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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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2
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Flores-Hidalgo A, Phero J, Steward-Tharp S, Williamson M, Paquette D, Krishnan D, Padilla R. Immunophenotypic and Gene Expression Analyses of the Inflammatory Microenvironment in High-Grade Oral Epithelial Dysplasia and Oral Lichen Planus. Head Neck Pathol 2024; 18:17. [PMID: 38456941 PMCID: PMC10923754 DOI: 10.1007/s12105-024-01624-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/30/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Oral lichen planus (OLP) and oral epithelial dysplasia (OED) present diagnostic challenges due to clinical and histologic overlap. This study explores the immune microenvironment in OED, hypothesizing that immune signatures could aid in diagnostic differentiation and predict malignant transformation. METHODS Tissue samples from OED and OLP cases were analyzed using immunofluorescence/immunohistochemistry (IF/IHC) for CD4, CD8, CD163/STAT1, and PD-1/PDL-1 expression. RNA-sequencing was performed on the samples, and data was subjected to CIBERSORTx analysis for immune cell composition. Gene Ontology analysis on the immune differentially expressed genes was also conducted. RESULTS In OED, CD8 + T-cells infiltrated dysplastic epithelium, correlating with dysplasia severity. CD4 + lymphocytes increased in the basal layer. STAT1/CD163 + macrophages correlated with CD4 + intraepithelial distribution. PD-1/PDL-1 expression varied. IF/IHC analysis revealed differential immune cell composition between OED and OLP. RNA-sequencing identified upregulated genes associated with cytotoxic response and immunosurveillance in OED. Downregulated genes were linked to signaling, immune cell recruitment, and tumor suppression. CONCLUSIONS The immune microenvironment distinguishes OED and OLP, suggesting diagnostic potential. Upregulated genes indicate cytotoxic immune response in OED. Downregulation of TRADD, CX3CL1, and ILI24 implies dysregulation in TNFR1 signaling, immune recruitment, and tumor suppression. This study contributes to the foundation for understanding immune interactions in OED and OLP, offering insights into future objective diagnostic avenues.
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Affiliation(s)
- Andres Flores-Hidalgo
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - James Phero
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Scott Steward-Tharp
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, USA
| | - Megumi Williamson
- Department of Surgical Sciences, East Carolina University School of Dental Medicine, Greenville, USA
| | - David Paquette
- Department of Surgical Sciences, East Carolina University School of Dental Medicine, Greenville, USA
| | - Deepak Krishnan
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ricardo Padilla
- Department of Diagnostic Sciences, University of North Carolina at Chapel Hill Adams School of Dentistry, Chapel Hill, USA
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3
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Tanner G, Barrow R, Ajaib S, Al-Jabri M, Ahmed N, Pollock S, Finetti M, Rippaus N, Bruns AF, Syed K, Poulter JA, Matthews L, Hughes T, Wilson E, Johnson C, Varn FS, Brüning-Richardson A, Hogg C, Droop A, Gusnanto A, Care MA, Cutillo L, Westhead DR, Short SC, Jenkinson MD, Brodbelt A, Chakrabarty A, Ismail A, Verhaak RGW, Stead LF. IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy. Genome Biol 2024; 25:45. [PMID: 38326875 PMCID: PMC10848526 DOI: 10.1186/s13059-024-03172-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur. RESULTS Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression. In two thirds of patients, a specific subset of genes is upregulated from primary to recurrence (Up responders), and in one third, the same genes are downregulated (Down responders), specifically in neoplastic cells. Characterization of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms that are associated with distinct changes in the tumor microenvironment. In Up responders, recurrent tumors are enriched in quiescent proneural GBM stem cells and differentiated neoplastic cells, with increased interaction with the surrounding normal brain and neurotransmitter signaling, whereas Down responders commonly undergo mesenchymal transition. ChIP-sequencing data from longitudinal GBM tumors suggests that the observed transcriptional reprogramming could be driven by Polycomb-based chromatin remodeling rather than DNA methylation. CONCLUSIONS We show that the responder subtype is cancer-cell intrinsic, recapitulated in in vitro GBM cell models, and influenced by the presence of the tumor microenvironment. Stratifying GBM tumors by responder subtype may lead to more effective treatment.
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Affiliation(s)
- Georgette Tanner
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Rhiannon Barrow
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Shoaib Ajaib
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Muna Al-Jabri
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Nazia Ahmed
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Steven Pollock
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Martina Finetti
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Nora Rippaus
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Alexander F Bruns
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - James A Poulter
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Laura Matthews
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Thomas Hughes
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- School of Science, Technology and Health, York St John University, York, YO31 7EX, UK
| | - Erica Wilson
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Colin Johnson
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Catherine Hogg
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | | | | | - Matthew A Care
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Luisa Cutillo
- School of Mathematics, University of Leeds, Leeds, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Susan C Short
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- Leeds Teaching Hospital, Leeds, UK
| | - Michael D Jenkinson
- The Walton Centre NHS Foundation Trust, Liverpool, UK
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | | | | | | | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Lucy F Stead
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.
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Ovchinnikova S, Anders S. Simple but powerful interactive data analysis in R with R/LinekdCharts. Genome Biol 2024; 25:43. [PMID: 38317238 PMCID: PMC10840235 DOI: 10.1186/s13059-024-03164-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
In research involving data-rich assays, exploratory data analysis is a crucial step. Typically, this involves jumping back and forth between visualizations that provide overview of the whole data and others that dive into details. For example, it might be helpful to have one chart showing a summary statistic for all samples, while a second chart provides details for points selected in the first chart. We present R/LinkedCharts, a framework that renders this task radically simple, requiring very few lines of code to obtain complex and general visualization, which later can be polished to provide interactive data access of publication quality.
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Affiliation(s)
- Svetlana Ovchinnikova
- Center for Molecular Biology and BioQuant Center of the University of Heidelberg, Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology and BioQuant Center of the University of Heidelberg, Heidelberg, Germany.
