paraffin-embedded (FFPE) tissue. Methods miR-18a and miR-221 expressions were assessed by reverse transcription and real-time quantitative reverse transcription polymerase chain reaction in 50 pairs of FFPE HCC and the adjacent noncancerous liver tissues. And we evaluated the expression level in HCC tissues as compared with their adjacent noncancerous counterparts. And the relationship between miR-18a, miR-221 level and clinicopathological data and survival rates were analyzed. Results miR-221 and miR-18a were overexpressed in HCC tissue as compared with their adjacent noncancerous liver tissue (P<0.001). miR-221 expression was found to be correlated with larger tumor size (P=0.048). miR-18a expression was correlated with modified Union for International Cancer Control stage (P=0.05). The overall survival (P=0.02) of HCC patients with high miR-221 expression was significantly poorer compared to those patients with low expression. Multivariate analyses demonstrated that miR-221 may be a poor prognostic factor of HCC patients. Conclusion High expression of miR-221 in FFPE tissues could provide significance for prognosis of HCC patients. Although, miR-18a expression was significantly upregulated in HCC tissues, they are not correlated with prognosis. Further large prospective studies are needed to determine their clinical significance.
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Affiliation(s)
- Jong Hyuk Yun
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Moo-Jun Baek
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Hae Il Jung
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
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13
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Zhou Y, Takano T, Li X, Wang Y, Wang R, Zhu Z, Tanokura M, Miyakawa T, Hachimura S. β-elemene regulates M1-M2 macrophage balance through the ERK/JNK/P38 MAPK signaling pathway. Commun Biol 2022; 5:519. [PMID: 35641589 PMCID: PMC9156783 DOI: 10.1038/s42003-022-03369-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
Macrophages are classified into classically activated M1 macrophages and alternatively activated M2 macrophages, and the two phenotypes of macrophages are present during the development of various chronic diseases, including obesity-induced inflammation. In the present study, β-elemene, which is contained in various plant substances, is predicted to treat high-fat diet (HFD)-induced macrophage dysfunction based on the Gene Expression Omnibus (GEO) database and experimental validation. β-elemene impacts the imbalance of M1-M2 macrophages by regulating pro-inflammatory cytokines in mouse white adipose tissue both in vitro and in vivo. In addition, the RAW 264 cell line, which are macrophages from mouse ascites, is used to identify the effects of β-elemene on inhibiting bacterial endotoxin lipopolysaccharide (LPS)-induced phosphorylation of mitogen-activated protein kinase (MAPK) pathways. These pathways both induce and are activated by pro-inflammatory cytokines, and they also participate in the process of obesity-induced inflammation. The results highlight that β-elemene may represent a possible macrophage-mediated therapeutic medicine. β-elemene regulates the balance of proinflammatory cytokines in mouse white adipose tissue through MAPK signaling. Targets of β -elemene are predicted based on its 3D structure and include regulators of macrophage-mediated processes.
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Affiliation(s)
- Yingyu Zhou
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tomohiro Takano
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Xuyang Li
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yimei Wang
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Rong Wang
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Zhangliang Zhu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.,Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, National Engineering Laboratory for Industrial Enzymes, Tianjin, 300457, P. R. China
| | - Masaru Tanokura
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Satoshi Hachimura
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
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14
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Khare S, Khare T, Ramanathan R, Ibdah JA. Hepatocellular Carcinoma: The Role of MicroRNAs. Biomolecules 2022; 12:biom12050645. [PMID: 35625573 PMCID: PMC9138333 DOI: 10.3390/biom12050645] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related deaths worldwide. HCC is diagnosed in its advanced stage when limited treatment options are available. Substantial morphologic, genetic and epigenetic heterogeneity has been reported in HCC, which poses a challenge for the development of a targeted therapy. In this review, we discuss the role and involvement of several microRNAs (miRs) in the heterogeneity and metastasis of hepatocellular carcinoma with a special emphasis on their possible role as a diagnostic and prognostic tool in the risk prediction, early detection, and treatment of hepatocellular carcinoma.
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Affiliation(s)
- Sharad Khare
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (S.K.); (T.K.); (R.R.)
- Harry S. Truman Veterans Hospital, Columbia, MO 65201, USA
| | - Tripti Khare
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (S.K.); (T.K.); (R.R.)
| | - Raghu Ramanathan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (S.K.); (T.K.); (R.R.)
- Harry S. Truman Veterans Hospital, Columbia, MO 65201, USA
| | - Jamal A. Ibdah
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (S.K.); (T.K.); (R.R.)
- Harry S. Truman Veterans Hospital, Columbia, MO 65201, USA
- Department of Medical Pharmacology and Physiology, University of Missouri, Columbia, MO 65212, USA
- Correspondence: ; Tel.: 1-573-882-7349; Fax: 1-573-884-4595
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15
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El-Mahdy HA, Sallam AAM, Ismail A, Elkhawaga SY, Elrebehy MA, Doghish AS. miRNAs inspirations in hepatocellular carcinoma: Detrimental and favorable aspects of key performers. Pathol Res Pract 2022; 233:153886. [PMID: 35405621 DOI: 10.1016/j.prp.2022.153886] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/23/2022] [Accepted: 04/01/2022] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related deaths worldwide. HCC initiation, progression, and therapy failure are all influenced by various variables, including microRNAs (miRNAs). miRNAs are short non-coding RNA sequences that modulate target mRNA expression by deteriorating or repressing translation. miRNAs play an imperative role in HCC pathogenesis by triggering the induction of cancer stem cells (CSCs) and their proliferation, while also delaying apoptosis, sustaining the cell cycle, and inspiring angiogenesis, invasion, and metastasis. Additionally, miRNAs modulate crucial HCC-related molecular pathways such as the p53 pathway, the Wnt/β-catenin pathway, VEGFR2, and PTEN/PI3K/AKT pathway. Consequently, the goal of this review was to give an up-to-date overview of oncogenic and tumor suppressor (TS) miRNAs, as well as their potential significance in HCC pathogenesis and treatment responses, highlighting their underpinning molecular pathways in HCC initiation and progression. Similarly, the biological importance and clinical application of miRNAs in HCC are summarized.
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Affiliation(s)
- Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Al-Aliaa M Sallam
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Samy Y Elkhawaga
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt.
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16
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Chen X, Li X, Wei C, Zhao C, Wang S, Gao J. High expression of SETDB1 mediated by miR-29a-3p associates with poor prognosis and immune invasion in breast invasive carcinoma. Transl Cancer Res 2022; 10:5065-5075. [PMID: 35116358 PMCID: PMC8797950 DOI: 10.21037/tcr-21-1527] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022]
Abstract
Background Breast invasive carcinoma (BRCA) has a poor prognosis. Numerous studies have shown that SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) is involved in the initiation and progression of many cancers. This study aims to reveal the potential mechanism of SETDB1 in the development and progression of BRCA. Methods The ONCOMINE database, TIMER database, UALCAN database and GEPIA database were used to analyze the expression of SETDB1 in human cancers. We evaluated the expression level of SETDB1 in cell lines by quantitative real-time polymerase chain reaction (qPCR), and the survival analysis of SETDB1 was performed on PrognoScan and Kaplan-Meier plotter websites. The upstream regulator was obtained from starBase database. Results We confirmed that SETDB1 messenger RNA (mRNA) level showed high expression in breast cell lines, and we also found that SETDB1 showed high expression in many types of cancers. Moreover, SETDB1 overexpression was positively correlated with poor prognosis in BRCA. Furthermore, we first predicted miR-29a-3p was a potential upstream regulator of SETDB1 in BRCA. Our findings indicated that SETDB1 might play a carcinogenic role by increasing the infiltration of immune cell and influencing immune checkpoint expression. Conclusions This study suggested that miR-29a-3p can mediate the expression of SETDB1 with poor prognosis and tumor immune infiltration in BRCA.
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Affiliation(s)
- Xiatian Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xin Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Chuang Wei
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Cheng Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Shaoying Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.,School of Basic Medicine, Qingdao University, Qingdao, China
| | - Jinning Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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17
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MicroRNA-494-3p prevents liver fibrosis and attenuates hepatic stellate cell activation by inhibiting proliferation and inducing apoptosis through targeting TRAF3. Ann Hepatol 2022; 23:100305. [PMID: 33434689 DOI: 10.1016/j.aohep.2021.100305] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
INTRODUCTION AND OBJECTIVES Alcoholic hepatitis (AH) is characterized by high morbidity and mortality. MicroRNA-494-3p is possibly involved in the regulation of cancers, but its role in AH has been rarely studied. MATERIALS AND METHODS AH mice model and primarily cultured mice hepatic stellate cells (HSCs) model were constructed. Levels of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were analyzed by ELISA. Expressions of miRNAs, HSC activation-related proteins and fibrosis-related protein were analyzed by qRT-PCR and Western blot. Cell counting kit, colony formation and flow cytometry assays were used to detect cell viability, proliferation and apoptosis, respectively. The relationship between TNF receptor-associated factor 3 (TRAF3) and miR-494-3p was predicted and verified by TargetScan and dual-luciferase assay, respectively. Results of the above experiments were verified by rescue experiments using TRAF3. RESULTS Liver damage and miRNA expression were observed in AH mice, and AST and ALT levels were increased in serum of AH mice. MiR-494-3p was reduced in AH liver tissues, and it decreased the levels of α-SMA and fibrosis-related proteins. HSCs were isolated, and activating HSCs or upregulating miR-494-3p had a regulatory effect on the levels of miR-494-3p, HSC activation-related proteins and fibrosis-related proteins as well as cell viability, proliferation and apoptosis. In addition, miR-494-3p targeted TRAF3 and inhibited TRAF3 expression, while overexpressed TRAF3 promoted TRAF3 expression and rescued the regulatory effect of miR-494-3p on the levels of related proteins as well as cell viability, proliferation and apoptosis. CONCLUSIONS This study provided a novel mechanistic comprehension of the anti-fibrotic effect of miR-494-3p.
