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Yi H, Liu L, Zhang J, Guo K, Cao Y, Sun P, Wang H. GALNT2 targeted by miR-139-5p promotes proliferation of clear cell renal cell carcinoma via inhibition of LATS2 activation. Discov Oncol 2024; 15:73. [PMID: 38478152 PMCID: PMC10937861 DOI: 10.1007/s12672-024-00930-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
Polypeptide N-Acetylgalactosaminyltransferase (GALNTs) are critical enzymes that initiate mucin type-O glycosylation, and are closely associated with the occurrence and development of multiple cancers. However, the significance of GALNT2 in clear cell renal cell carcinoma (ccRCC) progression remains largely undetermined. Based on public multi-omics analysis, GALNT2 was strongly elevated in ccRCC versus adjoining nontumor tissues, and it displayed a relationship with poor overall survival (OS) of ccRCC patients. In addition, GALNT2 over-expression accelerated proliferation of renal cancer cell (RCC) lines. In contrast, GALNT2 knockdown using shRNAs suppressed cell proliferation, and this was rescued by LATS2 knockdown. Similarly, GALNT2 deficiency enhanced p-LATS2/LATS2 expression. LATS2 is activated by phosphorylation (p-LATS2) and, in turn, phosphorylate the downstream substrate protein YAP. Phosphorylated YAP (p-YAP) stimulated its degradation and cytoplasmic retention, as it was unable to translocate to the nucleus. This resulted in reduced cell proliferation. Subsequently, we explored the upstream miRNAs of GALNT2. Using dual luciferase reporter assay, we revealed that miR-139-5p interacted with the 3' UTR of GALNT2. Low miR-139-5p expression was associated with worse ccRCC patient outcome. Based on our experiments, miR-139-5p overexpression inhibited RCC proliferation, and this phenotype was rescued by GALNT2 overexpression. Given these evidences, the miR-139-5p-GALNT2-LATS2 axis is critical for RCC proliferation, and it is an excellent candidate for a new therapeutic target in ccRCC.
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Affiliation(s)
- Haisheng Yi
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Lingyun Liu
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Jingshun Zhang
- Reproductive Medical Center, Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, 130041, China
| | - Kaimin Guo
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Yin Cao
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Penghao Sun
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Hongliang Wang
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China.
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Yao Y, Chen X, Wang X, Li H, Zhu Y, Li X, Xiao Z, Zi T, Qin X, Zhao Y, Yang T, Wang L, Wu G, Fang X, Wu D. Glycolysis related lncRNA SNHG3 / miR-139-5p / PKM2 axis promotes castration-resistant prostate cancer (CRPC) development and enzalutamide resistance. Int J Biol Macromol 2024; 260:129635. [PMID: 38266860 DOI: 10.1016/j.ijbiomac.2024.129635] [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: 05/23/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Although androgen deprivation therapy (ADT) by the anti-androgen drug enzalutamide (Enz) may improve the survival level of patients with castration-resistant prostate cancer (CRPC), most patients may eventually fail due to the acquired resistance. The reprogramming of glucose metabolism is one type of the paramount hallmarks of cancers. PKM2 (Pyruvate kinase isozyme typeM2) is a speed-limiting enzyme in the glycolytic mechanism, and has high expression in a variety of cancers. Emerging evidence has unveiled that microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have impact on tumor development and therapeutic efficacy by regulating PKM2 expression. Herein, we found that lncRNA SNHG3, a highly expressed lncRNA in CRPC via bioinformatics analysis, promoted the invasive ability and the Enz resistance of the PCa cells. KEGG pathway enrichment analysis indicated that glucose metabolic process was tightly correlated with lncRNA SNHG3 level, suggesting lncRNA SNHG3 may affect glucose metabolism. Indeed, glucose uptake and lactate content determinations confirmed that lncRNA SNHG3 promoted the process of glycolysis. Mechanistic dissection demonstrated that lncRNA SNHG3 facilitated the advance of CRPC by adjusting the expression of PKM2. Further explorations unraveled the role of lncRNA SNHG3 as a 'sponge' of miR-139-5p and released its binding with PKM2 mRNA, leading to PKM2 up-regulation. Together, Our studies suggest that lncRNA SNHG3 / miR-139-5p / PKM2 pathway promotes the development of CRPC via regulating glycolysis process and provides valuable insight into a novel therapeutic approach for the disordered disease.
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Affiliation(s)
- Yicong Yao
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Xi Chen
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Xin'an Wang
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Haopeng Li
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Yaru Zhu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Xilei Li
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Zhihui Xiao
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Tong Zi
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Xin Qin
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Yan Zhao
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Tao Yang
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China; School of Medicine, Tongji University, Shanghai 200092, China
| | - Licheng Wang
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
| | - Gang Wu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
| | - Xia Fang
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.
| | - Denglong Wu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
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Bohosova J, Kozelkova K, Al Tukmachi D, Trachtova K, Naar O, Ruckova M, Kolarikova E, Stanik M, Poprach A, Slaby O. Long non-coding RNAs enable precise diagnosis and prediction of early relapse after nephrectomy in patients with renal cell carcinoma. J Cancer Res Clin Oncol 2023; 149:7587-7600. [PMID: 36988708 PMCID: PMC10374689 DOI: 10.1007/s00432-023-04700-7] [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: 01/29/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
PURPOSE Renal cell carcinoma belongs among the deadliest malignancies despite great progress in therapy and accessibility of primary care. One of the main unmet medical needs remains the possibility of early diagnosis before the tumor dissemination and prediction of early relapse and disease progression after a successful nephrectomy. In our study, we aimed to identify novel diagnostic and prognostic biomarkers using next-generation sequencing on a novel cohort of RCC patients. METHODS Global expression profiles have been obtained using next-generation sequencing of paired tumor and non-tumor tissue of 48 RCC patients. Twenty candidate lncRNA have been selected for further validation on an independent cohort of paired tumor and non-tumor tissue of 198 RCC patients. RESULTS Sequencing data analysis showed significant dysregulation of more than 2800 lncRNAs. Out of 20 candidate lncRNAs selected for validation, we confirmed that 14 of them are statistically significantly dysregulated. In order to yield better discriminatory results, we combined several best performing lncRNAs into diagnostic and prognostic models. A diagnostic model consisting of AZGP1P1, CDKN2B-AS1, COL18A1, and RMST achieved AUC 0.9808, sensitivity 95.96%, and specificity 90.4%. The model for prediction of early relapse after nephrectomy consists of COLCA1, RMST, SNHG3, and ZNF667-AS1 and achieved AUC 0.9241 with sensitivity 93.75% and specificity 71.07%. Notably, no combination has outperformed COLCA1 alone. Lastly, a model for stage consists of ZNF667-AS1, PVT1, RMST, LINC00955, and TCL6 and achieves AUC 0.812, sensitivity 85.71%, and specificity 69.41%. CONCLUSION In our work, we identified several lncRNAs as potential biomarkers and developed models for diagnosis and prognostication in relation to stage and early relapse after nephrectomy.
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Affiliation(s)
- Julia Bohosova
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Katerina Kozelkova
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Dagmar Al Tukmachi
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Karolina Trachtova
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Ondrej Naar
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Michaela Ruckova
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Eva Kolarikova
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk University, Zluty Kopec 543/7, 602 00, Brno, Czech Republic
| | - Michal Stanik
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk University, Zluty Kopec 543/7, 602 00, Brno, Czech Republic
| | - Alexandr Poprach
- Masaryk Memorial Cancer Institute, Department of Comprehensive Cancer Care, Faculty of Medicine, Masaryk University, Zluty Kopec 543/7, 602 00, Brno, Czech Republic
| | - Ondrej Slaby
- Masaryk University, Central European Institute of Technology, Kamenice 753/5, 625 00, Brno, Czech Republic.
- Faculty of Medicine, Department of Biology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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Li JS, Chen X, Luo A, Chen D. TFRC-RNA interactions show the regulation of gene expression and alternative splicing associated with IgAN in human renal tubule mesangial cells. Front Genet 2023; 14:1176118. [PMID: 37547464 PMCID: PMC10397801 DOI: 10.3389/fgene.2023.1176118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction: IgA nephropathy (IgAN) is the most common primary glomerular disease (PGD) which could progress to renal failure and is characterized by aberrant IgA immune complex deposition. Transferrin receptor1 (TFRC), an IgA receptor, is a potential RNA binding protein (RBP) which regulates expression of genes positively associated with the cell cycle and proliferation and is involved in IgAN. Molecular mechanisms by which TFRC affects IgAN development remain unclear. Methods: In this study, TFRC was overexpressed in human renal tubular mesangial cells (HRMCs) and RNA-sequencing (RNA-seq) and improved RNA immunoprecipitation sequencing (iRIP-seq) were performed. The aim was to identify potential RNA targets of TFRC at transcriptional and alternative splicing (AS) levels. Results: TFRC-regulated AS genes were enriched in mRNA splicing and DNA repair, consistent with global changes due to TFRC overexpression (TFRC-OE). Expression of TFRC-regulated genes potentially associated with IgAN, including CENPH, FOXM1, KIFC1, TOP2A, FABP4, ID1, KIF20A, ATF3, H19, IRF7, and H1-2, and with AS, CYGB, MCM7 and HNRNPH1, were investigated by RT-qPCR and iRIP-seq data analyzed to identify TFRC-bound RNA targets. RCC1 and RPPH1 were found to be TFRC-bound RNA targets involved in cell proliferation. Discussion: In conclusion, molecular TFRC targets were identified in HRMCs and TFRC found to regulate gene transcription and AS. TFRC is considered to have potential as a clinical therapeutic target.
