51
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Genetic variant rs10251977 (G>A) in EGFR-AS1 modulates the expression of EGFR isoforms A and D. Sci Rep 2021; 11:8808. [PMID: 33888812 PMCID: PMC8062556 DOI: 10.1038/s41598-021-88161-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
Tyrosine kinase inhibitor is an effective chemo-therapeutic drug against tumors with deregulated EGFR pathway. Recently, a genetic variant rs10251977 (G>A) in exon 20 of EGFR reported to act as a prognostic marker for HNSCC. Genotyping of this polymorphism in oral cancer patients showed a similar frequency in cases and controls. EGFR-AS1 expressed significantly high level in tumors and EGFR-A isoform expression showed significant positive correlation (r = 0.6464, p < 0.0001) with reference to EGFR-AS1 expression levels, consistent with larger TCGA HNSCC tumor dataset. Our bioinformatic analysis showed enrichment of alternative splicing marks H3K36me3 and presence of intronic polyA sites spanning around exon 15a and 15b of EGFR facilitates skipping of exon 15b, thereby promoting the splicing of EGFR-A isoform. In addition, high level expression of PTBP1 and its binding site in EGFR and EGFR-AS1 enhances the expression of EGFR-A isoform (r = 0.7404, p < 0.0001) suggesting that EGFR-AS1 expression modulates the EGFR-A and D isoforms through alternative splicing. In addition, this polymorphism creates a binding site for miR-891b in EGFR-AS1 and may negatively regulate the EGFR-A. Collectively, our results suggested the presence of genetic variant in EGFR-AS1 modulates the expression of EGFR-D and A isoforms.
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Wu QN, Luo XJ, Liu J, Lu YX, Wang Y, Qi J, Liu ZX, Huang QT, Liu ZK, Lu JB, Jin Y, Pu HY, Hu PS, Zheng JB, Zeng ZL, Ju HQ, Xie D, Zhao Q, Xu R. MYC-Activated LncRNA MNX1-AS1 Promotes the Progression of Colorectal Cancer by Stabilizing YB1. Cancer Res 2021; 81:2636-2650. [PMID: 33782099 DOI: 10.1158/0008-5472.can-20-3747] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/20/2021] [Accepted: 03/25/2021] [Indexed: 11/16/2022]
Abstract
Long noncoding RNAs (lncRNA) are involved in tumorigenesis and drug resistance. However, the roles and underlying mechanisms of lncRNAs in colorectal cancer are still unknown. In this work, through transcriptomic profiling analysis of 21 paired tumor and normal samples, we identified a novel colorectal cancer-related lncRNA, MNX1-AS1. MNX1-AS1 expression was significantly upregulated in colorectal cancer and associated with poor prognosis. In vitro and in vivo gain- and loss-of-function experiments showed that MNX1-AS1 promotes the proliferation of colorectal cancer cells. MNX1-AS1 bound to and activated Y-box-binding protein 1 (YB1), a multifunctional RNA/DNA-binding protein, and prevented its ubiquitination and degradation. A marked overlap between genes that are differentially expressed in MNX1-AS1 knockdown cells and transcriptional targets of YB1 was observed. YB1 knockdown mimicked the loss of viability phenotype observed upon depletion of MNX1-AS1. In addition, MYC bound the promoter of the MNX1-AS1 locus and activated its transcription. In vivo experiments showed that ASO inhibited MNX1-AS1, which suppressed the proliferation of colorectal cancer cells in both cell-based and patient-derived xenograft models. Collectively, these findings suggest that the MYC-MNX1-AS1-YB1 axis might serve as a potential biomarker and therapeutic target in colorectal cancer. SIGNIFICANCE: This study highlights the discovery of a novel colorectal cancer biomarker and therapeutic target, MNX1-AS1, a long noncoding RNA that drives proliferation via a MYC/MNX1-AS1/YB1 signaling pathway. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/10/2636/F1.large.jpg.
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Affiliation(s)
- Qi-Nian Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Jing Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun-Xin Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jingjing Qi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi-Tao Huang
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ze-Kun Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Bin Lu
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Jin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Heng-Ying Pu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Pei-Shan Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital (Guangdong Gastrointestinal and Anal Hospital), Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia-Bo Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhao-Lei Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huai-Qiang Ju
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Ruihua Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, China
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53
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Luo Y, Zheng S, Wu Q, Wu J, Zhou R, Wang C, Wu Z, Rong X, Huang N, Sun L, Bin J, Liao Y, Shi M, Liao W. Long noncoding RNA (lncRNA) EIF3J-DT induces chemoresistance of gastric cancer via autophagy activation. Autophagy 2021; 17:4083-4101. [PMID: 33764843 DOI: 10.1080/15548627.2021.1901204] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chemotherapy is currently the main treatment for unresectable or advanced postoperative gastric cancers. However, its efficacy is negatively affected by the occurrence of chemoresistance, which severely affects patient prognosis. Recently, dysregulation in autophagy has been suggested as a potential mechanism for chemoresistence, and long noncoding RNA (lncRNA) also shows its regulatory role in cancer drug resistance. Using RNA sequencing, we found that lncRNA EIF3J-DT was highly expressed in drug-resistant gastric cancer cells. In-vitro and in-vivo experiments showed that EIF3J-DT activated autophagy and induced drug resistance in gastric cancer cells by targeting ATG14. Bioinformatics and experimental results showed that EIF3J-DT regulated the expression of ATG14 through direct binding to enhance stabilization of ATG14 mRNA and via blocking the degradation of ATG14 mRNA through competitively binding with microRNA (miRNA) MIR188-3p. Therefore, EIF3J-DT increased the expression of ATG14, contributing to activation of autophagy and chemoresistance. Furthermore, it was confirmed that EIF3J-DT and ATG14 were highly expressed in gastric cancer patients resistant to chemotherapy, and this was closely associated with patient prognosis. In conclusion, EIF3J-DT is involved in the regulation of autophagy and chemoresistance in gastric cancer cells by targeting ATG14. It may be a suitable new target for enhancing chemosensitivity and improving prognosis.Abbreviations: 3-MA: 3-methyladenine; 5-Fu: 5-fluorouracil; ATG: autophagy related; C-CASP3: cleaved caspase 3; C-CASP7: cleaved caspase 7; C-PARP: cleaved PARP; CQ: chloroquine; CR: complete response; DIG: digoxigenin; ESR1: estrogen receptor 1; FBS: fetal bovine serum; FISH: fluorescence in situ hybridization; IHC: immunohistochemistry; ISH: in situ hybridization; lncRNA: long noncoding RNA; miRNA: microRNA; MUT: mutant; NC: negative control; OXA: oxaliplatin; PBS: phosphate-buffered saline; PD: progressive disease; PFA: paraformaldehyde; PR: partial response; qPCR: quantitative polymerase chain reaction; RAPA: rapamycin; SD: stable disease; TEM: transmission electron microscopy; WT: wild type.
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Affiliation(s)
- Yuhao Luo
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Siting Zheng
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qianying Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianhua Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Rui Zhou
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chunling Wang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhenzhen Wu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoxiang Rong
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Na Huang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Li Sun
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jianping Bin
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yulin Liao
- Department of Cardiology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Min Shi
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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54
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Geng Q, Li Z, Li X, Wu Y, Chen N. LncRNA NORAD, sponging miR-363-3p, promotes invasion and EMT by upregulating PEAK1 and activating the ERK signaling pathway in NSCLC cells. J Bioenerg Biomembr 2021; 53:321-332. [PMID: 33742335 DOI: 10.1007/s10863-021-09892-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/09/2021] [Indexed: 12/30/2022]
Abstract
Lung cancer is one of the most common malignant tumors in the world. Non-small cell lung cancer (NSCLC) accounts for about 80% of all lung cancers. About 75% of patients are in the middle and advanced stages at the time of discovery, and the 5-year survival rate is very low. The aim of this study was to investigate the role of long non-coding RNA (lncRNA) NORAD in the pathogenesis of NSCLC. We found that lncRNA NORAD was highly expressed in human NSCLC tissues and cell lines. The CCK-8 assay results showed that lncRNA NORAD had no effect on cell proliferation. The Transwell assay and Western blotting results showed that overexpression of lncRNA NORAD promoted the invasion and epithelial-mesenchymal transition (EMT) of NSCLC cells. Then bioinformatics analysis was used to screen for candidate miRNA bound with lncRNA NORAD and the target gene of miRNA in NSCLC. The luciferase reporter gene assay and RNA pull-down assay were used to verify the relationship. We found that miR-363-3p expression was down-regulated, whereas PEAK1 expression was upregulated in NSCLC cells. We performed gain and loss function test of lncRNA NORAD, miR-363-3p and PEAK1, the results showed that while miR-363-3p-mimic inhibited cell invasion and EMT by targeting PEAK1, lncRNA NORAD acted as a sponge of miR-363-3p and promoted cell invasion and EMT by increasing the expression of PEAK1. In addition, p-ERK expression was detected by Western blotting to observe the effects of lncRNA NORAD, miR-363-3p and PEAK1 on activation of the ERK signaling pathway. Taken together, lncRNA NORAD upregulated the expression of PEAK1 through sponging miR-363-3p, and then activated the ERK signaling pathway, thereby promoting the development of NSCLC.
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Affiliation(s)
- Qianqian Geng
- Department of Nuclear Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Zhubin Li
- Department of Minimally Invasive Intervention, Shaanxi Province Tumor Hospital, Xi'an, 710061, China
| | - Xintao Li
- The Second Department of Internal Medicine, Shaanxi Province Tumor Hospital, Xi'an, 710061, China
| | - Yunhua Wu
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Nanzheng Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China.
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55
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Kalhori MR, Khodayari H, Khodayari S, Vesovic M, Jackson G, Farzaei MH, Bishayee A. Regulation of Long Non-Coding RNAs by Plant Secondary Metabolites: A Novel Anticancer Therapeutic Approach. Cancers (Basel) 2021; 13:cancers13061274. [PMID: 33805687 PMCID: PMC8001769 DOI: 10.3390/cancers13061274] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/05/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Cancer is caused by the rapid and uncontrolled growth of cells that eventually lead to tumor formation. Genetic and epigenetic alterations are among the most critical factors in the onset of carcinoma. Phytochemicals are a group of natural compounds that play an essential role in cancer prevention and treatment. Long non-coding RNAs (lncRNAs) are potential therapeutic targets of bioactive phytochemicals, and these compounds could regulate the expression of lncRNAs directly and indirectly. Here, we critically evaluate in vitro and in vivo anticancer effects of phytochemicals in numerous human cancers via regulation of lncRNA expression and their downstream target genes. Abstract Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs that play an essential role in various cellular activities, such as differentiation, proliferation, and apoptosis. Dysregulation of lncRNAs serves a fundamental role in the progression and initiation of various diseases, including cancer. Precision medicine is a suitable and optimal treatment method for cancer so that based on each patient’s genetic content, a specific treatment or drug is prescribed. The rapid advancement of science and technology in recent years has led to many successes in this particular treatment. Phytochemicals are a group of natural compounds extracted from fruits, vegetables, and plants. Through the downregulation of oncogenic lncRNAs or upregulation of tumor suppressor lncRNAs, these bioactive compounds can inhibit metastasis, proliferation, invasion, migration, and cancer cells. These natural products can be a novel and alternative strategy for cancer treatment and improve tumor cells’ sensitivity to standard adjuvant therapies. This review will discuss the antineoplastic effects of bioactive plant secondary metabolites (phytochemicals) via regulation of expression of lncRNAs in various human cancers and their potential for the treatment and prevention of human cancers.
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Affiliation(s)
- Mohammad Reza Kalhori
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6714415185, Iran;
| | - Hamid Khodayari
- International Center for Personalized Medicine, 40235 Düsseldorf, Germany; (H.K.); (S.K.)
- Breast Disease Research Center, Tehran University of Medical Sciences, Tehran 1419733141, Iran
| | - Saeed Khodayari
- International Center for Personalized Medicine, 40235 Düsseldorf, Germany; (H.K.); (S.K.)
- Breast Disease Research Center, Tehran University of Medical Sciences, Tehran 1419733141, Iran
| | - Miko Vesovic
- Department of Mathematics, Statistics, and Computer Science, University of Illinois at Chicago, Chicago, IL 60607, USA;
| | - Gloria Jackson
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
| | - Mohammad Hosein Farzaei
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6718874414, Iran
- Correspondence: (M.H.F.); or (A.B.)
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton, FL 34211, USA;
- Correspondence: (M.H.F.); or (A.B.)
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56
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Sur S, Ray RB. Diverse roles of bitter melon ( Momordica charantia) in prevention of oral cancer. JOURNAL OF CANCER METASTASIS AND TREATMENT 2021; 7:12. [PMID: 34765739 PMCID: PMC8580380 DOI: 10.20517/2394-4722.2020.126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is one of the common lethal malignancies which is increasing rapidly in the world. Increasing risks from alcohol and tobacco habits, lack of early detection markers, lack of effective chemotherapeutic agents, recurrence and distant metastasis make the disease more complicated to manage. Laboratory-based studies and epidemiological studies indicate important roles of nutraceuticals to manage different cancers. The plant bitter melon (Momordica charantia) is a good source of nutrients and bio-active phytochemicals such as triterpenoids, triterpene glycosides, phenolic acids, flavonoids, lectins, sterols and proteins. The plant is widely grown in Asia, Africa, and South America. Bitter melon has traditionally been used as a folk medicine and Ayurvedic medicine in Asian culture to treat diseases such as diabetes, since ancient times. The crude extract and some of the isolated pure compounds of bitter melon show potential anticancer effects against different cancers. In this review, we shed light on its effect on OSCC. Bitter melon extract has been found to inhibit cell proliferation and metabolism, induce cell death and enhance the immune defense system in the prevention of OSCC in vitro and in vivo. Thus, bitter melon may be used as an attractive chemopreventive agent in progression towards OSCC clinical study.
