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Huang X, Yi G, Xu J, Gou S, Chen H, Chen X, Quan X, Xie L, Teichmann AT, Yang G, Chi H, Wang Q. Angiogenesis-related lncRNAs index: A predictor for CESC prognosis, immunotherapy efficacy, and chemosensitivity. J Cancer 2024; 15:3095-3113. [PMID: 38706901 PMCID: PMC11064265 DOI: 10.7150/jca.94332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/26/2024] [Indexed: 05/07/2024] Open
Abstract
Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) is a common gynecologic tumor and patients with advanced and recurrent disease usually have a poor clinical outcome. Angiogenesis is involved in the biological processes of tumors and can promote tumor growth and invasion. In this paper, we created a signature for predicting prognosis based on angiogenesis-related lncRNAs (ARLs). This provides a prospective direction for enhancing the efficacy of immunotherapy in CESC patients. We screened seven OS-related ARLs by univariate and multivariate regression analyses and Lasso analysis and developed a prognostic signature at the same time. Then, we performed an internal validation in the TCGA-CESC cohort to increase the precision of the study. In addition, we performed a series of analyses based on ARLs, including immune cell infiltration, immune function, immune checkpoint, tumor mutation load, and drug sensitivity analysis. Our created signature based on ARLs can effectively predict the prognosis of CESC patients. To strengthen the prediction accuracy of the signature, we built a nomogram by combining signature and clinical features.
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Affiliation(s)
- Xueyuan Huang
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Guangming Yi
- Department of Oncology, The Third Hospital of Mianyang (Sichuan Mental Health Center), Mianyang, Sichuan 621000, China
| | - Jiayu Xu
- School of Science, Minzu University of China, Beijing 100081, China
| | - Siqi Gou
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Haiqing Chen
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Xiaoyan Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, China
| | - Xiaomin Quan
- Beijing University of Chinese Medicine, 100029, Beijing, China
- Department of Oncology, Beijing University of Chinese Medicine second affiliated Dong Fang hospital, 100078, Beijing, China
| | - Linjia Xie
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Alexander Tobias Teichmann
- Sichuan Provincial Center for Gynecology and Breast Diseases (Gynecology), Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens 45701, OH, United States
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Qin Wang
- Sichuan Provincial Center for Gynecology and Breast Diseases (Gynecology), Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
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Zhou X, Li Z, Li M. LncRNA WWTR1-AS1 upregulates Notch3 through miR-136 to increase cancer cell stemness in cervical squamous cell carcinoma. BMC Womens Health 2024; 24:104. [PMID: 38331752 PMCID: PMC10851613 DOI: 10.1186/s12905-024-02905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 01/13/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND This Study investigated the role of WWTR1-AS1 in cervical squamous cell carcinoma (CSCC). RESULTS WWTR1-AS1 expression was upregulated in CSCC tissues. WWTR1-AS1 was predicted to interact with miR-136, whereas correlation analysis revealed that there was no close correlation between WWTR1-AS1 and miR-136 across CSCC samples. Moreover, WWTR1-AS1 and miR-136 did not regulate the expression of each other. In addition, overexpression of WWTR1-AS1 increased the expression levels of Notch3, which could be targeted by miR-136. Cell stemness analysis indicated that the overexpression of WWTR1-AS1 and Notch3 increased CSCC cell stemness and the capacity of CSCC cell to grow as spheroids. Overexpression of miR-136 decreased CSCC cell stemness and reversed the effects of overexpression of WWTR1-AS1 on Notch3 in CSCC cells. CONCLUSION Therefore, WWTR1-AS1 may upregulate Notch3 through miR-136 to increase cancer cell stemness in CSCC.
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Affiliation(s)
- Xiaofeng Zhou
- Department of Obstetrics and Gynecology, Bishan hospital of Chongqing medical university, Bishan Hospital of Chongqing, No. 9 Shuangxing Avenue, Biquan Street, Bishan District, 402760, Chongqing City, P. R. China
| | - Zhizun Li
- Department of Obstetrics and Gynecology, Bishan hospital of Chongqing medical university, Bishan Hospital of Chongqing, No. 9 Shuangxing Avenue, Biquan Street, Bishan District, 402760, Chongqing City, P. R. China
| | - Moyu Li
- Department of Obstetrics and Gynecology, Bishan hospital of Chongqing medical university, Bishan Hospital of Chongqing, No. 9 Shuangxing Avenue, Biquan Street, Bishan District, 402760, Chongqing City, P. R. China.
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Wang S, Pang X, Tong L, Fan H, Jiang J, Zhao M, Yu X, Li M, Liang J, Fan Y, Zhang X, Tang Y, Sun Y, Liang X. LncRNA SELL/L-selectin Promotes HPV-Positive HNSCC Progression and Drives Fucoidan-Mediated Therapeutic Strategies. Acta Biomater 2023:S1742-7061(23)00335-5. [PMID: 37330030 DOI: 10.1016/j.actbio.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/18/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
Positive human papillomavirus (HPV+) head and neck squamous cell carcinoma (HNSCC) presents a higher risk of lymph node metastasis and poor prognosis. Here, advanced microarray analysis of clinically collected HNSCC tissues revealed significant upregulation of the lncRNA SELL in HPV+ HNSCC, and its overexpression was obviously associated with lymph node metastasis. The lncRNA SELL could function as a promigratory and proinvasive mediator as well as an inducer of M1-like tumour-associated macrophages (TAM) by increasing the level of L-selectin. Furthermore, fucoidan, as an L-selectin inhibitor, obviously weakened the formation of tongue lesions induced by 4-Nitroquinoline N-oxide (4-NQO) in HPV16 E6/E7 transgenic mice. This result drove us to synchronously develop a nanodelivery platform to verify fucoidan-mediated anti-growth and anti-metastasis effects. This work highlighted the important influence of the lncRNA SELL/L-selectin on promoting HPV+ HNSCC progression and proposed a potential fucoidan-mediated therapeutic strategy. STATEMENT OF SIGNIFICANCE: Head and neck squamous cell carcinoma (HNSCC) patients with human papillomavirus (HPV) involvement present a greater risk of lymph node metastasis than HPV negative HNSCC patients. However, treatment protocols, including surgery and platinum-based chemo- and radiotherapy, have not improved the 5-year overall survival due to the high tendency of lymphatic metastasis. Here, microarray of clinical HNSCC samples confirms the oncogenic significance of lncRNA SELL, which acts as an M1-like TAM inducer and promotes tumorigenesis by upregulating L-selectin. Fucoidan, as an L-selectin inhibitor, suppresses tongue lesions in transgenic mice, and a fucoidan-mediated nanodelivery platform inhibits HPV+ HNSCC growth. The present study highlights lncRNA SELL/L-selectin on promoting HPV+ HNSCC progression and proposes a potential fucoidan-mediated therapeutic.
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Affiliation(s)
- Shasha Wang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Pang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lei Tong
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, China
| | - Huayang Fan
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jian Jiang
- Department of Head and Neck Surgery, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Mingda Zhao
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, China
| | - Xianghua Yu
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Oral Pathology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mao Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Oral Pathology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jie Liang
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, China
| | - Yujiang Fan
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, China
| | - Xingdong Zhang
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, China
| | - Yaling Tang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Oral Pathology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yong Sun
- National Engineering Research Center for Biomaterials, College of Biomedical Engineering, Sichuan University, Chengdu, China.
| | - Xinhua Liang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Guo D, Yang M, Li S, Zhu W, Chen M, Pan J, Long D, Liu Z, Zhang C. Expression and molecular regulation of non-coding RNAs in HPV-positive head and neck squamous cell carcinoma. Front Oncol 2023; 13:1122982. [PMID: 37064141 PMCID: PMC10090466 DOI: 10.3389/fonc.2023.1122982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent malignancy worldwide. Accumulating evidence suggests that persistent HPV infection is closely related to a subset of HNSCC types, and the incidence of human papillomavirus (HPV)-positive HNSCC has been annually increasing in recent decades. Although the carcinogenesis of HPV-positive HNSCC has not been completely elucidated, it has been well confirmed that E6 and E7, the main viral oncoproteins are responsible for the maintenance of malignant transformation, promotion of cell proliferation, and increase in tumor invasion. Moreover, compared with HPV-negative HNSCC, HPV-positive HNSCC shows some special clinical-pathological features, which are possibly related to HPV infection and their specific regulatory mechanisms. Non-coding RNA (ncRNA) is a class of RNA lacking the protein-coding function and playing a critical regulatory role via multiple complex molecular mechanisms. NcRNA is an important regulatory pattern of epigenetic modification, which can exert significant effects on HPV-induced tumorigenesis and progression by deregulating downstream genes. However, the knowledge of ncRNAs is still limited, hence, a better understanding of ncRNAs could provide some insights for exploring the carcinogenesis mechanism and identifying valuable biomarkers in HPV-positive HNSCC. Therefore, in this review, we mainly focused on the expression profile of ncRNAs (including lncRNA, miRNA, and circRNA) and explored their regulatory role in HPV-positive HNSCC, aiming to clarify the regulatory mechanism of ncRNAs and identify valuable biomarkers for HPV-positive HNSCC.
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Sekar AA, Veeraraghavan VP, Raj AT, Patil S. Unravelling the long non-coding RNA, CYTOR can serve as a potential therapeutic target in oral cancer. Oral Oncol 2022; 135:106195. [DOI: 10.1016/j.oraloncology.2022.106195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
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Jafer M, Crutzen R, Halboub E, Moafa I, van den Borne B, Bajonaid A, Jafer A, Hedad I. Dentists Behavioral Factors Influencing Early Detection of Oral Cancer: Direct Clinical Observational Study. JOURNAL OF CANCER EDUCATION : THE OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER EDUCATION 2022; 37:932-941. [PMID: 33094387 PMCID: PMC9399221 DOI: 10.1007/s13187-020-01903-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/16/2020] [Indexed: 05/21/2023]
Abstract
This study aimed to investigate the possible factors affecting dentists' behavior relating to performing oral cancer examinations as part of routine clinical examination. A total of 95 direct clinical observation sessions-utilizing an instrument consisting of 19 evidence-based observational criteria for oral cancer examinations-were observed by four calibrated dentists. Thirty-two final-year students, 32 interns, and 31 faculty members of Jazan Dental School were examined between April 9 and May 4, 2017. A descriptive analysis was conducted to investigate the frequencies/percentages of the performed observing criteria by all examiners. ANOVA and Tukey tests were carried out to investigate the difference between the examiner groups. A total number of 32 patients participated in the study, whereby each patient was examined by three different examiners from each group, as well as by the attending observer/s. Fewer than 50% of the examiners performed the clinical steps necessary for an oral cancer examination-for example, taking into account past medical history, as well as extra and intra-oral examinations. More than 90% of the examiners examined hard tissue, whereas fewer than 30% of them educated their patients about possible risk factors. A significant difference between examiner groups was found in favor of faculty members. A gap between knowledge and actual practice of oral cancer examinations was evident: majority of participants failed to perform the necessary steps for an oral cancer examination. Previous experience and confidence in performing oral cancer examination are possible explanations for the dentist's behavior toward oral cancer examination.
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Affiliation(s)
- Mohammed Jafer
- Department of Preventive Dental Science, College of Dentistry, Jazan University, Jazan, Saudi Arabia.