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Affiliation(s)
- Jian-Si Li
- Department of Nephrology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiao Chen
- Heilongjiang Provincial Hospital Affiliated to Harbin Institute of Technology, Harbin, China
| | - Ailing Luo
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, China
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Huang X, Jia Y, Shi H, Fan H, Sun L, Zhang H, Wang Y, Chen J, Han J, Wang M, Du J, Zhang J. miR-30c-2-3p suppresses the proliferation of human renal cell carcinoma cells by targeting TOP2A. ASIAN BIOMED 2023; 17:124-135. [PMID: 37818158 PMCID: PMC10561683 DOI: 10.2478/abm-2023-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
Abstract
Background The ambiguity of renal cell carcinoma (RCC) symptoms hinders early diagnosis, thereby contributing to high mortality rates. By attaching to the 3'-untranslated region (UTR) of the target gene, microRNAs (miRNAs) exert significant control over the expression of genes. Objectives To investigate the influence of miR-30c-2-3p and DNA topoisomerase II alpha (TOP2A) on RCC growth and the mechanisms underlying the regulation of its expression. Methods The expression of miRNA-30c-2-3p and TOP2A in RCC cells was examined using quantitative real-time polymerase chain reaction (qRT-PCR). MiR-30c-2-3p mimics, its inhibitors, and controls, as well as TOP2A short hairpin RNA (shRNA) and controls, were used to transfect the human RCC cell lines 786-O, Caki-1, and ACHN. Additionally, the roles of miRNA-30c-2-3p and TOP2A in the growth of RCC were evaluated using the cell counting kit (CCK)-8 test, colony formation assay, apoptosis analysis, and Western blotting. Meanwhile, binding of miRNA-30c-2-3p and TOP2A was verified using dual-luciferase reporter assays and Western blotting. Results miR-30c-2-p is underexpressed in RCC cells. Overexpression of miR-30c-2-p promotes apoptosis and inhibits proliferation of ACHN, Caki-1, and 786-O cells. miR-30c-2-3p targets TOP2A, which is elevated in RCC tissues and cells, whereas TOP2A silencing inhibits the proliferation ability of RCC cells. The miRNA-30c-2-3p inhibitor compromises TOP2A shRNA-induced apoptosis of RCC. RCC cells cotransfected with miRNA-30c-2-3p inhibitors and TOP2A shRNAs have a higher proliferation rate than those transfected with only TOP2A shRNAs. Conclusions Collectively, our results verify that miRNA-30c-2-3p has a tumor suppressor property. miRNA-30c-2-3p inhibits the proliferation of RCC through regulation of TOP2A. The data provide a viable therapeutic target for RCC.
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Affiliation(s)
- Xiaoyong Huang
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Yuna Jia
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Haiyan Shi
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Haiyan Fan
- Department of Laboratory, The First Hospital of Yulin, Yulin719000, China
| | - Lingbo Sun
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Huahua Zhang
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Yanfeng Wang
- Clinical Laboratory of Affiliated Hospital of Yan’an University, Yan’an, Shaanxi716000, China
| | - Jie Chen
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Jiaqi Han
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Mingming Wang
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Juan Du
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
| | - Jing Zhang
- Department of Clinical Medicine, Medical College of Yan’an University, Yan’an, Shaanxi716000, China
- Yan’an Key Laboratory of Chronic Disease Prevention and Research, Yan’an, Shaanxi716000, China
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Zhang L, Di L, Liu J, Lei X, Gu M, Zhang W, Wang Y. The LncRNA signature associated with cuproptosis as a novel biomarker of prognosis in immunotherapy and drug screening for clear cell renal cell carcinoma. Front Genet 2023; 14:1039813. [PMID: 36755568 PMCID: PMC9899836 DOI: 10.3389/fgene.2023.1039813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Cuproptosis is a new form of cell death, the second form of metal ion-induced cell death defined after ferroptosis. Recently, cuproptosis has been suggested to be associated with tumorigenesis. However, the relationship between cuproptosis and patient prognosis in clear cell renal cell carcinoma (ccRCC) in the context of immunotherapy remains unknown. The aim of this study was to investigate the correlation between cuproptosis-related long non-coding RNA (lncRNA) and ccRCC in terms of immunity as well as prognosis. Clinical information on lncRNAs associated with differences in cuproptosis genes in ccRCC and normal tissues was collected from The Cancer Genome Atlas (TCGA) dataset. Univariate Cox regression was used to screen lncRNAs. A total of 11 lncRNAs closely associated with cuproptosis were further screened and established using the least absolute shrinkage and selection operator (LASSO) algorithm and multivariate Cox regression, and the samples were randomly divided into training and test groups. A risk prognostic model was constructed using the training group, and the model was validated using the test group. We investigated the predictive ability of the prognostic risk model in terms of clinical prognosis, tumor mutation, immune escape, immunotherapy, tumor microenvironment, immune infiltration levels, and tumor drug treatment of ccRCC. Using the median risk score, patients were divided into low and high-risk groups. Kaplan-Meier curves showed that the overall survival (OS) of patients in the high-risk group was significantly worse than low-risk group (p < 0.001). Receiver operating characteristic (ROC) curves further validated the reliability of our model. The model consistently and accurately predicted prognosis at 1, 3, and 5 years, with an AUC above 0.7. Tumor cell genes generally precede morphological abnormalities; therefore, the model we constructed can effectively compensate for the traditional method of evaluating the prognosis of patients with renal cancer, and our model was also clinically meaningful in predicting ccRCC staging. In addition, lower model risk scores determined by mutational load indicated a good chance of survival. The high-risk group had greater recruitment of immune cells, while the anti-immune checkpoint immunotherapy was less efficacious overall than that of the low-risk group. Tumor and immune-related pathways were enriched, and anti-tumor agents were selected to improve the survival of ccRCC. This prognostic risk model is based on the levels of cuproptosis-associated lncRNAs and provides a new perspective in the clinical assessment and precise treatment of ccRCC.
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Affiliation(s)
- Lishuo Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Longjiang Di
- College of Basic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jinhui Liu
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xianli Lei
- Harbin Medical University, Harbin, Heilongjiang, China
| | - Maoli Gu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wenjing Zhang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Yufu Wang, ; Wenjing Zhang,
| | - Yufu Wang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Yufu Wang, ; Wenjing Zhang,
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Guan Y, Yue S, Chen Y, Pan Y, An L, Du H, Liang C. Molecular Cluster Mining of Adrenocortical Carcinoma via Multi-Omics Data Analysis Aids Precise Clinical Therapy. Cells 2022; 11:cells11233784. [PMID: 36497046 PMCID: PMC9737968 DOI: 10.3390/cells11233784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Adrenocortical carcinoma (ACC) is a malignancy of the endocrine system. We collected clinical and pathological features, genomic mutations, DNA methylation profiles, and mRNA, lncRNA, microRNA, and somatic mutations in ACC patients from the TCGA, GSE19750, GSE33371, and GSE49278 cohorts. Based on the MOVICS algorithm, the patients were divided into ACC1-3 subtypes by comprehensive multi-omics data analysis. We found that immune-related pathways were more activated, and drug metabolism pathways were enriched in ACC1 subtype patients. Furthermore, ACC1 patients were sensitive to PD-1 immunotherapy and had the lowest sensitivity to chemotherapeutic drugs. Patients with the ACC2 subtype had the worst survival prognosis and the highest tumor-mutation rate. Meanwhile, cell-cycle-related pathways, amino-acid-synthesis pathways, and immunosuppressive cells were enriched in ACC2 patients. Steroid and cholesterol biosynthetic pathways were enriched in patients with the ACC3 subtype. DNA-repair-related pathways were enriched in subtypes ACC2 and ACC3. The sensitivity of the ACC2 subtype to cisplatin, doxorubicin, gemcitabine, and etoposide was better than that of the other two subtypes. For 5-fluorouracil, there was no significant difference in sensitivity to paclitaxel between the three groups. A comprehensive analysis of multi-omics data will provide new clues for the prognosis and treatment of patients with ACC.
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Affiliation(s)
- Yu Guan
- Department of Urology, The First Affifiliated Hospital of Anhui Medical University, 218th Jixi Road, Hefei 230022, China
- Institute of Urology, Anhui Medical University, 81th Meishan Road, Hefei 230022, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University (AHMU), 81th Meishan Road, Hefei 230022, China
| | - Shaoyu Yue
- Department of Urology, The First Affifiliated Hospital of Anhui Medical University, 218th Jixi Road, Hefei 230022, China
- Institute of Urology, Anhui Medical University, 81th Meishan Road, Hefei 230022, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University (AHMU), 81th Meishan Road, Hefei 230022, China
| | - Yiding Chen
- Department of Urology, The First Affifiliated Hospital of Anhui Medical University, 218th Jixi Road, Hefei 230022, China
- Institute of Urology, Anhui Medical University, 81th Meishan Road, Hefei 230022, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University (AHMU), 81th Meishan Road, Hefei 230022, China
| | - Yuetian Pan
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, D-81377 Munich, Germany
| | - Lingxuan An
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, D-81377 Munich, Germany
| | - Hexi Du
- Department of Urology, The First Affifiliated Hospital of Anhui Medical University, 218th Jixi Road, Hefei 230022, China
- Institute of Urology, Anhui Medical University, 81th Meishan Road, Hefei 230022, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University (AHMU), 81th Meishan Road, Hefei 230022, China
- Correspondence: (H.D.); (C.L.); Tel.: +86-18856040979 (H.D.); +86-13505604595 (C.L.)
| | - Chaozhao Liang
- Department of Urology, The First Affifiliated Hospital of Anhui Medical University, 218th Jixi Road, Hefei 230022, China
- Institute of Urology, Anhui Medical University, 81th Meishan Road, Hefei 230022, China
- Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University (AHMU), 81th Meishan Road, Hefei 230022, China
- Correspondence: (H.D.); (C.L.); Tel.: +86-18856040979 (H.D.); +86-13505604595 (C.L.)
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Hu K, Yu H, Liu S, Liao D, Zhang Y. Systematic pan-cancer analysis on the expression and role of regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene 12. Front Mol Biosci 2022; 9:946507. [PMID: 36148010 PMCID: PMC9486007 DOI: 10.3389/fmolb.2022.946507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Regulator of chromatin condensation 1 (RCC1) is the major guanine nucleotide exchange factor of RAN GTPase, which plays a key role in various biological processes such as cell cycle and DNA damage repair. Small nucleolar RNA host gene 3 (SNHG3) and small nucleolar RNA host gene12 are long-stranded non-coding RNAs (lncRNAs) and are located on chromatin very close to the sequence of Regulator of chromatin condensation 1. Many studies have shown that they are aberrantly expressed in tumor tissues and can affect the proliferation and viability of cancer cells. Although the effects of Regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene12 on cellular activity have been reported, respectively, their overall analysis on the pan-cancer level has not been performed. Here, we performed a comprehensive analysis of Regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene12 in 33 cancers through the Cancer Genome Atlas and Gene Expression Database. The results showed that Regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene12 were highly expressed in a variety of tumor tissues compared to normal tissues. The expression of Regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene12 in BRCA, LGG and LIHC was associated with TP53 mutations. In addition, Regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene12 expression was closely associated with the prognosis of patients with multiple tumors. Immunocorrelation analysis indicated that Regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene12 showed a correlation with multiple immune cell infiltration. The results of enrichment analysis suggested that Regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene12 was involved in the regulation of cell cycle, apoptosis and other pathways. We found that these effects were mainly mediated by Regulator of chromatin condensation 1, while the trend of small nucleolar RNA host gene 3/small nucleolar RNA host gene12 regulation was also consistent with regulator of chromatin condensation 1. The important role played by Regulator of chromatin condensation 1 in tumor diseases was further corroborated by the study of adjacent lncRNAs.These findings provide new and comprehensive insights into the role of Regulator of chromatin condensation 1/small nucleolar RNA host gene 3/small nucleolar RNA host gene12 in tumor development and show their potential as clinical monitoring and therapy.