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Affiliation(s)
- Subhayan Sur
- Department of Pathology, Saint Louis University, St. Louis, MO 63104, USA
| | - Ratna B. Ray
- Department of Pathology, Saint Louis University, St. Louis, MO 63104, USA
- Cancer Center, Saint Louis University, St. Louis, MO 63104, USA
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de Kort WWB, Spelier S, Devriese LA, van Es RJJ, Willems SM. Predictive Value of EGFR-PI3K-AKT-mTOR-Pathway Inhibitor Biomarkers for Head and Neck Squamous Cell Carcinoma: A Systematic Review. Mol Diagn Ther 2021; 25:123-136. [PMID: 33686517 PMCID: PMC7956931 DOI: 10.1007/s40291-021-00518-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Understanding molecular pathogenesis of head and neck squamous cell carcinomas (HNSCC) has considerably improved in the last decades. As a result, novel therapeutic strategies have evolved, amongst which are epidermal growth factor receptor (EGFR)-targeted therapies. With the exception of cetuximab, targeted therapies for HNSCC have not yet been introduced into clinical practice. One important aspect of new treatment regimes in clinical practice is presence of robust biomarkers predictive for therapy response. METHODS We performed a systematic search in PubMed, Embase and the Cochrane library. Articles were included if they investigated a biomarker for targeted therapy in the EGFR-PI3K-AKT-mTOR-pathway. RESULTS Of 83 included articles, 52 were preclinical and 33 were clinical studies (two studies contained both a preclinical and a clinical part). We classified EGFR pathway inhibitor types and investigated the type of biomarker (biomarker on epigenetic, DNA, mRNA or protein level). CONCLUSION Several EGFR-PI3K-AKT-mTOR-pathway inhibitor biomarkers have been researched for HNSCC but few of the investigated biomarkers have been adequately confirmed in clinical trials. A more systematic approach is needed to discover proper biomarkers as stratifying patients is essential to prevent unnecessary costs and side effects.
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Affiliation(s)
- W W B de Kort
- Department of Pathology, University Medical Center Utrecht, PO Box 885500, 3508 GA, Utrecht, The Netherlands.
| | - S Spelier
- Department of Pathology, University Medical Center Utrecht, PO Box 885500, 3508 GA, Utrecht, The Netherlands
| | - L A Devriese
- Department of Medical Oncology, University Medical Center Utrecht, PO Box 885500, 3508 GA, Utrecht, The Netherlands
| | - R J J van Es
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, PO Box 885500, 3508 GA, Utrecht, The Netherlands.,Department of Head and Neck Surgical Oncology, Utrecht Cancer Center, University Medical Center Utrecht, PO Box 885500, 3508 GA, Utrecht, The Netherlands
| | - S M Willems
- Department of Pathology, University Medical Center Utrecht, PO Box 885500, 3508 GA, Utrecht, The Netherlands.,Department of Pathology, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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58
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Low JL, Lau DP, Zhang X, Kwang XL, Rohatgi N, Chan JV, Chong FT, Wong SQR, Leong HS, Thangavelu MT, Rikka S, Skanderup AMJ, Tan DSW, Periyasamy G, Koh JLY, Iyer NG, DasGupta R. A chemical genetic screen identifies Aurora kinases as a therapeutic target in EGFR T790M negative, gefitinib-resistant head and neck squamous cell carcinoma (HNSCC). EBioMedicine 2021; 64:103220. [PMID: 33529999 PMCID: PMC7851772 DOI: 10.1016/j.ebiom.2021.103220] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 01/03/2021] [Accepted: 01/10/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Overexpression of epidermal growth factor receptor (EGFR), and downstream pathway activation appears to be a common oncogenic driver in the majority of head and neck squamous cell cancers (HNSCCs); yet targeting EGFR for the treatment of HNSCC has met with limited success. Apart from the anti-EGFR antibody cetuximab, no small molecule EGFR/tyrosine kinase inhibitors (TKIs) have progressed to routine clinical use. The aim of this study was to determine factors contributing to the lack of response to TKIs and identify alternative therapeutic vulnerabilities. METHODS Genomic and transcriptomic sequencing, high-throughput compound screens, overexpression and siRNA knockdown, western blot, in vivo xenograft studies. FINDINGS We derived three pairs of isogenic gefitinib (TKI)-sensitive and resistant patient-derived HNSCC cell lines. Genomic sequencing of gefitinib-resistant cell lines identified a lack of activating and resistance-associated EGFR mutations. Instead, transcriptomic sequencing showed upregulated EMT gene signature in the gefitinib-resistant cells with a corresponding increase in their migratory phenotype. Additionally, the resistant cell displayed reduced growth rate. Surprisingly, while gefitinib-resistant cells were independent of EGFR for survival, they nonetheless displayed activation of downstream ERK and AKT signalling. High-throughput screening (HTS) of druggable, small molecule libraries revealed that the gefitinib-resistant cells were particularly sensitive to inhibitors of genes involved in cell cycle and mitosis, such as Aurora kinase inhibitors (AKIs), cyclin-dependent kinase (CDK) inhibitors, and microtubule inhibitors. Notably our results showed that in the EGFR inhibited state, Aurora kinases are essential for cell survival. INTERPRETATION Our study demonstrates that in the absence of activating EGFR mutations, HNSCCs may gain resistance to gefitinib through decreased cell proliferation, which makes them exceptionally vulnerable to cell-cycle inhibitors. FUNDING Agency for Science, Technology, and Research (A*STAR), National Medical Research Council (NMRC), and the National Institutes of Health (NIH)/National Cancer Institute (NCI).
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Affiliation(s)
- Joo-Leng Low
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - Dawn Pingxi Lau
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Xiaoqian Zhang
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - Xue-Lin Kwang
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Neha Rohatgi
- Laboratory of Computational Cancer Genomics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Jane Vin Chan
- Computational Phenomics Platform, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Fui-Teen Chong
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Stephen Qi Rong Wong
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - Hui-Sun Leong
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Matan Thangavelu Thangavelu
- Centre for High Throughput Phenomics (CHiP-GIS), Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Shivaji Rikka
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore; Centre for High Throughput Phenomics (CHiP-GIS), Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Anders Martin Jacobsen Skanderup
- Laboratory of Computational Cancer Genomics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Daniel Shao Weng Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore
| | - Giridharan Periyasamy
- Centre for High Throughput Phenomics (CHiP-GIS), Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Judice Lie Yong Koh
- Computational Phenomics Platform, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - N Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore 169610, Singapore.
| | - Ramanuj DasGupta
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore.
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EGFR Protein Expression Relates with Tumor Histology, Methylation Status of EGFR and HPV16 E6 Viral Load in Oropharyngeal Carcinoma. Head Neck Pathol 2021; 15:743-756. [PMID: 33428063 PMCID: PMC8385027 DOI: 10.1007/s12105-020-01261-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 10/22/2022]
Abstract
The epidermal growth factor receptor (EGFR) pathway is important in tumorigenesis of oropharyngeal carcinoma (OPC). However, the molecular mechanisms contributing to EGFR expression in OPC are not well-known. To detect relating factors and clinicopathological impact of EGFR protein expression in OPC, gene amplification/loss, point mutations including synonymous mutations, and promoter methylation of EGFR, and the viral genome load of human papillomavirus type 16 (HPV16)-E5, -E6, and -E7, after extracting HPV16-related OPCs with qPCR of HPV16-E6 and E7, were investigated in 74 OPC surgical cases, including 52 HPV-related (HPV-OPC) and 22 HPV-unrelated (nHPV-OPC). Immunohistochemical (IHC) data of EGFR expression (high, weak, and negative), validated by the qPCR of EGFR mRNA, were compared with molecular, viral, and clinicopathological data of patients. All nHPV-OPC cases were EGFR-IHC-high, whereas 21.2%, 65.4%, and 13.5% of HPV-OPC cases showed EGFR-IHC-high, -weak, -negative (p < 0.01), respectively. In HPV-OPC cases, EGFR-IHC-weak/negative status was related to promoter methylation of EGFR (p = 0.009), but not with gene amplification/loss or the point mutation of EGFR and was more often seen in HPV16-OPC cases (p = 0.049). Among HPV16-OPC cases, EGFR-IHC-weak/negative was related to high E6 expression. EGFR protein-loss was related to the tumor histology of non-keratinizing squamous cell carcinoma (SCC) (p = 0.035) but not with patient prognosis. In conclusion, decreased EGFR protein expression was more frequent in HPV-OPC than in nHPV-OPC and was related to EGFR methylation, infection of HPV16, and the viral genome load of HPV16-E6. Clinicopathologically, it was related to the tumor histology of non-keratinizing SCC.
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Lin Z, Gong J, Zhong G, Hu J, Cai D, Zhao L, Zhao Z. Identification of Mutator-Derived Alternative Splicing Signatures of Genomic Instability for Improving the Clinical Outcome of Cholangiocarcinoma. Front Oncol 2021; 11:666847. [PMID: 34055632 PMCID: PMC8160381 DOI: 10.3389/fonc.2021.666847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/26/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Cholangiocarcinoma is an aggressive carcinoma with increasing incidence and poor outcomes worldwide. Genomic instability and alternative splicing (AS) events are hallmarks of carcinoma development and progression. The relationship between genomic instability, AS events, and tumor immune microenvironment remain unclear. METHODS The splicing profiles of patients with cholangiocarcinoma were obtained from The Cancer Genome Atlas (TCGA) spliceSeq database. The transcriptomics, simple nucleotide variation (SNP) and clinical data of patients with cholangiocarcinoma were obtained from TCGA database. Patients were divided into genomic unstable (GU-like) and genomic stable (GS-like) groups according to their somatic mutations. Survival-related differential AS events were identified through integrated analysis of splicing profiling and clinical data. Kyoto Encyclopedia of Genes and Genomes enrichment analysis was used to identify AS events occurring in genes enriched in cancer pathways. Pearson correlation was applied to analyze the splicing factors regulating AS events. CIBERSORT was used identify differentially infiltrating immune cells. RESULTS A prognostic signature was constructed with six AS events. Using this signature, the hazard ratio of risk score for overall survival is 2.362. For TCGA patients with cholangiocarcinoma, the area under the receiver operating characteristic curve is 0.981. CDK11A is a negative regulator of survival associated AS events. Additionally, the CD8+ T cell proportion and PD-L1 expression are upregulated in patients with cholangiocarcinoma and high splicing signatures. CONCLUSION We provide a prognostic signature for cholangiocarcinoma overall survival. The CDK11A splicing factor and SLC46A1-39899-ES and IARS-86836-ES AS events may be potential targets for cholangiocarcinoma therapy. Patients with high AS risk score may be more sensitive to anti-PD-L1/PD1 immunotherapy.
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Affiliation(s)
- Zijing Lin
- Department of Breast and Thyroid Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianping Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Guochao Zhong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Jiejun Hu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Dong Cai
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Lei Zhao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital & Centre for Lipid Research & Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Chongqing Medical University, Chongqing, China
- *Correspondence: Zhibo Zhao, ; Lei Zhao,
| | - Zhibo Zhao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
- *Correspondence: Zhibo Zhao, ; Lei Zhao,
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Wang L, Xiao B, Yu T, Gong L, Wang Y, Zhang X, Zou Q, Zuo Q. lncRNA PVT1 promotes the migration of gastric cancer by functioning as ceRNA of miR-30a and regulating Snail. J Cell Physiol 2021; 236:536-548. [PMID: 32557622 DOI: 10.1002/jcp.29881] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/26/2020] [Accepted: 06/03/2020] [Indexed: 01/17/2023]
Abstract
Although the incidence and mortality of gastric cancer (GC) are slowly decreasing, the overall prognosis of GC patients with distal metastasis remains dismal. Long non-coding RNA PVT1 has been verified to function as a tumor promoter in several types of cancer. However, the role of PVT1 in GC metastasis remains obscure. Herein, we found that PVT1 was highly expressed in GC tissues and high PVT1 level was associated with tumor stage, lymph node metastasis, and poor prognosis. Overexpression of PVT1 significantly elevated epithelial-to-mesenchymal transition (EMT) marker (N-cadherin, ZEB1, and ZEB2) levels and promoted GC cell EMT process and tumor metastasis in vitro and in vivo. Mechanistically, Snail was identified as a direct target of miR-30a. PVT1 could bind with miR-30a and increase the expression of Snail by acting as a competing endogenous RNA, whereas re-expression of miR-30a in GC cells rescued the EMT markers, decreased Snail level, and inhibited GC cell migration. Taken together, these findings provide a new light on PVT1 in the pathogenesis and development of GC and an important implication for future therapy of the GC.
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Affiliation(s)
- Lina Wang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, China
| | - Bin Xiao
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Ting Yu
- Department of Clinical Laboratory, The 89th Hospital of The People's Liberation Army, Weifang, China
| | - Li Gong
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University (General Hospital), Chongqing, China
| | - Yu Wang
- Department of Basic Courses, NCO School, Army Medical University, Shijiazhuang, China
| | - Xiaokai Zhang
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Army Medical University, Chongqing, China
| | - Quanming Zou
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Army Medical University, Chongqing, China
| | - Qianfei Zuo
- Department of Microbiology and Biochemical Pharmacy, National Engineering Research Center of Immunological Products, College of Pharmacy, Army Medical University, Chongqing, China
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EGFR-AS1 Promotes Bladder Cancer Progression by Upregulating EGFR. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6665974. [PMID: 33426060 PMCID: PMC7781701 DOI: 10.1155/2020/6665974] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/13/2020] [Indexed: 11/17/2022]
Abstract
Long noncoding RNAs play an essential role in bladder cancer progression. The role of long noncoding RNA EGFR-AS1 in bladder cancer needs further study. We used clinical specimens to analyze the relationship between EGFR-AS1 and bladder cancer patients' characteristics. The functional experiments and mechanism studies were performed using qRT-PCR, transwell assay, survival analysis, and correlation analysis. We found that high expression of EGFR-AS1 was nearly related to aggressive bladder cancer and indicated poor prognosis for patients. The functional experiments in vivo and in vitro suggested that EGFR-AS1 promoted the proliferation and invasion of bladder cancer cells. Mechanically, EGFR-AS1 promoted the expression of EGFR by inhibiting the degradation of EGFR mRNA, thereby promoting the metastasis of bladder cancer. In addition, EGFR-AS1/EGFR may be involved in the immune-related pathways of bladder cancer. These studies indicate that the EGFR-AS1/EGFR pathway may be a potential diagnostic marker and therapeutic target for bladder cancer.