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Radaic A, Shamir ER, Jones K, Villa A, Garud NR, Tward AD, Kamarajan P, Kapila YL. Specific Oral Microbial Differences in Proteobacteria and Bacteroidetes Are Associated with Distinct Sites When Moving from Healthy Mucosa to Oral Dysplasia-A Microbiome and Gene Profiling Study and Focused Review. Microorganisms 2023; 11:2250. [PMID: 37764094 PMCID: PMC10534919 DOI: 10.3390/microorganisms11092250] [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: 07/18/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Oral potentially malignant disorders (OPMDs) are a group of conditions that carry a risk of oral squamous cell carcinoma (OSCC) development. Recent studies indicate that periodontal disease-associated pathogenic bacteria may play a role in the transition from healthy mucosa to dysplasia and to OSCC. Yet, the microbial signatures associated with the transition from healthy mucosa to dysplasia have not been established. To characterize oral microbial signatures at these different sites, we performed a 16S sequencing analysis of both oral swab and formalin-fixed, paraffin-embedded tissue (FFPE) samples. We collected oral swabs from healthy mucosa (from healthy patients), histologically normal mucosa adjacent to dysplasia, and low-grade oral dysplasia. Additionally, FFPE samples from histologically normal mucosa adjacent to OSCC, plus low grade and high-grade oral dysplasia samples were also collected. The collected data demonstrate significant differences in the alpha and beta microbial diversities of different sites in oral mucosa, dysplasia, and OSCC, as well as increased dissimilarities within these sites. We found that the Proteobacteria phyla abundance increased, concurrent with a progressive decrease in the Firmicutes phyla abundance, as well as altered levels of Enterococcus cecorum, Fusobacterium periodonticum, Prevotella melaninogenica, and Fusobacterium canifelinum when moving from healthy to diseased sites. Moreover, the swab sample analysis indicates that the oral microbiome may be altered in areas that are histologically normal, including in mucosa adjacent to dysplasia. Furthermore, trends in specific microbiome changes in oral swab samples preceded those in the tissues, signifying early detection opportunities for clinical diagnosis. In addition, we evaluated the gene expression profile of OSCC cells (HSC-3) infected with either P. gingivalis, T. denticola, F. nucelatum, or S. sanguinis and found that the three periodontopathogens enrich genetic processes related to cancer progression, including skin keratinization/cornification, while the commensal enriched processes related to RNA processing and adhesion. Finally, we reviewed the dysplasia microbiome literature and found a significant decrease in commensal bacteria, such as the Streptococci genus, and a simultaneous increase in pathogenic bacteria, mainly Bacteroidetes phyla and Fusobacterium genus. These findings suggest that features of the oral microbiome can serve as novel biomarkers for dysplasia and OSCC disease progression.
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Affiliation(s)
- Allan Radaic
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; (A.R.); (P.K.)
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
| | - Eliah R. Shamir
- School of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (E.R.S.); (A.D.T.)
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Kyle Jones
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
- Genentech, Inc., South San Francisco, CA 94080, USA
| | - Alessandro Villa
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | - Nandita R. Garud
- College of Life Sciences, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA;
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Aaron D. Tward
- School of Medicine, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (E.R.S.); (A.D.T.)
| | - Pachiyappan Kamarajan
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; (A.R.); (P.K.)
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
| | - Yvonne L. Kapila
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; (A.R.); (P.K.)
- School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA; (K.J.); (A.V.)
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6
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Zhang T, Kutler D, Scognamiglio T, Gudas LJ, Tang XH. Transcriptomic analysis predicts the risk of progression of premalignant lesions in human tongue. Discov Oncol 2023; 14:24. [PMID: 36820942 PMCID: PMC9950315 DOI: 10.1007/s12672-023-00629-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/12/2023] [Indexed: 02/24/2023] Open
Abstract
The 5-year survival rate for patients with oral squamous cell carcinomas (SCC), including tongue SCC, has not significantly improved over the last several decades. Oral potentially malignant disorders (OPMD), including oral dysplasias, are oral epithelial disorders that can develop into oral SCCs. To identify molecular characteristics that might predict conversion of OPMDs to SCCs and guide treatment plans, we performed global transcriptomic analysis of human tongue OPMD (n = 9) and tongue SCC (n = 11) samples with paired normal margin tissue from patients treated at Weill Cornell Medicine. Compared to margin tissue, SCCs showed more transcript changes than OPMDs. OPMDs and SCCs shared some altered transcripts, but these changes were generally greater in SCCs than OPMDs. Both OPMDs and SCCs showed altered signaling pathways related to cell migration, basement membrane disruption, and metastasis. We suggest that OPMDs are on the path toward malignant transformation. Based on patterns of gene expression, both OPMD and tongue SCC samples can be categorized into subclasses (mesenchymal, classical, basal, and atypical) similar to those seen in human head and neck SCC (HNSCC). These subclasses of OPMDs have the potential to be used to stratify patient prognoses and therapeutic options for tongue OPMDs. Lastly, we identified a gene set (ELF5; RPTN; IGSF10; CRMP1; HTR3A) whose transcript changes have the power to classify OPMDs and SCCs and developed a Firth logistic regression model using the changes in these transcripts relative to paired normal tissue to validate pathological diagnosis and potentially predict the likelihood of an OPMD developing into SCC, as data sets become available.
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Affiliation(s)
- Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - David Kutler
- Division of Head and Neck Surgery in the Department of Otolaryngology at New York Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, 10065, USA
| | - Theresa Scognamiglio
- Division of Anatomic Pathology, New York Presbyterian Hospital, Department of Pathology and Laboratory Medicine, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY, 10065, USA.
| | - Xiao-Han Tang
- Department of Pharmacology, Weill Cornell Medical College of Cornell University, 1300 York Avenue, New York, NY, 10065, USA.