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18
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Identification of MCM4 as a Prognostic Marker of Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2021; 2021:7479326. [PMID: 34961841 PMCID: PMC8710152 DOI: 10.1155/2021/7479326] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022]
Abstract
Methods MCM4 expression difference in HCC were analyzed from TCGA and GEO data and verified by real-time PCR and western blot. ROC curve was used to analyze the diagnostic value of MCM4 and AFP. Additionally, the relationship between MCM4 and stage or nodal metastasis status or grade or age in TCGA cohort with HCC was observed from the UALCAN website. The univariate and multivariate Cox and functional analyses were done to explore the prognostic value of MCM4 in TCGA cohort. Results It was found that MCM4 was significantly highly expressed in HCC tissues from TCGA, GEO, and experimental data. Furthermore, ROC curve analysis showed that MCM4 was superior to be a diagnostic biomarker than AFP from TCGA (AUCMCM4 = 0.9461, AUCAFP = 0.7056) and GEO (GSE19665: AUCMCM4 = 0.8800, AUCAFP = 0.5100; GSE64041 AUCMCM4 = 0.8038, AUCAFP = 0.6304). AUC of MCM4 from real-time PCR result in 60 pairs of HCC and adjacent tissues was 0.7172, demonstrating the prediction value of MCM4. Besides, different expression tendencies of MCM4 among different stages or nodal metastasis status or grade or age were observed from the UALCAN website. In addition, multiROC analysis showed the advantage of MCM4 as a survival prediction at 1, 3, and 5 years with the higher AUC at 0.69 of 1 year, 0.65 of 3 years, and 0.61 of 5 years. It was shown that MCM4 was independently associated with OS in univariate and multivariate Cox analysis. And GSEA displayed that MCM4 was highly enriched in KEGG_CELL_CYCLE signaling pathway following higher correlation positively with CDC6, PLK1, CRC1, and BUB1B in HCC. Conclusion MCM4 might be a potential biomarker in guiding the prognostic status of HCC patients.
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19
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Resaz R, Cangelosi D, Segalerba D, Morini M, Uva P, Bosco MC, Banderali G, Estrella A, Wanner C, Weinstein DA, Sechi A, Paci S, Melis D, Di Rocco M, Lee YM, Eva A. Exosomal MicroRNAs as Potential Biomarkers of Hepatic Injury and Kidney Disease in Glycogen Storage Disease Type Ia Patients. Int J Mol Sci 2021; 23:328. [PMID: 35008754 PMCID: PMC8745197 DOI: 10.3390/ijms23010328] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/15/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
Glycogen storage disease type Ia (GSDIa) is an inherited metabolic disorder caused by mutations in the enzyme glucose-6-phosphatase-α (G6Pase-α). Affected individuals develop renal and liver complications, including the development of hepatocellular adenoma/carcinoma and kidney failure. The purpose of this study was to identify potential biomarkers of the evolution of the disease in GSDIa patients. To this end, we analyzed the expression of exosomal microRNAs (Exo-miRs) in the plasma exosomes of 45 patients aged 6 to 63 years. Plasma from age-matched normal individuals were used as controls. We found that the altered expression of several Exo-miRs correlates with the pathologic state of the patients and might help to monitor the progression of the disease and the development of late GSDIa-associated complications.
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Affiliation(s)
- Roberta Resaz
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (R.R.); (D.S.); (M.M.); (M.C.B.)
| | - Davide Cangelosi
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (D.C.); (P.U.)
| | - Daniela Segalerba
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (R.R.); (D.S.); (M.M.); (M.C.B.)
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (R.R.); (D.S.); (M.M.); (M.C.B.)
| | - Paolo Uva
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (D.C.); (P.U.)
| | - Maria Carla Bosco
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (R.R.); (D.S.); (M.M.); (M.C.B.)
| | - Giuseppe Banderali
- Clinical Department of Pediatrics, ASST Santi Paolo e Carlo, Presidio San Paolo, Università degli Studi di Milano, Via Antonio di Rudinì 8, 20142 Milano, Italy; (G.B.); (S.P.)
| | - Ana Estrella
- Department of Pediatrics, University of Connecticut School of Medicine, 400 Farmington Ave, Farmington, CT 06030, USA; (A.E.); (C.W.); (D.A.W.)
| | - Corbinian Wanner
- Department of Pediatrics, University of Connecticut School of Medicine, 400 Farmington Ave, Farmington, CT 06030, USA; (A.E.); (C.W.); (D.A.W.)
| | - David A. Weinstein
- Department of Pediatrics, University of Connecticut School of Medicine, 400 Farmington Ave, Farmington, CT 06030, USA; (A.E.); (C.W.); (D.A.W.)
| | - Annalisa Sechi
- Regional Coordinating Center for Rare Diseases, Presidio Ospedaliero Universitario di Udine, P.zzale SM Della Misericordia 15, 33100 Udine, Italy;
| | - Sabrina Paci
- Clinical Department of Pediatrics, ASST Santi Paolo e Carlo, Presidio San Paolo, Università degli Studi di Milano, Via Antonio di Rudinì 8, 20142 Milano, Italy; (G.B.); (S.P.)
| | - Daniela Melis
- Department of Medicine, Surgery and Dentistry, Scuola Medica Salernitana, Section of Pediatrics, Università Degli Studi di Salerno, Via Salvador Allende 43, Baronissi, 84100 Salerno, Italy;
| | - Maja Di Rocco
- Department of Pediatrics, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy;
| | - Young Mok Lee
- Department of Pediatrics, University of Connecticut School of Medicine, 400 Farmington Ave, Farmington, CT 06030, USA; (A.E.); (C.W.); (D.A.W.)
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (R.R.); (D.S.); (M.M.); (M.C.B.)
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Zhou Y, Li X, Morita Y, Hachimura S, Miyakawa T, Takahashi S, Tanokura M. Identification of the Effects of Chondroitin Sulfate on Inhibiting CDKs in Colorectal Cancer Based on Bioinformatic Analysis and Experimental Validation. Front Oncol 2021; 11:705939. [PMID: 34595111 PMCID: PMC8477652 DOI: 10.3389/fonc.2021.705939] [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: 05/06/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
With a high occurrence rate and high mortality, the treatment of colorectal cancer (CRC) is increasingly attracting the attention of scholars. Hub genes that determine the phenotypes of CRC become essential for targeted therapy. In the present study, the importance of cyclin-dependent kinases (CDKs) on the occurrence of CRC was identified by data mining of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The results showed that the gene expression levels of CDK1, CDK4, and CDK6 were obviously changed in different stages of CRC. Among the CDKs, CDK4 was suggested as an independent risk factor for CRC based on Cox analysis. Furthermore, chondroitin sulfate (CS), a kind of dietary supplement to treat osteoarthritis, was predicted to treat CRC based on its chemical structure and GEO datasets. Cell assay experiments with the human CRC cell line HCT-116 also verified this prediction. CS inhibited the gene and protein expression levels of CDKs and increased the ratios of apoptotic or dead HCT-116 cells by regulating mitogen-activated protein (MAP) kinase pathways. Our data highlight the essential roles of CDKs in CRC carcinogenesis and the effects of CS on treating CRC, both of which will contribute to the future CRC treatment.
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Affiliation(s)
- Yingyu Zhou
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Xuyang Li
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuki Morita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Department of Research, Medical Viara, Tokyo, Japan.,Department of Research, MAF Clinic, Tokyo, Japan
| | - Satoshi Hachimura
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Sachiko Takahashi
- Department of Research, Medical Viara, Tokyo, Japan.,Department of Research, MAF Clinic, Tokyo, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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21
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He L, Wang X, Jin Y, Xu W, Guan Y, Wu J, Han S, Liu G. Identification and validation of the miRNA-mRNA regulatory network in fetoplacental arterial endothelial cells of gestational diabetes mellitus. Bioengineered 2021; 12:3503-3515. [PMID: 34233591 PMCID: PMC8806558 DOI: 10.1080/21655979.2021.1950279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Gestational diabetes mellitus (GDM) increases the risk of fetal heart malformations, though little is known about the mechanism of hyperglycemia-induced heart malformations. Thus, we aimed to reveal the global landscape of miRNAs and mRNAs in GDM-exposed fetoplacental arterial endothelial cells (dAECs) and establish regulatory networks for exploring the pathophysiological mechanism of fetal heart malformations in maternal hyperglycemia. Gene Expression Omnibus (GEO) datasets were used, and identification of differentially expressed miRNAs (DEMs) and genes (DEGs) in GDM was based on a previous sequencing analysis of dAECs. A miRNA-mRNA network containing 20 DEMs and 65 DEGs was established using DEMs altered in opposite directions to DEGs. In an in vivo study, we established a streptozotocin-induced pregestational diabetes mellitus (PGDM) mouse model and found the fetal cardiac wall thickness in different regions to be dramatically increased in the PGDM grouValidation of DEMs and DEGs in the fetal heart showed significantly upregulated expression of let-7e-5p, miR-139-5p and miR-195-5p and downregulated expression of SGOL1, RRM2, RGS5, CDK1 and CENPA. In summary, we reveal the miRNA-mRNA regulatory network related to fetal cardiac development disorders in offspring, which may shed light on the potential molecular mechanisms of fetal cardiac development disorders during maternal hyperglycemia.
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Affiliation(s)
- Longkai He
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Xiaotong Wang
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Ya Jin
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Weipeng Xu
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Yi Guan
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Jingchao Wu
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Shasha Han
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Guosheng Liu
- Department of Pediatrics, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
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22
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Tao H, Li J, Liu J, Yuan T, Zhang E, Liang H, Huang Z. Construction of a ceRNA Network and a Prognostic lncRNA Signature associated with Vascular Invasion in Hepatocellular Carcinoma based on Weighted Gene Co-Expression Network Analysis. J Cancer 2021; 12:3754-3768. [PMID: 34093785 PMCID: PMC8176257 DOI: 10.7150/jca.57260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/21/2021] [Indexed: 12/28/2022] Open
Abstract
Background: Understanding risk factors for vascular invasion (VI) is crucial for assessing the risk of recurrence and overall prognosis of hepatocellular carcinoma (HCC). This study aimed to construct a prognostic long non-coding RNA (lncRNA) signature and a ceRNA Network associated with vascular invasion in HCC. Methods: Differentially expressed genes (DEGs) of HCC patients associated with VI were identified by analyzing data from TCGA. Weighted gene co-expression network analysis (WGCNA) was used to identify associations between gene expression modules and clinical features. A VI-related prognostic lncRNA signature was then established using univariate, LASSO and multivariate Cox proportional hazards regression analyses. Based on the hub modules identified by the WGCNA, we constructed a VI-related lncRNA-miRNA-mRNA ceRNA network and screened hub lncRNAs for further research. Finally, we conducted in vitro and in vivo experiments to determine the biological roles of the identified hub gene BBOX1-AS1. Results: The key module related to VI and OS was identified using WGCNA, after which a prognostic model consisting of eight lncRNAs was established, and verified using time-dependent receiver operating characteristic (ROC) curve analysis. BBOX1-AS1 was confirmed to be highly expressed in HCC tissues, and its expression was significantly correlated with a poor prognosis. Silencing BBOX1-AS1 in vitro significantly suppressed the proliferation, migration and invasion of HCC cells. In vivo experiments demonstrated that knocking down of BBOX1-AS1 could result in significant decrease of tumor volume and tumor weight. Conclusions: The VI-related lncRNA signature established in this study can be used to predict the clinical outcomes of HCC patients. In addition, we constructed a VI-related lncRNA-miRNA-mRNA ceRNA network and demonstrated that BBOX1-AS1 might be a novel biomarker associated with VI in HCC.