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Sur S, Nakanishi H, Steele R, Zhang D, Varvares MA, Ray RB. Long non-coding RNA ELDR enhances oral cancer growth by promoting ILF3-cyclin E1 signaling. EMBO Rep 2020; 21:e51042. [PMID: 33043604 PMCID: PMC7726807 DOI: 10.15252/embr.202051042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/22/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the sixth most common cancer with a 5-year overall survival rate of 50%. Thus, there is a critical need to understand the disease process, and to identify improved therapeutic strategies. Previously, we found the long non-coding RNA (lncRNA) EGFR long non-coding downstream RNA (ELDR) induced in a mouse tongue cancer model; however, its functional role in human oral cancer remained unknown. Here, we show that ELDR is highly expressed in OSCC patient samples and in cell lines. Overexpression of ELDR in normal non-tumorigenic oral keratinocytes induces cell proliferation, colony formation, and PCNA expression. We also show that ELDR depletion reduces OSCC cell proliferation and PCNA expression. Proteomics data identifies the RNA binding protein ILF3 as an interacting partner of ELDR. We further show that the ELDR-ILF3 axis regulates Cyclin E1 expression and phosphorylation of the retinoblastoma (RB) protein. Intratumoral injection of ELDR-specific siRNA reduces OSCC and PDX tumor growth in mice. These findings provide molecular insight into the role of ELDR in oral cancer and demonstrate that targeting ELDR has promising therapeutic potential.
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Affiliation(s)
- Subhayan Sur
- Department of PathologySaint Louis UniversitySaint LouisMOUSA
| | | | - Robert Steele
- Department of PathologySaint Louis UniversitySaint LouisMOUSA
| | - Dapeng Zhang
- Department of BiologySaint Louis UniversitySaint LouisMOUSA
| | - Mark A Varvares
- Saint Louis University Cancer CenterSaint LouisMOUSA
- Department of Otolaryngology, Head and Neck SurgeryMassachusetts Eye and EarHarvard Medical SchoolBostonMAUSA
| | - Ratna B Ray
- Department of PathologySaint Louis UniversitySaint LouisMOUSA
- Saint Louis University Cancer CenterSaint LouisMOUSA
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Zhang W, Zeng B, Yang M, Yang H, Wang J, Deng Y, Zhang H, Yao G, Wu S, Li W. ncRNAVar: A Manually Curated Database for Identification of Noncoding RNA Variants Associated with Human Diseases. J Mol Biol 2020; 433:166727. [PMID: 33275967 DOI: 10.1016/j.jmb.2020.166727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/22/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022]
Abstract
While variants of noncoding RNAs (ncRNAs) have been experimentally validated as a new class of biomarkers and drug targets, the discovery and interpretation of relationships between ncRNA variants and human diseases become important and challenging. Here we present ncRNAVar (http://www.liwzlab.cn/ncrnavar/), the first database that provides association data between validated ncRNA variants and human diseases through manual curation on 2650 publications and computational annotation. ncRNAVar contains 4565 associations between 711 human disease phenotypes and 3112 variants from 2597 ncRNAs. Each association was reviewed by professional curators, incorporated with valuable annotation and cross references, and designated with an association score by our refined score model. ncRNAVar offers web applications including association prioritization, network visualization, and relationship mapping. ncRNAVar, presenting a landscape of ncRNA variants in human diseases and a useful resource for subsequent software development, will improve our insight of relationships between ncRNA variants and human health.
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Affiliation(s)
- Wenliang Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Binghui Zeng
- Guanghua School of Stomatology, Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Minglei Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Huan Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jianbo Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yongjie Deng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Haiyue Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Guocai Yao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Song Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Ministry of Education, Guangzhou 510080, China.
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Yao L, Ye PC, Tan W, Luo YJ, Xiang WP, Liu ZL, Fu ZM, Lu F, Tang LH, Xiao JW. Decreased expression of the long non-coding RNA HOXD-AS2 promotes gastric cancer progression by targeting HOXD8 and activating PI3K/Akt signaling pathway. World J Gastrointest Oncol 2020; 12:1237-1254. [PMID: 33250958 PMCID: PMC7667460 DOI: 10.4251/wjgo.v12.i11.1237] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/27/2020] [Accepted: 10/21/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been shown to be associated with many tumors. However, the specific mechanism of lncRNAs in the occurrence and development of gastric cancer (GC) has not been fully elucidated.
AIM To explore the expression level and molecular mechanism of HOXD-AS2 in GC tissues and cells, and analyze its significance in the prognosis of GC.
METHODS Real-time quantitative PCR was used to detect the expression of HOXD-AS2 in 79 pairs of GC tissues and five cell lines. The pcHOXD-AS2 plasmid vector was constructed and transfected into SGC-7901 and SNU-1 GC cells. Matrigel Transwell and wound healing assays were used to confirm the effect of HOXD-AS2 on invasion and migration of GC cells. Cell counting kit-8 assay and flow cytometry were used to verify the effect of HOXD-AS2 on the proliferation, cell cycle, and apoptosis of GC cells. The relevant regulatory mechanism between HOXD-AS2 and HOXD8 and PI3K/Akt signaling pathway was verified by Western blot analysis.
RESULTS The low expression of lncRNA HOXD-AS2 was associated with lymph node metastasis and tumor-node-metastasis stage in GC. In vitro functional experiments demonstrated that overexpression of HOXD-AS2 inhibited GC cell progression. Mechanistic studies revealed that HOXD-AS2 regulated the expression of its nearby gene HOXD8 and inhibited the activity of the PI3K/Akt signaling pathway.
CONCLUSION These results indicate that downregulation of HOXD-AS2 significantly promotes the progression of GC cells by regulating HOXD8 expression and activating the PI3K/Akt signaling pathway. HOXD-AS2 may be a novel diagnostic biomarker and effective therapeutic target for GC.
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Affiliation(s)
- Lin Yao
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu 610000, Sichuan Province, China, The Hepatobiliary Research Institute, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
- Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, The Hepatobiliary Research Institute, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Peng-Cheng Ye
- Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, The Hepatobiliary Research Institute, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Wang Tan
- Department of Gastrointestinal Surgery, Yaan People’s Hospital, Yaan 625000, Sichuan Province, China
| | - Ya-Jun Luo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Wan-Ping Xiang
- Department of Thoracic Surgery, Nanchong Central Hospital, Nanchong 637000, Sichuan Province, China
| | - Zi-Lin Liu
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu 610000, Sichuan Province, China
| | - Zhi-Ming Fu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, The Hepatobiliary Research Institute, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Fei Lu
- Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, The Hepatobiliary Research Institute, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Ling-Han Tang
- Department of Gastrointestinal Surgery, The Affiliated Hospital of North Sichuan Medical College, The Hepatobiliary Research Institute, North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Jiang-Wei Xiao
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu 610000, Sichuan Province, China
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lncRNA HotairM1 Depletion Promotes Self-Renewal of Cancer Stem Cells through HOXA1-Nanog Regulation Loop. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:456-470. [PMID: 33230449 PMCID: PMC7554324 DOI: 10.1016/j.omtn.2020.09.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/11/2020] [Indexed: 01/10/2023]
Abstract
In cancer cells, a gain of stemness may have profound implications for tumor initiation, aggressiveness, and clinical outcome. However, the molecular mechanisms underlying the self-renewal maintenance of cancer stem-like cells (CSCs) remain elusive. Here, based on analysis of transcriptome sequencing, we identified a long noncoding RNA (lncRNA) named HotairM1, which is weakly expressed in human colorectal carcinoma and uveal melanoma, and a much lower expression in corresponding CSCs. Our results showed that HotairM1 depletion could promote CSC self-renewal and tumor propagation. Mechanistically, HotairM1 recruit EZH2 and SUZ12 to the promoter of its target gene HOXA1, leading to histone H3K27 trimethylation and epigenetic silencing of HOXA1. The silence of HOXA1 subsequently induces the H3K27 acetylation at the enhancer site of Nanog gene to upregulate its expression. The enrichment of Nanog could further inhibit HOXA1 expression, forming a reciprocal regulation loop augmenting the stemness maintaining effect. In summary, our results revealed a lncRNA-based regulatory loop that sustains self-renewal of CSCs, which highlights the critical role of HotairM1 in CSC development through the HOXA1-Nanog signaling loop.
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Schuch LF, Silveira FM, Wagner VP, Borgato GB, Rocha GZ, Castilho RM, Vargas PA, Martins MD. Head and neck cancer patient-derived xenograft models - A systematic review. Crit Rev Oncol Hematol 2020; 155:103087. [PMID: 32992152 DOI: 10.1016/j.critrevonc.2020.103087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Patient-derived xenograft (PDX) involve the direct surgical transfer of fresh human tumor samples to immunodeficient mice. This systematic review aimed to identify publications of head and neck cancer PDX (HNC-PDX) models, describing the main methodological characteristics and outcomes. METHODS An electronic search was undertaken in four databases, including publications having used HNC-PDX. Data were analyzed descriptively. RESULTS 63 articles were yielded. The nude mouse was one most commonly animal model used (38.8 %), and squamous cell carcinoma accounted for the majority of HNC-PDX (80.6 %). Tumors were mostly implanted in the flank (86.3 %), and the latency period ranged from 30 to 401 days. The successful rate ranged from 17 % to 100 %. Different drugs and pathways were identified. CONCLUSION HNC-PDX appears to significantly recapitulate the morphology of the original HNC and represents a valuable method in translational research for the assessment of the in vivo effect of novel therapies for HNC.
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Affiliation(s)
- Lauren F Schuch
- Department of Oral Diagnosis, Piracicaba Dental School, Universidade de Campinas, Piracicaba, SP, Brazil
| | - Felipe M Silveira
- Department of Oral Diagnosis, Piracicaba Dental School, Universidade de Campinas, Piracicaba, SP, Brazil
| | - Vivian P Wagner
- Department of Oral Diagnosis, Piracicaba Dental School, Universidade de Campinas, Piracicaba, SP, Brazil
| | - Gabriell B Borgato
- Department of Oral Diagnosis, Piracicaba Dental School, Universidade de Campinas, Piracicaba, SP, Brazil
| | - Guilherme Z Rocha
- Department of Oral Diagnosis, Piracicaba Dental School, Universidade de Campinas, Piracicaba, SP, Brazil
| | - Rogerio M Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, 48109-1078, United States; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Pablo A Vargas
- Department of Oral Diagnosis, Piracicaba Dental School, Universidade de Campinas, Piracicaba, SP, Brazil
| | - Manoela D Martins
- Department of Oral Diagnosis, Piracicaba Dental School, Universidade de Campinas, Piracicaba, SP, Brazil; Department of Oral Pathology, School of Dentistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Ji Y, Xue Y. Identification and Clinical Validation of 4-lncRNA Signature for Predicting Survival in Head and Neck Squamous Cell Carcinoma. Onco Targets Ther 2020; 13:8395-8411. [PMID: 32904613 PMCID: PMC7457573 DOI: 10.2147/ott.s257200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/26/2020] [Indexed: 12/24/2022] Open
Abstract
Background The prognosis of patients with head and neck squamous cell carcinoma (HNSCC) is still poor due to the lack of effective prognostic biomarkers. lncRNA is an important survival prognostic indicator and has important biological functions in tumorigenesis. Methods RNA-seq was re-annotated, and comprehensive clinical information was obtained from the GEO database. Univariate and multivariate Cox regression analyses were used to construct the lncRNA prognosis signature. Gene set enrichment analysis (GSEA) enrichment analysis method is used to explore the possible mechanism of the selected lncRNA influencing HNSCC development. The rms package was used to calculate the C-index to evaluate the overall prediction performance between different signature. PCR is used to detect the expression of selected lncRNA in cancer and adjacent tissues. Results In the GSE65858 training cohort, 124 probes significantly related to prognosis were identified, 11 significant lncRNAs were further selected by rbsurv dimensionality reduction analysis. Finally, 4-lncRNA signature was constructed by multivariate Cox analysis. This signature was associated with tumor-associated pathway and is an independent factor of the patient’s prognosis. 4-lncRNA signature has strong robustness and can exert stable prediction performance in different cohorts. A nomogram comprising the prognostic model to predict the overall survival was established. The 4-lncRNA signature was significantly upregulated in HNSCC samples. Conclusion The predictive model and nomogram will enable patients to be more accurately managed in trials and clinical practices and could be applied as a new prognostic model for predicting survival of HNSCC patients.
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Affiliation(s)
- Yanping Ji
- Department of Pathology, Eye, Ear, Nose and Throat Hospital, Fudan University, Shanghai, People's Republic of China
| | - Yu Xue
- Department of General Surgery, Pudong Hospital, Shanghai, People's Republic of China
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Peng X, Zhou Y, Chen Y, Tang L, Wang G, Jiang H, Wang X, Tao Y, Zhuang W. Reduced LINC00551 expression promotes proliferation and invasion of esophageal squamous cancer by increase in HSP27 phosphorylation. J Cell Physiol 2020; 236:1418-1431. [PMID: 32677057 DOI: 10.1002/jcp.29947] [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: 01/06/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/21/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers, and long noncoding RNAs (lncRNAs) regulate gene expression or activities. This study investigated the role of lncRNA LINC00551 in ESCC development and progression. Three paired ESCC and normal tissues were subjected to next-generation sequencing and we identified 82 upregulated and 60 downregulated lncRNAs, including LINC00551, which was confirmed to markedly downregulated in 78 ESCC tissues and in the Gene Expression Profiling Interactive Analysis data set. Downregulated LINC00551 expression was associated with lymph node metastasis, advanced TNM stage, and tumor size. Moreover, downregulated LINC00551 expression was also associated with poor progression-free survival and overall survival of ESCC patients. In vitro and in vivo, LINC00551 overexpression inhibited ESCC cell proliferation and invasion, whereas knockdown of LINC00551 expression promoted ESCC cell proliferation and invasion. RNA pull-down and mass spectrometry assays identified the potential LINC00551 binding proteins, and HSP27 was a promising LINC00551 targeting proteins after RNA immunoprecipitation assay. At the protein level, LINC00551 bound to and decreased HSP27 phosphorylation, and in turn, downregulated ESCC cell proliferation and invasion. The current study demonstrated the functional significance of LINC00551 in ESCC development, progression, and prognosis. Further study will assess LINC00551 as a novel prognostic marker or therapeutic target for ESCC.