- Department of Health Promotion, Maastricht University/CAPHRI, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
| | - Rik Crutzen
- Department of Health Promotion, Maastricht University/CAPHRI, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Esam Halboub
- Department of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia
| | - Ibtisam Moafa
- Department of Preventive Dental Science, College of Dentistry, Jazan University, Jazan, Saudi Arabia
- Department of Health Promotion, Maastricht University/CAPHRI, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Bart van den Borne
- Department of Health Promotion, Maastricht University/CAPHRI, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Amal Bajonaid
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Harvard University, Cambridge, USA
| | - Alhassen Jafer
- Dental Division, Ministry of Health, Jazan, Saudi Arabia
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Ousati Ashtiani Z, Abbasi S, Pourmand G, Ghafouri-Fard S. Overexpression of long intergenic noncoding RNAs in bladder cancer: A new insight to cancer diagnosis. Pathol Res Pract 2022; 235:153961. [DOI: 10.1016/j.prp.2022.153961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 12/24/2022]
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8
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Hu XL, Huang XT, Zhang JN, Liu J, Wen LJ, Xu X, Zhou JY. Long noncoding RNA MIR210HG is induced by hypoxia-inducible factor 1α and promotes cervical cancer progression. Am J Cancer Res 2022; 12:2783-2797. [PMID: 35812055 PMCID: PMC9251695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023] Open
Abstract
Increasing evidence has indicated that long noncoding RNAs (lncRNAs) play essential roles in various types of cancer, especially the ability of tumor cells to adapt to hypoxia conditions. However, only a few of them have been experimentally validated in cervical squamous cell carcinoma (CSCC). In the current study, we identified a hypoxia-induced lncRNA MIR210HG was excessively expressed in CSCC tissues and regulated by human papillomavirus (HPV) type 16 E6 and E7 via hypoxia-inducible factor 1α (HIF-1α). Functional assays revealed the role of MIR210HG in promoting proliferation, migration and invasion of CSCC cells in vitro under normoxia as well as hypoxia conditions. Meanwhile, stable MIR210HG silencing dramatically repressed tumor growth and pulmonary metastasis in vivo. Mechanistically, the depletion of MIR210HG or HIF-1α decreased each other's expression level, while silencing MIR210HG or HIF-1α respectively downregulated the expression levels of phosphoglycerate kinase 1 (PGK1), one of key metabolic enzymes in the glycolysis pathway. Furthermore, decreased expression of PGK1 by HIF-1α knockdown was reversed through the overexpression of MIR210HG. Also, we demonstrated HIF-1α can activate the transcription of MIR210HG via binding its promoter. Taken together, these results expand our understanding of the cancer-associated functions of hypoxia-induced lncRNAs, and highlight MIR210HG forms a feedback loop with HIF-1α contributing to cervical carcinogenesis, with potential implications for therapeutic targeting.
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Affiliation(s)
- Xiao-Lin Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
| | - Xia-Tong Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
- The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
| | - Jia-Ni Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
- The First School of Clinical Medicine, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
| | - Jie Liu
- Department of Gynaecology and Obstetrics, Nanfang Hospital, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
| | - Li-Jun Wen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
- School of Basic Medical Sciences, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
| | - Xin Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
| | - Jue-Yu Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical UniversityGuangzhou 510515, Guangdong, P. R. China
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Chen X, Liu Y, Liu H, Wang ZW, Zhu X. Unraveling diverse roles of noncoding RNAs in various human papillomavirus negative cancers. Pharmacol Ther 2022; 238:108188. [PMID: 35421419 DOI: 10.1016/j.pharmthera.2022.108188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 12/17/2022]
Abstract
Human papillomavirus (HPV)-negative tumors distinguish from cancers associated with HPV infection. Due to its high rate of lymph node metastasis and difficulty in inchoate discover and diagnosis, the treatment efficacy of HPV-negative cancers is unsatisfactory. Epidemiological evidence suggests that HPV-negative tumor patients have a poor prognosis, and the mortality is higher than that of cancer patients caused by HPV infection. Evidence has demonstrated that noncoding RNAs (ncRNAs) play a crucial role in regulation of physiological and developmental processes. Therefore, dysregulated ncRNAs are involved in the occurrence of diversified diseases, including cancer. In cumulative studies, ncRNAs are concerned with pathogenetic mechanisms of HPV-negative tumors via regulating gene expression and signal transduction. It is important to decipher the functions of ncRNAs in HPV-negative cancers and identify the potential biomarkers, which will bring new treatment strategies for improving outcome of cancer therapy. In this review, we demonstrated the effects of ncRNAs via regulating the development and progression of HPV- negative tumors by directly or indirectly acting on target molecules, which provide a basis for future tumor targeted therapy by targeting ncRNAs for HPV-negative cancers.
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Affiliation(s)
- Xin Chen
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Hejing Liu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Zhi-Wei Wang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China; Department of Research and Development, Beijing Zhongwei Research Center of Biological and Translational Medicine, Beijing 100161, China.
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China.
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Jiang M, Liu F, Yang AG, Wang W, Zhang R. The role of long non-coding RNAs in the pathogenesis of head and neck squamous cell carcinoma. Mol Ther Oncolytics 2022; 24:127-138. [PMID: 35024439 PMCID: PMC8717422 DOI: 10.1016/j.omto.2021.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Head and neck cancers are a heterogeneous collection of malignancies of the upper aerodigestive tract, salivary glands, and thyroid. However, the molecular mechanisms underlying the carcinogenesis of head and neck squamous cell carcinomas (HNSCCs) remain poorly understood. Over the past decades, overwhelming evidence has demonstrated the regulatory roles of long non-coding RNAs (lncRNAs) in tumorigenesis, including HNSCC. Notably, these lncRNAs have vital roles in gene regulation and affect various aspects of cellular homeostasis, including proliferation, survival, and metastasis. They exert regulating functions by interacting with nucleic acids or proteins and affecting cancer cell signaling. LncRNAs represent a burgeoning field of cancer research, and we are only beginning to understand the importance and complicity of lncRNAs in HNSCC. In this review, we summarize the deregulation and function of lncRNAs in human HNSCC. We also review the working mechanism of lncRNAs in HNSCC pathogenesis and discuss the potential application of lncRNAs as diagnostic/prognostic tools and therapeutic targets in human HNSCC.
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Affiliation(s)
- Man Jiang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710032, China.,State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Fang Liu
- Department of Dermatology, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - An-Gang Yang
- State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wei Wang
- State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Rui Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China.,State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
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Fu Y, Liu Y, Nasiroula A, Wang Q, Cao X. Long non‑coding RNA HCG22 inhibits the proliferation, invasion and migration of oral squamous cell carcinoma cells by downregulating miR‑425‑5p expression. Exp Ther Med 2022; 23:246. [PMID: 35222723 PMCID: PMC8815030 DOI: 10.3892/etm.2022.11171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/28/2021] [Indexed: 11/05/2022] Open
Affiliation(s)
- Yating Fu
- Department of Radiology, Urumqi Stomatological Hospital, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China
| | - Ying Liu
- Department of General Special Requirements, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China
| | - Aheli Nasiroula
- Department of General Special Requirements, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China
| | - Qichao Wang
- Department of Oncology II, Dalian Fifth People's Hospital, Dalian, Liaoning 116021, P.R. China
| | - Xinhua Cao
- Department of Radiology, Urumqi Stomatological Hospital, Urumqi, Xinjiang Uygur Autonomous Region 830011, P.R. China
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Chen Y, Zhao Y, Lu R, Zhao H, Guo Y. Identification and Validation of a Novel Genomic Instability-Associated Long Non-Coding RNA Prognostic Signature in Head and Neck Squamous Cell Carcinoma. Front Cell Dev Biol 2022; 9:787766. [PMID: 35127708 PMCID: PMC8812830 DOI: 10.3389/fcell.2021.787766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most aggressive malignant cancers worldwide, and accurate prognostic models are urgently needed. Emerging evidence revealed that long non-coding RNAs (lncRNAs) are related to genomic instability. We sought to identify and validate a genomic instability-associated lncRNA prognostic signature to assess HNSCC patient survival outcomes. Methods: RNA-sequencing data, somatic mutation files, and patient clinical data were downloaded from The Cancer Genome Atlas database. A total of 491 patients with completely clinical files were randomly divided into training and testing sets. In the training set, genomic instability-associated lncRNAs were screened through univariate Cox regression analyses and least absolute shrinkage and selection operator regression analyses to build a genomic instability-associated lncRNA signature (GILncSig). In addition, time-dependent receiver operating characteristic (ROC) curve, Kaplan-Meier survival curve, and clinical stratification analyses were used to evaluate the signature’s reliability. Finally, in situ hybridization experiments were performed to validate GILncSig expression levels between adjacent non-tumor tissues and tumor tissues from HNSCC patients. Results: Four genomic instability-associated lncRNAs (AC023310.4, AC091729.1, LINC01564, and MIR3142HG) were selected for the prognostic signature. The model was successfully validated using the testing cohort. ROC analysis demonstrated its strong predictive ability for HNSCC prognosis. Univariate and multivariate Cox analyses revealed that the GILncSig was an independent predictor of prognosis. HNSCC patients with a low-risk score showed a substantially better prognosis than the high-risk groups. The in situ hybridization experiments using human HNSCC tissue revealed high GILncSig expression in HNSCC tissues compared with adjacent non-tumor tissues. Conclusion: We developed a novel GILncSig for prognosis prediction in HNSCC patients, and the components of that signature might be therapeutic targets for HNSCC.
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Affiliation(s)
- Yun Chen
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yaqiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ruohuang Lu
- Department of Stomatology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose and Throat Hospital of Fudan University, Shanghai, China
- Laboratory of Myopia, NHC Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai, China
- *Correspondence: Han Zhao, ; Yue Guo,
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Han Zhao, ; Yue Guo,
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Dong A, Xu B, Wang Z, Miao X. Survival‑related DLEU1 is associated with HPV infection status and serves as a biomarker in HPV‑infected cervical cancer. Mol Med Rep 2022; 25:77. [PMID: 35014679 PMCID: PMC8778738 DOI: 10.3892/mmr.2022.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/01/2021] [Indexed: 11/06/2022] Open
Abstract
Human papillomavirus (HPV) is the most common risk factor for the occurrence of cervical cancer (CC). In recent years, the important roles of long non‑coding RNAs (lncRNAs) in CC have emerged, but studies on the relationship between lncRNAs and HPV‑positive (HPV+) CC remain scarce. The present study aimed to investigate whether lncRNA deleted in lymphocytic leukemia 1 (DLEU1) is associated with HPV infection and explore the clinical significance of DLEU1 in HPV+ patients with CC. DLEU1 expression was detected by reverse transcription‑quantitative PCR. The ability of DLEU1 to screen patients with CC from controls and differentiate individuals with different HPV infection status was evaluated by receiver operating characteristic analysis. The association of DLEU1 with the survival prognosis of patients with CC was assessed by Kaplan‑Meier survival analysis and Cox regression analysis. The RNA Interactome Database was used to predict molecules interacting with DLEU1. The results indicated that DLEU1 expression was significantly upregulated in CC tissues and cell lines, particularly in those that were HPV+. In addition, DLEU1 had a high diagnostic value in discriminating patients with CC and differentiating between HPV+ and HPV‑ patients with CC, and had a certain ability to screen HPV+ controls. DLEU1 was correlated with HPV infection in CC patients. Furthermore, DLEU1 was indicated to be associated with survival prognosis in both total patients with CC and HPV+ patients with CC, and independently predict the prognosis of patients with CC. Most of the molecules interacting with DLEU1 were microRNAs. In conclusion, abnormal DLEU1 expression is associated with HPV infection and may serve as a diagnostic and prognostic biomarker for HPV+ patients with CC.
