1
|
Mei Z, Zhengdong L, Shupeng L, Xin Z, Lei W, Wang C. Identification of an 8 HPV-related RNA signature as a novel prognostic biomarker for squamous cell carcinoma of the head and neck. Medicine (Baltimore) 2024; 103:e36448. [PMID: 38335428 PMCID: PMC10860974 DOI: 10.1097/md.0000000000036448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 02/12/2024] Open
Abstract
Squamous cell carcinoma of the head and neck (SCCHN) is a commonly detected cancer worldwide. Human papillomavirus (HPV) is emerging as an important risk factor affecting SCCHN prognosis. Therefore, identification of HPV status is essential for effective therapies in SCCHN. The aim of this study was to investigate the prognostic value of HPV-associated RNA biomarkers for SCCHN. The clinical data, survival data, and RNA-seq data of SCCHN were downloaded from The Cancer Genome Atlas database. Before the differential expression analysis, the heterogeneity between the 2 groups (HPV+ vs HPV-) of samples was analyzed using principal component analysis. The differentially expressed genes (DEGs) between HPV+ and HPV- SCCHN samples were analyzed using the R edgeR package. The Gene Ontology functional annotations, including biological process, molecular function and cellular component (CC), and Kyoto Encyclopedia of Genes And Genomes pathways enriched by the DEGs were analyzed using DAVID. The obtained matrix was analyzed by weighed gene coexpression network analysis. A total of 350 significant DEGs were identified through differential analysis, and these DEGs were significantly enriched in functions associated with keratinization, and the pathway of neuroactive ligand-receptor interaction. Moreover, 72 hub genes were identified through weighed gene coexpression network analysis. After the hub genes and DEGs were combined, we obtained 422 union genes, including 65 survival-associated genes. After regression analysis, a HPV-related prognostic model was established, which consisted of 8 genes, including Clorf105, CGA, CHRNA2, CRIP3, CTAG2, ENPP6, NEFH, and RNF212. The obtained regression model could be expressed by an equation as follows: risk score = 0.065 × Clorf105 + 0.012 × CGA + 0.01 × CHRNA2 + 0.047 × CRIP3 + 0.043 × CTAG2-0.034 × ENPP6 - 0.003 × NEFH - 0.068 × RNF212. CGA interacted with 3 drugs, and CHRNA2 interacted with 11 drugs. We have identified an 8 HPV-RNA signature associated with the prognosis of SCCHN patients. Such prognostic model might serve as possible candidate biomarker and therapeutic target for SCCHN.
Collapse
Affiliation(s)
- Zhang Mei
- Department of Dental, Shandong Medical College, Jinan, China
| | - Luo Zhengdong
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Liu Shupeng
- Department of Outpatient, Yidu Central Hospital of Weifang, Weifang, China
| | - Zhang Xin
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Wang Lei
- Department of Orthodontics, Qilu Hospital of Shandong University, Jinan, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, the Second Hospital of Shandong University, Jinan, China
| |
Collapse
|
2
|
Wang CS, Lee YC, Jhan JH, Li WM, Chang LL, Huang AM, Lin HH, Wu YR, Hsu WC, Ke HL. MicroRNA-299-3p inhibits cell proliferation, motility, invasion and angiogenesis via VEGFA in upper tract urothelial carcinoma. J Gene Med 2024; 26:e3616. [PMID: 38049938 DOI: 10.1002/jgm.3616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Upper tract urothelial carcinoma (UTUC) is a rare tumor with extraordinarily different features between Eastern and Western countries. Vascular endothelial growth factor-A (VEGFA) was originally identified as a secreted signaling protein and regulator of vascular development and cancer progression. In this study, we aimed to elucidate the molecular mechanisms underlying the regulation of VEGFA by microRNA in UTUC. METHODS VEGFA expression was evaluated by immunohistochemistry in 140 human UTUC tissue samples. Next, we assessed the regulatory relationship between VEGFA and miR-299-3p by real-time PCR, western blotting, ELISA and dual-luciferase reporter assays using two UTUC cell lines. The role of miR-299-3p/VEGFA in cell proliferation, motility, invasion, and tube formation was analyzed in vitro. RESULTS High VEGFA expression was significantly associated with tumor stage, grade, distant metastasis and cancer-related death and correlated with poor progression-free and cancer-specific survival. VEGFA knockdown repressed proliferation, migration, invasion and angiogenesis in UTUC cell lines. miR-299-3p significantly reduced VEGFA protein expression and miR-299-3p overexpression inhibited VEGFA mRNA and protein expression by directly targeting its 3'-UTR. Functional studies indicated that VEGFA overexpression reversed the miR-299-3p-mediated suppression of tumor cell proliferation, migration, invasion and angiogenesis. In addition, miR-299-3p/VEGFA suppressed cellular functions in UTUC by modulating the expression of P18 and cyclin E2. CONCLUSIONS Our findings suggest that miR-299-3p possibly suppresses UTUC cell proliferation, motility, invasion and angiogenesis via VEGFA. VEGFA may act as a prognostic predictor, and both VEGFA and miR-299-3p could be potential therapeutic targets for UTUC.
Collapse
Affiliation(s)
- Chien-Shen Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yi-Chen Lee
- Department of Anatomy, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jhen-Hao Jhan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Municipal Siaogang Hospital, Kaohsiung, Taiwan
| | - Wei-Ming Li
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, Ministry of Health and Welfare Pingtung Hospital, Pingtung, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Lin-Li Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Microbiology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - A-Mei Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biochemistry, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hui-Hui Lin
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yi-Ru Wu
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wei-Chi Hsu
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hung-Lung Ke
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| |
Collapse
|
3
|
Shen Y, Chen H, Huang Q, Du H, Zhou L. Transcriptomic signature associated with RNA-binding proteins for survival stratification of laryngeal cancer. Aging (Albany NY) 2022; 14:6605-6625. [PMID: 35985767 PMCID: PMC9467394 DOI: 10.18632/aging.204234] [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: 03/11/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022]
Abstract
RNA-binding proteins (RBPs) have been suggested as important prognostic indicators in different human cancers. This study was designed to search the prognostic value of RBPs of laryngeal squamous cell carcinoma (LSCC). Differentially expressed RBPs (DERBPs) were screened via The Cancer Genome Atlas (TCGA). Bioinformatics methods were used to identify prognostic DERBPs. Expression profiling of training cohort were calculated to develop a transcriptomic signature, which was validated by three independent cohorts (TCGA cohort, GSE65858 cohort and GSE27020 cohort). We identified DERBPs and a set of signatures (GTPBP3, KHDRBS3 and RBM38) were confirmed as prognosis-related hub DERBPs in LSCC, which was also tested and verified by bioinformatics method and molecular biology experiment. The role of immune cell infiltration and drug resistance between subgroups was explored. Furthermore, the risk score based on transcriptomic signature was turned out to be an independent prognostic indicator for LSCC. Finally, a nomogram for further clinical application was established. Our study demonstrated that the transcriptomic signature we constructed could serve as a novel therapeutic target and biomarker for LSCC from the perspective of RBPs.