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Affiliation(s)
- Xiong Peng
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Zhou
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yuqiao Chen
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Tang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital of Central South University, Changsha, China.,Institute of Clinical Pharmacrology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, China
| | - Xiang Wang
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Yongguang Tao
- Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, China
| | - Wei Zhuang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
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Pucci P, Venalainen E, Alborelli I, Quagliata L, Hawkes C, Mather R, Romero I, Rigas SH, Wang Y, Crea F. LncRNA HORAS5 promotes taxane resistance in castration-resistant prostate cancer via a BCL2A1-dependent mechanism. Epigenomics 2020; 12:1123-1138. [DOI: 10.2217/epi-2019-0316] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Castration-resistant prostate cancer (CRPC) is an incurable malignancy. Long noncoding RNAs (lncRNAs) play key roles in drug resistance. Materials & methods: LncRNA HORAS5 role in cabazitaxel resistance (i.e., cell-count, IC50 and caspase activity) was studied via lentiviral-mediated overexpression and siRNA-based knockdown. Genes expression was analyzed with RNA-sequencing, reverse transcription quantitative PCR (RT-qPCR) and western blot. HORAS5 expression was queried in clinical database. Results: Cabazitaxel increased HORAS5 expression that upregulated BCL2A1, thereby protecting CRPC cells from cabazitaxel-induced apoptosis. BCL2A1 knockdown decreased cell-count and increased apoptosis in CRPC cells. HORAS5-targeting antisense oligonucleotide decreased cabazitaxel IC50. In CRPC clinical samples, HORAS5 expression increased upon taxane treatment. Conclusion: HORAS5 stimulates the expression of BCL2A1 thereby decreasing apoptosis and enhancing cabazitaxel resistance in CRPC cells.
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Affiliation(s)
- Perla Pucci
- School of Life, Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, Buckinghamshire, MK7 6AA, UK
- Present address: Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, CB20QQ, UK
| | - Erik Venalainen
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Ilaria Alborelli
- Institute of Pathology, University Hospital Basel, Basel 4031, Switzerland
| | - Luca Quagliata
- Global Head of Medical Affairs, Clinical NGS & Oncology Division, Life Sciences Solutions, Thermo Fisher Scientific, Baarerstrasse, Switzerland
| | - Cheryl Hawkes
- School of Life, Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, Buckinghamshire, MK7 6AA, UK
| | - Rebecca Mather
- School of Life, Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, Buckinghamshire, MK7 6AA, UK
| | - Ignacio Romero
- School of Life, Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, Buckinghamshire, MK7 6AA, UK
| | - Sushilaben H Rigas
- School of Life, Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, Buckinghamshire, MK7 6AA, UK
| | - Yuzhuo Wang
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
- The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, BC V6H 3Z6, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Francesco Crea
- School of Life, Health & Chemical Sciences, The Open University, Walton Hall, Milton Keynes, Buckinghamshire, MK7 6AA, UK
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
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71
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Abstract
Non-communicable diseases contribute to 71% of the deaths worldwide, of which cancers rank second after cardiovascular diseases. Among all the cancers, head and neck cancers (HNC) are consequential in augmenting the global cancer incidence as well as mortality. Receptor tyrosine kinases (RTKs) are emphatic for the matter that they serve as biomarkers aiding the analysis of tumor progression and metastasis as well as diagnosis, prognosis and therapeutic progression in the patients. The extensive researches on HNC have made significant furtherance in numerous targeted therapies, but for the escalating therapeutic resistance. This review explicates RTKs in HNC, their signaling pathways involved in tumorigenesis, metastasis and stemness induction, the association of non-coding RNAs with RTKs, an overview of RTK based therapy and associated resistance in HNC, as well as a sneak peek into the HPV positive HNC and its therapy. The review extrapolates the cardinal role of RTKs and RTK based therapy as superior to other existing therapeutic interventions for HNC.
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Affiliation(s)
- Revathy Nadhan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - Priya Srinivas
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India.
| | - M Radhakrishna Pillai
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
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72
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Yang X, Wu S, Li X, Yin Y, Chen R. MAGI2-AS3 rs7783388 polymorphism contributes to colorectal cancer risk through altering the binding affinity of the transcription factor GR to the MAGI2-AS3 promoter. J Clin Lab Anal 2020; 34:e23431. [PMID: 32533587 PMCID: PMC7595890 DOI: 10.1002/jcla.23431] [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: 03/11/2020] [Revised: 04/29/2020] [Accepted: 05/20/2020] [Indexed: 12/15/2022] Open
Abstract
Background It has been indicated that the single nuclear polymorphisms (SNPs) in the long noncoding RNA (lncRNA) have association with colorectal cancer (CRC) susceptibility. Methods We enrolled 1078 cases with CRC and 1175 age‐ and gender‐matched cancer‐free controls to explore whether the polymorphisms in MAGI2‐AS3 have associations with CRC risk. qRT‐PCR, expression quantitative trait loci (eQTL) analyses, dual‐luciferase reporter assay, chromatin immunoprecipitation (ChIP), flow cytometry, and transwell assays were performed to explore the specific mechanisms in which MAGI2‐AS3 rs7783388 variation influenced the tumorigenesis of CRC. Results Subjects carrying rs7783388 GG genotype presented a higher risk of CRC compared with the AG/AA genotypes. Mechanistically, we found that the functional genetic variant of rs7783388 A > G decreased binding affinity of transcription factor glucocorticoid receptor (GR) to the MAGI2‐AS3 promoter, resulting in decreased transcriptional activity that subsequently downregulated MAGI2‐AS3 expression. Furthermore, functional experiments elucidated that MAGI2‐AS3 overexpression suppressed CRC cell proliferation, migration, and invasion capacities, arrested cell cycle at G0/G1 phase, and promoted cell apoptosis. Conclusion Taken together, our study demonstrated that the potential function of MAGI2‐AS3 as a tumor suppressor for CRC, and the MAGI2‐AS3 rs7783388 polymorphism is associated with the increased susceptibility to CRC by altering the binding ability of GR to the MAGI2‐AS3 promoter.
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Affiliation(s)
- Xi Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Shenshen Wu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Ying Yin
- Department of Gastroenterology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Rui Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
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73
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Six long noncoding RNAs as potentially biomarkers involved in competitive endogenous RNA of hepatocellular carcinoma. Clin Exp Med 2020; 20:437-447. [PMID: 32514710 DOI: 10.1007/s10238-020-00634-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/06/2020] [Indexed: 01/19/2023]
Abstract
To investigate lncRNAs acting as competing endogenous RNAs (ceRNAs) involved in oncogenesis and progression of HCC. Different expressed lncRNAs, microRNAs, and mRNAs (DElncRNAs, DEmiRNAs, DEmRNAs), downloaded from The Cancer Genome Atlas (TCGA) database, were identified by edgeR package. CeRNA network was constructed based on miRcode, TargetScan, and miRTarBase. Target DEmRNAs were annotated by KEGG pathway and GO analysis. Negatively correlated lncRNA-miRNA pairs were analyzed by Pearson correlation coefficient, simultaneously, overall survival (OS) were evaluated. The expression of these lncRNAs were examined in HCC cell lines and tissues through qRT-PCR. 1070 DElncRNAs, 147 DEmiRNAs and 1993 DEmRNAs were acquired. CeRNA network was successfully established, including 27 lncRNAs, 5 miRNAs, and 30 mRNAs significantly correlated with OS. The DEmRNAs were significantly enriched in "Cell Cycle" and "pathways in cancer". Six lncRNAs and 2 miRNAs were negatively correlated. These lncRNAs were validated by qRT-PCR. These observations will provide a novel perspective to elucidate HCC pathogenesis.
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74
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Zaheed O, Samson J, Dean K. A bioinformatics approach to identify novel long, non-coding RNAs in breast cancer cell lines from an existing RNA-sequencing dataset. Noncoding RNA Res 2020; 5:48-59. [PMID: 32206740 PMCID: PMC7078458 DOI: 10.1016/j.ncrna.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 01/17/2023] Open
Abstract
Breast cancer research has traditionally centred on genomic alterations, hormone receptor status and changes in cancer-related proteins to provide new avenues for targeted therapies. Due to advances in next generation sequencing technologies, there has been the emergence of long, non-coding RNAs (lncRNAs) as regulators of normal cellular events, with links to various disease states, including breast cancer. Here we describe our bioinformatic analyses of a previously published RNA sequencing (RNA-seq) dataset to identify lncRNAs with altered expression levels in a subset of breast cancer cell lines. Using a previously published RNA-seq dataset of 675 cancer cell lines, a subset of 18 cell lines was selected for our analyses that included 16 breast cancer lines, one ductal carcinoma in situ line and one normal-like breast epithelial cell line. Principal component analysis demonstrated correlation with well-established categorisation methods of breast cancer (i.e. luminal A/B, HER2 enriched and basal-like A/B). Through detailed comparison of differentially expressed lncRNAs in each breast cancer sub-type with normal-like breast epithelial cells, we identified 15 lncRNAs with consistently altered expression, including three uncharacterised lncRNAs. Utilising data from The Cancer Genome Atlas (TCGA) and The Genotype Tissue Expression (GETx) project via Gene Expression Profiling Interactive Analysis (GEPIA2), we assessed clinical relevance of several identified lncRNAs with invasive breast cancer. Lastly, we determined the relative expression level of six lncRNAs across a spectrum of breast cancer cell lines to experimentally confirm the findings of our bioinformatic analyses. Overall, we show that the use of existing RNA-seq datasets, if re-analysed with modern bioinformatic tools, can provide a valuable resource to identify lncRNAs that could have important biological roles in oncogenesis and tumour progression.
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Affiliation(s)
| | | | - Kellie Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, T12XF62, Ireland
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75
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Erlotinib sensitivity of MAPK1p.D321N mutation in head and neck squamous cell carcinoma. NPJ Genom Med 2020; 5:17. [PMID: 32351709 PMCID: PMC7171136 DOI: 10.1038/s41525-020-0124-5] [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] [Received: 09/12/2019] [Accepted: 02/14/2020] [Indexed: 11/08/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) lacks predictive biomarkers for drug responses. By targeted sequencing, we identified two MAPK1 mutations in recurrent HNSCC, MAPK1p.D321N, and p.R135K. We previously reported an exceptional erlotinib responder with MAPK1p.E322K. Here, by in silico and drug studies, we determined functions of these two recurrence-associated MAPK1 mutations. Residues D321, R135, and E322 are in 3D proximity. MAPK1p.D321N drives marked in vivo erlotinib sensitivity, while p.R135K's effect is moderate.
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76
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Zang X, Gu J, Zhang J, Shi H, Hou S, Xu X, Chen Y, Zhang Y, Mao F, Qian H, Zhu T, Xu W, Zhang X. Exosome-transmitted lncRNA UFC1 promotes non-small-cell lung cancer progression by EZH2-mediated epigenetic silencing of PTEN expression. Cell Death Dis 2020; 11:215. [PMID: 32242003 PMCID: PMC7118073 DOI: 10.1038/s41419-020-2409-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs (LncRNAs) have been suggested as important regulators of cancer development and progression in non-small cell lung cancer (NSCLC). Nevertheless, the biological roles and clinical significance of lncRNA UFC1 in NSCLC remain unclear. We detected the expression of UFC1 in tumor tissues, serum, and serum exosomes of NSCLC patients by qRT-PCR. Gene overexpression or silencing were used to examine the biological roles of UFC1 in NSCLC. RNA immunoprecipitation and ChIP assays were performed to evaluate the interaction between UFC1 and enhancer of zeste homolog 2 (EZH2) and the binding of EZH2 to PTEN gene promoter. Rescue study was used to access the importance of PTEN regulation by UFC1 in NSCLC progression. UFC1 expression was upregulated in tumor tissues, serum, and serum exosomes of NSCLC patients and high level of UFC1 was associated with tumor infiltration. UFC1 knockdown inhibited NSCLC cell proliferation, migration and invasion while promoted cell cycle arrest and apoptosis. UFC1 overexpression led to the opposite effects. Mechanistically, UFC1 bound to EZH2 and mediated its accumulation at the promoter region of PTEN gene, resulting in the trimethylation of H3K27 and the inhibition of PTEN expression. UFC1 knockdown inhibited NSCLC growth in mouse xenograft tumor models while the simultaneous depletion of PTEN reversed this effect. NSCLC cells derived exosomes could promote NSCLC cell proliferation, migration and invasion through the transfer of UFC1. Moreover, Exosome-transmitted UFC1 promotes NSCLC progression by inhibiting PTEN expression via EZH2-mediated epigenetic silencing. Exosome-mediated transmit of UFC1 may represent a new mechanism for NSCLC progression and provide a potential marker for NSCLC diagnosis.
