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Dong F, Yan J, Zhang X, Zhang Y, Liu D, Pan X, Xue L, Liu Y. Artificial intelligence-based predictive model for guidance on treatment strategy selection in oral and maxillofacial surgery. Heliyon 2024; 10:e35742. [PMID: 39170321 PMCID: PMC11336844 DOI: 10.1016/j.heliyon.2024.e35742] [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: 03/05/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024] Open
Abstract
Application of deep learning (DL) and machine learning (ML) is rapidly increasing in the medical field. DL is gaining significance for medical image analysis, particularly, in oral and maxillofacial surgeries. Owing to the ability to accurately identify and categorize both diseased and normal soft- and hard-tissue structures, DL has high application potential in the diagnosis and treatment of tumors and in orthognathic surgeries. Moreover, DL and ML can be used to develop prediction models that can aid surgeons to assess prognosis by analyzing the patient's medical history, imaging data, and surgical records, develop more effective treatment strategies, select appropriate surgical modalities, and evaluate the risk of postoperative complications. Such prediction models can play a crucial role in the selection of treatment strategies for oral and maxillofacial surgeries. Their practical application can improve the utilization of medical staff, increase the treatment accuracy and efficiency, reduce surgical risks, and provide an enhanced treatment experience to patients. However, DL and ML face limitations, such as data drift, unstable model results, and vulnerable social trust. With the advancement of social concepts and technologies, the use of these models in oral and maxillofacial surgery is anticipated to become more comprehensive and extensive.
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Affiliation(s)
- Fanqiao Dong
- School of Stomatology, China Medical University, Shenyang, China
| | - Jingjing Yan
- Hospital of Stomatology, China Medical University, Shenyang, China
| | - Xiyue Zhang
- School of Stomatology, China Medical University, Shenyang, China
| | - Yikun Zhang
- School of Stomatology, China Medical University, Shenyang, China
| | - Di Liu
- School of Stomatology, China Medical University, Shenyang, China
| | - Xiyun Pan
- School of Stomatology, China Medical University, Shenyang, China
| | - Lei Xue
- School of Stomatology, China Medical University, Shenyang, China
- Hospital of Stomatology, China Medical University, Shenyang, China
| | - Yu Liu
- First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
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Cai XJ, Peng CR, Zhang JY, Li XF, Wang X, Han Y, Zhang HY, Peng X, Li TJ. Mast Cell Infiltration and Subtype Promote Malignant Transformation of Oral Precancer and Progression of Oral Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:2203-2214. [PMID: 39087378 PMCID: PMC11339667 DOI: 10.1158/2767-9764.crc-24-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/28/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
The role of mast cell (MC), a common myeloid-derived immune cell, in the development of oral squamous cell carcinoma (OSCC) is unclear. The aim of this study was to investigate MC infiltration in oral precancer and oral cancer. The evaluation of immune cell infiltration and its association with prognosis in OSCC used RNA sequencing and multiple public datasets. Multiplex immunofluorescence was used to explore the infiltration of MC in the microenvironment of OSCC and oral precancer and the interaction with CD8+ cells. The role of MC in OSCC progression was verified by in vivo experiments. The resting MC infiltration was mainly present in oral precancer, whereas activated MC infiltration was significantly higher in OSCC. Activated MC was associated with malignant transformation of oral precancer and poor prognosis of OSCC. In vivo studies showed that MC promoted the growth of OSCC. The infiltration of activated MC was negatively correlated with the infiltration of CD8+ T cells. The subtype of MC containing tryptase without chymase (MCT) was significantly higher in OSCC compared with oral precancer and was associated with poor survival. Furthermore, spatial distance analysis revealed a greater distance between MCT and CD8+ cells, which was also linked to poor prognosis in OSCC. Cox regression analysis showed that MCT could be a potential diagnostic and prognostic biomarker. This study provides new insights into the role of MC in the immune microenvironment of OSCC. It might enhance the immunotherapeutic efficacy of OSCC by developing targeted therapies against MC. SIGNIFICANCE In this study, we investigated the role of mast cells (MC) in oral precancer and oral cancer and demonstrated that MCs are involved in oral cancer progression and may serve as a potential diagnostic and prognostic marker. It might improve the immunotherapeutic efficacy through developing targeted therapies against MCs.
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Affiliation(s)
- Xin-Jia Cai
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
| | - Chao-Ran Peng
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China.
| | - Jian-Yun Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China.
| | - Xue-Fen Li
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
| | - Xu Wang
- Department of Oral Medicine, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
| | - Ying Han
- Department of Oral Medicine, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
| | - He-Yu Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
| | - Xin Peng
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
| | - Tie-Jun Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Beijing, China.
- National Center for Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, National Engineering Research Center of Oral Biomaterials and Digital Medical Devices, Beijing, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, China.
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3
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Umapathy VR, Natarajan PM, Swamikannu B. Molecular and Therapeutic Roles of Non-Coding RNAs in Oral Cancer-A Review. Molecules 2024; 29:2402. [PMID: 38792263 PMCID: PMC11123887 DOI: 10.3390/molecules29102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Oral cancer (OC) is among the most common malignancies in the world. Despite advances in therapy, the worst-case scenario for OC remains metastasis, with a 50% survival rate. Therefore, it is critical to comprehend the pathophysiology of the condition and to create diagnostic and treatment plans for OC. The development of high-throughput genome sequencing has revealed that over 90% of the human genome encodes non-coding transcripts, or transcripts that do not code for any proteins. This paper describes the function of these different kinds of non-coding RNAs (ncRNAs) in OC as well as their intriguing therapeutic potential. The onset and development of OC, as well as treatment resistance, are linked to dysregulated ncRNA expression. These ncRNAs' potentially significant roles in diagnosis and prognosis have been suggested by their differing expression in blood or saliva. We have outlined every promising feature of ncRNAs in the treatment of OC in this study.
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Affiliation(s)
- Vidhya Rekha Umapathy
- Department of Public Health Dentistry, Dr. M.G.R. Educational and Research Institute, Thai Moogambigai Dental College and Hospital, Chennai 600107, Tamil Nadu, India
| | - Prabhu Manickam Natarajan
- Department of Clinical Sciences, Centre of Medical and Bio-Allied Health Sciences and Research Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Bhuminathan Swamikannu
- Department of Prosthodontics, Sree Balaji Dental College and Hospital, Pallikaranai, BIHER, Chennai 600100, Tamil Nadu, India;
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Brennan K, Espín-Pérez A, Chang S, Bedi N, Saumyaa S, Shin JH, Plevritis SK, Gevaert O, Sunwoo JB, Gentles AJ. Loss of p53-DREAM-mediated repression of cell cycle genes as a driver of lymph node metastasis in head and neck cancer. Genome Med 2023; 15:98. [PMID: 37978395 PMCID: PMC10656821 DOI: 10.1186/s13073-023-01236-w] [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: 01/14/2023] [Accepted: 09/20/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The prognosis for patients with head and neck cancer (HNC) is poor and has improved little in recent decades, partially due to lack of therapeutic options. To identify effective therapeutic targets, we sought to identify molecular pathways that drive metastasis and HNC progression, through large-scale systematic analyses of transcriptomic data. METHODS We performed meta-analysis across 29 gene expression studies including 2074 primary HNC biopsies to identify genes and transcriptional pathways associated with survival and lymph node metastasis (LNM). To understand the biological roles of these genes in HNC, we identified their associated cancer pathways, as well as the cell types that express them within HNC tumor microenvironments, by integrating single-cell RNA-seq and bulk RNA-seq from sorted cell populations. RESULTS Patient survival-associated genes were heterogenous and included drivers of diverse tumor biological processes: these included tumor-intrinsic processes such as epithelial dedifferentiation and epithelial to mesenchymal transition, as well as tumor microenvironmental factors such as T cell-mediated immunity and cancer-associated fibroblast activity. Unexpectedly, LNM-associated genes were almost universally associated with epithelial dedifferentiation within malignant cells. Genes negatively associated with LNM consisted of regulators of squamous epithelial differentiation that are expressed within well-differentiated malignant cells, while those positively associated with LNM represented cell cycle regulators that are normally repressed by the p53-DREAM pathway. These pro-LNM genes are overexpressed in proliferating malignant cells of TP53 mutated and HPV + ve HNCs and are strongly associated with stemness, suggesting that they represent markers of pre-metastatic cancer stem-like cells. LNM-associated genes are deregulated in high-grade oral precancerous lesions, and deregulated further in primary HNCs with advancing tumor grade and deregulated further still in lymph node metastases. CONCLUSIONS In HNC, patient survival is affected by multiple biological processes and is strongly influenced by the tumor immune and stromal microenvironments. In contrast, LNM appears to be driven primarily by malignant cell plasticity, characterized by epithelial dedifferentiation coupled with EMT-independent proliferation and stemness. Our findings postulate that LNM is initially caused by loss of p53-DREAM-mediated repression of cell cycle genes during early tumorigenesis.
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Affiliation(s)
- Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Almudena Espín-Pérez
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Serena Chang
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Nikita Bedi
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Saumyaa Saumyaa
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - June Ho Shin
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - John B Sunwoo
- Department of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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5
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Shang Q, Peng J, Jiang Y, Qing M, Zhou Y, Xu H, Chen Q. SNAI2 promotes the malignant transformation of oral leukoplakia by modulating p-EMT. Oral Dis 2023; 29:3232-3242. [PMID: 35894087 DOI: 10.1111/odi.14321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Snail family transcriptional repressor 2 (SNAI2) is a key regulator of partial epithelial-mesenchymal transition (p-EMT) and is associated with tumorigenesis. Whether SNAI2 promotes oral leukoplakia (OLK) malignant transformation by modulating p-EMT is unclear. MATERIALS AND METHODS This study utilized two clinical datasets (GSE26549 and GSE85195) from the Gene Expression Omnibus database, cytological experiments, and a 4-nitroquinoline 1-oxide-induced mice model to explore the role of SNAI2 in OLK malignant transformation. RESULTS The clinical cohort found SNAI2, as a risk factor (HR = 2.50, 95% CI: 1.08-5.79, p = 0.033), could promote OLK malignant transformation (p = 0.012). Cytological experiments indicated that SNAI2 overexpression promoted DOK cell proliferation, invasion, migration, and increase the protein expression of p-EMT relative signatures, whereas SNAI2 silencing has opposite effects. Furthermore, the mice model and clinical datasets demonstrated the expression of SNAI2 and p-EMT relative signatures were increased with OLK malignant transformation. And SNAI2 was strongly correlated with p-EMT. Besides, co-expressed genes of SNAI2 were also enriched in p-EMT relative biological processes and signaling pathways. CONCLUSIONS p-EMT plays a significant role in promoting the OLK malignant transformation. As an important regulator of p-EMT, SNAI2 could be a target to block the OLK malignant transformation.
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Affiliation(s)
- Qianhui Shang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Jiakuan Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Yuchen Jiang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Maofeng Qing
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Hao Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Research Unit of Oral Carcinogenesis and Management, Chinese Academy of Medical Sciences, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
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Khan MM, Frustino J, Villa A, Nguyen BC, Woo SB, Johnson WE, Varelas X, Kukuruzinska M, Monti S. Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer. Hum Genomics 2023; 17:72. [PMID: 37542347 PMCID: PMC10403884 DOI: 10.1186/s40246-023-00519-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
Head and neck cancers are a complex malignancy comprising multiple anatomical sites, with cancer of the oral cavity ranking among the deadliest and the most disfiguring cancers globally. Oral cancer (OC) constitutes a subset of head and neck cancer cases, presenting primarily as tobacco- and alcohol-associated oral squamous cell carcinoma (OSCC), with a 5-year survival rate of ~ 65%, partly due to the lack of early detection and effective treatments. OSCC arises from premalignant lesions (PMLs) in the oral cavity through a multi-step series of clinical and histopathological stages, including varying degrees of epithelial dysplasia. To gain insights into the molecular mechanisms associated with the progression of PMLs to OSCC, we profiled the whole transcriptome of 66 human PMLs comprising leukoplakia with dysplasia and hyperkeratosis non-reactive (HkNR) pathologies, alongside healthy controls and OSCC. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome toward PML evolution to OSCC. Collectively, this study reveals molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage.