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7
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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
- *Correspondence:Kue Peng Lim,
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Duhen T, Gough MJ, Leidner RS, Stanton SE. Development and therapeutic manipulation of the head and neck cancer tumor environment to improve clinical outcomes. FRONTIERS IN ORAL HEALTH 2022; 3:902160. [PMID: 35937775 PMCID: PMC9354490 DOI: 10.3389/froh.2022.902160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
The clinical response to cancer therapies involves the complex interplay between the systemic, tumoral, and stromal immune response as well as the direct impact of treatments on cancer cells. Each individual's immunological and cancer histories are different, and their carcinogen exposures may differ. This means that even though two patients with oral tumors may carry an identical mutation in TP53, they are likely to have different pre-existing immune responses to their tumors. These differences may arise due to their distinct accessory mutations, genetic backgrounds, and may relate to clinical factors including previous chemotherapy exposure and concurrent medical comorbidities. In isolation, their cancer cells may respond similarly to cancer therapy, but due to their baseline variability in pre-existing immune responses, patients can have different responses to identical therapies. In this review we discuss how the immune environment of tumors develops, the critical immune cell populations in advanced cancers, and how immune interventions can manipulate the immune environment of patients with pre-malignancies or advanced cancers to improve therapeutic outcomes.
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Affiliation(s)
| | - Michael J. Gough
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
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Chen X, Liu Y, Liu H, Wang ZW, Zhu X. Unraveling diverse roles of noncoding RNAs in various human papillomavirus negative cancers. Pharmacol Ther 2022; 238:108188. [PMID: 35421419 DOI: 10.1016/j.pharmthera.2022.108188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 12/17/2022]
Abstract
Human papillomavirus (HPV)-negative tumors distinguish from cancers associated with HPV infection. Due to its high rate of lymph node metastasis and difficulty in inchoate discover and diagnosis, the treatment efficacy of HPV-negative cancers is unsatisfactory. Epidemiological evidence suggests that HPV-negative tumor patients have a poor prognosis, and the mortality is higher than that of cancer patients caused by HPV infection. Evidence has demonstrated that noncoding RNAs (ncRNAs) play a crucial role in regulation of physiological and developmental processes. Therefore, dysregulated ncRNAs are involved in the occurrence of diversified diseases, including cancer. In cumulative studies, ncRNAs are concerned with pathogenetic mechanisms of HPV-negative tumors via regulating gene expression and signal transduction. It is important to decipher the functions of ncRNAs in HPV-negative cancers and identify the potential biomarkers, which will bring new treatment strategies for improving outcome of cancer therapy. In this review, we demonstrated the effects of ncRNAs via regulating the development and progression of HPV- negative tumors by directly or indirectly acting on target molecules, which provide a basis for future tumor targeted therapy by targeting ncRNAs for HPV-negative cancers.
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Affiliation(s)
- Xin Chen
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Hejing Liu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Zhi-Wei Wang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China; Department of Research and Development, Beijing Zhongwei Research Center of Biological and Translational Medicine, Beijing 100161, China.
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China.
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Genes and pathways monotonically dysregulated during progression from normal through leukoplakia to gingivo-buccal oral cancer. NPJ Genom Med 2021; 6:32. [PMID: 33980865 PMCID: PMC8115176 DOI: 10.1038/s41525-021-00195-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 01/17/2023] Open
Abstract
Oral squamous cell carcinoma of the gingivo-buccal region (OSCC-GB) accounts for the highest cancer morbidity and mortality among men in India. It has been observed that about one-third of individuals with oral leukoplakia, a dysplastic precancerous lesion in the oral cavity, progress to oral cancer. We aimed to identify systematic transcriptomic changes as a normal tissue in the oral cavity progresses to frank OSCC-GB. Seventy-two OSCC-GB patients, from multiple hospitals, were recruited, and transcriptome analysis of tumor and adjacent normal tissue (of all patients) and adjacent leukoplakia tissue (of a subset of 25 unselected patients with concomitant leukoplakia) was performed. We have identified many differences in the transcriptomic profiles between OSCC-GB and squamous cell carcinoma of the head and neck regions. Compared to the normal/precancerous tissue, significant enrichment of ECM−receptor interaction, PI3K-Akt signaling, cytokine−cytokine receptor interaction, focal adhesion, and cell cycle pathways were observed in OSCC-GB. Using gene set enrichment analysis, we identified a profound role of interferon receptor signaling in tumor growth by activating immune evasion mechanisms. The role of tumor-infiltrating immune cells further supported the growth and immunosuppressive mechanism of tumor tissues. Some immune evasion genes—CD274, CD80, and IDO1—were found to be activated even in the precancerous tissue. Taken together, our findings provide a clear insight into the sequential genetic dysregulation associated with progression to oral cancer. This insight provides a window to the development of predictive biomarkers and therapeutic targets for gingivo-buccal oral cancer.
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Odell E, Eckel HE, Simo R, Quer M, Paleri V, Klussmann JP, Remacle M, Sjögren E, Piazza C. European Laryngological Society position paper on laryngeal dysplasia Part I: aetiology and pathological classification. Eur Arch Otorhinolaryngol 2020; 278:1717-1722. [PMID: 33051798 PMCID: PMC8131293 DOI: 10.1007/s00405-020-06403-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/24/2020] [Indexed: 11/29/2022]
Abstract
Purpose of review To give an overview of the current knowledge regarding the aetiology, epidemiology, and classification of laryngeal dysplasia (LD) and to highlight the contributions of recent literature. As most cases of dysplasia occur at the glottic level and data on diagnosis and management are almost exclusively from this location, laryngeal dysplasia in this position paper is taken to be synonymous with dysplasia of the vocal folds. Summary LD has long been recognized as a precursor lesion to laryngeal squamous cell carcinoma (SCC). Tobacco and alcohol consumption are the two single most important etiological factors for the development of LD. There is currently insufficient evidence to support a role of reflux. Although varying levels of human papillomavirus have been identified in LD, its causal role is still uncertain, and there are data suggesting that it may be limited. Dysplasia has a varying presentation including leukoplakia, erythroleukoplakia, mucosal reddening or thickening with exophytic, “tumor-like” alterations. About 50% of leukoplakic lesions will contain some form of dysplasia. It has become clear that the traditionally accepted molecular pathways to cancer, involving accumulated mutations in a specific order, do not apply to LD. Although the molecular nature of the progression of LD to SCC is still unclear, it can be concluded that the risk of malignant transformation does rise with increasing grade of dysplasia, but not predictably so. Consequently, grading systems are inherently troubled by the weak correlation between the degree of the dysplasia and the risk of malignant transformation. The best data on LD grading and outcomes come from the Ljubljana group, forming the basis for the World Health Organization classification published in 2017.