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Affiliation(s)
- Haisu Tao
- Hepatic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, China
| | - Jiang Li
- Hepatic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, China
| | - Junjie Liu
- Hepatic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, China
| | - Tong Yuan
- Hepatic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, China
| | - Erlei Zhang
- Hepatic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, China
| | - Zhiyong Huang
- Hepatic Surgery Center, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, China
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23
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KRT8 and KRT19, associated with EMT, are hypomethylated and overexpressed in lung adenocarcinoma and link to unfavorable prognosis. Biosci Rep 2021; 40:225236. [PMID: 32519739 PMCID: PMC7335829 DOI: 10.1042/bsr20193468] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 05/20/2020] [Accepted: 06/01/2020] [Indexed: 12/30/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. To date, the prognosis of patients with LUAD remains dismal. Methods: Three datasets were downloaded from the GEO database. Differentially expressed genes (DEGs) were obtained. FunRich was used to perform pathway enrichment analysis. Protein–protein interaction (PPI) networks were established and hub genes were obtained by Cytoscape software. GEPIA was utilized to conduct correlation and survival analysis. Upstream miRNAs of DEGs were predicted via miRNet database, and methylation status of promoters of DEGs was determined through UALCAN database. Results: A total of 375 DEGs, including 105 and 270 up-regulated and down-regulated genes in LUAD, were commonly appeared in three datasets. These DEGs were significantly enriched in mesenchymal-to-epithelial transition (MET) and epithelial-to-mesenchymal transition (EMT). About 8 up-regulated and 5 down-regulated DEGs were commonly appeared in EMT/MET-related gene set and the top 50 hub gene set. Among the 13 genes, increased expression of KRT8 and KRT19 indicated unfavorable prognosis whereas high expression of DCN and CXCL12 suggested favorable prognosis in LUAD. Correlation analysis showed that KRT8 (DCN) expression was linked to KRT19 (CXCL12) expression. Further analysis displayed that KRT8 and KRT19 could jointly forecast poor prognosis in LUAD. About 42 and 2 potential miRNAs were predicted to target KRT8 and KRT19, respectively. Moreover, methylation level analysis demonstrated that KRT8 and KRT19 were significantly hypomethylated in LUAD compared with normal controls. Conclusions: All these findings suggest that KRT8 and KRT19 are hypomethylated and overexpressed in LUAD and associated with unfavorable prognosis.
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24
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Gao Y, Xu J, Li H, Hu Y, Yu G. Identification of Metastasis-Associated MicroRNAs in Metastatic Melanoma by miRNA Expression Profile and Experimental Validation. Front Genet 2021; 12:663110. [PMID: 33897771 PMCID: PMC8063111 DOI: 10.3389/fgene.2021.663110] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
It is reported that microRNAs (miRNA) have paramount functions in many cellular biological processes, development, metabolism, differentiation, survival, proliferation, and apoptosis included, some of which are involved in metastasis of tumors, such as melanoma. Here, three metastasis-associated miRNAs, miR-18a-5p (upregulated), miR-155-5p (downregulated), and miR-93-5p (upregulated), were identified from a total of 63 different expression miRNAs (DEMs) in metastatic melanoma compared with primary melanoma. We predicted 262 target genes of miR-18a-5p, 904 miR-155-5p target genes, and 1220 miR-93-5p target genes. They participated in pathways concerning melanoma, such as TNF signaling pathway, pathways in cancer, FoxO signaling pathway, cell cycle, Hippo signaling pathway, and TGF-beta signaling pathway. We identified the top 10 hub nodes whose degrees were higher for each survival-associated miRNA as hub genes through constructing the PPI network. Using the selected miRNA and the hub genes, we constructed the miRNA-hub gene network, and PTEN and CCND1 were found to be regulated by all three miRNAs. Of note, miR-155-5p was obviously downregulated in metastatic melanoma tissues, and miR-18a-5p and miR-93-5p were obviously regulated positively in metastatic melanoma tissues. In validating experiments, miR-155-5p's overexpression inhibited miR-18a-5p's and miR-93-5p's expression, which could all significantly reduce SK-MEL-28 cells' invasive ability. Finally, miR-93-5p and its potential target gene UBC were selected for further validation. We found that miR-93-5p's inhibition could reduce SK-MEL-28 cell's invasive ability through upregulated the expression of UBC, and the anti-invasive effect was reserved by downregulation of UBC. The results show that the selected three metastasis-associated miRNAs participate in the process of melanoma metastasis via regulating their target genes, providing a potential molecular mechanism for this disease.
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Affiliation(s)
- Yunshu Gao
- Department of Oncology, People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Jiahua Xu
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongwei Li
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Hu
- Department of Oncology, People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Guanzhen Yu
- Department of Oncology, Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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25
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Lou W, Wang W, Chen J, Wang S, Huang Y. ncRNAs-mediated high expression of SEMA3F correlates with poor prognosis and tumor immune infiltration of hepatocellular carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:845-855. [PMID: 34026328 PMCID: PMC8121632 DOI: 10.1016/j.omtn.2021.03.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/25/2021] [Indexed: 01/04/2023]
Abstract
Hepatocellular carcinoma (HCC) is notorious for its poor prognosis. Increasing evidence has demonstrated that semaphorin 3F (SEMA3F) plays key roles in initiation and progression of several types of human cancer. However, the specific role and mechanism of SEMA3F in HCC remains not fully determined. In this study, we first performed pan-cancer analysis for SEMA3F’s expression and prognosis using The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) data and found that SEMA3F might be a potential oncogene in HCC. Subsequently, noncoding RNAs (ncRNAs) contributing to SEMA3F overexpression were identified by a combination of a series of in silico analyses, including expression analysis, correlation analysis, and survival analysis. Finally, the TMPO-AS1/SNHG16-let-7c-5p axis was identified as the most potential upstream ncRNA-related pathway of SEMA3F in HCC. Moreover, SEMA3F level was significantly positively associated with tumor immune cell infiltration, biomarkers of immune cells, and immune checkpoint expression. Collectively, our findings elucidated that ncRNAs-mediated upregulation of SEMA3F correlated with poor prognosis and tumor immune infiltration in HCC.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003 Zhejiang, China
| | - Wenlong Wang
- Intensive Care Unit, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Jing Chen
- Department of Oncology, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314000 Zhejiang, China
| | - Shuqian Wang
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003 Zhejiang, China
| | - Yuan Huang
- Department of Breast Medical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022 Zhejiang, China
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26
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Dong M, Xu T, Cui X, Li H, Li X, Xia W. NCAPG upregulation mediated by four microRNAs combined with activation of the p53 signaling pathway is a predictor of poor prognosis in patients with breast cancer. Oncol Lett 2021; 21:323. [PMID: 33692855 PMCID: PMC7933778 DOI: 10.3892/ol.2021.12585] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
The role of non-SMC condensin I complex subunit G (NCAPG) in breast cancer remains unclear. The present study used online databases, reverse transcription-quantitative PCR, flow cytometry and western blotting to determine the expression levels, prognosis and potential molecular mechanisms underlying the role of NCAPG in breast cancer. The association between NCAPG expression and several different clinicopathological parameters in patients with breast cancer was determined, and the results revealed that NCAPG expression was negatively associated with estrogen receptor and progesterone receptor positive status, but was positively associated with HER2 positive status, Nottingham Prognostic Index score and Scarff-Bloom-Richardson grade status. Furthermore, upregulated expression levels of NCAPG resulted in a poor prognosis in patients with breast cancer. A total of 27 microRNAs (miRNAs/miRs) were predicted to target NCAPG, among which four miRNAs (miR-101-3p, miR-195-5p, miR-214-3p and miR-944) were predicted to most likely regulate NCAPG expression in breast cancer. A total of 261 co-expressed genes of NCAPG were identified, including cell division cyclin 25 homolog C (CDC25C), and pathway enrichment analysis indicated that these co-expressed genes were significantly enriched in the p53 signaling pathway. CDC25C expression was downregulated in breast cancer and was associated with a poor prognosis. These findings suggested that upregulated NCAPG expression may be a prognostic biomarker of breast cancer.
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Affiliation(s)
- Menglu Dong
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Tao Xu
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xiaoqing Cui
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Hanning Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Xingrui Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Wenfei Xia
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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27
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Lou W, Chen J, Ding B, Fan W. XIAP, commonly targeted by tumor suppressive miR-3607-5p and miR-3607-3p, promotes proliferation and inhibits apoptosis in hepatocellular carcinoma. Genomics 2021; 113:933-945. [PMID: 33588071 DOI: 10.1016/j.ygeno.2021.02.003] [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] [Received: 10/11/2020] [Revised: 12/17/2020] [Accepted: 02/09/2021] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are frequently aberrantly expressed in hepatocellular carcinoma (HCC) and are involved in its development. However, their role and mechanism in HCC are still not fully elucidated. Differential expression analysis and survival analysis were performed to identify potential miRNAs in HCC and miR-3607 was identified as a candidate therapeutic target and prognostic biomarker. RT-qPCR confirmed the low expression of mature miR-3607-3p and miR-3607-5p in HCC. Functional experiments suggested that both miR-3607-3p and miR-3607-5p significantly inhibited HCC proliferation and induced apoptosis. Next, the detailed mechanism of miR-3607-3p and miR-3607-5p in HCC was explored by combination of bioinformatic analysis and experimental validation, and uncovered that XIAP, a common target gene of miR-3607-3p and miR-3607-5p, was involoved in their tumor suppressive effects. Finally, a XIAP-associated protein-protein interaction network, consisting of 10 positively correlated genes, was established. Collectively, we for the first time suggest that miR-3607-3p and miR-3607-5p inhibit HCC by acting one common target XIAP.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China.