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Affiliation(s)
- Mohammed Muzamil Khan
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, 75 E. Newton St. E609, Boston, MA, 02118, USA
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
| | - Jennifer Frustino
- Department of Dentistry/Oral Oncology & Maxillofacial Prosthetics, Erie County Medical Center, Buffalo, NY, USA
| | - Alessandro Villa
- Oral Medicine, Oral Oncology and Dentistry, Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bach-Cuc Nguyen
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, 700 Albany Street, W-201, Boston, MA, 02118, USA
| | - Sook-Bin Woo
- Division of Oral Medicine and Dentistry, Brigham and Women's Hospital and Harvard University, Boston, MA, USA
| | - William Evan Johnson
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Maria Kukuruzinska
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, 700 Albany Street, W-201, Boston, MA, 02118, USA.
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, 75 E. Newton St. E609, Boston, MA, 02118, USA.
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
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Kabzinski J, Kucharska-Lusina A, Majsterek I. RNA-Based Liquid Biopsy in Head and Neck Cancer. Cells 2023; 12:1916. [PMID: 37508579 PMCID: PMC10377854 DOI: 10.3390/cells12141916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.
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Affiliation(s)
- Jacek Kabzinski
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
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8
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Lai TY, Ko YC, Chen YL, Lin SF. The Way to Malignant Transformation: Can Epigenetic Alterations Be Used to Diagnose Early-Stage Head and Neck Cancer? Biomedicines 2023; 11:1717. [PMID: 37371812 PMCID: PMC10296077 DOI: 10.3390/biomedicines11061717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Identifying and treating tumors early is the key to secondary prevention in cancer control. At present, prevention of oral cancer is still challenging because the molecular drivers responsible for malignant transformation of the 11 clinically defined oral potentially malignant disorders are still unknown. In this review, we focused on studies that elucidate the epigenetic alterations demarcating malignant and nonmalignant epigenomes and prioritized findings from clinical samples. Head and neck included, the genomes of many cancer types are largely hypomethylated and accompanied by focal hypermethylation on certain specific regions. We revisited prior studies that demonstrated that sufficient uptake of folate, the primary dietary methyl donor, is associated with oral cancer reduction. As epigenetically driven phenotypic plasticity, a newly recognized hallmark of cancer, has been linked to tumor initiation, cell fate determination, and drug resistance, we discussed prior findings that might be associated with this hallmark, including gene clusters (11q13.3, 19q13.43, 20q11.2, 22q11-13) with great potential for oral cancer biomarkers, and successful examples in screening early-stage nasopharyngeal carcinoma. Although one-size-fits-all approaches have been shown to be ineffective in most cancer therapies, the rapid development of epigenome sequencing methods raises the possibility that this nonmutagenic approach may be an exception. Only time will tell.
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Affiliation(s)
- Ting-Yu Lai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan;
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan; (Y.-C.K.); (Y.-L.C.)
| | - Ying-Chieh Ko
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan; (Y.-C.K.); (Y.-L.C.)
| | - Yu-Lian Chen
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan; (Y.-C.K.); (Y.-L.C.)
| | - Su-Fang Lin
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan; (Y.-C.K.); (Y.-L.C.)
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9
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Khan MM, Frustino J, Villa A, Nguyen BC, Woo SB, Johnson WE, Varelas X, Kukuruzinska M, Monti S. Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534064. [PMID: 36993637 PMCID: PMC10055367 DOI: 10.1101/2023.03.24.534064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
UNLABELLED Head and neck cancers are a complex malignancy comprising multiple anatomical sites, with cancer of the oral cavity ranking among the deadliest and most disfiguring cancers globally. Oral cancer (OC) constitutes a subset of head and neck cancer cases, presenting primarily as tobacco-and alcohol-associated oral squamous cell carcinoma (OSCC), with a 5-year survival rate of ∼65%, partly due to the lack of early detection and effective treatments. OSCC arises from premalignant lesions (PMLs) in the oral cavity through a multi-step series of clinical and histopathological stages, including varying degrees of epithelial dysplasia. To gain insights into the molecular mechanisms associated with the progression of PMLs to OSCC, we profiled the whole transcriptome of 66 human PMLs comprising leukoplakia with dysplasia and hyperkeratosis non-reactive (HkNR) pathologies, alongside healthy controls and OSCC. Our data revealed that PMLs were enriched in gene signatures associated with cellular plasticity, such as partial EMT (p-EMT) phenotypes, and with immune response. Integrated analyses of the host transcriptome and microbiome further highlighted a significant association between differential microbial abundance and PML pathway activity, suggesting a contribution of the oral microbiome towards PML evolution to OSCC. Collectively, this study reveals molecular processes associated with PML progression that may help early diagnosis and disease interception at an early stage. AUTHOR SUMMARY Patients harboring oral premalignant lesions (PMLs) have an increased risk of developing oral squamous cell carcinoma (OSCC), but the underlying mechanisms driving transformation of PMLs to OSCC remain poorly understood. In this study, Khan et al., analyzed a newly generated dataset of gene expression and microbial profiles of oral tissues from patients diagnosed with PMLs from differing histopathological groups, including hyperkeratosis not reactive ( HkNR ) and dysplasia, comparing these profiles with OSCC and normal oral mucosa. Significant similarities between PMLs and OSCC were observed, with PMLs manifesting several cancer hallmarks, including oncogenic and immune pathways. The study also demonstrates associations between the abundance of multiple microbial species and PML groups, suggesting a potential contribution of the oral microbiome to the early stages of OSCC development. The study offers insights into the nature of the molecular, cellular and microbial heterogeneity of oral PMLs and suggests that molecular and clinical refinement of PMLs may provide opportunities for early disease detection and interception.
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Affiliation(s)
- Mohammed Muzamil Khan
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
| | - Jennifer Frustino
- Department of Dentistry/Oral Oncology & Maxillofacial Prosthetics, Erie County Medical Center, Buffalo, NY, USA
| | - Alessandro Villa
- Oral Medicine, Oral Oncology and Dentistry, Miami Cancer Institute, Baptist Health South Florida, Miami, FL, and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bach-Cuc Nguyen
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, MA, USA
| | - Sook-Bin Woo
- Division of Oral Medicine and Dentistry, Brigham and Women’s Hospital and Harvard University, Boston, MA, USA
| | - William Evan Johnson
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Maria Kukuruzinska
- Department of Translational Dental Medicine, Boston University School of Dental Medicine, Boston, MA, USA
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Bioinformatics Graduate Program, Boston University, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
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10
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Role of E2F transcription factor in Oral cancer: Recent Insight and Advancements. Semin Cancer Biol 2023; 92:28-41. [PMID: 36924812 DOI: 10.1016/j.semcancer.2023.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023]
Abstract
The family of mammalian E2F transcription factors (E2Fs) comprise of 8 members (E2F1-E2F8) classified as activators (E2F1-E2F3) and repressors (E2F4-E2F8) primarily regulating the expression of several genes related to cell proliferation, apoptosis and differentiation, mainly in a cell cycle-dependent manner. E2F activity is frequently controlled via the retinoblastoma protein (pRb), cyclins, p53 and the ubiquitin-proteasome pathway. Additionally, genetic or epigenetic changes result in the deregulation of E2F family genes expression altering S phase entry and apoptosis, an important hallmark for the onset and development of cancer. Although studies reveal E2Fs to be involved in several human malignancies, the mechanisms underlying the role of E2Fs in oral cancer lies nascent and needs further investigations. This review focuses on the role of E2Fs in oral cancer and the etiological factors regulating E2Fs activity, which in turn transcriptionally control the expression of their target genes, thus contributing to cell proliferation, metastasis, and drug/therapy resistance. Further, we will discuss therapeutic strategies for E2Fs, which may prevent oral tumor growth, metastasis, and drug resistance.
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11
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Tapak L, Ghasemi MK, Afshar S, Mahjub H, Soltanian A, Khotanlou H. Identification of gene profiles related to the development of oral cancer using a deep learning technique. BMC Med Genomics 2023; 16:35. [PMID: 36849997 PMCID: PMC9972685 DOI: 10.1186/s12920-023-01462-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 02/15/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Oral cancer (OC) is a debilitating disease that can affect the quality of life of these patients adversely. Oral premalignant lesion patients have a high risk of developing OC. Therefore, identifying robust survival subgroups among them may significantly improve patient therapy and care. This study aimed to identify prognostic biomarkers that predict the time-to-development of OC and survival stratification for patients using state-of-the-art machine learning and deep learning. METHODS Gene expression profiles (29,096 probes) related to 86 patients from the GSE26549 dataset from the GEO repository were used. An autoencoder deep learning neural network model was used to extract features. We also used a univariate Cox regression model to select significant features obtained from the deep learning method (P < 0.05). High-risk and low-risk groups were then identified using a hierarchical clustering technique based on 100 encoded features (the number of units of the encoding layer, i.e., bottleneck of the network) from autoencoder and selected by Cox proportional hazards model and a supervised random forest (RF) classifier was used to identify gene profiles related to subtypes of OC from the original 29,096 probes. RESULTS Among 100 encoded features extracted by autoencoder, seventy features were significantly related to time-to-OC-development, based on the univariate Cox model, which was used as the inputs for the clustering of patients. Two survival risk groups were identified (P value of log-rank test = 0.003) and were used as the labels for supervised classification. The overall accuracy of the RF classifier was 0.916 over the test set, yielded 21 top genes (FUT8-DDR2-ATM-CD247-ETS1-ZEB2-COL5A2-GMAP7-CDH1-COL11A2-COL3A1-AHR-COL2A1-CHORDC1-PTP4A3-COL1A2-CCR2-PDGFRB-COL1A1-FERMT2-PIK3CB) associated with time to developing OC, selected among the original 29,096 probes. CONCLUSIONS Using deep learning, our study identified prominent transcriptional biomarkers in determining high-risk patients for developing oral cancer, which may be prognostic as significant targets for OC therapy. The identified genes may serve as potential targets for oral cancer chemoprevention. Additional validation of these biomarkers in experimental prospective and retrospective studies will launch them in OC clinics.
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Affiliation(s)
- Leili Tapak
- Department of Biostatistics, School of Public Health and Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mohammad Kazem Ghasemi
- Department of Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Saeid Afshar
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Hossein Mahjub
- Department of Biostatistics, School of Public Health and Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Alireza Soltanian
- Department of Biostatistics, School of Public Health and Modeling of Noncommunicable Diseases Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hassan Khotanlou
- Department of Computer Engineering, Bu-Ali Sina University, Hamadan, Iran
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12
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Screening for Biomarkers for Progression from Oral Leukoplakia to Oral Squamous Cell Carcinoma and Evaluation of Diagnostic Efficacy by Multiple Machine Learning Algorithms. Cancers (Basel) 2022; 14:cancers14235808. [PMID: 36497288 PMCID: PMC9738227 DOI: 10.3390/cancers14235808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
The aim of the study is to identify key genes during the progression from oral leukoplakia (OL) to oral squamous cell carcinoma (OSCC) and predict effective diagnoses. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were performed to identify seven genes associated with the progression from OL to OSCC. Twelve machine learning algorithms including k-nearest neighbor (KNN), neural network (NNet), and extreme gradient boosting (XGBoost) were used to construct multi-gene models, which revealed that each model had good diagnostic efficacy. The functional mechanism or the pathways associated with these genes were evaluated using enrichment analysis, subtype clustering, and immune infiltration analysis. The enrichment analysis revealed that the genes enriched were associated with the cell cycle, cell division, and intracellular energy metabolism. The immunoassay results revealed that the genes primarily affected the infiltration of proliferating T cells and macrophage polarization. Finally, a nomogram and Kaplan-Meier survival analysis were used to predict the prognostic efficacy of key genes in OSCC patients. The results showed that genes could predict the prognosis of the patients, and patients in the high-risk group had a poor prognosis. Our study identified that the seven key genes, including DHX9, BCL2L12, RAD51, MELK, CDC6, ANLN, and KIF4A, were associated with the progression from OL to OSCC. These genes had good diagnostic efficacy and could be used as potential biomarkers for the prognosis of OSCC patients.
