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Wang J, Dou P, Sun Y, Zheng J, Wu G, Liu H, Tao L. Epigenetic dysregulated long non-coding RNAs in renal cell carcinoma based on multi-omics data and their influence on target drugs sensibility. Front Genet 2024; 15:1406150. [PMID: 39156959 PMCID: PMC11327069 DOI: 10.3389/fgene.2024.1406150] [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: 03/24/2024] [Accepted: 07/16/2024] [Indexed: 08/20/2024] Open
Abstract
Purpose Epigenetic modifications play a crucial role in cancer development, and our study utilized public data to analyze which leads to the discovery of significant epigenetic abnormalities in lncRNAs, offering valuable insights into prognosis and treatment strategies for renal carcinoma. Methods Public data were obtained from the Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and Gene Expression Omnibus (GEO) database. The analysis of the online public data was all completed in R software. Results We discovered a great number of epigenetic abnormalities of lncRNA in renal cancer, which is achieved by comparing the following modification and methylation of histone region changes on the promoter and enhancer of lncRNA: H3K27ac, H3K4me1, H3K4me3. As a result, 12 specific epigenetic disorders of lncRNA genes in renal cancer were identified. Finally, based on this lncRNA, we investigated the prognosis of renal cancer samples, among which 8 lncRNA can be seen as markers of prognosis in renal cancer, which had great prediction ability for ccRCC prognosis. Meanwhile, high risk score may pose response better to axitinib and nilotinib, but not sorafenib or sunitinib. Beyond, we observed an elevated level of risk score in immunotherapy non-responders. Further, biological enrichment and immuno-infiltration analysis was conducted to investigate the fundamental differences between patients categorized as high or low risk. Conclusion Our research improves the understanding in the function of epigenetic dysregulated long non-coding RNAs in renal carcinoma.
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Affiliation(s)
- Jiawei Wang
- Department of Urology, The Second People’s Hospital of Wuhu, Wuhu, China
| | - Pingnan Dou
- Department of Urology, The Second People’s Hospital of Wuhu, Wuhu, China
- School of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Yunwen Sun
- Department of Urology, The Second People’s Hospital of Wuhu, Wuhu, China
- The First Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Jie Zheng
- Department of Urology, The Second People’s Hospital of Wuhu, Wuhu, China
| | - Guanwei Wu
- Department of Urology, The Second People’s Hospital of Wuhu, Wuhu, China
| | - Heqian Liu
- Department of Urology, The Second People’s Hospital of Wuhu, Wuhu, China
| | - Lingsong Tao
- Department of Urology, The Second People’s Hospital of Wuhu, Wuhu, China
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A Computationally Constructed lncRNA-Associated Competing Triplet Network in Clear Cell Renal Cell Carcinoma. DISEASE MARKERS 2022; 2022:8928282. [DOI: 10.1155/2022/8928282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) are revealed to be involved in the tumorigenesis and progression of human malignancies mediated by microRNA (miRNA) via the competing endogenous RNA (ceRNA) mechanism, a newly proposed “RNA language.” However, the lncRNA-associated competing triplet (lncACT) network among ceRNA transcripts in clear cell renal cell carcinoma (ccRCC) is currently lacking. We carried out differential expression analysis to identify aberrantly expressed lncRNAs, miRNAs, and mRNAs by analyzing the RNA-seq data of 420 ccRCC tissues and 71 noncancerous kidney tissues obtained from The Cancer Genome Atlas (TCGA). Then, a ccRCC-specific ceRNA network was built using computational algorithms, including miRcode, TargetScan, miRanda, and miRTarBase. In total, 1491 dysregulated lncRNAs were found between normal renal tissues and ccRCC (fold
and false discovery
). A ceRNA network that comprised of 46 DElncRNAs, 11 DEmiRNAs, and 55 DEmRNAs was established by integrating the lncRNA/miRNA and miRNA/mRNA interactions into lncACTs. Several lncRNAs were identified to be significantly associated with clinical features of ccRCC patients. Notably, four key lncRNAs (TCL6, HOTTIP, HULC, and PCGEM1) were tightly correlated with both patients’ clinical characteristics and overall survival (log-rank
), indicating their potential important roles in ccRCC. HOTTIP may be a potential prognostic and therapeutic molecular marker for ccRCC patients. Collectively, our results provide a comprehensive view of the lncRNA-associated ceRNA regulatory network for a better understanding of the mechanisms and prognosis biomarkers for ccRCC.
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Liu T, Zhao H. Long Non-Coding RNAs: A Double-Edged Sword in Renal Cell Carcinoma Carcinogenesis. INT J PHARMACOL 2022. [DOI: 10.3923/ijp.2022.1537.1549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ssc-MiR-21-5p and Ssc-MiR-615 Regulates the Proliferation and Apoptosis of Leydig Cells by Targeting SOX5. Cells 2022; 11:cells11142253. [PMID: 35883696 PMCID: PMC9324347 DOI: 10.3390/cells11142253] [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: 06/10/2022] [Revised: 07/06/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
Leydig cells (LCs) are the predominant cells of androgen production, which plays key roles in spermatogenesis and maintaining male secondary sexual characteristics. Abnormal development of LCs affects androgen levels in vivo, affects fertility and may even lead to infertility. Little is known about the regulation mechanism on LCs’ development and maturation in domestic animals, especially the regulation of non-coding RNAs. In this study, we continued to dig deeper in the previous RNA-seq data of porcine LCs from our group, combined with detecting the expression profiles in different tissues and different types of cells in the testis, to screen out candidate microRNAs (miRNAs) that may affect the regulation of LCs. A total of two miRNAs, ssc-miR-21-5p and ssc-miR-615 (“ssc” is omitted below), were finally determined. After overexpression and interference of miRNAs in vitro, the effects of candidate miRNAs on the proliferation and apoptosis of TM3 (mouse Leydig cell line) were explored. The results showed that miR-21-5p led to a decrease in TM3 cell density and p53 (apoptosis related protein) expression. Meanwhile, miR-21-5p decreased EdU positive cell numbers, but increased TUNEL positive cell numbers, suggesting miR-21-5p could inhibit proliferation and promote apoptosis. Conversely, miR-615 could increase TM3 cell density. Western blot and TUNEL assay indicated miR-615 inhibited apoptosis, but had no effect on proliferation. In addition, Sox5 was identified a potential target gene of these two miRNAs by Dual-Luciferase reporter system assay. Our findings about functions of miRNAs in TM3 and the mapping of miRNAs-target gene regulatory network would provide an important basis for the further elucidation of miRNAs in regulating pig LCs.
