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HOTTIP Functions as a Key Candidate Biomarker in Head and Neck Squamous Cell Carcinoma by Integrated Bioinformatic Analysis. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5450617. [PMID: 31032351 PMCID: PMC6457310 DOI: 10.1155/2019/5450617] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 02/10/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023]
Abstract
Background Accumulating evidence has demonstrated the pivotal role of long noncoding RNAs (lncRNAs) in competing endogenous RNA (ceRNA) networks for predicting survival and evaluating prognosis in cancer patients. However, the pathogenesis of head and neck squamous cell carcinoma (HNSCC) remains unclear, and prognostic biomarkers for HNSCC are still lacking. Methods A total of 546 RNA sequencing profiles of HNSCC patients with clinical outcome data were obtained from the Cancer Genome Atlas (TCGA) database, providing a large sample of RNA sequencing data. From these, 71 Long noncoding RNAs lncRNAs, 8 microRNAs (miRNAs), and 16 messenger RNAs (mRNAs) were identified to construct a HNSCC-specific ceRNA network (fold change >2, P < 0.05). Univariate and multivariate Cox proportional regression models were used to assess independent indicators of prognosis. Then the expression of lncRNAs harboring prognostic value was validated in human HNSCC cell lines and tumor samples from our cohort and another two datasets from GEO (Gene Expression Omnibus) databases. Results As a result, a 3-mRNA signature and 6-lncRNA signature were identified. The six-lncRNA signature exhibited the highest prognostic value. Notably, in the six lncRNAs, HOTTIP showed the greatest prognostic value and was significantly correlated with clinical stage and histological grade of HNSCC patients. Furthermore, it was proved that HOTTIP was upregulated in HNSCC cell lines and cancerous tissues compared with corresponding normal cell lines and normal tissues. Functional assessment analysis revealed that HOTTIP might play a key role in the oncogenesis and progression of HNSCC. Conclusion The present study deepened our understanding of the ceRNA-related regulatory mechanism in the pathogenesis of HNSCC and identified candidate prognostic biomarkers for clinical outcome prediction in HNSCC. HOTTIP may function as a key candidate biomarker in HNSCC and serve as a prognostic marker for HNSCC patients.
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Gu X, Wang L, Boldrup L, Coates PJ, Fahraeus R, Sgaramella N, Wilms T, Nylander K. AP001056.1, A Prognosis-Related Enhancer RNA in Squamous Cell Carcinoma of the Head and Neck. Cancers (Basel) 2019; 11:cancers11030347. [PMID: 30862109 PMCID: PMC6468641 DOI: 10.3390/cancers11030347] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 12/24/2022] Open
Abstract
A growing number of long non-coding RNAs (lncRNAs) have been linked to squamous cell carcinoma of the head and neck (SCCHN). A subclass of lncRNAs, termed enhancer RNAs (eRNAs), are derived from enhancer regions and could contribute to enhancer function. In this study, we developed an integrated data analysis approach to identify key eRNAs in SCCHN. Tissue-specific enhancer-derived RNAs and their regulated genes previously predicted using the computational pipeline PreSTIGE, were considered as putative eRNA-target pairs. The interactive web servers, TANRIC (the Atlas of Noncoding RNAs in Cancer) and cBioPortal, were used to explore the RNA levels and clinical data from the Cancer Genome Atlas (TCGA) project. Requiring that key eRNAs should show significant associations with overall survival (Kaplan⁻Meier log-rank test, p < 0.05) and the predicted target (correlation coefficient r > 0.4, p < 0.001), we identified five key eRNA candidates. The most significant survival-associated eRNA was AP001056.1 with ICOSLG encoding an immune checkpoint protein as its regulated target. Another 1640 genes also showed significant correlation with AP001056.1 (r > 0.4, p < 0.001), with the "immune system process" being the most significantly enriched biological process (adjusted p < 0.001). Our results suggest that AP001056.1 is a key immune-related eRNA in SCCHN with a positive impact on clinical outcome.
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Affiliation(s)
- Xiaolian Gu
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden.
| | - Lixiao Wang
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden.
| | - Linda Boldrup
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden.
| | - Philip J Coates
- RECAMO, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.
| | - Robin Fahraeus
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden.
- RECAMO, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.
- Équipe Labellisée Ligue Contre le Cancer, INSERM UMRS1162, Institut de Génétique Moléculaire, Université Paris 7, IUH Hôpital St. Louis, 75010 Paris, France.
| | - Nicola Sgaramella
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden.
| | - Torben Wilms
- Department of Clinical Sciences/ENT, Umeå University, 90185 Umeå, Sweden.
| | - Karin Nylander
- Department of Medical Biosciences/Pathology, Umeå University, 90185 Umeå, Sweden.