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Affiliation(s)
- Edward Odell
- Head and Neck Pathology, King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Hans Edmund Eckel
- Department of Oto-Rhino-Laryngology, Klagenfurt General Hospital, Feschnigstr. 11, Klagenfurt, Austria
| | - Ricard Simo
- Department of Otorhinolaryngology Head and Neck Surgery, Guy's and St Thomas' Hospital NHS Foundation Trust, London, UK
| | - Miquel Quer
- Department of Otorhinolaryngology and Head and Neck Surgery, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vinidh Paleri
- Head and Neck Unit, Royal Marsden Hospital, London, UK
| | - Jens Peter Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, Cologne, Germany
| | - Marc Remacle
- Department of Otorhinolaryngology, Head and Neck Surgery, CH Luxembourg, Luxembourg, Belgium
| | - Elisabeth Sjögren
- Department of Otorhinolaryngology, Head and Neck Surgery, Leiden University Medical Center, Leiden, The Netherlands.
| | - Cesare Piazza
- Department of Otorhinolaryngology- Head and Neck Surgery, ASST Spedali Civili of Brescia, University of Brescia, Brescia, Italy
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12
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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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13
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Increased expression of PD-1 and PD-L1 in oral lesions progressing to oral squamous cell carcinoma: a pilot study. Sci Rep 2020; 10:9705. [PMID: 32546692 PMCID: PMC7297711 DOI: 10.1038/s41598-020-66257-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 04/24/2020] [Indexed: 02/07/2023] Open
Abstract
Oral cancer is a devastating disease and is commonly preceded by a range of oral premalignant disorders. We investigated the expression of PD-1 and PD-L1 in oral epithelial dysplasia (OED) that progressed to oral squamous cell carcinoma (OSCC) compared to non-progressing dysplasia. 49 oral biopsies were analyzed, including 19 progressing cases, 20 cases did not progress, and 10 OSCC. Samples were stained with monoclonal antibodies for PD-1 and PD-L1, followed by conventional peroxidase reaction immunohistochemistry (IHC) imaged under light microscopy or fluorescent immunohistochemistry (FIHC) imaged using a confocal microscope. Images were analyzed using a novel semi-automated analysis protocol. PD-1/PD-L1 expression was assessed at the epithelium/tumor cells (TC) and at inflammatory cells in lamina propria. Our results show a significant increase in PD-L1 expression in progressing compared to non-progressing dysplasia. Using FIHC, we showed increased PD-L1 expression, increased nuclear density in progressing dysplasia and a better interobserver agreement compared with IHC. We developed a new FIHC-based quantitative method to study PD-1/PD-L1 expression in FFPE samples and showed that PD-L1 is highly expressed in premalignant lesions progressing to cancer. Our results suggest that immunomodulation via PD-L1/PD-1 pathway occurs prior to malignant transformation.
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14
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da Silva B, Irving BK, Polson ES, Droop A, Griffiths HBS, Mathew RK, Stead LF, Marrison J, Williams C, Williams J, Short SC, Scarcia M, O'Toole PJ, Allison SJ, Mavria G, Wurdak H. Chemically induced neurite-like outgrowth reveals a multicellular network function in patient-derived glioblastoma cells. J Cell Sci 2019; 132:jcs.228452. [PMID: 31515278 DOI: 10.1242/jcs.228452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 09/02/2019] [Indexed: 12/22/2022] Open
Abstract
Tumor stem cells and malignant multicellular networks have been separately implicated in the therapeutic resistance of glioblastoma multiforme (GBM), the most aggressive type of brain cancer in adults. Here, we show that small-molecule inhibition of RHO-associated serine/threonine kinase proteins (ROCKi) significantly promoted the outgrowth of neurite-like cell projections in cultures of heterogeneous patient-derived GBM stem-like cells. These projections formed de novo-induced cellular network (iNet) 'webs', which regressed after withdrawal of ROCKi. Connected cells within the iNet web exhibited long range Ca2+ signal transmission, and significant lysosomal and mitochondrial trafficking. In contrast to their less-connected vehicle control counterparts, iNet cells remained viable and proliferative after high-dose radiation. These findings demonstrate a link between ROCKi-regulated cell projection dynamics and the formation of radiation-resistant multicellular networks. Our study identifies means to reversibly induce iNet webs ex vivo, and may thereby accelerate future studies into the biology of GBM cellular networks.
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Affiliation(s)
| | | | - Euan S Polson
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Alastair Droop
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
- Leeds Institute for Data Analytics, University of Leeds, Leeds, LS2 9JT, UK
| | - Hollie B S Griffiths
- School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | - Ryan K Mathew
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
- Department of Neurosurgery, Leeds General Infirmary, Leeds, LS1 3EX, UK
| | - Lucy F Stead
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Joanne Marrison
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Courtney Williams
- School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | | | - Susan C Short
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Peter J O'Toole
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Simon J Allison
- School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK
| | - Georgia Mavria
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
| | - Heiko Wurdak
- School of Medicine, University of Leeds, Leeds, LS2 9JT, UK
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15
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Farah CS, Fox SA. Dysplastic oral leukoplakia is molecularly distinct from leukoplakia without dysplasia. Oral Dis 2019; 25:1715-1723. [DOI: 10.1111/odi.13156] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Camile S. Farah
- UWA Dental School University of Western Australia Nedlands WA Australia
- Australian Centre for Oral Oncology Research & Education Nedlands WA Australia
| | - Simon A. Fox
- UWA Dental School University of Western Australia Nedlands WA Australia
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16
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Diniz MG, França JA, Vilas-Boas FA, de Souza FTA, Calin GA, Gomez RS, de Sousa SF, Gomes CC. The long noncoding RNA KIAA0125 is upregulated in ameloblastomas. Pathol Res Pract 2019; 215:466-469. [DOI: 10.1016/j.prp.2018.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/03/2018] [Accepted: 12/25/2018] [Indexed: 02/06/2023]
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17
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Prasad K, Rao R, Augustine D, Sowmya SV, Haragannavar V, Sagar P, Sreedhar P. Pathway based prognostic gene expression profile of buccal and gingivo-buccal oral squamous cell carcinoma in smokeless tobacco chewers. Head Neck 2018; 41:388-397. [PMID: 30536474 DOI: 10.1002/hed.25494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/14/2018] [Accepted: 08/31/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The objective was to study comprehensive mRNA expression profiles of buccal mucosa oral squamous cell carcinoma (OSCC-BM) and gingivo-buccal OSCC (OSCC-GB) in smokeless tobacco chewers to understand the biological behavior of OSCC at these specific sites and identify diagnostic and prognostic markers. METHODS High throughput RNA sequencing transcriptome of fresh buccal mucosa (4 samples) and gingivo-buccal (4 samples) OSCC with normal oral mucosa (3 samples) was performed on Illumina NextSeq500 paired end sequencing with 75x2bp. RESULTS In the comparison between OSCC and normal, there were 402 differentially expressed genes (DEGs); between OSCC-BM and normal, there were 467 DEGs; and between OSCC-GB and normal oral tissue, there were 608 DEGs. Pathway-based analysis of gene expression was done. The inflammation mediated by chemokine and cytokine signaling pathway had the maximum gene hits. CONCLUSIONS FZD2 and its interactions with the cadherins have a role in invasion and metastasis. immunosurveillance is evident in OSCC-GB with the downregulation of CADM1.