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Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. NPJ Precis Oncol 2022; 6:40. [PMID: 35729321 PMCID: PMC9213432 DOI: 10.1038/s41698-022-00283-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers. Cell-free nucleic acids (cfNA) such as circulating long noncoding RNAs (lncRNAs) have been proposed as a new class of potential biomarkers for cancer diagnosis. The reported correlation between the presence of tumors and abnormal levels of lncRNAs in the blood of cancer patients has notably triggered a worldwide interest among clinicians and oncologists who have been actively investigating their potentials as reliable cancer biomarkers. In this report, we review the progress achieved (“the Good”) and challenges encountered (“the Bad”) in the development of circulating lncRNAs as potential biomarkers for early cancer diagnosis. We report and discuss the diagnostic performance of more than 50 different circulating lncRNAs and emphasize their numerous potential clinical applications (“the Beauty”) including therapeutic targets and agents, on top of diagnostic and prognostic capabilities. This review also summarizes the best methods of investigation and provides useful guidelines for clinicians and scientists who desire conducting their own clinical studies on circulating lncRNAs in cancer patients via RT-qPCR or Next Generation Sequencing (NGS).
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Li Z, Li M, Xia P, Lu Z. HOTTIP Mediated Therapy Resistance in Glioma Cells Involves Regulation of EMT-Related miR-10b. Front Oncol 2022; 12:873561. [PMID: 35402278 PMCID: PMC8987496 DOI: 10.3389/fonc.2022.873561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/03/2022] [Indexed: 12/16/2022] Open
Abstract
The advanced grade glioblastomas are characterized by dismal five-year survival rates and are associated with worse outcomes. Additionally, resistance to therapies is an additional burden responsible for glioma associated mortality. We studied the resistance against temozolomide (TMZ) as a surrogate to understand the mechanism of therapy resistance in glioma cancer cells. Screening of three glioma cells lines, A172, LN229 and SF268 revealed that SF268 glioma cells were particularly resistant to TMZ with the IC-50 of this cell line for TMZ ten times higher than for the other two cell lines. A role of lncRNAs in glioma progression has been identified in recent years and, therefore, we focused on lncRNAs for their role in regulating TMZ resistance in glioma cancer cells. lncRNA HOTTIP was found to be particularly elevated in SF268 cells and over-expression of HOTTIP in both A172 and LN229 remarkably increased their TMZ IC-50s, along with increased cell proliferation, migration, clonogenicity and markers of angiogenesis and metastasis. As a mechanism we observed increased expression of miRNA-10b and mesenchymal markers Zeb1/Zeb2 and reduced expression of E-cadherin in SF268 cells indicating a role of EMT in TMZ resistance. A172 and LN229 cells with overexpressed HOTTIP also had similarly induced EMT and the elevated miR-10b levels. Further, silencing of miR-10b in HOTTIP overexpressing cells as well as the SF268 cells reversed EMT with associated sensitization of all the tested cells to TMZ. Our results thus present a case for HOTTIP in native as well as acquired resistance of glioma cells against chemotherapy, with a key mechanistic role of EMT and the miR-10b. Thus, HOTTIP as well as miR-10b are critical targets for glioma therapy, and need to be tested further.
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Ren F, Li B, Wang C, Wang Y, Cui B. Iodine-125 seed represses the growth and facilitates the apoptosis of colorectal cancer cells by suppressing the methylation of miR-615 promoter. BMC Cancer 2022; 22:49. [PMID: 34998382 PMCID: PMC8742920 DOI: 10.1186/s12885-021-09141-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) represents a common malignancy in gastrointestinal tract. Iodine-125 (125I) seed implantation is an emerging treatment technology for unresectable tumors. This study investigated the mechanism of 125I seed in the function of CRC cells. METHODS The CRC cells were irradiated with different doses of 125I seed (0.4, 0.6 and 0.8 mCi). miR-615 expression in CRC tissues and adjacent tissues was detected by RT-qPCR. miR-615 expression was intervened with miR-615 mimic or miR-615 inhibitor, and then the CRC cells were treated with 5-AZA (methylation inhibitor). The CRC cell growth, invasion and apoptosis were measured. The methylation level of miR-615 promoter region was detected. The xenograft tumor model irradiated by 125I seed was established in nude mice. The methylation of miR-615, Ki67 expression and CRC cell apoptosis were detected. RESULTS 125I seed irradiation repressed the growth and facilitated apoptosis of CRC cells in a dose-dependent manner. Compared with adjacent tissues, miR-615 expression in CRC tissues was downregulated and miR-615 was poorly expressed in CRC cells. Overexpression of miR-615 suppressed the growth of CRC cells. 125I seed-irradiated CRC cells showed increased miR-615 expression, reduced growth rate and enhanced apoptosis. The methylation level of miR-615 promoter region in CRC cells was decreased after 125I seed treatment. In vivo experiments confirmed that 125I seed-irradiated xenograft tumors showed reduced methylation of the miR-615 promoter and increased miR-615 expression, as well as decreased Ki67 expression and enhanced apoptosis. The target genes of miR-615 and its regulatory downstream pathway were further predicted by bioinformatics analysis. CONCLUSIONS 125I seed repressed the growth and facilitated the apoptosis of CRC cells by suppressing the methylation of the miR-615 promoter and thus activating miR-615 expression. The possible mechanism was that miR-615-5p targeted MAPK13, thus affecting the MAPK pathway and the progression of CRC.
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Affiliation(s)
- Fenghai Ren
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, Heilongjiang, China
| | - Baojun Li
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, Heilongjiang, China
| | - Chao Wang
- Department of Prenatal Diagnosis, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yanbo Wang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, Heilongjiang, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150081, Heilongjiang, China.