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53
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Guo YZ, Sun HH, Wang XT, Wang MT. Transcriptomic analysis reveals key lncRNAs associated with ribosomal biogenesis and epidermis differentiation in head and neck squamous cell carcinoma. J Zhejiang Univ Sci B 2019; 19:674-688. [PMID: 30178634 DOI: 10.1631/jzus.b1700319] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE In this study, we aimed to expand current knowledge of head and neck squamous cell carcinoma (HNSCC)-associated long noncoding RNAs (lncRNAs), and to discover potential lncRNA prognostic biomarkers for HNSCC based on next-generation RNA-seq. METHODS RNA-seq data of 546 samples from patients with HNSCC were downloaded from The Cancer Genome Atlas (TCGA), including 43 paired samples of tumor tissue and adjacent normal tissue. An integrated analysis incorporating differential expression, weighted gene co-expression networks, functional enrichment, clinical parameters, and survival analysis was conducted to discover HNSCC-associated lncRNAs. The function of CYTOR was verified by cell-based experiments. To further identify lncRNAs with prognostic significance, a multivariate Cox proportional hazard regression analysis was performed. The identified lncRNAs were validated with an independent cohort using clinical feature relevance analysis and multivariate Cox regression analysis. RESULTS We identified nine HNSCC-relevant lncRNAs likely to play pivotal roles in HNSCC onset and development. By functional enrichment analysis, we revealed that CYTOR might participate in the multistep pathological processes of cancer, such as ribosome biogenesis and maintenance of genomic stability. CYTOR was identified to be positively correlated with lymph node metastasis, and significantly negatively correlated with overall survival (OS) and disease free survival (DFS) of HNSCC patients. Moreover, CYTOR inhibited cell apoptosis following treatment with the chemotherapeutic drug diamminedichloroplatinum (DDP). HCG22, the most dramatically down-regulated lncRNA in tumor tissue, may function in epidermis differentiation. It was also significantly associated with several clinical features of patients with HNSCC, and positively correlated with patient survival. CYTOR and HCG22 maintained their prognostic values independent of several clinical features in multivariate Cox hazards analysis. Notably, validation either based on an independent HNSCC cohort or by laboratory experiments confirmed these findings. CONCLUSIONS Our transcriptomic analysis suggested that dysregulation of these HNSCC-associated lncRNAs might be involved in HNSCC oncogenesis and progression. Moreover, CYTOR and HCG22 were confirmed as two independent prognostic factors for HNSCC patient survival, providing new insights into the roles of these lncRNAs in HNSCC as well as clinical applications.
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Affiliation(s)
- Yu-Zhu Guo
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Hui-Hui Sun
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xiang-Ting Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Mei-Ting Wang
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China.,College of Liren, Yanshan University, Qinhuangdao 066004, China
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Farah CS, Shearston K, Nguyen AP, Kujan O. Oral Carcinogenesis and Malignant Transformation. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/978-981-13-2931-9_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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55
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Zhou D, Wu F, Cui Y, Wei F, Meng Q, Lv Q. Long non-coding RNA-OIS1 inhibits HPV-positive, but not HPV-negative cervical squamous cell carcinoma by upregulating MTK-1. Oncol Lett 2019; 17:2923-2930. [PMID: 30854069 DOI: 10.3892/ol.2019.9891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/27/2018] [Indexed: 11/05/2022] Open
Abstract
Long non-coding RNA-oncogene-induced senescence 1 (lncRNA-OIS1) is a novel lncRNA that is involved in oncogene-induced senescence, while its functionality in cervical squamous cell carcinoma is unknown. In the present study, 68 human papillomavirus (HPV)-positive and 22 HPV-negative patients with cervical squamous cell carcinoma were recruited. Additionally, 40 healthy females were employed as healthy controls. Tumor tissues and adjacent healthy tissues were collected from all patients with cervical squamous cell carcinoma, and blood samples were obtained. Expression of OIS1 was detected by reverse transcription-quantitative polymerase chain reaction. Receiver operating characteristic curve analysis was used to evaluate the diagnostic value of OIS1 for cervical squamous cell carcinoma. HPV-positive and HPV-negative cervical squamous cell carcinoma and normal cervical cell lines were used, and the effects of OIS1 or mitogen-activated protein kinase kinase kinase 4, (MTK-1) expression vector transfection on the proliferation of cell lines and MTK-1 expression were detected by CCK-8 assay and western blotting, respectively. It was established that a reduction in OIS1 expression level in tumor tissues was apparent only in HPV-positive patients. Serum levels of OIS1 were lower in HPV-positive patients compared with that in HPV-negative patients and healthy controls, and no significant differences were observed between HPV-negative patients and healthy controls. Serum levels of OIS1 were significantly associated with tumor size, but not distant tumor metastasis. OIS1 expression level was lower in HPV-positive cancer cell lines compared with that in HPV-negative cancer cell lines, while no significant differences were observed between HPV-positive and HPV-negative normal cell lines. OIS1 overexpression inhibited and MTK-1 overexpression promoted the proliferation of HPV-positive, but not HPV-negative cancer or normal cell lines. OIS1 transfection also decreased the expression of MTK-1 in HPV-positive cancer cell lines, but not in any of the other cell lines. Therefore, it was concluded that OIS1 inhibited HPV-positive, but not HPV-negative cervical squamous cell carcinoma by upregulating MTK-1.