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Affiliation(s)
- Kavitha Prasad
- MDS, Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Roopa Rao
- MDS, Department of Oral and Maxillofacial Pathology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Dominic Augustine
- MDS, Department of Oral and Maxillofacial Pathology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Samudrala Venkatesiah Sowmya
- MDS, Department of Oral and Maxillofacial Pathology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Vanishri Haragannavar
- MDS, Department of Oral and Maxillofacial Pathology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Parimala Sagar
- MDS, Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Prathibha Sreedhar
- MDS, Department of Oral and Maxillofacial Surgery, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
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18
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Takkem A, Barakat C, Zakaraia S, Zaid K, Najmeh J, Ayoub M, Seirawan MY. Ki-67 Prognostic Value in Different Histological Grades of Oral Epithelial Dysplasia and Oral Squamous Cell Carcinoma. Asian Pac J Cancer Prev 2018; 19:3279-3286. [PMID: 30486632 PMCID: PMC6318382 DOI: 10.31557/apjcp.2018.19.11.3279] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Introduction: Abnormal cell proliferation appears to be a possible predictor of tumorigenesis, Ki-67 protein expression is closely related to the cell proliferation and could be used as a biomarker for the growth in the most of human tumors. The aim of the study: Investigating of Ki-67 expression in the pathological grades of oral epithelial dysplasia and oral squamous cell carcinomas. Materials and Methods: The sample consisted of 30 formalin-fixed, paraffin-embedded specimens of oral epithelial dysplasia (OED), 30 other of oral squamous cell carcinomas (OSCC), and 10 normal oral epithelium (NOE) were conventionally stained with hematoxylin and eosin and immunohistochemically stained with Ki-67 monoclonal antibody. Results: Expression of Ki-67 was restricted to the basal layers in the normal oral epithelium whereas Ki-67 positive cells in oral epithelial dysplasia (OED) were located in the basal, suprabasal and spinous layers, Ki-67 expression was increased in high-risk cases. Ki-67 positive cells in well-differentiated (OSCC) were located mainly in the periphery of the tumor nests, in moderately-differentiated (OSCC) were located in both peripheral and part of a center of the tumor nests whereas it was diffused in most of the Poorly-differentiated (OSCC). Statistical analysis indicated a significant difference between the expression in (OED) and (NOE), (OSCC) and (NOE), and no differences between (OED) and (OSCC). Conclusion: This study has concluded that Ki-67 antigen could be used as a marker for the histological grading of OED and OSCC, Expression of Ki 67 increased according to the severity of oral epithelial dysplasia.
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Affiliation(s)
- Amer Takkem
- Department of Oral Histology and Pathology, University of Damascus, Damascus, Syria.
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19
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Kanatas A, Mitchell DA. Genomic mutations and proof of causation between dysplasia and squamous cell carcinoma in medicolegal cases: a useful approach or a waste of resources? Br J Oral Maxillofac Surg 2018; 56:777-778. [PMID: 30340778 DOI: 10.1016/j.bjoms.2018.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/17/2018] [Indexed: 11/27/2022]
Affiliation(s)
- A Kanatas
- Leeds Teaching Hospitals and St James Institute of Oncology, Leeds Dental Institute and Leeds General Infirmary, LS1 3EX.
| | - D A Mitchell
- Leeds South and East Clinical Commissioning Group.