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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: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Lun P, Ji T, Wan DH, Liu X, Chen XD, Yu S, Sun P. HOTTIP downregulation reduces neuronal damage and microglial activation in Parkinson's disease cell and mouse models. Neural Regen Res 2021; 17:887-897. [PMID: 34472490 PMCID: PMC8530116 DOI: 10.4103/1673-5374.322475] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
HOXA transcript at the distal tip (HOTTIP), a newly identified long noncoding RNA, has been shown to exhibit anti-inflammatory effects and inhibit oxygen-glucose deprivation-induced neuronal apoptosis. However, its role in Parkinson’s disease (PD) remains unclear. 1-Methyl-4-phenylpyridium (MPP+) and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) were used to establish PD models in SH-SY5Y and BV2 cells and in C57BL/6 male mice, respectively. In vitro, after HOTTIP knockdown by sh-HOTTIP transfection, HOTTIP and FOXO1 overexpression promoted SH-SY5Y apoptosis, BV2 microglial activation, proinflammatory cytokine expression, and nuclear factor kappa-B and NACHT, LRR and PYD domains-containing protein 3 inflammasome activation. Overexpression of miR-615-3p inhibited MPP+-induced neuronal apoptosis and microglial inflammation and ameliorated HOTTIP- and FOXO1-mediated nerve injury and inflammation. In vivo, HOTTIP knockdown alleviated motor dysfunction in PD mice and reduced neuronal apoptosis and microglial activation in the substantia nigra. These findings suggest that inhibition of HOTTIP mitigates neuronal apoptosis and microglial activation in PD models by modulating miR-615-3p/FOXO1. This study was approved by the Ethics Review Committee of the Affiliated Hospital of Qingdao University, China (approval No. UDX-2018-042) in June 2018.
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Affiliation(s)
- Peng Lun
- Department of Neurosurgery, the Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Tao Ji
- Department of Neurosurgery, Laiyang People's Hospital, Yantai, Shandong Province, China
| | - De-Hong Wan
- Department of Neurosurgery, the Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Xia Liu
- Department of Endocrine and Metabolic Diseases, the Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Xiao-Dong Chen
- Emergency Department, the Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Shuai Yu
- Emergency Department, the Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Peng Sun
- Department of Neurosurgery, the Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
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Liu B, Jiang HY, Yuan T, Zhou WD, Xiang ZD, Jiang QQ, Wu DL. Long non-coding RNA AFAP1-AS1 facilitates prostate cancer progression by regulating miR-15b/IGF1R axis. Curr Pharm Des 2021; 27:4261-4269. [PMID: 34126893 DOI: 10.2174/1381612827666210612052317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Prostate cancer (PCa) is a commonly diagnosed malignant cancer and is the second highest cause of cancer related death in men worldwide. Enzalutamide is the second-generation inhibitor of androgen receptor signaling and is the fundamental drug for the treatment of advanced PCa. However, the disease will eventually progress to metastatic castration-resistant prostate cancer (CRPC) and aggressive neuroendocrine prostate cancer (NEPC) because of androgen-deprivation therapy (ADT) resistance. The aim of the study was to investigate the role of long non-coding RNA (lncRNA) AFAP1-AS1 in ADT resistance. METHODS Quantitative real-time PCR analysis (qPCR) was used to assess the expression of AFAP1-AS1 in PCa cell lines and tissues. Cell proliferation and invasion were assessed after AFAP1-AS1 knockdown using Cell Counting Kit (CCK)-8 and Transwell assay, respectively. A dual-luciferase reporter gene assay was carried out to validate the regulatory relationship among AFAP1-AS1, microRNA (miR)-15b, and insulin-like growth factor1 receptor (IGF1R). RESULTS AFAP1-AS1 level was markedly increased in castration-resistant C4-2 cells and NE-like cells (PC3, DU145, and NCI-H660), compared with androgen-sensitive LNCaP cells. Enzalutamide treatment increased the expression of AFAP1-AS1 in vitro and in vivo. Functionally, AFAP1-AS1 knockdown repressed tumor cell proliferation and invasion. Mechanistically, AFAP1-AS1 functioned as an oncogene in PCa through binding to miR-15b and destroying its tumor suppressor function. Finally, we identified that AFAP1-AS1 up-regulated IGF1R expression by competitively binding to miR-15b to de-repress IGF1R. CONCLUSION AFAP1-AS1 facilitates PCa progression by regulating miR-15b/IGF1R axis, indicating that AFAP1-AS1 may serve as a diagnostic biomarker and therapeutic target for PCa.