Collapse
Affiliation(s)
- Yujie Shen
- Department of Otorhinolaryngology Head and Neck Surgery, Eye, Ear, Nose, and Throat Hospital, Fudan University, Shanghai 200031, Shanghai, China
| | - Huijun Chen
- Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, Southeast University, Nanjing 210009, Jiangsu, China
| | - Qiang Huang
- Department of Otorhinolaryngology Head and Neck Surgery, Eye, Ear, Nose, and Throat Hospital, Fudan University, Shanghai 200031, Shanghai, China
| | - Huaidong Du
- Department of Otorhinolaryngology Head and Neck Surgery, Eye, Ear, Nose, and Throat Hospital, Fudan University, Shanghai 200031, Shanghai, China
| | - Liang Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, Eye, Ear, Nose, and Throat Hospital, Fudan University, Shanghai 200031, Shanghai, China
| |
Collapse
|
4
|
Thomaidou AC, Batsaki P, Adamaki M, Goulielmaki M, Baxevanis CN, Zoumpourlis V, Fortis SP. Promising Biomarkers in Head and Neck Cancer: The Most Clinically Important miRNAs. Int J Mol Sci 2022; 23:ijms23158257. [PMID: 35897831 PMCID: PMC9367895 DOI: 10.3390/ijms23158257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 02/01/2023] Open
Abstract
Head and neck cancers (HNCs) comprise a heterogeneous group of tumors that extend from the oral cavity to the upper gastrointestinal tract. The principal etiologic factors for oral tumors include tobacco smoking and alcohol consumption, while human papillomavirus (HPV) infections have been accused of a high incidence of pharyngeal tumors. Accordingly, HPV detection has been extensively used to categorize carcinomas of the head and neck. The diverse nature of HNC highlights the necessity for novel, sensitive, and precise biomarkers for the prompt diagnosis of the disease, its successful monitoring, and the timely prognosis of patient clinical outcomes. In this context, the identification of certain microRNAs (miRNAs) and/or the detection of alterations in their expression patterns, in a variety of somatic fluids and tissues, could serve as valuable biomarkers for precision oncology. In the present review, we summarize some of the most frequently studied miRNAs (including miR-21, -375, -99, -34a, -200, -31, -125a/b, -196a/b, -9, -181a, -155, -146a, -23a, -16, -29, and let-7), their role as biomarkers, and their implication in HNC pathogenesis. Moreover, we designate the potential of given miRNAs and miRNA signatures as novel diagnostic and prognostic tools for successful patient stratification. Finally, we discuss the currently ongoing clinical trials that aim to identify the diagnostic, prognostic, or therapeutic utility of miRNAs in HNC.
Collapse
Affiliation(s)
- Arsinoe C. Thomaidou
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece; (A.C.T.); (M.A.)
| | - Panagiota Batsaki
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (P.B.); (M.G.); (C.N.B.)
| | - Maria Adamaki
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece; (A.C.T.); (M.A.)
| | - Maria Goulielmaki
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (P.B.); (M.G.); (C.N.B.)
| | - Constantin N. Baxevanis
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (P.B.); (M.G.); (C.N.B.)
| | - Vassilis Zoumpourlis
- Biomedical Applications Unit, Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), 11635 Athens, Greece; (A.C.T.); (M.A.)
- Correspondence: (V.Z.); (S.P.F.); Tel.: +30-210-727-3730 (V.Z.); +30-210-640-9462 (S.P.F.)
| | - Sotirios P. Fortis
- Cancer Immunology and Immunotherapy Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (P.B.); (M.G.); (C.N.B.)
- Correspondence: (V.Z.); (S.P.F.); Tel.: +30-210-727-3730 (V.Z.); +30-210-640-9462 (S.P.F.)
| |
Collapse
|
5
|
Sayyed AA, Gondaliya P, Bhat P, Mali M, Arya N, Khairnar A, Kalia K. Role of miRNAs In Cancer Diagnostics And Therapy: A Recent Update. Curr Pharm Des 2021; 28:471-487. [PMID: 34751112 DOI: 10.2174/1381612827666211109113305] [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: 02/03/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022]
Abstract
The discovery of miRNAs has been one of the revolutionary developments and has led to the advent of new diagnostic and therapeutic opportunities for the management of cancer. In this regard, miRNA dysregulation has been shown to play a critical role in various stages of tumorigenesis, including tumor invasion, metastasis as well as angiogenesis. Therefore, miRNA profiling can provide accurate fingerprints for the development of diagnostic and therapeutic platforms. This review discusses the recent discoveries of miRNA-based tools for early detection of cancer as well as disease monitoring in cancers that are common, like breast, lung, hepatic, colorectal, oral and brain cancer. Based on the involvement of miRNA in different cancers as oncogenic miRNA or tumor suppressor miRNA, the treatment with miRNA inhibitors or mimics is recommended. However, the stability and targeted delivery of miRNA remain the major limitations of miRNA delivery. In relation to this, several nanoparticle-based delivery systems have been reported which have effectively delivered the miRNA mimics or inhibitors and showed the potential for transforming these advanced delivery systems from bench to bedside in the treatment of cancer metastasis and chemoresistance. Based on this, we attempted to uncover recently reported advanced nanotherapeutic approaches to deliver the miRNAs in the management of different cancers.
Collapse
Affiliation(s)
- Adil A Sayyed
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat. India
| | - Piyush Gondaliya
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat. India
| | - Palak Bhat
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat. India
| | - Mukund Mali
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat. India
| | - Neha Arya
- Department of Medical Devices, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat. India
| | - Amit Khairnar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat. India
| | - Kiran Kalia
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat. India
| |
Collapse
|
6
|
Hsieh JCH, Wang HM, Wu MH, Chang KP, Chang PH, Liao CT, Liau CT. Review of emerging biomarkers in head and neck squamous cell carcinoma in the era of immunotherapy and targeted therapy. Head Neck 2020; 41 Suppl 1:19-45. [PMID: 31573749 DOI: 10.1002/hed.25932] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Biomarkers in head and neck squamous cell carcinoma (HNSCC) emerge rapidly in recent years, especially for new targeted therapies and immunotherapies. METHODS Recent, relevant peer-reviewed evidence were critically reviewed and summarized. RESULTS This review article briefly introduces essential biomarker concepts, including purposes and classifications (predictive, prognostic, and diagnostic markers), and the phases of biomarker development. We summarize current biomarkers in order of clinical utility; p16 and human papillomavirus status remain the most important and validated biomarkers in HNSCC. The rationale for biomarker study design continues to evolve with technological advances, especially whole-exome or whole-genomic sequencing. Noninvasive body fluid and liquid biopsy biomarkers appear to hold strong potential for development as tools for early cancer detection, cancer diagnosis, monitoring of disease recurrence, and outcome prediction. In light of discrepancies among different technologies, standardized approaches are needed. CONCLUSION Biomarkers from cancer tissue or blood in HNSCC could direct new anticancer therapies.