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Affiliation(s)
- Dan Zhou
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Beijing 100730, P.R. China
| | - Fengli Wu
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Beijing 100730, P.R. China
| | - Ying Cui
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Beijing 100730, P.R. China
| | - Fenghua Wei
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Beijing 100730, P.R. China
| | - Qingwei Meng
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Beijing 100730, P.R. China
| | - Qiubo Lv
- Department of Obstetrics and Gynecology, Beijing Hospital, National Center of Gerontology, Beijing 100730, P.R. China
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Wu H, Yu DH, Wu MH, Huang T. Long non-coding RNA LOC541471: A novel prognostic biomarker for head and neck squamous cell carcinoma. Oncol Lett 2018; 17:2457-2464. [PMID: 30675311 DOI: 10.3892/ol.2018.9831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 09/14/2018] [Indexed: 12/26/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive cancer. Early detection and management of HNSCC may prevent progression of the disease. Long non-coding RNAs (lncRNAs) may serve as prognostic biomarkers for various cancer types. The current study downloaded an RNA-Seq dataset containing 43 tumor-normal pairs. An independent t-test identified that the expression level of lncRNA LOC541471 was significantly increased in tumor tissues compared with healthy tissues. Additionally, the current study demonstrated that high lncRNA LOC541471 expression was significantly associated with increasing lymph node metastasis classification and perineural invasion. A multivariate Cox regression analysis revealed that high lncRNA LOC541471 expression levels were an independent predictor for reduced overall survival (n=487) and relapse-free survival (n=355). According to the anatomic neoplasm subdivision, HNSCC samples were classified as oropharyngeal carcinoma (n=297), oral carcinoma (n=80), laryngeal carcinoma and hypopharyngeal carcinoma (n=123). A negative association was revealed between lncRNA LOC541471 expression and overall survival in all subtypes of HNSCC. Therefore, lncRNA LOC541471 is significantly negatively associated with overall survival and relapse-free survival of patients with HNSCC and may be considered a potential prognostic factor for HNSCC.
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Affiliation(s)
- Hua Wu
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
| | - Da Hai Yu
- Department of Radiation Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China.,Department of Radiation Oncology, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
| | - Mian Hua Wu
- First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
| | - Teng Huang
- Department of Radiation Oncology, Affiliated Hospital of Nanjing University of Traditional Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China.,Department of Radiation Oncology, Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing, Jiangsu 210000, P.R. China
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Rodríguez-Álvarez MI, Gómez-Urquiza JL, Husein-El Ahmed H, Albendín-García L, Gómez-Salgado J, Cañadas-De la Fuente GA. Prevalence and Risk Factors of Human Papillomavirus in Male Patients: A Systematic Review and Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15102210. [PMID: 30309014 PMCID: PMC6210641 DOI: 10.3390/ijerph15102210] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/30/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
Abstract
Human papillomavirus (HPV) is one of the most prevalent sexually transmitted infections. Although the research focus has been on women, men are also affected. Thus, the aim was to estimate the prevalence of HPV in men and to analyse its risk factors. A systematic review with meta-analysis was performed. The main health science databases were consulted. The search terms were was: "papilloma virus AND (prevalence OR risk factors) AND men". The final sample of studies was n = 16 and the men sample for the meta-analysis was n = 18,106. The meta-analysis revealed a prevalence of 49% (95% Confidence Interval (CI): 35⁻64%) of any type of human papillomavirus in men and 35% (95% CI: 26⁻45%) of high-risk human papillomavirus in men. The included studies showed that stable sexual habits, circumcision and condom use are protective factors against HPV. In addition, there is a certain positive association with tobacco use and the early initiation of sexual intercourse. In conclusion, the prevalence of HPV in men is high. The risk factors for HPV infection are sexual promiscuity, early sexual debut, absence of circumcision, lack of condom use and smoking. Further study in this field about the effectiveness of the vaccine and health education should be conducted.
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Affiliation(s)
| | | | - Husein Husein-El Ahmed
- Hospital of Baza, Department of Dermatology, Andalusian Health Service, 18016 Granada, Spain.
| | - Luis Albendín-García
- Hospital of Baza, Department of Dermatology, Andalusian Health Service, 18016 Granada, Spain.
- Department of Nursing, University of Granada, 18016 Granada, Spain.
| | - Juan Gómez-Salgado
- Department of Nursing, University of Huelva, 21007 Huelva, Spain.
- Safety and Health Posgrade Program, Espíritu Santo University, Guayaquil 091650, Ecuador.
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58
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Cui GX, Gao XL, Liang XH. [Invasion and metastasis mechanism of human papillomavirus in head and neck squamous cell carcinomas]. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2018; 36:544-551. [PMID: 30465350 DOI: 10.7518/hxkq.2018.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Human papillomavirus (HPV) is a major causative agent of head and neck squamous cell carcinomas (HNSCC). Over the past several decades, an increasing number of studies established the strong association of HPV with the invasion and metastasis of HNSCC. In the present study, we reviewed the gene mutations in HPV-associated HNSCC and the unique mechanism of E6- and E7-mediated carcinogenesis via interactions with an array of cellular elements. We further discussed the progress in the mechanisms of invasion and metastasis; these mechanisms include non-coding RNAs, deregulating cellular energetics, tumor microenvironment, cancer stem cells, angiogenesis, and lymphangiogenesis.