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Affiliation(s)
- Bo Liu
- Department of Urology, Tongji Hospital, Tongji University of Medicine, 389 Xincun Road, Putuo, Shanghai, 200065, China
| | - Hui-Yang Jiang
- Department of Urology, Tongji Hospital, Tongji University of Medicine, 389 Xincun Road, Putuo, Shanghai, 200065, China
| | - Tao Yuan
- Department of Urology, Tongji Hospital, Tongji University of Medicine, 389 Xincun Road, Putuo, Shanghai, 200065, China
| | - Wei-Dong Zhou
- Department of Urology, Tongji Hospital, Tongji University of Medicine, 389 Xincun Road, Putuo, Shanghai, 200065, China
| | - Zhen-Dong Xiang
- Department of Urology, Tongji Hospital, Tongji University of Medicine, 389 Xincun Road, Putuo, Shanghai, 200065, China
| | - Qi-Quan Jiang
- Department of Urology, Tongji Hospital, Tongji University of Medicine, 389 Xincun Road, Putuo, Shanghai, 200065, China
| | - Deng-Long Wu
- Department of Urology, Tongji Hospital, Tongji University of Medicine, 389 Xincun Road, Putuo, Shanghai, 200065, China
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Abdelaleem OO, Shaker OG, AbdelHafez MN, Abdelghaffar NK, Eid HM, Zaidan M, Khalefa AA, Ahmed NA, Hemeda NF, Zaki OM, Awaji AAA, Mohammed SR. The Influence of rs1859168 Polymorphism on Serum Expression of HOTTIP and Its Target miR-615-3p in Egyptian Patients with Breast Cancer. Biomolecules 2021; 11:733. [PMID: 34069089 PMCID: PMC8156858 DOI: 10.3390/biom11050733] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/02/2021] [Accepted: 05/07/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Polymorphisms of long noncoding RNAs are lately documented as hazardous factors for the development of numerous tumors. Furthermore, the evaluation of noncoding RNAs has emerged as a novel detector of breast cancer patients. We aimed to genotype the HOXA transcript at the distal tip (HOTTIP) rs1859168 and assess its relationship with the levels of the serum HOTTIP and its target miR-615-3p in patients with breast cancer (BC). METHODS One hundred and fifty-one patients with BC, 139 patients with fibroadenoma (FA), and 143 healthy participants were incorporated into the current study. The genotyping of rs1859168 and the measurements of the HOTTIP and miR-615-3p levels were assessed using quantitative real-time PCR. RESULTS We revealed a significant association between each of the CC genotypes, C allele, dominant and recessive models, and the increased risk of BC (p = 0.013, p < 0.001, p < 0.001, and p < 0.001, respectively) relative to the healthy controls. Similarly, the CC genotype, C allele, and recessive model were observed to be related to the increased incidence of BC with respect to FA (p < 0.001 for all). A significant upregulation of HOTTIP and a marked decrease of miR-615-3p were verified in patients with BC compared to each of the healthy individuals, patients with FA, and the non-BC group (healthy subjects + FA) (p < 0.001 for all). A significant negative correlation was demonstrated between the expression of HOTTIP and miR-615-3p in the serum of patients with BC. The HOTTIP expression was upregulated, while that of miR-615-3p was downregulated in patients with BC who carried the CC genotype with respect to those who carried the AA or AC genotypes (p < 0.05 for all). CONCLUSIONS The genetic variants of rs1859168 are linked to an increased susceptibility to BC. Moreover, HOTTIP and miR-615-3p may be used as novel indicators and targets for the treatment of patients with BC.
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Affiliation(s)
- Omayma O. Abdelaleem
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum 63511, Egypt; (O.O.A.); (S.R.M.)
| | - Olfat G. Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo 11511, Egypt;
| | - Marwa N. AbdelHafez
- Department of Medical Oncology, National Cancer Institute, Cairo University, Cairo 11511, Egypt;
| | - Noha K. Abdelghaffar
- Department of Clinical pathology, Faculty of Medicine, Fayoum University, Fayoum 63511, Egypt;
| | - Hanaa M. Eid
- Department of Microbiology and Immunology, Faculty of Medicine, Fayoum University, Fayoum 63511, Egypt
| | - Mohamed Zaidan
- Department of General Surgery, Faculty of Medicine, Fayoum University, Fayoum 63511, Egypt;
| | - Abeer A. Khalefa
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig 44523, Egypt; (A.A.K.); (N.A.A.)
| | - Naglaa A. Ahmed
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig 44523, Egypt; (A.A.K.); (N.A.A.)
| | - Nada F. Hemeda
- Department of Genetics, Faculty of Agriculture, Fayoum University, Fayoum 63511, Egypt;
| | - Othman M. Zaki
- Department of Clinical Pathology, Faculty of Medicine, Damietta University, Damietta 34511, Egypt;
| | - Aeshah Ali A. Awaji
- Department of Biology, Faculty of Science, University College of Taymaa, Tabuk University, Tabuk 47711, Saudi Arabia;
| | - Shereen R. Mohammed
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum 63511, Egypt; (O.O.A.); (S.R.M.)
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Yuan X, Sun Z, Cui C. Knockdown of lncRNA HOTTIP Inhibits Retinoblastoma Progression by Modulating the miR-101-3p/STC1 Axis. Technol Cancer Res Treat 2021; 20:1533033821997831. [PMID: 33784880 PMCID: PMC8020084 DOI: 10.1177/1533033821997831] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Objective: Retinoblastoma (RB) is a frequent eye cancer in children. Long non-coding RNA
(LncRNA) HOXA transcript at the distal tip (HOTTIP) is aberrantly expressed
in cancer tissues. This study explores the underlying mechanism of lncRNA
HOTTIP in RB. Methods: HOTTIP expression in normal retinal cells and RB cell lines was detected
using qRT-PCR. The proliferation of RB cells was measured using CCK-8 and
EdU assays, and apoptosis was detected using flow cytometry and Western
blotting after the transfection of si-HOTTIP into Y79 cells and pc-HOTTIP
into HXO-RB-44 cells. The target relationships between HOTTIP and
miR-101-3p, and miR-101-3p and STC1 were predicted by bioinformatics website
and verified using dual-luciferase reporter gene assay. The binding of
HOTTIP and miR-101-3p was verified using RNA pull-down assay. STC1 mRNA and
protein in RB cells were measured using qRT-PCR and Western blotting.
Moreover, si-HOTTIP and in-miR-101-3p/in-NC, and si-HOTTIP and pc-STC1/pcDNA
were co-transfected into Y79 cells respectively to evaluate cell
proliferation and apoptosis. Xenograft study was conducted, and
Ki67-positive expression was detected using immunohistochemical
staining. Results: HOTTIP expression was promoted in RB tissues and cells. Downregulation of
HOTTIP inhibited proliferation and promoted apoptosis of Y79 cells, while
upregulation of HOTTIP promoted proliferation and inhibited apoptosis of
HXO-RB-44 cells. There were target relationships between HOTTIP and
miR-101-3p, and miR-101-3p and STC1. Inhibition of miR-101-3p or
overexpression of STC1 reversed the effect of si-HOTTIP on the proliferation
and apoptosis of RB cells. Xenograft study showed that knockdown of HOTTIP
suppressed the growth of RB in vitro. Conclusion: It could be concluded that HOTTIP sponged miR-101-3p to upregulate STC1
expression, thereby promoting RB cell proliferation and inhibiting
apoptosis.
