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Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples
Hypomethylation of DNA is a hallmark of cancer and its analysis as tumor biomarker has been proposed, but its determination in clinical settings is hampered by lack of standardized methodologies. Here, we present QUAlu (Quantification of Unmethylated Alu), a new technique to estimate the Percentage...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Impact Journals LLC
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891138/ https://www.ncbi.nlm.nih.gov/pubmed/26859682 http://dx.doi.org/10.18632/oncotarget.7233 |
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author | Buj, Raquel Mallona, Izaskun Díez-Villanueva, Anna Barrera, Víctor Mauricio, Dídac Puig-Domingo, Manel Reverter, Jordi L. Matias-Guiu, Xavier Azuara, Daniel Ramírez, Jose L. Alonso, Sergio Rosell, Rafael Capellà, Gabriel Perucho, Manuel Robledo, Mercedes Peinado, Miguel A. Jordà, Mireia |
author_facet | Buj, Raquel Mallona, Izaskun Díez-Villanueva, Anna Barrera, Víctor Mauricio, Dídac Puig-Domingo, Manel Reverter, Jordi L. Matias-Guiu, Xavier Azuara, Daniel Ramírez, Jose L. Alonso, Sergio Rosell, Rafael Capellà, Gabriel Perucho, Manuel Robledo, Mercedes Peinado, Miguel A. Jordà, Mireia |
author_sort | Buj, Raquel |
collection | PubMed |
description | Hypomethylation of DNA is a hallmark of cancer and its analysis as tumor biomarker has been proposed, but its determination in clinical settings is hampered by lack of standardized methodologies. Here, we present QUAlu (Quantification of Unmethylated Alu), a new technique to estimate the Percentage of UnMethylated Alu (PUMA) as a surrogate for global hypomethylation. QUAlu consists in the measurement by qPCR of Alu repeats after digestion of genomic DNA with isoschizomers with differential sensitivity to DNA methylation. QUAlu performance has been evaluated for reproducibility, trueness and specificity, and validated by deep sequencing. As a proof of use, QUAlu has been applied to a broad variety of pathological examination specimens covering five cancer types. Major findings of the preliminary application of QUAlu to clinical samples include: (1) all normal tissues displayed similar PUMA; (2) tumors showed variable PUMA with the highest levels in lung and colon and the lowest in thyroid cancer; (3) stools from colon cancer patients presented higher PUMA than those from control individuals; (4) lung squamous cell carcinomas showed higher PUMA than lung adenocarcinomas, and an increasing hypomethylation trend associated with smoking habits. In conclusion, QUAlu is a simple and robust method to determine Alu hypomethylation in human biospecimens and may be easily implemented in research and clinical settings. |
format | Online Article Text |
id | pubmed-4891138 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Impact Journals LLC |
record_format | MEDLINE/PubMed |
spelling | pubmed-48911382016-06-23 Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples Buj, Raquel Mallona, Izaskun Díez-Villanueva, Anna Barrera, Víctor Mauricio, Dídac Puig-Domingo, Manel Reverter, Jordi L. Matias-Guiu, Xavier Azuara, Daniel Ramírez, Jose L. Alonso, Sergio Rosell, Rafael Capellà, Gabriel Perucho, Manuel Robledo, Mercedes Peinado, Miguel A. Jordà, Mireia Oncotarget Research Paper Hypomethylation of DNA is a hallmark of cancer and its analysis as tumor biomarker has been proposed, but its determination in clinical settings is hampered by lack of standardized methodologies. Here, we present QUAlu (Quantification of Unmethylated Alu), a new technique to estimate the Percentage of UnMethylated Alu (PUMA) as a surrogate for global hypomethylation. QUAlu consists in the measurement by qPCR of Alu repeats after digestion of genomic DNA with isoschizomers with differential sensitivity to DNA methylation. QUAlu performance has been evaluated for reproducibility, trueness and specificity, and validated by deep sequencing. As a proof of use, QUAlu has been applied to a broad variety of pathological examination specimens covering five cancer types. Major findings of the preliminary application of QUAlu to clinical samples include: (1) all normal tissues displayed similar PUMA; (2) tumors showed variable PUMA with the highest levels in lung and colon and the lowest in thyroid cancer; (3) stools from colon cancer patients presented higher PUMA than those from control individuals; (4) lung squamous cell carcinomas showed higher PUMA than lung adenocarcinomas, and an increasing hypomethylation trend associated with smoking habits. In conclusion, QUAlu is a simple and robust method to determine Alu hypomethylation in human biospecimens and may be easily implemented in research and clinical settings. Impact Journals LLC 2016-02-07 /pmc/articles/PMC4891138/ /pubmed/26859682 http://dx.doi.org/10.18632/oncotarget.7233 Text en Copyright: © 2016 Buj et al. http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Paper Buj, Raquel Mallona, Izaskun Díez-Villanueva, Anna Barrera, Víctor Mauricio, Dídac Puig-Domingo, Manel Reverter, Jordi L. Matias-Guiu, Xavier Azuara, Daniel Ramírez, Jose L. Alonso, Sergio Rosell, Rafael Capellà, Gabriel Perucho, Manuel Robledo, Mercedes Peinado, Miguel A. Jordà, Mireia Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples |
title | Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples |
title_full | Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples |
title_fullStr | Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples |
title_full_unstemmed | Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples |
title_short | Quantification of Unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples |
title_sort | quantification of unmethylated alu (qualu): a tool to assess global hypomethylation in routine clinical samples |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4891138/ https://www.ncbi.nlm.nih.gov/pubmed/26859682 http://dx.doi.org/10.18632/oncotarget.7233 |
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