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Affiliation(s)
- Guang-Xue Cui
- Dept. of Oral and Maxillofacial Surgery, Affiliated Hospital of Chifeng University, Chifeng 024000, China
| | - Xiao-Lei Gao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Xin-Hua Liang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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Hu JC, Wang Q, Jiang LX, Cai L, Zhai HY, Yao ZW, Zhang ML, Feng Y. Effect of long non-coding RNA AOC4P on gastrointestinal stromal tumor cells. Onco Targets Ther 2018; 11:6259-6269. [PMID: 30288061 PMCID: PMC6163024 DOI: 10.2147/ott.s174524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Objective In this research, we explored the effect of long non-coding RNA (lncRNA) AOC4P on gastrointestinal stromal tumor (GIST) cells. Materials and methods The expression of lncRNA AOC4P in tissues was detected by real-time PCR (RT-PCR). The epithelial–mesenchymal transition (EMT)-related proteins in tissues were analyzed by Western blot. The experiment included negative control group (CN), silence AOC4P group (si AOC4P), and silence negative control group (si CT). RT-PCR, MTT, Scratch, Transwell, and Annexin V-FITC methods were used to detect the expression of lncRNA AOC4P, cell proliferation, cell migration ability, cell invasion ability, and apoptosis, respectively. The EMT-related proteins including TGF-β, ZEB1, Vimentin, Snail, and E-cadherin were analyzed by Western blot. Results The expression of lncRNA AOC4P and the expression of EMT-related proteins in high-risk GISTs were higher than that in low- and intermediate-risk GISTs (P<0.05). It was revealed that cell proliferative migration and invasive ability in si AOC4P group was decreased than that in CN and si CT groups (P<0.05), and cell apoptosis in si AOC4P group was higher than that in si CT group. The results of Western blot demonstrated that the expression of TGF-β1, ZEB1, Vimentin, and Snail in si AOC4P group were lower than that in si CT and CN group (P<0.05), and the expression of E-cadherin in si AOC4P group was higher than that in si CT and CN group (P<0.05).
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Affiliation(s)
- Jin-Chen Hu
- Department of Gastrointestinal Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Quan Wang
- Department of Gastrointestinal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Li-Xin Jiang
- Department of Gastrointestinal Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Li Cai
- Department of Pathology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Hui-Yuan Zhai
- Department of Gastrointestinal Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Zeng-Wu Yao
- Department of Gastrointestinal Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Meng-Lai Zhang
- Department of Gastrointestinal Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, China
| | - Ye Feng
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China,
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Wang X, Wang G, Zhang L, Cong J, Hou J, Liu C. LncRNA PVT1 promotes the growth of HPV positive and negative cervical squamous cell carcinoma by inhibiting TGF-β1. Cancer Cell Int 2018; 18:70. [PMID: 29760583 PMCID: PMC5941374 DOI: 10.1186/s12935-018-0567-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/27/2018] [Indexed: 01/08/2023] Open
Abstract
Background Our study aimed to investigate the role of lncRNA PVT1 in cervical squamous cell carcinoma. Materials and methods A total of 156 patients with cervical squamous cell carcinoma were enrolled in this study and human papillomavirus (HPV) infection was detected by highly sensitive PCR techniques. Serum levels of PVT1 in patients infected with different HPVs and healthy controls was detected by qRT-PCR and compared. Serum levels of PVT1 were also compared among patients with different sizes of tumor. ROC curve analysis was performed to evaluate the diagnostic values of serum for cervical squamous cell carcinoma. Survival curves were plotted by Kaplan–Meier method and compared to evaluate the prognostic values of serum PVT1 for this disease. Effects of PVT1 siRNA silencing and overexpression on proliferation of cervical squamous cell carcinoma cells were explored by CCK-8 assay. Western blot was performed to detect the expression of TGF-β1 after PVT1 siRNA silencing and overexpression. Results No significant differences in serum levels of PVT1 were detected among patients infected with different HPVs and HPV-negative patients. However, serum levels of PVT1 were significantly higher in all patient groups than in healthy control group. Serum level of PVT1 increased with the increased sizes of primary tumor. Serum PVT1 accurately predicted the disease and its prognosis. PVT1 siRNA silencing inhibited the proliferation of cancer cells and reduced the expression of TGF-β1, while PVT1 overexpression played an opposite role. Conclusion LncRNA PVT1 promotes the growth HPV positive and negative cervical squamous cell carcinoma by inhibiting TGF-β1.
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Affiliation(s)
- Xiuli Wang
- 1Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000 Shandong People's Republic of China
| | - Guichan Wang
- 2Department of Obstetrics and Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000 Shandong People's Republic of China
| | - Lijuan Zhang
- 2Department of Obstetrics and Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000 Shandong People's Republic of China
| | - Jianglin Cong
- 1Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000 Shandong People's Republic of China
| | - Jianqing Hou
- 1Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000 Shandong People's Republic of China
| | - Chunyan Liu
- 1Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, 264000 Shandong People's Republic of China
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61
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Feng L, Houck JR, Lohavanichbutr P, Chen C. Transcriptome analysis reveals differentially expressed lncRNAs between oral squamous cell carcinoma and healthy oral mucosa. Oncotarget 2018; 8:31521-31531. [PMID: 28415559 PMCID: PMC5458226 DOI: 10.18632/oncotarget.16358] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/09/2017] [Indexed: 01/09/2023] Open
Abstract
Oral cavity and oropharyngeal squamous cell carcinoma (OSCC) is a major cancer type in the head and neck region. To better understand the roles long non-coding RNA (lncRNA) play in OSCC carcinogenesis, we compared the expression levels of 3,054 probe sets for lncRNAs between 167 OSCCs and 45 healthy oral mucosa using an Affymetrix HG U133 plus 2.0 array dataset. We found 658 lncRNA transcripts (790 probe sets) to be significantly differentially expressed using a criteria of FDR < 0.01, with 36 of them (39 probe sets) showing more than a 2-fold change. We further validated the top differentially expressed lncRNAs in three independent datasets from Gene Expression Omnibus (GEO) repository: GSE42743, GSE9844, and GSE6791. Fourteen lncRNAs (15 probe sets) were validated in all three datasets using the criteria FDR < 0.01: LOC441178, C5orf66-AS1, HCG22, FLG-AS1, CCL14/CCL15-CCL14, LOC100506990, TRIP10, PCBP1-AS1, LINC01315, LINC00478, COX10-AS1/LOC100506974, MLLT4-AS1, MIR31HG, and DUXAP10/LINC01296. Three lncRNAs in the validated list which showed the highest fold change (LOC441178, HCG22 and C5orf66-AS1) were verified by quantitative RT-PCR in a subset of 20 OSCCs and 10 control samples. In silico prediction of their functional role has given us directions for further investigation.