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Affiliation(s)
- XiangWen Yuan
- Department of Ophthalmology, Jinan People's Hospital, Jinan, Shandong, People's Republic of China
| | - Zhaoyan Sun
- Department of Ophthalmology, Jinan People's Hospital, Jinan, Shandong, People's Republic of China.,Department of Ophthalmology, Tai'an Second Hospital of Traditional Chinese Medicine, Ophthalmology, Tai'an, Shandong, People's Republic of China
| | - Congxian Cui
- The Procurement Office of Logistics Management Department, Affiliated Hospital of Qingdao University, Qingdao, Shandong, People's Republic of China
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Ghafouri-Fard S, Abak A, Mohaqiq M, Shoorei H, Taheri M. The Interplay Between Non-coding RNAs and Insulin-Like Growth Factor Signaling in the Pathogenesis of Neoplasia. Front Cell Dev Biol 2021; 9:634512. [PMID: 33768092 PMCID: PMC7985092 DOI: 10.3389/fcell.2021.634512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
The insulin-like growth factors (IGFs) are polypeptides with similar sequences with insulin. These factors regulate cell growth, development, maturation, and aging via different processes including the interplay with MAPK, Akt, and PI3K. IGF signaling participates in the pathogenesis of neoplasia, insulin resistance, diabetes mellitus, polycystic ovarian syndrome, cerebral ischemic injury, fatty liver disease, and several other conditions. Recent investigations have demonstrated the interplay between non-coding RNAs and IGF signaling. This interplay has fundamental roles in the development of the mentioned disorders. We designed the current study to search the available data about the role of IGF-associated non-coding RNAs in the evolution of neoplasia and other conditions. As novel therapeutic strategies have been designed for modification of IGF signaling, identification of the impact of non-coding RNAs in this pathway is necessary for the prediction of response to these modalities.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atefe Abak
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Mohaqiq
- School of Advancement, Centennial College, Ashtonbee Campus, Toronto, ON, Canada
- Wake Forest Institute for Regenerative Medicine, School of Medicine, Wake Forest University, Winston-Salem, NC, United States
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Biranjd University of Medical Sciences, Birjand, Iran
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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14
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Sun L, Wang P, Zhang Z, Zhang K, Xu Z, Li S, Mao J. MicroRNA-615 functions as a tumor suppressor in osteosarcoma through the suppression of HK2. Oncol Lett 2020; 20:226. [PMID: 32968448 PMCID: PMC7500052 DOI: 10.3892/ol.2020.12089] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
At present, the regulatory mechanisms of various microRNAs (miRNAs/miRs) have been elucidated in human cancers including osteosarcoma (OS). This study mainly focused on the role of miR-615 in OS, which has not yet been reported. Ninety-two OS tissues and normal samples were used in this study. Human osteoblast hFOB1.19 cells and OS cell line HOS were utilized to detect the expression of miR-615. The expression of miR-615 and gene expression were assessed by RT-qPCR and western blot analysis. Transwell, MTT and luciferase reporter assays were used to investigate the regulatory mechanism of miR-615 in OS. The results revealed that miR-615 expression was reduced in OS tissues and cells, and was associated with poor clinical outcomes and prognosis in OS patients. In addition, overexpression of miR-615 restrained cell viability and metastasis in OS. Furthermore, hexokinase 2 (HK2) was confirmed as a direct target of miR-615. Upregulation of HK2 was detected in OS tissues. The upregulation of HK2 weakened the tumor-suppressive effect of miR-615 in OS. Moreover, miR-615 blocked epithelial-mesenchymal transition (EMT) and inactivated the PI3K/AKT pathway in OS. To conclude, miR-615 acts as a tumor suppressor in OS, thus miR-615 can be used as a target for OS treatment.
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Affiliation(s)
- Limin Sun
- Department of Orthopedics, Shandong Provincial Third Hospital, Jinan, Shandong 250031, P.R. China
| | - Peng Wang
- Department of Orthopedics, Shandong Provincial Third Hospital, Jinan, Shandong 250031, P.R. China
| | - Zhiqiang Zhang
- Department of Orthopedics, Shandong Provincial Third Hospital, Jinan, Shandong 250031, P.R. China
| | - Kai Zhang
- Department of Orthopedics, Shandong Provincial Third Hospital, Jinan, Shandong 250031, P.R. China
| | - Zheng Xu
- Department of Orthopedics, Shandong Provincial Third Hospital, Jinan, Shandong 250031, P.R. China
| | - Siyuan Li
- Department of Orthopedics, Shandong Provincial Third Hospital, Jinan, Shandong 250031, P.R. China
| | - Junsheng Mao
- Department of Orthopedic Surgery, Taishan Hospital of Shandong Province, Tai'an, Shandong 271000, P.R. China
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15
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Barth DA, Drula R, Ott L, Fabris L, Slaby O, Calin GA, Pichler M. Circulating Non-coding RNAs in Renal Cell Carcinoma-Pathogenesis and Potential Implications as Clinical Biomarkers. Front Cell Dev Biol 2020; 8:828. [PMID: 33042985 PMCID: PMC7523432 DOI: 10.3389/fcell.2020.00828] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
Liquid biopsy-the determination of circulating cells, proteins, DNA or RNA from biofluids through a "less invasive" approach-has emerged as a novel approach in all cancer entities. Circulating non-(protein) coding RNAs including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and YRNAs can be passively released by tissue or cell damage or actively secreted as cell-free circulating RNAs, bound to lipoproteins or carried by exosomes. In renal cell carcinoma (RCC), a growing body of evidence suggests circulating non-coding RNAs (ncRNAs) such as miRNAs, lncRNAs, and YRNAs as promising and easily accessible blood-based biomarkers for the early diagnosis of RCC as well as for the prediction of prognosis and treatment response. In addition, circulating ncRNAs could also play a role in RCC pathogenesis and progression. This review gives an overview over the current study landscape of circulating ncRNAs and their involvement in RCC pathogenesis as well as their potential utility as future biomarkers in RCC diagnosis and treatment.