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20
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Sieviläinen M, Passador-Santos F, Almahmoudi R, Christopher S, Siponen M, Toppila-Salmi S, Salo T, Al-Samadi A. Immune checkpoints indoleamine 2,3-dioxygenase 1 and programmed death-ligand 1 in oral mucosal dysplasia. J Oral Pathol Med 2018; 47:773-780. [DOI: 10.1111/jop.12737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Meri Sieviläinen
- Department of Oral and Maxillofacial Diseases; Clinicum; University of Helsinki; Helsinki Finland
| | | | - Rabeia Almahmoudi
- Department of Oral and Maxillofacial Diseases; Clinicum; University of Helsinki; Helsinki Finland
| | - Solomon Christopher
- Department of Mathematics and Statistics; University of Helsinki; Helsinki Finland
| | - Maria Siponen
- Department of Oral and Maxillofacial Diseases; Kuopio University Hospital; Kuopio Finland
- Institute of Dentistry; University of Eastern Finland; Kuopio Finland
| | - Sanna Toppila-Salmi
- Department of Allergy; Helsinki University Hospital; University of Helsinki; Helsinki Finland
| | - Tuula Salo
- Department of Oral and Maxillofacial Diseases; Clinicum; University of Helsinki; Helsinki Finland
- Medical Research Centre; Oulu University Hospital; Oulu Finland
- Department of Diagnostics and Oral Medicine; Research Group of Cancer Research and Translational Medicine; Medical Faculty; University of Oulu; Oulu Finland
| | - Ahmed Al-Samadi
- Department of Oral and Maxillofacial Diseases; Clinicum; University of Helsinki; Helsinki Finland
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21
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Samson A, Scott KJ, Taggart D, West EJ, Wilson E, Nuovo GJ, Thomson S, Corns R, Mathew RK, Fuller MJ, Kottke TJ, Thompson JM, Ilett EJ, Cockle JV, van Hille P, Sivakumar G, Polson ES, Turnbull SJ, Appleton ES, Migneco G, Rose AS, Coffey MC, Beirne DA, Collinson FJ, Ralph C, Alan Anthoney D, Twelves CJ, Furness AJ, Quezada SA, Wurdak H, Errington-Mais F, Pandha H, Harrington KJ, Selby PJ, Vile RG, Griffin SD, Stead LF, Short SC, Melcher AA. Intravenous delivery of oncolytic reovirus to brain tumor patients immunologically primes for subsequent checkpoint blockade. Sci Transl Med 2018; 10:eaam7577. [PMID: 29298869 PMCID: PMC6276984 DOI: 10.1126/scitranslmed.aam7577] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 09/08/2017] [Accepted: 11/27/2017] [Indexed: 12/23/2022]
Abstract
Immune checkpoint inhibitors, including those targeting programmed cell death protein 1 (PD-1), are reshaping cancer therapeutic strategies. Evidence suggests, however, that tumor response and patient survival are determined by tumor programmed death ligand 1 (PD-L1) expression. We hypothesized that preconditioning of the tumor immune microenvironment using targeted, virus-mediated interferon (IFN) stimulation would up-regulate tumor PD-L1 protein expression and increase cytotoxic T cell infiltration, improving the efficacy of subsequent checkpoint blockade. Oncolytic viruses (OVs) represent a promising form of cancer immunotherapy. For brain tumors, almost all studies to date have used direct intralesional injection of OV, because of the largely untested belief that intravenous administration will not deliver virus to this site. We show, in a window-of-opportunity clinical study, that intravenous infusion of oncolytic human Orthoreovirus (referred to herein as reovirus) leads to infection of tumor cells subsequently resected as part of standard clinical care, both in high-grade glioma and in brain metastases, and increases cytotoxic T cell tumor infiltration relative to patients not treated with virus. We further show that reovirus up-regulates IFN-regulated gene expression, as well as the PD-1/PD-L1 axis in tumors, via an IFN-mediated mechanism. Finally, we show that addition of PD-1 blockade to reovirus enhances systemic therapy in a preclinical glioma model. These results support the development of combined systemic immunovirotherapy strategies for the treatment of both primary and secondary tumors in the brain.
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Affiliation(s)
- Adel Samson
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK.
| | - Karen J Scott
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - David Taggart
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Emma J West
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Erica Wilson
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Gerard J Nuovo
- Ohio State University, Comprehensive Cancer Centre, Columbus, OH 43210, USA
| | - Simon Thomson
- Leeds Teaching Hospitals National Health Service Trust, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Robert Corns
- Leeds Teaching Hospitals National Health Service Trust, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Ryan K Mathew
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Martin J Fuller
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | | | - Jill M Thompson
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Elizabeth J Ilett
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Julia V Cockle
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Philip van Hille
- Leeds Teaching Hospitals National Health Service Trust, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Gnanamurthy Sivakumar
- Leeds Teaching Hospitals National Health Service Trust, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Euan S Polson
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Samantha J Turnbull
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Elizabeth S Appleton
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Gemma Migneco
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Ailsa S Rose
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | | | - Deborah A Beirne
- Leeds Teaching Hospitals National Health Service Trust, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Fiona J Collinson
- Leeds Institute of Clinical Trials Research, Faculty of Medicine and Health, University of Leeds, Leeds, West Yorkshire LS2 9JT, UK
| | - Christy Ralph
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - D Alan Anthoney
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Christopher J Twelves
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | | | | | - Heiko Wurdak
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Fiona Errington-Mais
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | | | | | - Peter J Selby
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Richard G Vile
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen D Griffin
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Lucy F Stead
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK
| | - Susan C Short
- Leeds Institute of Cancer and Pathology, Faculty of Medicine and Health, University of Leeds, St James's University Hospital, Beckett Street, Leeds, West Yorkshire LS9 7TF, UK.
| | - Alan A Melcher
- Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, UK.
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22
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Droop A, Bruns A, Tanner G, Rippaus N, Morton R, Harrison S, King H, Ashton K, Syed K, Jenkinson MD, Brodbelt A, Chakrabarty A, Ismail A, Short S, Stead LF. How to analyse the spatiotemporal tumour samples needed to investigate cancer evolution: A case study using paired primary and recurrent glioblastoma. Int J Cancer 2017; 142:1620-1626. [PMID: 29194603 DOI: 10.1002/ijc.31184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/09/2017] [Accepted: 11/15/2017] [Indexed: 12/19/2022]
Abstract
Many traits of cancer progression (e.g., development of metastases or resistance to therapy) are facilitated by tumour evolution: Darwinian selection of subclones with distinct genotypes or phenotypes that enable such progression. Characterising these subclones provide an opportunity to develop drugs to better target their specific properties but requires the accurate identification of somatic mutations shared across multiple spatiotemporal tumours from the same patient. Current best practices for calling somatic mutations are optimised for single samples, and risk being too conservative to identify shared mutations with low prevalence in some samples. We reasoned that datasets from multiple matched tumours can be used for mutual validation and thus propose an adapted two-stage approach: (1) low-stringency mutation calling to identify mutations shared across samples irrespective of the weight of evidence in a single sample; (2) high-stringency mutation calling to further characterise mutations present in a single sample. We applied our approach to three-independent cohorts of paired primary and recurrent glioblastoma tumours, two of which have previously been analysed using existing approaches, and found that it significantly increased the amount of biologically relevant shared somatic mutations identified. We also found that duplicate removal was detrimental when identifying shared somatic mutations. Our approach is also applicable when multiple datasets e.g. DNA and RNA are available for the same tumour.