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Oncogenic role and potential regulatory mechanism of topoisomerase IIα in a pan-cancer analysis. Sci Rep 2022; 12:11161. [PMID: 35778520 PMCID: PMC9249858 DOI: 10.1038/s41598-022-15205-7] [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: 02/24/2022] [Accepted: 06/20/2022] [Indexed: 11/08/2022] Open
Abstract
Topoisomerase IIα (TOP2A) plays an oncogenic role in multiple tumor types. However, no pan-cancer analysis about the function and the upstream molecular mechanism of TOP2A is available. For the first time, we analyzed potential oncogenic roles of TOP2A in 33 cancer types via The Cancer Genome Atlas (TCGA) database. Overexpression of TOP2A was existed in almost all cancer types, and related to poor prognosis and advanced pathological stages in most cases. Besides, the high frequency of TOP2A genetic alterations was observed in several cancer types, and related to prognosis in some cases. Moreover, we conduct upstream miRNAs and lncRNAs of TOP2A to establish ceRNA networks in kidney renal clear cell carcinoma (SNHG3-miR-139-5p), kidney renal papillary cell carcinoma (TMEM147-AS1/N4BP2L2-IT2/THUMPD3-AS1/ERICD/TTN-AS1/SH3BP5-AS1/THRB-IT1/SNHG3/NEAT1-miR-139-5p), liver hepatocellular carcinoma (SNHG3/THUMPD3-AS1/NUTM2B-AS1/NUTM2A-AS1-miR-139-5p and SNHG6/GSEC/SNHG1/SNHG14/LINC00265/MIR3142HG-miR-101-3p) and lung adenocarcinoma (TYMSOS/HELLPAR/SNHG1/GSEC/SNHG6-miR-101-3p). TOP2A expression was generally positively correlated with cancer associated fibroblasts, M0 and M1 macrophages in most cancer types. Furthermore, TOP2A was positively associated with expression of immune checkpoints (CD274, CTLA4, HAVCR2, LAG3, PDCD1 and TIGIT) in most cancer types. Our first TOP2A pan-cancer study contributes to understanding the prognostic roles, immunological roles and potential upstream molecular mechanism of TOP2A in different cancers.
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10
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Jiang Y, Han D, Zhao Y, Zhang C, Shi X, Gu W. Multi-Omics Analysis of the Prognosis and Biological Function for TRPV Channel Family in Clear Cell Renal Cell Carcinoma. Front Immunol 2022; 13:872170. [PMID: 35558077 PMCID: PMC9086597 DOI: 10.3389/fimmu.2022.872170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
Background The transient receptor potential vanilloid (TRPV) channels family, TRPV1-6, has been identified to profoundly affect a wide spectrum of pathological processes in various cancers. However, the biological function and prognostic value of TRPVs in clear cell renal cell carcinoma (ccRCC) are still largely unknown. Methods We obtained the gene expression data and clinical information of 539 ccRCC patients from The Cancer Genome Atlas (TCGA) database. A series of databases were used for data processing and visualization, including GEPIA, GeneMANIA, MethSurv, GSCA, TIMER, and starBase databases. Results The mRNA expression of TRPV2/3 was upregulated while the expression of TRPV5/6 was downregulated in ccRCC tumor tissues. TRPV family members in ccRCC were rarely mutated (nearly 7 frequencies). The ROC curve showed that TRPV2/5/6 had a high diagnostic ability in discriminating ccRCC from the control samples (AUC>0.9). Higher levels of TRPV3 expression were associated with poor prognosis of ccRCC patients, while higher expression of TRPV4 was associated with favorable prognosis. The expression of TRPV3 in normal and ccRCC tissues was validated by Immunohistochemistry, and its expression was remarkably related to high histologic grade and advanced stage. Besides, TRPV3 exhibit a reduction of DNA methylation level with tumor progression, and 12 CpGs of TRPV3 were associated with a significant prognosis. In addition, TRPV3 expression was significantly associated with the accumulation of several tumor-infiltrating immune cells, especially regulatory T cells. Furthermore, high levels of TRPV3 induced the expression of immune checkpoints such as LAG3, CTLA4, PDCD1, and TIGIT. Finally, we predicted a key SNHG3/AL513497.1-miR-10b-5p-TRPV3 axis linking to carcinogenesis and progression of ccRCC. Conclusion Our study may uncover TRPV channels–associated molecular mechanisms involved in the tumorigenesis and progression of ccRCC. TRPV family members might be diagnosed and prognostic markers and potential therapeutic targets for ccRCC patients.
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Affiliation(s)
- Yuxiong Jiang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Dongxu Han
- School of Medicine, Tongji University, Shanghai, China
| | - Yifan Zhao
- Department of Hematology, Mianyang Central Hospital, Mianyang, China
| | - Chen Zhang
- School of Medicine, Tongji University, Shanghai, China
| | - Xiujuan Shi
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
| | - Wenyu Gu
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,School of Medicine, Tongji University, Shanghai, China
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11
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Identification of m6A-Related lncRNA to Predict the Prognosis of Patients with Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4169150. [PMID: 35592519 PMCID: PMC9112178 DOI: 10.1155/2022/4169150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/16/2022] [Accepted: 04/01/2022] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. In the past decades, HCC treatment has achieved great progress; however, the overall prognosis remains poor. Therefore, it is the need of the hour to identify new prognostic biomarkers which can advance our understanding related to the underlying molecular mechanism of adverse prognosis and apply them to clinical work in prognosis prediction. In the present study, data of 576 HCC patients and 292 normal control cases from TCGA and ICGC databases were enrolled to our bioinformatic analysis. SNHG1 and SNHG3 were identified as overlapping genes in TCGA and ICGC databases using Pearson correlation analysis and univariate Cox regression analysis. Further, we used the median of the SNHG1 and SNHG3 expression values as the cutoff values to define the HCC patient groups with high or low expression level. The subsequent analysis revealed that abnormal high expression of SNHG1 or SNHG3 affected the immune infiltration patterns and the crosstalk among immune cells. Moreover, high expression of SNHG1 or SNHG3 resulted in drug resistant to AKT inhibitor VII, bexarotene, bicalutamide, dasatinib, erlotinib, and gefitinib. In addition, lower tumor neoantigen burden was observed in high SNHG1 or SNHG3 group. Further, we found significant relation between the aberrant upregulation of SNHG1 and SNHG3 in tumor grade and stage. We established a nomogram to systematically predict the 5- and 8-year overall survival of liver cancer patients with good accuracy. Finally, the in vitro assays suggest that SNHG1 and SNHG3 promote the proliferative, migratory, and invasive abilities of HCC cells.
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12
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Shan DD, Zheng QX, Wang J, Chen Z. Small nucleolar RNA host gene 3 functions as a novel biomarker in liver cancer and other tumour progression. World J Gastroenterol 2022; 28:1641-1655. [PMID: 35581965 PMCID: PMC9048787 DOI: 10.3748/wjg.v28.i16.1641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/09/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023] Open
Abstract
Cancer has become the most life-threatening disease in the world. Mutations in and aberrant expression of genes encoding proteins and mutations in noncoding RNAs, especially long noncoding RNAs (lncRNAs), have significant effects in human cancers. LncRNAs have no protein-coding ability but function extensively in numerous physiological and pathological processes. Small nucleolar RNA host gene 3 (SNHG3) is a novel lncRNA and has been reported to be differentially expressed in various tumors, such as liver cancer, gastric cancer, and glioma. However, the interaction mechanisms for the regulation between SNHG3 and tumor progression are poorly understood. In this review, we summarize the results of SNHG3 studies in humans, animal models, and cells to underline the expression and role of SNHG3 in cancer. SNHG3 expression is upregulated in most tumors and is detrimental to patient prognosis. SNHG3 expression in lung adenocarcinoma remains controversial. Concurrently, SNHG3 affects oncogenes and tumor suppressor genes through various mechanisms, including competing endogenous RNA effects. A deeper understanding of the contribution of SNHG3 in clinical applications and tumor development may provide a new target for cancer diagnosis and treatment.
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Affiliation(s)
- Dan-Dan Shan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China
| | - Qiu-Xian Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China
| | - Jing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China
| | - Zhi Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China
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13
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Abedi Kichi Z, Soltani M, Rezaei M, Shirvani-Farsani Z, Rojhannezhad M. The Emerging role of EMT-related lncRNAs in therapy resistance and their application as biomarkers. Curr Med Chem 2022; 29:4574-4601. [PMID: 35352644 DOI: 10.2174/0929867329666220329203032] [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: 12/02/2021] [Revised: 01/15/2022] [Accepted: 01/19/2022] [Indexed: 12/09/2022]
Abstract
Cancer is the world's second largest cause of death. The most common cancer treatments are surgery, radiation therapy, and chemotherapy. Drug resistance, epithelial-to-mesenchymal transition (EMT), and metastasis are all pressing issues in cancer therapy today. Increasing evidence showed that drug-resistant and EMT are co-related with each other. Indeed, drug-resistant cancer cells possess enhanced EMT and invasive ability. Recent researches have demonstrated lncRNAs (long noncoding RNAs) are noncoding transcripts, which play an important role in the regulation of EMT, metastasis, and drug resistance in different cancers. However, the relationships among lncRNAs, EMT, and drug resistance are still unclear. These effects could be exerted via several signaling pathways such as TGF-β, PI3K-AKT, and Wnt/β-catenin. Identifying the crucial regulatory roles of lncRNAs in these pathways and processes leads to the development of novel targeted therapies. We review the key aspects of lncRNAs associated with EMT and therapy resistance. We focus on the crosstalk between lncRNAs and molecular signaling pathways affecting EMT and drug resistance. Moreover, each of the mentioned lncRNAs could be used as a potential diagnostic, prognostic, and therapeutic biomarker for cancer. Although, there are still many challenges to investigate lncRNAs for clinical applications.