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Affiliation(s)
- Dominik A Barth
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Clinical Oncology, Department of Internal Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, Graz, Austria.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rares Drula
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Research Centre for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Leonie Ott
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Tumor Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Linda Fabris
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czechia.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czechia
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing, Division of Clinical Oncology, Department of Internal Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, Graz, Austria.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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16
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Dasgupta P, Kulkarni P, Majid S, Hashimoto Y, Shiina M, Shahryari V, Bhat NS, Tabatabai L, Yamamura S, Saini S, Tanaka Y, Dahiya R. LncRNA CDKN2B-AS1/miR-141/cyclin D network regulates tumor progression and metastasis of renal cell carcinoma. Cell Death Dis 2020; 11:660. [PMID: 32814766 PMCID: PMC7438482 DOI: 10.1038/s41419-020-02877-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 11/09/2022]
Abstract
The molecular heterogeneity of renal cell carcinoma (RCC) complicates the therapeutic interventions for advanced metastatic disease and thus its management remains a significant challenge. This study investigates the role of the lncRNA CDKN2B-AS1 and miR-141-3p interactions in the progression and metastasis of kidney cancer. Human renal cancer cell lines (ACHN and Caki1), normal RPTEC cells, tissue cohorts, and a series of in vitro assays and in vivo mouse model were used for this study. An overexpression of CDKN2B-AS1 was observed in RCC compared to normal samples in TCGA and our in-house SFVAMC tissue cohorts. Reciprocally, we observed reduced expression of miR-141 in RCC compared to normal in the same cohorts. CDKN2B-AS1 shares regulatory miR-141 binding sites with CCND1 and CCND2 genes. Direct interactions of CDKN2B-AS1/miR-141/Cyclin D1-D2 were confirmed by RNA immunoprecipitation and luciferase reporter assays indicating that CDKN2B-AS1/miR-141/Cyclin D1-D2 acts as a ceRNA network in RCC. Functionally, attenuation of CDKN2B-AS1 and/or overexpression of miR-141 inhibited proliferation, clonogenicity, migration/invasion, induced apoptosis in vitro and suppressed tumor growth in xenograft mouse model. Further, overexpression of CDKN2B-AS1 is positively correlated with poor overall survival of RCC patients. Expression of miR-141 also robustly discriminated malignant from non-malignant tissues and its inhibition in normal RPTEC cells induced pro-cancerous characteristics. CDKN2B-AS1 attenuation or miR-141 overexpression decreased CCND1/CCND2 expression, resulting in reduced RAC1/pPXN that are involved in migration, invasion and epithelial-mesenchymal transition. This study, for the first time, deciphered the role of CDKN2B-AS1/miR-141/Cyclin D axis in RCC and highlights this network as a promising therapeutic target for the regulation of EMT driven metastasis in RCC.
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Affiliation(s)
- Pritha Dasgupta
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Priyanka Kulkarni
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Shahana Majid
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Yutaka Hashimoto
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Marisa Shiina
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Varahram Shahryari
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Nadeem S Bhat
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Laura Tabatabai
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Soichiro Yamamura
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Sharanjot Saini
- Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Yuichiro Tanaka
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA
| | - Rajvir Dahiya
- Department of Urology, Veterans Affairs Medical Center, San Francisco and University of California San Francisco, San Francisco, CA, USA.
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17
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miR-615 Fine-Tunes Growth and Development and Has a Role in Cancer and in Neural Repair. Cells 2020; 9:cells9071566. [PMID: 32605009 PMCID: PMC7408929 DOI: 10.3390/cells9071566] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/21/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that function as epigenetic modulators regulating almost any gene expression. Similarly, other noncoding RNAs, as well as epigenetic modifications, can regulate miRNAs. This reciprocal interaction forms a miRNA-epigenetic feedback loop, the deregulation of which affects physiological processes and contributes to a great diversity of diseases. In the present review, we focus on miR-615, a miRNA highly conserved across eutherian mammals. It is involved not only during embryogenesis in the regulation of growth and development, for instance during osteogenesis and angiogenesis, but also in the regulation of cell growth and the proliferation and migration of cells, acting as a tumor suppressor or tumor promoter. It therefore serves as a biomarker for several types of cancer, and recently has also been found to be involved in reparative processes and neural repair. In addition, we present the pleiad of functions in which miR-615 is involved, as well as their multiple target genes and the multiple regulatory molecules involved in its own expression. We do this by introducing in a comprehensible way the reported knowledge of their actions and interactions and proposing an integral view of its regulatory mechanisms.
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18
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Yang N, Dong B, Song Y, Li Y, Kou L, Yang J, Qin Q. Downregulation of miR-637 promotes vascular smooth muscle cell proliferation and migration via regulation of insulin-like growth factor-2. Cell Mol Biol Lett 2020; 25:30. [PMID: 32399056 PMCID: PMC7203897 DOI: 10.1186/s11658-020-00222-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/13/2020] [Indexed: 02/08/2023] Open
Abstract
Background Dysregulation of the proliferation and migration of vascular smooth muscle cells (VSMCs) is a crucial cause of atherosclerosis. MiR-637 exerts an antiproliferative effect on multiple human cells. Its impact on atherosclerosis remains largely unexplored. Methods Real-time PCR was used to determine miR-637 expression in samples from atherosclerosis patients and animal models. Its expression in VSMC dysfunction models (induced by ox-LDL) was also measured. The proliferation and migration of VSMCs were respectively tested using CCK-8 and Transwell assays, and apoptosis was measured using flow cytometry. The Targetscan database was used to predict the target genes of miR-637. Interaction between miR-637 and the potential target gene was validated via real-time PCR, western blotting and a luciferase reporter assay. Results MiR-637 expression was significantly lower in atherosclerosis patient and animal model samples. It also decreased in a dose- and time-dependent manner in animal models with ox-LDL-induced atherosclerosis. Transfection with miR-637 mimics suppressed the proliferation and migration of VSMCs while promoting apoptosis, while transfection with miR-637 inhibitors had the opposite effects. We also validated that insulin-like growth factor-2 (IGF-2), a crucial factor in the pathogenesis of atherosclerosis, serves as a target gene for miR-637. Conclusion MiR-637 targeting IGF-2 contributes to atherosclerosis inhibition and could be a potential target for this disease.