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Affiliation(s)
- Aiping Dong
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
| | - Bin Xu
- Department of Clinical Laboratory, Weifang Center for Disease Control and Prevention, Weifang, Shandong 261061, P.R. China
| | - Zhanzhao Wang
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
| | - Xia Miao
- Department of Clinical Laboratory, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
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14
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Salinas-Montalvo AM, Supramaniam A, McMillan NA, Idris A. RNA-based gene targeting therapies for human papillomavirus driven cancers. Cancer Lett 2021; 523:111-120. [PMID: 34627949 DOI: 10.1016/j.canlet.2021.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 12/22/2022]
Abstract
While platinum-based chemotherapy, radiation therapy and or surgery are effective in reducing human papillomavirus (HPV) driven cancer tumours, they have some significant drawbacks, including low specificity for tumour, toxicity, and severe adverse effects. Though current therapies for HPV-driven cancers are effective, severe late toxicity associated with current treatments contributes to the deterioration of patient quality of life. This warrants the need for novel therapies for HPV derived cancers. In this short review, we examined RNA-based therapies targeting the major HPV oncogenes, including short-interfering RNAs (siRNAs) and clustered regularly interspaced short palindromic repeats (CRISPR) as putative treatment modalities. We also explore other potential RNA-based targeting approaches such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and mRNA vaccines as future treatment modalities for HPV cancers. Some of these technologies have already been approved for clinical use for a range of other human diseases but not for HPV cancers. Here we explore the emerging evidence supporting the effectiveness of some of these gene-based therapies for HPV malignancies. In short, the evidence sheds promising light on the feasibility of translating these technologies into a clinically relevant treatment modality for HPV derived cancers and potentially other virally driven human cancers.
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Affiliation(s)
- Ana María Salinas-Montalvo
- Menzies Health Institute Queensland and School of Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Aroon Supramaniam
- Menzies Health Institute Queensland and School of Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Nigel Aj McMillan
- Menzies Health Institute Queensland and School of Medical Sciences, Griffith University, Gold Coast, QLD, Australia
| | - Adi Idris
- Menzies Health Institute Queensland and School of Medical Sciences, Griffith University, Gold Coast, QLD, Australia.
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15
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Mumtaz PT, Taban Q, Bhat B, Ahmad SM, Dar MA, Kashoo ZA, Ganie NA, Shah RA. Expression of lncRNAs in response to bacterial infections of goat mammary epithelial cells reveals insights into mammary gland diseases. Microb Pathog 2021; 162:105367. [PMID: 34963641 DOI: 10.1016/j.micpath.2021.105367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2022]
Abstract
Mastitis or inflammation of the mammary gland is a highly economic and deadly alarming disease for the dairy sector as well as policymakers caused by microbial infection. Transcriptomic and proteomic approaches have been widely employed to identify the underlying molecular mechanisms of bacterial infections in the mammary gland. Numerous differentially expressed mRNAs, miRNAs, and proteins together with their associated signaling pathways have been identified during bacterial infection, paving the way for analysis of their biological functions. Long noncoding RNAs (lncRNAs) are important regulators of multiple biological processes. However, little is known regarding their role in bacterial infection in mammary epithelial cells. Hence, RNA-sequencing was performed by infecting primary mammary epithelial cells (pMECs) with both gram-negative (E. coli) and gram-positive bacteria (S. aureus). Using stringent pipeline, a set of 1957 known and 1175 novel lncRNAs were identified, among which, 112 lncRNAs were found differentially expressed in bacteria challenged PMECs compared with the control. Additionally, potential targets of the lncRNAs were predicted in cis- and trans-configuration. KEGG analysis revealed that DE lncRNAs were associated with at least 15 immune-related pathways. Therefore, our study revealed that bacterial challenge triggers the expression of lncRNAs associated with immune response and defense mechanisms in goat mammary epithelial cells.
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Affiliation(s)
- Peerzada Tajamul Mumtaz
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India; Department of Biochemistry, School of Life Sciences Jaipur National University, India
| | - Qamar Taban
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India.
| | - Mashooq Ahmad Dar
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Zahid Amin Kashoo
- Division of Veterinary Microbiology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Nazir A Ganie
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Riaz Ahmad Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
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16
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Dong H, Shu X, Xu Q, Zhu C, Kaufmann AM, Zheng ZM, Albers AE, Qian X. Current Status of Human Papillomavirus-Related Head and Neck Cancer: From Viral Genome to Patient Care. Virol Sin 2021. [PMID: 34152564 DOI: 10.1007/s12250-021-00413-8/figures/2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023] Open
Abstract
Human papillomavirus (HPV) infection identified as a definitive human carcinogen is increasingly being recognized for its role in carcinogenesis of human cancers. Up to 38%-80% of head and neck squamous cell carcinoma (HNSCC) in oropharyngeal location (OPSCC) and nearly all cervical cancers contain the HPV genome which is implicated in causing cancer through its oncoproteins E6 and E7. Given by the biologically distinct HPV-related OPSCC and a more favorable prognosis compared to HPV-negative tumors, clinical trials on de-escalation treatment strategies for these patients have been studied. It is therefore raised the questions for the patient stratification if treatment de-escalation is feasible. Moreover, understanding the crosstalk of HPV-mediated malignancy and immunity with clinical insights from the proportional response rate to immune checkpoint blockade treatments in patients with HNSCC is of importance to substantially improve the treatment efficacy. This review discusses the biology of HPV-related HNSCC as well as successful clinically findings with promising candidates in the pipeline for future directions. With the advent of various sequencing technologies, further biomolecules associated with HPV-related HNSCC progression are currently being identified to be used as potential biomarkers or targets for clinical decisions throughout the continuum of cancer care.
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Affiliation(s)
- Haoru Dong
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinhua Shu
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Qiang Xu
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Chen Zhu
- Department of Cancer Prevention, Cancer Hospital University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Andreas M Kaufmann
- Clinic for Gynecology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, 12203, Germany
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Andreas E Albers
- Department of Otolaryngology, Head and Neck Surgery, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, 13353, Germany
| | - Xu Qian
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
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17
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Prevalence of HPV in Mexican Patients with Head and Neck Squamous Carcinoma and Identification of Potential Prognostic Biomarkers. Cancers (Basel) 2021; 13:cancers13225602. [PMID: 34830760 PMCID: PMC8616077 DOI: 10.3390/cancers13225602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Head and neck squamous cell carcinomas (HNSCC) are a heterogeneous group of neoplasms that show diverse clinical and biological characteristics associated with human papillomavirus (HPV). Biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. The biological features of HNSCC may change according to geography and population characteristics. Studies on the molecular biology of HNSCC in Mexico are scarce. In the present study, we analyzed 414 Mexican patients with HNSCC and determined the presence and genotype of HPV, p16 expression, and global gene expression profiles. Twenty-two percent of total cases were HPV+, and 32% were p16+. We identified genes associated with survival, such as SLIRP, KLF10, AREG, ACT1, and LIMA. In addition, CSF1R, MYC, and SRC genes were identified as potential therapeutic targets. This study offers information that may be relevant for our understanding of the biology of HNSCC and the development of therapeutic strategies. Abstract Head and neck squamous cell carcinomas (HNSCC) show a variety of biological and clinical characteristics that could depend on the association with the human papillomavirus (HPV). Biological and clinical characterization is essential to stratify patients based on prognostic and predictive factors. Reports on HNSCC are scarce in Mexico. Herein, we analyzed 414 Mexican patients with HNSCC, including oropharynx (OPSCC), larynx (LASCC), and oral cavity (OCSCC), and identified HPV DNA and p16 expression. Global gene expression profiles were analyzed in 25 HPV+/p16+ vs. HPV−/p16− cases. We found 32.3% p16+ and 22.3% HPV+ samples, HPV 16, 18, 39, 52, and 31 being the most frequent genotypes. For OPSCC, LASCC and OCSCC, 39.2, 14.7, and 9.6% were HPV+/p16+, respectively. High expression of SLIRP, KLF10, AREG, and LIMA was associated with poor survival; in contrast, high expression of MYB and SYCP2 correlated with better survival. In HPV+ cases, high expression of SLC25A39 and GJB2 was associated with poor survival. Likewise, EGFR, IL-1, IL-6, JAK-STAT, WNT, NOTCH, and ESR1 signaling pathways were downregulated in HPV+ cases. CSF1R, MYC, and SRC genes were identified as key hubs and therapeutic targets. Our study offers information regarding the molecular and clinical characteristics of HNSCC in Mexican patients.
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18
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Dong H, Shu X, Xu Q, Zhu C, Kaufmann AM, Zheng ZM, Albers AE, Qian X. Current Status of Human Papillomavirus-Related Head and Neck Cancer: From Viral Genome to Patient Care. Virol Sin 2021; 36:1284-1302. [PMID: 34152564 PMCID: PMC8692589 DOI: 10.1007/s12250-021-00413-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022] Open
Abstract
Human papillomavirus (HPV) infection identified as a definitive human carcinogen is increasingly being recognized for its role in carcinogenesis of human cancers. Up to 38%–80% of head and neck squamous cell carcinoma (HNSCC) in oropharyngeal location (OPSCC) and nearly all cervical cancers contain the HPV genome which is implicated in causing cancer through its oncoproteins E6 and E7. Given by the biologically distinct HPV-related OPSCC and a more favorable prognosis compared to HPV-negative tumors, clinical trials on de-escalation treatment strategies for these patients have been studied. It is therefore raised the questions for the patient stratification if treatment de-escalation is feasible. Moreover, understanding the crosstalk of HPV-mediated malignancy and immunity with clinical insights from the proportional response rate to immune checkpoint blockade treatments in patients with HNSCC is of importance to substantially improve the treatment efficacy. This review discusses the biology of HPV-related HNSCC as well as successful clinically findings with promising candidates in the pipeline for future directions. With the advent of various sequencing technologies, further biomolecules associated with HPV-related HNSCC progression are currently being identified to be used as potential biomarkers or targets for clinical decisions throughout the continuum of cancer care.
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Affiliation(s)
- Haoru Dong
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xinhua Shu
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Qiang Xu
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Chen Zhu
- Department of Cancer Prevention, Cancer Hospital University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Andreas M Kaufmann
- Clinic for Gynecology, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, 12203, Germany
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Andreas E Albers
- Department of Otolaryngology, Head and Neck Surgery, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, 13353, Germany
| | - Xu Qian
- Department of Clinical Laboratory, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
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19
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Alfeghaly C, Sanchez A, Rouget R, Thuillier Q, Igel-Bourguignon V, Marchand V, Branlant C, Motorin Y, Behm-Ansmant I, Maenner S. Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL. Nucleic Acids Res 2021; 49:4954-4970. [PMID: 33872355 PMCID: PMC8136789 DOI: 10.1093/nar/gkab245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 03/20/2021] [Accepted: 03/26/2021] [Indexed: 11/14/2022] Open
Abstract
Long non-coding RNAs have emerged as critical regulators of cell homeostasis by modulating gene expression at chromatin level for instance. Here, we report that the lncRNA ANRIL, associated with several pathologies, binds to thousands of loci dispersed throughout the mammalian genome sharing a 21-bp motif enriched in G/A residues. By combining ANRIL genomic occupancy with transcriptomic analysis, we established a list of 65 and 123 genes potentially directly activated and silenced by ANRIL in trans, respectively. We also found that Exon8 of ANRIL, mainly made of transposable elements, contributes to ANRIL genomic association and consequently to its trans-activity. Furthermore, we showed that Exon8 favors ANRIL's association with the FIRRE, TPD52L1 and IGFBP3 loci to modulate their expression through H3K27me3 deposition. We also investigated the mechanisms engaged by Exon8 to favor ANRIL's association with the genome. Our data refine ANRIL's trans-activity and highlight the functional importance of TEs on ANRIL's activity.