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Affiliation(s)
- Zahra Abedi Kichi
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Germany
| | - Mona Soltani
- Department of Plant Production & Genetics, Faculty of Agriculture, Zanjan University, Zanjan, Iran
| | - Mina Rezaei
- Department of Cell and Molecular Biology, Faculty of life Sciences and Technology, Shahid Beheshti University, Tehran, IR Iran
| | - Zeinab Shirvani-Farsani
- Department of Cell and Molecular Biology, Faculty of life Sciences and Technology, Shahid Beheshti University, Tehran, IR Iran
| | - Mahbubeh Rojhannezhad
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, IR Iran
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14
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Li F, Lai L, You Z, Cheng H, Guo G, Tang C, Xu L, Liu H, Zhong W, Lin Y, Wang Q, Lin Y, Wei Y. Identification of UBE2I as a Novel Biomarker in ccRCC Based on a Large-Scale CRISPR-Cas9 Screening Database and Immunohistochemistry. Front Mol Biosci 2022; 9:813428. [PMID: 35211510 PMCID: PMC8861443 DOI: 10.3389/fmolb.2022.813428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Background: The genome-wide CRISPR-cas9 dropout screening has emerged as an outstanding approach for characterization of driver genes of tumor growth. The present study aims to investigate core genes related to clear cell renal cell carcinoma (ccRCC) cell viability by analyzing the CRISPR-cas9 screening database DepMap, which may provide a novel target in ccRCC therapy. Methods: Candidate genes related to ccRCC cell viability by CRISPR-cas9 screening from DepMap and genes differentially expressed between ccRCC tissues and normal tissues from TCGA were overlapped. Weighted gene coexpression network analysis, pathway enrichment analysis, and protein–protein interaction network analysis were applied for the overlapped genes. The least absolute shrinkage and selection operator (LASSO) regression was used to construct a signature to predict the overall survival (OS) of ccRCC patients and validated in the International Cancer Genome Consortium (ICGC) and E-MTAB-1980 database. Core protein expression was determined using immunohistochemistry in 40 cases of ccRCC patients. Results: A total of 485 essential genes in the DepMap database were identified and overlapped with differentially expressed genes in the TCGA database, which were enriched in the cell cycle pathway. A total of four genes, including UBE2I, NCAPG, NUP93, and TOP2A, were included in the gene signature based on LASSO regression. The high-risk score of ccRCC patients showed worse OS compared with these low-risk patients in the ICGC and E-MTAB-1980 validation cohort. UBE2I was screened out as a key gene. The immunohistochemistry indicated UBE2I protein was highly expressed in ccRCC tissues, and a high-level nuclear translocation of UBE2I occurs in ccRCC. Based on the area under the curve (AUC) values, nuclear UBE2I had the best diagnostic power (AUC = 1). Meanwhile, the knockdown of UBE2I can inhibit the proliferation of ccRCC cells. Conclusion: UBE2I, identified by CRISPR-cas9 screening, was a core gene-regulating ccRCC cell viability, which accumulated in the nucleus and acted as a potential novel promising diagnostic biomarker for ccRCC patients. Blocking the nuclear translocation of UBE2I may have potential therapeutic value with ccRCC patients.
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Affiliation(s)
- Feng Li
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of Pathology, Fujian Provincial Hospital, Fuzhou, China
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- *Correspondence: Feng Li, ; Qingshui Wang, ; Yao Lin, ; Yongbao Wei,
| | - Li Lai
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- Central Laboratory, Fujian Provincial Hospital, Fuzhou, China
| | - Zhijie You
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of Pathology, Fujian Provincial Hospital, Fuzhou, China
| | - Hui Cheng
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of Pathology, Fujian Provincial Hospital, Fuzhou, China
| | - Guodong Guo
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of Pathology, Fujian Provincial Hospital, Fuzhou, China
| | - Chenchen Tang
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Luyun Xu
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Hongxia Liu
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Wenting Zhong
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Youyu Lin
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qingshui Wang
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
- Fujian Provincial Key Laboratory of Hepatic Drug Research, Fuzhou, China
- *Correspondence: Feng Li, ; Qingshui Wang, ; Yao Lin, ; Yongbao Wei,
| | - Yao Lin
- Key Laboratory of Optoelectronic Science and Technology for Medicine of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
- Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- *Correspondence: Feng Li, ; Qingshui Wang, ; Yao Lin, ; Yongbao Wei,
| | - Yongbao Wei
- Shengli Clinical Medical College, Fujian Medical University, Fuzhou, China
- Department of Urology, Fujian Provincial Hospital, Fuzhou, China
- *Correspondence: Feng Li, ; Qingshui Wang, ; Yao Lin, ; Yongbao Wei,
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Wang D, Zou L, Luo J, Zhang C, Feng H, Qin G. Potential diagnostic and prognostic value of the long non-coding RNA SNHG3 in human cancers: A systematic review and meta-analysis. Int J Biol Markers 2022; 37:3-12. [PMID: 35130083 DOI: 10.1177/03936155221077121] [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] [Indexed: 12/24/2022]
Abstract
BACKGROUND Small nucleolar RNA host gene 3 (SNHG3), as a novel long non-coding RNA (lncRNA) participates in the oncogenic processes of various cancers. We combined a systematic review and a meta-analysis to assess the potential role of SNHG3 as a pan-cancer marker for cancer diagnosis and prognosis. METHODS Our study comprehensively searched for SNHG3 expression profiling studies from PubMed, Web of Science, Excerpta Medica Database (EMBASE), Cochrane Library, Google Scholar, and The Cancer Genome Atlas (TCGA). The diagnostic capacity of SNHG3 for all cancers in TCGA database was evaluated from the perspective of pooled sensitivity, specificity, diagnostic odds ratio (DOR), area under the curve (AUC) of the summary receiver operating characteristic (sROC) curve. Also, this research studied the correlation of SNHG3 expression and the overall survival to access its prognostic value. RESULTS A sum total of 11,888 cancer patients and 730 controls from 44 eligible studies were enrolled in this integrated analysis. In TCGA database, SNHG3 was significantly upregulated in most types of cancers (16/33, 48%). The pooled sensitivity, specificity, and DOR with 95% CIs was 0.72 (95% CI: 0.60-0.82), 0.87 (95% CI: 0.84-0.90), and 18 (95% CI: 11-30), respectively. Similarly, the AUC of the sROC curve was 0.89 (95% CI: 0.86-0.92), indicating SNHG3 was highly conserved as a diagnosis biomarker. Additionally, SNHG3 overexpression significantly deteriorated the overall survival of cancer patients (pooled HR = 1.28, 95% CI:1.11-1.48; P < 0.05). CONCLUSIONS These findings suggest that the lncRNA SNHG3 could serve as a promising diagnostic and prognostic biomarker.
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Affiliation(s)
- Dingting Wang
- Department of Otolaryngology Head and Neck Surgery, 556508Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Longfei Zou
- Department of Orthopedic Surgery, 556508Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jian Luo
- Department of Otolaryngology Head and Neck Surgery, The First People's Hospital of Yibin, Yibin, China
| | - Conghong Zhang
- Department of Otolaryngology Head and Neck Surgery, Sichuan Province Panzhihua Central Hospital, Panzhihua, China * These authors contributed equally to this work
| | - Huajun Feng
- Department of Otolaryngology Head and Neck Surgery, 556508Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Gang Qin
- Department of Otolaryngology Head and Neck Surgery, 556508Affiliated Hospital of Southwest Medical University, Luzhou, China
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A diagnostic and prognostic value of blood-based circulating long non-coding RNAs in Thyroid, Pancreatic and Ovarian Cancer. Crit Rev Oncol Hematol 2022; 171:103598. [PMID: 35033662 DOI: 10.1016/j.critrevonc.2022.103598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/12/2022] Open
Abstract
Several studies have demonstrated the potential of circulating long non-coding RNAs (lncRNAs) as promising cancer biomarkers. Herein, we addressed the regulatory role of circulating lncRNAs and their potential value as diagnostic/prognostic markers for thyroid, pancreatic and ovarian cancers. Furthermore, we analyzed and measured the clinical implications and association of lncRNAs with sensitivity, specificity, and area under the ROC curve (AUC). Based on our meta-analysis, we found that GAS8-AS1 could discriminate thyroid cancer from non-cancer and other cancers with higher accuracy (AUC = 0.746; sensitivity = 61.70%, and specificity = 90.00%). Similarly, for ovarian cancer, lncRNA RP5-837J1.2 was found to have ideal diagnostic potential with critical clinical specifications of AUC = 0.996; sensitivity = 97.30% and specificity = 94.60%. Whereas we could not find any lncRNA having high diagnostic/prognostic efficiency in pancreatic cancer. We believe that lncRNAs mentioned above may explore clinical settings for the diagnosis and prognosis of cancer patients.
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Popławski P, Bogusławska J, Hanusek K, Piekiełko-Witkowska A. Nucleolar Proteins and Non-Coding RNAs: Roles in Renal Cancer. Int J Mol Sci 2021; 22:ijms222313126. [PMID: 34884928 PMCID: PMC8658237 DOI: 10.3390/ijms222313126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Renal cell cancer is the most frequent kidney malignancy. Most RCC cases are classified as clear cell renal cell carcinoma (ccRCC), characterized by high aggressiveness and poor prognosis for patients. ccRCC aggressiveness is defined by classification systems based on changes in morphology of nucleoli, the membraneless substructures of nuclei. The latter act as the sites of ribosome biogenesis as well as the hubs that trap and immobilize proteins, preventing their action in other cellular compartments. Thereby, nucleoli control cellular functioning and homeostasis. Nucleoli are also the sites of activity of multiple noncoding RNAs, including snoRNAs, IGS RNA, and miRNAs. Recent years have brought several remarkable discoveries regarding the role of nucleolar non-coding RNAs, in particular snoRNAs, in ccRCC. The expression of snoRNAs is largely dysregulated in ccRCC tumors. snoRNAs, such as SNHG1, SNHG4 and SNHG12, act as miRNA sponges, leading to aberrant expression of oncogenes and tumor suppressors, and directly contributing to ccRCC development and progression. snoRNAs can also act without affecting miRNA functioning, by altering the expression of key oncogenic proteins such as HIF1A. snoRNAs are also potentially useful biomarkers of ccRCC progression. Here, we comprehensively discuss the role of nucleolar proteins and non-coding RNAs in ccRCC.