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Affiliation(s)
- Xueyan Zang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Jianmei Gu
- Departmemt of Clinical Laboratory Medicine, Nantong Tumor Hospital, 30 Tongyang North Road, 226361, Nantong, Jiangsu, China
| | - Jiayin Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Hui Shi
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Sinan Hou
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Xueying Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Yanke Chen
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Yu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Fei Mao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Hui Qian
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China
| | - Taofeng Zhu
- Department of Respiratory Medicine, the Affiliated Yixing Hospital of Jiangsu University, 75 Tongzhenguan Road, 214200, Yixing, Jiangsu, China.
| | - Wenrong Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China.
| | - Xu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, 212013, Zhenjiang, Jiangsu, China.
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77
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Lyu K, Li Y, Xu Y, Yue H, Wen Y, Liu T, Chen S, Liu Q, Yang W, Zhu X, Wang Z, Chai L, Wen W, Li C, Lei W. Using RNA sequencing to identify a putative lncRNA-associated ceRNA network in laryngeal squamous cell carcinoma. RNA Biol 2020; 17:977-989. [PMID: 32174248 DOI: 10.1080/15476286.2020.1741282] [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] [Indexed: 12/17/2022] Open
Abstract
Accumulating evidence indicates that lncRNAs can interact with miRNAs to regulate target mRNAs through competitive interactions. However, this mechanism remains largely unexplored in laryngeal squamous cell carcinoma (LSCC). In this study, transcriptome-wide RNA sequencing was performed on 3 pairs of LSCC tissues and adjacent normal tissues to investigate the expression profiles of lncRNAs, miRNAs and mRNAs, with differential expression of 171 lncRNAs, 36 miRNAs and 1709 mRNAs detected. Seven lncRNAs, eight mRNAs and three miRNAs were identified to be dysregulated in patients' tissues by using qRT-PCR. GO and KEGG pathway enrichment analyses were performed to elucidate the potential functions of these differentially expressed genes in LSCC. Subsequently, a ceRNA (lncRNA-miRNA-mRNA) network including 4631 ceRNA pairs was constructed based on predicted miRNAs shared by lncRNAs and mRNAs. Cis- and transregulatory lncRNAs were analysed by bioinformatics-based methods. Importantly, mRNA-related ceRNA networks (mRCNs) were further obtained based on potential cancer-related coding genes. Coexpression between lncRNAs and downstream mRNAs was used as a criterion for the validation of mRCNs, with the ZNF561-AS1-miR217-WNT5A and SATB1-AS1-miR1299-SAV1/CCNG2/SH3 KBP1/JADE1/HIPK2 ceRNA regulatory interactions determined, followed by experimental validation after siRNA transfection. Moreover, ceRNA activity analysis revealed that different activities of ceRNA modules existing in specific pathological environments may contribute to the tumorigenesis of LSCC. Consistently, both downregulated SATB1-AS1 and ZNF561-AS1 significantly promoted laryngeal cancer cell migration and invasion, indicating their important roles in LSCC via a ceRNA regulatory mechanism. Taken together, the results of this investigation uncovered and systemically characterized a lncRNA-related ceRNA regulatory network that may be valuable for the diagnosis and treatment of LSCC.
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Affiliation(s)
- Kexing Lyu
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Yun Li
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Yang Xu
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Huijun Yue
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Yihui Wen
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Tesi Liu
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Siyu Chen
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Qihong Liu
- Department of Otolaryngology, The Eighth Affiliated Hospital, Sun Yat-sen University , Shenzhen, Guangdong, P.R. China
| | - Weiqiang Yang
- Department of Otolaryngology, Peking University Shenzhen Hospital , Shenzhen, Guangdong, P.R. China
| | - Xiaolin Zhu
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Zhangfeng Wang
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Liping Chai
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Weiping Wen
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Chunwei Li
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
| | - Wenbin Lei
- Otorhinolaryngology Hospital, The First Affiliated Hospital, Sun Yat-sen University , Guangzhou, Guangdong, China
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78
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Yuan S, Luan X, Chen H, Shi X, Zhang X. Long non-coding RNA EGFR-AS1 sponges micorRNA-381 to upregulate ROCK2 in bladder cancer. Oncol Lett 2020; 19:1899-1905. [PMID: 32194685 PMCID: PMC7039139 DOI: 10.3892/ol.2020.11283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/14/2019] [Indexed: 01/06/2023] Open
Abstract
The present study aimed to investigate the role of the long non-coding RNA EGFR-AS1 in bladder cancer (BC). In this study gene expression of both BC and non-tumor tissues from BC patients were measured by quantitative PCR. Cell transfections were performed to analyze gene interactions in HT-1197 cells. Transwell assays were performed to analyze cell invasion and migration of HT-1197 cells. It was revealed that epidermal growth factor receptor-antisense RNA 1 (EGFR-AS1) was upregulated in BC and positively associated with rho associated coiled-coil containing protein kinase 2 (ROCK2). Analysis of data collected in follow-ups indicated that EGFR-AS1 expression was significantly associated with poorer overall survival of patients with BC. Moreover, in bladder cancer cells, EGFR-AS1 overexpression mediated the upregulation of ROCK2, while microRNA (miR)-381 mediated the downregulation of ROCK2. However, EGFR-AS1 and ROCK2 failed to affect each other. Bioinformatics analysis indicated that miR-381 binds EGFR-AS1. In addition, EGFR-AS1 and ROCK2 overexpression resulted in the promotion of cell invasiveness and migration of HT-1197 BC cells. Conversely, miR-381 was revealed to partially reverse the effect of EGFR-AS1 overexpression. Therefore, EGFR-AS1 may sponge miR-381 to upregulate ROCK2 in BC, thereby promoting cell invasion and migration.
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Affiliation(s)
- Shouxian Yuan
- Department of Urology Surgery, The Second People's Hospital of Liaocheng, Linqing, Shandong 252600, P.R. China
| | - Xiuhua Luan
- Department of Urology Surgery, The Second People's Hospital of Liaocheng, Linqing, Shandong 252600, P.R. China
| | - Haixia Chen
- Department of Medical Records, The Second People's Hospital of Liaocheng, Linqing, Shandong 252600, P.R. China
| | - Xiuqing Shi
- Department of Urology Surgery, The Second People's Hospital of Liaocheng, Linqing, Shandong 252600, P.R. China
| | - Xiangkai Zhang
- Department of Urology Surgery, Shanxi Provincial People's Hospital, Taiyuan, Shanxi 030012, P.R. China
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79
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Zhang Y, Wu D, Wang D. Long non-coding RNA ARAP1-AS1 promotes tumorigenesis and metastasis through facilitating proto-oncogene c-Myc translation via dissociating PSF/PTB dimer in cervical cancer. Cancer Med 2020; 9:1855-1866. [PMID: 31953923 PMCID: PMC7050100 DOI: 10.1002/cam4.2860] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/05/2020] [Accepted: 01/06/2020] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNA (lncRNA) is emerging as a pivotal regulator in tumorigenesis and aggressive progression. Here, we focused on an oncogenic lncRNA, ARAP1 antisense RNA 1 (ARAP1-AS1), which was notably upregulated in cervical cancer (CC) tissues, cell lines and serum. High ARAP1-AS1 expression was closely associated with larger tumor size, advanced FIGO stage as well as lymph node metastasis. Importantly, it was identified as an effective diagnostic and prognostic biomarker for CC. In vitro and in vivo assays showed that knockdown of ARAP1-AS1 inhibited, while overexpression of ARAP1-AS1 promoted CC cell growth and dissemination. Stepwise mechanistic dissection unveiled that ARAP1-AS1 could directly interact with PSF to release PTB, resulting in accelerating the internal ribosome entry site (IRES)-driven translation of proto-oncogene c-Myc, thereby facilitating CC development and progression. Moreover, c-Myc was able to transcriptionally activate ARAP1-AS1 by directly binding to the E-box motif located on ARAP1-AS1 promoter. Taken together, our findings clearly reveal the crucial role of ARAP1-AS1 in CC tumorigenesis and metastasis via regulation of c-Myc translation, targeting ARAP1-AS1 and its related regulatory loop implicates the therapeutic possibility for CC patients.
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Affiliation(s)
- Yao Zhang
- Department of Gynaecology and ObstetricsShengjing Hospital of China Medical UniversityShenyangChina
| | - Dan Wu
- Department of Gynaecology and ObstetricsShengjing Hospital of China Medical UniversityShenyangChina
| | - Dian Wang
- Department of Gynaecology and ObstetricsShengjing Hospital of China Medical UniversityShenyangChina
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80
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Long noncoding RNA FOXD2-AS1 enhances chemotherapeutic resistance of laryngeal squamous cell carcinoma via STAT3 activation. Cell Death Dis 2020; 11:41. [PMID: 31959918 PMCID: PMC6971019 DOI: 10.1038/s41419-020-2232-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 01/24/2023]
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a common head and neck cancer. Despite recently improved management of LSCC, chemotherapy resistance of patients remains a challenge. In this study, we identified that long noncoding RNA FOXD2-AS1 regulates LSCC therapeutic resistance by augmenting LSCC stemness. LSCC chemotherapy-resistant patients showed increased FOXD2-AS1 expression compared with that in chemotherapy-sensitive patients, which predicted poor prognosis. Gain- or loss-of-function experiments showed that upregulated FOXD2-AS1 maintained cancer stemness, reducing the response to chemotherapy, while FOXD2-AS1 downregulation had the opposite effects. FOXD2-AS1 acted as a scaffold for STAT3 and PRMT5, promoting STAT3 transcriptional activity, which is essential to maintain cancer stemness and promote chemotherapeutic resistance. Interfering with FOXD2-AS1 using short hairpin RNA rescued LSCC’s chemotherapeutic sensitivity. Thus, FOXD2-AS1 promotes LSCC chemotherapeutic resistance and is an upstream activator of STAT3, making FOXD2-AS1 a potential therapeutic target to improve the chemotherapy effect in LSCC patients.
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81
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Zhang T, Hu H, Yan G, Wu T, Liu S, Chen W, Ning Y, Lu Z. Long Non-Coding RNA and Breast Cancer. Technol Cancer Res Treat 2020; 18:1533033819843889. [PMID: 30983509 PMCID: PMC6466467 DOI: 10.1177/1533033819843889] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Breast cancer, one of the most common diseases among women, is regarded as a
heterogeneous and complicated disease that remains a major public health concern.
Recently, owing to the development of next-generation sequencing technologies, long
non-coding RNAs have received extensive attention. Numerous studies reveal that long
non-coding RNAs are playing important roles in tumor development. Although the biological
function and molecular mechanisms of long non-coding RNAs remain enigmatic, recent
researchers have demonstrated that an array of long non-coding RNAs express abnormally in
cancers, including breast cancer. Herein, we summarized the latest literature about long
non-coding RNAs in breast cancer, with a particular focus on the multiple molecular roles
of regulatory long non-coding RNAs that regulate cell proliferation, invasion, metastasis,
and apoptosis.
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Affiliation(s)
- Tianzhu Zhang
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Hui Hu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ge Yan
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Tangwei Wu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuiyi Liu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiqun Chen
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,4 Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Ning
- 2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Zhongxin Lu
- 1 Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,2 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China.,3 Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,4 Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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82
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Hoque M, Elmaghrabi YA, Köse M, Beevi SS, Jose J, Meneses-Salas E, Blanco-Muñoz P, Conway JRW, Swarbrick A, Timpson P, Tebar F, Enrich C, Rentero C, Grewal T. Annexin A6 improves anti-migratory and anti-invasive properties of tyrosine kinase inhibitors in EGFR overexpressing human squamous epithelial cells. FEBS J 2020; 287:2961-2978. [PMID: 31869496 DOI: 10.1111/febs.15186] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/22/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
Annexin A6 (AnxA6), a member of the calcium (Ca2+ ) and membrane binding annexins, is known to stabilize and establish the formation of multifactorial signaling complexes. At the plasma membrane, AnxA6 is a scaffold for protein kinase Cα (PKCα) and GTPase-activating protein p120GAP to promote downregulation of epidermal growth factor receptor (EGFR) and Ras/mitogen-activated protein kinase (MAPK) signaling. In human squamous A431 epithelial carcinoma cells, which overexpress EGFR, but lack endogenous AnxA6, restoration of AnxA6 expression (A431-A6) promotes PKCα-mediated threonine 654 (T654)-EGFR phosphorylation, which inhibits EGFR tyrosine kinase activity. This is associated with reduced A431-A6 cell growth, but also decreased migration and invasion in wound healing, matrigel, and organotypic matrices. Here, we show that A431-A6 cells display reduced EGFR activity in vivo, with xenograft analysis identifying increased pT654-EGFR levels, but reduced tyrosine EGFR phosphorylation compared to controls. In contrast, PKCα depletion in A431-A6 tumors is associated with strongly reduced pT654 EGFR levels, yet increased EGFR tyrosine phosphorylation and MAPK activity. Moreover, tyrosine kinase inhibitors (TKIs; gefitinib, erlotinib) more effectively inhibit cell viability, clonogenic growth, and wound healing of A431-A6 cells compared to controls. Likewise, the ability of AnxA6 to inhibit A431 motility and invasiveness strongly improves TKI efficacy in matrigel invasion assays. This correlates with a greatly reduced invasion of the surrounding matrix of TKI-treated A431-A6 when cultured in 3D spheroids. Altogether, these findings implicate that elevated AnxA6 scaffold levels contribute to improve TKI-mediated inhibition of growth and migration, but also invasive properties in EGFR overexpressing human squamous epithelial carcinoma.