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Affiliation(s)
| | | | - Raphael Rouget
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | | | - Valérie Igel-Bourguignon
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France
| | | | - Yuri Motorin
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
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20
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Long Non-Coding RNAs as Functional Codes for Oral Cancer: Translational Potential, Progress and Promises. Int J Mol Sci 2021; 22:ijms22094903. [PMID: 34063159 PMCID: PMC8124393 DOI: 10.3390/ijms22094903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/24/2022] Open
Abstract
Oral cancer is one of the leading malignant tumors worldwide. Despite the advent of multidisciplinary approaches, the overall prognosis of patients with oral cancer is poor, mainly due to late diagnosis. There is an urgent need to develop valid biomarkers for early detection and effective therapies. Long non-coding RNAs (lncRNAs) are recognized as key elements of gene regulation, with pivotal roles in various physiological and pathological processes, including cancer. Over the past few years, an exponentially growing number of lncRNAs have been identified and linked to tumorigenesis and prognosis outcomes in oral cancer, illustrating their emerging roles in oral cancer progression and the associated signaling pathways. Herein, we aim to summarize the most recent advances made concerning oral cancer-associated lncRNA, and their expression, involvement, and potential clinical impact, reported to date, with a specific focus on the lncRNA-mediated molecular regulation in oncogenic signaling cascades and oral malignant progression, while exploring their potential, and challenges, for clinical applications as biomarkers or therapeutic targets for oral cancer.
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21
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Identification of crucial long non-coding RNAs and mRNAs along with related regulatory networks through microarray analysis in esophageal carcinoma. Funct Integr Genomics 2021; 21:377-391. [PMID: 33864185 DOI: 10.1007/s10142-021-00784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 03/22/2021] [Accepted: 04/06/2021] [Indexed: 02/01/2023]
Abstract
Esophageal carcinoma (EC) is a tremendous threat to human health and life worldwide. Long non-coding RNAs (lncRNAs) have been identified as crucial players in carcinomas including EC. An in-depth understanding on regulatory networks of lncRNAs contributes to the better management of EC. In this text, 2052 lncRNAs and 3240 mRNAs were found to be differentially expressed in 5 EC tumor tissues versus adjacent normal tissues by microarray analysis. Moreover, 297 carcinoma-related genes were screened out according to pathway and disease annotation analyses. In addition, 410 potential lncRNA-mRNA cis-regulation pairs and 395 lncRNA-mRNA trans-regulation pairs were screened out. Among these genes, 14 trans-regulated and 19 cis-regulated genes were found to be related with carcinomas. Additionally, 42 possible lncRNA-mRNA trans-regulation pairs and 26 cis-regulation pairs were found to be related with carcinomas. Also, 4 differentially expressed transcription factors in EC and lncRNAs possibly regulated by these transcription factors were screened out. Moreover, plenty of common upregulated or downregulated lncRNAs and mRNAs in EC were identified by comparative analysis for our microarray outcomes and previous high-throughput data. Furthermore, we demonstrated that ENST00000437781.1 knockdown inhibited cell proliferation and facilitated cell apoptosis by downregulating SIX homeobox 4 (SIX4) and ENST00000524987.1 knockdown had no influence on anoctamin 1 calcium activated chloride channel (ANO1) expression in EC cells. In conclusion, we identified some crucial lncRNAs and genes along with potential regulatory networks of lncRNAs/genes, deepening our understanding on pathogenesis of EC.
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22
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Dias TR, Santos JMO, Gil da Costa RM, Medeiros R. Long non-coding RNAs regulate the hallmarks of cancer in HPV-induced malignancies. Crit Rev Oncol Hematol 2021; 161:103310. [PMID: 33781867 DOI: 10.1016/j.critrevonc.2021.103310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
High-risk human papillomavirus (HPV) is the most frequent sexually transmitted agent worldwide and is responsible for approximately 5% of human cancers. Identifying novel biomarkers and therapeutic targets for these malignancies requires a deeper understanding of the mechanisms involved in the progression of HPV-induced cancers. Long non-coding RNAs (lncRNAs) are crucial in the regulation of biological processes. Importantly, these molecules are key players in the progression of multiple malignancies and are able to regulate the development of the different hallmarks of cancer. This review highlights the action of lncRNAs in the regulation of cellular processes leading to the typical hallmarks of cancer. The regulation of lncRNAs by HPV oncogenes, their targets and also their mechanisms of action are also discussed, in the context of HPV-induced malignancies. Overall, accumulating data indicates that lncRNAs may have a significant potential to become useful tools for clinical practice as disease biomarkers or therapy targets.
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Affiliation(s)
- Tânia R Dias
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; Faculty of Medicine of the University of Porto (FMUP), 4200-319, Porto, Portugal; Research Department of the Portuguese League Against Cancer-Regional Nucleus of the North (Liga Portuguesa Contra o Cancro-Núcleo Regional do Norte), 4200-177, Porto, Portugal.
| | - Joana M O Santos
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; Faculty of Medicine of the University of Porto (FMUP), 4200-319, Porto, Portugal.
| | - Rui M Gil da Costa
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; Center for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), 5001-911 Vila Real, Portugal; LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465, Porto, Portugal; Postgraduate Programme in Adult Health (PPGSAD), Tumour and DNA Biobank, Federal University of Maranhão (UFMA), 65080-805, São Luís, Brazil.
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; Faculty of Medicine of the University of Porto (FMUP), 4200-319, Porto, Portugal; Research Department of the Portuguese League Against Cancer-Regional Nucleus of the North (Liga Portuguesa Contra o Cancro-Núcleo Regional do Norte), 4200-177, Porto, Portugal; Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072, Porto, Portugal; CEBIMED, Faculty of Health Sciences of the Fernando Pessoa University, 4249-004, Porto, Portugal.
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Assessment of multiple pathways involved in the inhibitory effect of HCG22 on oral squamous cell carcinoma progression. Mol Cell Biochem 2021; 476:2561-2571. [PMID: 33649984 DOI: 10.1007/s11010-021-04091-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/29/2021] [Indexed: 12/24/2022]
Abstract
LncRNAs have been proposed to be associated with the tumorigenesis and progression of oral squamous cell carcinoma (OSCC). LncRNA HLA complex group 22 (HCG22) was reported to be lowly expressed and associated with poor prognosis in head and neck squamous cell carcinoma (HNSCC). However, the biological role and related mechanism of HCG22 in OSCC have not been characterized. HCG22 expression in OSCC cells was detected by qRT-PCR. Cell proliferation, invasion, and apoptosis were evaluated by Bromodeoxyuridine (BrdU) proliferation assay, Transwell invasion assay, and flow cytometry analysis, respectively. The protein levels of proliferating cell nuclear antigen (PCNA), E-cadherin, Vimentin, Bcl-2, Bax, protein kinase B (Akt), phosphorylated Akt (p-Akt), mammalian target of rapamycin (mTOR), phosphorylated mTOR (p-mTOR), and β-catenin were detected by western blot. Cell growth evaluation was performed using in vitro colony formation assay and in vivo tumor xenograft assay. We found that HCG22 was weakly expressed in OSCC cells. HCG22 overexpression inhibited cell proliferation and invasion and induced apoptosis in OSCC cells. The levels of PCNA, Vimentin, and Bcl-2 were decreased and E-cadherin and Bax expression was elevated in OSCC cells after HCG22 overexpression. Additionally, HCG22 overexpression inhibited the Akt, mTOR and Wnt/β-catenin pathways. Activation of Akt, mTOR, and Wnt/β-catenin pathways attenuated the anti-tumor property of HCG22 in OSCC cells. Furthermore, HCG22 overexpression inhibited the growth of OSCC cells in vitro and in vivo. In conclusion, HCG22 exerted anti-tumor property in OSCC by inhibiting the Akt, mTOR, and Wnt/β-catenin pathways.
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24
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Cao W, Shen Q, Lim MY. Editorial: "Non-Coding RNAs in Head and Neck Squamous Cell Carcinoma". Front Oncol 2021; 11:785001. [PMID: 35004307 PMCID: PMC8732768 DOI: 10.3389/fonc.2021.785001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/09/2021] [Indexed: 02/05/2023] Open
Affiliation(s)
- Wei Cao
- Department of Oral and Maxillofacial, Head and Neck Oncology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
- *Correspondence: Wei Cao,
| | - Qiang Shen
- Department of Genetics, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Ming Yann Lim
- Department of Otorhinolaryngology, Tan Tock Seng Hospital, Singapore, Singapore
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Jiang H, Ma B, Xu W, Luo Y, Lu Z, Liao T, Wang X, Wen S, Yang S, Wang Y. ASO Author Reflections: A Novel Three-lncRNA Signature Predictive of Prognoses of HNSCC Patients. Ann Surg Oncol 2020; 28:3407. [PMID: 33200328 DOI: 10.1245/s10434-020-09235-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 11/18/2022]
Affiliation(s)
- Hongyi Jiang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China. .,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China.
| | - Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Weibo Xu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yi Luo
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Zhongwu Lu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Xiao Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shishuai Wen
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shuwen Yang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College of Fudan University, Shanghai, China
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Jiang H, Ma B, Xu W, Luo Y, Wang X, Wen S, Liao T, Lu Z, Yang S, Wang Y. A Novel Three-lncRNA Signature Predicts the Overall Survival of HNSCC Patients. Ann Surg Oncol 2020; 28:3396-3406. [PMID: 33095358 DOI: 10.1245/s10434-020-09210-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/18/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND A number of long non-coding RNAs (lncRNAs) have been found to be involved in tumor progression and associated with disease prognoses in various types of cancer. Our study identified a novel three-lncRNA signature to predict survival of head and neck squamous cell caner (HNSCC) patients. METHODS We utilized The Cancer Genome Atlas (TCGA) cohort to screen out overall survival (OS)-associated lncRNAs in HNSCC and further developed a model to identify a lncRNA signature for evaluating disease status and prognosis. The lncRNA signature was then validated in HNSCC patients from our Fudan University Shanghai Cancer Center (FUSCC) cohort. RESULTS LINC02434, AL139327.2, and AC126175.1 were identified by multivariable Cox regression analyses of independent risk factors for deceased status. We built a risk score model based on the three-lncRNA signature using coefficient of multivariable Cox regression and expression value of the three lncRNAs. The high-risk signature score was significantly associated with decreased OS in both the TCGA cohort and the FUSCC cohort. The high-risk group had worse overall survival than the low-risk group in TCGA cohort. To further validate the robustness of three-lncRNA signature risk score model developed in the TCGA dataset, the performance of risk score also evaluated in our institute FUSCC cohort. Additionally, the signature score showed a positive correlation with aggressive outcomes of HNSCC, such as III/IV stage, TP53 mutation, and PI3KCA mutation. The gene set enrichment analysis indicates that the risk score is associated with cancer metastasis-related pathways. Several cancer-related pathways, such as epithelial mesenchymal transition, TNFα signaling via NF-κB, MYC targets, and angiogenesis. CONCLUSIONS The three-lncRNA signature could provide a novel prediction insight into the prognosis of HNSCC patients. The three-lncRNA signature was identified as a predictor of poor prognoses in HNSCC, which may serve as a potential therapeutic target.