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Affiliation(s)
- Lu Feng
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Head and Neck Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, P.R.China
| | - John R Houck
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pawadee Lohavanichbutr
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA.,Department of Otolaryngology, Head and Neck Surgery, University of Washington, Seattle, Washington, USA
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62
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Haque SU, Niu L, Kuhnell D, Hendershot J, Biesiada J, Niu W, Hagan MC, Kelsey KT, Casper KA, Wise-Draper TM, Medvedovic M, Langevin SM. Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma. Head Neck 2018; 40:1555-1564. [PMID: 29575229 DOI: 10.1002/hed.25136] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/30/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Long non-coding RNA (lncRNA) has emerged as a new avenue of interest due to its various biological functions in cancer. Abnormal expression of lncRNA has been reported in other malignancies but has been understudied in head and neck squamous cell carcinoma (HNSCC). METHODS The lncRNA expression was interrogated via quantitative real-time polymerase chain reaction (qRT-PCR) array for 19 human papillomavirus (HPV)-negative HNSCC tumor-normal pairs. The Cancer Genome Atlas (TCGA) was used to validate these results. The association between differentially expressed lncRNA and survival outcomes was analyzed. RESULTS Differential expression was validated for 5 lncRNA (SPRY4-IT1, HEIH, LUCAT1, LINC00152, and HAND2-AS1). There was also an inverse association between MEG3 expression (not significantly differentially expressed in TCGA tumors but highly variable expression) and 3-year recurrence-free survival (RFS). CONCLUSION We identified and validated differential expression of 5 lncRNA in HPV-negative HNSCC. Low MEG3 expression was associated with favorable 3-year RFS, although the significance of this finding remains unclear.
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Affiliation(s)
- Sulsal-Ul Haque
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Liang Niu
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Damaris Kuhnell
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jacob Hendershot
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Jacek Biesiada
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Wen Niu
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Matthew C Hagan
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Keith A Casper
- Department of Otolaryngology, University of Michigan, Ann Arbor, Michigan
| | - Trisha M Wise-Draper
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati College of Medicine, Cincinnati, Ohio.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
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63
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Unravelling the Long Non-Coding RNA Profile of Undifferentiated Large Cell Lung Carcinoma. Noncoding RNA 2018; 4:ncrna4010004. [PMID: 29657301 PMCID: PMC5890391 DOI: 10.3390/ncrna4010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 12/14/2022] Open
Abstract
Undifferentiated large cell lung carcinoma (LCLC) accounts for 2.9-9% of total lung cancers. Recently, RNA-seq based studies have revealed major genomic aberrations in LCLC. In this study, we aim to identify long non-coding RNAs (LncRNAs) expression pattern specific to LCLC. The RNA-seq profile of LCLC and other non-small cell lung carcinoma (NSCLC) was downloaded from Gene Expression Omnibus (GEO) and analyzed. Using 10 LCLC samples, we found that 18% of all the annotated LncRNAs are expressed in LCLC samples. Among 1794 expressed LncRNAs, 11 were overexpressed and 14 were downregulated in LCLC compared to normal samples. Based on receiver operating characteristic (ROC) analysis, we showed that the top five differentially expressed LncRNAs were able to differentiate between LCLC and normal samples with high sensitivity and specificity. Guilt by association analysis using genes correlating with differentially expressed LncRNAs identified several cancer-associated pathways, suggesting the role of these deregulated LncRNA in LCLC biology. We also identified the LncRNA differentially expressed in LCLC compared to lung squamous carcinoma (LUSC) and Lung-adenocarcinoma (LUAD). We found that LCLC sample showed more deregulated LncRNA in LUSC than LUAD. Interestingly, LCLC had more downregulated LncRNA compared to LUAD and LUSC. Our study provides novel insight into LncRNA deregulation in LCLC. This study also finds tools to diagnose LCLC and differentiate LCLC with other Non-Small Cell Lung Cancer.