| | - Jing Chen
- Department of Oncology, First Affiliated Hospital of Jiaxing University, Jiaxing, 314000 Zhejiang, China
| | - Bisha Ding
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - Weimin Fan
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou 310003, Zhejiang Province, China
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28
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Poleto Spinola L, F Vieira G, Fernandes Ferreira R, Calastri MCJ, D Tenani G, Aguiar FL, Santana Ferreira Boin IF, B E Da Costa L, Chaim Correia MF, Zanovelo EM, B De Souza DC, Martins Alves Da Silva RC, Ferreira Da Silva R, Coelho Abrantes AM, R R Botelho MF, L R Tralhão JG, R S Souza D. Underexpression of miR-126-3p in Patients with Cholangiocarcinoma. Asian Pac J Cancer Prev 2021; 22:573-579. [PMID: 33639676 PMCID: PMC8190345 DOI: 10.31557/apjcp.2021.22.2.573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Objectives: To evaluate the expression of miR-126-3p and its potential as a biomarker for cholangiocarcinoma (CCA) and to better understand the prognosis, comorbidities, and lifestyle habits associated with the disease. Methods: Fifty-nine individuals were distributed into either the study group (38 CCA patients) or the control group (21 individuals without liver diseases). Total RNA was extracted, cDNA synthesis was performed, and miR-126-3p expression was assessed using real-time PCR. For statistical analysis, alpha error was set at 5%. Results: MiR-126-3p was found to be underexpressed in the study group relative to the controls (0.42; P=0.001). Additionally, marked underexpression was found in the study group in when associated with smoking (0.28; P=0.0001), alcoholism (0.19; P=0.0001), hypertension (0.29; P=000.1), and diabetes (0.12; P=0.0003) relative to the controls. No association was found between miR-126-3p expression and tumor subtypes (iCCA=0.42; pCCA=0.45; dCCA=0.72; P=0.9155). A total of 67% of dCCA patients were event-free at 16 months of follow up, while both pCCA and iCCA exhibited event-free survival rates of 25%, though there was no significant difference between these subgroups (P=0.273). Conclusion: The underexpression of mir-126-3p is associated with cholangiocarcinoma and can be potentiated by alcoholism, hypertension, diabetes, and smoking, the latter of which is an independent risk factor for this cancer. Furthermore, dCCA patients exhibit higher survival rates relative to patients with pCCA and iCCA.
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Affiliation(s)
- Lucas Poleto Spinola
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São Paulo, Brazil
| | - Gabriel F Vieira
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São Paulo, Brazil
| | | | - Maria C J Calastri
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São Paulo, Brazil
| | - Graciele D Tenani
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São Paulo, Brazil
| | - Franciana L Aguiar
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São Paulo, Brazil
| | | | - Larissa B E Da Costa
- School of Medical Sciences of the State University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | | | | | | | | | | | | | - Doroteia R S Souza
- Department of Molecular Biology, São José do Rio Preto Medical School (FAMERP), São Paulo, Brazil
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29
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Huang C, Tang S, Shen D, Li X, Liang L, Ding Y, Xu B. Circulating plasma exosomal miRNA profiles serve as potential metastasis-related biomarkers for hepatocellular carcinoma. Oncol Lett 2021; 21:168. [PMID: 33552286 PMCID: PMC7798106 DOI: 10.3892/ol.2021.12429] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 12/02/2020] [Indexed: 12/19/2022] Open
Abstract
Exosomes carry functional molecules that can regulate cancer progression. Understanding the function of exosomal markers may provide invaluable insights into the mechanism of metastasis in hepatocellular carcinoma (HCC). The aim of the present study was to identify metastasis-associated microRNAs (miRNAs/miRs) expressed in plasma exosomes. A miRNA microarray and reverse transcription-quantitative PCR were used to analyze the plasma exosome miRNA expression profiles of patients with metastatic or non-metastatic HCC. Receiver operating characteristic (ROC) curve and Kaplan-Meier analyses were used to evaluate the predictive performance and prognostic efficacy of candidate miRNAs identified in the Gene Expression Omnibus database (dataset accession no. GSE67140). Bioinformatics analysis was used to examine the role of exosomal miRNAs in HCC metastasis. A total of 32 miRNAs were differentially expressed in plasma exosomes of patients with metastatic HCC compared with in those of patients with non-metastatic HCC. Additionally, the expression levels of six miRNAs were consistent between plasma exosome samples and matched tissue samples. ROC analysis demonstrated that miR-18a, miR-27a and miR-20b could discriminate metastatic HCC from non-metastatic HCC. Furthermore, the prognostic efficacy of the combination of three miRNAs (miR-18a, miR-20b and miR-221) was superior to that of individual miRNAs. Survival analysis demonstrated that high expression levels of the candidate miRNAs were associated with poor prognosis. Bioinformatics analysis indicated that the potential target genes of these miRNAs were involved in biological processes, molecular functions and cellular components that were associated with metastasis. The present findings suggested that these exosomal miRNAs may serve important roles in HCC lung metastasis and could represent a complementary clinical tool for the assessment of HCC prognosis.
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Affiliation(s)
- Chunyu Huang
- Department of Endoscopy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China.,State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China.,Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong 510060, P.R. China
| | - Shuiying Tang
- Department of Interventional Radiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Dong Shen
- Department of Epidemiology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xiangzhao Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Department of Pathology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Department of Pathology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Department of Pathology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Bihong Xu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Department of Pathology, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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30
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Sharma A, Colonna G. System-Wide Pollution of Biomedical Data: Consequence of the Search for Hub Genes of Hepatocellular Carcinoma Without Spatiotemporal Consideration. Mol Diagn Ther 2021; 25:9-27. [PMID: 33475988 PMCID: PMC7847983 DOI: 10.1007/s40291-020-00505-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 12/17/2022]
Abstract
Biomedical institutions rely on data evaluation and are turning into data factories. Big-data storage centers, supercomputing systems, and increased algorithmic efficiency allow us to analyze the ever-increasing amount of data generated every day in biomedical research centers. In network science, the principal intrinsic problem is how to integrate the data and information from different experiments on genes or proteins. Data curation is an essential process in annotating new functional data to known genes or proteins, undertaken by a biobank curator, which is then reflected in the calculated networks. We provide an example of how protein-protein networks today have space-time limits. The next step is the integration of data and information from different biobanks. Omics data and networks are essential parts of this step but also have flawed protocols and errors. Consider data from patients with cancer: from biopsy procedures to experimental tests, to archiving methods and computational algorithms, these are continuously handled so require critical and continuous "updates" to obtain reproducible, reliable, and correct results. We show, as a second example, how all this distorts studies in cellular hepatocellular carcinoma. It is not unlikely that these flawed data have been polluting biobanks for some time before stringent conditions for the veracity of data were implemented in Big data. Therefore, all this could contribute to errors in future medical decisions.
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Affiliation(s)
- Ankush Sharma
- Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Informatics, University of Oslo, Oslo, Norway.
- Institute of Cancer Research, Institute of Clinical medicine, University of Oslo, Oslo, Norway.
| | - Giovanni Colonna
- Medical Informatics, AOU-Vanvitelli, Università della Campania, Naples, Italy
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Liu AG, Pang YY, Chen G, Wu HY, He RQ, Dang YW, Huang ZG, Zhang R, Ma J, Yang LH. Downregulation of miR-199a-3p in Hepatocellular Carcinoma and Its Relevant Molecular Mechanism via GEO, TCGA Database and In Silico Analyses. Technol Cancer Res Treat 2020; 19:1533033820979670. [PMID: 33327879 PMCID: PMC7750904 DOI: 10.1177/1533033820979670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Existing reports have demonstrated that miR-199a-3p plays a role as a tumor suppressor in a variety of human cancers. This study aims to further validate the expression of miR-199a-3p in HCC and to explore its underlying mechanisms by using multiple data sets. Chip data or sequencing data and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were integrated to assess the expression of miR-199a-3p in HCC. The potential targets and transcription factor regulatory network of miR-199a-3p in HCC were determined and possible biological mechanism of miR-199a-3p was analyzed with bioinformatics methods. In the results, miR-199a-3p expression was significantly lower in HCC tissues compared to normal tissues according to chip data or sequencing data and qRT-PCR. Moreover, 455 targets of miR-199a-3p were confirmed, and these genes were involved in the PI3K-Akt signaling pathway, pathways in cancer, and focal adhesions. LAMA4 was considered a key target of miR-199a-3p. In CMTCN, 11 co-regulatory pairs, 3 TF-FFLs, and 2 composite-FFLs were constructed. In conclusion, miR-199a-3p was down regulated in HCC and LAMA4 may be a potential target of miR-199a-3p in HCC.
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Affiliation(s)
- An-Gui Liu
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yu-Yan Pang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hua-Yu Wu
- Departments of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Rong-Quan He
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Rui Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jie Ma
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China.,Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Li-Hua Yang
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
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Lin C, Xin S, Huang X, Zhang F. PTPRA facilitates cancer growth and migration via the TNF-α-mediated PTPRA-NF-κB pathway in MCF-7 breast cancer cells. Oncol Lett 2020; 20:131. [PMID: 32934700 PMCID: PMC7471670 DOI: 10.3892/ol.2020.11992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 04/20/2020] [Indexed: 02/05/2023] Open
Abstract
Protein tyrosine phosphatase receptor type A (PTPRA), one of the classic protein tyrosine phosphatases, is crucial for modulating tumorigenesis and metastasis in breast cancer; however, its functional mechanism has not fully elucidated. The present study assessed PTPRA expression and estimated its clinical impact on survival using the Gene Expression Profiling Interactive Analysis database (GEPIA). Growth curves, colony formations and Transwell assays were utilized to examine cell proliferation and migration. Additionally, luciferase reporter assays were used to examine the potential tumor signaling pathways targeted by PTPRA in HEK293T cells. Furthermore, quantitative PCR (qPCR) was utilized to confirm the transcriptional regulation of PTPRA expression. Bioinformatic analyses of data from GEPIA identified PTPRA overexpression in patients with breast cancer. The growth curve, colony formation and transwell experiments demonstrated that PTPRA upregulation significantly promoted the cell proliferation and migration of MCF-7 breast cancer cells. In contrast, PTPRA knockdown significantly attenuated cell proliferation and migration. Mechanistic experiments revealed that the transcriptional activity of NF-κB was higher compared with other classic tumor pathways when they were activated by PTPRA in HEK293T cells. Furthermore, the transcriptional activity of NF-κB was altered in a PTPRA-dose-dependent manner. Additionally, following exposure to TNF-α, PTPRA-deficient MCF-7 cells exhibited lower NF-κB transcriptional activity compared with normal control cells. The results of the present study demonstrate that PTPRA overexpression accelerates inflammatory tumor phenotypes in breast cancer and that the TNF-α-mediated PTPRA-NF-κB pathway may offer novel insight into early diagnosis and optimum treatment for breast cancer.