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Affiliation(s)
- Hongyi Jiang
- 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
| | - 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
| | - Weibo Xu
- 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
| | - Yi Luo
- 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
| | - Xiao 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
| | - Shishuai 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
| | - 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
| | - Zhongwu Lu
- 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.
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PRINS lncRNA Is a New Biomarker Candidate for HPV Infection and Prognosis of Head and Neck Squamous Cell Carcinomas. Diagnostics (Basel) 2020; 10:diagnostics10100762. [PMID: 32998396 PMCID: PMC7599931 DOI: 10.3390/diagnostics10100762] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/18/2022] Open
Abstract
Numerous studies have shown that human papillomavirus (HPV) infection is one of the important risk factors for head and neck squamous cell carcinoma (HNSCC) progression and affects the expression of multiple genes, which might serve as new biomarkers. This study examines the effects of HPV infection on long non-coding RNA (lncRNA) expression and the immune system, particularly PRINS (Psoriasis susceptibility-related RNA Gene Induced by Stress). The Cancer Genome Atlas (TCGA) expression data for lncRNA genes and clinical data were analyzed by GraphPad Prism 5/7. The expressions of PRINS, CDKN2B-AS1, TTTY14, TTTY15, MEG3, and H19 were significantly different in HPV-positive and HPV-negative patients. HPV-positive patients with high PRINS expression demonstrated significantly better overall survival (OS) and disease-free survival (DFS). HPV-positive patients with high PRINS expression showed changes in gene expression associated with immune and antiviral responses. A majority of HPV-positive patients with high PRINS expression demonstrated a high number of immune cells within tumors. PRINS expression was significantly associated with HPV-infection HNSCC tumors. Validation of these results using data set from Gene Expression Omnibus (GEO) indicated that PRINS is upregulated in HPV active infections and in “atypical 1 (IR)” HNSCC clusters, negatively influencing patients’ overall survival. Patients with high PRINS expression display different immunological profiles than those with low expression levels. For instance, they have active HPV infection status or are clustered in the “atypical 1 (IR)” subtype of HNSCC which influences both viral infection and patients’ survival. It is likely that PRINS could be used as a potential biomarker for HNSCC patients, but its role is dual. On the one hand, it stimulates patients’ immune response, while on the other it can be favorable in virus replication.
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Chen FB, Wu P, Zhou R, Yang QX, Zhang X, Wang RR, Qi SC, Yang X. LINC01315 Impairs microRNA-211-Dependent DLG3 Downregulation to Inhibit the Development of Oral Squamous Cell Carcinoma. Front Oncol 2020; 10:556084. [PMID: 33117688 PMCID: PMC7549330 DOI: 10.3389/fonc.2020.556084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/18/2020] [Indexed: 12/20/2022] Open
Abstract
Recent studies have revealed that long non-coding RNAs (lncRNAs) involve in the progression of oral squamous cell carcinoma (OSCC). These lncRNAs have emerged as biomarkers or therapeutic targets for OSCC. We here aimed to investigate the role of lncRNA LINC01315 in OSCC and the related mechanisms. LINC01315 and DLG3 were determined to be poorly expressed while microRNA-211 (miR-211) was highly expressed in OSCC tissues and cells using RT-qPCR and western blot analysis. Based on the results obtained from dual-luciferase reporter gene, RIP, and FISH assays, LINC01315 was found to upregulate DLG3 expression by competitively binding to miR-211. Upon altering the expression of LINC01315, and/or miR-211 in OSCC cells with shRNA, mimic, or an inhibitor, we assessed their effects on OSCC cell proliferation, migration, invasion, and apoptosis. LINC01315 knockdown enhanced OSCC cell proliferation, migration and invasion, but dampened their apoptosis, all of which could be reversed by miR-211 inhibition. Elevation of DLG3, a target gene of miR-211, activated the Hippo signaling pathway, whereby suppressing OSCC progression in vitro. Finally, their roles in tumor growth were validated in vivo. These findings suggest that LINC01315 elevates DLG3 expression by competitively binding to miR-211, thereby suppressing OSCC progression.
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Affiliation(s)
- Fu-Bo Chen
- Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Peng Wu
- Department of Othorpaedics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rong Zhou
- Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qi-Xiang Yang
- Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xu Zhang
- Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rao-Rao Wang
- Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Sheng-Cai Qi
- Department of Stomatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Yang
- Department of Oral & Maxillofacial - Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Zhao J, Liu D, Yang H, Yu S, He H. Long noncoding RNAs in head and neck squamous cell carcinoma: biological functions and mechanisms. Mol Biol Rep 2020; 47:8075-8090. [PMID: 32914266 DOI: 10.1007/s11033-020-05777-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/28/2020] [Indexed: 12/22/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the primary malignant tumor of the oral cavity, larynx, nasopharynx, esophagus and tongue. Although several novel therapeutic methods for HNSCC have been developed, the final therapeutic effect on the patient is still not satisfactory. Thus, it is imperative that scientists identify novel distinguishable markers with specific molecular characteristics that can be used in therapeutic and prognostic evaluation. Previous reports have shown that long noncoding RNAs (lncRNAs) are important regulators of gene expression in many cancers, including head and neck squamous cell carcinomas. Translational studies of lncRNAs in HNSCC are urgently required before their application as a treatment can be realized. We aimed to address the most relevant findings on lncRNAs as biomarkers or treatment targets in head and neck squamous cell carcinoma and to summarize their discovered pathways and mechanisms of action to reveal the possible future applications of these novel biomarkers in clinical translational research.
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Affiliation(s)
- Jiayu Zhao
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081, Heilongjiang, China
| | - Daming Liu
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081, Heilongjiang, China
| | - Hao Yang
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081, Heilongjiang, China
| | - Shan Yu
- Department of Pathology, Second Affiliated Hospital of Harbin Medical University, No. 246 XueFu Avenue, Harbin, 150086, Heilongjiang, China.
| | - Hongjiang He
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, No. 150 Haping Road, Nangang District, Harbin, 150081, Heilongjiang, China.
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A lncRNA landscape in breast cancer reveals a potential role for AC009283.1 in proliferation and apoptosis in HER2-enriched subtype. Sci Rep 2020; 10:13146. [PMID: 32753692 PMCID: PMC7403317 DOI: 10.1038/s41598-020-69905-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 07/19/2020] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is the most commonly diagnosed neoplasm in women worldwide with a well-recognized heterogeneous pathology, classified into four molecular subtypes: Luminal A, Luminal B, HER2-enriched and Basal-like, each one with different biological and clinical characteristics. Long non-coding RNAs (lncRNAs) represent 33% of the human transcriptome and play critical roles in breast carcinogenesis, but most of their functions are still unknown. Therefore, cancer research could benefit from continued exploration into the biology of lncRNAs in this neoplasm. We characterized lncRNA expression portraits in 74 breast tumors belonging to the four molecular subtypes using transcriptome microarrays. To infer the biological role of the deregulated lncRNAs in the molecular subtypes, we performed co-expression analysis of lncRNA-mRNA and gene ontology analysis. We identified 307 deregulated lncRNAs in tumor compared to normal tissue and 354 deregulated lncRNAs among the different molecular subtypes. Through co-expression analysis between lncRNAs and protein-coding genes, along with gene enrichment analysis, we inferred the potential function of the most deregulated lncRNAs in each molecular subtype, and independently validated our results taking advantage of TCGA data. Overexpression of the AC009283.1 was observed in the HER2-enriched subtype and it is localized in an amplification zone at chromosome 17q12, suggesting it to be a potential tumorigenic lncRNA. The functional role of lncRNA AC009283.1 was examined through loss of function assays in vitro and determining its impact on global gene expression. These studies revealed that AC009283.1 regulates genes involved in proliferation, cell cycle and apoptosis in a HER2 cellular model. We further confirmed these findings through ssGSEA and CEMITool analysis in an independent HER2-amplified breast cancer cohort. Our findings suggest a wide range of biological functions for lncRNAs in each breast cancer molecular subtype and provide a basis for their biological and functional study, as was conducted for AC009283.1, showing it to be a potential regulator of proliferation and apoptosis in the HER2-enriched subtype.
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Yin J, Zeng X, Ai Z, Yu M, Wu Y, Li S. Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer. BMC Med Genomics 2020; 13:84. [PMID: 32571304 PMCID: PMC7310129 DOI: 10.1186/s12920-020-00741-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/15/2020] [Indexed: 12/24/2022] Open
Abstract
Background A growing evidence suggests that long non-coding RNAs (lncRNAs) can function as a microRNA (miRNA) sponge in various diseases including oral cancer. However, the pathophysiological function of lncRNAs remains unclear. Methods Based on the competitive endogenous RNA (ceRNA) theory, we constructed a lncRNA-miRNA-mRNA network in oral cancer with the human expression profiles GSE74530 from the Gene Expression Omnibus (GEO) database. We used topological analysis to determine the hub lncRNAs in the regulatory ceRNA network. Then, function enrichment analysis was performed using the clusterProfiler R package. Clinical information was downloaded from The Cancer Genome Atlas (TCGA) database and survival analysis was performed with Kaplan-Meier analysis. Results A total of 238 potential co-dysregulated competing triples were obtained in the lncRNA-associated ceRNA network in oral cancer, which consisted of 10 lncRNA nodes, 41 miRNA nodes and 122 mRNA nodes. Additionally, we found lncRNA HCG22 exhibiting superior potential as a diagnostic and prognostic marker of oral cancer. Conclusions Our findings provide novel insights to understand the ceRNA regulation in oral cancer and identify a novel lncRNA as a potential molecular biomarker.
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Affiliation(s)
- Junhao Yin
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, 200072, China.,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Xiaoli Zeng
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, 200072, China.,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Zexin Ai
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, 200072, China.,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Miao Yu
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, 200072, China.,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Yang'ou Wu
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, 200072, China.,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China
| | - Shengjiao Li
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, 200072, China. .,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, 200072, China.
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Casarotto M, Fanetti G, Guerrieri R, Palazzari E, Lupato V, Steffan A, Polesel J, Boscolo-Rizzo P, Fratta E. Beyond MicroRNAs: Emerging Role of Other Non-Coding RNAs in HPV-Driven Cancers. Cancers (Basel) 2020; 12:cancers12051246. [PMID: 32429207 PMCID: PMC7281476 DOI: 10.3390/cancers12051246] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
Persistent infection with high-risk Human Papilloma Virus (HPV) leads to the development of several tumors, including cervical, oropharyngeal, and anogenital squamous cell carcinoma. In the last years, the use of high-throughput sequencing technologies has revealed a number of non-coding RNA (ncRNAs), distinct from micro RNAs (miRNAs), that are deregulated in HPV-driven cancers, thus suggesting that HPV infection may affect their expression. However, since the knowledge of ncRNAs is still limited, a better understanding of ncRNAs biology, biogenesis, and function may be challenging for improving the diagnosis of HPV infection or progression, and for monitoring the response to therapy of patients affected by HPV-driven tumors. In addition, to establish a ncRNAs expression profile may be instrumental for developing more effective therapeutic strategies for the treatment of HPV-associated lesions and cancers. Therefore, this review will address novel classes of ncRNAs that have recently started to draw increasing attention in HPV-driven tumors, with a particular focus on ncRNAs that have been identified as a direct target of HPV oncoproteins.