Collapse
Affiliation(s)
- Jason Chia-Hsun Hsieh
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and Chang Gung University, Taoyuan, Taiwan
| | - Hung-Ming Wang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and Chang Gung University, Taoyuan, Taiwan
| | - Min-Hsien Wu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan, Taiwan.,Department of Chemical Engineering, Ming Chi University of Technology, New Taipei City, Taiwan
| | - Kai-Ping Chang
- Department of Otorhinolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Pei-Hung Chang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan and Chang Gung University, Taoyuan, Taiwan.,Cancer Center, Chang Gung Memorial Hospital, Keelung, and Chang Gung University, Taoyuan, Taiwan
| | - Chun-Ta Liao
- Department of Otorhinolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Chi-Ting Liau
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Linkou and Chang Gung University, Taoyuan, Taiwan
| |
Collapse
|
7
|
Zhao X, Cui L. A robust six-miRNA prognostic signature for head and neck squamous cell carcinoma. J Cell Physiol 2020; 235:8799-8811. [PMID: 32342519 DOI: 10.1002/jcp.29723] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) remains a major health problem worldwide. We aimed to identify a robust microRNA (miRNA)-based signature for predicting HNSCC prognosis. The miRNA expression profiles of HNSCC were obtained from The Cancer Genome Atlas (TCGA) database. The TCGA HNSCC cohort was randomly divided into the discovery and validation cohort. A miRNA-based prognostic signature was built up based on TGCA discovery cohort, and then further validated. The downstream targets of prognostic miRNAs were subjected to functional enrichment analyses. The role of miR-1229-3p, a prognosis-related miRNA, in tumorigenesis of HNSCC was further evaluated. A total of 305 significantly differentially expressed miRNAs were found between HNSCC samples and normal tissues. A six-miRNA prognostic signature was constructed, which exhibited a strong association with overall survival (OS) in the TCGA discovery cohort. In addition, these findings were successfully confirmed in TCGA validation cohort and our own independent cohort. The miRNA-based signature was demonstrated as an independent prognostic indicator for HNSCC. A risk signature-based nomogram model was constructed and showed good performance for predicting the OS for HNSCC. The functional analyses revealed that the downstream targets of these prognostic miRNAs were closely linked to cancer progression. Mechanistically, in vitro analysis revealed that miR-1229-3p played a tumor promoting role in HNSCC. In conclusion, our study has developed a robust miRNA-based signature for predicting the prognosis of HNSCC with high accuracy, which will contribute to improve the therapeutic outcome.
Collapse
Affiliation(s)
- Xinyuan Zhao
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, China
| | - Li Cui
- Division of Oral Biology and Medicine, School of Dentistry, UCLA, Los Angeles, California
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Abstract
microRNAs are small non-coding RNA molecules playing a central role in gene regulation. miRBase is the standard reference source for analysis and interpretation of experimental studies. However, the richness and complexity of the annotation is often underappreciated by users. Moreover, even for experienced users, the size of the resource can make it difficult to explore annotation to determine features such as species coverage, the impact of specific characteristics and changes between successive releases. A further consideration is that each new miRBase release contains entries that have had limited review and which may subsequently be removed in a future release to ensure the quality of annotation. To aid the miRBase user, we developed a software tool, miRBaseMiner, for investigating miRBase annotation and generating custom annotation sets. We apply the tool to characterize each release from v9.2 to v22 to examine how annotation has changed across releases and highlight some of the annotation features that users should keep in mind when using for miRBase for data analysis. These include: (1) entries with identical or very similar sequences; (2) entries with multiple annotated genome locations; (3) hairpin precursor entries with extremely low-estimated minimum free energy; (4) entries possessing reverse complementary; (5) entries with 3ʹ poly(A) ends. As each of these factors can impact the identification of dysregulated features and subsequent clinical or biological conclusions, miRBaseMiner is a valuable resource for any user using miRBase as a reference source.
Collapse
Affiliation(s)
- Xiangfu Zhong
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
| | - Fatima Heinicke
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
| | - Simon Rayner
- Department of Medical Genetics, Oslo University Hospital and University of Oslo , Oslo , Norway
| |
Collapse
|
10
|
Kamińska K, Białkowska A, Kowalewski J, Huang S, Lewandowska MA. Differential gene methylation patterns in cancerous and non‑cancerous cells. Oncol Rep 2019; 42:43-54. [PMID: 31115550 PMCID: PMC6549081 DOI: 10.3892/or.2019.7159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022] Open
Abstract
Large-scale projects, such as The Cancer Genome Atlas (TCGA), Human Epigenome Project (HEP) and Human Epigenome Atlas (HEA), provide an insight into DNA methylation and histone modification markers. Changes in the epigenome significantly contribute to the initiation and progression of cancer. The goal of the present study was to characterize the prostate cancer malignant transformation model using the CpG island methylation pattern. The Human Prostate Cancer EpiTect Methyl II Signature PCR Array was used to evaluate the methylation status of 22 genes in prostate cancer cell lines: PC3, PC3M, PC3MPro4 and PC3MLN4, each representing different metastatic potential in vivo. Subsequently, it was ascertained whether DNA methylation plays a role in the expression of these genes in prostate cancer cells. Hypermethylation of APC, DKK3, GPX3, GSTP1, MGMT, PTGS2, RASSF1, TIMP2 and TNFRSF10D resulted in downregulation of their expression in prostate cancer cell lines as compared to WT fibroblasts. Mining of the TCGA data deposited in the MetHC database found increases in the methylation status of these 9 genes in prostate cancer patients, further supporting the role of methylation in altering the expression of these genes in prostate cancer. Future studies are warranted to investigate the role of these proteins in prostate cancer development.
Collapse
Affiliation(s)
- Katarzyna Kamińska
- Department of Molecular Oncology and Genetics, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
| | - Aneta Białkowska
- Department of Molecular Oncology and Genetics, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
| | - Janusz Kowalewski
- Department of Thoracic Surgery and Tumors, The Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, 85‑796 Bydgoszcz, Poland
| | - Sui Huang
- Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marzena A Lewandowska
- Department of Molecular Oncology and Genetics, Innovative Medical Forum, The F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
| |
Collapse
|
11
|
A gene expression profile associated with perineural invasion identifies a subset of HNSCC at risk of post-surgical recurrence. Oral Oncol 2018; 86:53-60. [PMID: 30409320 DOI: 10.1016/j.oraloncology.2018.09.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/03/2018] [Accepted: 09/08/2018] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Perineural invasion (PNI) is a common histopathological finding in head and neck squamous cell carcinoma (HNSCC). We aimed to explore the molecular mechanisms involved in PNI and the role of PNI as an aggressive pathological feature. MATERIALS AND METHODS We used data from The Cancer Genome Atlas (TCGA) to relate the histological presentation of 528 HNSCC tumours to clinical, whole genome expression and proteomic data. RESULTS We identified a specific gene expression profile highly enriched in genes related to muscle differentiation/function and associated with PNI in HNSCC. We explored the clinical significance of this profile in three groups of HNSCC tumours stratified according to their low, intermediate or high risk of post-surgical recurrence. In the "low-risk" group, defined as tumours indicated for surgery without adjuvant radiotherapy (n = 51), the PNI gene expression profile identified a subset of HNSCC with a higher rate of tumour recurrence, decreased Disease Free Survival (DFS) and Overall Survival (OS) (p < 0.0001 and p = 0.0064, respectively). Comparable results were observed in "intermediate risk" tumours (n = 112), but not in "high risk" tumours (n = 147), whose prognosis was driven by the presence of lymph node extracapsular spread. Finally, we found that tumours with histological PNI had increased activation levels of the Akt/PKB and mTOR (mammalian Target Of Rapamycin) kinases. CONCLUSION PNI is characterised by a specific gene expression profile and distinct biological characteristics. Analysing the PNI gene expression profile holds potential for therapeutic stratification of HNSCC and identification of a subset of tumours with a higher risk of recurrence.