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Affiliation(s)
- Canfeng Lin
- Department of Oncology, Shantou Central Hospital, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Shubo Xin
- Department of Pharmacy, Shantou Central Hospital, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Xiaoguang Huang
- Department of Oncology, Shantou Central Hospital, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
| | - Feiran Zhang
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, P.R. China
- Correspondence to: Dr Feiran Zhang, Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, 57 Changping Road, Shantou, Guangdong 515041, P.R. China, E-mail:
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Liu CZ, Guo WP, Peng JB, Chen G, Lin P, Huang XL, Liu XF, Yang H, He Y, Pang YY, Ma W. Clinical significance of CCNE2 protein and mRNA expression in thyroid cancer tissues. Adv Med Sci 2020; 65:442-456. [PMID: 33059229 DOI: 10.1016/j.advms.2020.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 06/22/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE Thyroid carcinoma (TC) is the most common endocrinal malignancy worldwide. Cyclin E2 (CCNE2), a member of the cyclin family, acts as a regulatory subunit of cyclin-dependent kinases (CDKs). It controls the transition of quiescent cells into the cell cycle, regulates the G1/S transition, promotes DNA replication, and activates CDK2. This study explored the role and potential molecular mechanisms of CCNE2 expression in TC tissues. MATERIAL/METHODS Immunohistochemistry was used to evaluate the CCNE2 protein expression levels in TC. High-throughput data on CCNE2 in TC were obtained from RNA sequencing (RNA-seq), microarray, and literature data. The CCNE2 expression levels in TC were comprehensively assessed through an integrated analysis. Analyses of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPIs) data facilitated the investigation of the relative molecular mechanisms of CCNE2 in TC. RESULTS The immunohistochemical experiment showed a significant increase in the expression of CCNE2 in the TC tissues. For 505 TC and 59 non-cancerous samples from RNA-seq data, the area under the curve (AUC) was 0.8016 (95% confidence interval [CI] 0.742-0.8612; p<0.001). With another 14 microarrays, the pool standard mean difference [SMD] was 1.01 (95% CI [0.82-1.19]). The pooled SMD of CCNE2 was 1.12 (95% CI [0.60-1.64]), and the AUC was 0.87 (95% CI [0.84-0.90]) for 1157 TC samples and 366 non-cancerous thyroid samples from all possible sources. Nine hub genes were upregulated in TC. CONCLUSIONS A high expression of CCNE2 may lead to carcinogenesis and the development of TC.
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MESH Headings
- Adenocarcinoma, Follicular/genetics
- Adenocarcinoma, Follicular/metabolism
- Adenocarcinoma, Follicular/pathology
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary/metabolism
- Carcinoma, Papillary/pathology
- Cell Proliferation
- Cyclins/genetics
- Cyclins/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Male
- Middle Aged
- Prognosis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Survival Rate
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/metabolism
- Thyroid Neoplasms/pathology
- Tumor Cells, Cultured
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Affiliation(s)
- Cui-Zhen Liu
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Wan-Ping Guo
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Jin-Bo Peng
- Department of Ultrasonography, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Peng Lin
- Department of Ultrasonography, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Xiao-Li Huang
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Xiao-Fan Liu
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Hong Yang
- Department of Ultrasonography, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Yun He
- Department of Ultrasonography, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China
| | - Yu-Yan Pang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China.
| | - Wei Ma
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, PR China.
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Chen N, Xiao B, Wang S, Wei B. Bioinformatics analysis of microRNA linked to ubiquitin proteasome system in traumatic osteonecrosis of the femoral head. Medicine (Baltimore) 2020; 99:e21706. [PMID: 32872046 PMCID: PMC7437855 DOI: 10.1097/md.0000000000021706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) have been suggested to act critical roles in the pathophysiology of traumatic osteonecrosis of the femoral head (TONFH). Unfortunately, their roles in the development of TONFH are still ambiguous. The purpose of this study is to identify promising miRNA biomarkers in traumatic osteonecrosis development.We conducted a comprehensive bioinformatics analysis using microarray datasets downloaded from the Gene Expression Omnibus database, and compared the expression of miRNAs in the serum of TONFH patients with controls. Next, we performed target prediction, function enrichment analysis, and protein-protein interaction network analysis based on differentially expressed (DE) miRNAs.We identified 26 DE miRNAs that may contribute to the pathophysiology of TONFH. The miRNAs were linked to ubiquitin proteasome system including conjugating protein ligase activity, ubiquitin-protein ligase activity and ubiquitin mediated proteolysis 5 pathway, and we exposed miR-181a-5p and miR-140-5p as promising biomarkers in TONFH.A predicting model consisting of 5 miRNAs may help discriminating high-risk patients who might develop TONFH after femur neck fracture. Among DE miRNAs, MiR-181a-5p and miR-140-5p may contribute to the development femoral head osteonecrosis after femur neck fracture via ubiquitin proteasome system.
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Affiliation(s)
- Ning Chen
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong
- Department of Femoral Head, Linyi People's Hospital, Linyi, Shandong, China
| | - Bolian Xiao
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong
- Department of Femoral Head, Linyi People's Hospital, Linyi, Shandong, China
| | - Shiying Wang
- Guangzhou University of Chinese Medicine, Guangzhou, Guangdong
- Department of Femoral Head, Linyi People's Hospital, Linyi, Shandong, China
| | - Biaofang Wei
- Department of Femoral Head, Linyi People's Hospital, Linyi, Shandong, China
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Wang W, Ding B, Lou W, Lin S. Promoter Hypomethylation and miR-145-5p Downregulation- Mediated HDAC11 Overexpression Promotes Sorafenib Resistance and Metastasis of Hepatocellular Carcinoma Cells. Front Cell Dev Biol 2020; 8:724. [PMID: 32903337 PMCID: PMC7434871 DOI: 10.3389/fcell.2020.00724] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022] Open
Abstract
Sorafenib resistance and tumor metastasis account for poor outcome of hepatocellular carcinoma (HCC). Histone deacetylase 11 (HDAC11) has been reported to exert oncogenic effects in several types of human cancer, but its specific functions and detailed mechanisms in HCC are not fully elucidated. Here we identified HDAC11 as a potential oncogene and promising biomarker in HCC by in silico analysis. Histone deacetylase 11 was upregulated in sorafenib-resistant SMMC7721 compared with its parental cell. Knockdown of HDAC11 suppressed proliferation and sorafenib resistance, which may be due to inhibition of drug metabolism cytochrome P450 predicted by gene-set enrichment analysis. Histone deacetylase expression was higher in highly metastatic MHCC97H than lowly metastatic MHCC97L. Downregulation of HDAC11 significantly attenuated the migrated and invaded abilities of HCC cells. Histone deacetylase 11 was directly targeted and suppressed by miR-145-5p. Inhibition of miR-145-5p enhanced sorafenib resistance and metastasis of HCC, and these effects could be attenuated by knockdown of HDAC11. The promoter methylation level of HDAC11 was markedly decreased in HCC tissues compared with normal controls. Administration of 5’-Aza-2’-deoxycytidine, a DNA methyltransferase inhibitor, facilitated HDAC11 expression in HCC cells. Our data indicate a role of miR-145-5p/HDAC11 axis in regulation of sorafenib resistance and metastasis in HCC.
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Affiliation(s)
- Wenlong Wang
- Intensive Care Unit, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou, China
| | - Weiyang Lou
- Department of Breast Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Zhejiang, China
| | - Shengyou Lin
- Department of Oncology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, China
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Lou W, Ding B, Zhong G, Yao J, Fan W, Fu P. RP11-480I12.5-004 Promotes Growth and Tumorigenesis of Breast Cancer by Relieving miR-29c-3p-Mediated AKT3 and CDK6 Degradation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:916-931. [PMID: 32810693 PMCID: PMC7452110 DOI: 10.1016/j.omtn.2020.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 12/11/2022]
Abstract
Pseudogenes have been reported to exert oncogenic or tumor-suppressive functions in cancer. However, the expression, role, and mechanism of pseudogene-derived RNAs in breast cancer remain unclear. The RNA levels and prognostic values of pseudogenes in breast cancer were determined. The levels of RP11-480I12.5 in cell lines and clinical samples were validated by quantitative real-time PCR. In vitro effects of RP11-480I12.5 on cell growth were measured by cell counting kit-8 (CCK-8) assay, colony formation assay, cell counting assay, and flow cytometry analysis. Xenograft model was established to detect its in vivo effect. The potential mechanism of RP11-480I12.5 was also studied by a combination of bioinformatic analysis and experimental confirmation. Finally, the possible functional parental genes of RP11-480I12.5 in breast cancer were explored. After a series of bioinformatic analyses, RP11-480I12.5 was selected as the most potential pseudogene in breast cancer. RP11-480I12.5 expression was significantly upregulated in breast cancer cell lines and clinical breast cancer tissues. Knockdown of RP11-480I12.5 markedly suppressed cell proliferation and colony formation, induced cell apoptosis of breast cancer in vitro, and inhibited tumor growth in vivo. Four transcripts of RP11-480I12.5 (001/002/003/004) were identified. Only overexpression of RP11-480I12.5-004 significantly enhanced cell growth of breast cancer both in vitro and in vivo. RP11-480I12.5-004 mainly located in cytoplasm and increased AKT3 and CDK6 mRNA expression, at least in part, by competitively binding to miR-29c-3p. Six parental genes of RP11-480I12.5 were found, among which TUBA1B and TUBA1C were statistically linked to RP11-480I12.5 expression, possessed prognostic values, and were upregulated in breast cancer. Our findings suggested that pseudogene-derived long non-coding RNA (lncRNA) RP11-480I12.5-004 promoted growth and tumorigenesis of breast cancer via increasing AKT3 and CDK6 expression by competitively binding to miR-29c-3p.