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Affiliation(s)
- Mariateresa Casarotto
- Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (M.C.); (R.G.); (A.S.)
| | - Giuseppe Fanetti
- Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (G.F.); (E.P.)
| | - Roberto Guerrieri
- Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (M.C.); (R.G.); (A.S.)
| | - Elisa Palazzari
- Division of Radiotherapy, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (G.F.); (E.P.)
| | - Valentina Lupato
- Division of Otolaryngology, General Hospital “Santa Maria degli Angeli”, 33170 Pordenone, Italy;
| | - Agostino Steffan
- Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (M.C.); (R.G.); (A.S.)
| | - Jerry Polesel
- Division of Cancer Epidemiology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy;
| | - Paolo Boscolo-Rizzo
- Section of Otolaryngology, Department of Neurosciences, University of Padova, 31100 Treviso, Italy;
| | - Elisabetta Fratta
- Division of Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, National Cancer Institute, 33081 Aviano (PN), Italy; (M.C.); (R.G.); (A.S.)
- Correspondence: ; Tel.: +390434659569
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Ata-abadi NS, Mowla SJ, Aboutalebi F, Dormiani K, Kiani-Esfahani A, Tavalaee M, Nasr-Esfahani MH. Hypoxia-related long noncoding RNAs are associated with varicocele-related male infertility. PLoS One 2020; 15:e0232357. [PMID: 32353040 PMCID: PMC7192471 DOI: 10.1371/journal.pone.0232357] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/13/2020] [Indexed: 12/19/2022] Open
Abstract
One of the main molecular causes that contributes to varicocele-related male infertility is excess production of reactive oxygen species (ROS). It is believed that hypoxia is an important stimulator of ROS in this condition. Recently, the significant roles of long non-coding RNAs (lncRNAs) in hypoxia response have emerged. Despite the investigation of hypoxia, there is scant information about the role of hypoxia-responding lncRNAs in varicocele-related male infertility. In the present study, we deduced eight hypoxia-responding lncRNAs based on high-throughput RNA sequencing data from two Gene Expression Omnibus (GEO) datasets. We used qRT-PCR to assess the expression levels of some of these lncRNAs in 42 ejaculated spermatozoa samples from 25 infertile men with varicocele and 17 fertile men as controls. We identified significant increases in expression levels of hypoxia-related lncRNAs, MIR210HG and MLLT4-AS1 in ejaculated spermatozoa of infertile men with varicocele. These lncRNAs also showed significant positive correlations with ROS levels and meaningful negative correlations with sperm parameters (count and motility). Besides, in silico studies identified several hypoxia response elements (HREs) within selected lncRNAs promoters. Delineation of hypoxia-related lncRNAs in varicocele-related infertility provides a valuable insight into male infertility.
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Affiliation(s)
- Nafiseh Sanei Ata-abadi
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail: (SJM); (MHN-E)
| | - Fatemeh Aboutalebi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Kianoush Dormiani
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Abbas Kiani-Esfahani
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Marziyeh Tavalaee
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
- Isfahan Fertility and Infertility Center, Isfahan, Iran
- * E-mail: (SJM); (MHN-E)
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Chaudhary R, Wang X, Cao B, De La Iglesia J, Masannat J, Song F, Hernandez-Prera JC, Gimbrone NT, Slebos RJC, Chung CH. Long noncoding RNA, LINC00460, as a prognostic biomarker in head and neck squamous cell carcinoma (HNSCC). Am J Transl Res 2020; 12:684-696. [PMID: 32194915 PMCID: PMC7061833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is an aggressive epithelial malignancy characterized by frequent mutations and metastasis. Long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis and serve as novel prognostic biomarkers in different cancers. To enhance our understanding of lncRNAs that may have biological significance in HNSCC and may serve as prognostic biomarkers, we globally profiled lncRNAs in HNSCC by analyzing the RNA-seq data from The Atlas of Noncoding RNAs in Cancer (TANRIC) database. Of 3576 lncRNAs, we identified 926 (higher-688, lower-238) lncRNAs with a 2-fold abundance difference among the forty HNSCC and paired adjacent normal tissue. We investigated differential abundance of lncRNAs based on TP53 mutation and p16 status. We found 133 lncRNAs to have differential abundance by 2-fold among the mutant vs wild-type TP53 samples, whereas among p16-negative vs positive samples, we identified 710 lncRNAs with the same criteria. Meanwhile, analysis of the 15 most abundant lncRNAs in the tumor samples identified five lncRNAs whose higher abundance was associated with poor overall patient survival. Among these five, higher abundance of LINC00460 associated with poor patient survival in an independent cohort of 82 HNSCC patients. To further evaluate the potential function of LINC00460, we performed lncRNA-mRNAs co-expression analysis and found that higher abundance of LINC00460 associated with cancer-related biological pathways including EMT and other inflammatory response pathways. In summary, we report LINC00460 is more abundant in tumors compared to adjacent normal tissue and that it may serve as a potential prognostic biomarker in HNSCC.
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Affiliation(s)
- Ritu Chaudhary
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, Moffitt Cancer CenterTampa, FL, USA
| | - Biwei Cao
- Department of Biostatistics and Bioinformatics, Moffitt Cancer CenterTampa, FL, USA
| | - Janis De La Iglesia
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Jude Masannat
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Feifei Song
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | | | - Nicholas T Gimbrone
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Robbert JC Slebos
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer CenterTampa, FL, USA
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Ghafouri-Fard S, Mohammad-Rahimi H, Jazaeri M, Taheri M. Expression and function of long non-coding RNAs in head and neck squamous cell carcinoma. Exp Mol Pathol 2020; 112:104353. [DOI: 10.1016/j.yexmp.2019.104353] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022]
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Serafini MS, Lopez-Perez L, Fico G, Licitra L, De Cecco L, Resteghini C. Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures. CANCERS OF THE HEAD & NECK 2020; 5:2. [PMID: 31988797 PMCID: PMC6971871 DOI: 10.1186/s41199-020-0047-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Indexed: 02/06/2023]
Abstract
For many years, head and neck squamous cell carcinoma (HNSCC) has been considered as a single entity. However, in the last decades HNSCC complexity and heterogeneity have been recognized. In parallel, high-throughput omics techniques had allowed picturing a larger spectrum of the behavior and characteristics of molecules in cancer and a large set of omics web-based tools and informative repository databases have been developed. The objective of the present review is to provide an overview on biological, prognostic and predictive molecular signatures in HNSCC. To contextualize the selected data, our literature survey includes a short summary of the main characteristics of omics data repositories and web-tools for data analyses. The timeframe of our analysis was fixed, encompassing papers published between January 2015 and January 2019. From more than 1000 papers evaluated, 61 omics studies were selected: 33 investigating mRNA signatures, 11 and 13 related to miRNA and other non-coding-RNA signatures and 4 analyzing DNA methylation signatures. More than half of identified signatures (36) had a prognostic value but only in 10 studies selection of a specific anatomical sub-site (8 oral cavity, 1 oropharynx and 1 both oral cavity and oropharynx) was performed. Noteworthy, although the sample size included in many studies was limited, about one-half of the retrieved studies reported an external validation on independent dataset(s), strengthening the relevance of the obtained data. Finally, we highlighted the development and exploitation of three gene-expression signatures, whose clinical impact on prognosis/prediction of treatment response could be high. Based on this overview on omics-related literature in HNSCC, we identified some limits and strengths. The major limits are represented by the low number of signatures associated to DNA methylation and to non-coding RNA (miRNA, lncRNA and piRNAs) and the availability of a single dataset with multiple omics on more than 500 HNSCC (i.e. TCGA). The major strengths rely on the integration of multiple datasets through meta-analysis approaches and on the growing integration among omics data obtained on the same cohort of patients. Moreover, new approaches based on artificial intelligence and informatic analyses are expected to be available in the next future.
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Affiliation(s)
- Mara S Serafini
- 1Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Laura Lopez-Perez
- 2Life Supporting Technologies, Universidad Politécnica de Madrid, Madrid, Spain
| | - Giuseppe Fico
- 2Life Supporting Technologies, Universidad Politécnica de Madrid, Madrid, Spain
| | - Lisa Licitra
- 3Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy.,4University of Milan, Milan, Italy
| | - Loris De Cecco
- 1Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Carlo Resteghini
- 3Head and Neck Medical Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
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Wang J, Zhang C, Wu Y, He W, Gou X. Identification and analysis of long non-coding RNA related miRNA sponge regulatory network in bladder urothelial carcinoma. Cancer Cell Int 2019; 19:327. [PMID: 31827401 PMCID: PMC6892182 DOI: 10.1186/s12935-019-1052-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022] Open
Abstract
Background The aim of this study was to investigate the regulatory network of lncRNAs as competing endogenous RNAs (ceRNA) in bladder urothelial carcinoma (BUC) based on gene expression data derived from The Cancer Genome Atlas (TCGA). Materials and methods RNA sequence profiles and clinical information from 414 BUC tissues and 19 non-tumor adjacent tissues were downloaded from TCGA. Differentially expressed RNAs derived from BUC and non-tumor adjacent samples were identified using the R package “edgeR”. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed using the “clusterProfiler” package. Gene ontology and protein–protein interaction (PPI) networks were analyzed for the differentially expressed mRNAs using the “STRING” database. The network for the dysregulated lncRNA associated ceRNAs was then constructed for BUC using miRcode, miRTarBase, miRDB, and TargetScan. Cox regression analysis was performed to identify independent prognostic RNAs associated with BUC overall survival (OS). Survival analysis for the independent prognostic RNAs within the ceRNA network was calculated using Kaplan–Meier curves. Results Based on our analysis, a total of 666, 1819 and 157 differentially expressed lncRNAs, mRNAs and miRNAs were identified respectively. The ceRNA network was then constructed and contained 59 lncRNAs, 23 DEmiRNAs, and 52 DEmRNAs. In total, 5 lncRNAs (HCG22, ADAMTS9-AS1, ADAMTS9-AS2, AC078778.1, and AC112721.1), 2 miRNAs (hsa-mir-145 and hsa-mir-141) and 6 mRNAs (ZEB1, TMEM100, MAP1B, DUSP2, JUN, and AIFM3) were found to be related to OS. Two lncRNAs (ADAMTS9-AS1 and ADAMTS9-AS2) and 4 mRNA (DUSP2, JUN, MAP1B, and TMEM100) were validated using GEPIA. Thirty key hub genes were identified using the ranking method of degree. KEGG analysis demonstrated that the majority of the DEmRNAs were involved in pathways associated with cancer. Conclusion Our findings provide an understanding of the important role of lncRNA–related ceRNAs in BUC. Additional experimental and clinical validations are required to support our findings.