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Affiliation(s)
- Alastair Droop
- MRC Medical Bioinformatics Centre, University of Leeds, Leeds, LS2 9NL, United Kingdom
| | - Alexander Bruns
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Georgette Tanner
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Nora Rippaus
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Ruth Morton
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Sally Harrison
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Henry King
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Katherine Ashton
- Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Preston, PR2 9HT, United Kingdom
| | - Khaja Syed
- Walton Centre NHS Trust, Liverpool, L9 7LJ, United Kingdom
| | - Michael D Jenkinson
- Walton Centre NHS Trust, Liverpool, L9 7LJ, United Kingdom.,Institute of Translational Medicine, University of Liverpool, Liverpool, L9 7LJ, United Kingdom
| | | | - Aruna Chakrabarty
- Leeds Teaching Hospitals NHS Trust, St James's University Hospital, Leeds, LS9 7TF, United Kingdom
| | - Azzam Ismail
- Leeds Teaching Hospitals NHS Trust, St James's University Hospital, Leeds, LS9 7TF, United Kingdom
| | - Susan Short
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Lucy F Stead
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
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23
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Singh R, De Sarkar N, Sarkar S, Roy R, Chattopadhyay E, Ray A, Biswas NK, Maitra A, Roy B. Analysis of the whole transcriptome from gingivo-buccal squamous cell carcinoma reveals deregulated immune landscape and suggests targets for immunotherapy. PLoS One 2017; 12:e0183606. [PMID: 28886030 PMCID: PMC5590820 DOI: 10.1371/journal.pone.0183606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/08/2017] [Indexed: 01/19/2023] Open
Abstract
Background Gingivo-buccal squamous cell carcinoma (GBSCC) is one of the most common oral cavity cancers in India with less than 50% patients surviving past 5 years. Here, we report a whole transcriptome profile on a batch of GBSCC tumours with diverse tobacco usage habits. The study provides an entire landscape of altered expression with an emphasis on searching for targets with therapeutic potential. Methods Whole transcriptomes of 12 GBSCC tumours and adjacent normal tissues were sequenced and analysed to explore differential expression of genes. Expression changes were further compared with those in TCGA head and neck cohort (n = 263) data base and validated in an independent set of 10GBSCC samples. Results Differentially expressed genes (n = 2176) were used to cluster the patients based on their tobacco habits, resulting in 3 subgroups. Immune response was observed to be significantly aberrant, along with cell adhesion and lipid metabolism processes. Different modes of immune evasion were seen across 12 tumours with up-regulation or consistent expression of CD47, unlike other immune evasion genes such as PDL1, FUT4, CTLA4 and BTLA which were downregulated in a few samples. Variation in infiltrating immune cell signatures across tumours also indicates heterogeneity in immune evasion strategies. A few actionable genes such as ITGA4, TGFB1 and PTGS1/COX1 were over expressed in most samples. Conclusion This study found expression deregulation of key immune evasion genes, such as CD47 and PDL1, and reasserts their potential as effective immunotherapeutic targets for GBSCC, which requires further clinical studies. Present findings reiterate the idea of using transcriptome profiling to guide precision therapeutic strategies.
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Affiliation(s)
- Richa Singh
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | | | - Sumanta Sarkar
- National Institute of Biomedical Genomics, Kalyani, India
| | - Roshni Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | | | - Anindita Ray
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | | | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, India
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
- * E-mail:
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24
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Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM. Precancer Atlas to Drive Precision Prevention Trials. Cancer Res 2017; 77:1510-1541. [PMID: 28373404 DOI: 10.1158/0008-5472.can-16-2346] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 02/07/2023]
Abstract
Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA - an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510-41. ©2017 AACR.
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Affiliation(s)
- Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts.,Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ludmil Alexandrov
- Theoretical Division, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Rafael Bejar
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Olivera J Finn
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Madhav Dhodapkar
- Department of Hematology and Immunology, Yale Cancer Center, New Haven, Connecticut
| | - Neil E Kay
- Department of Hematology, Mayo Clinic Hospital, Rochester, Minnesota
| | - Esteban Braggio
- Department of Hematology, Mayo Clinic Hospital, Phoenix, Arizona
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah A Mazzilli
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts.,Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Timothy R Rebbeck
- Division of Hematology and Oncology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor E Velculescu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland.,Department of Pathology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Mary L Disis
- Department of Medicine, Center for Translational Medicine in Women's Health, University of Washington, Seattle, Washington
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott M Lippman
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California.
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25
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Wood HM, Daly C, Chalkley R, Senguven B, Ross L, Egan P, Chengot P, Graham J, Sethi N, Ong TK, MacLennan K, Rabbitts P, Conway C. The genomic road to invasion-examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples. Genome Med 2017; 9:53. [PMID: 28592326 PMCID: PMC5461742 DOI: 10.1186/s13073-017-0442-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND It is frequently assumed that pre-invasive lesions are simpler precursors of cancer and will contain a limited subset of the genomic changes seen in their associated invasive disease. Driver mutations are thought to occur early, but it is not known how many of these are present in pre-invasive lesions. These assumptions need to be tested with the increasing focus on both personalised cancer treatments and early detection methodologies. METHODS We examined genomic copy number changes in 256 pre-invasive and invasive samples from 69 oral cancer patients. Forty-eight samples from 16 patients were further examined using exome sequencing. RESULTS Evidence of a shared ancestor of both dysplasia and carcinoma was seen in all but one patient. One-third of dysplasias showed independent copy number events. The remainder had a copy number pattern that was similar to or simpler than that of the carcinoma. All dysplasias examined contained somatic mutations absent in the related carcinoma. Previously observed copy number changes and TP53 mutations were very frequently observed, and almost always shared between dysplasia and carcinoma. Other gene changes were more sporadic. Pathway analysis confirmed that each patient's disease developed in a different way. Examining the numbers of shared mutations and the rate of accumulation of mutations showed evidence that all samples contain a population of sub-clones, with little evidence of selective advantage of a subset of these. CONCLUSIONS These findings suggest that most of the genomic changes driving oral cancer occur in the pre-cancerous state by way of gradual random accumulation rather than a dramatic single event.