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Affiliation(s)
- Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China; Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou 310003, Zhejiang, Province, China.
| | - Bisha Ding
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou 310003, Zhejiang, Province, China
| | - Guansheng Zhong
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - Jia Yao
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China
| | - Weimin Fan
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Zhejiang University, Hangzhou 310003, Zhejiang, Province, China
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, Zhejiang 310003, China.
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Five miRNAs-mediated PIEZO2 downregulation, accompanied with activation of Hedgehog signaling pathway, predicts poor prognosis of breast cancer. Aging (Albany NY) 2020; 11:2628-2652. [PMID: 31058608 PMCID: PMC6535055 DOI: 10.18632/aging.101934] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/23/2019] [Indexed: 12/16/2022]
Abstract
Roles of Piezo-type mechanosensitive ion channel component 2 (PIEZO2) in cancer remain largely unknown. Herein, we explored PIEZO2 expression, prognosis and underlying mechanisms in cancer. Breast was selected as the candidate as its relatively higher expression level of PIEZO2 than other human tissues. Next, we identified a decreased expression of PIEZO2 in breast cancer compared with normal controls, and found that PIEZO2 expression positively correlated with estrogen receptor (ER) and progesterone receptor (PR) status but negatively correlated with human epidermal growth factor receptor 2 (HER2) status, Nottingham Prognostic Index (NPI) score, Scarff-Bloom-Richardson (SBR) grade, basal-like and triple-negative status. Subsequent analysis revealed that high expression of PIEZO2 had a favorable prognosis in breast cancer. 182 miRNAs were predicted to target PIEZO2. Among these miRNAs, five miRNAs (miR-130b-3p, miR-196a-5p, miR-301a-3p, miR-421 and miR-454-3p) possess the greatest potential in targeting PIEZO2. 109 co-expressed genes of PIEZO2 were identified. Pathway enrichment analysis showed that these genes were enriched in Hedgehog signaling pathway, including Cell adhesion molecule-related/downregulated by oncogenes (CDON). CDON expression was decreased in breast cancer and downregulation of CDON indicated a poor prognosis. Altogether, these findings suggest that decreased expression of PIEZO2 may be utilized as a prognostic biomarker of breast cancer.
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A novel mRNA-miRNA-lncRNA competing endogenous RNA triple sub-network associated with prognosis of pancreatic cancer. Aging (Albany NY) 2020; 11:2610-2627. [PMID: 31061236 PMCID: PMC6535056 DOI: 10.18632/aging.101933] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/22/2019] [Indexed: 12/11/2022]
Abstract
Background: Recently, increasing evidence has uncovered the roles of mRNA-miRNA-lncRNA network in multiple human cancers. However, a systematic mRNA-miRNA-lncRNA network linked to pancreatic cancer prognosis is still absent. Methods: Differentially expressed genes (DEGs) were first identified by mining GSE16515 and GSE15471 datasets. DAVID database was utilized to conduct functional enrichment analysis. Protein-protein interaction (PPI) network was built using STRING database, and hub genes were identified by Cytoscape plug-in CytoHubba. Upstream miRNAs and lncRNAs of mRNAs were predicted by miRTarBase and miRNet, respectively. Expression, survival and correlation analysis for genes, miRNAs and lncRNAs were performed via GEPIA, Kaplan-Meier plotter and starBase. Results: 734 and 180 upregulated and downregulated significant DEGs were identified, respectively. Functional enrichment analysis revealed that they were significantly enriched in focal adhesion, pathways in cancer and metabolic pathways. According to node degree, hub genes in the PPI networks were screened, such as TGFB1 and ALB. Among the top 20 hub genes, 7 upregulated genes and 2 downregulated hub genes had significant prognostic values in pancreatic cancer. 33 miRNAs were predicted to target the 9 key genes. But only high expression of 8 miRNAs indicated favorable prognosis in pancreatic cancer. Then, 90 lncRNAs were predicted to potentially bind to the 8 miRNAs. SCAMP1, HCP5, MAL2 and LINC00511 were finally identified as key lncRNAs. By combination of results from expression, survival and correlation analysis demonstrated that MMP9/ITGB1-miR-29b-3p-HCP5 competing endogenous RNA (ceRNA) sub-network was linked to prognosis of pancreatic cancer. Conclusions: In a word, we established a novel mRNA-miRNA-lncRNA sub-network, among which each RNA may be utilized as a prognostic biomarker of pancreatic cancer.
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Yang H, Gao S, Chen J, Lou W. UBE2I promotes metastasis and correlates with poor prognosis in hepatocellular carcinoma. Cancer Cell Int 2020; 20:234. [PMID: 32536822 PMCID: PMC7291483 DOI: 10.1186/s12935-020-01311-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/30/2020] [Indexed: 12/13/2022] Open
Abstract
Background A comprehensive investigation of ubiquitin-conjugating enzyme E2I (UBE2I) in cancer is still insufficiency. In this study, we aimed to analyze its role and mechanism in cancer by combination of bioinformatic analysis and experimental validation. Methods The expression profile of UBE2I in human cancers were obtained using GEPIA. Kaplan–Meier plotter was used to assess the prognostic values of UBE2I in diverse types of cancer. ROC curve analysis was employed to determine the diagnostic role of UBE2I in hepatocellular carcinoma (HCC). The expression differences based on various clinicopathological features was evaluated by UALCAN. Wound healing assay and transwell invasion assay were used to detected the effects of UBE2I on migration and invasion of HCC cells, respectively. The miRNA regulatory mechanism of UBE2I was successively investigated by binding prediction, expression analysis, survival analysis and dual-luciferase reporter assay. The correlation of UBE2I mRNA expression and UBE2I promoter methylation level was assessed using cBioPortal. STRING was finally introduced to perform co-expression analysis and enrichment analysis for UBE2I. Results UBE2I was upregulated in HCC, correlated with cancer progression and poor prognosis of HCC. We also found a significant diagnostic value of UBE2I in HCC. Functional experiments revealed that knockdown of UBE2I significantly inhibited HCC migration and invasion. Further research on mechanism suggested that loss of inhibition of hsa-miR-195-3p and dysregulation of UBE2I promoter methylation might account for UBE2I overexpression in HCC. Analysis of UBE2I-invovled regulatory network identified six key genes (NSMCE2, SAE1, UBA2, RANGAP1, SUMO1 and SUMO2) whose expression linked to poor prognosis in HCC. Conclusions In conclusion, UBE2I may be a promising therapeutic target and biomarker in cancer, especially HCC.
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Affiliation(s)
- Hao Yang
- Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical Hospital, Hangzhou, 310014 Zhejiang China
| | - Shan Gao
- Department of Anus & Intestine Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014 Zhejiang China
| | - Jing Chen
- Department of Oncology, First Affiliated Hospital of Jiaxing University, Jiaxing, 314000 Zhejiang China
| | - Weiyang Lou
- Department of Breast Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003 Zhejiang China
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Gao S, Ding B, Lou W. microRNA-Dependent Modulation of Genes Contributes to ESR1's Effect on ERα Positive Breast Cancer. Front Oncol 2020; 10:753. [PMID: 32500028 PMCID: PMC7243797 DOI: 10.3389/fonc.2020.00753] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Dysregulation of ESR1 accounts for endocrine therapy resistance and metastasis of ERα positive breast cancer. However, the underlying molecular mechanism of ESR1 in ERα positive breast cancer remains insufficiency. Notably, to date, a comprehensive miRNA-mRNA regulatory network involved in modulation of ESR1 in development and progression of ERα positive breast cancer is still not established. Methods: Microarray miRNA and mRNA expression profiling from GEO database were used to obtained significant DE-miRNAs and DE-mRNAs in ERα positive breast cancer. Functional enrichment analysis was conducted by Enrichr database. STRING database was utilized to construct protein-protein interaction network, after which hub genes were identified through Cytoscape. Kaplan-Meier plotter was introduced to perform survival analysis. The relationship between ESR1-miRNA or miRNA-target gene pairs were experimentally validated. Results: 74 DE-miRNAs, including 19 upregulated and 55 downregulated miRNAs, and 830 DE-mRNAs, including 359 upregulated and 471 downregulated mRNAs, in ERα positive breast cancer were identified. Potential DE-mRNAs were statistically enriched in several cancer-associated pathways, such as cell cycle and pathway in cancer. Fifty-one hub genes with node degree more than 10 were screened. Twenty-seven of 51 hub genes had significant prognostic values in ERα positive breast cancer. Based on the 27 hub genes, a miRNA-hub gene network, containing 26 miRNAs, was established. Seven of 26 miRNAs were found to possess prognostic predictive roles for patients with ERα positive breast cancer by combination of TCGA and METABRIC data. Intriguingly, ESR1 positively correlated and regulated the 7 miRNAs and the 7 miRNAs inversely correlated and modulated their corresponding downstream targets in MCF-7 and T47D cells, supporting the accuracy of in silico analysis. The relationship between ESR1-miRNA, miRNA-mRNA, or ESR1-mRNA pairs was validated in clinical ERα positive breast cancer. Conclusions: In total, the current findings from this work add substantially to the understanding of ESR1's molecular regulatory mechanism in ERα positive breast cancer.