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LncRNAs in the Regulation of Genes and Signaling Pathways through miRNA-Mediated and Other Mechanisms in Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2021; 22:ijms222011193. [PMID: 34681854 PMCID: PMC8539140 DOI: 10.3390/ijms222011193] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
The fundamental novelty in the pathogenesis of renal cell carcinoma (RCC) was discovered as a result of the recent identification of the role of long non-coding RNAs (lncRNAs). Here, we discuss several mechanisms for the dysregulation of the expression of protein-coding genes initiated by lncRNAs in the most common and aggressive type of kidney cancer-clear cell RCC (ccRCC). A model of competitive endogenous RNA (ceRNA) is considered, in which lncRNA acts on genes through the lncRNA/miRNA/mRNA axis. For the most studied oncogenic lncRNAs, such as HOTAIR, MALAT1, and TUG1, several regulatory axes were identified in ccRCC, demonstrating a number of sites for various miRNAs. Interestingly, the LINC00973/miR-7109/Siglec-15 axis represents a novel agent that can suppress the immune response in patients with ccRCC, serving as a valuable target in addition to the PD1/PD-L1 pathway. Other mechanisms of action of lncRNAs in ccRCC, involving direct binding with proteins, mRNAs, and genes/DNA, are also considered. Our review briefly highlights methods by which various mechanisms of action of lncRNAs were verified. We pay special attention to protein targets and signaling pathways with which lncRNAs are associated in ccRCC. Thus, these new data on the different mechanisms of lncRNA functioning provide a novel basis for understanding the pathogenesis of ccRCC and the identification of new prognostic markers and targets for therapy.
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Deng R, Li J, Zhao H, Zou Z, Man J, Cao J, Yang L. Identification of potential biomarkers associated with immune infiltration in papillary renal cell carcinoma. J Clin Lab Anal 2021; 35:e24022. [PMID: 34606125 PMCID: PMC8605132 DOI: 10.1002/jcla.24022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/06/2021] [Accepted: 09/12/2021] [Indexed: 12/27/2022] Open
Abstract
Background Immunotherapeutic approaches have recently emerged as effective treatment regimens against various types of cancer. However, the immune‐mediated mechanisms surrounding papillary renal cell carcinoma (pRCC) remain unclear. This study aimed to investigate the tumor microenvironment (TME) and identify the potential immune‐related biomarkers for pRCC. Methods The CIBERSORT algorithm was used to calculate the abundance ratio of immune cells in each pRCC samples. Univariate Cox analysis was used to select the prognostic‐related tumor‐infiltrating immune cells (TIICs). Multivariate Cox regression analysis was performed to develop a signature based on the selected prognostic‐related TIICs. Then, these pRCC samples were divided into low‐ and high‐risk groups according to the obtained signature. Analyses using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were performed to investigate the biological function of the DEGs (differentially expressed genes) between the high‐ and low‐risk groups. The hub genes were identified using a weighted gene co‐expression network analysis (WGCNA) and a protein‐protein interaction (PPI) analysis. The hub genes were subsequently validated by multiple clinical traits and databases. Results According to our analyses, nine immune cells play a vital role in the TME of pRCC. Our analyses also obtained nine potential immune‐related biomarkers for pRCC, including TOP2A, BUB1B, BUB1, TPX2, PBK, CEP55, ASPM, RRM2, and CENPF. Conclusion In this study, our data revealed the crucial TIICs and potential immune‐related biomarkers for pRCC and provided compelling insights into the pathogenesis and potential therapeutic targets for pRCC.
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Affiliation(s)
- Ran Deng
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-urology, Lanzhou, China
| | - Jianpeng Li
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-urology, Lanzhou, China
| | - Hong Zhao
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-urology, Lanzhou, China
| | - Zhirui Zou
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-urology, Lanzhou, China
| | - Jiangwei Man
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-urology, Lanzhou, China
| | - Jinlong Cao
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-urology, Lanzhou, China
| | - Li Yang
- Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.,Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.,Clinical Center of Gansu Province for Nephron-urology, Lanzhou, China
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20
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Xu Z, Ye J, Bao P, Wu Q, Xie F, Li P. Long non-coding RNA SNHG3 promotes the progression of clear cell renal cell carcinoma via regulating BIRC5 expression. Transl Cancer Res 2021; 10:4502-4513. [PMID: 35116306 PMCID: PMC8798718 DOI: 10.21037/tcr-21-1802] [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: 08/17/2021] [Accepted: 09/29/2021] [Indexed: 01/02/2023]
Abstract
Background Research has shown that the progression of clear cell renal cell carcinoma (ccRCC) is modulated by long non-coding RNAs (lncRNAs). However, the roles of specific lncRNAs in the malignancy of ccRCC are still unknown. Methods TCGA and GSE66272 datasets were used to predict differentially expressed genes (DEGs) in ccRCC. ENCORI database was employed to display BIRC5 miRNA network and potential lncRNA interactions for miRNAs. KM plotter and correlation analyses were performed to identify the overall survival (OS)- and BIRC5-related miRNAs. Quantitative real-time PCR (qRT-PCR) was used to verify the BIRC5 mRNA in the seventy paired clinical samples of ccRCC tissues. The ccRCC A498 and 786-O were individually transfected with lncRNA SNHG3 and LINC00997 and then western blotting was used to detect the BIRC5 protein expression. The Dual-luciferase reporter assay was used to examine the regulatory interaction between lncRNA SNHG3 and microRNA (miRNA/miR)-10b-5p. Results BICR5 is associated with the progression of ccRCC. The two novel lncRNAs (LINC00997, SNHG3) were up-regulated in ccRCC tissues and positively with the BICR5 protein expression. However, Suppressing SNHG3 expression reduced BIRC5 protein expression compared with the LINC00997, most importantly, Suppressing SNHG3 expression suppressed tumor progression in vitro. In addition, SNHG3 promotes the expression of BIRC5 protein by sponging microRNA-10b-5p. Conclusions Our findings suggest that SNHG3 plays a vital role in promoting ccRCC via the microRNA-10b-5p/BIRC5 axis and may serve as a novel therapeutic target for the treatment of patients with ccRCC.
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Affiliation(s)
- Zhaoyu Xu
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Junjie Ye
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Pengfei Bao
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Qi Wu
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Fuchen Xie
- Department of Urology, Lishui People's Hospital, Lishui, China
| | - Peng Li
- Department of Urology, Lishui People's Hospital, Lishui, China
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21
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Tian X, Shen L, Wang Z, Zhou L, Peng L. A novel lncRNA-protein interaction prediction method based on deep forest with cascade forest structure. Sci Rep 2021; 11:18881. [PMID: 34556758 PMCID: PMC8460650 DOI: 10.1038/s41598-021-98277-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate many biological processes by interacting with corresponding RNA-binding proteins. The identification of lncRNA-protein Interactions (LPIs) is significantly important to well characterize the biological functions and mechanisms of lncRNAs. Existing computational methods have been effectively applied to LPI prediction. However, the majority of them were evaluated only on one LPI dataset, thereby resulting in prediction bias. More importantly, part of models did not discover possible LPIs for new lncRNAs (or proteins). In addition, the prediction performance remains limited. To solve with the above problems, in this study, we develop a Deep Forest-based LPI prediction method (LPIDF). First, five LPI datasets are obtained and the corresponding sequence information of lncRNAs and proteins are collected. Second, features of lncRNAs and proteins are constructed based on four-nucleotide composition and BioSeq2vec with encoder-decoder structure, respectively. Finally, a deep forest model with cascade forest structure is developed to find new LPIs. We compare LPIDF with four classical association prediction models based on three fivefold cross validations on lncRNAs, proteins, and LPIs. LPIDF obtains better average AUCs of 0.9012, 0.6937 and 0.9457, and the best average AUPRs of 0.9022, 0.6860, and 0.9382, respectively, for the three CVs, significantly outperforming other methods. The results show that the lncRNA FTX may interact with the protein P35637 and needs further validation.
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Affiliation(s)
- Xiongfei Tian
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China
| | - Ling Shen
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China
| | - Zhenwu Wang
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China.
| | - Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China.
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22
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Zhou X, Dou M, Liu Z, Jiao D, Li Z, Chen J, Li J, Yao Y, Li L, Li Y, Han X. Screening Prognosis-Related lncRNAs Based on WGCNA to Establish a New Risk Score for Predicting Prognosis in Patients with Hepatocellular Carcinoma. J Immunol Res 2021; 2021:5518908. [PMID: 34426790 PMCID: PMC8380184 DOI: 10.1155/2021/5518908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) remains an important cause of cancer death. The molecular mechanism of hepatocarcinogenesis and prognostic factors of HCC have not been completely uncovered. METHODS In this study, we screened out differentially expressed lncRNAs (DE lncRNAs), miRNAs (DE miRNAs), and mRNAs (DE mRNAs) by comparing the gene expression of HCC and normal tissue in The Cancer Genome Atlas (TCGA) database. DE mRNAs were used to perform Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Then, the miRNA and lncRNA/mRNA modules that were most closely related to the survival time of patients with HCC were screened to construct a competitive endogenous RNA (ceRNA) network by weighted gene coexpression network analysis (WGCNA). Moreover, univariable Cox regression and Kaplan-Meier curve analyses of DE lncRNAs and DE mRNAs were conducted. Finally, the lasso-penalized Cox regression analysis and nomogram model were used to establish a new risk scoring system and predict the prognosis of patients with liver cancer. The expression of survival-related DE lncRNAs was verified by qRT-PCR. RESULTS A total of 1896 DEmRNAs, 330 DElncRNAs, and 76 DEmiRNAs were identified in HCC and normal tissue samples. Then, the turquoise miRNA and turquoise lncRNA/mRNA modules that were most closely related to the survival time of patients with HCC were screened to construct a ceRNA network by WGCNA. In this ceRNA network, there were 566 lncRNA-miRNA-mRNA regulatory pairs, including 30 upregulated lncRNAs, 16 downregulated miRNAs, and 75 upregulated mRNAs. Moreover, we screened out 19 lncRNAs and 14 hub mRNAs related to prognosis from this ceRNA network by univariable Cox regression and Kaplan-Meier curve analyses. Finally, a new risk scoring system was established by selecting the optimal risk lncRNAs from the 19 prognosis-related lncRNAs through lasso-penalized Cox regression analysis. In addition, we established a nomogram model consisting of independent prognostic factors to predict the survival rate of HCC patients. Finally, the correlation between the risk score and immune cell infiltration and gene set enrichment analysis were determined. CONCLUSIONS In conclusion, the results may provide potential biomarkers or therapeutic targets for HCC and the establishment of the new risk scoring system and nomogram model provides the new perspective for predicting the prognosis of HCC.