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13
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Taherkhani A, Dehto SS, Jamshidi S, Shojaei S. Pathogenesis and prognosis of primary oral squamous cell carcinoma based on microRNAs target genes: a systems biology approach. Genomics Inform 2022; 20:e27. [PMID: 36239104 PMCID: PMC9576470 DOI: 10.5808/gi.22038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/30/2022] [Indexed: 11/20/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most prevalent head and neck malignancy, with frequent cervical lymph-node metastasis, leading to a poor prognosis in OSCC patients. The present study aimed to identify potential markers, including microRNAs (miRNAs) and genes, significantly involved in the etiology of early-stage OSCC. Additionally, the main OSCC's dysregulated Gene Ontology annotations and significant signaling pathways were identified. The dataset GSE45238 underwent multivariate statistical analysis in order to distinguish primary OSCC tissues from healthy oral epithelium. Differentially expressed miRNAs (DEMs) with the criteria of p-value < 0.001 and |Log2 fold change| > 1.585 were identified in the two groups, and subsequently, validated targets of DEMs were identified. A protein interaction map was constructed, hub genes were identified, significant modules within the network were illustrated, and significant pathways and biological processes associated with the clusters were demonstrated. Using the GEPI2 database, the hub genes' predictive function was assessed. Compared to the healthy controls, main OSCC had a total of 23 DEMs. In patients with head and neck squamous cell carcinoma (HNSCC), upregulation of CALM1, CYCS, THBS1, MYC, GATA6, and SPRED3 was strongly associated with a poor prognosis. In HNSCC patients, overexpression of PIK3R3, GIGYF1, and BCL2L11 was substantially correlated with a good prognosis. Besides, “proteoglycans in cancer” was the most significant pathway enriched in the primary OSCC. The present study results revealed more possible mechanisms mediating primary OSCC and may be useful in the prognosis of the patients with early-stage OSCC.
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Affiliation(s)
- Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahab Shahmoradi Dehto
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shokoofeh Jamshidi
- Dental Research Center, Department of Oral and Maxillofacial Pathology, School of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Setareh Shojaei
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Hamadan University of Medical Sciences, Hamadan, Iran
- Corresponding author E-mail:
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14
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Gan CP, Lee BKB, Lau SH, Kallarakkal TG, Zaini ZM, Lye BKW, Zain RB, Sathasivam HP, Yeong JPS, Savelyeva N, Thomas G, Ottensmeier CH, Ariffin H, Cheong SC, Lim KP. Transcriptional analysis highlights three distinct immune profiles of high-risk oral epithelial dysplasia. Front Immunol 2022; 13:954567. [PMID: 36119104 PMCID: PMC9479061 DOI: 10.3389/fimmu.2022.954567] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/12/2022] [Indexed: 11/20/2022] Open
Abstract
Oral potentially malignant disorders (OPMD) are precursors of oral squamous cell carcinoma (OSCC), and the presence of oral epithelial dysplasia (OED) in OPMD confers an increased risk of malignant transformation. Emerging evidence has indicated a role for the immune system in OPMD disease progression; however, the underlying immune mechanisms remain elusive. In this study, we used immune signatures established from cancer to delineate the immune profiles of moderate and severe OED, which are considered high-risk OPMD. We demonstrated that moderate and severe OEDs exhibit high lymphocyte infiltration and upregulation of genes involved in both immune surveillance (major histocompatibility complex-I, T cells, B cells and cytolytic activity) and immune suppression (immune checkpoints, T regulatory cells, and tumor-associated macrophages). Notably, we identified three distinct subtypes of moderate and severe OED: immune cytotoxic, non-cytotoxic and non-immune reactive. Active immune surveillance is present in the immune cytotoxic subtype, whereas the non-cytotoxic subtype lacks CD8 immune cytotoxic response. The non-immune reactive subtype showed upregulation of genes involved in the stromal microenvironment and cell cycle. The lack of T cell infiltration and activation in the non-immune reactive subtype is due to the dysregulation of CTNNB1, PTEN and JAK2. This work suggests that moderate and severe OED that harbor the non-cytotoxic or non-immune reactive subtype are likely to progress to cancer. Overall, we showed that distinct immune responses are present in high-risk OPMD, and revealed targetable pathways that could lead to potential new approaches for non-surgical management of OED.
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Affiliation(s)
- Chai Phei Gan
- Cancer Immunology and Immunotherapy Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- Department of Paediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Bernard Kok Bang Lee
- Cancer Immunology and Immunotherapy Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Shin Hin Lau
- Cancer Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Malaysia
| | - Thomas George Kallarakkal
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Zuraiza Mohamad Zaini
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Bryan Kit Weng Lye
- Cancer Immunology and Immunotherapy Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Rosnah Binti Zain
- Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
- Faculty of Dentistry, Malaysian Allied Health Sciences Academy (MAHSA) University, Jenjarom, Malaysia
| | - Hans Prakash Sathasivam
- Cancer Research Center, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Malaysia
| | - Joe Poh Sheng Yeong
- Integrative Biology for Theranostics, Institute of Molecular Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Natalia Savelyeva
- Head and Neck Center, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Gareth Thomas
- Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | - Christian H. Ottensmeier
- Head and Neck Center, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | - Hany Ariffin
- Department of Paediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sok Ching Cheong
- Cancer Immunology and Immunotherapy Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- Department of Oral and Maxillofacial Clinical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Kue Peng Lim
- Cancer Immunology and Immunotherapy Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
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15
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Schalk D, Bischl B, Rügamer D. Accelerated Componentwise Gradient Boosting using Efficient Data Representation and Momentum-based Optimization. J Comput Graph Stat 2022. [DOI: 10.1080/10618600.2022.2116446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Evaluation Criteria for Chromosome Instability Detection by FISH to Predict Malignant Progression in Premalignant Glottic Laryngeal Lesions. Cancers (Basel) 2022; 14:cancers14133260. [PMID: 35805032 PMCID: PMC9265082 DOI: 10.3390/cancers14133260] [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: 05/31/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 01/27/2023] Open
Abstract
Background: The definition of objective, clinically applicable evaluation criteria for FISH 1c/7c in laryngeal precursor lesions for the detection of chromosome instability (CI). Copy Number Variations (CNV) for chromosomes 1 and 7 reflect the general ploidy status of premalignant head and neck lesions and can therefore be used as a marker for CI. Methods: We performed dual-target FISH for chromosomes 1 and 7 centromeres on 4 µm formalin-fixed, paraffin-embedded tissue sections of 87 laryngeal premalignancies to detect CNVs. Thirty-five normal head and neck squamous cell samples were used as a control. First, the chromosome 7:1 ratio (CR) was evaluated per lesion. The normal range of CRs (≥0.84 ≤ 1.16) was based on the mean CR +/− 3 x SD found in the normal population. Second, the percentage of aberrant nuclei, harboring > 2 chromosomes of chromosome 1 and/or 7 (PAN), was established (cut-off value for abnormal PAN ≥ 10%). Results: PAN showed a stronger correlation with malignant progression than CR (resp. OR 5.6, p = 0.001 and OR 3.8, p = 0.009). PAN combined with histopathology resulted in a prognostic model with an area under the ROC curve (AUC) of 0.75 (s.e. 0.061, sensitivity 71%, specificity 70%). Conclusions: evaluation criteria for FISH 1c/7c based on PAN ≥ 10% provide the best prognostic information on the risk of malignant progression of premalignant laryngeal lesions as compared with criteria based on the CR. FISH 1c/7c detection can be applied in combination with histopathological assessment.
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17
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Cheung VKY, Hulme K, Schifter M, Palme C, Low THH, Clark J, Gupta R. Oral Epithelial Dysplasia: A Review of Diagnostic Criteria for Anatomic Pathologists. Adv Anat Pathol 2022; 29:227-240. [PMID: 35435865 DOI: 10.1097/pap.0000000000000343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Oral epithelial dysplasia (OED) represents a spectrum of histologic changes in the oral cavity mucosa that has the potential to transform into oral squamous cell carcinoma. Predicting the risk of malignant transformation is predominantly based on clinicopathologic correlation, histologic examination and grading. OED often poses a diagnostic challenge, primarily due to its histologic mimics and a large number of terminologies used in the literature. The grading system for OED is also fraught with significant interobserver variability. This review summarizes the essential clinical and histopathologic features of OED and its mimics. Practical preanalytical, analytical, and postanalytical considerations for anatomic pathologists are discussed to improve the diagnostic accuracy and increase the reproducibility in the grading of OED.
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Affiliation(s)
- Veronica K Y Cheung
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital
- Faculty of Medicine and Health, Sydney Medical School
| | - Katherine Hulme
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital
| | - Mark Schifter
- Westmead Centre for Oral Health, Westmead Hospital, a Teaching Hospital of the Sydney Dental School, Faculty of Medicine and Health, University of Sydney
- The Skin Hospital, Darlinghurst (Sydney)
- Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse
| | - Carsten Palme
- Faculty of Medicine and Health, Sydney Medical School
- Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse
| | - Tsu-Hui Hubert Low
- Faculty of Medicine and Health, Sydney Medical School
- Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse
- Department of Otolaryngology - Head & Neck Surgery, Faculty of Medicine and Health Sciences, Macquarie University
| | - Jonathan Clark
- Faculty of Medicine and Health, Sydney Medical School
- Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse
- Institute of Academic Surgery, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Ruta Gupta
- Department of Tissue Pathology and Diagnostic Oncology, NSW Health Pathology, Royal Prince Alfred Hospital
- Faculty of Medicine and Health, Sydney Medical School
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18
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Molecular Signatures of Tumour and Its Microenvironment for Precise Quantitative Diagnosis of Oral Squamous Cell Carcinoma: An International Multi-Cohort Diagnostic Validation Study. Cancers (Basel) 2022; 14:cancers14061389. [PMID: 35326543 PMCID: PMC8945999 DOI: 10.3390/cancers14061389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Heterogeneity in oral potentially malignant disorder (OPMD) poses a problem for accurate prognosis that impacts on treatment strategy and patient outcome. A holistic assessment based on gene expression signatures from both the tumour cells and their microenvironment is necessary to provide a more precise prognostic assessment than just tumour cell signatures alone. METHODS We reformulated our previously established multigene qPCR test, quantitative Malignancy Index Diagnostic System (qMIDS) with new genes involved in matrix/stroma and immune modulation of the tumour microenvironment. An algorithm calculates and converts a panel of 16 gene mRNA expression levels into a qMIDS index to quantify risk of malignancy for each sample. RESULTS The new qMIDSV2 assay was validated in a UK oral squamous cell carcinoma (OSCC) cohort (n = 282) of margin and tumour core samples demonstrating significantly better diagnostic performance (AUC = 0.945) compared to previous qMIDSV1 (AUC = 0.759). Performance of qMIDSV2 were independently validated in Chinese (n = 35; AUC = 0.928) and Indian (n = 95; AUC = 0.932) OSCC cohorts. Further, 5-year retrospective analysis on an Indian dysplastic lesion cohort (n = 30) showed that qMIDSV2 was able to significantly differentiate between lesions without transformation and those with malignant transformation. CONCLUSIONS This study validated a novel multi-gene qPCR test on a total of 535 tissue specimens from UK, China and India, demonstrating a rapid minimally invasive method that has a potential application for dysplasia risk stratification. Further study is required to establish if qMIDSV2 could be used to improve OPMD patient management, guide treatment strategy and reduce oral cancer burden.