Collapse
|
12
|
Hess J, Unger K, Maihoefer C, Schüttrumpf L, Wintergerst L, Heider T, Weber P, Marschner S, Braselmann H, Samaga D, Kuger S, Pflugradt U, Baumeister P, Walch A, Woischke C, Kirchner T, Werner M, Werner K, Baumann M, Budach V, Combs SE, Debus J, Grosu AL, Krause M, Linge A, Rödel C, Stuschke M, Zips D, Zitzelsberger H, Ganswindt U, Henke M, Belka C. A Five-MicroRNA Signature Predicts Survival and Disease Control of Patients with Head and Neck Cancer Negative for HPV Infection. Clin Cancer Res 2018; 25:1505-1516. [PMID: 30171046 DOI: 10.1158/1078-0432.ccr-18-0776] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/19/2018] [Accepted: 08/27/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is associated with unfavorable prognosis, while independent prognostic markers remain to be defined. EXPERIMENTAL DESIGN We retrospectively performed miRNA expression profiling. Patients were operated for locally advanced HPV-negative HNSCC and had received radiochemotherapy in eight different hospitals (DKTK-ROG; n = 85). Selection fulfilled comparable demographic, treatment, and follow-up characteristics. Findings were validated in an independent single-center patient sample (LMU-KKG; n = 77). A prognostic miRNA signature was developed for freedom from recurrence and tested for other endpoints. Recursive-partitioning analysis was performed on the miRNA signature, tumor and nodal stage, and extracapsular nodal spread. Technical validation used qRT-PCR. An miRNA-mRNA target network was generated and analyzed. RESULTS For DKTK-ROG and LMU-KKG patients, the median follow-up was 5.1 and 5.3 years, and the 5-year freedom from recurrence rate was 63.5% and 75.3%, respectively. A five-miRNA signature (hsa-let-7g-3p, hsa-miR-6508-5p, hsa-miR-210-5p, hsa-miR-4306, and hsa-miR-7161-3p) predicted freedom from recurrence in DKTK-ROG [hazard ratio (HR) 4.42; 95% confidence interval (CI), 1.98-9.88, P < 0.001], which was confirmed in LMU-KKG (HR 4.24; 95% CI, 1.40-12.81, P = 0.005). The signature also predicted overall survival (HR 3.03; 95% CI, 1.50-6.12, P = 0.001), recurrence-free survival (HR 3.16; 95% CI, 1.65-6.04, P < 0.001), and disease-specific survival (HR 5.12; 95% CI, 1.88-13.92, P < 0.001), all confirmed in LMU-KKG data. Adjustment for relevant covariates maintained the miRNA signature predicting all endpoints. Recursive-partitioning analysis of both samples combined classified patients into low (n = 17), low-intermediate (n = 80), high-intermediate (n = 48), or high risk (n = 17) for recurrence (P < 0.001). CONCLUSIONS The five-miRNA signature is a strong and independent prognostic factor for disease recurrence and survival of patients with HPV-negative HNSCC.See related commentary by Clump et al., p. 1441.
Collapse
Affiliation(s)
- Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany. .,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Cornelius Maihoefer
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Lars Schüttrumpf
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Ludmila Wintergerst
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Theresa Heider
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Peter Weber
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Institute for Diabetes and Cancer (IDC), Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Joint Heidelberg-IDC Translational Diabetes Program, Heidelberg University Hospital, Heidelberg, Germany
| | - Sebastian Marschner
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Herbert Braselmann
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Daniel Samaga
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Sebastian Kuger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Ulrike Pflugradt
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Philipp Baumeister
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Christine Woischke
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristin Werner
- Institute for Surgical Pathology, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Baumann
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Budach
- Department of Radiooncology and Radiotherapy, Charité University Hospital Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie E Combs
- German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.,Institute of Innovative Radiotherapy (iRT), Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Jürgen Debus
- Department of Radiation Oncology, Heidelberg Ion Therapy Center (HIT), University of Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anca-Ligia Grosu
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiation Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mechthild Krause
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany
| | - Annett Linge
- German Cancer Consortium (DKTK), Partner Site Dresden, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiotherapy and Radiation Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,OncoRay - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Partner Site Dresden, Dresden, Germany.,Helmholtz-Zentrum Dresden - Rossendorf, Institute of Radiooncology - OncoRay Dresden, Dresden, Germany
| | - Claus Rödel
- Department of Radiotherapy and Oncology, Goethe-University Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK), Partner Site Frankfurt, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Stuschke
- Department of Radiotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site Essen, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel Zips
- Department of Radiation Oncology, Faculty of Medicine and University Hospital Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tübingen, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Horst Zitzelsberger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Ute Ganswindt
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,Department of Therapeutic Radiology and Oncology, Innsbruck Medical University, Innsbruck, Austria
| | - Michael Henke
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiation Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claus Belka
- Clinical Cooperation Group "Personalized Radiotherapy in Head and Neck Cancer," Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany.,Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
13
|
MicroRNA-155, -185 and -193b as biomarkers in human papillomavirus positive and negative tonsillar and base of tongue squamous cell carcinoma. Oral Oncol 2018; 82:8-16. [PMID: 29909906 DOI: 10.1016/j.oraloncology.2018.04.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/23/2018] [Accepted: 04/26/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Three-year disease-free survival (DFS) is 80% for human papillomavirus (HPV) positive tonsillar and base of tongue cancer (TSCC/BOTSCC) treated with radiotherapy alone, and today's intensified therapy does not improve prognosis. More markers are therefore needed to more accurately identify patients with good prognosis or in need of alternative therapy. Here, microRNAs (miRs) 155, 185 and 193b were examined as potential prognostic markers in TSCC/BOTSCC. MATERIAL AND METHODS 168 TSCC/BOTSCC patients diagnosed 2000-2013, with known data on HPV-status, CD8+ tumour infiltrating lymphocytes, tumour staging and survival were examined for expression of miR-155, -185 and -193b using Real-Time PCR. Associations between miR expression and patient and tumour characteristics were analysed using univariate testing and multivariate regression. RESULTS Tumours compared to normal tonsils showed decreased miR-155 and increased miR-193b expression. miR-155 expression was associated with HPV-positivity, low T-stage, high CD8+ TIL counts and improved survival. miR-185 expression was associated with HPV-negativity and a tendency towards decreased survival, while miR-193b expression was associated with higher T-stage, male gender and lower CD8+ TIL counts, but not with outcome. Upon Cox regression, miR-185 was the only miR significantly associated with survival. Combining miR-155 and miR-185 to predict outcome in HPV+ patients yielded an area under curve (AUC) of 71%. CONCLUSION Increased miR-155 expression was found as a positive predictor of survival, with the effect mainly due to its association with high CD8+ TIL numbers, while miR-185 independently associated with decreased survival. Addition of these miRs to previously validated prognostic biomarkers could improve patient stratification accuracy.