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Affiliation(s)
- Henry M Wood
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK.
| | - Catherine Daly
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK
| | - Rebecca Chalkley
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK
| | - Burcu Senguven
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK.,Department of Oral Pathology, Faculty of Dentistry, Gazi University, Ankara, Turkey
| | - Lisa Ross
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK
| | - Philip Egan
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK.,Northern Ireland Centre for Stratified Medicine, University of Ulster, Altnagelvin Hospital, Londonderry, Northern Ireland, BT47 6SB, UK
| | - Preetha Chengot
- St James's Institute of Oncology, St James's University Hospital, Leeds, LS9 7TF, UK
| | - Jennifer Graham
- St James's Institute of Oncology, St James's University Hospital, Leeds, LS9 7TF, UK
| | - Neeraj Sethi
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK
| | - Thian K Ong
- Leeds Dental Institute, Leeds General Infirmary, Leeds, LS2 9LU, UK
| | - Kenneth MacLennan
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK.,St James's Institute of Oncology, St James's University Hospital, Leeds, LS9 7TF, UK
| | - Pamela Rabbitts
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK
| | - Caroline Conway
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK.,Northern Ireland Centre for Stratified Medicine, University of Ulster, Altnagelvin Hospital, Londonderry, Northern Ireland, BT47 6SB, UK
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26
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Shaikh MH, Clarke DTW, Johnson NW, McMillan NAJ. Can gene editing and silencing technologies play a role in the treatment of head and neck cancer? Oral Oncol 2017; 68:9-19. [PMID: 28438299 DOI: 10.1016/j.oraloncology.2017.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 01/25/2017] [Accepted: 02/19/2017] [Indexed: 01/04/2023]
Abstract
Conventional treatment strategies have done little to improve the prognosis or disease-free survival in head and neck cancer (HNC) patients. Recent progress in our understanding of molecular aspects of head and neck squamous cell carcinoma (HNSCC) has provided insights into the potential use of molecular targeted therapies in combination with current treatment strategies. Here we review the current understanding of treatment modalities for both HPV-positive and HPV-negative HNSCCs with the potential to use gene editing and silencing technologies therapeutically. The development of sequence-specific RNA interference (RNAi) with its strong gene-specific silencing ability, high target specificity, greater potency and reduced side effects, has shown it to be a promising therapeutic candidate for treating cancers. CRISPR/Cas gene editing is the newest technology with the ability to delete, mutate or replace genes of interest and has great potential for treating HNSCCs. We also discuss the major challenge in using these approaches in HNSCC; that being the choice of target and the ability to deliver the payload. Finally, we highlight the potential combination of RNAi or CRIPSR/Cas with current treatment strategies and outline the possible path to the clinic.
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Affiliation(s)
- Mushfiq H Shaikh
- School of Dentistry and Oral Health, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; School of Medical Science, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Australia.
| | - Daniel T W Clarke
- School of Medical Science, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Australia.
| | - Newell W Johnson
- School of Dentistry and Oral Health, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Australia.
| | - Nigel A J McMillan
- School of Medical Science, Griffith University, Gold Coast Campus, Southport 4222, Queensland, Australia; Understanding Chronic Conditions Program, Menzies Health Institute Queensland, Australia.
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27
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Yang Q, Guo B, Sun H, Zhang J, Liu S, Hexige S, Yu X, Wang X. Identification of the key genes implicated in the transformation of OLP to OSCC using RNA-sequencing. Oncol Rep 2017; 37:2355-2365. [PMID: 28259920 DOI: 10.3892/or.2017.5487] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/02/2017] [Indexed: 11/06/2022] Open
Abstract
Oral lichen planus (OLP) is a chronic inflammatory disease that may transform to oral squamous cell carcinoma (OSCC), while its carcinogenesis mechanisms are not entirely clear. This study was designed to identify the important genes involved in the malignant transformation of OLP to OSCC. After RNA-sequencing, the differently expressed genes (DEGs) in OLP vs. normal and OSCC vs. normal groups, respectively, were identified by limma package in R language, and then clustering analysis were conducted by Pheatmap package in R language. Weighed gene co-expression network analysis (WGCNA) was performed for the DEGs to screen disease-associated modules. Using Cytoscape software, co-expression networks were constructed for the genes involved in the modules. Enrichment analysis was conducted for the genes involved in the co-expression networks using GOstat package in R language. Finally, quantitative real-time PCR (qRT-PCR) experiments were conducted to validate the key genes. There were, respectively, 223 and 548 DEGs in OLP vs. normal and OSCC vs. normal groups. WGCNA identified the blue modules for the DEGs in the two groups as disease-associated modules. Moreover, 19 common DEGs (including upregulated BCL9L, PER2 and TSPAN33, and downregulated GMPS and HES1) associated with both OLP and OSCC were identified. In the co-expression networks, BCL9L, HES1, PER2 and TSPAN33 might function in OLP via interactions (such as BCL9L-TSPAN33 and HES1-PER2). qRT-PCR analysis showed that BCL9L, PER2 and TSPAN33 were significantly upregulated, and GMP and HES1 were downregulated. These findings indicated that BCL9L, GMPS, HES1, PER2 and TSPAN33 affected the transformation of OLP to OSCC.
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Affiliation(s)
- Qiaozhen Yang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Bin Guo
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Hongying Sun
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jie Zhang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Shangfeng Liu
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Saiyin Hexige
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Xuedi Yu
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xiaxia Wang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
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28
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The emerging role of long noncoding RNAs in oral cancer. Oral Surg Oral Med Oral Pathol Oral Radiol 2016; 123:235-241. [PMID: 27989708 DOI: 10.1016/j.oooo.2016.10.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/12/2016] [Accepted: 10/04/2016] [Indexed: 01/01/2023]
Abstract
Although less than 3% of the genome encodes proteins, at least 75% of the genome is transcribed into RNAs with no protein-coding potential (noncoding RNAs [ncRNAs]). On the basis of their size and the arbitrary 200 nucleotides cutoff, ncRNAs are classified into long ncRNAs (lncRNAs) or small ncRNAs (including microRNAs). Over the last few years, the role of microRNAs in oral squamous cells carcinoma (OSCC) has been extensively addressed, but the possible role of lncRNAs in OSCC remains unclear. We aimed to explore and discuss the potential role of lncRNAs in OSCC. The detection of lncRNAs in saliva holds promise not only as a noninvasive diagnostic tool in OSCC but also in the early detection of oral cancer recurrence. lncRNAs are promising future therapeutic targets in the OSCC scenario, and research in this field may expand greatly in the next decade.
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