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Gintoni I, Vassiliou S, Chrousos GP, Yapijakis C. Identification of Stage-Specific microRNAs that Govern the Early Stages of Sequential Oral Oncogenesis by Strategically Bridging Human Genetics with Epigenetics and Utilizing an Animal Model. Int J Mol Sci 2024; 25:7642. [PMID: 39062890 PMCID: PMC11277563 DOI: 10.3390/ijms25147642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/02/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a highly prevalent and aggressive malignancy, with mortality rates reaching 60%, mainly due to its excessive diagnostic delay. MiRNAs, a class of crucial epigenetic gene-expression regulators, have emerged as potential diagnostic biomarkers, with >200 molecules exhibiting expressional dysregulation in OSCC. We had previously established an in silico methodology for the identification of the most disease-specific molecules by bridging genetics and epigenetics. Here, we identified the stage-specific miRNAs that govern the asymptomatic early stages of oral tumorigenesis by exploiting seed-matching and the reverse interplay between miRNA levels and their target genes' expression. Incorporating gene-expression data from our group's experimental hamster model of sequential oral oncogenesis, we bioinformatically detected the miRNAs that simultaneously target/regulate >75% of the genes that are characteristically upregulated or downregulated in the consecutive stages of hyperplasia, dysplasia, and early invasion, while exhibiting the opposite expressional dysregulation in OSCC-derived tissue and/or saliva specimens. We found that all stages share the downregulation of miR-34a-5p, miR124-3p, and miR-125b-5p, while miR-1-3p is under-expressed in dysplasia and early invasion. The malignant early-invasion stage is distinguished by the downregulation of miR-147a and the overexpression of miR-155-5p, miR-423-3p, and miR-34a-5p. The identification of stage-specific miRNAs may facilitate their utilization as biomarkers for presymptomatic OSCC diagnosis.
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Affiliation(s)
- Iphigenia Gintoni
- Unit of Orofacial Genetics, 1st Department of Pediatrics, School of Medicine, National Kapodistrian University of Athens, “Aghia Sophia” Children’s Hospital, 115 27 Athens, Greece;
- Department of Molecular Genetics, Cephalogenetics Center, 176 72 Athens, Greece
- Department of Oral and Maxillofacial Surgery, School of Medicine, National Kapodistrian University of Athens, Attikon Hospital, 124 62 Athens, Greece;
- University Research Institute for the Study of Genetic and Malignant Disorders in Childhood, Choremion Laboratory, “Aghia Sophia” Children’s Hospital, 115 27 Athens, Greece
| | - Stavros Vassiliou
- Department of Oral and Maxillofacial Surgery, School of Medicine, National Kapodistrian University of Athens, Attikon Hospital, 124 62 Athens, Greece;
| | - George P. Chrousos
- University Research Institute for the Study of Genetic and Malignant Disorders in Childhood, Choremion Laboratory, “Aghia Sophia” Children’s Hospital, 115 27 Athens, Greece
| | - Christos Yapijakis
- Unit of Orofacial Genetics, 1st Department of Pediatrics, School of Medicine, National Kapodistrian University of Athens, “Aghia Sophia” Children’s Hospital, 115 27 Athens, Greece;
- Department of Molecular Genetics, Cephalogenetics Center, 176 72 Athens, Greece
- Department of Oral and Maxillofacial Surgery, School of Medicine, National Kapodistrian University of Athens, Attikon Hospital, 124 62 Athens, Greece;
- University Research Institute for the Study of Genetic and Malignant Disorders in Childhood, Choremion Laboratory, “Aghia Sophia” Children’s Hospital, 115 27 Athens, Greece
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Gopalakrishnan S, Pandi A, Arumugam P, Jayaseelan VP. MicroRNAs targeting CDKN2A gene as a potential prognostic marker in head and neck squamous cell carcinoma. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2024; 13:21-27. [PMID: 38164368 PMCID: PMC10644311 DOI: 10.22099/mbrc.2023.48081.1853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Epigenetic factors are known to markedly influence the functions of a gene by modification of transcripts, via methylation or acetylation and degradation of mRNA transcripts. The CDKN2A encodes cyclin-dependent kinase inhibitor 2A, a tumour suppressor protein. Genetic and epigenetic alterations in this gene have been demonstrated in several cancer types. The non-coding RNAs with a special emphasis on microRNAs have long been explored for their potential role in the epigenetic modification of gene expression. The present study aims to identify the microRNAs targeting CDKN2A gene transcripts and demonstrate their prognostic significance in head and neck squamous cell carcinoma (HNSCC). Computational approaches were employed to identify the microRNAs targeting CDKN2A. The gene and protein expression profile of CDKN2A was analyzed using UALCAN. A significant upregulation of CDKN2A was observed in the primary tumour tissues (p=<10-12). Interestingly, the protein expression, although found to be statistically significant (p=0.0129) did not correlate well with the gene expression profile. The microRNAs targeting CDKN2A were further analyzed to identify the possible reason for the decrease in protein expression. Among the 44 microRNAs targeting CDKN2A gene transcripts, hsa-miR-3681-3p, hsa-miR-542-5p, hsa-miR-4519 were found to be upregulated and hsa-miR-134-5p was found to be downregulated with a significant association with survival status of HNSCC patients. The hsa-miR-542-5p was found to correlate well with the survival and hence can be considered as the key microRNA associated with HNSCC. However, further validation of this microRNA is warranted to confirm its role in the process of carcinogenesis.
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Affiliation(s)
- Sivakumar Gopalakrishnan
- Clinical Genetics Lab, Centre for Cellular and Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Chennai, India
- Department of Oral Pathology and Microbiology, Madha Dental College and Hospital, Kundrathur, Chennai-69
| | - Anitha Pandi
- Clinical Genetics Lab, Centre for Cellular and Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Chennai, India
| | - Paramasivam Arumugam
- Molecular Biology Lab, Centre for Cellular and Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Chennai, India
| | - Vijayashree Priyadharsini Jayaseelan
- Clinical Genetics Lab, Centre for Cellular and Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Chennai, India
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