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Affiliation(s)
- Xueliang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengmeng Dou
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dechao Jiao
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhaonan Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianjian Chen
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuan Yao
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lifeng Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yahua Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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23
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Overexpression of lncRNA SNGH3 Predicts Unfavorable Prognosis and Clinical Outcomes in Human Cancers: Evidence from a Meta-Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2020:7974034. [PMID: 32802874 PMCID: PMC7335396 DOI: 10.1155/2020/7974034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/23/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to play a crucial role in human disease, especially in tumor development and progression. Small nucleolar RNA host gene (SNHG3), a newly identified lncRNA, has been found dysregulated in various cancers. Nevertheless, the results remain controversial. Thus, we aim to analyze the comprehensive data to elaborate the association between SNHG3 expression and clinical outcomes in multiple cancers. We searched PubMed, Web of Science, Cochrane Library, Embase, and MEDLINE database to identify eligible articles. STATA software was applied to calculate the hazard ratio (HR) and odds ratio (OR) with 95% confidence interval (95% CI) for survival outcomes and clinical parameters, respectively. Besides, the data from The Cancer Genome Atlas (TCGA) dataset was extracted to verify the results in our meta-analysis. There were thirteen studies totaling 919 cancer patients involved in this meta-analysis. The results demonstrated that high SNHG3 expression was significantly associated with poor overall survival (OS) (HR = 2.53, 95% CI: 1.94-3.31) in cancers, disease-free survival (DFS) (HR = 3.89, 95% CI: 1.34-11.3), and recurrence-free survival (RFS) (HR = 2.42, 95% CI: 1.14-5.15) in hepatocellular carcinoma. Analysis stratified by analysis method, sample size, follow-up time, and cancer type further verified the prognostic value of SNHG3. Additionally, patients with high SNHG3 expression tended to have more advanced clinical stage, higher histological grade, earlier distant metastasis, and earlier lymph node metastasis. Excavation of TCGA dataset valuated that SNHG3 was upregulated in various cancers and predicted worse OS and DFS. Overexpressed SNHG3 was strongly associated with poor survival and clinical outcomes in human cancers and therefore can serve as a promising biomarker for predicting patients' prognosis.
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24
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Yang Z, Li Q, Zheng X, Xie L. Long Noncoding RNA Small Nucleolar Host Gene: A Potential Therapeutic Target in Urological Cancers. Front Oncol 2021; 11:638721. [PMID: 33968736 PMCID: PMC8100577 DOI: 10.3389/fonc.2021.638721] [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: 12/07/2020] [Accepted: 03/31/2021] [Indexed: 12/12/2022] Open
Abstract
The incidence of urological cancer has been gradually increasing in the last few decades. However, current diagnostic tools and treatment strategies continue to have limitations. Substantial evidence shows that long noncoding RNAs (lncRNAs) play essential roles in carcinogenesis and the progression, treatment response and prognosis of multiple human cancers, including urological cancers, gastrointestinal tumours, reproductive cancers and respiratory neoplasms. LncRNA small nucleolar RNA host genes (SNHGs), a subgroup of lncRNAs, have been found to be dysregulated in tumour cell biology. In this review, we summarize the impacts of lncRNA SNHGs in urological malignancies and the underlying mechanisms.
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Affiliation(s)
- Zitong Yang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qinchen Li
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangyi Zheng
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liping Xie
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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25
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Zhan C, Wang Z, Xu C, Huang X, Su J, Chen B, Wang M, Qi Z, Bai P. Development and Validation of a Prognostic Gene Signature in Clear Cell Renal Cell Carcinoma. Front Mol Biosci 2021; 8:609865. [PMID: 33968978 PMCID: PMC8098777 DOI: 10.3389/fmolb.2021.609865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC), one of the most common urologic cancer types, has a relatively good prognosis. However, clinical diagnoses are mostly done during the medium or late stages, when mortality and recurrence rates are quite high. Therefore, it is important to perform real-time information tracking and dynamic prognosis analysis for these patients. We downloaded the RNA-seq data and corresponding clinical information of ccRCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A total of 3,238 differentially expressed genes were identified between normal and ccRCC tissues. Through a series of Weighted Gene Co-expression Network, overall survival, immunohistochemical and the least absolute shrinkage selection operator (LASSO) analyses, seven prognosis-associated genes (AURKB, FOXM1, PTTG1, TOP2A, TACC3, CCNA2, and MELK) were screened. Their risk score signature was then constructed. Survival analysis showed that high-risk scores exhibited significantly worse overall survival outcomes than low-risk patients. Accuracy of this prognostic signature was confirmed by the receiver operating characteristic curve and was further validated using another cohort. Gene set enrichment analysis showed that some cancer-associated phenotypes were significantly prevalent in the high-risk group. Overall, these findings prove that this risk model can potentially improve individualized diagnostic and therapeutic strategies.
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Affiliation(s)
| | - Zichu Wang
- Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Chao Xu
- Shaoxing people's Hospital, Shaoxing, China
| | - Xiao Huang
- Nanchang Five Elements Bio-Technology Co., Ltd, Nanchang, China
| | - Junzhou Su
- Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Bisheng Chen
- Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Mingshan Wang
- Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Zhihong Qi
- Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Peiming Bai
- Zhongshan Hospital, Xiamen University, Xiamen, China
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26
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Du Y, Yang H, Li Y, Guo W, Zhang Y, Shen H, Xing L, Li Y, Wu W, Zhang X. Long non-coding RNA LINC01137 contributes to oral squamous cell carcinoma development and is negatively regulated by miR-22-3p. Cell Oncol (Dordr) 2021; 44:595-609. [PMID: 33797737 DOI: 10.1007/s13402-021-00586-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 01/02/2021] [Accepted: 01/05/2021] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Long noncoding RNAs (lncRNAs) are emerging as key regulators in cancer initiation and progression. LINC01137 is a recently identified lncRNA of which the functional role in the development of oral squamous cell carcinoma (OSCC) has not been determined yet. METHODS We analyzed the expression of LINC01137 using a microarray-based OSCC gene expression dataset (GSE31056), and validated the results obtained using RT-qPCR in 26 pairs of primary OSCC tumor tissues and adjacent non-tumor tissues. The proliferative and invasive effects of LINC01137 on OSCC cells were determined using CCK-8, colony formation and transwell assays, respectively. Targeted binding between miR-22-3p and LINC01137 was verified using a dual luciferase reporter assay. RESULTS We found that LINC01137 was significantly upregulated in primary OSCCs. LINC01137 knockdown inhibited OSCC cell proliferation, migration and invasion, whereas LINC01137 overexpression induced opposite effects. LINC01137 upregulation along with p53 inhibition enhanced the malignant transformation of oral cells. In addition, we found that miR-22-3p can directly target LINC01137 through interaction with a putative miR-22-3p-binding site present within the LINC01137 sequence. A significant negative correlation was observed between LINC01137 and miR-22-3p expression in primary OSCC specimens. Exogenous overexpression of miR-22-3p markedly reduced the endogenous expression level of LINC01137 in OSCC cells. Additional functional assays showed that miR-22-3p overexpression enhanced the inhibitory effect of siRNA-mediated LINC01137 silencing on OSCC cell proliferation, migration and invasion, whereas miR-22-3p inhibition had the opposite effect. CONCLUSIONS Our results indicate that LINC01137 functions as an oncogenic lncRNA in OSCC. miR-22-3p can directly target LINC01137 and negatively regulate its expression and function.
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Affiliation(s)
- Yong Du
- Department of Stomatology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Haiyan Yang
- Laboratory of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Yue Li
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Department of Pathology, The Fourth Hospital of Shijiazhuang, Shijiazhuang, China
| | - Wenli Guo
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yufeng Zhang
- Department of Radiotherapy, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Haitao Shen
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Lingxiao Xing
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yuehong Li
- Laboratory of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Wenxin Wu
- Laboratory of Pathology, Hebei Medical University, Shijiazhuang, China
| | - Xianghong Zhang
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
- Laboratory of Pathology, Hebei Medical University, Shijiazhuang, China.
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27
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Yu L, Ren Y. Long Noncoding RNA Small Nucleolar RNA Host Gene 3 Mediates Prostate Cancer Migration, Invasion, and Epithelial-Mesenchymal Transition by Sponging miR-487a-3p to Regulate TRIM25. Cancer Biother Radiopharm 2021; 37:451-465. [PMID: 33416420 DOI: 10.1089/cbr.2020.3988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background: Long noncoding RNA small nucleolar RNA host gene 3 (SNHG3) is related to the proliferation and metastasis of cancer cells. This study aims to reveal the role of SNHG3 in prostate cancer (PCa), which may help prevent PCa metastasis. Methods: SNHG3 plasmid, SNHG3 siRNA, miR-487a-3p mimic, miR-487a-3p inhibitor, TRIM25 plasmid, and TRIM25 siRNA were transfected or cotransfected into LNCaP and PC-3 cells. The proliferation, migration, and invasion of PCa cells were measured by Cell Counting Kit-8, wound-healing, and transwell assays, respectively. The expressions of SNHG3, miR-487a-3p, E-cadherin, N-cadherin, Snail, and TRIM25 in PCa tissues and cells were measured by quantitative reverse transcription polymerase chain reaction or western blot. Results: SNHG3 expression level was upregulated in PCa tissues and cells. SNHG3 overexpression and miR-487a-3p inhibitor promoted cell viability, migration, invasion, and N-cadherin and Snail levels, and inhibited E-cadherin level in LNCaP cells, while SNHG3 silencing and miR-487a-3p mimic had the opposite effects on PC-3 cells. The inhibitory effect of miR-487a-3p mimic on the migration, invasion, and epithelial-mesenchymal transition (EMT) of LNCaP cells was inversed by both SNHG3 and TRIM25 plasmids. Similarly, the function of miR-487a-3p inhibitor in PC-3 cells was also inversed by SNHG3 siRNA and TRIM25 siRNA. Conclusion: SNHG3 mediates PCa migration, invasion, and EMT by sponging miR-487a-3p to regulate TRIM25. The Clinical Trial Registration number: Y20180831.
