1. A Landscape of Pharmacogenomic Interactions in Cancer.

    Cell 166(3):740 (2016) PMID 27397505 PMCID PMC4967469

    Systematic studies of cancer genomes have provided unprecedented insights into the molecular nature of cancer. Using this information to guide the development and application of therapies in the clinic is challenging. Here, we report how cancer-driven alterations identified in 11,289 tumors from...
  2. Arachidonic and oleic acid exert distinct effects on the DNA methylome.

    Epigenetics 11(5):321 (2016) PMID 27088456 PMCID PMC4889238

    Abnormal fatty acid metabolism and availability are landmarks of metabolic diseases, which in turn are associated with aberrant DNA methylation profiles. To understand the role of fatty acids in disease epigenetics, we sought DNA methylation profiles specifically induced by arachidonic (AA) or o...
  3. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences.

    Epigenomics 8(3):389 (2016) PMID 26673039 PMCID PMC4864062

    DNA methylation is the best known epigenetic mark. Cancer and other pathologies show an altered DNA methylome. However, delivering complete DNA methylation maps is compromised by the price and labor-intensive interpretation of single nucleotide methods. Following the success of the HumanMethylat...
  4. Epigenetic inactivation of the putative DNA/RNA helicase SLFN11 in human cancer confers resistance to platinum drugs.

    Oncotarget 7(3):3084 (2016) PMID 26625211 PMCID PMC4823092

    Platinum-derived drugs such as cisplatin and carboplatin are among the most commonly used cancer chemotherapy drugs, but very few specific molecular and cellular markers predicting differential sensitivity to these agents in a given tumor type have been clearly identified. Epigenetic gene silenc...
  5. Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer.

    Genome Biology 17(1):11 (2016) PMID 26813288 PMCID PMC4728783

    One of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recognized. Much of the research effort in this area has examined proximal promoter regions a...
  6. Corrigendum. Identification of a new locus and validation of previously reported loci showing differential methylation associated with smoking. The REGICOR study.

    Epigenetics 11(2):174 (2016) PMID 27058811 PMCID PMC4846141

  7. Aberrant DNA methylation in non-small cell lung cancer-associated fibroblasts.

    Carcinogenesis 36(12):1453 (2015) PMID 26449251 PMCID PMC4662832

    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 o...
  8. KAT6B Is a Tumor Suppressor Histone H3 Lysine 23 Acetyltransferase Undergoing Genomic Loss in Small Cell Lung Cancer.

    Cancer Research 75(18):3936 (2015) PMID 26208904

    Recent efforts to sequence human cancer genomes have highlighted that point mutations in genes involved in the epigenetic setting occur in tumor cells. Small cell lung cancer (SCLC) is an aggressive tumor with poor prognosis, where little is known about the genetic events related to its developm...
  9. Epigenetic mechanisms involved in melanoma pathogenesis and chemoresistance.

    Annals of translational medicine 3(15):209 (2015) PMID 26488005 PMCID PMC4583598

    The discovery of highly recurrent mutations in melanoma, such as BRAF(V600E), completely changed the clinical management including therapy of melanoma patients. In the era of Personalized Medicine targeted melanoma therapies showed high response rates, currently evidenced by BRAF inhibitors or i...
  10. DNA methylation dynamics in human carotid plaques after cerebrovascular events.

    Arteriosclerosis, Thrombosis, and Vascular Biology 35(8):1835 (2015) PMID 26088578

    To understand whether cerebrovascular events, a major complication of atherosclerosis, are associated with any specific DNA methylation changes in the carotid plaque. We profiled the DNA methylomes of human symptomatic carotid plaques obtained from patients who had cerebrovascular events (n=19) ...
  11. Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR.

    Nature Medicine 21(7):741 (2015) PMID 26030178 PMCID PMC4968631

    Metastasis is responsible for most cancer-related deaths, and, among common tumor types, melanoma is one with great potential to metastasize. Here we study the contribution of epigenetic changes to the dissemination process by analyzing the changes that occur at the DNA methylation level between...
  12. Whole-exome sequencing identifies MDH2 as a new familial paraganglioma gene.

    JNCI Journal of the National Cancer Institute 107(5) (2015) PMID 25766404

    Disruption of the Krebs cycle is a hallmark of cancer. IDH1 and IDH2 mutations are found in many neoplasms, and germline alterations in SDH genes and FH predispose to pheochromocytoma/paraganglioma and other cancers. We describe a paraganglioma family carrying a germline mutation in MDH2, which ...
  13. A DNA methylation-based definition of biologically distinct breast cancer subtypes.

    Molecular Oncology 9(3):555 (2015) PMID 25468711

    In cancer, epigenetic states are deregulated and thought to be of significance in cancer development and progression. We explored DNA methylation-based signatures in association with breast cancer subtypes to assess their impact on clinical presentation and patient prognosis. DNA methylation was...
  14. The DNA methylation drift of the atherosclerotic aorta increases with lesion progression.

    BMC Medical Genomics 8(1):7 (2015) PMID 25881171 PMCID PMC4353677

    Atherosclerosis severity-independent alterations in DNA methylation, a reversible and highly regulated DNA modification, have been detected in aortic atheromas, thus supporting the hypothesis that epigenetic mechanisms participate in the pathogenesis of atherosclerosis. One yet unaddressed issue...
  15. H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells.

    Genome Research 25(1):27 (2015) PMID 25271306 PMCID PMC4317171

    In differentiated cells, aging is associated with hypermethylation of DNA regions enriched in repressive histone post-translational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA meth...
  16. Identification of a new locus and validation of previously reported loci showing differential methylation associated with smoking. The REGICOR study.

    Epigenetics 10(12):1156 (2015) PMID 26829059 PMCID PMC4844221

    Smoking increases the risk of many diseases and could act through changes in DNA methylation patterns. The aims of this study were to determine the association between smoking and DNA methylation throughout the genome at cytosine-phosphate-guanine (CpG) site level and genomic regions. A discover...
  17. Caveolin-1 is down-regulated in alveolar rhabdomyosarcomas and negatively regulates tumor growth.

    Oncotarget 5(20):9744 (2014) PMID 25313138 PMCID PMC4259434

    Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood and adolescence. Despite advances in therapy, patients with histological variant of rhabdomyosarcoma known as alveolar rhabdomyosarcoma (ARMS) have a 5-year survival of less than 30%. Caveolin-1 (CAV1), encoding the structural ...
  18. DNA methylation map of human atherosclerosis.

    Circulation: Cardiovascular Genetics 7(5):692 (2014) PMID 25091541

    Epigenetic alterations may contribute to the development of atherosclerosis. In particular, DNA methylation, a reversible and highly regulated DNA modification, could influence disease onset and progression because it functions as an effector for environmental influences, including diet and life...
  19. A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition.

    Cancer Research 74(19):5608 (2014) PMID 25106427

    Epithelial-to-mesenchymal transition (EMT) is a plastic process in which fully differentiated epithelial cells are converted into poorly differentiated, migratory and invasive mesenchymal cells, and it has been related to the metastasis potential of tumors. This is a reversible process and cells...
  20. Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray.

    Epigenetics 9(6):829 (2014) PMID 24732293 PMCID PMC4065180

    A formalin-fixed paraffin-embedded (FFPE) sample usually yields highly degraded DNA, which limits the use of techniques requiring high-quality DNA, such as Infinium Methylation microarrays. To overcome this restriction, we have applied an FFPE restoration procedure consisting of DNA repair and l...