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Affiliation(s)
- Ning Yang
- Department of Cardiology, Tianjin Chest hospital, Taierzhuang South Road No.261, Jinnan District, Tianjin, 300222 China
| | - Bo Dong
- Department of Cardiology, Tianjin Chest hospital, Taierzhuang South Road No.261, Jinnan District, Tianjin, 300222 China
| | - Yanqiu Song
- Department of Cardiology, Tianjin Chest hospital, Taierzhuang South Road No.261, Jinnan District, Tianjin, 300222 China
| | - Yang Li
- Department of Cardiology, Tianjin Chest hospital, Taierzhuang South Road No.261, Jinnan District, Tianjin, 300222 China
| | - Lu Kou
- Department of Cardiology, Tianjin Chest hospital, Taierzhuang South Road No.261, Jinnan District, Tianjin, 300222 China
| | - Jingyu Yang
- Department of Cardiology, Tianjin Chest hospital, Taierzhuang South Road No.261, Jinnan District, Tianjin, 300222 China
| | - Qin Qin
- Department of Cardiology, Tianjin Chest hospital, Taierzhuang South Road No.261, Jinnan District, Tianjin, 300222 China
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19
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Ju Q, Zhao YJ, Ma S, Li XM, Zhang H, Zhang SQ, Yang YM, Yan SX. Genome-wide analysis of prognostic-related lncRNAs, miRNAs and mRNAs forming a competing endogenous RNA network in lung squamous cell carcinoma. J Cancer Res Clin Oncol 2020; 146:1711-1723. [PMID: 32356177 DOI: 10.1007/s00432-020-03224-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE As a type of cancer with the highest morbidity and mortality, lung squamous cell carcinoma (LUSC) has a very poor prognosis. Long-non-coding RNA (lncRNA) has recently attracted attentions because it can play the role of competing endogenous RNA (ceRNA) to inhibit microRNA (miRNA) functions. In this study, we aimed to find prognosis-related lncRNAs, miRNAs and mRNAs and construct a prognosis-related ceRNA network. METHODS The original LUSC RNA-sequencing data and miRNA profiles data were downloaded from the cancer genome atlas (TCGA) database. Differentially expressed lncRNAs, miRNAs and mRNAs were then identified between patients with lymph node metastasis and no lymph node metastasis. Univariate Cox regression analysis was performed to find the survival-associated lncRNAs, miRNAs and mRNAs. Subsequently, prognostic-related ceRNA network was established. By multivariate Cox regression analysis, three lncRNA signatures and three mRNA signatures were developed and used for predicting LUSC patients' survival. RESULTS A total of 224 lncRNAs, 160 miRNAs, 913 mRNAs were identified between samples with lymph node metastasis and no lymph node metastasis. Univariate Cox regression analysis showed that, among them, 28 lncRNAs, 8 miRNAs, 105 mRNAs were significantly associated with patients' overall survival time. Further pathway and enrichment analysis suggested that these mRNAs were associated with the regulation of transmembrane transport, regulation of blood circulation, plasma lipoprotein particle organization. Then we constructed a survival-related ceRNA network including 9 lncRNAs, 8 miRNAs and 23 mRNAs. Additionally, a multivariate Cox regression analysis demonstrated that three lncRNAs (AL161431.1, LINC02389, APCDD1L.DT) and three mRNAs (KLK6, SLITRK5, CCDC177) had a significant prognostic value. Risk score indicated that lncRNA signature and mRNA signature could independently predict overall survival in LUSC patients. CONCLUSION The current study provided a better understanding of the ceRNA network in the progression of LUSC and laid a theoretical foundation for LUSC prognosis.
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Affiliation(s)
- Qiang Ju
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Yan-Jie Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Sai Ma
- Qingdao International Travel Health Center, Qingdao, China
| | - Xin-Mei Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Heng Zhang
- School of Public Health, Qingdao University, Qingdao, China
| | - Shao-Qiang Zhang
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yuan-Ming Yang
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Song-Xia Yan
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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20
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Han L, Yan Y, Zhao L, Liu Y, Lv X, Zhang L, Zhao Y, Zhao H, He M, Wei M. LncRNA HOTTIP facilitates the stemness of breast cancer via regulation of miR-148a-3p/WNT1 pathway. J Cell Mol Med 2020; 24:6242-6252. [PMID: 32307830 PMCID: PMC7294123 DOI: 10.1111/jcmm.15261] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/27/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence suggests that dysregulation of long non‐coding RNA (lncRNA) plays a key role in tumorigenesis. The lncRNA, HOXA transcript at the distal tip (HOTTIP), has been reported to be up‐regulated in multiple cancers, including breast cancer, and is involved in various biological processes, including the maintenance of stemness. However, the biological function and underlying modulatory mechanism of HOTTIP in breast cancer stem cells (BCSCs) remains unknown. In this study, we found that HOTTIP was markedly up‐regulated in BCSCs and had a positive correlation with breast cancer progression. Functional studies revealed that overexpression of HOTTIP markedly promoted cell clonogenicity, increased the expression of the stem cell markers, OCT4 and SOX2, and decreased the expression of the differentiation markers, CK14 and CK18, in breast cancer cells. Knockdown of HOTTIP inhibited the CSC‐like properties of BCSCs. Consistently, depletion of HOTTIP suppressed tumour growth in a humanized model of breast cancer. Mechanistic studies demonstrated that HOTTIP directly binds to miR‐148a‐3p and inhibits the mediation of WNT1, which leads to inactivation of the Wnt/β‐catenin signalling pathway. Our study is the first to report that HOTTIP regulates the CSC‐like properties of BCSCs by as a molecular sponge for miR‐148a‐3p to increase WNT1 expression, offering a new target for breast cancer therapy.