Collapse
|
14
|
Yang Y, Lu Q, Shao X, Mo B, Nie X, Liu W, Chen X, Tang Y, Deng Y, Yan J. Development Of A Three-Gene Prognostic Signature For Hepatitis B Virus Associated Hepatocellular Carcinoma Based On Integrated Transcriptomic Analysis. J Cancer 2018; 9:1989-2002. [PMID: 29896284 PMCID: PMC5995946 DOI: 10.7150/jca.23762] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/14/2018] [Indexed: 02/07/2023] Open
Abstract
Integration of public genome-wide gene expression data together with Cox regression analysis is a powerful weapon to identify new prognostic gene signatures for cancer diagnosis and prognosis. Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC), however, it remains largely unknown about the specific gene prognostic signature of HBV-associated HCC. Using Robust Rank Aggreg (RRA) method to integrate seven whole genome expression datasets, we identified 82 up-regulated genes and 577 down-regulated genes in HBV-associated HCC patients. Combination of several enrichment analysis, univariate and multivariate Cox proportional hazards regression analysis, we revealed that a three-gene (SPP2, CDC37L1, and ECHDC2) prognostic signature could act as an independent prognostic indicator for HBV-associated HCC in both the discovery cohort and the internal testing cohort. Gene set enrichment analysis showed that the high-risk group with lower expression levels of the three genes was enriched in bladder cancer and cell cycle pathway, whereas the low-risk group with higher expression levels of the three genes was enriched in drug metabolism-cytochrome P450, PPAR signaling pathway, fatty acid and histidine metabolisms. This indicates that patients of HBV-associated HCC with higher expression of these three genes may preserve relatively good hepatic cellular metabolism and function, which may also protect HCC patients from persistent drug toxicity in response to various medication. Our findings suggest a three-gene prognostic model that serves as a specific prognostic signature for HBV-associated HCC.
Collapse
Affiliation(s)
- Yao Yang
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Qian Lu
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Xuejun Shao
- Brigade 315th of Territorial Defense Force, Chinese People's Liberation Army Ground Force, Xishuangbanna District, Yunan 666200, China
| | - Banghui Mo
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Xuqiang Nie
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Wei Liu
- Health Physical Examination Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Xianhua Chen
- Diagnosis and Treatment Center for Servicemen, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Yuan Tang
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Youcai Deng
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jun Yan
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing 102218, China.,Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400042, China
| |
Collapse
|
15
|
Liao X, Zhu G, Huang R, Yang C, Wang X, Huang K, Yu T, Han C, Su H, Peng T. Identification of potential prognostic microRNA biomarkers for predicting survival in patients with hepatocellular carcinoma. Cancer Manag Res 2018; 10:787-803. [PMID: 29713196 PMCID: PMC5912208 DOI: 10.2147/cmar.s161334] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background The aim of the present study was to identify potential prognostic microRNA (miRNA) biomarkers for hepatocellular carcinoma (HCC) prognosis prediction based on a dataset from The Cancer Genome Atlas (TCGA). Materials and methods A miRNA sequencing dataset and corresponding clinical parameters of HCC were obtained from TCGA. Genome-wide univariate Cox regression analysis was used to screen prognostic differentially expressed miRNAs (DEMs), and multivariable Cox regression analysis was used for prognostic signature construction. Comprehensive survival analysis was performed to evaluate the prognostic value of the prognostic signature. Results Five miRNAs were regarded as prognostic DEMs and used for prognostic signature construction. The five-DEM prognostic signature performed well in prognosis prediction (adjusted P < 0.0001, adjusted hazard ratio = 2.249, 95% confidence interval =1.491-3.394), and time-dependent receiver-operating characteristic (ROC) analysis showed an area under the curve (AUC) of 0.765, 0.745, 0.725, and 0.687 for 1-, 2-, 3-, and 5-year HCC overall survival (OS) prediction, respectively. Comprehensive survival analysis of the prognostic signature suggests that the risk score model could serve as an independent factor of HCC and perform better in prognosis prediction than other traditional clinical indicators. Functional assessment of the target genes of hsa-mir-139 and hsa-mir-5003 indicates that they were significantly enriched in multiple biological processes and pathways, including cell proliferation and cell migration regulation, pathways in cancer, and the cyclic adenosine monophosphate (cAMP) signaling pathway. Conclusion Our study indicates that the novel miRNA expression signature may be a potential prognostic biomarker for HCC patients.
Collapse
Affiliation(s)
- Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Ketuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Hao Su
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| |
Collapse
|
16
|
Identification of molecular targets for esophageal carcinoma diagnosis using miRNA-seq and RNA-seq data from The Cancer Genome Atlas: a study of 187 cases. Oncotarget 2018; 8:35681-35699. [PMID: 28415685 PMCID: PMC5482608 DOI: 10.18632/oncotarget.16051] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/28/2017] [Indexed: 12/14/2022] Open
Abstract
Esophageal carcinoma (ESCA) is one of the most common malignancies worldwide, and its pathogenesis is complex. In this study, we identified differentially expressed miRNAs (DEMs) and genes (DEGs) of ESCA from The Cancer Genome Atlas (TCGA) database. The diagnostic values of DEMs were determined by receiver operating characteristic (ROC) analyses and validated based on data from Gene Expression Omnibus (GEO). The top five DEMs with the best diagnostic values were selected, and their potential targets were predicted by various in silico methods. These target genes were then identified among the DEGs from TCGA. Furthermore, the overlapping genes were subjected to protein-protein interaction (PPI) analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The miRNA-transcription factor (TF) regulatory relations were determined using CircuitsDB and TransmiR. Finally, the regulatory networks of miRNA-TF and miRNA-gene were constructed and analyzed. A total of 136 DEMs and 3541 DEGs were identified in ESCA. The top five DEMs with the highest area under the receiver operating characteristic curve (AUC) values were miRNA-93 (0.953), miRNA-21 (0.928), miRNA-4746 (0.915), miRNA-196a-1 (0.906) and miRNA-196a-2 (0.906). The combined AUC of these five DEMs was 0.985. The KEGG analysis with 349 overlapping genes showed that the calcium signaling pathway and the neuroactive ligand-receptor interaction were the most relevant pathways. The regulatory networks of miRNA-TF and miRNA-gene, including 38 miRNA-TF and 560 miRNA-gene pairs, were successfully established. Our findings may provide new insights into the molecular mechanisms of ESCA pathogenesis. Future research will aim to explore the role of novel miRNAs in the pathogenesis and improve the early diagnosis of ESCA.
Collapse
|
17
|
A novel microRNA signature predicts survival in stomach adenocarcinoma. Oncotarget 2018; 8:28144-28153. [PMID: 28423653 PMCID: PMC5438638 DOI: 10.18632/oncotarget.15961] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/22/2017] [Indexed: 01/07/2023] Open
Abstract
Recent microRNA (miRNA) expression profiling studies suggest the clinical use of miRNAs as potential prognostic biomarkers in various malignancies. In this study, aiming to identify microRNAs with prognostic value for overall survival (OS) in stomach adenocarcinoma (STAD) patients, we analyzed the miRNA expression profiles and the associated clinical characteristics in 380 STAD samples from The Cancer Genome Atlas (TCGA) dataset. An eight-miRNA signature for predicting OS in STAD patients was identified and self-validated by survival analysis and semi-supervised principal components method. We developed a linear prognostic model composed of these miRNAs to divide patients into high- and low-risk groups according to the calculated prognostic scores. Kaplan-Meier analysis demonstrated that patients in the high-risk group had worse OS compared with patients in the low-risk group. Notably, this miRNA prognostic model showed prognostic significance to the STAD patients in early stages and the chemo-resistant patients, who would potentially benefit from additional medical interventions. Finally, this eight-miRNA signature is an independent prognostic biomarker and demonstrates a good predictive performance for 5-year survival. Thus, this signature may serve as a novel biomarker for predicting survival as well as chemotherapy response in STAD patients.