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Affiliation(s)
- Monira Hoque
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Yasmin A Elmaghrabi
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Meryem Köse
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Syed S Beevi
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Jaimy Jose
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Elsa Meneses-Salas
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Centre de Recerca Biomèdica CELLEX, IDIBAPS, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Spain
| | - Patricia Blanco-Muñoz
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Centre de Recerca Biomèdica CELLEX, IDIBAPS, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Spain
| | - James R W Conway
- Cancer Research Program, Garvan Institute of Medical Research and Kinghorn Cancer Centre, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Alexander Swarbrick
- Cancer Research Program, Garvan Institute of Medical Research and Kinghorn Cancer Centre, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Paul Timpson
- Cancer Research Program, Garvan Institute of Medical Research and Kinghorn Cancer Centre, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Francesc Tebar
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Centre de Recerca Biomèdica CELLEX, IDIBAPS, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Spain
| | - Carlos Enrich
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Centre de Recerca Biomèdica CELLEX, IDIBAPS, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Spain
| | - Carles Rentero
- Departament de Biomedicina, Unitat de Biologia Cel·lular, Centre de Recerca Biomèdica CELLEX, IDIBAPS, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Spain
| | - Thomas Grewal
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, NSW, Australia
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Grépin R, Guyot M, Dumond A, Durivault J, Ambrosetti D, Roussel JF, Dupré F, Quintens H, Pagès G. The combination of bevacizumab/Avastin and erlotinib/Tarceva is relevant for the treatment of metastatic renal cell carcinoma: the role of a synonymous mutation of the EGFR receptor. Theranostics 2020; 10:1107-1121. [PMID: 31938054 PMCID: PMC6956821 DOI: 10.7150/thno.38346] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/14/2019] [Indexed: 01/25/2023] Open
Abstract
Metastatic clear cell renal cell carcinomas (mRCC) over-express the vascular endothelial growth factor (VEGF). Hence, the anti-VEGF antibody bevacizumab/Avastin (BVZ) combined with interferon alpha (IFN) was approved for the treatment of mRCC. However, approval was lost in July 2016 due to the absence of sustained efficacy. We previously showed that BVZ accelerates tumor growth in experimental models of mRCC in mice, results in part explained by down-regulation of the phospho tyrosine phosphatase receptor kappa (PTPRκ) in tumor cells. The epidermal growth factor receptor (EGFR) is a direct target of PTPRκ. Its down-regulation leads to constitutive activation of EGFR, an observation which prompted us to test the effect of the EGFR inhibitor erlotinib/Tarceva (ERLO) in addition to BVZ/IFN. The influence of the long non-coding RNA, EGFR-AS1, on ERLO efficacy was also addressed. Methods: The effect of BVZ/IFN/ERLO was tested on the growth of experimental tumors in nude mice. The presence of germline mutation in the EGFR was evaluated on cell lines and primary RCC cells. In vitro translation and transfections of expression vectors coding the wild-type or the EGFR mutated gene in HEK-293 cells were used to test the role of EGFR mutation of the ERLO efficacy. Correlation between EGFR/EGFR-AS1 expression and survival was analyzed with an online available data base (TCGA). Results: Tumor growth was strongly reduced by the triple combination BVZ/IFN/ERLO and linked to reduced levels of pro-angiogenic/pro-inflammatory cytokines of the ELR+CXCL family and to subsequent inhibition of vascularization, a decreased number of lymphatic vessels and polarization of macrophages towards the M1 phenotype. Cells isolated from surgical resection of human tumors presented a range of sensitivity to ERLO depending on the presence of a newly detected mutation in the EGFR and to the presence of EGFR-AS1. Conclusions: Our results point-out that the BVZ/IFN/ERLO combination deserves testing for the treatment of mRCC that have a specific mutation in the EGFR.
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84
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Sun R, Wang R, Chang S, Li K, Sun R, Wang M, Li Z. Long Non-Coding RNA in Drug Resistance of Non-Small Cell Lung Cancer: A Mini Review. Front Pharmacol 2019; 10:1457. [PMID: 31920650 PMCID: PMC6930187 DOI: 10.3389/fphar.2019.01457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/13/2019] [Indexed: 12/29/2022] Open
Abstract
Lung cancer is one of main causes of cancer mortality and 83% of lung cancer cases are classified as non-small cell lung cancer (NSCLC). Patients with NSCLC usually have a poor prognosis and one of the leading causes is drug resistance. With the progress of drug therapy, the emergence and development of drug resistance affected the prognosis of patients severely. Accumulating evidence reveals that long non-coding RNAs (lncRNAs), as “dark matters” of the human genome, is of great significance to drug resistance in NSCLC. Herein, we review the role of lncRNAs in drug resistance in NSCLC.
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Affiliation(s)
- Ruizheng Sun
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Ranran Wang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Siyuan Chang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Kexin Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Rongsi Sun
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Mengnan Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Zheng Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, Cancer Research Institute and School of Basic Medical, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
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85
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EGFR vIII: An Oncogene with Ambiguous Role. JOURNAL OF ONCOLOGY 2019; 2019:1092587. [PMID: 32089685 PMCID: PMC7024087 DOI: 10.1155/2019/1092587] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/22/2019] [Indexed: 12/21/2022]
Abstract
Epidermal growth factor receptor variant III (EGFRvIII) seems to constitute the perfect therapeutic target for glioblastoma (GB), as it is specifically present on up to 28–30% of GB cells. In case of other tumor types, expression and possible role of this oncogene still remain controversial. In spite of EGFRvIII mechanism of action being crucial for the design of small active anticancer molecules and immunotherapies, i.e., CAR-T technology, it is yet to be precisely defined. EGFRvIII is known to be resistant to degradation, but it is still unclear whether it heterodimerizes with EGF-activated wild-type EGFR (EGFRWT) or homodimerizes (including covalent homodimerization). Constitutive kinase activity of this mutated receptor is relatively low, and some researchers even claim that a nuclear, but not a membrane function, is crucial for its activity. Based on the analyses of recurrent tumors that are often lacking EGFRvIII expression despite its initial presence in corresponding primary foci, this oncogene is suggested to play a marginal role during later stages of carcinogenesis, while even in primary tumors EGFRvIII expression is detected only in a small percentage of tumor cells, undermining the rationality of EGFRvIII-targeting therapies. On the other hand, EGFRvIII-positive cells are resistant to apoptosis, more invasive, and characterized with enhanced proliferation rate. Moreover, expression of this oncogenic receptor was also postulated to be a marker of cancer stem cells. Opinions regarding the role that EGFRvIII plays in tumorigenesis and for tumor aggressiveness are clearly contradictory and, therefore, it is crucial not only to determine its mechanism of action, but also to unambiguously define its role at early and advanced cancer stages.
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86
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Fan Y, Li J, Yang Q, Gong C, Gao H, Mao Z, Yuan X, Zhu S, Xue Z. Dysregulated Long Non-coding RNAs in Parkinson's Disease Contribute to the Apoptosis of Human Neuroblastoma Cells. Front Neurosci 2019; 13:1320. [PMID: 31920490 PMCID: PMC6923663 DOI: 10.3389/fnins.2019.01320] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
The molecular mechanism underlying Parkinson's disease (PD), an increasingly common neurodegenerative disease, remains unclear. Long non-coding RNA (lncRNA) plays essential roles in gene expression and human diseases. We hypothesize that lncRNAs are involved in neuronal degeneration of PD. Using microarray, we identified 122 differentially expressed (DE) lncRNAs and 48 DE mRNAs between the circulating leukocytes from PD patients and healthy controls. There were 714 significant correlations (r ≥ 0.8 or ≤-0.8, p < 0.05) among the DE lncRNAs and mRNAs. Gene function and pathway analysis of the 48 DE mRNAs revealed biological pathways related to PD pathogenesis, including immune response, inflammatory response, MAPK, and Jak-STAT pathway. In a cohort of 72 PD patients and 22 healthy controls, the upregulation of four lncRNAs (AC131056.3-001, HOTAIRM1, lnc-MOK-6:1, and RF01976.1-201) in circulating leukocytes of PD patients were further confirmed. These lncRNAs were also upregulated in THP-1 cells, a human monocytic cell line, after inflammatory stimulation. Interestingly, the conditioned culture medium of THP-1 cells or 6-OHDA significantly increased the expression of these lncRNAs in SH-SY5Y cells, a human neuroblastoma cell line expressing dopaminergic markers. Importantly, overexpression of AC131056.3-001 or HOTAIRM1 increased baseline and 6-OHDA-induced apoptosis of SH-SY5Y cells. Taken together, we identified distinct expression profiles of lncRNA and mRNA in circulating leukocytes between PD patients and healthy controls. Dysregulated lncRNAs such as HOTAIRM1 and AC131056.3-001 may contribute to PD pathogenesis by promoting the apoptosis of dopaminergic neuron.
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Affiliation(s)
- Yun Fan
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingyi Li
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingmei Yang
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chengwu Gong
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongling Gao
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhijuan Mao
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao Yuan
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Suiqiang Zhu
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng Xue
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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87
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Ge H, Yan Y, Yue C, Liang C, Wu J. Long Noncoding RNA LINC00265 Targets EGFR and Promotes Deterioration of Colorectal Cancer: A Comprehensive Study Based on Data Mining and in vitro Validation. Onco Targets Ther 2019; 12:10681-10692. [PMID: 31824175 PMCID: PMC6901053 DOI: 10.2147/ott.s227482] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/21/2019] [Indexed: 12/12/2022] Open
Abstract
Background LncRNAs are found to be aberrantly expressed in human cancers and could function as potential oncogenes or tumor suppressor genes. LINC00265 is a newly discovered LncRNA and its function in colorectal cancer (CRC) remains unknown. Methods Comprehensive bioinformatics analysis were performed to investigate the expression, clinical significance and potential biologic functions of LINC00265 in CRC based on the data from the Cancer Genome Atlas (TCGA). To further investigate the potential role of LINC00265 in CRC, we knocked down the LINC00265 expression in HT29 cells. The cell proliferation, invasion, cycle distribution, and apoptosis were evaluated in control, NC and siRNA groups. Additionally, effect of LINC00265 on the expression of EGFR was also measured. Results The expression level of LINC00265 is increased in CRC tissues. Elevated level of LINC00265 is correlated with lymph node metastases and advanced pathological stage. We obtained 269 LINC00265 related genes; the results of functional analysis of these genes revealed that LINC00265 might involve in carcinogenesis of CRC. In addition, further experiments indicated that LINC00265 knockdown impaired cell proliferation and invasion, promoted cell cycle distribution and apoptosis in HT29 cells. Moreover, Western blot analysis revealed that downregulation of LINC00265 suppressed the expression of EGFR. Conclusion Our results indicate that LINC00265 induces cell proliferation, migration and inhibits CRC cells apoptosis by targeting EGFR. LINC00265 could be served as a diagnostic factor and therapeutic target for CRC patients.
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Affiliation(s)
- Hua Ge
- Department of Gastrointestinal Surgery, The First People's Hospital of Zunyi, The Third Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Yan Yan
- Quality Control Department, The First People's Hospital of Zunyi, The Third Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, People's Republic of China
| | - Chaosen Yue
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Chaojie Liang
- Department of General Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, People's Republic of China
| | - Jixiang Wu
- Department of General Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, People's Republic of China
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88
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Liu Z, Tao H. Small nucleolar RNA host gene 3 facilitates cell proliferation and migration in oral squamous cell carcinoma via targeting nuclear transcription factor Y subunit gamma. J Cell Biochem 2019; 121:2150-2158. [PMID: 31762107 DOI: 10.1002/jcb.29421] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022]
Abstract
Oral squamous cell carcinoma (OSCC) has been reported to be the most common oral carcinoma. Emerging evidence has revealed the key role that long noncoding RNAs (lncRNAs) play in numerous malignancies, including OSCC. LncRNA small nucleolar RNA host gene 3 (SNHG3) has been reported as an oncogenic factor in some cancers. Nonetheless, the role of SNHG3 in OSCC has never been clarified. In this study, we analyzed the expression patterns of SNHG3 in OSCC through quantitative real-time polymerase chain reaction. It was revealed that the expression level of SNHG3 was remarkably elevated in OSCC cell lines compared with the nontumor cell line. It was demonstrated by functional experiments that SNHG3 knockdown notably inhibited cell proliferation and migration in OSCC. RNA immunoprecipitation, RNA pull down, and messenger RNA (mRNA) stability test verified that SNHG3 decoyed ELAV like RNA-binding protein 1 (ELAVL1) and therefore stabilized nuclear transcription factor Y subunit gamma (NFYC) mRNA to upregulate the expression levels of NFYC in OSCC cells. At last, it was confirmed by rescue experiments that the inhibiting impacts of SNHG3 knockdown on OSCC cell proliferation and migration could be partly revived by NFYC overexpression. Besides, we validated that Wnt/β-catenin pathway was also involved in SNHG3-regulated OSCC progression. In conclusion, SNHG3 might serve as a novel biomarker for OSCC.
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Affiliation(s)
- Zhi Liu
- Department of Oral, The First Affiliated Hospital of Xi'an JiaoTong University, Xi'an, Shaanxi, China
| | - Hong Tao
- Department of Oral, The First Affiliated Hospital of Xi'an JiaoTong University, Xi'an, Shaanxi, China
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89
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Zhao W, Shan B, He D, Cheng Y, Li B, Zhang C, Duan C. Recent Progress in Characterizing Long Noncoding RNAs in Cancer Drug Resistance. J Cancer 2019; 10:6693-6702. [PMID: 31777598 PMCID: PMC6856905 DOI: 10.7150/jca.30877] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 09/18/2019] [Indexed: 12/13/2022] Open
Abstract
Drug resistance is an important cause of failure in cancer chemotherapies. A large number of long noncoding RNAs (lncRNAs) have been found to be related to drug resistance in cancers. Therefore, lncRNAs provide potential targets for cancer therapies. The lncRNAs involved in cancer drug resistance are attracting interest from an increasing number of researchers. This review summarizes the latest research on the mechanisms and functions of lncRNAs in cancer drug resistance and envisages their future developments and therapeutic applications. This research suggests that lncRNAs regulate drug resistance through multiple mechanisms. LncRNAs do not affect drug resistance directly; usually, they do so by regulating the expression of some intermediate regulatory factors. In addition, lncRNAs exhibit a diversity of functions in cancer drug resistance. The overexpression of most lncRNAs promotes drug resistance, while a few lncRNAs have inhibitory effects.