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19
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Identification of Biomarkers Associated with Cancerous Change in Oral Leukoplakia Based on Integrated Transcriptome Analysis. JOURNAL OF ONCOLOGY 2022; 2022:4599305. [PMID: 35096060 PMCID: PMC8791753 DOI: 10.1155/2022/4599305] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/04/2022] [Indexed: 12/21/2022]
Abstract
Objective Oral leukoplakia (OLK) is the most common precancerous lesion in the oral cavity. This study aimed to explore key biomarkers for monitoring OLK for early diagnosis of oral squamous cell carcinoma (OSCC) and screen small-molecule drugs for the prevention of OSCC. Method The Gene Expression Omnibus (GEO) database was explored to extract two microarray datasets, namely, GSE85195 and GSE25099. The data of the normal group, OLK group, and OSCC group were analyzed by weighted gene coexpression network analysis (WGCNA) to identify the most significant gene module and differentially expressed genes (DEGs). The intersection genes were extracted as the key genes of OLK carcinogenesis. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed in the module. Connectivity Map and molecular docking were used to screen small-molecule drugs. The diagnostic values of four key genes were identified and verified in the GSE26549 dataset. Results WGCNA obtained the red module (r = −0.91, p < 0.05) with the strongest correlation with cancerous phenotype. GO enrichment analysis showed 60 pathways, including 28 biological processes, 11 cell components, and 21 molecular functions, and KEGG enrichment analysis showed 4 pathways (p < 0.05). In the differential expression analysis, there was no intersection between the upregulated genes and the red module genes. However, the intersection of the downregulated genes and the red module genes yielded 4 key genes: dopachrome tautomerase (DCT), keratin 3 (KRT3), keratin 76 (KRT76), and FAM3 metabolic regulation signal molecule B (FAM3B). The area under the curve of the diagnostic model constructed by these four genes was 0.963 (CI = 0.913–1.000). The sensitivity was 0.933, and the specificity was 0.923. The diagnostic model was successfully verified in GSE26549 (AUC = 0.745, CI = 0.638–0.851). Compared with the diagnostic models of the previous studies, the diagnostic efficiency of this model was the highest. The small-molecule drugs, selumetinib and benidipine, were selected according to the gene expression profile and showed binding activity when docking with the above molecules. Conclusions This study provides new targets and drugs for OLK. These targets could be used as the key diagnostic molecules for long-term follow-up of OLK. The small-molecule drugs selumetinib and benidipine could be used for the prevention and treatment of OSCC.
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20
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Cai X, Zhang H, Li T. The role of SPP1 as a prognostic biomarker and therapeutic target in head and neck squamous cell carcinoma. Int J Oral Maxillofac Surg 2021; 51:732-741. [PMID: 34489157 DOI: 10.1016/j.ijom.2021.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/05/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies and has a low 5-year survival rate. Mounting evidence suggests that oral potentially malignant disorders, such as oral leukoplakia (OLK), may progress to HNSCC. Given that OLK and HNSCC are often insidious and asymptomatic, the identification of markers of OLK malignant transformation and therapeutic targets in HNSCC is critical. Using various online tools and publicly available gene expression datasets, the secreted phosphoprotein 1 gene (SPP1) was identified as a significant differentially expressed gene among OLK, HNSCC, and non-cancerous tissues. SPP1 mRNA levels were elevated in HNSCC tissues and were associated with cancer stage, tumor grade, and human papillomavirus infection status. High SPP1 mRNA levels were correlated with poor overall survival of HNSCC patients. In contrast, SPP1 mutations were not significantly associated with overall survival, although their frequency in HNSCC was very low (0.6%). Furthermore, SPP1 expression levels in HNSCC were positively correlated with the infiltration of CD4+ cells, macrophages, neutrophils, and dendritic cells. The study results suggest that SPP1 may represent a diagnostic and prognostic biomarker, as well as a potential therapeutic target in HNSCC.
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Affiliation(s)
- X Cai
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Haidian District, Beijing, People's Republic of China; Research Unit of Precision Pathological Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, People's Republic of China
| | - H Zhang
- Research Unit of Precision Pathological Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, People's Republic of China; Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China.
| | - T Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, Haidian District, Beijing, People's Republic of China; Research Unit of Precision Pathological Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, People's Republic of China.
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21
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Spirko-Burns L, Devarajan K. Supervised Dimension Reduction for Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2032-2044. [PMID: 31940547 DOI: 10.1109/tcbb.2020.2965934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The past two decades have witnessed significant advances in high-throughput "omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive "omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential time-varying effects of features, and methods for handling them have been lacking. In this paper, we propose supervised methods for feature selection and survival prediction that simultaneously deal with both issues. Our approach utilizes continuum power regression (CPR) - a framework that includes a variety of regression methods - in conjunction with the parametric or semi-parametric accelerated failure time (AFT) model. Both CPR and AFT fall within the linear models framework and, unlike black-box models, the proposed prognostic index has a simple yet useful interpretation. We demonstrate the utility of our methods using simulated and publicly available cancer genomics data.
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22
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Odell E, Kujan O, Warnakulasuriya S, Sloan P. Oral epithelial dysplasia: Recognition, grading and clinical significance. Oral Dis 2021; 27:1947-1976. [PMID: 34418233 DOI: 10.1111/odi.13993] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/14/2021] [Accepted: 07/31/2021] [Indexed: 12/29/2022]
Abstract
Histopathological grading of epithelial dysplasia remains the principal laboratory method for assessing the risk of malignant transformation in oral potentially malignant disorders (OPMDs). Current views on the molecular pathogenesis and histological interpretation of the features of epithelial dysplasia are described, and the use of grading systems for epithelial dysplasia is discussed. Changes to the current 2017 WHO criteria for diagnosis are proposed with emphasis on the architectural features of epithelial dysplasia. The predictive values of three-grade and binary systems are summarised, and categories of epithelial dysplasia are reviewed, including lichenoid and verrucous lesions, keratosis of unknown significance, HPV-associated dysplasia, differentiated and basaloid epithelial dysplasia. The implications of finding epithelial dysplasia in an oral biopsy for clinical management are discussed from the pathologists' viewpoint.
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Affiliation(s)
- Edward Odell
- King's College London and Head and Neck Pathology Guy's Hospital, London, UK
| | - Omar Kujan
- UWA Dental School, The University of Western Australia, Perth, WA, Australia
| | - Saman Warnakulasuriya
- Faculty of Dentistry, Oral and Craniofacial Sciences King's College London and The WHO Collaborating Centre for Oral Cancer, King's College London, London, UK
| | - Philip Sloan
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.,Chief Histopathologist, AMLo Biosciences, Newcastle upon Tyne, UK
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23
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Sathasivam HP, Kist R, Sloan P, Thomson P, Nugent M, Alexander J, Haider S, Robinson M. Predicting the clinical outcome of oral potentially malignant disorders using transcriptomic-based molecular pathology. Br J Cancer 2021; 125:413-421. [PMID: 33972745 PMCID: PMC8329212 DOI: 10.1038/s41416-021-01411-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/06/2021] [Accepted: 04/16/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND This study was undertaken to develop and validate a gene expression signature that characterises oral potentially malignant disorders (OPMD) with a high risk of undergoing malignant transformation. METHODS Patients with oral epithelial dysplasia at one hospital were selected as the 'training set' (n = 56) whilst those at another hospital were selected for the 'test set' (n = 66). RNA was extracted from formalin-fixed paraffin-embedded (FFPE) diagnostic biopsies and analysed using the NanoString nCounter platform. A targeted panel of 42 genes selected on their association with oral carcinogenesis was used to develop a prognostic gene signature. Following data normalisation, uni- and multivariable analysis, as well as prognostic modelling, were employed to develop and validate the gene signature. RESULTS A prognostic classifier composed of 11 genes was developed using the training set. The multivariable prognostic model was used to predict patient risk scores in the test set. The prognostic gene signature was an independent predictor of malignant transformation when assessed in the test set, with the high-risk group showing worse prognosis [Hazard ratio = 12.65, p = 0.0003]. CONCLUSIONS This study demonstrates proof of principle that RNA extracted from FFPE diagnostic biopsies of OPMD, when analysed on the NanoString nCounter platform, can be used to generate a molecular classifier that stratifies the risk of malignant transformation with promising clinical utility.
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Affiliation(s)
- Hans Prakash Sathasivam
- grid.1006.70000 0001 0462 7212School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK ,Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Ralf Kist
- grid.1006.70000 0001 0462 7212School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK ,grid.1006.70000 0001 0462 7212Newcastle University Biosciences Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
| | - Philip Sloan
- grid.1006.70000 0001 0462 7212School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK ,grid.420004.20000 0004 0444 2244Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter Thomson
- grid.194645.b0000000121742757Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Michael Nugent
- grid.416726.00000 0004 0399 9059Oral and Maxillofacial Surgery, Sunderland Royal Hospital, Sunderland, UK
| | - John Alexander
- grid.18886.3f0000 0001 1271 4623The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Syed Haider
- grid.18886.3f0000 0001 1271 4623The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Max Robinson
- grid.1006.70000 0001 0462 7212School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK ,grid.420004.20000 0004 0444 2244Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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24
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Li X, Liu L, Zhang J, Ma M, Sun L, Li X, Zhang H, Wang J, Huang Y, Li T. Improvement in the risk assessment of oral leukoplakia through morphology-related copy number analysis. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1379-1391. [PMID: 34351567 DOI: 10.1007/s11427-021-1965-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/08/2021] [Indexed: 10/20/2022]
Abstract
Oral leukoplakia is the most common type of oral potentially malignant disorders and considered a precursor lesion to oral squamous cell carcinoma. However, a predictor of oral leukoplakia prognosis has not yet been identified. We investigated whether copy number alteration patterns may effectively predict the prognostic outcomes of oral leukoplakia using routinely processed paraffin sections. Comparison of copy number alteration patterns between oral leukoplakia with hyperplasia (HOL, n=22) and dysplasia (DOL, n=21) showed that oral leukoplakia with dysplasia had a higher copy number alteration rate (86%) than oral leukoplakia with hyperplasia (46%). Oral leukoplakia with dysplasia exhibited a wider range of genomic variations across all chromosomes compared with oral leukoplakia with hyperplasia. We also examined a retrospective cohort of 477 patients with oral leukoplakia with hyperplasia with detailed follow-up information. The malignant transformation (MT, n=19) and leukoplakia recurrence (LR, n=253) groups had higher frequencies of aneuploidy events and copy number loss rate than the free of disease (FD, n=205) group. Together, our results revealed the association between the degree of copy number alterations and the histological grade of oral leukoplakia and demonstrated that copy number alteration may be effective for prognosis prediction in oral leukoplakia patients with hyperplasia.
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Affiliation(s)
- Xiaotian Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Lu Liu
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jianyun Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Ming Ma
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Lisha Sun
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Xuefen Li
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, China.,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Heyu Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, China. .,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China.
| | - Jianbin Wang
- School of Life Sciences and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China. .,College of Chemistry and Molecular Engineering and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China. .,Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, 528107, China.
| | - Tiejun Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, Beijing, 100081, China. .,Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China.