Collapse
|
18
|
Gao X, Wu Y, Yu W, Li H. Identification of a seven-miRNA signature as prognostic biomarker for lung squamous cell carcinoma. Oncotarget 2018; 7:81670-81679. [PMID: 27835574 PMCID: PMC5348421 DOI: 10.18632/oncotarget.13164] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Specific biomarkers for outcome prediction of lung squamous cell carcinoma (LUSC) are still lacking. This study assessed the prognostic value of differentially expressed miRNAs of LUSC patients. RESULTS Twelve of the 133 most significantly altered miRNAs were associated with overall survival (OS) across different clinical subclasses of the Cancer Genome Atlas (TCGA) LUSC cohort. A linear prognostic model of seven miRNAs was developed to divide patients into high- and low-risk groups. Patients assigned to the high-risk group exhibited poor OS compared with patients in the low-risk group, which was further validated in the validation cohort and entire LUSC cohort. METHODS MiRNA expression profiles with clinical information of 447 LUSC patients were obtained from TCGA. Most significantly altered miRNAs were identified between tumor and normal samples. Using survival analysis and supervised principal components method, a seven-miRNA signature for prediction of OS of LUSC patients was established. Survival receiver operating characteristic (ROC) analysis was used to assess the performance of survival prediction. The biological relevance of predicted miRNA targets was also analyzed using bioinformatics method. CONCLUSIONS The current study suggests that seven-miRNA signature may have clinical implications in the outcome prediction of LUSC.
Collapse
Affiliation(s)
- Xujie Gao
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Yupeng Wu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Wenwen Yu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Hui Li
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| |
Collapse
|
19
|
Li L, Zhang S, Jiang X, Liu Y, Liu K, Yang C. MicroRNA-let-7e regulates the progression and development of allergic rhinitis by targeting suppressor of cytokine signaling 4 and activating Janus kinase 1/signal transducer and activator of transcription 3 pathway. Exp Ther Med 2018; 15:3523-3529. [PMID: 29545878 DOI: 10.3892/etm.2018.5827] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
The present study aimed to explore the microRNA-let-7e (miR-let-7e) expression in allergic rhinitis (AR), and to investigate the underlying molecular mechanisms. miR-let-7e expression in the nasal mucosa of mice and patients with AR were detected. The expression levels of three inflammatory factors, including histamine, immunoglobulin E and tumor necrosis factor-α (TNF-α), in the blood of AR mice and in interleukin (IL)-13-stimulated nasal epithelial cells (NECs) were also measured. Furthermore, the target gene of miR-let-7e was predicted and validated using a luciferase reporter assay. The expression levels of Janus kinase 1 (JAK1) and signal transducer and activator of transcription 3 (STAT3) were detected. The results demonstrated that miR-let-7e was downregulated in patients and mice with AR compared with the controls. In addition, the expression levels of inflammatory factors were higher in the blood of mice with AR compared with the control group, while miR-let-7e overexpression inhibited these levels in AR mice and IL-13-stimulated NECs. Furthermore, suppressor of cytokine signaling 4 (SOCS4) was revealed as a potential target gene of miR-let-7e and was negatively regulated by miR-let-7e. Overexpression of SOCS4 abrogated the anti-inflammatory activity of miR-let-7e overexpression. Finally, miR-let-7e overexpression activated the JAK1/STAT3 signaling pathway. In conclusion, miR-let-7e may serve an important role in the progression and development of AR, while overexpression of miR-let-7e had an anti-inflammatory effect by targeting SOCS4, which may be achieved by activation of the JAK1/STAT3 signaling pathway.
Collapse
Affiliation(s)
- Lihua Li
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Shaorong Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xunshuo Jiang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yuehui Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Ke Liu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chunping Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| |
Collapse
|
20
|
Liu GW, Qin ZM, Shen QH. An ensemble method integrated with miRNA expression data for predicting miRNA targets in stomach adenocarcinoma. Cancer Biomark 2017; 20:617-625. [DOI: 10.3233/cbm-170595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Guang-Wei Liu
- Department of Gastroenterology, The First Affiliated Hospital, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Zhao-Min Qin
- Department of Nursing, Shandong Medical College, Jinan, Shandong, China
| | - Qin-Hai Shen
- Department of Medicine, Shandong Medical College, Jinan, Shandong, China
| |
Collapse
|
21
|
Sannigrahi MK, Sharma R, Panda NK, Khullar M. Role of non-coding RNAs in head and neck squamous cell carcinoma: A narrative review. Oral Dis 2017; 24:1417-1427. [PMID: 28941018 DOI: 10.1111/odi.12782] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/23/2017] [Accepted: 09/08/2017] [Indexed: 12/13/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide with high recurrence, metastasis, and poor treatment outcome. Recent studies have reported that non-coding RNA (ncRNA) might play critical role in regulating different types of cancer. MicroRNAs (miRs) are short ncRNAs (20-25 nucleotides) responsible for post-transcriptional regulation of gene expression and may have a role in oncogenesis by acting as oncomiRs or tumor suppressor miRs. Long non-coding RNAs (lncRNAs) are heterogenous group of ncRNAs more than 200 nucleotides long, can act in cis and/or in trans, and have been also implicated in carcinogenesis. These molecules have been suggested to be promising candidates as diagnostic and prognostic biomarkers and for development of novel therapeutic approaches. In this review, we have summarized recent findings on role of these ncRNAs in HPV-negative (HPV-ve) and HPV-positive (HPV+ve) HNSCC. The available literature supports differential expression of both microRNAs and long non-coding RNAs, which include oncogenic ncRNAs (miR-21, miR-31, miR-155, miR-211, HOTAIR, and MALAT1) and tumor suppressor ncRNAs (let7d, miR-17, miR-375, miR-139, and MEG3) in HPV+ve HNSCC tumors as compared to HPV-ve tumors and they have distinct role in the pathophysiology of these two types of HNSCCs.
Collapse
Affiliation(s)
- M K Sannigrahi
- Department of Otolaryngology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - R Sharma
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
| | - N K Panda
- Department of Otolaryngology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - M Khullar
- Department of Experimental Medicine and Biotechnology, PGIMER, Chandigarh, India
| |
Collapse
|
22
|
Liang L, Wei DM, Li JJ, Luo DZ, Chen G, Dang YW, Cai XY. Prognostic microRNAs and their potential molecular mechanism in pancreatic cancer: A study based on The Cancer Genome Atlas and bioinformatics investigation. Mol Med Rep 2017; 17:939-951. [PMID: 29115476 PMCID: PMC5780175 DOI: 10.3892/mmr.2017.7945] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/02/2017] [Indexed: 01/17/2023] Open
Abstract
Although certain biomarkers that are directly associated with the overall survival (OS) of patients with pancreatic adenocarcinoma (PAAD) have been identified, the efficacy of a single factor is limited to predicting the prognosis. The aim of the present study was to identify a combination micro (mi)RNA signature that enhanced the prognostic prediction for PAAD. Following analysis of the data available from The Cancer Genome Atlas (TCGA), 175 PAAD samples were selected for the present study, and the associations between 494 miRNAs and OS were investigated. The prognostic value of all miRNAs was analyzed by multivariate Cox regression, and the miRNAs were ranked according to the hazard ratio (HR) and P-values. The top 5 miRNAs (miR-1301, miR-125a, miR-376c, miR-328 and miR-376b) were significantly associated with OS (HR=0.139; 95% confidence interval, 0.043–0.443; P<0.001), thus demonstrating that this panel was able to serve as an independent prognostic factor for PAAD. In addition, the present study also predicted the target genes of the top 10 miRNAs with the highest prognostic values using 12 different prediction software, and enrichment signaling pathway analyses elucidated that several pathways may be markedly associated with these miRNAs, including ‘Pathways in cancer’, ‘Chronic myeloid leukemia’, ‘Glioma’ and ‘MicroRNAs in cancer’. Lastly, ubiquitin C, epidermal growth factor receptor, estrogen receptor 1, mitogen-activated protein kinase 1, mothers against decapentaplegic homolog 4 and androgen receptor may be the hub genes revealed by STRING analysis. The present study identified several miRNAs, particularly a five-miRNA-pool, that may be reliable, independent factors for predicting survival in patients with PAAD. However, the underlying molecular mechanisms require further investigation in the future.
