Whole-exome sequencing of oral epithelial dysplasia samples reveals an association with new genes

Daniela Adorno-Farias; Jean Nunes Dos Santos; Wilfredo González-Arriagada; Sandra Tarquinio; Rodrigo Alberto Santibáñez Palominos; Alberto Jesus Martín Martín; Ricardo Fernandez-Ramires

doi:10.1590/1807-3107BOR-2023.VOL37.0016

Whole-exome sequencing of oral epithelial dysplasia samples reveals an association with new genes

Daniela Adorno-Farias, Jean Nunes Dos Santos, Wilfredo González-Arriagada, Sandra Tarquinio, Rodrigo Alberto Santibáñez Palominos, Alberto Jesus Martín Martín, Ricardo Fernandez-Ramires^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

2 Scopus citations

Abstract

The genetic basis of oral epithelial (OED) is unknown, and there is no reliable method for evaluating the risk of malignant transformation. Somatic mutations are responsible for the transformation of dysplastic mucosa to invasive cancer. In addition, these genomic variations could represent objective markers of the potential for malignant transformation. We performed whole-exome sequencing of 10 OED samples from Brazilian and Chilean patients. Using public genetic repositories, we identified 41 deleterious variants that could produce high-impact changes in the amino acid structures of 38 genes. In addition, the variants were filtered according to normal skin and Native American genome profiles. Finally, 13 genes harboring 15 variants were found to be exclusively related to OED. High-grade epithelial dysplasia samples showed a tendency to accumulate highly deleterious variants. We observed that 62% of 13 OED genes identified in our study were also found in head and neck squamous cell carcinoma. Among the shared genes, eight were not identified in oral squamous cell carcinoma. To our knowledge, we have described for the first time 13 genes that are found in OED in a Latin American population, of which five genes have already been observed in oral squamous cell carcinoma.

Original language	English
Article number	e016
Pages (from-to)	e016
Journal	Brazilian Oral Research
Volume	37
DOIs	https://doi.org/10.1590/1807-3107BOR-2023.VOL37.0016
State	Published - 2023

Bibliographical note

Funding Information:
All procedures performed in this study were in accordance with the ethical standards of the Scholl Dentistry of the University of Chile (Approval No. 2014/29) committee and with the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards. The patients were not directly involved in this study. Funding: FONDECYT nº 11140281 (Ricardo Fernandez-Ramires), Centro Ciencia & Vida, FB210008, Financiamiento Basal para Centros Científicos y Tecnológicos de Excelencia de ANID

Publisher Copyright:
© 2023, Brazilian Oral Research. All rights reserved

ASJC Scopus subject areas

General Dentistry

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1590/1807-3107BOR-2023.VOL37.0016

Cite this

@article{e1deaeaf6d874bdcbb58038e720230a4,

title = "Whole-exome sequencing of oral epithelial dysplasia samples reveals an association with new genes",

abstract = "The genetic basis of oral epithelial (OED) is unknown, and there is no reliable method for evaluating the risk of malignant transformation. Somatic mutations are responsible for the transformation of dysplastic mucosa to invasive cancer. In addition, these genomic variations could represent objective markers of the potential for malignant transformation. We performed whole-exome sequencing of 10 OED samples from Brazilian and Chilean patients. Using public genetic repositories, we identified 41 deleterious variants that could produce high-impact changes in the amino acid structures of 38 genes. In addition, the variants were filtered according to normal skin and Native American genome profiles. Finally, 13 genes harboring 15 variants were found to be exclusively related to OED. High-grade epithelial dysplasia samples showed a tendency to accumulate highly deleterious variants. We observed that 62% of 13 OED genes identified in our study were also found in head and neck squamous cell carcinoma. Among the shared genes, eight were not identified in oral squamous cell carcinoma. To our knowledge, we have described for the first time 13 genes that are found in OED in a Latin American population, of which five genes have already been observed in oral squamous cell carcinoma.",