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Affiliation(s)
- Lihang Yu
- Department of Urology, Shaoxing People's Hospital, Shaoxing, China
| | - Yu Ren
- Department of Urology, Shaoxing People's Hospital, Shaoxing, China
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28
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Xu B, Mei J, Ji W, Bian Z, Jiao J, Sun J, Shao J. LncRNA SNHG3, a potential oncogene in human cancers. Cancer Cell Int 2020; 20:536. [PMID: 33292213 PMCID: PMC7640707 DOI: 10.1186/s12935-020-01608-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are composed of > 200 nucleotides; they lack the ability to encode proteins but play important roles in a variety of human tumors. A large number of studies have shown that dysregulated expression of lncRNAs is related to tumor oncogenesis and progression. Emerging evidence shows that SNHG3 is a novel oncogenic lncRNA that is abnormally expressed in various tumors, including osteosarcoma, liver cancer, lung cancer, etc. SNHG3 primarily competes as a competitive endogenous RNA (ceRNA) that targets tumor suppressor microRNAs (miRNAs) and ceRNA mechanisms that regulate biological processes of tumors. In addition, abnormal expression of SNHG3 is significantly correlated with patient clinical features. Upregulation of SNHG3 contributes to biological functions, including tumor cell proliferation, migration, invasion and EMT. Therefore, SNHG3 may represent a potential diagnostic and prognostic biomarker, as well as a novel therapeutic target.
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Affiliation(s)
- Bin Xu
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jie Mei
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, P. R. China
| | - Wei Ji
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Zheng Bian
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jiantong Jiao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China
| | - Jun Sun
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China.
| | - Junfei Shao
- Department of Neurosurgery, Wuxi People's Hospital Affiliated to Nanjing Medical University, No. 299 Qing Yang Road, Wuxi, 214023, Jiangsu, China.
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29
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Dolicka D, Sobolewski C, Gjorgjieva M, Correia de Sousa M, Berthou F, De Vito C, Colin DJ, Bejuy O, Fournier M, Maeder C, Blackshear PJ, Rubbia-Brandt L, Foti M. Tristetraprolin Promotes Hepatic Inflammation and Tumor Initiation but Restrains Cancer Progression to Malignancy. Cell Mol Gastroenterol Hepatol 2020; 11:597-621. [PMID: 32987153 PMCID: PMC7806869 DOI: 10.1016/j.jcmgh.2020.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Tristetraprolin (TTP) is a key post-transcriptional regulator of inflammatory and oncogenic transcripts. Accordingly, TTP was reported to act as a tumor suppressor in specific cancers. Herein, we investigated how TTP contributes to the development of liver inflammation and fibrosis, which are key drivers of hepatocarcinogenesis, as well as to the onset and progression of hepatocellular carcinoma (HCC). METHODS TTP expression was investigated in mouse/human models of hepatic metabolic diseases and cancer. The role of TTP in nonalcoholic steatohepatitis and HCC development was further examined through in vivo/vitro approaches using liver-specific TTP knockout mice and a panel of hepatic cancer cells. RESULTS Our data demonstrate that TTP loss in vivo strongly restrains development of hepatic steatosis and inflammation/fibrosis in mice fed a methionine/choline-deficient diet, as well as HCC development induced by the carcinogen diethylnitrosamine. In contrast, low TTP expression fostered migration and invasion capacities of in vitro transformed hepatic cancer cells likely by unleashing expression of key oncogenes previously associated with these cancerous features. Consistent with these data, TTP was significantly down-regulated in high-grade human HCC, a feature further correlating with poor clinical prognosis. Finally, we uncover hepatocyte nuclear factor 4 alpha and early growth response 1, two key transcription factors lost with hepatocyte dedifferentiation, as key regulators of TTP expression. CONCLUSIONS Although TTP importantly contributes to hepatic inflammation and cancer initiation, its loss with hepatocyte dedifferentiation fosters cancer cells migration and invasion. Loss of TTP may represent a clinically relevant biomarker of high-grade HCC associated with poor prognosis.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/immunology
- Carcinogenesis/pathology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Datasets as Topic
- Diethylnitrosamine/administration & dosage
- Diethylnitrosamine/toxicity
- Down-Regulation
- Female
- Gene Expression Regulation, Neoplastic/immunology
- Hepatocytes
- Humans
- Liver/immunology
- Liver/pathology
- Liver Cirrhosis/genetics
- Liver Cirrhosis/immunology
- Liver Cirrhosis/pathology
- Liver Neoplasms/genetics
- Liver Neoplasms/immunology
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Liver Neoplasms, Experimental/chemistry
- Liver Neoplasms, Experimental/genetics
- Liver Neoplasms, Experimental/immunology
- Liver Neoplasms, Experimental/pathology
- Male
- Mice
- Non-alcoholic Fatty Liver Disease
- Primary Cell Culture
- Prognosis
- RNA-Seq
- Survival Analysis
- Tristetraprolin/genetics
- Tristetraprolin/metabolism
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Affiliation(s)
- Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Flavien Berthou
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Claudio De Vito
- Division of Clinical Pathology, University Hospitals, Geneva, Switzerland
| | - Didier J Colin
- Centre for Biomedical Imaging and Preclinical Imaging Platform, University of Geneva, Geneva, Switzerland
| | - Olivia Bejuy
- Centre for Biomedical Imaging and Preclinical Imaging Platform, University of Geneva, Geneva, Switzerland
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Perry J Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Translational Research Centre in Onco-haematology, Faculty of Medicine, University of Geneva, Switzerland.
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30
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Wu J, Li R, Li L, Gu Y, Zhan H, Zhou C, Zhong C. MYC-activated lncRNA HNF1A-AS1 overexpression facilitates glioma progression via cooperating with miR-32-5p/SOX4 axis. Cancer Med 2020; 9:6387-6398. [PMID: 33448691 PMCID: PMC7476832 DOI: 10.1002/cam4.3186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/27/2020] [Accepted: 05/01/2020] [Indexed: 12/15/2022] Open
Abstract
Mounting literatures have revealed the crucial effects of long noncoding RNA (lncRNA) in various cancers, including glioma. HNF1A‐AS1, a novel lncRNA, is reported to modulate tumorigenesis and development of multiple cancers. However, the tumorigenic function of lncRNA HNF1A‐AS1 in glioma remains largely unknown. quantitative reverse transcription and polymerase chain reaction and western blot assays were applied to evaluate the expression of relevant mRNAs and proteins. 5‐Ethynyl‐2’‐ deoxyuridine, terminal deoxynucleotidyl transferase dUTP nick‐end labeling, flow cytometry, and transwell assays were conducted for examining the influence of HNF1A‐AS1 on glioma cell functions. The relationship among RNAs was investigated by mechanical experiments. The results demonstrated that HNF1A‐AS1 was predominantly highly expressed in glioma cell lines compared with nontumor glial epithelial cell, which was associated with the stimulation of transcription factor myelocytomatosis oncogene. Knockdown of HNF1A‐AS1 remarkably inhibited glioma cells proliferation, migration, and invasion, while accelerating cell apoptosis in vitro. Mechanically, HNF1A‐AS1 served as a miR‐32‐5p sponge. Moreover, SOX4 was discovered as a target of miR‐32‐5p. Inhibited miR‐32‐5p or upregulated SOX4 could markedly counteract the inhibitory effects of silencing HNF1A‐AS1 on glioma malignant biological behaviors. HNF1A‐AS1 exerted oncogenic property in glioma progression via upregulating miR‐32‐5p–mediated SOX4 expression, suggesting potential novel therapeutic target for future glioma treatment.
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Affiliation(s)
- Jianheng Wu
- Department of Neurosurgery, Gaozhou People's Hospital, Gaozhou, Guangdong, China
| | - Rong Li
- Department of Radiation Oncology, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Linfan Li
- Department of Neurosurgery, Gaozhou People's Hospital, Gaozhou, Guangdong, China
| | - Yimian Gu
- Department of Neurosurgery, Gaozhou People's Hospital, Gaozhou, Guangdong, China
| | - Hui Zhan
- Department of Neurosurgery, Gaozhou People's Hospital, Gaozhou, Guangdong, China
| | - Changbao Zhou
- Department of Neurosurgery, Gaozhou People's Hospital, Gaozhou, Guangdong, China
| | - Chuanhong Zhong
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Neurosurgical Clinical Research Center of Sichuan Province, Luzhou, Sichuan, China
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31
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Jiao M, Guo H, Chen Y, Li L, Zhang L. DARS-AS1 promotes clear cell renal cell carcinoma by sequestering miR-194-5p to up-regulate DARS. Biomed Pharmacother 2020; 128:110323. [PMID: 32526457 DOI: 10.1016/j.biopha.2020.110323] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 02/01/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC), the most frequent subtype of renal cell carcinoma (RCC), is characterized by high relapse rate and mortality. Long non-coding RNAs (lncRNAs) are critical participants during cancer development. LncRNA DARS antisense RNA 1 (DARS-AS1), a newly-found lncRNA, is not specifically reported in ccRCC. However, Gene Expression Profiling Interactive Analysis (GEPIA) and starBase databases revealed the up-regulation of DARS-AS1 in ccRCC. Current study investigated the function and mechanism of DARS-AS1 in ccRCC. Functional assays including colony formation assay, EdU assay, caspase-3 activity detection, flow cytometry analysis and JC-1 assay were implemented to identify the role of DARS-AS1 in ccRCC. As a result, silencing of DARS-AS1 retarded proliferation and facilitated apoptosis in ccRCC cells. Moreover, mainly a cytoplasmic localization of lncRNA DARS-AS1 was verified in ccRCC cells. Then, we demonstrated that DARS-AS1 positively regulated its nearby gene, aspartyl-tRNA synthetase (DARS), by sequestering miR-194-5p. Moreover, DARS was testified as the oncogene in ccRCC and DARS-AS1 worked as a tumor-facilitator in ccRCC through miR-194-5p/DARS signaling. In a summary, this study firstly uncovered that DARS-AS1 boosted DARS expression via absorbing miR-194-5p, therefore contributing to malignancy in ccRCC. Our findings may be helpful for opening new strategies for ccRCC treatment.
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Affiliation(s)
- Min Jiao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, PR China
| | - Hui Guo
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, PR China
| | - Yule Chen
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, PR China
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, PR China
| | - Linlin Zhang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, PR China.
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32
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Khalili N, Nouri-Vaskeh M, Hasanpour Segherlou Z, Baghbanzadeh A, Halimi M, Rezaee H, Baradaran B. Diagnostic, prognostic, and therapeutic significance of miR-139-5p in cancers. Life Sci 2020; 256:117865. [PMID: 32502540 DOI: 10.1016/j.lfs.2020.117865] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/23/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022]
Abstract
miRNAs are a group of non-coding RNAs that have regulatory functions in post-transcriptional gene expression. These molecules play a fundamental role in cellular processes, for instance cell proliferation, apoptosis, migration, and invasion. Scientific investigations have previously established that miRNAs can either promote or suppress tumor development by mediating different signaling pathways. miR-139-5p, located on chromosome 11q13.4, has been examined extensively in cancers. Studies have demonstrated that miR-139-5p might be an attractive cancer biomarker. Herein, we will review how miR-139-5p acts in cancer diagnosis, prognosis, and therapy, as well as elucidating its major target genes and associated signaling pathways.