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64
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Guglas K, Bogaczyńska M, Kolenda T, Ryś M, Teresiak A, Bliźniak R, Łasińska I, Mackiewicz J, Lamperska K. lncRNA in HNSCC: challenges and potential. Contemp Oncol (Pozn) 2017; 21:259-266. [PMID: 29416430 PMCID: PMC5798417 DOI: 10.5114/wo.2017.72382] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 01/17/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cause of cancer mortality in the world. Some progress has been made in the therapy of HNSCC, however treatment remains unsatisfactory. Recent studies have shown that different types of long non-coding RNAs (lncRNAs) are dysregulated in HNSCC and correlate with tumor progression, lymph node metastasis, clinical stage and poor prognosis. lncRNAs are a class of functional RNA molecules that can not be translated into proteins but can modulate the activity of transcription factors or regulate changes in chromatin structure. The lncRNAs might have potential of biomarker in HNSCC diagnosis, prognosis, prediction and targeted treatment. In this review we describe the potential role of lncRNAs as new biomarkers and discuss their features including source of origin, extraction methods, stability, detection methods and data normalization and potential function as biomarkers in HNSCC.
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Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Bogaczyńska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- HAN University of Applied Sciences, Nijmegen, Netherlands
| | - Tomasz Kolenda
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Marcel Ryś
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
| | - Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poland
- Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
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65
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Han W, Zhang Z, He B, Xu Y, Zhang J, Cao W. Integrated analysis of long non-coding RNAs in human gastric cancer: An in silico study. PLoS One 2017; 12:e0183517. [PMID: 28841672 PMCID: PMC5571953 DOI: 10.1371/journal.pone.0183517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/04/2017] [Indexed: 02/04/2023] Open
Abstract
Accumulating evidence highlights the important role of long non-coding RNAs (lncRNAs) in a large number of biological processes. However, the knowledge of genome scale expression of lncRNAs and their potential biological function in gastric cancer is still lacking. Using RNA-seq data from 420 gastric cancer patients in The Cancer Genome Atlas (TCGA), we identified 1,294 lncRNAs differentially expressed in gastric cancer compared with adjacent normal tissues. We also found 247 lncRNAs differentially expressed between intestinal subtype and diffuse subtype. Survival analysis revealed 33 lncRNAs independently associated with patient overall survival, of which 6 lncRNAs were validated in the internal validation set. There were 181 differentially expressed lncRNAs located in the recurrent somatic copy number alterations (SCNAs) regions and their correlations between copy number and RNA expression level were also analyzed. In addition, we inferred the function of lncRNAs by construction of a co-expression network for mRNAs and lncRNAs. Together, this study presented an integrative analysis of lncRNAs in gastric cancer and provided a valuable resource for further functional research of lncRNAs in gastric cancer.
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Affiliation(s)
- Weiwei Han
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenyu Zhang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Bangshun He
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yijun Xu
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Jun Zhang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Weijun Cao
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- * E-mail:
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66
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Kolenda T, Guglas K, Ryś M, Bogaczyńska M, Teresiak A, Bliźniak R, Łasińska I, Mackiewicz J, Lamperska KM. Biological role of long non-coding RNA in head and neck cancers. Rep Pract Oncol Radiother 2017; 22:378-388. [PMID: 28794691 DOI: 10.1016/j.rpor.2017.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/26/2017] [Accepted: 07/11/2017] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) are one of the worst prognosis cancers with high mortality of patients. The treatment strategy is primarily based on surgery and radiotherapy but chemotherapy is also used. Every year the knowledge concerning HNSCC biology is updated with new elements such as the recent discovered molecules - long non-coding RNAs. Long non-coding RNAs are involved in regulatory processes in the cells. It has been revealed that the expression levels of lncRNAs are disturbed in tumor cells what results in the acquisition of their specific phenotype. lncRNAs influence cell growth, cell cycle, cell phenotype, migration and invasion ability as well as apoptosis. Development of the lncRNA panel characteristic for HNSCC and validation of specific lncRNA functions are yet to be elucidated. In this work, we collected available data concerning lncRNAs in HNSCC and characterized their biological role. We believe that the tumor examination, in the context of lncRNA expression, may lead to understanding complex biology of the cancer and improve therapeutic methods in the future.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61th Zwirki i Wigury Street, 02-091 Warszawa, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Marcel Ryś
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland
| | - Marta Bogaczyńska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland.,HAN University of Applied Sciences, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands
| | - Anna Teresiak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
| | - Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18th Grunwaldzka Street, 60-786 Poznan, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18th Grunwaldzka Street, 60-786 Poznan, Poland.,Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, 8th Rokietnicka Street, 60-806 Poznan, Poland.,Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15th Garbary Street, 61-866 Poznan, Poland
| | - Katarzyna M Lamperska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866 Poznan, Poland
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67
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Li S, Chen X, Liu X, Yu Y, Pan H, Haak R, Schmidt J, Ziebolz D, Schmalz G. Complex integrated analysis of lncRNAs-miRNAs-mRNAs in oral squamous cell carcinoma. Oral Oncol 2017; 73:1-9. [PMID: 28939059 DOI: 10.1016/j.oraloncology.2017.07.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/24/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES This study aims to reveal regulatory network of lncRNAs-miRNAs-mRNAs in oral squamous cell carcinoma (OSCC) through gene expression data. MATERIAL AND METHODS Differentially expressed lncRNAs, miRNAs and mRNAs (cut-off: False discovery rate (FDR)<0.05 and |fold change|>1.5) were unveiled by package edgeR of R. Cox regression analysis was performed to screen prognostic factors in OSCC related with overall survival (OS) and relapse-free survival (RFS). Protein-protein interaction (PPI) network was constructed for differentially expressed mRNAs using BioGRID, HPRD and DIP. Key hub genes were identified from top 100 differentially expressed mRNAs ranked by betweenness centrality using recursive feature elimination. LncRNA-miRNA and miRNA-mRNA regulatory network were constructed and combined into ceRNAs regulatory network. Gene ontology biological terms and Kyoto Encyclopedia of Genes and Genomes pathways were identified using Fisher's exact test. RESULTS A total of 929 differentially expressed mRNAs, 23 differentially expressed lncRNAs and 29 differentially expressed miRNAs were identified. 59 mRNAs, 6 miRNAs (hsa-mir-133a-1, hsa-mir-1-2, hsa-mir-486, hsa-mir-135b, hsa-mir-196b, hsa-mir-193b) and 6 lncRNAs (C10orf91, C2orf48, SFTA1P, FLJ41941,PART1,TTTY14) were related with OS; and 52 mRNAs, 4 miRNAs (hsa-mir-133a-1, hsa-mir-135b, hsa-mir-196b, hsa-mir-193b) and 2 lncRNAs (PART1, TTTY14) were associated with RFS. A support vector machine (SVM) classifier containing 37 key hub genes was obtained. A ceRNA regulatory network containing 417 nodes and 696 edges was constructed. ECM-receptor interaction, cytokine-cytokine receptor interaction, focal adhesion, arachidonic acid metabolism, and p53 signaling pathway were significantly enriched in the network. CONCLUSION These findings uncover the pathogenesis of OSCC and might provide potential therapeutic targets.