Collapse
Affiliation(s)
- Liang Liang
- Department of General Surgery, Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Dan-Ming Wei
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jian-Jun Li
- Department of General Surgery, Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Dian-Zhong Luo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yi-Wu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Xiao-Yong Cai
- Department of General Surgery, Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| |
Collapse
|
23
|
Shen S, Bai J, Wei Y, Wang G, Li Q, Zhang R, Duan W, Yang S, Du M, Zhao Y, Christiani DC, Chen F. A seven-gene prognostic signature for rapid determination of head and neck squamous cell carcinoma survival. Oncol Rep 2017; 38:3403-3411. [PMID: 29130107 PMCID: PMC5783586 DOI: 10.3892/or.2017.6057] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/02/2017] [Indexed: 12/15/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer and displays divergent clinical outcomes. Prognostic biomarkers might improve risk stratification and survival prediction. We aimed to investigate the prognostic genes associated with overall survival. A two-step gene selection method was used to develop a seven-gene-based prognostic model based on the training set collected from The Cancer Genome Atlas (TCGA). In addition, the prognostic model was validated in an independent testing set from Gene Expression Omnibus (GEO). The score based on the model successfully distinguished HNSCC survival into high-risk and low-risk groups in the training set (HR, 2.79; 95% CI, 1.98–3.92; P=4.05×10−9) and the testing set (HR, 2.05; 95% CI, 1.35–3.11; P=7.98×10−4). In addition, the score could significantly predict 5-year survival by ROC curves (AUCs for training set, 0.73; testing set, 0.66). Combining risk scores with clinical characteristics improved the AUCs beyond using clinical characteristics alone (training set, from 0.57 to 0.75; testing set, from 0.63 to 0.72). A subgroup sensitivity analysis with HPV status and tumor sites revealed that the risk score was significant in all subgroups except oral cavity tumors of the testing set. Furthermore, HPV-positive status improves survival in oropharyngeal HNSCC but not non-oropharyngeal HNSCC. In conclusion, the seven-gene prognostic signature is a reliable and practical prognostic tool for HNSCC. This approach can add prognostic value to clinical characteristics and provides a new possibility for individualized treatment.
Collapse
Affiliation(s)
- Sipeng Shen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Jianling Bai
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Yongyue Wei
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Guanrong Wang
- NPFPC Contraceptive Adverse Reaction Surveillance Center, Jiangsu Institute of Planned Parenthood Research, Nanjing, Jiangsu, P.R. China
| | - Qingya Li
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Ruyang Zhang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Weiwei Duan
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Sheng Yang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Mulong Du
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Yang Zhao
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - David C Christiani
- China International Cooperation Center of Environment and Human Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Feng Chen
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| |
Collapse
|
24
|
Rabinowits G, Bowden M, Flores LM, Verselis S, Vergara V, Jo VY, Chau N, Lorch J, Hammerman PS, Thomas T, Goguen LA, Annino D, Schoenfeld JD, Margalit DN, Tishler RB, Haddad RI. Comparative Analysis of MicroRNA Expression among Benign and Malignant Tongue Tissue and Plasma of Patients with Tongue Cancer. Front Oncol 2017; 7:191. [PMID: 28900608 PMCID: PMC5581802 DOI: 10.3389/fonc.2017.00191] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
Background Identification of a microRNA (miRNA) pattern to be used as a biomarker for HNSCC is challenging given the heterogeneity of the disease and different methodologies used. To better define the field, we performed a prospective analysis of blood, tumor, and paired benign tissues in tongue squamous cell carcinoma (SCC) patients. Methods Plasma samples were collected prior to surgery, and paired tumor and benign tissue blocks were collected from tongue cancer resections. Circulating free and exosomal miRNA, and paired tumor and benign tissues miRNA were analyzed. TaqMan-based miRNA arrays were used to quantitate the expression of 747 human miRNAs. The comparative Ct method assessed the miRNA profile results, and Student’s t-test determined statistical significance between tumor and benign samples. Results Sixteen of 359 miRNAs detected were differentially expressed between paired tumor and benign tissue. Nine were upregulated, and seven downregulated in tumor tissue. All nine upregulated and six of seven downregulated tumor miRNAs were expressed in circulating exosomes. In contrast, eight of nine upregulated and four of seven downregulated tumor miRNAs were circulating free in the plasma. Conclusion An aberrantly expressed pattern of miRNA was identified in both tumor and plasma of patients with tongue SCC, suggesting this may be a biomarker for SCC of the oral tongue. Circulating exosomes appear to be a more reliable method for evaluation of circulating tumor-miRNA expression. Further studies with a larger cohort of patients and serial blood samples are needed to validate our findings.