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Affiliation(s)
- Neda Khalili
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Masoud Nouri-Vaskeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | | | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Monireh Halimi
- Department of Pathology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Haleh Rezaee
- Infectious Diseases and Tropical Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Clinical Pharmacy (Pharmacotherapy), Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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33
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Dacheng W, Songhe L, Weidong J, Shutao Z, Jingjing L, Jiaming Z. RETRACTED: LncRNA SNHG3 promotes the growth and metastasis of colorectal cancer by regulating miR-539/RUNX2 axis. Biomed Pharmacother 2020; 125:110039. [PMID: 32187965 DOI: 10.1016/j.biopha.2020.110039] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Authors and Editor-in-Chief. The corresponding author notified the journal that “LncRNA SNHG3 did not affect colorectal cancer cell invasion, which was inconsistent with our published results”. As the results were unreliable the authors requested its retraction. The journal was also alerted to suspected image similarities within Figure 2D, that appear to be present in another publication, as detailed here: https://pubpeer.com/publications/7855CA1A494A20F55AAE1463D1B648. The journal requested the authors provide an explanation and source data relating to the affected figure. The Authors did not provide an explanation in response to these concerns. The Editor-in-Chief assessed this case and decided to retract the article.
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Affiliation(s)
- Wen Dacheng
- Department of Gastrointestinal Nutrition and Hernia Surgery, the Second Hospital of Jilin University, Nanguan District, Changchun, 130041, China
| | - Li Songhe
- Department of Ophthalmology, the First Hospital of Jilin University, Chaoyang District, Changchun, 130021, China.
| | - Jiang Weidong
- Department of Hepatobiliary and Pancreatic Surgery, the Second Hospital of Jilin University, Nanguan District, Changchun, 130041, China
| | - Zhao Shutao
- Department of Gastrointestinal Nutrition and Hernia Surgery, the Second Hospital of Jilin University, Nanguan District, Changchun, 130041, China
| | - Liu Jingjing
- Department of Gastrointestinal Nutrition and Hernia Surgery, the Second Hospital of Jilin University, Nanguan District, Changchun, 130041, China
| | - Zhu Jiaming
- Department of Gastrointestinal Nutrition and Hernia Surgery, the Second Hospital of Jilin University, Nanguan District, Changchun, 130041, China
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34
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Li T, Xing Y, Yang F, Sun Y, Zhang S, Wang Q, Zhang W. LncRNA SNHG3 sponges miR-577 to up-regulate SMURF1 expression in prostate cancer. Cancer Med 2020; 9:3852-3862. [PMID: 32248648 PMCID: PMC7286463 DOI: 10.1002/cam4.2992] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/25/2020] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer remains one of the most prevalent cancers and the main causes of cancer-related deaths in males. Various articles introduced that long noncoding RNAs (lncRNAs) are found in vital functions in the development and progression of cancers. Although SNHG3 (small nucleolar RNA host gene 3) has been investigated in many cancers, now researches on the role and mechanism of SNHG3 in prostate cancer are lacked. In this work, SNHG3 exerted high expression in prostate cancer cell lines. Suppression of SNHG3 inhibited cell proliferation, migration, EMT (epithelial-mesenchymal transition) process and promoted cell apoptosis. Additionally, it was found that SNHG3 could bind with miR-577. Subsequently, SMURF1 (Smad ubiquitination regulatory factor 1) was identified as a downstream target of miR-577 and had a negative correlation with miR-577. SNHG3 was found to positively regulate SMURF1 expression. Furthermore, rescue assays demonstrated that co-transfection of pcDNA3.1/SMURF1 reversed the effects of SNHG3 knockdown in cell proliferation, migration, EMT process and cell apoptosis. SNHG3 also promoted tumorigenesis in vivo. All the results above explained that SNHG3 accelerated prostate cancer progression by sponging miR-577 to up-regulate SMURF1 expression, suggesting that SNHG3 may act as a biomarker for prostate cancer patients.
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Affiliation(s)
- Teng Li
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Xing
- Department of Opthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fan Yang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yangyang Sun
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shaojin Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qingwei Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weixing Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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35
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Duan Y, Wang Z, Xu L, Sun L, Song H, Yin H, He F. lncRNA SNHG3 acts as a novel Tumor Suppressor and regulates Tumor Proliferation and Metastasis via AKT/mTOR/ERK pathway in Papillary Thyroid Carcinoma. J Cancer 2020; 11:3492-3501. [PMID: 32284745 PMCID: PMC7150443 DOI: 10.7150/jca.42070] [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: 11/13/2019] [Accepted: 01/19/2020] [Indexed: 12/11/2022] Open
Abstract
The incidence of papillary thyroid carcinoma (PTC) has been increased rapidly in recent decades. Long noncoding RNAs (lncRNA) are a class of non-protein-coding transcripts and play critical roles in regulating gene expression and influence biological behaviors of multiple cancers, including PTC. Here, we discovered that lncRNA SNHG3 was significantly downregulated in PTC tissues and cell lines, the expression of SNHG3 was negatively correlated with the TNM stage and poor prognosis of PTC patients. Functional studies illustrated that the depletion of SNHG3 via CRISPR/Cas9 technology promoted the proliferation, migration and invasion abilities of PTC cells. Tumor xenograft models confirmed the tumor-promoting role of silenced SNHG3 in vivo. Further mechanistic analyses revealed that knockout of SNHG3 activated the AKT/mTOR/ERK pathway in PTC cell lines and the mTOR inhibitor AZD8055 abrogated the tumor-promoting effect induced by SNHG3 inhibition. Taken together, our findings identified a lncRNA SNHG3 that functions its tumor-suppressor role during PTC development and SNHG3 might serve as a promising candidate for target therapy of PTC.
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Affiliation(s)
- Yu Duan
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Zhiyong Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Lijuan Xu
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Li Sun
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Hairong Song
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Huiqing Yin
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Fucheng He
- Department of Medical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
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36
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Yang W, Zhang K, Li L, Ma K, Hong B, Gong Y, Gong K. Discovery and validation of the prognostic value of the lncRNAs encoding snoRNAs in patients with clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12:4424-4444. [PMID: 32126023 PMCID: PMC7093172 DOI: 10.18632/aging.102894] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/25/2020] [Indexed: 12/11/2022]
Abstract
Some lncRNAs can encode small nucleolar RNAs (snoRNAs), called small nucleolar RNA host genes (SNHGs), which have exerted certain predictive values for the prognosis of some cancer patients. In this study, using RNA-seq and survival data in TCGA-KIRC, we examined the expression profile of 20 SNHGs and explored their prognostic values in ccRCC. Results showed that SNHG1, GAS5, SNHG3-8, SNHG11, SNHG12, SNHG15-17, SNHG20, SNHG22 and SNHG25 were significantly upregulated in ccRCC tissues compared with adjacent normal tissues. After adjustment for confounding factors, the multivariate analysis confirmed that increased SNHG3 expression was independently associated with shorter OS, while increased SNHG15 expression was an independent predictor of shorter RFS. Using the methylation data, the methylation status of 2 CpG sites (cg07807470 and cg15161854) and 2 CpG sites (cg00953154 and cg16459265) were negatively correlated with SNHG3 and SNHG15 expression, respectively. Moreover, low methylation levels of the 4 CpG sites were significantly associated with shorter OS. Furthermore, we validated the expression patterns, methylation status and prognostic value of SNHG3 and SNHG15 using clinical ccRCC samples. Taken together, SNHG3 and SNHG15 might be valuable prognostic markers in ccRCC, and DNA hypomethylation might play an important role in elevated SNHG3 and SNHG15 transcription in ccRCC.
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Affiliation(s)
- Wuping Yang
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Beijing 100034, P.R. China.,National Urological Cancer Center, Beijing 100034, P.R. China
| | - Kenan Zhang
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Beijing 100034, P.R. China.,National Urological Cancer Center, Beijing 100034, P.R. China
| | - Lei Li
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Beijing 100034, P.R. China.,National Urological Cancer Center, Beijing 100034, P.R. China
| | - Kaifang Ma
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Beijing 100034, P.R. China.,National Urological Cancer Center, Beijing 100034, P.R. China
| | - Baoan Hong
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Beijing 100034, P.R. China.,National Urological Cancer Center, Beijing 100034, P.R. China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Beijing 100034, P.R. China.,National Urological Cancer Center, Beijing 100034, P.R. China
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing 100034, P.R. China.,Hereditary Kidney Cancer Research Center, Peking University First Hospital, Beijing 100034, P.R. China.,Institute of Urology, Peking University, Beijing 100034, P.R. China.,National Urological Cancer Center, Beijing 100034, P.R. China
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37
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Wang Y, Wang X, Ma Y, Wang YX, Di Y. Expression profiles of long noncoding RNAs in retinopathy of prematurity. Neural Regen Res 2020; 15:1962-1968. [PMID: 32246647 PMCID: PMC7513972 DOI: 10.4103/1673-5374.280328] [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] [Indexed: 12/22/2022] Open
Abstract
Long noncoding RNA (lncRNA) regulates the proliferation and migration of human retinal endothelial cells, as well as retinal neovascularization in diabetic retinopathy. Based on similarities between the pathogenesis of retinopathy of prematurity (ROP) and diabetic retinopathy, lncRNA may also play a role in ROP. Seven-day-old mice were administered 75 ± 2% oxygen for 5 days and normoxic air for another 5 days to establish a ROP model. Expression of lncRNA and mRNA in the retinal tissue of mice was detected by high-throughput sequencing technology, and biological functions of the resulted differentially expressed RNAs were evaluated by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. The results showed that compared with the control group, 57 lncRNAs were differentially expressed, including 43 upregulated and 14 downregulated, in the retinal tissue of ROP mice. Compared with control mice, 42 mRNAs were differentially expressed in the retinal tissue of ROP mice, including 24 upregulated and 18 downregulated mRNAs. Differentially expressed genes were involved in ocular development and related metabolic pathways. The differentially expressed lncRNAs may regulate ROP in mice via microRNAs and multiple signaling pathways. Our results revealed that these differentially expressed lncRNAs may be therapeutic targets for ROP treatment. This study was approved by the Medical Ethics Committee of Shengjing Hospital of China Medical University on February 25, 2016 (approval No. 2016PS074K).
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Affiliation(s)
- Yue Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Xue Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Yuan Ma
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Yue-Xia Wang
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Yu Di
- Department of Ophthalmology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China
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