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Affiliation(s)
- Shan Gao
- Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China.,Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Bisha Ding
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Liu Y, Cao Y, Cai W, Wu L, Zhao P, Liu XG. Aberrant expression of two miRNAs promotes proliferation, hepatitis B virus amplification, migration and invasion of hepatocellular carcinoma cells: evidence from bioinformatic analysis and experimental validation. PeerJ 2020; 8:e9100. [PMID: 32377460 PMCID: PMC7195830 DOI: 10.7717/peerj.9100] [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: 12/13/2019] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
Background As key negative regulators of gene expression, microRNAs (miRNAs) play an important role in the onset and progression of hepatocellular carcinoma (HCC). This study aimed to identify the miRNAs involved in HCC carcinogenesis and their regulated genes. Methods The Gene Expression Omnibus (GEO) dataset (GSE108724) was chosen and explored to identify differentially expressed miRNAs using GEO2R. For the prediction of potential miRNA target genes, the miRTarBase was explored. Enrichment analysis of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed by the DAVID online tool. The hub genes were screened out using the CytoHubba plug-in ranked by degrees. The networks between miRNAs and hub genes were constructed by Cytoscape software. MiRNA mimics and negative control were transfected into HCC cell lines and their effects on proliferation, hepatitis B virus DNA (HBV-DNA) replication, TP53 expression, migration, and invasion were investigated. The following methods were employed: MTT assay, quantitative PCR (qPCR) assay, western blotting, wound healing assay, and transwell assay. Results A total of 50 differentially expressed miRNAs were identified, including 20 upregulated and 30 downregulated miRNAs, in HCC tumor tissues compared to matched adjacent tumor-free tissues. The top three upregulated (miR-221-3p, miR-222-3p, and miR-18-5p) and downregulated (miR-375, miR-214-3p and miR-378d) miRNAs, ranked by |log2 fold change (log2FC)|, were chosen and their potential target genes were predicted. Two gene sets, targeted by the upregulated and the downregulated miRNAs, were identified respectively. GO and KEGG pathway analysis showed that the predicted target genes of upregulated and downregulated miRNAs were mainly enriched in the cell cycle and cancer-related pathways. The top ten hub nodes of gene sets ranked by degrees were identified as hub genes. Analysis of miRNA-hub gene network showed that miR-221-3p and miR-375 modulated most of the hub genes, especially involving regulation of TP53. The q-PCR results showed that miR-221-3p and miR-375 were markedly upregulated and downregulated, respectively, in HCC cells and HCC clinical tissue samples compared to non-tumoral tissues. Furthermore, miR-221-3p overexpression significantly enhanced proliferation, HBV-DNA replication, as well as the migration and invasion of HCC cells, whereas miR-375 overexpression resulted in opposite effects. Western blotting analysis showed that the overexpression of miR-221-3p and miR-375 reduced and increased TP53 expression, respectively. Conclusion The present study revealed that miR-211-3p and miR-375 may exert vital effects on cell proliferation, HBV-DNA replication, cell migration, and invasion through the regulation of TP53 expression in HCC.
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Affiliation(s)
- Yanming Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, Guangdong, China.,Department of Clinical Laboratory, YueBei People's Hospital, Shaoguan, Guangdong, China
| | - Yue Cao
- Department of Medical Technology, Medical College of Shaoguan University, Shaogguan, Guangdong, China
| | - Wencan Cai
- Department of Clinical Laboratory, YueBei People's Hospital, Shaoguan, Guangdong, China
| | - Liangyin Wu
- Department of Clinical Laboratory, YueBei People's Hospital, Shaoguan, Guangdong, China
| | - Pingsen Zhao
- Department of Clinical Laboratory, YueBei People's Hospital, Shaoguan, Guangdong, China
| | - Xin-Guang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, Guangdong, China
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Ding B, Yao M, Fan W, Lou W. Whole-transcriptome analysis reveals a potential hsa_circ_0001955/hsa_circ_0000977-mediated miRNA-mRNA regulatory sub-network in colorectal cancer. Aging (Albany NY) 2020; 12:5259-5279. [PMID: 32221048 PMCID: PMC7138558 DOI: 10.18632/aging.102945] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/09/2020] [Indexed: 12/15/2022]
Abstract
Background: Circular RNAs (circRNAs), a novel class of non-coding RNAs, have been found to act as microRNA (miRNA) sponges and thus play key roles in biological processes and pathogenesis. However, studies regarding circRNAs in colorectal cancer (CRC) remain inadequate. Results: By differential expression analysis, 10 candidate circRNAs (6 upregulated and 4 downregulated circRNAs) were chosen. 9 of 10 circRNAs were available on CSCD and their structure showed the binding potential of miRNA. Intersection analysis revealed that miR-145-5p, miR-3127-5p, miR-761, miR-4766-3p, miR-135a-5p, miR-135b-5p, miR-374a-3p and miR-330-3p were 8 miRNAs with the most potential in binding circRNAs. Further expression validation and correlation analysis demonstrated hsa_circ_0001955/miR-145-5p and hsa_circ_0000977/miR-135b-5p axes as key pathways in CRC. Subsequently, target gene prediction, differential expression analysis, intersection analysis and correlation analysis showed that CDK6, MMP12 and RAB3IP were the three potential downstream targets of hsa_circ_0001955/miR-145-5p axis and FOXO1, MBNL1, MEF2C, RECK, PPM1E, TTLL7 and PCP4L1 were the seven potential downstream targets of hsa_circ_0000977/miR-135b-5p axis in CRC. Finally, we also confirmed that expression of hsa_circ_0001955 or hsa_circ_0000977 was significantly positively correlated with their individual targets in CRC. Conclusions: In the present work, we constructed a potential hsa_circ_0001955/hsa_circ_0000977-mediated circRNA-miRNA-mRNA regulatory network in CRC by a series of in silico analysis and experimental validation. Methods: Whole-transcriptome microarrays from CRC and matched normal samples were obtained from GEO. The structure of circRNA was identified by CSCD. starBase and miRNet were successively used to predict miRNA of circRNA and target gene of miRNA. Expression correlation between RNA-RNA interactions was assessed using GEO and TCGA data. Finally, a potential circRNA-miRNA-mRNA network was established based on competing endogenous RNA (ceRNA) hypothesis.
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Affiliation(s)
- Bisha Ding
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China.,Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang Province, China
| | - Minya Yao
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Weimin Fan
- Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang Province, China
| | - Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China.,Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, Hangzhou, Zhejiang Province, China
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Zhang J, Lou W. A Key mRNA-miRNA-lncRNA Competing Endogenous RNA Triple Sub-network Linked to Diagnosis and Prognosis of Hepatocellular Carcinoma. Front Oncol 2020; 10:340. [PMID: 32257949 PMCID: PMC7092636 DOI: 10.3389/fonc.2020.00340] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/26/2020] [Indexed: 01/27/2023] Open
Abstract
Growing evidence has illustrated critical roles of competing endogenous RNA (ceRNA) regulatory network in human cancers including hepatocellular carcinoma. In this study, we aimed to find promising diagnostic and prognostic biomarkers for patients with hepatocellular carcinoma. Three novel unfavorable prognosis-associated genes (CELSR3, GPSM2, and CHEK1) was first identified. We also demonstrated that these genes were significantly upregulated in hepatocellular carcinoma cell lines and tissues. Next, 154 potential miRNAs of CELSR3, GPSM2, and CHEK1 were predicted. CHEK1-hsa-mir-195-5p/hsa-mir-497-5p and GPSM2-hsa-mir-122-5p axes were defined as two key pathways in carcinogenesis of hepatocellular carcinoma by combination of in silico analysis and experimental validation. Subsequently, lncRNAs binding to hsa-mir-195-5p, hsa-mir-497-5p, and hsa-mir-122-5p were predicted via starBase and miRNet databases. After performing expression analysis and survival analysis for these predicted lncRNAs, we showed that nine lncRNAs (SNHG1, SNHG12, LINC00511, HCG18, FGD5-AS1, CERS6-AS1, NUTM2A-AS1, SNHG16, and ASB16-AS1) were markedly increased in hepatocellular carcinoma and their upregulation indicated poor prognosis. Moreover, a similar mRNA-miRNA-lncRNA analysis for six “known” genes (CLEC3B, DNASE1L3, PTTG1, KIF2C, XPO5, and UBE2S) was performed. Subsequently, a comprehensive mRNA-miRNA-lncRNA triple ceRNA network linked to prognosis of patients with hepatocellular carcinoma was established. Moreover, all RNAs in this network exhibited significantly diagnostic values for patients with hepatocellular carcinoma. In summary, the current study constructed a mRNA-miRNA-lncRNA ceRNA network associated with diagnosis and prognosis of hepatocellular carcinoma.
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Affiliation(s)
- Junjie Zhang
- Department of Hepatobiliary Surgery, The First People's Hospital of Fuyang Hangzhou, Hangzhou, China
| | - Weiyang Lou
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang University, College of Medicine, Zhejiang University, Hangzhou, China
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Zou H, Yang L. miR-378a-5p improved the prognosis and suppressed the progression of hepatocellular carcinoma by targeting the VEGF pathway. Transl Cancer Res 2020; 9:1558-1566. [PMID: 35117503 PMCID: PMC8798882 DOI: 10.21037/tcr.2020.01.46] [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: 11/02/2019] [Accepted: 12/26/2019] [Indexed: 12/23/2022]
Abstract
Background The malignant tumor hepatocellular carcinoma (HCC) has a poor prognosis and ineffective therapeutic options. miR-378a-5p is a micro-ribonucleic acid (miRNA) that is overexpressed in many cancers. However, its role in the progression of human HCC is unclear. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure miR-378a-5p levels in tissues from patients with HCC and from HCC cell lines. Following transfection, flow cytometry and cell viability assays were used to measure cell proliferation. HCC cell invasive and migration capacities were assessed using Transwell assays. Western blots were performed with HCC cells to identify the expression of vascular endothelial growth factor (VEGF). Results The HCC tissues and cells had significantly reduced miR-378a-5p expression compared with normal liver tissues and cells, while miR-378a-5p mimics suppressed the colony formation, viability, migration and invasive capacity of HCC cells. The HCC tissues and cell lines had upregulated VEGF expression. In HCC cells, miR-378a-5p expression was negatively correlated with VEGF expression, and miR-378a-5p targeted VEGF in HCC cells. Conclusions miR-378a-5p improved the HCC prognosis and suppressed HCC progression by targeting the VEGF pathway.
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Affiliation(s)
- Haibo Zou
- Department of Hepatobiliary Surgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu 610072, China
| | - Lan Yang
- Department of Oncology Centre, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu 610072, China
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Deng F, Chen D, Wei X, Lu S, Luo X, He J, Liu J, Meng T, Yang A, Chen H. Development and validation of a prognostic classifier based on HIF-1 signaling for hepatocellular carcinoma. Aging (Albany NY) 2020; 12:3431-3450. [PMID: 32084009 PMCID: PMC7066907 DOI: 10.18632/aging.102820] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
HIF-1 (hypoxia-inducible factor 1) signaling played a vital role in HCC (hepatocellular carcinoma) prognosis. We aimed to establish an accurate risk scoring system for HCC prognosis prediction and treatment guidance. 424 samples from TCGA (The Cancer Genome Atlas) and 445 samples from GSE14520 dataset were included as the derivation and validation cohort, respectively. In the derivation cohort, prognostic relevant signatures were selected from sixteen HIF-1 related genes and LASSO regression was adopted for model construction. Tumor-infiltrating immune cells were calculated using CIBERSORT algorithm. HIF-1 signaling significantly increased in HCC samples compared with normal tissues. Scoring system based on SLC2A1, ENO1, LDHA and GAPDH exhibited a continuous predictive ability for OS (overall survival) in HCC patients. PCA and t-SNE analysis confirmed a reliable clustering ability of risk score in both cohorts. Patients were classified into high-risk and low-risk groups and the survival outcomes between the two groups showed significant differences. In the derivation cohort, Cox regression indicated the scoring system was an independent predictor for OS, which was validated in the validation cohort. Different infiltrating immune cells fraction and immune scores were also observed in different groups. Herein, a novel integrated scoring system was developed based on HIF-1 related genes, which would be conducive to the precise treatment of patients.