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25
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McCarthy C, Fedele S, Ottensmeier C, Shaw RJ. Early-Phase Interventional Trials in Oral Cancer Prevention. Cancers (Basel) 2021; 13:cancers13153845. [PMID: 34359746 PMCID: PMC8345124 DOI: 10.3390/cancers13153845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/24/2021] [Accepted: 07/28/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Oral cancer is a devastating disease with increasing incidence worldwide. Oral epithelial dysplasia (OED) is a potentially malignant disorder and patients with OED are at increased risk of developing oral cancer. Current strategies for management of OED include surgery or close observation and both fail to address the underlying pathogenesis of the disease. There is an urgent need for evidence-based medical treatments for OED to prevent oral cancer development in this cohort. Chemoprevention trials to date have not delivered therapeutic agents for routine clinical practice. Historically, there has been significant heterogeneity in the design of oral cancer chemoprevention trials, with most failing to selectively recruit patients with biopsy-proven OED, which limits the usefulness of the findings in the OED population. The present paper aims to review the current evidence and the methodology of early-phase trials in oral cancer chemoprevention. Novel strategies in oral cancer chemoprevention will also be discussed. Abstract The increasing breadth of molecular targets, promise of immune-targeted therapies and repurposed agents have heightened interest in cancer prevention. While, to date, testing of oral cancer chemoprevention strategies has failed to deliver therapeutic agents for routine clinical practice, there remains an urgent need for further clinical research to overcome this hurdle. Patients at the greatest risk of disease stand to benefit the most from inclusion in clinical trials; therefore, there is a need to carefully define this population using validated clinical and molecular markers. Safety, tolerability and the efficacy of interventions is assessed through carefully selected endpoints. These endpoints may include pharmacodynamic, clinical, histological and on-target molecular modifications as an individual or as a composite endpoint. Early-phase trials provide an area of opportunity to explore novel and repurposed agents in the setting of oral cancer chemoprevention, eventually leading to phase III trials with clinical endpoints such as transformation and clinical outcome; these studies are large, lengthy and expensive and should be reserved for the most promising of agents. This paper will explore current evidence in oral cancer chemoprevention, drug repurposing, selection of appropriate endpoints for early-phase trials and novel therapeutic angles in oral cancer chemoprevention.
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Affiliation(s)
- Caroline McCarthy
- Liverpool Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 9TA, UK; (C.O.); (R.J.S.)
- Department of Oral Medicine, Liverpool University Dental Hospital, Liverpool L3 9TA, UK
- Correspondence: ; Tel.: +44-7904-363-109
| | - Stefano Fedele
- Eastman Dental Institute, University College London, 21 University Street, London WC1E 6DE, UK;
- National Institute for Health Research, University College London Hospitals Biomedical Research Centre, Maple House Suite A 1st floor, 149 Tottenham Court Road, London W1T 7DN, UK
| | - Christian Ottensmeier
- Liverpool Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 9TA, UK; (C.O.); (R.J.S.)
| | - Richard J. Shaw
- Liverpool Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L3 9TA, UK; (C.O.); (R.J.S.)
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26
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Overview of oral cavity squamous cell carcinoma: Risk factors, mechanisms, and diagnostics. Oral Oncol 2021; 121:105451. [PMID: 34329869 DOI: 10.1016/j.oraloncology.2021.105451] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 02/07/2023]
Abstract
Oral cavity squamous cell carcinoma (OCSCC) is the most common malignancy of the oral cavity. The substantial risk factors for OCSCC are the consumption of tobacco products, alcohol, betel quid, areca nut, and genetic alteration. However, technological advancements have occurred in treatment, but the survival decreases with late diagnosis; therefore, new methods are continuously being investigated for treatment. In addition, the rate of secondary tumor formation is 3-7% yearly, which is incomparable to other malignancies and can lead to the disease reoccurrence. Oral cavity cancer (OCC) arises from genetic alterations, and a complete understanding of the molecular mechanism involved in OCC is essential to develop targeted treatments. This review aims to update the researcher on oral cavity cancer, risk factors, genetic alterations, molecular mechanism, classification, diagnostic approaches, and treatment.
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27
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Zhang X, Yang M, Liu Y, Liu H, Yang J, Luo J, Zhou H. A novel 4-gene signature model simultaneously predicting malignant risk of oral potentially malignant disorders and oral squamous cell carcinoma prognosis. Arch Oral Biol 2021; 129:105203. [PMID: 34252587 DOI: 10.1016/j.archoralbio.2021.105203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 06/10/2021] [Accepted: 06/26/2021] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Oral squamous cell carcinoma (OSCC) is often diagnosed at late stage with a poor prognosis. The study hereunder aimed to construct a multi-gene model to simultaneously promote early diagnosis of OSCC by evaluating malignant risk of oral potentially malignant disorders (OPMDs) and predict prognosis. MATERIALS AND METHODS 3 GEO datasets including OPMDs and OSCC samples were obtained for overlapping differentially expressed genes (DEGs) being screened. The predictive model was built with optimal DEGs by SVM algorithm, estimated by receiver operator characteristic curves and validated for double prediction via oral cancer-free survival (for malignant risk of OPMDs) and overall survival time (for OSCC) analysis respectively compared to other models. The protein expression of biomarkers in the model was validated in human samples by immunohistochemistry. RESULTS A novel predictive model of 4-gene signature was built based on 12 common DEGs revealed from 3 GEO datasets. It could well distinguish OSCC from OPMDs and normal tissues. Both oral cancer-free survival and overall survival time analysis were significantly poorer in high-risk patients than in low-risk ones in Kaplan Meier survival curve respectively. The protein expression of biomarkers in OSCC was with significant difference compared to normal and OPMDs. CONCLUSIONS The novel 4-gene signature model presents strong ability in simultaneous prediction of the malignant risk of OPMDs and OSCC progression, potentially benefiting both the early diagnosis and therapeutic outcomes of OSCC.
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Affiliation(s)
- Xinyue Zhang
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China; Department of Stomatology, Chengdu Fifth People's Hospital/The Second Clinical Medical College, Chengdu University of TCM, Chengdu, Sichuan, People's Republic of China
| | - Miao Yang
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Yangfan Liu
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
| | - Hailong Liu
- Freelance Computer Engineer, Chengdu, Sichuan, People's Republic of China
| | - Jin Yang
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China.
| | - Jingjing Luo
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China.
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People's Republic of China
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28
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Bouaoud J, Foy JP, Tortereau A, Michon L, Lavergne V, Gadot N, Boyault S, Valantin J, De Souza G, Zrounba P, Bertolus C, Bendriss-Vermare N, Saintigny P. Early changes in the immune microenvironment of oral potentially malignant disorders reveal an unexpected association of M2 macrophages with oral cancer free survival. Oncoimmunology 2021; 10:1944554. [PMID: 34239777 PMCID: PMC8238000 DOI: 10.1080/2162402x.2021.1944554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Understanding the dynamics of the immune microenvironment is critical to the development of immuno-based strategies for the prevention of oral potentially malignant disorders transformation to oral squamous cell carcinoma (OSCC). We used laser capture microdissection and RNA-sequencing to profile the expression of 13 matched pairs of epithelial versus stromal compartments from normal mucosa, hyperplasia, dysplasia, and invasive tumors in the 4-nitroquinolein (4-NQO) murine model of oral carcinogenesis. Genes differentially expressed at each step of transformation were defined. Immune cell deconvolution and enrichment scores of various biological processes including immune-related ones were computed. Immunohistochemistry was also performed to characterize the immune infiltrates by T-cells (T-cells CD3+, helper CD4+, cytotoxic CD8+, regulatory FoxP3+), B-cells (B220+), and macrophages (M1 iNOS+, M2 CD163+) at each histological step. Enrichment of three independent M2 macrophages signatures were computed in 86 oral leukoplakia with available clinical outcome. Most gene expression changes were observed in the stromal compartment and related to immune biological processes. Immune cell deconvolution identified infiltration by the macrophage population as the most important quantitatively especially at the stage of dysplasia. In 86 patients with oral leukoplakia, three M2 macrophages signatures were independently associated with improved oral cancer-free survival. This study provides a better understanding of the dynamics of the immune microenvironment during oral carcinogenesis and highlights an unexpected association of M2 macrophages gene expression signatures with oral cancer free survival in patients with oral leukoplakia.
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Affiliation(s)
- Jebrane Bouaoud
- Tumor Escape, Resistance and Immunity Department, Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre De Recherche En Cancérologie De Lyon, Lyon, France.,Department of Translational Medicine, Centre Léon Bérard, Lyon, France.,Department of Maxillo-Facial Surgery, Sorbonne Université, Hôpital Pitié-Salpêtrière, Assistance Publique Des Hôpitaux De Paris, Paris, France
| | - Jean-Philippe Foy
- Tumor Escape, Resistance and Immunity Department, Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre De Recherche En Cancérologie De Lyon, Lyon, France.,Department of Translational Medicine, Centre Léon Bérard, Lyon, France.,Department of Maxillo-Facial Surgery, Sorbonne Université, Hôpital Pitié-Salpêtrière, Assistance Publique Des Hôpitaux De Paris, Paris, France
| | | | - Lucas Michon
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France
| | - Vincent Lavergne
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France
| | - Nicolas Gadot
- Tumor Escape, Resistance and Immunity Department, Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre De Recherche En Cancérologie De Lyon, Lyon, France.,Department of Translational Medicine, Centre Léon Bérard, Lyon, France
| | - Sandrine Boyault
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France
| | - Julie Valantin
- Tumor Escape, Resistance and Immunity Department, Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre De Recherche En Cancérologie De Lyon, Lyon, France.,Department of Translational Medicine, Centre Léon Bérard, Lyon, France
| | | | - Philippe Zrounba
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France.,Department of Surgery, Centre Léon Bérard, Lyon, France
| | - Chloé Bertolus
- Department of Translational Medicine, Centre Léon Bérard, Lyon, France.,Department of Maxillo-Facial Surgery, Sorbonne Université, Hôpital Pitié-Salpêtrière, Assistance Publique Des Hôpitaux De Paris, Paris, France
| | - Nathalie Bendriss-Vermare
- Tumor Escape, Resistance and Immunity Department, Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre De Recherche En Cancérologie De Lyon, Lyon, France
| | - Pierre Saintigny
- Tumor Escape, Resistance and Immunity Department, Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre De Recherche En Cancérologie De Lyon, Lyon, France.,Department of Translational Medicine, Centre Léon Bérard, Lyon, France.,Department of Medical Oncology, Centre Léon Bérard, Lyon, France
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29
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Prime SS, Cirillo N, Cheong SC, Prime MS, Parkinson EK. Targeting the genetic landscape of oral potentially malignant disorders has the potential as a preventative strategy in oral cancer. Cancer Lett 2021; 518:102-114. [PMID: 34139286 DOI: 10.1016/j.canlet.2021.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022]
Abstract
This study reviews the molecular landscape of oral potentially malignant disorders (OPMD). We examine the impact of tumour heterogeneity, the spectrum of driver mutations (TP53, CDKN2A, TERT, NOTCH1, AJUBA, PIK3CA, CASP8) and gene transcription on tumour progression. We comment on how some of these mutations impact cellular senescence, field cancerization and cancer stem cells. We propose that OPMD can be monitored more closely and more dynamically through the use of liquid biopsies using an appropriate biomarker of transformation. We describe new gene interactions through the use of a systems biology approach and we highlight some of the first studies to identify functional genes using CRISPR-Cas9 technology. We believe that this information has translational implications for the use of re-purposed existing drugs and/or new drug development. Further, we argue that the use of digital technology encompassing clinical and laboratory-based data will create relevant datasets for machine learning/artificial intelligence. We believe that therapeutic intervention at an early molecular premalignant stage should be an important preventative strategy to inhibit the development of oral squamous cell carcinoma and that this approach is applicable to other aerodigestive tract cancers.
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Affiliation(s)
- S S Prime
- Centre for Immunology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 4NS, UK.
| | - N Cirillo
- Melbourne Dental School, University of Melbourne, 720 Swanson Street, Carlton, Melbourne, Victoria, 3053, Australia.
| | - S C Cheong
- Head and Neck Cancer Research Team, Cancer Research Malaysia, 1 Jalan SS12/1A, Subang Jaya, Selangor, Malaysia.
| | - M S Prime
- Roche Diagnostics Information Solutions, Hoffman-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - E K Parkinson
- Centre for Immunology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 4NS, UK.