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Affiliation(s)
- Li Han
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Yuanyuan Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Yinuo Liu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Xuemei Lv
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Liwen Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Yanyun Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Haishan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
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21
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Zhao K, Zhang Q, Wang Y, Zhang J, Cong R, Song N, Wang Z. The construction and analysis of competitive endogenous RNA (ceRNA) networks in metastatic renal cell carcinoma: a study based on The Cancer Genome Atlas. Transl Androl Urol 2020; 9:303-311. [PMID: 32420136 PMCID: PMC7215020 DOI: 10.21037/tau.2020.02.17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The pathogenesis of metastatic renal cell carcinoma (mRCC), one of the most common malignant neoplasms, remains unknown. Studies on competitive endogenous RNAs (ceRNAs) have uncovered new interactions between RNAs, which suggest their roles in cancer pathogenesis. However, the role of ceRNA networks in mRCC has not yet been studied. Thus, this study aims to explore the role of ceRNA networks in mRCC development and identify potential prognostic indicators. Methods We analyzed RNA sequencing data of mRCC patients, which had been obtained from The Cancer Genome Atlas (TCGA) database. Next, differentially expressed long-noncoding RNAs (DElncRNAs), differentially expressed micro RNAs (DEmiRNAs), and differentially expressed messenger RNAs (DEmRNAs) in mRCC and clear cell RCC (ccRCC) samples were identified using the edgeR package that is available in R software. Moreover, based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID), enrichment analyses for biological processes and pathways functional were performed. As such, we built a ceRNA network and performed a survival analysis using the survival package in R. Results A total of 369 DElncRNAs, 12 DEmiRNAs, and 728 DEmRNAs were identified for further analysis. Of these, 11 lncRNAs, 20 mRNAs, and 2 miRNAs were included in the ceRNA network. Moreover, 7 of the 11 lncRNAs and 3 of the 20 mRNAs were associated with the overall survival of mRCC patients (P<0.05). Conclusions Collectively, our findings allow a deepened understanding of the molecular mechanism of the ceRNA network and its role in mRCC development, which can guide both mRCC therapy and related future research.
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Affiliation(s)
- Kai Zhao
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Qijie Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yamin Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jiayi Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Rong Cong
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Ninghong Song
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Zengjun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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22
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HOTTIP Functions as a Key Candidate Biomarker in Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatic Analysis. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5450617. [PMID: 31032351 PMCID: PMC6457310 DOI: 10.1155/2019/5450617] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 02/10/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023]
Abstract
Background Accumulating evidence has demonstrated the pivotal role of long noncoding RNAs (lncRNAs) in competing endogenous RNA (ceRNA) networks for predicting survival and evaluating prognosis in cancer patients. However, the pathogenesis of head and neck squamous cell carcinoma (HNSCC) remains unclear, and prognostic biomarkers for HNSCC are still lacking. Methods A total of 546 RNA sequencing profiles of HNSCC patients with clinical outcome data were obtained from the Cancer Genome Atlas (TCGA) database, providing a large sample of RNA sequencing data. From these, 71 Long noncoding RNAs lncRNAs, 8 microRNAs (miRNAs), and 16 messenger RNAs (mRNAs) were identified to construct a HNSCC-specific ceRNA network (fold change >2, P < 0.05). Univariate and multivariate Cox proportional regression models were used to assess independent indicators of prognosis. Then the expression of lncRNAs harboring prognostic value was validated in human HNSCC cell lines and tumor samples from our cohort and another two datasets from GEO (Gene Expression Omnibus) databases. Results As a result, a 3-mRNA signature and 6-lncRNA signature were identified. The six-lncRNA signature exhibited the highest prognostic value. Notably, in the six lncRNAs, HOTTIP showed the greatest prognostic value and was significantly correlated with clinical stage and histological grade of HNSCC patients. Furthermore, it was proved that HOTTIP was upregulated in HNSCC cell lines and cancerous tissues compared with corresponding normal cell lines and normal tissues. Functional assessment analysis revealed that HOTTIP might play a key role in the oncogenesis and progression of HNSCC. Conclusion The present study deepened our understanding of the ceRNA-related regulatory mechanism in the pathogenesis of HNSCC and identified candidate prognostic biomarkers for clinical outcome prediction in HNSCC. HOTTIP may function as a key candidate biomarker in HNSCC and serve as a prognostic marker for HNSCC patients.
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Zhao Q, Liu S. [High expression of MMP20 may be a potential prognostic factor for poor outcomes of patients with endometrial carcinoma]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:1239-1244. [PMID: 30377136 DOI: 10.3969/j.issn.1673-4254.2018.10.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To explore the expression of MMP20 in endometrial carcinoma and its clinical significance. METHODS Bioinformatics analysis was used to explore the correlation of MMP20 expression with the prognosis of the patients with endometrial carcinoma. We collected 21 pairs of fresh endometrial carcinoma and adjacent endometrial tissues to detect the expression of MMP20 mRNA using real-time PCR. We also examined MMP20 protein expressions in 134 paraffin-embedded endometrial carcinoma tissues and 34 paraffin-embedded endometrial tissues using immunohistochemistry. The correlation of MMP20 expression with the clinicopathological features and prognosis of the patients were analyzed. RESULTS Based on TCGA database analysis, the patients with endometrial carcinoma showing an increased MMP20 mRNA expression had a significantly poorer prognosis than those with a low MMP20 mRNA expression (P=0.00065). Real-time PCR analysis and immunohistochemistry confirmed the up-regulated expressions of MMP20 at both the mRNA (P=0.0062) and protein (P=0.005) levels in endometrial carcinoma tissues compared to the adjacent endometrial tissues. An elevated MMP20 protein expression was positively associated with FIGO stage of endometrial carcinoma (P=0.014) and inversely correlated with the survival time of the patients (P=0.019). The Cox regression model analysis showed that an increased MMP20 expression was an independent predictor of a poor prognosis of the patients with endometrial carcinoma (P=0.067). CONCLUSIONS High expression of MMP20 is a potential prognostic factor for poor outcomes of patients with endometrial carcinoma.
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Affiliation(s)
- Qian Zhao
- Department of Infection, Guiyang Maternal and Children's Healthcare Hospital, Guiyang 550003, China
| | - Shu Liu
- Department of Breast, Guiyang Maternal and Children's Healthcare Hospital, Guiyang 550003, China
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