Collapse
Affiliation(s)
- Guilherme Rabinowits
- Medical Oncology Department, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Michaela Bowden
- Medical Oncology Department, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Ludmila M Flores
- Internal Medicine Department, Brigham and Women's Hospital, Boston, MA, United States
| | - Sigitas Verselis
- Dana-Farber Cancer Institute, Molecular Diagnostics Laboratory, Boston, MA, United States
| | - Victoria Vergara
- Medical Oncology Department, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Vickie Y Jo
- Anatomic Pathology Department, Brigham and Women's Hospital, Boston, MA, United States
| | - Nicole Chau
- Medical Oncology Department, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Jochen Lorch
- Medical Oncology Department, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Peter S Hammerman
- Radiation Oncology Department, Dana-Farber, Brigham and Women's Hospital, Boston, MA, United States
| | - Tom Thomas
- Brigham and Women's Hospital, Otolaryngology Division, Boston, MA, United States
| | - Laura A Goguen
- Brigham and Women's Hospital, Otolaryngology Division, Boston, MA, United States
| | - Donald Annino
- Brigham and Women's Hospital, Otolaryngology Division, Boston, MA, United States
| | - Jonathan D Schoenfeld
- Radiation Oncology Department, Dana-Farber, Brigham and Women's Hospital, Boston, MA, United States
| | - Danielle N Margalit
- Radiation Oncology Department, Dana-Farber, Brigham and Women's Hospital, Boston, MA, United States
| | - Roy B Tishler
- Radiation Oncology Department, Dana-Farber, Brigham and Women's Hospital, Boston, MA, United States
| | - Robert I Haddad
- Medical Oncology Department, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, United States
| |
Collapse
|
25
|
Luo W, Wang L, Luo M, Huang Y, Yang H, Zhou Y, Jia H, Wang X. hsa‐mir‐3199‐2 and hsa‐mir‐1293 as Novel Prognostic Biomarkers of Papillary Renal Cell Carcinoma by COX Ratio Risk Regression Model Screening. J Cell Biochem 2017; 118:3488-3494. [DOI: 10.1002/jcb.26008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 03/22/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Wen Luo
- Department of Urological SurgeryRenmin HospitalHubei University of MedicineShiyanHubei Province442000China
| | - Lei Wang
- Department of UrologyThe Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'anHuai'anChina
| | - Mao‐Hua Luo
- Department of Urological SurgeryRenmin HospitalHubei University of MedicineShiyanHubei Province442000China
| | - Yu‐Zhu Huang
- Department of Urological SurgeryRenmin HospitalHubei University of MedicineShiyanHubei Province442000China
| | - Hua Yang
- Department of Urological SurgeryRenmin HospitalHubei University of MedicineShiyanHubei Province442000China
| | - Yu Zhou
- Department of Urological SurgeryRenmin HospitalHubei University of MedicineShiyanHubei Province442000China
| | - Hong‐Tao Jia
- Department of Urological SurgeryRenmin HospitalHubei University of MedicineShiyanHubei Province442000China
| | - Xiu‐Xin Wang
- Department of Urological SurgeryRenmin HospitalHubei University of MedicineShiyanHubei Province442000China
| |
Collapse
|
26
|
Xiong DD, Lv J, Wei KL, Feng ZB, Chen JT, Liu KC, Chen G, Luo DZ. A nine-miRNA signature as a potential diagnostic marker for breast carcinoma: An integrated study of 1,110 cases. Oncol Rep 2017; 37:3297-3304. [PMID: 28440475 DOI: 10.3892/or.2017.5600] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/14/2016] [Indexed: 11/05/2022] Open
Abstract
Growing evidence indicates that microRNAs (miRNAs) play critical roles in the initiation and progression of breast carcinoma (BC) and are promising diagnostic biomarkers. In the present study, we aimed to identify a multi-marker miRNA pool with high diagnostic performance for BC. We collected miRNA expression profiles of BC samples and normal breast tissues from The Cancer Genome Atlas (TCGA) and screened differentially expressed miRNAs by conducting two‑sample t-tests and by calculating log2 fold-change (log2FC) ratios. Statistical significance was established at p<0.001 and |log2FC| >1. Then, we generated receiver operating characteristic (ROC) curves, calculated the area under the curve (AUC) with a 95% confidence interval (95% CI), and calculated the diagnostic sensitivity and specificity using MedCalc software. Additionally, we predicted the targets of candidate miRNAs using 10 online databases: TarBase, miRTarBase, TargetScan, TargetMiner, microRNA.org, RNA22, PicTar-vert, miRDB, PITA and PolymiRTS. Target genes that were predicted by at least four algorithms were chosen, and cooperative targets of multiple miRNAs were further selected for GO and KEGG pathway analyses through the DAVID online tool. Eventually, a total of 66 differentially expressed miRNAs were identified after miRNA expression profiles were analyzed in BC and normal breast samples. Of these, we selected nine dysregulated miRNAs as candidate diagnostic markers: seven upregulated miRNAs (hsa-miR-21, hsa-miR-96, hsa-miR-183, hsa-miR‑182, hsa-miR-141, hsa-miR-200a and hsa-miR-429) and two downregulated miRNAs (hsa-miR-139 and hsa-miR‑145). The ROC curve for the combination of these nine differently expressed miRNAs showed extremely high diagnostic accuracy, with an AUC of 0.995 (95% CI, 0.988‑0.999) and diagnostic sensitivity and specificity of 98.7 and 98.9%, respectively. In conclusion, the combination of these nine miRNAs significantly improved the accuracy of breast cancer diagnosis.
Collapse
Affiliation(s)
- Dan-Dan Xiong
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Jun Lv
- Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Kang-Lai Wei
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ji-Tian Chen
- Department of Pathology, People's Hospital of Ling Shan, Ling Shan, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ke-Cheng Liu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Dian-Zhong Luo
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| |
Collapse
|
27
|
Improving accuracy of RNA-based diagnosis and prognosis of oral cancer by using noninvasive methods. Oral Oncol 2017; 69:62-67. [PMID: 28559022 DOI: 10.1016/j.oraloncology.2017.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 03/23/2017] [Accepted: 04/01/2017] [Indexed: 12/13/2022]
Abstract
RNA-based diagnosis and prognosis of squamous cell carcinoma has been slow to come to the clinic. Improvements in RNA measurement, statistical evaluation, and sample preservation, along with increased sample numbers, have not made these methods reproducible enough to be used clinically. We propose that, in the case of squamous cell carcinoma of the oral cavity, a chief source of variability is sample dissection, which leads to variable amounts of stroma mixed in with tumor epithelium. This heterogeneity of the samples, which requires great care to avoid, makes it difficult to see changes in RNA levels specific to tumor cells. An evaluation of the data suggests that, paradoxically, brush biopsy samples of oral lesions may provide a more reproducible method than surgical acquisition of samples for miRNA measurement. The evidence also indicates that body fluid samples can show similar changes in miRNAs with oral squamous cell carcinoma (OSCC) as those seen in tumor brush biopsy samples - suggesting much of the miRNA in these samples is coming from the same source: tumor epithelium. We conclude that brush biopsy or body fluid samples may be superior to surgical samples in allowing miRNA-based diagnosis and prognosis of OSCC in that they feature a rapid method to obtain homogeneous tumor cells and/or RNA.
Collapse
|
28
|
Cao W, Liu JN, Liu Z, Wang X, Han ZG, Ji T, Chen WT, Zou X. A three-lncRNA signature derived from the Atlas of ncRNA in cancer (TANRIC) database predicts the survival of patients with head and neck squamous cell carcinoma. Oral Oncol 2017; 65:94-101. [PMID: 28109476 DOI: 10.1016/j.oraloncology.2016.12.017] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/12/2016] [Accepted: 12/17/2016] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Long non-coding RNAs (lncRNAs) have important biological functions and can be used as prognostic biomarkers in cancer. To identify a lncRNA prognostic signature for head and neck squamous cell carcinoma (HNSCC). METHOD We analysed RNA-seq data derived from the TANRIC database to identify a lncRNA prognostic signature model using the orthogonal partial least squares discrimination analysis (OPLS-DA) and 1.5-fold expression change criterion methods. The prognosis prediction model based on the lncRNA signatures and clinical parameters were evaluated using the 5-fold cross validation method. RESULTS A total of 84 out of 3199 lncRNAs were significantly associated with the survival of patients with HNSCC (log-rank test P<0.01). Using the OPLS-DA and 1.5-fold change selection criterion, 5 lncRNAs (KTN1-AS1, LINC00460, GUSBP11, LINC00923 and RP5-894A10.6) were further selected. The prediction power of each combination of the 5 lncRNAs was evaluated through the receiver operating characteristic (ROC) curve and a three-lncRNA panel (KTN1-AS1, LINC00460 and RP5-894A10.6) achieved the highest prognostic prediction power (AUC 0.68, 95% CI 0.60-0.76, P<0.0001) in the cohort. The patients were categorized into high- and low-risk groups based on their three-lncRNA profiles. Patients with high-risk scores had worse overall survival than those with low risk scores in the cohort (log-rank test P=0.0003). Multivariable Cox regression analyses showed that the lncRNA signature and tumour grade were independent prognostic factors for patients with HNSCC. CONCLUSIONS Our findings showed that the three-lncRNA signature might be a novel biomarker for the accurate prognosis prediction of patients with HNSCC.
Collapse
Affiliation(s)
- Wei Cao
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Jian-Nan Liu
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Zeqi Liu
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Xu Wang
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tong Ji
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.
| | - Wan-Tao Chen
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.
| | - Xin Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|