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30
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Chan HC, Chattopadhyay A, Chuang EY, Lu TP. Development of a Gene-Based Prediction Model for Recurrence of Colorectal Cancer Using an Ensemble Learning Algorithm. Front Oncol 2021; 11:631056. [PMID: 33692961 PMCID: PMC7938710 DOI: 10.3389/fonc.2021.631056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/05/2021] [Indexed: 01/21/2023] Open
Abstract
It is difficult to determine which patients with stage I and II colorectal cancer are at high risk of recurrence, qualifying them to undergo adjuvant chemotherapy. In this study, we aimed to determine a gene signature using gene expression data that could successfully identify high risk of recurrence among stage I and II colorectal cancer patients. First, a synthetic minority oversampling technique was used to address the problem of imbalanced data due to rare recurrence events. We then applied a sequential workflow of three methods (significance analysis of microarrays, logistic regression, and recursive feature elimination) to identify genes differentially expressed between patients with and without recurrence. To stabilize the prediction algorithm, we repeated the above processes on 10 subsets by bagging the training data set and then used support vector machine methods to construct the prediction models. The final predictions were determined by majority voting. The 10 models, using 51 differentially expressed genes, successfully predicted a high risk of recurrence within 3 years in the training data set, with a sensitivity of 91.18%. For the validation data sets, the sensitivity of the prediction with samples from two other countries was 80.00% and 91.67%. These prediction models can potentially function as a tool to decide if adjuvant chemotherapy should be administered after surgery for patients with stage I and II colorectal cancer.
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Affiliation(s)
- Han-Ching Chan
- Department of Public Health, College of Public Health, National Taiwan University, Institute of Epidemiology and Preventive Medicine, Taipei, Taiwan
| | - Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Eric Y Chuang
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Department of Electrical Engineering, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Department of Public Health, College of Public Health, National Taiwan University, Institute of Epidemiology and Preventive Medicine, Taipei, Taiwan.,Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
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31
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Monteiro L, Mello FW, Warnakulasuriya S. Tissue biomarkers for predicting the risk of oral cancer in patients diagnosed with oral leukoplakia: A systematic review. Oral Dis 2020; 27:1977-1992. [PMID: 33290585 DOI: 10.1111/odi.13747] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/15/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES We performed a systematic review to evaluate the published biomarkers related to oral leukoplakia (OL), aiming to identify the biomarkers that indicate any future risk of cancer in patients with oral leukoplakia. METHODS A search strategy was developed for three main electronic databases: PubMed, Cochrane Library, and EBSCO, and also for Google Scholar, until February 28, 2020. The study selection was performed in a two-phase process aiming at studies assessing tissue biomarkers for "malignant transformation of OL." Risk of bias analysis of included studies was performed using the Quality in Prognosis Studies Tool. RESULTS From 3,130 articles initially identified by searching databases, a total of 46 studies were included in this systematic review, with a combined sample of 3,783 patients, of whom 1,047 presented with malignant transformation of a previously diagnosed OL as reported by the authors. The cancer incidence in the whole group was 27.6% (range: 5.4% to 54.1%). The studies were derived from different geographic areas, including Asia (n = 21), Europe (n = 15), North America (n = 9), and Oceania (n = 1). There were 49 different molecular biomarkers evaluated in the 46 included studies: p53 and podoplanin proteins were the most frequently reported, followed by abnormalities at particular chromosomal loci (e.g., LOH). Risk of bias analysis revealed concerns associated with "measurement of prognostic factor," "study confounding" and "statistical analysis and reporting." CONCLUSIONS Substantial heterogeneity and lack of standardized reporting of data among the studies were identified. The most promising biomarkers reported to have a significant association with the malignant transformation in OL included podoplanin and chromosomal loci abnormalities. A critical examination of the follow-up studies on OL published so far indicated that tissue biomarkers that could predict the risk of oral cancer in patients with OL are still in a discovery phase.
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Affiliation(s)
- Luis Monteiro
- Medicine and Oral Surgery Department, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS), IUCS - Instituto Universitário de Ciências da Saúde (CESPU), Gandra, Portugal
| | - Fernanda Weber Mello
- Postgraduate Program in Dentistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Saman Warnakulasuriya
- Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London and WHO Collaborating Centre for Oral Cancer, London, UK
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Spirko-Burns L, Devarajan K. Unified methods for feature selection in large-scale genomic studies with censored survival outcomes. Bioinformatics 2020; 36:3409-3417. [PMID: 32154833 DOI: 10.1093/bioinformatics/btaa161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 12/20/2019] [Accepted: 03/05/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous datasets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards (PH), which is unlikely to hold for each feature. When applied to genomic features exhibiting some form of non-proportional hazards (NPH), these methods could lead to an under- or over-estimation of the effects. We propose a broad array of marginal screening techniques that aid in feature ranking and selection by accommodating various forms of NPH. First, we develop an approach based on Kullback-Leibler information divergence and the Yang-Prentice model that includes methods for the PH and proportional odds (PO) models as special cases. Next, we propose R2 measures for the PH and PO models that can be interpreted in terms of explained randomness. Lastly, we propose a generalized pseudo-R2 index that includes PH, PO, crossing hazards and crossing odds models as special cases and can be interpreted as the percentage of separability between subjects experiencing the event and not experiencing the event according to feature measurements. RESULTS We evaluate the performance of our measures using extensive simulation studies and publicly available datasets in cancer genomics. We demonstrate that the proposed methods successfully address the issue of NPH in genomic feature selection and outperform existing methods. AVAILABILITY AND IMPLEMENTATION R code for the proposed methods is available at github.com/lburns27/Feature-Selection. CONTACT karthik.devarajan@fccc.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Karthik Devarajan
- Department of Biostatistics & Bioinformatics, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA, USA
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33
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Farah CS. Molecular, genomic and mutational landscape of oral leukoplakia. Oral Dis 2020; 27:803-812. [PMID: 33448555 DOI: 10.1111/odi.13608] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022]
Abstract
Oral leukoplakia (OLK) and its more aggressive clinical variant proliferative verrucous leukoplakia (PVL) remain enigmatic disorders clinically and histopathologically. Despite decades of research into both, there has been only incremental advancement in our understanding of their aetiology and pathogenesis and only minimal improvement in effective management strategies. Currently, no specific prognostic genetic or molecular marker has been reported for leukoplakia. There is, however, an emerging body of evidence characterising the genomic and transcriptomic profile of OLK. Regardless of the significance of cellular and architectural features of OLK and PVL, it is clear from studies reported in this review that new emerging evidence points to the presence of premalignant molecular subtypes of leukoplakia which require further investigation. This up-to-date review explores the contemporary genomic, transcriptomic and mutational landscape of leukoplakia broadly, discusses concepts that may not be widely recognised or accepted and purposefully highlights studies with juxtaposed findings in an effort to challenge dogma. It also highlights the urgent need for a concerted international effort of original collaborative research which will only occur by pooling collective efforts, resources and intellect to define the molecular fingerprint of this enigmatic disorder, in the hope it will better inform diagnosis, stratification and treatment.
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Affiliation(s)
- Camile S Farah
- Australian Centre for Oral Oncology Research & Education, Nedlands, WA, Australia.,Perth Oral Medicine & Dental Sleep Centre, West Leederville, WA, Australia.,Oral, Maxillofacial and Dental Surgery, Fiona Stanley Hospital, Murdoch, WA, Australia.,Australian Clinical Labs, Subiaco, WA, Australia.,Genomics for Life, Brisbane, QLD, Australia
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34
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Sathasivam HP, Casement J, Bates T, Sloan P, Thomson P, Robinson M, Kist R. Gene expression changes associated with malignant transformation of oral potentially malignant disorders. J Oral Pathol Med 2020; 50:60-67. [PMID: 32740996 DOI: 10.1111/jop.13090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND A large number of oral squamous cell carcinomas (OSCCs) are believed to be preceded by oral potentially malignant disorders (OPMD) that have an increased likelihood of malignant transformation compared to clinically normal mucosa. This study was performed to identify differentially expressed genes between OPMDs that underwent malignant transformation (MT) and those that did not, termed "non-transforming" (NT) cases. METHODS Total RNA was extracted from formalin-fixed paraffin-embedded tissue biopsies of 20 OPMD cases with known clinical outcomes (10 MT vs. 10 NT). Samples were assessed for quantity, quality and integrity of RNA prior to sequencing. Analysis for differential gene expression between MT and NT was performed using statistical packages in R. Genes were considered to be significantly differentially expressed if the False Discovery Rate corrected P-value was < 0.05. RESULTS RNA yield was variable but RNA purity was good (A260/A280 > 1.90). Analysis of RNA-Sequencing outputs revealed 41 genes (34 protein-coding; 7 non-coding) that were significantly differentially expressed between MT and NT cases. The log2 fold change for the statistically significant differentially expressed genes ranged from -2.63 to 2.48, with 23 protein-coding genes being downregulated and 11 protein-coding genes being upregulated in MT cases compared to NT cases. CONCLUSION Several candidate genes that may play a role in malignant transformation of OPMD have been identified. Experiments to validate these candidates are underway. It is anticipated that this work will contribute to better understanding of the etiopathogenesis of OPMD and development of novel biomarkers.
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Affiliation(s)
- Hans P Sathasivam
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Cancer Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Malaysia
| | - John Casement
- Bioinformatics Support Unit, Newcastle University, Newcastle upon Tyne, UK
| | | | - Philip Sloan
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Newcastle upon Tyne Hospital NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter Thomson
- Oral and Maxillofacial Surgery, Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, Hong Kong
| | - Max Robinson
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Newcastle upon Tyne Hospital NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ralf Kist
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Newcastle University Biosciences Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
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35
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Gene Expression Clustering and Selected Head and Neck Cancer Gene Signatures Highlight Risk Probability Differences in Oral Premalignant Lesions. Cells 2020; 9:cells9081828. [PMID: 32756466 PMCID: PMC7466020 DOI: 10.3390/cells9081828] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Oral premalignant lesions (OPLs) represent the most common oral precancerous conditions. One of the major challenges in this field is the identification of OPLs at higher risk for oral squamous cell cancer (OSCC) development, by discovering molecular pathways deregulated in the early steps of malignant transformation. Analysis of deregulated levels of single genes and pathways has been successfully applied to head and neck squamous cell cancers (HNSCC) and OSCC with prognostic/predictive implications. Exploiting the availability of gene expression profile and clinical follow-up information of a well-characterized cohort of OPL patients, we aim to dissect tissue OPL gene expression to identify molecular clusters/signatures associated with oral cancer free survival (OCFS). MATERIALS AND METHODS The gene expression data of 86 OPL patients were challenged with: an HNSCC specific 6 molecular subtypes model (Immune related: HPV related, Defense Response and Immunoreactive; Mesenchymal, Hypoxia and Classical); one OSCC-specific signature (13 genes); two metabolism-related signatures (3 genes and signatures raised from 6 metabolic pathways associated with prognosis in HNSCC and OSCC, respectively); a hypoxia gene signature. The molecular stratification and high versus low expression of the signatures were correlated with OCFS by Kaplan-Meier analyses. The association of gene expression profiles among the tested biological models and clinical covariates was tested through variance partition analysis. RESULTS Patients with Mesenchymal, Hypoxia and Classical clusters showed an higher risk of malignant transformation in comparison with immune-related ones (log-rank test, p = 0.0052) and they expressed four enriched hallmarks: "TGF beta signaling" "angiogenesis", "unfolded protein response", "apical junction". Overall, 54 cases entered in the immune related clusters, while the remaining 32 cases belonged to the other clusters. No other signatures showed association with OCFS. Our variance partition analysis proved that clinical and molecular features are able to explain only 21% of gene expression data variability, while the remaining 79% refers to residuals independent of known parameters. CONCLUSIONS Applying the existing signatures derived from HNSCC to OPL, we identified only a protective effect for immune-related signatures. Other gene expression profiles derived from overt cancers were not able to identify the risk of malignant transformation, possibly because they are linked to later stages of cancer progression. The availability of a new well-characterized set of OPL patients and further research is needed to improve the identification of adequate prognosticators in OPLs.