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Affiliation(s)
- Simin Li
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany
| | - Xiujie Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xiangqiong Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yang Yu
- Department of Periodontology, The Stomatology Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Hongying Pan
- Department of Orthopedic surgery, Brigham and Women's Hospital, Harvard Medical School, Harvard University, Boston, USA
| | - Rainer Haak
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany
| | - Jana Schmidt
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany
| | - Dirk Ziebolz
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany.
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany
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68
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de Lena PG, Paz-Gallardo A, Paramio JM, García-Escudero R. Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates. Clin Epigenetics 2017; 9:36. [PMID: 28405244 PMCID: PMC5385094 DOI: 10.1186/s13148-017-0334-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/24/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have emerged as key players in a remarkably variety of biological processes and pathologic conditions, including cancer. Next-generation sequencing technologies and bioinformatics procedures predict the existence of tens of thousands of lncRNAs, from which we know the functions of only a handful of them, and very little is known in cancer types such as head and neck squamous cell carcinomas (HNSCCs). RESULTS Here, we use RNAseq expression data from The Cancer Genome Atlas (TCGA) and various statistic and software tools in order to get insight about the lncRNome in HNSCC. Based on lncRNA expression across 426 samples, we discover five distinct tumor clusters that we compare with reported clusters based on various genomic/genetic features. Results demonstrate significant associations between lncRNA-based clustering and DNA methylation, TP53 mutation, and human papillomavirus infection. Using "guilt-by-association" procedures, we infer the possible biological functions of representative lncRNAs of each cluster. Furthermore, we found that lncRNA clustering is correlated with some important clinical and pathologic features, including patient survival after treatment, tumor grade, or sub-anatomical location. CONCLUSIONS We present a landscape of lncRNAs in HNSCC and provide associations with important genotypic and phenotypic features that may help to understand the disease.
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Affiliation(s)
- Pelayo G de Lena
- Molecular Oncology Unit, CIEMAT, Ave Complutense 40 (ed70A), 28040 Madrid, Spain
| | | | - Jesús M Paramio
- Molecular Oncology Unit, CIEMAT, Ave Complutense 40 (ed70A), 28040 Madrid, Spain.,Biomedical Research Institute I+12, University Hospital 12 de Octubre, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT, Ave Complutense 40 (ed70A), 28040 Madrid, Spain.,Biomedical Research Institute I+12, University Hospital 12 de Octubre, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
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69
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Seven LncRNA-mRNA based risk score predicts the survival of head and neck squamous cell carcinoma. Sci Rep 2017; 7:309. [PMID: 28331188 PMCID: PMC5428014 DOI: 10.1038/s41598-017-00252-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/15/2017] [Indexed: 02/06/2023] Open
Abstract
Dysregulation of mRNAs and long non-coding RNAs (lncRNAs) is one of the most important features of carcinogenesis and cancer development. However, studies integrating the expression of mRNAs and lncRNAs to predict the survival of head and neck squamous cell carcinoma (HNSC) are still limited, hitherto. In current work, we identified survival related mRNAs and lncRNAs in three datasets (TCGA dataset, E-TABM-302, GSE41613). By random forest, seven gene signatures (six mRNAs and lncRNA) were further selected to develop the risk score model. The risk score was significantly associated with survival in both training and testing datasets (E-TABM-302, GSE41613, and E-MTAB-1324). Furthermore, correlation analyses showed that the risk score is independent from clinicopathological features. According to Cox multivariable hazard model and nomogram, the risk score contributes the most to survival than the other clinical information, including gender, age, histologic grade, and alcohol taking. The Gene Set Enrichment Analysis (GSEA) indicates that the risk score is associated with cancer related pathways. In summary, the lncRNA-mRNA based risk score model we developed successfully predicts the survival of 755 HNSC samples in five datasets and two platforms. It is independent from clinical information and performs better than clinical information for prognosis.