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Affiliation(s)
- Jiawu Wang
- 1Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Chengyao Zhang
- 2Department of Head and Neck Cancer Center, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Shapingba District, Chongqing, China
| | - Yan Wu
- 3Department of General Surgery, University-Town Hospital of Chongqing Medical University, Shapingba District, Chongqing, China
| | - Weiyang He
- 1Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Xin Gou
- 1Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Yuzhong District, Chongqing, China
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Li H, Wang FL, Li W, Fei YH, Wang YT, Zhang JE, Bi HY, Zhang M. Aberrant expressed long non-coding RNAs in laryngeal squamous-cell carcinoma. Am J Otolaryngol 2019; 40:615-625. [PMID: 31128861 DOI: 10.1016/j.amjoto.2019.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/08/2019] [Indexed: 11/17/2022]
Abstract
PURPOSE Laryngeal squamous-cell carcinoma (LSCC) is the second most common malignant tumor of head and neck squamous cell carcinoma. The study was aimed to identify key long non-coding RNAs (lncRNAs) biomarkers for LSCC. METHODS Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) between LSCC and adjacent tissues were obtained based on The Cancer Genome Atlas. DElncRNA-DEmRNAs co-expression and DElncRNA-nearby-target DEmRNA interaction networks were constructed. Receiver operating characteristic and survival analysis were performed. A published dataset were as used to validate the result of bioinformatics analysis. RESULTS We obtained 1103 DEmRNAs and 306 DElncRNAs between LSCC and adjacent tissues. A total of 338 DElncRNA-DEmRNA co-expression pairs and 229 DElncRNA-nearby-target DEmRNA pairs were obtained. Ten DElncRNAs and six DEmRNAs has great diagnostic value for LSCC. HOXB9 has potential prognostic value for LSCC. The results of GSE84957 validation were generally consistent with our results. CONCLUSION Our study provided clues for understanding the mechanism and developing potential biomarkers for LSCC.
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Affiliation(s)
- Hu Li
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong, China
| | - Fu-Ling Wang
- Department of Obstetrics, Maternal and Child Health Hospital of RenCheng District, Jining, Jining, Shandong, China
| | - Wei Li
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong, China
| | - Yong-Hua Fei
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong, China
| | - Ya-Ting Wang
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong, China
| | - Jing-E Zhang
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong, China
| | - Hui-Yun Bi
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong, China
| | - Mei Zhang
- Department of Otolaryngology, Head and Neck Surgery, The First People's Hospital of Jining, Jining, Shandong, China.
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Long Non-Coding RNA Expression Profile Associated with Malignant Progression of Oral Submucous Fibrosis. JOURNAL OF ONCOLOGY 2019; 2019:6835176. [PMID: 31467541 PMCID: PMC6699286 DOI: 10.1155/2019/6835176] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/27/2019] [Indexed: 02/03/2023]
Abstract
Oral submucous fibrosis (OSF) as one of the premalignant disorders endures a series of histopathological stages to invasive oral squamous cell carcinoma (OSCC) eventually. However, the role of long non-coding RNA (lncRNA) expression in OSF malignant progression still remains poorly understood. Through RNA-sequencing normal mucous, OSF and OSCC tissues, we found 687 lncRNA transcripts significantly and differentially expressed during OSF progression, including 231 upregulated lncRNAs and 456 downregulated lncRNAs, indicating that lncRNAs are involved in the regulation of different stages of OSF development. Further functional enrichment analysis showed these differentially expressed lncRNAs participated in inflammation signaling, Wnt signaling, angiogenesis, CCKR signaling, integrin signaling, PDGF signaling, p53 signaling, and EGF receptor (EGFR) signaling pathways, which contribute to inflammatory and fibroelastic pathogenetic changes of OSF and further malignant progression. Five novel lncRNAs were differentially expressed during OSF progression with varied expression levels, indicating the importance of these lncRNAs in OSF malignant development. Moreover, some lncRNAs have been previously identified to be associated with OSCC pathogenesis, including HCG22, RP11-397A16.1, LINC00271, CTD-3179P9.1, and ZNF667-AS1. Thus, our study firstly comprehensively elucidated lncRNAs expression profile of malignant procession from OSF premalignant lesion to OSCC, which will enlighten our understanding of the importance of lncRNA involved in OSF malignant development.
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Xing L, Zhang X, Chen A. Prognostic 4-lncRNA-based risk model predicts survival time of patients with head and neck squamous cell carcinoma. Oncol Lett 2019; 18:3304-3316. [PMID: 31452809 PMCID: PMC6704293 DOI: 10.3892/ol.2019.10670] [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: 12/06/2018] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common malignant disease with high mortality rates. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to participate in a number of important biological functions and could serve as prognostic biomarkers in the field of oncology. Therefore, the present study aimed to identify an lncRNA-based model that was associated with prognosis. RNA-sequencing data was downloaded from The Cancer Genome Atlas and R software was used to analyze the data. Univariate analyses, robust likelihood analyses and multivariate analyses were performed to screen out key lncRNA candidates associated with prognosis and construct a risk model. A Kaplan-Meier plot was constructed for survival analysis. LncBase and Starbase were used to identify the miRNA and protein targets. Gene set enrichment analysis was used for functional analysis. As a result, a 4-lncRNA (ALMS1-IT1, RP11-359J14.2, CTB-178M22.2 and RP11-347C18.5) based risk model was identified and patients in the high-risk group were revealed to have a lower survival rate than patients in the low-risk group. A nomogram that could predict the survival of patients was plotted. A total of 79 target miRNAs and 61 target proteins were identified. The gene set enrichment analysis results revealed that nutrient metabolism pathways were enriched in the high-risk group and immune regulation pathways were enriched in the low-risk group. In summary, a 4-lncRNA based risk model was identified that was associated with prognosis, which may serve as a prognosis prediction biomarker for HNSCC.
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Affiliation(s)
- Lu Xing
- School of Stomatology, Shandong University, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Jinan, Shandong 250012, P.R. China
| | - Xiaoqian Zhang
- Department of Stomatology, Haiyuan College of Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Anwei Chen
- Department of Oral and Maxillofacial Surgery, Qilu Hospital, Institute of Stomatology, Shandong University, Jinan, Shandong 250000, P.R. China
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Long Non-coding RNAs as Important Biomarkers in Laryngeal Cancer and Other Head and Neck Tumours. Int J Mol Sci 2019; 20:ijms20143444. [PMID: 31336999 PMCID: PMC6678449 DOI: 10.3390/ijms20143444] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/28/2022] Open
Abstract
Head and neck carcinoma (HNC) is a heterogeneous disease encompassing a variety of tumors according to the origin. Laryngeal cancer (LC) represents one of the most frequent tumors in the head and neck region. Despite clinical studies and advance in treatment, satisfactory curative strategy has not yet been reached. Therefore, there is an urgent need for the identification of specific molecular signatures that better predict the clinical outcomes and markers that serve as suitable therapeutic targets. Long non-coding RNAs (lncRNA) are reported as important regulators of gene expression and represent an innovative pharmacological application as molecular biomarkers in cancer. The purpose of this review is to discuss the most relevant epigenetic and histological prognostic biomarkers in HNC, with particular focus on LC. We summarize the emerging roles of long non-coding RNAs in HNC and LC development and their possible use in early diagnosis.
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Weng SL, Huang KY, Weng JTY, Hung FY, Chang TH, Lee TY. Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes. Brief Bioinform 2019; 19:1102-1114. [PMID: 28531277 DOI: 10.1093/bib/bbx046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Indexed: 12/18/2022] Open
Abstract
In mammals, microRNAs (miRNAs) play key roles in controlling posttranscriptional regulation through binding to the mRNAs of target genes. Recently, it was discovered that viral miRNAs may be involved in human cancers and diseases. It is likely that viral miRNAs help viruses enter the latent phase of their life cycle and become undetected by the host's immune system, while increasing the host's risk for cancer development. Cervical cancer is typically related to the infection of human papillomavirus (HPV) through sexual transmission. To further understand the molecular mechanisms underlying the associations of HPV infection with genital diseases, we developed a systematic method for viral miRNA identification and viral miRNA-mediated regulatory network construction based on genome-wide sequence analysis. The complete genomes of certain high-risk HPV subtypes were used to predict putative viral pre-miRNAs by bioinformatics approaches. In addition, small RNA libraries in human cervical lesions from existing publications were collected to validate the predicted HPV pre-miRNAs. For the construction of virally encoded miRNA-mediated regulatory network of HPV infection, cervical squamous epithelial carcinoma gene expression data were extracted from the RNA sequencing platform in The Cancer Genome Atlas; the differentially expressed genes were used to identify the putative targets of viral miRNAs. Predicted cellular target genes of HPV-encoded miRNAs provide an overview of these viral miRNA's putative functions. Finally, a large-scale genome analysis was carried out to examine the phylogenetic relationship and structural evolution among genital HPV types that have the potential to cause genital cancer. In this study, we discovered putative HPV-encoded miRNAs, which were validated against the small RNA libraries in human cervical lesions. Furthermore, as indicated by their biological functions, host genes targeted by HPV-encoded miRNAs may play significant roles in virus infection and carcinogenesis. These viral miRNAs pose as promising candidates for the development of antiviral drugs. More importantly, the identified subtype-specific miRNAs have the potential to be used as biomarkers for HPV subtype determination.
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Affiliation(s)
| | - Kai-Yao Huang
- Department of Computer Science and Engineering, Graduate Program in Biomedical Informatics, Yuan Ze University
| | - Julia Tzu-Ya Weng
- Graduate Program of Biomedical Informatics at Yuan Ze University in Taiwan
| | | | - Tzu-Hao Chang
- Institute of Biomedical Informatics, Taipei Medical University
| | - Tzong-Yi Lee
- Department of Computer Science and Engineering, Graduate Program in Biomedical Informatics, Yuan Ze University
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Qiu X, Lei Z, Wang Z, Xu Y, Liu C, Li P, Wu H, Gong Z. Knockdown of LncRNA RHPN1-AS1 Inhibits Cell Migration, Invasion and Proliferation in Head and Neck Squamous Cell Carcinoma. J Cancer 2019; 10:4000-4008. [PMID: 31417644 PMCID: PMC6692605 DOI: 10.7150/jca.29029] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/26/2019] [Indexed: 12/27/2022] Open
Abstract
Previous studies have revealed that long non-coding RNAs (lncRNAs) are involved in head and neck squamous cell carcinoma (HNSCC) progression. However, the detailed roles of lncRNA RHPN1-AS1 remain to be elucidated. In this study, by analyzing online RNA-Seq data, we found that RHPN1-AS1 was upregulated in HNSCC tissues and that its expression level was associated with neoplasm histologic grade. High expression of RHPN1-AS1 was also confirmed in HNSCC tissues. Knockdown of RHPN1-AS1 inhibited tumor cell migration, invasion and proliferation in HNSCC. Furthermore, inhibition of RHPN1-AS1 suppressed the expression of epithelial-mesenchymal transition (EMT)-related genes (β-Catenin, Claudin-1 and Vimentin) in HNSCC cells. Collectively, our results suggest that RHPN1-AS1, acting as an oncogene, may be a potential diagnostic and therapeutic target in HNSCC.