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36
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Yu X, Wang Z, Zeng T. Essential gene expression pattern of head and neck squamous cell carcinoma revealed by tumor-specific expression rule based on single-cell RNA sequencing. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165791. [PMID: 32234410 DOI: 10.1016/j.bbadis.2020.165791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/14/2020] [Accepted: 03/25/2020] [Indexed: 01/05/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) has been widely reported and considered as one of the most threatening diseases to human health. Derived from complicated tissue subtypes, HNSCC has diverse symptoms and pathogenesis. They make the identification of the core carcinogenic factors of such diseases at the multi-cell level difficult. With the development of single-cell sequencing technologies, the effects of non-malignant cells on traditional bulk sequencing data can be eliminated directly. On the basis of fresh single-cell RNA-seq data, we set up a computational filtering strategy for tumor cell identification in an expression rule manner. This strategy can reveal the accurate expression distinction between tumor cells and adjacent tumor microenvironment, which are all supported by literature reports. Validated by several independent datasets, these rule genes can further group HNSCC patients with significant difference on survival risks. Thus, the establishment of our computational approach may not only provide an efficient tool to identify malignant cells in the tumor ecosystem but also deepen our understanding of tumor heterogeneity and tumorigenesis.
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Affiliation(s)
- Xiangtian Yu
- Clinical Research Center, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 201210, China.
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37
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Zhao Z, Li Y, Wu Y, Chen R. Deep learning-based model for predicting progression in patients with head and neck squamous cell carcinoma. Cancer Biomark 2020; 27:19-28. [PMID: 31658045 DOI: 10.3233/cbm-190380] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE This study endeavors to build a deep learning (DL)-based model for predicting disease progression in head and neck squamous cell carcinoma (HNSCC) patients by integrating multi-omics data. METHODS RNA sequencing, miRNA sequencing, and methylation data from The Cancer Genome Atlas (TCGA) were used as input for autoencoder, a DL approach. An autoencoder-based prognosis model for PFS was built by SVM algorithm and tested in three confirmation sets. Predictive performance of the model was compared to two alternative approaches. Differential expression analysis for mRNAs, microRNAs (miRNA) and methylation was conducted. Moreover, functional annotation of differentially expressed genes (DEGs) was achieved through function enrichment analysis. RESULT The DL-based prognosis model identified two subgroups of patients with significantly different PFS, and showcased a good model fitness (C-index = 0.73). The two identified PFS subtypes were successfully validated in three confirmation sets. The DL-based model was more accurate and efficient than principal component analysis (PCA) or individual Cox-PH-based models. There were 348 DEGs, 23 differentially expressed miRNAs and 55 differentially methylated genes between the two PFS subtypes. These genes were significantly involved in several immune-related biological processes and primary immunodeficiency, cell adhesion molecules (CAMs), B cell receptor signaling and leukocyte transendothelial migration pathways. CONCLUSION The DL-based model introduced in this study is reliable and robust in predicting disease progression in HNSCC patients. A number of pathways and genes targets are unraveled to be implicated in cancer progression. Utility of this model would facilitate development of more individualized therapy for HNSCC patients and improve prognosis.
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Affiliation(s)
- Zhen Zhao
- Department of Otolaryngology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu 210006, China.,Department of Otolaryngology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu 210006, China
| | - Yingli Li
- Department of Plastic Surgery, The 960th Hospital of the PLA Joint Logistic Support Force, Jinan, Shandong 250000, China.,Department of Otolaryngology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu 210006, China
| | - Yuanqing Wu
- Department of Otolaryngology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu 210006, China
| | - Rongrong Chen
- Department of Otolaryngology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu 210006, China
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Adaptive ERK signalling activation in response to therapy and in silico prognostic evaluation of EGFR-MAPK in HNSCC. Br J Cancer 2020; 123:288-297. [PMID: 32424150 PMCID: PMC7374086 DOI: 10.1038/s41416-020-0892-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/25/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) patients frequently develop treatment resistance to cetuximab, a monoclonal antibody against EGFR, as well as radiotherapy. Here we addressed extracellular signal-regulated kinase 1/2 (ERK1/2) regulation by cetuximab or fractionated irradiation (IR) and conducted in silico prognostic evaluation of the EGFR-MAPK axis in HNSCC. METHODS Expression of ERK1/2 phosphorylation (pERK1/2) was determined in HNSCC cell lines, which were treated with cetuximab or fractionated-IR. Furthermore, the effect of fractionated IR on pERK1/2 was confirmed in an ex vivo HNSCC tissue culture model. Expression and prognostic significance of EGFR-ERK axis was evaluated in a cohort of radiotherapy plus cetuximab-treated HNSCC. Correlations among EGFR-MAPK signalling components and association between transcript and protein expression profiles and patient survival in HNSCC were analysed using publicly available databases. RESULTS ERK1/2 phosphorylation was rebounded by prolonged cetuximab administration and was induced by fractionated IR, which could be suppressed by a MEK inhibitor as a radiosensitiser. In silico assessments suggested that EGFR-MAPK cascade genes and proteins could predict HNSCC patients' survival as a prognostic signature. CONCLUSIONS Activation of ERK1/2 signalling contributes to the cellular defence of HNSCC against cetuximab and fractionated IR treatment. EGFR-MAPK axis has a prognostic significance in HNSCC.
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Oral potentially malignant disorders: A scoping review of prognostic biomarkers. Crit Rev Oncol Hematol 2020; 153:102986. [PMID: 32682268 DOI: 10.1016/j.critrevonc.2020.102986] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 02/08/2023] Open
Abstract
This scoping review aimed to map evidence regarding biomarkers for malignant transformation of oral potentially malignant disorders (OPMD). Seventy-three longitudinal studies investigating prognostic biomarkers for OPMD malignant transformation were included, encompassing 5612 disorders and 108 biomarkers, of which 72 were investigated by immunohistochemistry. Most biomarkers were assessed in one or two studies, while five (p53, Ki-67, podoplanin, p16, and DNA ploidy) were analyzed in five or more studies. All studies investigating podoplanin (n = 8) reported a significant association between positive/high immunoexpression and malignant transformation. Similarly, all studies assessing DNA ploidy (n = 5) found that aneuploidy or gross genomic aberrations were significantly associated with malignant transformation. Included studies often presented mixed data from different OPMD subtypes, inadequate description of population characteristics, and lack of adjusted analysis for confounding factors. One hundred and eight biomarkers were identified and, from these, podoplanin immunoexpression and DNA ploidy were considered promising candidates for future long-term clinical research.
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40
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Elsewify WAE, Hassan EA, Mekky MA, Abd El-Rehim ASED, Sayed ZEAA, Abdel Malek MO, ElMelegy TTH, Sabry A. Usefulness of Circulating Methylated p16 as a Noninvasive Molecular Biomarker for Hepatitis C-Related Hepatocellular Carcinoma with Normal Serum Alpha-Fetoprotein Levels. Int J Gen Med 2020; 13:147-155. [PMID: 32431531 PMCID: PMC7200244 DOI: 10.2147/ijgm.s249272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Background Screening of hepatocellular carcinoma (HCC) is challenged especially in patients with normal alpha-fetoprotein (AFP) levels. Aberrant p16 methylation has been implicated in HCC. Objectives and Aims This study aimed to assess serum methylated p16 (MP16) expression levels and to evaluate MP16 diagnostic performance in HCC detection among HCV-infected Egyptian patients with normal AFP levels. Methods MP16 levels were quantified using real-time PCR in 230 serum samples (30 healthy controls, 95 with HCV-HCC, 40 with chronic hepatitis C "CHC" and 65 with HCV cirrhosis). Diagnostic performance of MP16 for diagnosis of HCC was done using receiver operator characteristic curve analysis. Results Serum MP16 levels were significantly higher in HCC than CHC, cirrhosis, and healthy subjects and significantly higher in HCC with normal AFP levels than those with higher AFP. ROC curves revealed promising diagnostic performance for MP16 in discriminating HCC with normal AFP levels from non-HCC cases. This predictive ability improved by combining MP16 and AFP (AUC of 0.872 with 100% sensitivity, 76.5% specificity, 79.1% positive predictive value, 100% negative predictive value, and 87.5% accuracy). Conclusion MP16 can be a potential noninvasive molecular biomarker for HCC detection in patients with hepatic mass(es) and normal AFP levels especially in those where liver biopsy and radiological imaging cannot be done.
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Affiliation(s)
| | - Elham Ahmed Hassan
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mohamed A Mekky
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | | | | | - Mohamed Omar Abdel Malek
- Department of Gastroenterology and Tropical Medicine, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Tarek T H ElMelegy
- Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Abeer Sabry
- Department of Internal Medicine, Faculty of Medicine, Helwan University, Cairo, Egypt
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Baig MS, Roy A, Rajpoot S, Liu D, Savai R, Banerjee S, Kawada M, Faisal SM, Saluja R, Saqib U, Ohishi T, Wary KK. Tumor-derived exosomes in the regulation of macrophage polarization. Inflamm Res 2020; 69:435-451. [DOI: 10.1007/s00011-020-01318-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/02/2020] [Accepted: 01/09/2020] [Indexed: 01/21/2023] Open
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42
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Diagnostic Adjuncts for Oral Cavity Squamous Cell Carcinoma and Oral Potentially Malignant Disorders. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-32316-5_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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43
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Zaini ZM, Neat M, Stokes A, Tavassoli M, Odell EW. DNA aneuploidy and tissue architecture in oral potentially malignant disorders with epithelial dysplasia assessed by a 10 locus FISH panel. Oncol Rep 2020; 43:877-885. [PMID: 32020221 PMCID: PMC7041104 DOI: 10.3892/or.2020.7461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/29/2019] [Indexed: 12/04/2022] Open
Abstract
Subjectivity in oral dysplasia grading has prompted evaluation of molecular-based tests to predict malignant transformation. Aneuploidy detected by DNA image-based cytometry (ICM) is currently the best predictor but fails to detect certain high risk lesions. A novel multiplex fluorescence in situ hybridization (FISH) panel was used to explore possible explanations by detecting aneuploidy at the single cell level. FISH was compared to reference standard DNA ICM in 19 oral lesions with epithelial dysplasia and used to characterize the cellular architecture. Copy number variation at 3q28, 7p11.2, 8q24.3, 11q13.3 and 20q13.12 and matched chromosome specific loci were assessed by dual-color FISH to assess numerical and spatial patterns of copy number increase and gene amplification. FISH revealed wide variation in copy number at different loci. Only low level copy number gain was present and often in only a small proportion of cells, although usually with all or all but one locus (9/12). Four cases showed gene amplification, one at two loci. Some probes revealed an internal presumed clonal structure within lesions not apparent in routine histological examination. Both methods produced similar diagnostic results with concordance in detection of aneuploidy by both methods in 17 out of 19 samples (89%). We have shown that oral dysplastic lesions may contain very few aneuploid cells at a cellular level, high copy number gain is rare and changes appear to arise from large chromosomal fragment duplications. Single stem lines are relatively homogeneous for loci with copy number gain but there is a subclonal structure revealed by gene amplification in some lesions.
