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Prognostic and therapeutic prediction by screening signature combinations from transcriptome-methylome interactions in oral squamous cell carcinoma. Sci Rep 2022; 12:11400. [PMID: 35794182 PMCID: PMC9259703 DOI: 10.1038/s41598-022-15534-7] [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: 01/11/2022] [Accepted: 06/24/2022] [Indexed: 02/05/2023] Open
Abstract
DNA methylation pattern in oral squamous cell carcinoma (OSCC) remains poorly described. This study aimed to perform a genome-wide integrated analysis of the transcriptome and methylome and assess the efficacy of their prognostic signature model in patients with OSCC. We analyzed transcriptome and methylome data from 391 OSCC samples and 41 adjacent normal samples. A total of 8074 differentially expressed genes (DEGs) and 10,084 differentially expressed CpGs (DMCpGs) were identified. Then 241 DEGs with DMCpGs were identified. According to the prognostic analysis, the prognostic signature of methylation-related differentially expressed genes (mrDEGPS) was established. mrDEGPS consisted of seven prognostic methylation-related genes, including ESRRG, CCNA1, SLC20A1, COL6A6, FCGBP, CDKN2A, and ZNF43. mrDEGPS was a significant stratification factor of survival (P < 0.00001) irrespective of the clinical stage. The immune effector components, including B cells, CD4+ T cells, and CD8+ T cells, were decreased in the tumor environment of patients with high mrDEGPS. Immune checkpoint expressions, including CTLA-4, PD-1, LAG3, LGALS9, HAVCR2, and TIGHT, were comprehensively elevated (P < 0.001). The estimated half-maximal inhibitory concentration difference between low- and high-risk patients was inconsistent among chemotherapeutic drugs. In conclusion, the transcriptome–methylome interaction pattern in OSCC is complex. mrDEGPS can predict patient survival and responses to immunotherapy and chemotherapy and facilitate clinical decision-making in patients with OSCC.
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On the Cutting Edge of Oral Cancer Prevention: Finding Risk-Predictive Markers in Precancerous Lesions by Longitudinal Studies. Cells 2022; 11:cells11061033. [PMID: 35326482 PMCID: PMC8947091 DOI: 10.3390/cells11061033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 02/06/2023] Open
Abstract
Early identification and management of precancerous lesions at high risk of developing cancers is the most effective and economical way to reduce the incidence, mortality, and morbidity of cancers as well as minimizing treatment-related complications, including pain, impaired functions, and disfiguration. Reliable cancer-risk-predictive markers play an important role in enabling evidence-based decision making as well as providing mechanistic insight into the malignant conversion of precancerous lesions. The focus of this article is to review updates on markers that may predict the risk of oral premalignant lesions (OPLs) in developing into oral squamous cell carcinomas (OSCCs), which can logically be discovered only by prospective or retrospective longitudinal studies that analyze pre-progression OPL samples with long-term follow-up outcomes. These risk-predictive markers are different from those that prognosticate the survival outcome of cancers after they have been diagnosed and treated, or those that differentiate between different lesion types and stages. Up-to-date knowledge on cancer-risk-predictive markers discovered by longitudinally followed studies will be reviewed. The goal of this endeavor is to use this information as a starting point to address some key challenges limiting our progress in this area in the hope of achieving effective translation of research discoveries into new clinical interventions.
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Pink R, Michalek J, Kral D, Mozola M, Benes P, Lenka S, Dvorak Z. Importance of evaluation of bone invasion type in squamous cell carcinomas of the oral cavity and oropharynx. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2021. [PMID: 34782797 DOI: 10.5507/bp.2021.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
AIMS The objective of this study was to compare bone invasion type with histopathological, clinical and immunohistochemical prognostic factors. METHODS The study included 49 patients who were treated for oral squamous cell carcinoma. Of which, 30 patients, with presence of bone invasion on histopathology, were divided according to the type of bone invasion (erosive, infiltrative, mixed). Each invasion type was compared to microvascular density using the CD34 marker. RESULTS The bone invasion was observed in 30 out of 49 patients (61.22%). On McNemar's test, statistically significant association was observed between bone invasion types and histopathological grade. In contrast, no significant correlation was observed between bone invasion type, and tumour volume or nodal metastases. In tumours with bone invasion of the infiltrative type, higher frequency of locoregional relapses was observed. The 5-year survival, since diagnosis, was approximately 60% in the erosive group, 40% in the mixed group, and merely 15% in the infiltrative group. CONCLUSION Peritumoural microvascular density was not significantly related to bone invasion types. Whereas, a significantly higher intratumoural microvascular density was observed in infiltrative type of the bone invasion, when compared to the erosive and mixed type.