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Affiliation(s)
- Wenyuan Zhao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, PR China
| | - Bin Shan
- College of Medical Sciences, Washington State University Spokane, WA, USA
| | - Dan He
- Hunan Cancer Hospital, The Affiliated Tumor Hospital of Xiangya Medical College, Central South University, Changsha, PR China
| | - Yuanda Cheng
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, PR China
| | - Bin Li
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, PR China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, PR China
| | - Chaojun Duan
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, PR China.,Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, PR China
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90
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Li ZX, Zheng ZQ, Wei ZH, Zhang LL, Li F, Lin L, Liu RQ, Huang XD, Lv JW, Chen FP, He XJ, Guan JL, Kou J, Ma J, Zhou GQ, Sun Y. Comprehensive characterization of the alternative splicing landscape in head and neck squamous cell carcinoma reveals novel events associated with tumorigenesis and the immune microenvironment. Am J Cancer Res 2019; 9:7648-7665. [PMID: 31695792 PMCID: PMC6831462 DOI: 10.7150/thno.36585] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing (AS) has emerged as a key event in tumor development and microenvironment formation. However, comprehensive analysis of AS and its clinical significance in head and neck squamous cell carcinoma (HNSC) is urgently required. Methods: Genome-wide profiling of AS events using RNA-Seq data from The Cancer Genome Atlas (TCGA) program was performed in a cohort of 464 patients with HNSC. Cancer-associated AS events (CASEs) were identified between paired HNSC and adjacent normal tissues and evaluated in functional enrichment analysis. Splicing networks and prognostic models were constructed using bioinformatics tools. Unsupervised clustering of the CASEs identified was conducted and associations with clinical, molecular and immune features were analyzed. Results: We detected a total of 32,309 AS events and identified 473 CASEs in HNSC; among these, 91 were validated in an independent cohort (n = 15). Functional protein domains were frequently altered, especially by CASEs affecting cancer drivers, such as PCSK5. CASE parent genes were significantly enriched in pathways related to HNSC and the tumor immune microenvironment, such as the viral carcinogenesis (FDR < 0.001), Human Papillomavirus infection (FDR < 0.001), chemokine (FDR < 0.001) and T cell receptor (FDR < 0.001) signaling pathways. CASEs enriched in immune-related pathways were closely associated with immune cell infiltration and cytolytic activity. AS regulatory networks suggested a significant association between splicing factor (SF) expression and CASEs and might be regulated by SF methylation. Eighteen CASEs were identified as independent prognostic factors for overall and disease-free survival. Unsupervised clustering analysis revealed distinct correlations between AS-based clusters and prognosis, molecular characteristics and immune features. Immunogenic features and immune subgroups cooperatively depict the immune features of AS-based clusters. Conclusion: This comprehensive genome-wide analysis of the AS landscape in HNSC revealed novel AS events related to carcinogenesis and immune microenvironment, with implications for prognosis and therapeutic responses.
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91
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Pan H, Guo C, Pan J, Guo D, Song S, Zhou Y, Xu D. Construction of a Competitive Endogenous RNA Network and Identification of Potential Regulatory Axis in Gastric Cancer. Front Oncol 2019; 9:912. [PMID: 31637209 PMCID: PMC6787165 DOI: 10.3389/fonc.2019.00912] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/02/2019] [Indexed: 12/31/2022] Open
Abstract
Background: Increasing studies has found that long non-coding RNAs (lncRNAs) play critical roles in carcinogenesis, but the underlying mechanisms remain unclear. The aim of this study is to construct a competitive endogenous RNA (ceRNA) network and to identify potential regulatory axis in gastric cancer (GC). Methods: Differentially expressed (DE) mRNAs, miRNAs, and lncRNAs were obtained by analyzing the RNA expression profiles of stomach adenocarcinoma (STAD) retrieved from The Cancer Genome Atlas (TCGA) database. The lncRNA-miRNA-mRNA regulatory networks of GC were constructed by comprehensive bioinformatics methods including functional annotation, RNA-RNA interactomes prediction, correlation analysis, and survival analysis. The interactions and correlations among ceRNAs were validated by experiments on cancer tissues and cell lines. Results: A total of 41 lncRNAs, 9 miRNAs, and 10 mRNAs were identified and selected to establish the ceRNA regulatory network of GC. Several ceRNA regulatory axes, which consist of 18 lncRNAs, 4 miRNAs, and 6 mRNAs, were obtained from the network. A potential ADAMTS9-AS2/miR-372/CADM2 axis which perfectly conformed to the ceRNA theory was further analyzed. qRT-PCR showed that ADAMTS9-AS2 knockdown remarkably increased miR-372 expression but reduced CADM2 expression, whereas ADAMTS9-AS2 overexpression had the opposite effects. Dual luciferase reporter assay indicated that miR-372 could bound to the ADAMTS9-AS2 and the 3′UTR of CADM2. Conclusion: The constructed novel ceRNA network and the potential regulatory axes might provide a novel approach of the exploring the potential mechanisms of development in GC. The ADAMTS9-AS2/miR-372/CADM2 could act as a promising target for GC treatment.
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Affiliation(s)
- Hongda Pan
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunmiao Guo
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Jingxin Pan
- The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Dongwei Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shibo Song
- Department of Gastrointestinal Surgery, Beijing Hospital, Beijing, China
| | - Ye Zhou
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dazhi Xu
- Department of Gastric Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Discovering long noncoding RNA predictors of anticancer drug sensitivity beyond protein-coding genes. Proc Natl Acad Sci U S A 2019; 116:22020-22029. [PMID: 31548386 DOI: 10.1073/pnas.1909998116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Large-scale cancer cell line screens have identified thousands of protein-coding genes (PCGs) as biomarkers of anticancer drug response. However, systematic evaluation of long noncoding RNAs (lncRNAs) as pharmacogenomic biomarkers has so far proven challenging. Here, we study the contribution of lncRNAs as drug response predictors beyond spurious associations driven by correlations with proximal PCGs, tissue lineage, or established biomarkers. We show that, as a whole, the lncRNA transcriptome is equally potent as the PCG transcriptome at predicting response to hundreds of anticancer drugs. Analysis of individual lncRNAs transcripts associated with drug response reveals nearly half of the significant associations are in fact attributable to proximal cis-PCGs. However, adjusting for effects of cis-PCGs revealed significant lncRNAs that augment drug response predictions for most drugs, including those with well-established clinical biomarkers. In addition, we identify lncRNA-specific somatic alterations associated with drug response by adopting a statistical approach to determine lncRNAs carrying somatic mutations that undergo positive selection in cancer cells. Lastly, we experimentally demonstrate that 2 lncRNAs, EGFR-AS1 and MIR205HG, are functionally relevant predictors of anti-epidermal growth factor receptor (EGFR) drug response.
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93
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Lyu K, Xu Y, Yue H, Li Y, Zhao J, Chen L, Wu J, Zhu X, Chai L, Li C, Wen W, Lei W. Long Noncoding RNA GAS5 Acts As A Tumor Suppressor In Laryngeal Squamous Cell Carcinoma Via miR-21. Cancer Manag Res 2019; 11:8487-8498. [PMID: 31572003 PMCID: PMC6756574 DOI: 10.2147/cmar.s213690] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/04/2019] [Indexed: 01/01/2023] Open
Abstract
Purpose Long noncoding RNAs (lncRNAs) have been identified as an important class of noncoding RNAs that are deeply involved in multiple biological processes in tumorigenesis. This study is to investigate the critical roles and biological function of lncRNA growth arrest-specific 5 (GAS5) in tumorigenesis of laryngeal squamous cell carcinoma (LSCC). Patients and methods A total of 59 samples of LSCC and paired adjacent tissue, as well as corresponding clinicopathological information were collected. GAS5 expression in both LSCC tissues and human SUN1076 and SNU899 cell lines were analyzed by Real-time quantitative RT-PCR method. Ectopic expression of GAS5 by vector transfection in LSCC cell lines and followed by in vitro experiments was to investigate the critical roles and function of GAS5 in LSCC. Cell Counting Kit 8 (CCK8) assay and PE/7AAD Annexin V Apoptosis analysis was to evaluate cell proliferation ability and cell apoptosis. Co-transfection of GAS5 and miR-21 was to explore the interaction between GAS5 and miR-21 in LSCC. BAX and CDK6 protein level were analyzed by western blot method. Results This study demonstrated that GAS5 was significantly downregulated in LSCC tissue and human LSCC cell lines. GAS5 levels were correlated with the clinicopathological features of LSCC patients. In addition, the ectopic expression of GAS5 significantly inhibited cell proliferation and promoted apoptosis. Co-expression analyses indicated that GAS5 is negatively correlated with miR-21 in LSCC tissues. Overexpression of miR-21 eliminated GAS5-mediated cell apoptosis and proliferation suppression. Furthermore, GAS5, which upregulated BAX mRNA expression and downregulated CDK6 mRNA expression, was reversed by ectopic expression of miR-21. Conclusion GAS5 suppresses LSCC progression through the negative regulation of miR-21 and its targets involved in cell proliferation and apoptosis, indicating that GAS5 may serve as a biomarker and potential target for LSCC therapy.
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Affiliation(s)
- Kexing Lyu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yang Xu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Huijun Yue
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yun Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jing Zhao
- Department of Otolaryngology, The Third Hospital of Heibei Medical University, Shijiazhuang, People's Republic of China
| | - Lin Chen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jianhui Wu
- Department of Otolaryngology, Meizhou People's Hospital, Meizhou, People's Republic of China
| | - Xiaolin Zhu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Liping Chai
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Chunwei Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Weiping Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Wenbin Lei
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
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Dong ZQ, Guo ZY, Xie J. The lncRNA EGFR-AS1 is linked to migration, invasion and apoptosis in glioma cells by targeting miR-133b/RACK1. Biomed Pharmacother 2019; 118:109292. [PMID: 31545240 DOI: 10.1016/j.biopha.2019.109292] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/18/2019] [Accepted: 07/31/2019] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common in situ neoplasms in central nervous system (CNS). However, the pathogenesis of GBM is poorly understood. Long noncoding RNAs (lncRNAs) have been implicated in GBM progression. In this study, we attempted to identify the biological role of the EGFR-AS1 in glioma cells and tissues, as well as reveal the molecular mechanism associated. The results indicated that lnc-EGFR-AS1 expression was increased in glioma cells and tissues. EGFR-AS1 knockdown suppressed proliferation, migration and invasion of glioma cells, but induced apoptosis. Additionally, lnc-EGFR-AS1 functioned as a sponge for miR-133b. Promoting lnc-EGFR-AS1 expression significantly reduced miR-133b expression. Furthermore, miR-133b could target the 3'-untranslated region (3'-UTR) of RACK1 and reduced its expression levels. What's more, lnc-EGFR-AS1 knockdown reduced RACK1 expression partly through enhancing miR-133b expression. In vivo experiments confirmed the anti-tumorigenesis capability of EGFR-AS1 knockdown. These findings elucidated that EGFR-AS1 accelerated cell proliferation, migration, invasion and prevented apoptosis in glioma cells by regulating miR-133b/RACK1, providing new insights for the diagnosis and molecular therapy of GBM.
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Affiliation(s)
- Zhi-Qiang Dong
- Department of Neurosurgery, Second Hospital of Lanzhou University, Lanzhou 730030, China
| | - Zhao-Yu Guo
- Department of Neurosurgery, Yangling Demonstration Zone Hospital, Xianyang 712100, China.
| | - Jun Xie
- Department of Neurosurgery, People's Hospital of Tongchuan City, Tongchuan 727000, China
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95
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Lin X, Xiaoqin H, Jiayu C, Li F, Yue L, Ximing X. Long non-coding RNA miR143HG predicts good prognosis and inhibits tumor multiplication and metastasis by suppressing mitogen-activated protein kinase and Wnt signaling pathways in hepatocellular carcinoma. Hepatol Res 2019; 49:902-918. [PMID: 30945380 DOI: 10.1111/hepr.13344] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/26/2019] [Accepted: 03/25/2019] [Indexed: 02/06/2023]
Abstract
AIM The expression of microRNA143HG (miR143HG) was significantly downregulated in hepatocellular carcinoma (HCC) tissues by bioinformatics analysis. This study aimed to determine the role of miR143HG in HCC cell proliferation and metastasis. METHODS Fifty patients with HCC were divided into two groups based on median miR143HG expression levels. The correlation between miR143HG expression and prognosis, and the correlations between miR143HG expression and the patients' clinicopathological characteristics were evaluated based on the two groups. Gain-of-function and loss-of-function measurements of miR143HG were carried out to verify the biological function of miR143HG by Cell Counting Kit-8, EdU, Transwell, and western blotting assays and flow cytometric analysis. The underlying mechanism was explored by quantitative real-time polymerase chain reaction of miRNA (miR-155-5p and miR-26b-5p), luciferase reporter assay, western blotting of Wnt signaling pathway-related proteins (β-catenin, adenomatous polyposis coli (APC), glycogen synthase kinase 3β (GSK3β), ZEB1, and E-cadherin), mitogen-activated protein kinase (MAPK) signaling pathway-related proteins (extracellular signal-regulated kinase [ERK]1/2, p-ERK1/2, c-Jun N-terminal kinase (JNK), p-JNK, P38, and p-P38), and immunofluorescence staining of β-catenin. RESULTS miR143HG expression was markedly downregulated in HCC tissues and cells. Its expression was associated with the presence or absence of portal vein tumor thrombus, hepatitis B virus infection, relapse and metastasis, and Barcelona Clinic Liver Cancer stage. Additionally, miR143HG expression predicted a good prognosis and acted as an independent prognostic factor in HCC for overall survival. Overexpression of miR143HG suppressed HCC cell proliferation and metastasis, and induced cell cycle arrest and apoptosis. Consistently, the depletion of miR143HG resulted in the opposite phenomenon of the aforementioned results. miR143HG inhibits miR-155 expression; miR-155 directly targets APC, which is a negative regulator of the Wnt/β-catenin pathway, so miR143HG can act on the Wnt pathway. miR143HG was further found to reduce the expression of β-catenin and block the nuclear accumulation of β-catenin, ultimately inhibiting the activation of the Wnt pathway. It inhibits the expression of Wnt downstream target gene ZEB1, and then E-cadherin expression is increased and cell motility is inhibited. Furthermore, miR143HG exerts its antiproliferative function by influencing the MAPK signaling pathway and then inducing G2 /M arrest in cells. CONCLUSION This study showed that miR143HG plays critical roles in the development and progression of HCC by suppressing the MAPK and Wnt signaling pathways.