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Affiliation(s)
| | - Michael Neat
- Cancer Genetics, ViaPath LLC, Guy's Hospital, London SE1 9RT, UK
| | - Angela Stokes
- Head and Neck Pathology, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Mahvash Tavassoli
- Molecular Oncology, King's College London, Guy's Campus, London SE1 1UL, UK
| | - Edward W Odell
- Head and Neck Pathology, King's College London, Guy's Hospital, London SE1 9RT, UK
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Visualization of mucosal field in HPV positive and negative oropharyngeal squamous cell carcinomas: combined genomic and radiology based 3D model. Sci Rep 2020; 10:40. [PMID: 31913295 PMCID: PMC6949264 DOI: 10.1038/s41598-019-56429-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/22/2019] [Indexed: 01/24/2023] Open
Abstract
The aim of this study was to visualize the tumor propagation and surrounding mucosal field in radiography-based 3D model for advanced stage HNSCC and combine it with HPV genotyping and miRNA expression characterization of the visualized area. 25 patients with T1-3 clinical stage HNSCC were enrolled in mapping biopsy sampling. Biopsy samples were evaluated for HPV positivity and miR-21-5p, miR-143, miR-155, miR-221-5p expression in Digital Droplet PCR system. Significant miRNA expression differences of HPV positive tumor tissue biopsies were found for miR-21-5p, miR-143 and miR-221-5p compared to the HPV negative tumor biopsy series. Peritumoral mucosa showed patchy pattern alterations of miR-21-5p and miR-155 in HPV positive cases, while gradual change of miR-21-5p and miR-221-5p was seen in HPV negative tumors. In our study we found differences of the miRNA expression patterns among the HPV positive and negative tumorous tissues as well as the surrounding mucosal fields. The CT based 3D models of the cancer field and surrounding mucosal surface can be utilized to improve proper preoperative planning. Complex evaluation of HNSCC tissue organization field can elucidate the clinical and molecular differentiation of HPV positive and negative cases, and enhance effective organ saving therapeutic strategies.
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Villa A, Celentano A, Glurich I, Borgnakke WS, Jensen SB, Peterson DE, Delli K, Ojeda D, Vissink A, Farah CS. World Workshop on Oral Medicine VII: Prognostic biomarkers in oral leukoplakia: A systematic review of longitudinal studies. Oral Dis 2020; 25 Suppl 1:64-78. [PMID: 31140698 DOI: 10.1111/odi.13087] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/24/2019] [Accepted: 03/03/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To identify the prognostic biomarker candidates for stratification and long-term surveillance of oral leukoplakia progressing to cancer via a systematic literature review. MATERIALS AND METHODS Systematic searches with no date restrictions were conducted on March 29, 2018, targeting the databases PubMed (Ovid), EMBASE (Ovid), EBM (Ovid), and Web of Science (ISI). Bias was assessed using the Quality in Prognosis Studies tool. Biomarkers were stratified based on hallmarks of cancer. RESULTS Inclusion criteria were met by 25 of 3,415 studies. A range of biomarkers were evaluated experimentally for risk stratification, prognosis, and surveillance of oral leukoplakia in tissue, blood, and saliva. However, the studies were highly heterogeneous and require further validation. Biomarkers reported in these studies included inflammatory or oxidative markers, growth factors, ion channels, genetic and cellular regulatory factors, and epigenetic biomarkers. Studies tended to include small sample sizes, under-reported or variably reported histopathological data, did not address potential confounding, reported limited/variable follow-up data, or lacked a control group. Inclusion of subsets from chemoprevention trials may have introduced bias regarding reported malignant transformation rates and accuracy of prognostic biomarkers. CONCLUSIONS This review identified insufficient longitudinal evidence to support validated prognostic biomarkers for oral leukoplakia. Further studies are needed to identify molecular targets with the potential to mitigate risk of malignant transformation.
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Affiliation(s)
- Alessandro Villa
- Division of Oral Medicine and Dentistry, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts
| | - Antonio Celentano
- Melbourne Dental School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid Glurich
- Center for Oral and Systemic Health, Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | - Wenche S Borgnakke
- Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, Michigan
| | - Siri Beier Jensen
- Department of Dentistry and Oral Health, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Douglas E Peterson
- Oral Medicine Section, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, Connecticut
| | - Konstantina Delli
- Department of Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David Ojeda
- Department of Comprehensive Dentistry, School of Dentistry, UT Health San Antonio, San Antonio, Texas
| | - Arjan Vissink
- Department of Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Camile S Farah
- Australian Centre for Oral Oncology Research & Education, Perth, Westren Australia, Australia
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46
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Chen JH, Wu ATH, Bamodu OA, Yadav VK, Chao TY, Tzeng YM, Mukhopadhyay D, Hsiao M, Lee JC. Ovatodiolide Suppresses Oral Cancer Malignancy by Down-Regulating Exosomal Mir-21/STAT3/β-Catenin Cargo and Preventing Oncogenic Transformation of Normal Gingival Fibroblasts. Cancers (Basel) 2019; 12:cancers12010056. [PMID: 31878245 PMCID: PMC7017298 DOI: 10.3390/cancers12010056] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/02/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is among the most commonly diagnosed malignancies in the world. Patients with OSCC often develop treatment resistance, resulting in a poor prognosis. Mounting evidence indicates that interactions between cancerous cells and other components of the tumor microenvironment (TME) determine their response to treatment. Herein, we examined the role of cancer stem cell-derived extracellular vesicles (CSC_EVs) generated from CAL27 and SCC-15 OSCC cells in the development of cisplatin (CDDP) resistance. We demonstrated that CSC_EVs enhance CDDP resistance, clonogenicity, and the tumorsphere formation potential of OSCC cells. Our bioinformatics analyses revealed that OSCC_EVs are enriched with microRNA (miR)-21-5p and are associated with increased metastasis, stemness, chemoresistance, and poor survival in patients with OSCC. Mechanistically, enhanced activity of CSC_EVs was positively correlated with upregulated β-catenin, phosphatidylinositol-3 kinase (PI3K), signal transducer and activator of transcription 3 (STAT3), mammalian target of rapamycin (mTOR), and transforming growth factor (TGF)-β1 messenger (m)RNA and protein expression levels. CSC_EVs also conferred a cancer-associated fibroblast (CAF) phenotype on normal gingival fibroblasts (NGFs), with the resultant CAFs enhancing the oncogenicity of OSCC cells. Interestingly, treatment with ovatodiolide (OV), the bioactive component of Anisomeles indica, suppressed OSCC tumorigenesis by reducing the cargo content of EVs derived from CSCs, suppressing self-renewal, and inhibiting the NGF-CAF transformation by disrupting EV-TME interactions. Moreover, by suppressing miR-21-5p, STAT3, and mTOR expressions in CSC_EVs, OV re-sensitized CSCs to CDDP and suppressed OSCC tumorigenesis. In vivo, treatment with OV alone or in combination with CDDP significantly reduced the tumor sphere-forming ability and decreased EV cargos containing mTOR, PI3K, STAT3, β-catenin, and miR-21-5p. In summary, our findings provide further strong evidence of OV’s therapeutic effect in OSCC.
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Affiliation(s)
- Jia-Hong Chen
- Graduate and Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
- Division of Hematology/Oncology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Alexander T. H. Wu
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Oluwaseun Adebayo Bamodu
- Department of Hematology and Oncology, Cancer Center, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan; (O.A.B.); (T.-Y.C.)
- Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan
| | - Vijesh Kumar Yadav
- The Program for Translational Medicine, Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 11031, Taiwan
| | - Tsu-Yi Chao
- Department of Hematology and Oncology, Cancer Center, Taipei Medical University-Shuang Ho Hospital, New Taipei City 23561, Taiwan; (O.A.B.); (T.-Y.C.)
- Taipei Cancer Center, Taipei Medical University, Taipei 11031, Taiwan
| | - Yew-Min Tzeng
- Center for General Education, National Taitung University, Taitung 95092, Taiwan;
- Department of Life Science, National Taitung University, Taitung 95092, Taiwan
| | - Debabrata Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA;
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei City 11529, Taiwan;
- Department of Biochemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Jih-Chin Lee
- Department of Otolaryngology, Head and Neck Surgery Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
- Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
- Correspondence:
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47
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Makarov V, Gorlin A. Meta-analysis of gene expression for development and validation of a diagnostic biomarker panel for Oral Squamous Cell Carcinoma. Comput Biol Chem 2019; 82:74-79. [DOI: 10.1016/j.compbiolchem.2019.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 12/16/2022]
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48
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Kim DW, Lee S, Kwon S, Nam W, Cha IH, Kim HJ. Deep learning-based survival prediction of oral cancer patients. Sci Rep 2019; 9:6994. [PMID: 31061433 PMCID: PMC6502856 DOI: 10.1038/s41598-019-43372-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/23/2019] [Indexed: 12/24/2022] Open
Abstract
The Cox proportional hazards model commonly used to evaluate prognostic variables in survival of cancer patients may be too simplistic to properly predict a cancer patient’s outcome since it assumes that the outcome is a linear combination of covariates. In this retrospective study including 255 patients suitable for analysis who underwent surgical treatment in our department from 2000 to 2017, we applied a deep learning-based survival prediction method in oral squamous cell carcinoma (SCC) patients and validated its performance. Survival prediction using DeepSurv, a deep learning based-survival prediction algorithm, was compared with random survival forest (RSF) and the Cox proportional hazard model (CPH). DeepSurv showed the best performance among the three models, the c-index of the training and testing sets reaching 0.810 and 0.781, respectively, followed by RSF (0.770/0.764), and CPH (0.756/0.694). The performance of DeepSurv steadily improved with added features. Thus, deep learning-based survival prediction may improve prediction accuracy and guide clinicians both in choosing treatment options for better survival and in avoiding unnecessary treatments.
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Affiliation(s)
- Dong Wook Kim
- Department of Oral & Maxillofacial Surgery, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Sanghoon Lee
- Department of Oral & Maxillofacial Surgery, Dankook University Jukjeon Dental Hospital, 152 Jukjeon-ro, Suji-gu, Yongin-Si, Gyeonggi-do, 16890, Republic of Korea
| | - Sunmo Kwon
- Department of Oral & Maxillofacial Surgery, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Woong Nam
- Department of Oral & Maxillofacial Surgery, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Oral Cancer Research Institute, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - In-Ho Cha
- Department of Oral & Maxillofacial Surgery, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.,Oral Cancer Research Institute, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyung Jun Kim
- Department of Oral & Maxillofacial Surgery, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea. .,Oral Cancer Research Institute, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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49
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Molecular Biomarkers Related to Oral Carcinoma: Clinical Trial Outcome Evaluation in a Literature Review. DISEASE MARKERS 2019; 2019:8040361. [PMID: 31019584 PMCID: PMC6452537 DOI: 10.1155/2019/8040361] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/02/2018] [Accepted: 01/15/2019] [Indexed: 02/07/2023]
Abstract
Backgrounds The objective of the present research was to systematically revise the international literature about the genetic biomarkers related to oral cancer (OC) evaluating the recent findings in clinical studies. Methods A comprehensive review of the current literature was conducted according to the PRISMA guidelines by accessing the NCBI PubMed database. The authors conducted the search of articles in the English language published from 2008 to 2018. The present systematic review included only papers with significant results about correlation between wound healing, genetic alteration, and OC. Prognostic capacity of genetic markers was not evaluated in vivo. Results The first analysis with filters recorded about 1884 published papers. Beyond reading and consideration of suitability, only 20 and then 8 papers, with case report exclusion, were recorded for the revision. Conclusion All the researches recorded the proteomic and genetic alterations in OC human biopsy cells. The gene modification level in the different studies, compared with samples of healthy tissues, has always been statistically significant, but it is not possible to associate publications with each other because each job is based on the measurement of different biomarkers and gene targets. Further investigations should be required in order to state scientific evidence about a clear advantage of using these biomarkers for diagnostic purpose.
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50
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Foy JP, Bertolus C, Saintigny P. Oral cancer prevention worldwide: Challenges and perspectives. Oral Oncol 2018; 88:91-94. [PMID: 30616804 DOI: 10.1016/j.oraloncology.2018.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 11/06/2018] [Indexed: 11/24/2022]
Affiliation(s)
- Jean-Philippe Foy
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69008, France; Department of Oral and Maxillo-Facial Surgery, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Chloé Bertolus
- Department of Oral and Maxillo-Facial Surgery, Sorbonne University, Pitié-Salpêtrière Hospital, Paris, France
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69008, France; Department of Medicine, Centre Léon Bérard, Lyon, France.
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