title: Aberrant DNA methylation in non-small cell lung cancer-associated fibroblasts.
abstract: Epigenetic changes through altered DNA methylation have been implicated in critical aspects of tumor progression, and have been extensively studied in a variety of cancer types. In contrast, our current knowledge of the aberrant genomic DNA methylation in tumor-associated fibroblasts (TAFs) or other stromal cells that act as critical coconspirators of tumor progression is very scarce. To address this gap of knowledge, we conducted genome-wide DNA methylation profiling on lung TAFs and paired control fibroblasts (CFs) from non-small cell lung cancer patients using the HumanMethylation450 microarray. We found widespread DNA hypomethylation concomitant with focal gain of DNA methylation in TAFs compared to CFs. The aberrant DNA methylation landscape of TAFs had a global impact on gene expression and a selective impact on the TGF-β pathway. The latter included promoter hypermethylation-associated SMAD3 silencing, which was associated with hyperresponsiveness to exogenous TGF-β1 in terms of contractility and extracellular matrix deposition. In turn, activation of CFs with exogenous TGF-β1 partially mimicked the epigenetic alterations observed in TAFs, suggesting that TGF-β1 may be necessary but not sufficient to elicit such alterations. Moreover, integrated pathway-enrichment analyses of the DNA methylation alterations revealed that a fraction of TAFs may be bone marrow-derived fibrocytes. Finally, survival analyses using DNA methylation and gene expression datasets identified aberrant DNA methylation on the EDARADD promoter sequence as a prognostic factor in non-small cell lung cancer patients. Our findings shed light on the unique origin and molecular alterations underlying the aberrant phenotype of lung TAFs, and identify a stromal biomarker with potential clinical relevance.
authors.affiliation: Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat 08907, Barcelona, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Vizoso
authors.affiliation: Unit of Biophysics and Bioengineering, School of Medicine, University of Barcelona, Barcelona 08036, Spain, Medical Oncology Department, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Institute (IDIBAPS), Barcelona 08036, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Puig
authors.affiliation: Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat 08907, Barcelona, Spain.
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Carmona
authors.affiliation: Department of ESAII, Center for Biomedical Engineering Research, Technical University of Catalonia (UPC), CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona 08028, Spain.
authors.forename: María
authors.initials: M
authors.lastname: Maqueda
authors.affiliation: Unit of Biophysics and Bioengineering, School of Medicine, University of Barcelona, Barcelona 08036, Spain.
authors.forename: Adriana
authors.initials: A
authors.lastname: Velásquez
authors.affiliation: Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat 08907, Barcelona, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Gómez
authors.affiliation: Institute for Bioengineering of Catalonia (IBEC), Barcelona 08028, Spain.
authors.forename: Anna
authors.initials: A
authors.lastname: Labernadie
authors.affiliation: Unit of Biophysics and Bioengineering, School of Medicine, University of Barcelona, Barcelona 08036, Spain.
authors.forename: Roberto
authors.initials: R
authors.lastname: Lugo
authors.affiliation: Unit of Biophysics and Bioengineering, School of Medicine, University of Barcelona, Barcelona 08036, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Gabasa
authors.affiliation: Department of ESAII, Center for Biomedical Engineering Research, Technical University of Catalonia (UPC), CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona 08028, Spain, Institute for Bioengineering of Catalonia (IBEC), Barcelona 08028, Spain.
authors.forename: Luis G
authors.initials: LG
authors.lastname: Rigat-Brugarolas
authors.affiliation: Unit of Biophysics and Bioengineering, School of Medicine, University of Barcelona, Barcelona 08036, Spain, Institute for Bioengineering of Catalonia (IBEC), Barcelona 08028, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain.
authors.forename: Xavier
authors.initials: X
authors.lastname: Trepat
authors.affiliation: Servei d'Anatomia Patològica, Hospital Clínic de Barcelona, Barcelona 08036, Spain.
authors.forename: Josep
authors.initials: J
authors.lastname: Ramírez
authors.affiliation: Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat 08907, Barcelona, Spain.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Moran
authors.affiliation: Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat 08907, Barcelona, Spain.
authors.forename: Enrique
authors.initials: E
authors.lastname: Vidal
authors.affiliation: Medical Oncology Department, Hospital Clínic of Barcelona, August Pi i Sunyer Biomedical Institute (IDIBAPS), Barcelona 08036, Spain.
authors.forename: Noemí
authors.initials: N
authors.lastname: Reguart
authors.affiliation: Department of ESAII, Center for Biomedical Engineering Research, Technical University of Catalonia (UPC), CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona 08028, Spain.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Perera
authors.affiliation: Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat 08907, Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain, Department of Physiological Sciences II, School of Medicine, University of L'Hospitalet de Llobregat 08907, Barcelona, Spain and jalcaraz@ub.edu.
authors.forename: Manel
authors.initials: M
authors.lastname: Esteller
authors.affiliation: Unit of Biophysics and Bioengineering, School of Medicine, University of Barcelona, Barcelona 08036, Spain, CIBER de Enfermedades Respiratorias (CIBERES), Madrid, 28029, Spain jalcaraz@ub.edu.
authors.forename: Jordi
authors.initials: J
authors.lastname: Alcaraz
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000473:pathology; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000473:pathology; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005109:Extracellular Matrix / Q000235:genetics / Q000378:metabolism; D005347:Fibroblasts / Q000378:metabolism*; D022001:Focal Adhesions / Q000235:genetics / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000473:pathology; D008297:Male; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D008875:Middle Aged; D017452:Receptors, IgG / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D051900:Smad3 Protein / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D053773:Transforming Growth Factor beta1 / Q000502:physiology; D014407:Tumor Cells, Cultured
chemical_list: D035683:MicroRNAs; D017452:Receptors, IgG; C497790:SMAD3 protein, human; D051900:Smad3 Protein; D053773:Transforming Growth Factor beta1