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Affiliation(s)
- Feiwen Deng
- Department of Liver and Pancreatic Surgery, The Affiliated Foshan Hospital, Sun Yat-Sen University, Foshan 528000, China
| | - Dong Chen
- Department of Pancreatobiliary Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiaoli Wei
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Shilin Lu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510008, China
| | - Xuan Luo
- Department of Pancreatobiliary Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
| | - Jincan He
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510008, China
| | - Junting Liu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510008, China
| | - Tiebao Meng
- Department of Medical Imaging, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Anli Yang
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Huanwei Chen
- Department of Liver and Pancreatic Surgery, The Affiliated Foshan Hospital, Sun Yat-Sen University, Foshan 528000, China
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Wang SS, Huang ZG, Wu HY, He RQ, Yang LH, Feng ZB, Dang YW, Lu HP, Fang YY, Chen G. Downregulation of miR-193a-3p is involved in the pathogenesis of hepatocellular carcinoma by targeting CCND1. PeerJ 2020; 8:e8409. [PMID: 32095323 PMCID: PMC7017797 DOI: 10.7717/peerj.8409] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second-highest cause of malignancy-related death worldwide, and many physiological and pathological processes, including cancer, are regulated by microRNAs (miRNAs). miR-193a-3p is an anti-oncogene that plays an important part in health and disease biology by interacting with specific targets and signals. Methods In vitro assays were performed to explore the influences of miR-193a-3p on the propagation and apoptosis of HCC cells. The sequencing data for HCC were obtained from The Cancer Genome Atlas (TCGA), and the expression levels of miR-193a-3p in HCC and non-HCC tissues were calculated. The differential expression of miR-193a-3p in HCC was presented as standardized mean difference (SMD) with 95% confidence intervals (CIs) in Stata SE. The impact of miR-193a-3p on the prognoses of HCC patients was determined by survival analysis. The potential targets of miR-193a-3p were then predicted using miRWalk 2.0 and subjected to enrichment analyses, including Gene Ontology (GO) annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Protein-Protein Interaction (PPI) network analysis. The interaction between miR-193a-3p and one predicted target, Cyclin D1 (CCND1), was verified by dual luciferase reporter assays and Pearson correlation analysis. Results MiR-193a-3p inhibited the propagation and facilitated the apoptosis of HCC cells in vitro. The pooled SMD indicated that miR-193a-3p had a low level of expression in HCC (SMD: −0.88, 95% CI [−2.36 −0.59]). Also, HCC patients with a higher level of miR-193a-3p expression tended to have a favorable overall survival (OS: HR = 0.7, 95% CI [0.43–1.13], P = 0.14). For the KEGG pathway analysis, the most related pathway was “proteoglycans in cancer”, while the most enriched GO term was “protein binding”. The dual luciferase reporter assays demonstrated the direct interaction between miR-193a-3p and CCND1, and the Pearson correlation analysis suggested that miR-193a-3p was negatively correlated with CCND1 in HCC tissues (R = − 0.154, P = 0.002). Conclusion miR-193a-3p could suppress proliferation and promote apoptosis by targeting CCND1 in HCC cells. Further, miR-193a-3p can be used as a promising biomarker for the diagnosis and treatment of HCC in the future.
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Affiliation(s)
- Shi-Shuo Wang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhi-Guang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hua-Yu Wu
- Department of Cell Biology & Genetics, Guangxi Medical University, Nanning, Guangxi, China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Li-Hua Yang
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hui-Ping Lu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ye-Ying Fang
- Department of Radiation Oncology, Radiation Oncology Clinical Medical Research Center of Guangxi, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Zhou B, Wang J, Gao J, Xie J, Chen Y. Fidgetin as a potential prognostic biomarker for hepatocellular carcinoma. Int J Med Sci 2020; 17:2888-2894. [PMID: 33162817 PMCID: PMC7645349 DOI: 10.7150/ijms.49913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/27/2020] [Indexed: 12/04/2022] Open
Abstract
Background: Fidgetin (FIGN), a conserved ATP-dependent enzyme, is regarded as a hepatocellular carcinoma (HCC) risk gene, but the prognostic implication of FIGN in HCC remains obscure. In this study, we investigate the expression of FIGN in HCC and to evaluate its prognostic value. Methods: A total of 216 patients with HCC who experienced hepatectomy were recruited in this study. The expression of FIGN in HCC samples was evaluated by quantitative real-time PCR, immunohistochemistry and immunoblotting analysis. And Cox regression model was used to evaluate the prognostic value of all covariates. Results: Of the 216 HCC patients, 67 (31.0%) had tumors with high FIGN expression and 149 (69.0%) had tumors with low FIGN expression. FIGN expression was positively correlated with TNM stage (P = 0.039), tumor with incomplete capsule (P = 0.036), microvascular invasion (P = 0.023), and portal vein tumor thrombus (P = 0.003). High expression of FIGN indicated shorter overall survival (OS) (hazard ratio: 4.569, P = 0.036) and disease-free survival (DFS) (hazard ratio: 6.487, P = 0.001). Conclusion: Our results indicate that high Fidgetin expression is associated with tumor progression and suggest a worse prognosis in HCC. Fidgetin might serve as a potential target for therapy.
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Affiliation(s)
- Bin Zhou
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Jisheng Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Jing Gao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Junqing Xie
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Yiming Chen
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
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Gupta MK, Vadde R. Applications of Computational Biology in Gastrointestinal Malignancies. IMMUNOTHERAPY FOR GASTROINTESTINAL MALIGNANCIES 2020:231-251. [DOI: 10.1007/978-981-15-6487-1_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
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Dysregulation of pseudogene/lncRNA-hsa-miR-363-3p-SPOCK2 pathway fuels stage progression of ovarian cancer. Aging (Albany NY) 2019; 11:11416-11439. [PMID: 31794425 PMCID: PMC6932902 DOI: 10.18632/aging.102538] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023]
Abstract
Objective: Ovarian cancer is one of the most common and lethal cancer types in women. The molecular mechanism of ovarian cancer progression is still unclear. Results: Here, we first reported that expression levels of three genes, GJB2, S100A2 and SPOCK2, were significantly higher in advanced stage than that in early stage of ovarian cancer, and upregulation of them indicated poor prognosis of patients with ovarian cancer. Subsequently, 8, 6 and 20 miRNAs were predicted to target GJB2, S100A2 and SPOCK2, respectively. Among these miRNA-mRNA pairs, hsa-miR-363-3p-SPOCK2 axis was the most potential in suppressing progression of ovarian cancer. Mechanistically, we found that hsa-miR-363-3p-SPOCK2 axis was involved in regulation of actin cytoskeleton. Moreover, 6 pseudogenes and 8 lncRNAs were identified to potentially inhibit hsa-miR-363-3p-SPOCK2 axis in ovarian cancer. Conclusions: Collectively, we elucidate a regulatory role of pseudogene/lncRNA-hsa-miR-363-3p-SPOCK2 pathway in progression of ovarian cancer, which may provide effective therapeutic approaches and promising prognostic biomarkers for ovarian cancer. Materials and methods: Differentially expressed genes (DEGs) in ovarian cancer were first screened using GSE12470, after which DEGs expression were validated using GEPIA. Kaplan-Meier analysis was employed to assess the prognostic values. Potential miRNAs were predicted by seven target prediction databases, and upstream lncRNAs and pseudogenes of hsa-miR-363-3p were forecasted through miRNet or starBase. UALCAN and starBase were used to obtain the co-expressed genes of SPOCK. Enrichment analysis for these co-expressed genes was performed by Enrichr.
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50
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Yang S, Wang X, Liu J, Ding B, Shi K, Chen J, Lou W. Distinct expression pattern and prognostic values of pituitary tumor transforming gene family genes in non-small cell lung cancer. Oncol Lett 2019; 18:4481-4494. [PMID: 31611957 PMCID: PMC6781778 DOI: 10.3892/ol.2019.10844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/05/2019] [Indexed: 01/26/2023] Open
Abstract
Members of the pituitary tumor transforming gene (PTTG) family, including PTTG1, PTTG2 and PTTG3P, exhibit pivotal roles in the onset and progression of certain types of human cancer. However, to the best of our knowledge, a systematic study regarding the expression pattern and the prognostic values of PTTG family genes in non-small cell lung cancer (NSCLC) remains to be performed. The expression levels of PTTG family genes in NSCLC were successively determined using the Gene Expression Profiling Interactive Analysis, UALCAN and Oncomine databases. Subsequently, the Kaplan-Meier plotter database was used to assess the prognostic value of the PTTG family genes in patients with NSCLC, and to determine the associations between PTTG expression levels and the prognosis of patients based on different clinicopathological features, including cancer stage, grade, chemotherapy, radiotherapy, lymph node status, smoking history, and sex. PTTG1 was identified to be significantly upregulated in NSCLC in all three databases, whereas PTTG2 and PTTG3P were significantly upregulated in NSCLC in only the UALCAN database. Patients with NSCLC with higher expression levels of the three PTTG genes demonstrated shorter overall survival times. In summary, the results of the present study suggested that increased expression of PTTG family genes may serve as promising prognostic biomarkers for patients with NSCLC.
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Affiliation(s)
- Shaolong Yang
- Department of Pathology, Zhengzhou Railway Vocational and Technical College, Zhengzhou, Henan 451460, P.R. China
| | - Xiaodi Wang
- Department of Emergency Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Jingxing Liu
- Department of Intensive Care Unit, Changxing People's Hospital of Zhejiang, Huzhou, Zhejiang 313100, P.R. China
| | - Bisha Ding
- Department of Surgery, Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang 310003, P.R. China
| | - Kairi Shi
- Department of Orthopedics and Traumatology, Traditional Chinese Medicine Hospital of Cixi, Ningbo, Zhejiang 315300, P.R. China
| | - Jing Chen
- Department of Oncology, First Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang 314000, P.R. China
| | - Weiyang Lou
- Department of Surgery, Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang 310003, P.R. China
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