keywords = "Leukoplakia, Whole Exome Sequencing",

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note = "Funding Information: All procedures performed in this study were in accordance with the ethical standards of the Scholl Dentistry of the University of Chile (Approval No. 2014/29) committee and with the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards. The patients were not directly involved in this study. Funding: FONDECYT nº 11140281 (Ricardo Fernandez-Ramires), Centro Ciencia & Vida, FB210008, Financiamiento Basal para Centros Cient{\'i}ficos y Tecnol{\'o}gicos de Excelencia de ANID Publisher Copyright: {\textcopyright} 2023, Brazilian Oral Research. All rights reserved",

year = "2023",

doi = "10.1590/1807-3107BOR-2023.VOL37.0016",

language = "English",

volume = "37",

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journal = "Brazilian Oral Research",

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AU - Adorno-Farias, Daniela

AU - Dos Santos, Jean Nunes

AU - González-Arriagada, Wilfredo

AU - Tarquinio, Sandra

AU - Palominos, Rodrigo Alberto Santibáñez

AU - Martín, Alberto Jesus Martín

AU - Fernandez-Ramires, Ricardo

N1 - Funding Information: All procedures performed in this study were in accordance with the ethical standards of the Scholl Dentistry of the University of Chile (Approval No. 2014/29) committee and with the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards. The patients were not directly involved in this study. Funding: FONDECYT nº 11140281 (Ricardo Fernandez-Ramires), Centro Ciencia & Vida, FB210008, Financiamiento Basal para Centros Científicos y Tecnológicos de Excelencia de ANID Publisher Copyright: © 2023, Brazilian Oral Research. All rights reserved

PY - 2023

Y1 - 2023

N2 - The genetic basis of oral epithelial (OED) is unknown, and there is no reliable method for evaluating the risk of malignant transformation. Somatic mutations are responsible for the transformation of dysplastic mucosa to invasive cancer. In addition, these genomic variations could represent objective markers of the potential for malignant transformation. We performed whole-exome sequencing of 10 OED samples from Brazilian and Chilean patients. Using public genetic repositories, we identified 41 deleterious variants that could produce high-impact changes in the amino acid structures of 38 genes. In addition, the variants were filtered according to normal skin and Native American genome profiles. Finally, 13 genes harboring 15 variants were found to be exclusively related to OED. High-grade epithelial dysplasia samples showed a tendency to accumulate highly deleterious variants. We observed that 62% of 13 OED genes identified in our study were also found in head and neck squamous cell carcinoma. Among the shared genes, eight were not identified in oral squamous cell carcinoma. To our knowledge, we have described for the first time 13 genes that are found in OED in a Latin American population, of which five genes have already been observed in oral squamous cell carcinoma.

AB - The genetic basis of oral epithelial (OED) is unknown, and there is no reliable method for evaluating the risk of malignant transformation. Somatic mutations are responsible for the transformation of dysplastic mucosa to invasive cancer. In addition, these genomic variations could represent objective markers of the potential for malignant transformation. We performed whole-exome sequencing of 10 OED samples from Brazilian and Chilean patients. Using public genetic repositories, we identified 41 deleterious variants that could produce high-impact changes in the amino acid structures of 38 genes. In addition, the variants were filtered according to normal skin and Native American genome profiles. Finally, 13 genes harboring 15 variants were found to be exclusively related to OED. High-grade epithelial dysplasia samples showed a tendency to accumulate highly deleterious variants. We observed that 62% of 13 OED genes identified in our study were also found in head and neck squamous cell carcinoma. Among the shared genes, eight were not identified in oral squamous cell carcinoma. To our knowledge, we have described for the first time 13 genes that are found in OED in a Latin American population, of which five genes have already been observed in oral squamous cell carcinoma.

KW - Leukoplakia

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SN - 1806-8324

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ER -

Whole-exome sequencing of oral epithelial dysplasia samples reveals an association with new genes

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

Access to Document

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