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Affiliation(s)
- Xiaowen Qiu
- Department of Stomatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China.,Department of Stomatology, Haikou people's Hospital, Haikou 570208, Hainan, China
| | - Zhuo Lei
- Xiangya Stomatological Hospital & School of Stomatology, Central South University, Changsha 410008, Hunan, China
| | - Zeyou Wang
- Department of Laboratory Medicine, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Yuming Xu
- Department of Stomatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Chang Liu
- Department of Stomatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Panchun Li
- Department of Stomatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Hanjiang Wu
- Department of Stomatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Zhaojian Gong
- Department of Stomatology, Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
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Chen L, Wang X, Song L, Yao D, Tang Q, Zhou J. Upregulation of lncRNA GATA6-AS suppresses the migration and invasion of cervical squamous cell carcinoma by downregulating MTK-1. Oncol Lett 2019; 18:2605-2611. [PMID: 31404324 DOI: 10.3892/ol.2019.10554] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 04/29/2019] [Indexed: 01/11/2023] Open
Abstract
The diagnosis and treatment of cervical squamous cell carcinoma is challenged by difficulties in the determination of tumor invasion. GATA binding protein 6 antisense (GATA6-AS) is a recently identified long non-coding RNA that exhibits critical functions in the growth of endothelial cells; however, to the best of our knowledge, its involvement in other physiological and pathological processes is unknown. By reverse transcription-quantitative polymerase chain reaction, the present study examined the expression of GATA6-AS in tumor tissues and adjacent healthy tissues, and the serum from patients with cervical squamous cell carcinoma and healthy controls. The diagnostic and prognostic potentials of GATA6-AS for cervical squamous cell carcinoma were analyzed by receiver operating characteristic curve analysis and survival curve analysis, respectively. Associations between the serum levels of GATA6-AS and clinical characteristics of patients with cervical squamous cell carcinoma were analyzed by a χ2 test. A GATA6-AS overexpression vector was transfected into cervical squamous cell carcinoma cells, and the effects on cell migration and invasion were investigated by Transwell migration and invasion assays, respectively. The expression of mitogen-activated protein kinase kinase 4 (MTK-1) following transfection with the GATA6-AS overexpression vector was detected by western blot analysis. It was identified that the expression levels of GATA6-AS were lower in tumor tissues compared with healthy tissues. In addition, serum levels of GATA6-AS were higher in patients compared with healthy controls. The serum levels of GATA6-AS were associated with tumor metastasis, and may serve as a potential diagnostic and prognostic marker for cervical squamous cell carcinoma. Furthermore, GATA6-AS overexpression inhibited cancer cell migration and invasion. The expression levels of MTK-1 were also reduced following GATA6-AS overexpression. Therefore, the present study proposed that downregulated GATA6-AS expression was associated with tumor metastasis in cervical squamous cell carcinoma, and that GATA6-AS expression may inhibit cancer cell migration and invasion by downregulating MTK-1.
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Affiliation(s)
- Lan Chen
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xuming Wang
- Department of Pathology and Pathophysiology, School of Medicine, Jianghan University, Wuhan, Hubei 430056, P.R. China
| | - Limian Song
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Dujuan Yao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Qianqian Tang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jun Zhou
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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Li X, Xiao X, Chang R, Zhang C. Comprehensive bioinformatics analysis identifies lncRNA HCG22 as a migration inhibitor in esophageal squamous cell carcinoma. J Cell Biochem 2019; 121:468-481. [PMID: 31236983 DOI: 10.1002/jcb.29218] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022]
Abstract
Esophageal cancer is one of the most lethal malignancies worldwide, and esophageal squamous cell carcinoma (ESCC) is the dominant histological type. However, the long noncoding RNA (lncRNA) alterations in ESCC have not been elucidated to date. In this study, reliable databases from Gene Expression Omnibus (GEO), which analyzed lncRNA expression in ESCC tumor tissues and adjacent normal tissues were searched, and common differentially expressed lncRNAs and genes were analyzed. Next, cis- trans analysis was performed to predict the underlying relationships between altered lncRNAs and mRNAs, and the lncRNA-mRNA regulatory network was established. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of altered lncRNA-related genes were performed. The promising lncRNA HCG22 was validated by quantitative polymerase chain reaction (qPCR), and clinicopathological data were collected to identify the relationship between lncRNA HCG22 expression level and clinical features. Finally, Transwell assays were performed to explore the biological functions of lncRNA HCG22 in ESCC cells. Two hundred forty-one lncRNAs and 835 mRNAs were observed to be remarkably altered between ESCC tumor tissues and adjacent normal tissues. The lncRNA-mRNA regulatory network showed the coexpression association between lncRNA HCG22 and SPINK7 and ADAMTS12. GO and KEGG analyses showed that HCG22 and ADAMTS12 had potential biological functions in the cell migration of ESCC. The downregulation of lncRNA HCG22 in ESCC tumor tissues was validated by qPCR, and the clinicopathological data showed a noticeable correlation between lncRNA HCG22 expression level and the ESCC differentiational degree and clinical TNM stage. Kaplan-Meier analysis showed that patients with ESCC having low lncRNA HCG22 expression in ESCC tissues had considerably shorter overall survival compared with patients with ESCC having high lncRNA HCG22 expression. Following Transwell assays confirmed the migratory role of lncRNA HCG22 in ESCC cells. In conclusion, lncRNA HCG22 was downregulated in ESCC tissues and can be a migration inhibitor of ESCC cells, and SPINK7 and ADAMTS12 are promising to be the regulatory targets of lncRNA HCG22.
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Affiliation(s)
- Xizhe Li
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoxiong Xiao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruimin Chang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Li Z, Jiang C, Yuan Y. TCGA based integrated genomic analyses of ceRNA network and novel subtypes revealing potential biomarkers for the prognosis and target therapy of tongue squamous cell carcinoma. PLoS One 2019; 14:e0216834. [PMID: 31141819 PMCID: PMC6541473 DOI: 10.1371/journal.pone.0216834] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES The study aimed to investigate the ceRNA network in biological development of Tongue Squamous Cell Carcinoma (TSCC) and to identify novel molecular subtypes of TSCC to screen potential biomarkers for target therapy and prognosis by using integrated genomic analysis based on The Cancer Genome Atlas (TCGA) database. MATERIAL AND METHODS Data on gene expressions were downloaded from TCGA and GEO database. Differentially expressed RNAs(DERNAs) were shown by DESeq2 package in R. Functional enrichment analysis of DEmRNAs was performed using clusterprofilers in R. PPI network was established by referring to String website. Survival analysis of DERNAs was carried out by survival package in R. Interactions among mRNAs, miRNAs and lncRNAs were obtained from Starbase v3.0 and used to construct ceRNA network. Consensus Cluster Plus package was applied to identify molecular subtypes. All key genes were validated by comparing them with GEO microarray data. Statistical analyses of clinical features among different subtypes were performed using SPSS 22.0. RESULTS A total of 2907 mRNAs (1366 up-regulated and 1541 down-regulated), 191miRNAs (98 up-regulated and 93 down-regulated) and 1831 lncRNAs (1151 up-regulated and 680 down-regulated) were identified from tumor and normal tissues. A ceRNA network was successfully constructed and 15 DEmRNAs, 1 DEmiRNA, 2 DElncRNAs associated with prognosis were employed. Furthermore, we firstly identified 2 molecular subtypes, basal and differentiated, and found that differentiated subtype consumed less alcohol and was related to a better overall survival. CONCLUSION The study constructed a ceRNA network and identified molecular subtypes of TSCC, and our findings provided a novel insight into this intractable cancer and potential therapeutic targets and prognostic indicators.
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Affiliation(s)
- Zaiye Li
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Canhua Jiang
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yongxiang Yuan
- Department of Oral and Maxillofacial Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Song L, Xie H, Tong F, Yan B, Zhang S, Fu E, Jing Q, Wei L. Association of lnc-IL17RA-11 with increased radiation sensitivity and improved prognosis of HPV-positive HNSCC. J Cell Biochem 2019; 120:17438-17448. [PMID: 31119798 DOI: 10.1002/jcb.29008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
Abstract
Human papillomavirus (HPV) associated head and neck squamous cell carcinoma (HNSCC) has a far better prognosis than HPV negative HNSCC. Recent studies suggest that long noncoding RNA (lncRNA) moieties may play a role in HPV associated differential HNSCC prognoses. In this study, we examined differential expression of lncRNAs in HPV+ vs HPV- HNSCC using The Cancer Genome Atlas database. LncRNAs were categorized based on expression level and survival analysis. A group of eight lncRNAs was identified in which altered expression was associated with both HPV infection and better prognosis. Subsequently, genes coexpressed with these lncRNAs in HNSCC cells were sorted into corresponding co-expression modules. The lnc-IL17RA-11 coexpression module exhibited the greatest correlation with HPV infection and radiotherapy efficacy. We identified the lnc-IL17RA-11 transcription factor ER-alpha as the most likely HPV infection associated factor promoting increased lnc-IL17RA-11 levels. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis revealed enrichment among lnc-IL17RA-11 co-expressed genes for functions related to DNA replication and cell proliferation. These observations are consistent with a model in which HPV infection upregulates transcription factor ER-alpha, which increases levels of lnc-IL17RA-11 and coexpressed genes that promote HNSCC cell sensitivity to radiotherapy, thereby improving disease prognosis.
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Affiliation(s)
- Lianhao Song
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Huanhuan Xie
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Fangjia Tong
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Bingqing Yan
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Siwei Zhang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Enhui Fu
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Qingxu Jing
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Lanlan Wei
- Department of Microbiology, Harbin Medical University, Harbin, China
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Kulski JK. Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. Cells 2019; 8:cells8050480. [PMID: 31137555 PMCID: PMC6562477 DOI: 10.3390/cells8050480] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
The HCP5 RNA gene (NCBI ID: 10866) is located centromeric of the HLA-B gene and between the MICA and MICB genes within the major histocompatibility complex (MHC) class I region. It is a human species-specific gene that codes for a long noncoding RNA (lncRNA), composed mostly of an ancient ancestral endogenous antisense 3′ long terminal repeat (LTR, and part of the internal pol antisense sequence of endogenous retrovirus (ERV) type 16 linked to a human leukocyte antigen (HLA) class I promoter and leader sequence at the 5′-end. Since its discovery in 1993, many disease association and gene expression studies have shown that HCP5 is a regulatory lncRNA involved in adaptive and innate immune responses and associated with the promotion of some autoimmune diseases and cancers. The gene sequence acts as a genomic anchor point for binding transcription factors, enhancers, and chromatin remodeling enzymes in the regulation of transcription and chromatin folding. The HCP5 antisense retroviral transcript also interacts with regulatory microRNA and immune and cellular checkpoints in cancers suggesting its potential as a drug target for novel antitumor therapeutics.
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Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA 6009, Australia.
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan.
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Zhang ZL, Zhao LJ, Xu L, Chai L, Wang F, Xu YP, Zhou SH, Fu Y. Transcriptomic model-based lncRNAs and mRNAs serve as independent prognostic indicators in head and neck squamous cell carcinoma. Oncol Lett 2019; 17:5536-5544. [PMID: 31186775 PMCID: PMC6507369 DOI: 10.3892/ol.2019.10213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 12/06/2017] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSC) is one of most common types of cancer worldwide, and mRNAs and long non-coding RNAs (lncRNAs) have been identified as prognostic biomarkers in HNSC. In the present study, using gene expression datasets from multiple platforms, survival-associated genes in HNSC were identified. Subsequently, a combination of 17 genes (14 mRNAs and 3 lncRNA) was optimized using random forest variable hunting and a risk score model for HNSC prognosis was developed using a cohort from The Cancer Genome Atlas. Patients with high-risk scores tend to have earlier disease recurrence and lower survival rates, compared with those with low-risk scores. This observation was further validated in three independent datasets (GSE41613, GSE10300 and E-MTAB-302). Association analysis revealed that the risk score is independent of other clinicopathological observations. On the basis of the results depicted in the nomogram, the risk score performs better in 3-year survival rate prediction than other clinical observations. In summary, the lncRNA-mRNA signature-based risk score successfully predicts the survival of HNSC and serves as an indicator of prognosis.
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Affiliation(s)
- Zhi-Li Zhang
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Li-Jing Zhao
- Ear, Nose and Throat Department, The Second Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Lin Xu
- Ear, Nose and Throat Department, The Second Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Liang Chai
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Feng Wang
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Ya-Ping Xu
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Shui-Hong Zhou
- Ear, Nose and Throat Department, The First Affiliated Hospital of Medical College, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, P.R. China
| | - Yong Fu
- Ear, Nose and Throat Department, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, P.R. China
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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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