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70
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Cao W, Liu JN, Liu Z, Wang X, Han ZG, Ji T, Chen WT, Zou X. A three-lncRNA signature derived from the Atlas of ncRNA in cancer (TANRIC) database predicts the survival of patients with head and neck squamous cell carcinoma. Oral Oncol 2017; 65:94-101. [PMID: 28109476 DOI: 10.1016/j.oraloncology.2016.12.017] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/12/2016] [Accepted: 12/17/2016] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Long non-coding RNAs (lncRNAs) have important biological functions and can be used as prognostic biomarkers in cancer. To identify a lncRNA prognostic signature for head and neck squamous cell carcinoma (HNSCC). METHOD We analysed RNA-seq data derived from the TANRIC database to identify a lncRNA prognostic signature model using the orthogonal partial least squares discrimination analysis (OPLS-DA) and 1.5-fold expression change criterion methods. The prognosis prediction model based on the lncRNA signatures and clinical parameters were evaluated using the 5-fold cross validation method. RESULTS A total of 84 out of 3199 lncRNAs were significantly associated with the survival of patients with HNSCC (log-rank test P<0.01). Using the OPLS-DA and 1.5-fold change selection criterion, 5 lncRNAs (KTN1-AS1, LINC00460, GUSBP11, LINC00923 and RP5-894A10.6) were further selected. The prediction power of each combination of the 5 lncRNAs was evaluated through the receiver operating characteristic (ROC) curve and a three-lncRNA panel (KTN1-AS1, LINC00460 and RP5-894A10.6) achieved the highest prognostic prediction power (AUC 0.68, 95% CI 0.60-0.76, P<0.0001) in the cohort. The patients were categorized into high- and low-risk groups based on their three-lncRNA profiles. Patients with high-risk scores had worse overall survival than those with low risk scores in the cohort (log-rank test P=0.0003). Multivariable Cox regression analyses showed that the lncRNA signature and tumour grade were independent prognostic factors for patients with HNSCC. CONCLUSIONS Our findings showed that the three-lncRNA signature might be a novel biomarker for the accurate prognosis prediction of patients with HNSCC.
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Affiliation(s)
- Wei Cao
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Jian-Nan Liu
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Zeqi Liu
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Xu Wang
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tong Ji
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.
| | - Wan-Tao Chen
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.
| | - Xin Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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71
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Ma B, Liao T, Wen D, Dong C, Zhou L, Yang S, Wang Y, Ji Q. Long intergenic non-coding RNA 271 is predictive of a poorer prognosis of papillary thyroid cancer. Sci Rep 2016; 6:36973. [PMID: 27833134 PMCID: PMC5105055 DOI: 10.1038/srep36973] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/21/2016] [Indexed: 12/02/2022] Open
Abstract
A number of long non-coding RNAs (lncRNAs) have been found to play critical roles in oncogenesis and tumor progression. We aimed to investigate whether lncRNAs could act as prognostic biomarkers for papillary thyroid cancer (PTC) that may assist us in evaluating disease status and prognosis for patients. We found 220 lncRNAs with expression alteration from the annotated 2773 lncRNAs approved by the HUGO gene nomenclature committee in The Cancer Genome Atlas (TCGA) dataset, of which FAM41C, CTBP1-AS2, LINC00271, HAR1A, LINC00310 and HAS2-AS1 were associated with recurrence. After adjusting classical clinicopathogical factors and BRAFV600E mutation, LINC00271 was found to be an independent risk factor for extrathyroidal extension, lymph node metastasis, advanced tumor stage III/IV and recurrence in multivariate analyses. Additionally, LINC00271 expression was significantly downregulated in PTCs versus adjacent normal tissues (P < 0.001). The Gene Set Enrichment Analysis (GSEA) revealed that genes associated with cell adhesion molecules, cell cycle, P53 signaling pathway and JAK/STAT signaling pathway were remarkably enriched in lower-LINC00271 versus higher-LINC00271 tumors. In conclusion, LINC00271 was identified as a possible suppressor gene in PTC in our study, and it may serve as a potential predictor of poor prognoses in PTC.
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Affiliation(s)
- Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Duo Wen
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Chuanpeng Dong
- Institute of Biomedical Science, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Li Zhou
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Shuwen Yang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Qinghai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
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72
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The emerging role of long noncoding RNAs in oral cancer. Oral Surg Oral Med Oral Pathol Oral Radiol 2016; 123:235-241. [PMID: 27989708 DOI: 10.1016/j.oooo.2016.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/12/2016] [Accepted: 10/04/2016] [Indexed: 01/01/2023]
Abstract
Although less than 3% of the genome encodes proteins, at least 75% of the genome is transcribed into RNAs with no protein-coding potential (noncoding RNAs [ncRNAs]). On the basis of their size and the arbitrary 200 nucleotides cutoff, ncRNAs are classified into long ncRNAs (lncRNAs) or small ncRNAs (including microRNAs). Over the last few years, the role of microRNAs in oral squamous cells carcinoma (OSCC) has been extensively addressed, but the possible role of lncRNAs in OSCC remains unclear. We aimed to explore and discuss the potential role of lncRNAs in OSCC. The detection of lncRNAs in saliva holds promise not only as a noninvasive diagnostic tool in OSCC but also in the early detection of oral cancer recurrence. lncRNAs are promising future therapeutic targets in the OSCC scenario, and research in this field may expand greatly in the next decade.
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