title: Quantification of unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples.
abstract: 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.
authors: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.|Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.
authors: Raquel
authors: R
authors: Buj
authors: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.|Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.
authors: Izaskun
authors: I
authors: Mallona
authors: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.|Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.
authors: Anna
authors: A
authors: Díez-Villanueva
authors: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.
authors: Víctor
authors: V
authors: Barrera
authors: Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.|Department of Endocrinology and Nutrition, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.|ISCIII Center for Biomedical Research on Diabetes and Metabolic Associated Diseases (CIBERDEM), Madrid, Spain.
authors: Dídac
authors: D
authors: Mauricio
authors: Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.|Department of Endocrinology and Nutrition, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.|ISCIII Center for Biomedical Research on Diabetes and Metabolic Associated Diseases (CIBERDEM), Madrid, Spain.
authors: Manel
authors: M
authors: Puig-Domingo
authors: Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.|Department of Endocrinology and Nutrition, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.
authors: Jordi L
authors: JL
authors: Reverter
authors: Department of Pathology and Molecular Genetics, University Hospital Arnau de Vilanova and University of Lleida, Biomedical Research Institute of Lleida (IRBLLEIDA), Lleida, Spain.
authors: Xavier
authors: X
authors: Matias-Guiu
authors: Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
authors: Daniel
authors: D
authors: Azuara
authors: Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.|Catalan Institute of Oncology (ICO), Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.
authors: Jose L
authors: JL
authors: Ramírez
authors: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.|Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.
authors: Sergio
authors: S
authors: Alonso
authors: Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.|Catalan Institute of Oncology (ICO), Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.
authors: Rafael
authors: R
authors: Rosell
authors: Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
authors: Gabriel
authors: G
authors: Capellà
authors: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.|Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.|Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
authors: Manuel
authors: M
authors: Perucho
authors: Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain.|ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain.
authors: Mercedes
authors: M
authors: Robledo
authors: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.|Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.
authors: Miguel A
authors: MA
authors: Peinado
authors: Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.|Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.
authors: Mireia
authors: M
authors: Jordà
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D020087:Alu Elements / Q000235:genetics*; D014408:Biomarkers, Tumor / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D045744:Cell Line, Tumor; D003110:Colonic Neoplasms / Q000235:genetics*; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics*; D045325:HCT116 Cells; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D013964:Thyroid Neoplasms / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; D004247:DNA
keywords: Alu repeats; DNA hypomethylation; biomarker; human cancer; routine clinical biospecimens