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Affiliation(s)
- Richard Pink
- Department of Oral and Maxillofacial Surgery, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Jaroslav Michalek
- Department of Clinical and Molecular Pathology, University Hospital Olomouc, Czech Republic
| | - David Kral
- Department of Oral and Maxillofacial Surgery, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Michal Mozola
- Department of Oral and Maxillofacial Surgery, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Pavel Benes
- Department of Oral and Maxillofacial Surgery, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Saskova Lenka
- Department of Oral and Maxillofacial Surgery, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic
| | - Zdenek Dvorak
- Department of Oral and Maxillofacial Surgery, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacky University Olomouc, Czech Republic.,Department of Plastic and Aesthetic Surgery, St. Anne's Faculty Hospital and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Gissi DB, Fabbri VP, Gabusi A, Lenzi J, Morandi L, Melotti S, Asioli S, Tarsitano A, Balbi T, Marchetti C, Montebugnoli L. Pre-Operative Evaluation of DNA Methylation Profile in Oral Squamous Cell Carcinoma Can Predict Tumor Aggressive Potential. Int J Mol Sci 2020; 21:ijms21186691. [PMID: 32937734 PMCID: PMC7555204 DOI: 10.3390/ijms21186691] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/21/2020] [Accepted: 09/08/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Prognosis of oral squamous cell carcinoma (OSCC) is difficult to exactly assess on pre-operative biopsies. Since OSCC DNA methylation profile has proved to be a useful pre-operative diagnostic tool, the aim of the present study was to evaluate the prognostic impact of DNA methylation profile to discriminate OSCC with high and low aggressive potential. METHODS 36 OSCC cases underwent neoplastic cells collection by gentle brushing of the lesion, before performing a pre-operative biopsy. The CpG islands methylation status of 13 gene (ZAP70, ITGA4, KIF1A, PARP15, EPHX3, NTM, LRRTM1, FLI1, MiR193, LINC00599, MiR296, TERT, GP1BB) was studied by bisulfite Next Generation Sequencing (NGS). A Cox proportional hazards model via likelihood-based component-wise boosting was used to evaluate the prognostic power of the CpG sites. RESULTS The boosting estimation identified five CpGs with prognostic significance: EPHX3-24, EPHX3-26, ITGA4-3, ITGA4-4, and MiR193-3. The combination of significant CpGs provided promising results for adverse events prediction (Brier score = 0.080, C-index = 0.802 and AUC = 0.850). ITGA4 had a strong prognostic power in patients with early OSCC. CONCLUSIONS These data confirm that the study of methylation profile provides new insights into the molecular mechanisms of OSCC and can allow a better OSCC prognostic stratification even before surgery.
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Affiliation(s)
- Davide B. Gissi
- Section of Oral Science, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40159 Bologna, Italy; (D.B.G.); (A.G.); (L.M.)
| | - Viscardo P. Fabbri
- Section of Anatomic Pathology at Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy; (V.P.F.); (S.M.); (S.A.)
| | - Andrea Gabusi
- Section of Oral Science, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40159 Bologna, Italy; (D.B.G.); (A.G.); (L.M.)
| | - Jacopo Lenzi
- Section of Hygiene, Public Health and Medical Statistics, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy;
| | - Luca Morandi
- Functional MR Unit, Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy
- Correspondence:
| | - Sofia Melotti
- Section of Anatomic Pathology at Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy; (V.P.F.); (S.M.); (S.A.)
| | - Sofia Asioli
- Section of Anatomic Pathology at Bellaria Hospital, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139 Bologna, Italy; (V.P.F.); (S.M.); (S.A.)
| | - Achille Tarsitano
- Unit of Oral and Maxillofacial Surgery, Azienda Ospedaliero-Universitaria di Bologna, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40138 Bologna, Italy; (A.T.); (C.M.)
| | - Tiziana Balbi
- Unit of Anatomic Pathology, S. Orsola Hospital, 40138 Bologna, Italy;
| | - Claudio Marchetti
- Unit of Oral and Maxillofacial Surgery, Azienda Ospedaliero-Universitaria di Bologna, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40138 Bologna, Italy; (A.T.); (C.M.)
| | - Lucio Montebugnoli
- Section of Oral Science, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40159 Bologna, Italy; (D.B.G.); (A.G.); (L.M.)
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Dai Y, Lv Q, Qi T, Qu J, Ni H, Liao Y, Liu P, Qu Q. Identification of hub methylated-CpG sites and associated genes in oral squamous cell carcinoma. Cancer Med 2020; 9:3174-3187. [PMID: 32155325 PMCID: PMC7196066 DOI: 10.1002/cam4.2969] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/07/2020] [Accepted: 02/16/2020] [Indexed: 12/15/2022] Open
Abstract
To improve personalized diagnosis and prognosis for oral squamous cell carcinoma (OSCC) by identification of hub methylated‐CpG sites and associated genes, weighted gene comethylation network analysis (WGCNA) was performed to examine and identify hub modules and CpG sites correlated with OSCC. Here, WGCNA modeling yielded blue and brown comethylation modules that were significantly associated with OSCC status. Following screening of the differentially expressed genes (DEGs) from gene expression microarrays and differentially methylated‐CpG sites (DCGs), integrated multiomics analysis of the DEGs, DCGs, and hub CpG sites from the modules was performed to investigate their correlations. Expression levels of 16 CpG sites‐associated genes were negatively correlated with methylation patterns of promoter. Moreover, Kaplan‐Meier survival analysis of the hub CpG sites and associated genes was carried out using 2 public databases, MethSurv and GEPIA. Only 5 genes, ACTA1, ACTN2, OSR1, SYNGR1, and ZNF677, had significant overall survival using GEPIA. Hypermethylated‐CpG sites ACTN2‐cg21376883 and OSR1‐cg06509239 were found to be associated with poor survival by MethSurv. Methylation status of specific site and expression levels of associated genes were determined using clinical samples by quantitative methylation‐specific PCR and real‐time PCR. Pearson's correlation analysis showed that methylation levels of cg06509239 and cg18335068 were negatively related to OSR1 and ZNF677 expression levels, respectively. Our classification schema using multiomics analysis represents a screening framework for identification of hub CpG sites and associated genes.
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Affiliation(s)
- Yuxin Dai
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiaoli Lv
- Department of Science and Education, Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Nanchang, Jiangxi, China
| | - Tingting Qi
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Qu
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongli Ni
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yongkang Liao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Peng Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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