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Affiliation(s)
- Xiong Lin
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - He Xiaoqin
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chen Jiayu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fan Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Li Yue
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xu Ximing
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
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96
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Wang J, Xie S, Yang J, Xiong H, Jia Y, Zhou Y, Chen Y, Ying X, Chen C, Ye C, Wang L, Zhou J. The long noncoding RNA H19 promotes tamoxifen resistance in breast cancer via autophagy. J Hematol Oncol 2019; 12:81. [PMID: 31340867 PMCID: PMC6657081 DOI: 10.1186/s13045-019-0747-0] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/31/2019] [Indexed: 12/16/2022] Open
Abstract
Background Tamoxifen resistance remains a clinical challenge for hormone receptor-positive breast cancer. Recently, dysregulations in autophagy have been suggested as a potential mechanism for tamoxifen resistance. Although the long noncoding RNA H19 is involved in various stages of tumorigenesis, its role in tamoxifen resistance remains unknown. Here, we assessed the role of H19 in the development of tamoxifen-resistant breast cancer. Methods Quantitative real-time PCR analyzed expression of H19 in tamoxifen-resistant breast cancer tissues. Knockdown of H19 was used to assess the sensitivity to tamoxifen in vitro and in vivo. Both knockdown and overexpression of H19 were used to analyze the status of autophagy. Real-time quantitative methylation-specific polymerase chain reaction, chromatin immunoprecipitation, immunofluorescence, and Western blot were used to explore the tamoxifen resistance mechanism of H19. Results In this study, we observed that the expression of H19 was substantially upregulated in tamoxifen-resistant breast cancer cell line and tumor tissues, and knockdown of H19 enhanced the sensitivity to tamoxifen both in vitro and in vivo. Furthermore, knockdown of H19 significantly inhibited autophagy in MCF7 tamoxifen-resistant (MCF7/TAMR) cells. Conversely, overexpression of H19 promoted autophagy. Interestingly, overexpression of H19 in MCF7 tamoxifen-sensitive cells could recapitulate tamoxifen resistance. Moreover, an increase in methylation in the promoter region of Beclin1 was observed in MCF7/TAMR-shH19 cells. In the double knockdown groups, both shH19+shSAHH and shH19+shDNMT3B rescued the Beclin1 promoter region methylation levels and reactivated autophagy functions. A chromatin immunoprecipitation assay further validated that DNMT3B binds to the Beclin1 promoter region and the knockdown of H19 increases this binding. Conclusions Our findings demonstrate that H19 induces autophagy activation via the H19/SAHH/DNMT3B axis, which could contribute to tamoxifen resistance in breast cancer. Electronic supplementary material The online version of this article (10.1186/s13045-019-0747-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ji Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Shuduo Xie
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Jingjing Yang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Hanchu Xiong
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Yunlu Jia
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Yulu Zhou
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Yongxia Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Xiaogang Ying
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Cong Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China.,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China
| | - Chenyang Ye
- Cancer Institute (Key Laboratory of Cancer Prevention & Intervention, National Ministry of Education), Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Linbo Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China. .,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China.
| | - Jichun Zhou
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No.3 Eastern Qingchun Road, Hangzhou, 310016, Zhejiang, China. .,Biomedical Research Center and Key Laboratory of Biotherapy of Zhejiang Province, Hangzhou, 310016, Zhejiang, China.
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97
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Zilberg C, Lee MW, Kraitsek S, Ashford B, Ranson M, Shannon K, Iyer NG, Ch'ng S, Low THH, Palme C, Clark J, Gupta R, Yu B. Is high-risk cutaneous squamous cell carcinoma of the head and neck a suitable candidate for current targeted therapies? J Clin Pathol 2019; 73:17-22. [PMID: 31300530 DOI: 10.1136/jclinpath-2019-206038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Cutaneous squamous cell carcinoma (cSCC) is the second most common malignancy, most frequently affecting the head and neck. Treatment often requires surgery and can have significant functional morbidity. Research into disease pathogenesis and second line medical management of cSCC is limited. We assess genetic mutations in high-risk, primary head and neck cutaneous squamous cell carcinomas (HNcSCC) that may hinder or be beneficial for use of targeted therapy in disease management. METHODS Genetic alterations and variant allele frequencies (VAFs) were analysed using a clinically relevant 48 gene panel in 10 primary high-risk non-metastatic treatment-naïve HNcSCC to evaluate applicability of targeted therapeutics. Variants present at all VAFs were evaluated for pathogenicity. Somatic mutation patterns of individual tumours were analysed. RESULTS High-risk HNcSCC showed a high proportion (82%) of C to T transitions in keeping with ultraviolet-mediated damage. There was significant intratumour genetic heterogeneity in this cohort (MATH scores 20-89) with the two patients <45 years of age showing highest intratumour heterogeneity. TP53 was altered at VAF >22% in all cases, and mutations with highest VAF were observed in tumour suppressor genes in 80%. 70% of cases demonstrated at least one mutation associated with treatment resistance (KIT S821F, KIT T670I, RAS mutations at codons 12 and 13). CONCLUSION We demonstrate high proportion tumour suppressor loss of function mutations, high intratumour genetic heterogeneity, and presence of well recognised resistance mutations in treatment naïve primary HNcSCC. These factors pose challenges for successful utilisation of targeted therapies.
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Affiliation(s)
- Catherine Zilberg
- Medicine, Gosford Hospital, Gosford, New South Wales, Australia .,Medicine, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Spiridoula Kraitsek
- Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Bruce Ashford
- Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Marie Ranson
- Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kerwin Shannon
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - N Gopalakrishna Iyer
- Sinnghealth/Duke-NUS Head and Neck Centre, National Cancer Centre Singapore, Singapore, Singapore
| | - Sydney Ch'ng
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.,Central Clinical School Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Tsu-Hui Hubert Low
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.,Central Clinical School Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Carsten Palme
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia.,Central Clinical School Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan Clark
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Camperdown, New South Wales, Australia
| | - Ruta Gupta
- Anatomic Pathology, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Bing Yu
- Molecular and Clinical Genetics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
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98
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Xiong HG, Li H, Xiao Y, Yang QC, Yang LL, Chen L, Bu LL, Zhang WF, Zhang JL, Sun ZJ. Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma. J Exp Clin Cancer Res 2019; 38:278. [PMID: 31238980 PMCID: PMC6593600 DOI: 10.1186/s13046-019-1254-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/28/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Partial epithelial mesenchymal transition (p-EMT) was found to play a potential role in the initial stage of metastasis in human head and neck squamous cell carcinoma (HNSCC). Some long noncoding RNAs (lncRNAs) have been reported to function as promoters or inhibitors of cancer metastasis. This study aimed to identify p-EMT-related lncRNAs in HNSCC. METHODS Differentially expressed lncRNAs (DE-lncRNAs) and mRNAs (DEGs) in HNSCC obtained from The Cancer Genome Atlas (TCGA) were screened out by using the "edgeR" package. DE-lncRNAs in the Oral squamous cell carcinoma (OSCC) lncRNA microarray dataset GSE84805 were screened out by using the "limma" package. Slug-related lncRNAs were determined by Pearson correlation analysis (|Pearson correlation coefficient| ≥ 0.4, p < 0.01) based on TCGA. Survival analysis were performed for the overlapping DE-lncRNAs by using the "Survival" package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were used to predict the potential functions of MYOSLID. RT-qPCR and In Site Hybridization (ISH) were used to explore the MYOSLID expression and its clinical significance in HNSCC specimens. Immunohistochemical staining, siRNA, wound healing assay, transwell assay, and western blot were used to explore the biological function and potential molecular mechanisms. RESULTS MYOSLID was identified as a Slug-related lncRNA and with prognostic value among the 9 overlapping DE-lncRNAs. GO and KEGG analyses revealed that MYOSLID was closely related to important biological processes and pathways that regulate cancer metastasis. The results of univariate and multivariate Cox regression analysis based on TCGA and HNSCC tissue microarray data suggested MYOSLID was an independent prognostic factor. MYOSLID expression in HNSCC was closely correlated with Slug, PDPN and LAMB3. The knockdown of MYOSLID in OSCC cell line significantly inhibited cell migration and invasion compared to those in the control cells. In addition, the knockdown of MYOSLID significantly reduced Slug, PDPN and LAMB3 expression levels. However, the knockdown of MYOSLID had no effect on the expression levels of the EMT biomarkers E-cadherin and Vimentin. CONCLUSIONS Our study revealed that MYOSLID expression was closely related to the p-EMT program in HNSCC, and it might be a new predictive biomarker for aggressive HNSCC.
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Affiliation(s)
- Hong-Gang Xiong
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hao Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yao Xiao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Qi-Chao Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Lei-Lei Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Lei Chen
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Lin-Lin Bu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Wen-Feng Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jia-Li Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral Pathology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhi-Jun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
- Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
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Zhang Y, Liao G, Bai J, Zhang X, Xu L, Deng C, Yan M, Xie A, Luo T, Long Z, Xiao Y, Li X. Identifying Cancer Driver lncRNAs Bridged by Functional Effectors through Integrating Multi-omics Data in Human Cancers. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 17:362-373. [PMID: 31302496 PMCID: PMC6626872 DOI: 10.1016/j.omtn.2019.05.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/23/2019] [Accepted: 05/15/2019] [Indexed: 01/18/2023]
Abstract
The accumulation of somatic driver mutations in the human genome enables cells to gradually acquire a growth advantage and contributes to tumor development. Great efforts on protein-coding cancer drivers have yielded fruitful discoveries and clinical applications. However, investigations on cancer drivers in non-coding regions, especially long non-coding RNAs (lncRNAs), are extremely scarce due to the limitation of functional understanding. Thus, to identify driver lncRNAs integrating multi-omics data in human cancers, we proposed a computational framework, DriverLncNet, which dissected the functional impact of somatic copy number alteration (CNA) of lncRNAs on regulatory networks and captured key functional effectors in dys-regulatory networks. Applying it to 5 cancer types from The Cancer Genome Atlas (TCGA), we portrayed the landscape of 117 driver lncRNAs and revealed their associated cancer hallmarks through their functional effectors. Moreover, lncRNA RP11-571M6.8 was detected to be highly associated with immunotherapeutic targets (PD-1, PD-L1, and CTLA-4) and regulatory T cell infiltration level and their markers (IL2RA and FCGR2B) in glioblastoma multiforme, highlighting its immunosuppressive function. Meanwhile, a high expression of RP11-1020A11.1 in bladder carcinoma was predictive of poor survival independent of clinical characteristics, and CTD-2256P15.2 in lung adenocarcinoma responded to the sensitivity of methyl ethyl ketone (MEK) inhibitors. In summary, this study provided a framework to decipher the mechanisms of tumorigenesis from driver lncRNA level, established a new landscape of driver lncRNAs in human cancers, and offered potential clinical implications for precision oncology.
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Affiliation(s)
- Yong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Jing Bai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Chunyu Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Aimin Xie
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Tao Luo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Zhilin Long
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China.
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150086, China; Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang 150086, China.
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Qi H, Wang S, Wu J, Yang S, Gray S, Ng CSH, Du J, Underwood MJ, Li MY, Chen GG. EGFR-AS1/HIF2A regulates the expression of FOXP3 to impact the cancer stemness of smoking-related non-small cell lung cancer. Ther Adv Med Oncol 2019; 11:1758835919855228. [PMID: 31275431 PMCID: PMC6598324 DOI: 10.1177/1758835919855228] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/13/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Early data showed that FOXP3 could induce epithelial-mesenchymal transition by stimulating the Wnt/β-catenin signaling pathway in non-small cell lung cancer (NSCLC). However, how the expression of FOXP3 is regulated in NSCLC remains unknown. We thus explored the impacts of the long noncoding RNA EGFR antisense RNA 1 (EGFR-AS1) and hypoxia-inducible factor-2A (HIF2A) on FOXP3 expression and the cancer stemness of NSCLC. Methods: Lung tissues samples from 87 patients with NSCLC and two NSCLC cell lines were used in this study. The regulation of FOXP3 and lung cancer cell stemness by EGFR-AS1 and HIF2A was determined at molecular levels in NSCLC tissue samples and cultured cells in the presence/absence of the smoking carcinogen, 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) (also known as nicotine-derived nitrosamine ketone). The results were confirmed in tumor xenograft models. Results: We found that NNK decreased the expression of EGFR-AS1 in the long term, but increased the expression of HIF2A and FOXP3 to stimulate lung cancer cell stemness. EGFR-AS1 significantly inhibited FOXP3 expression and NSCLC cell stemness, whereas HIF2A obviously promoted both. The enhancement of lung cancer stemness by FOXP3 was, at least partially, via stimulating Notch1, as the inhibition of Notch1 could markedly diminish the effect of FOXP3. Conclusions: FOXP3, the expression of which is under the fine control of EGFR-AS1, is a critical molecule that promotes NSCLC cancer cell stemness through stimulating the Notch1 pathway.
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Affiliation(s)
- Haolong Qi
- Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Shanshan Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Juekun Wu
- Department of Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shucai Yang
- Department of Clinical Laboratory, Pingshan District People's Hospital of Shenzhen, Shenzhen, China
| | - Steven Gray
- Thoracic Oncology Research Group, Trinity Centre for Health Sciences, St James's Hospital, Dublin, Ireland
| | - Calvin S H Ng
- Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Jing Du
- Peking University Shenzhen Hospital, Shenzhen, China
| | - Malcolm J Underwood
- Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Ming-Yue Li
- Department of Surgery, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong, China
| | - George G Chen
- Department of Surgery, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong, China
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