Publications

First Barcelona Conference on Epigenetics and Cancer

The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled “Challenges, opportunities and perspectives” took place November 21–22, 2013 in Barcelona. The 2013 BCEC is the first edition of a series of annual conferences jointly organized by five leading research centers in Barcelona. These centers are the Institute of Predictive and Personalized Medicine of Cancer (IMPPC), the Biomedical Campus Bellvitge with its Program of Epigenetics and Cancer Biology (PEBC), the Centre for Genomic Regulation (CRG), the Institute for Biomedical Research (IRB), and the Molecular Biology Institute of Barcelona (IBMB). Manuel Perucho and Marcus Buschbeck from the Institute of Predictive and Personalized Medicine of Cancer put together the scientific program of the first conference broadly covering all aspects of epigenetic research ranging from fundamental molecular research to drug and biomarker development and clinical application. In one and a half days, 23 talks and 50 posters were presented to a completely booked out audience counting 270 participants.

A Role for Methyl-CpG Binding Domain Protein 2 in the Modulation of the Estrogen Response of pS2/TFF1 Gene

Background In human Estrogen Receptor α (ERα)-positive breast cancers, 5′ end dense methylation of the estrogen-regulated pS2/TFF1 gene correlates with its transcriptional inhibition. However, in some ERα-rich biopsies, pS2 expression is observed despite the methylation of its TATA-box region. Herein, we investigated the methylation-dependent mechanism of pS2 regulation. Methodology/Principal Findings We observed interplay between Methyl-CpG Binding Domain protein 2 (MBD2) transcriptional repressor and ERα transactivator: (i) the pS2 gene is poised for transcription upon demethylation limited to the enhancer region containing the estrogen responsive element (ERE); (ii) MBD2-binding sites overlapped with the methylation status of the pS2 5′ end; (iii) MBD2 depletion elevated pS2 expression and ectopic expression of ERα partially overcame the inhibitory effect of MBD2 when the ERE is unmethylated. Furthermore, serial chromatin immunoprecipitation assays indicated that MBD2 and ERα could simultaneously occupy the same pS2 DNA molecule; (iv) concomitant ectopic ERα expression and MBD2 depletion resulted in synergistic transcriptional stimulation, while the pS2 promoter remains methylated. Conclusions/Significance MBD2 and ERα drive opposite effects on pS2 expression, which are associated with specific steady state levels of histone H3 acetylation and methylation marks. Thus, epigenetic silencing of pS2 could be dependent on balance of the relative intracellular concentrations of ERα and MBD2.

Supplementary Table 5 from ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms

<p>Whole exome sequencing data, including single nucleotide variants and copy number variants.</p>

Figure S5 from ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms

<p>Parental (green) and resistant (orange) levels of DNA promoter methylation (A) and gene expression (RNA-seq, B) of DUSP4, and p-ERK upon 1µM of idelalisib (Flow cytometry).</p>

P1.02-076 DNA Methylation Profiling Unravels a TGF-β Hyperresponse in Tumor Associated Fibroblasts from Lung Cancer Patients

DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker

Using whole blood from 15 twin pairs discordant for breast cancer and high-resolution (450K) DNA methylation analysis, we identified 403 differentially methylated CpG sites including known and novel potential breast cancer genes. Confirming the results in an independent validation cohort of 21 twin pairs determined the docking protein DOK7 as a candidate for blood-based cancer diagnosis. DNA hypermethylation of the promoter region was also seen in primary breast cancer tissues and cancer cell lines. Hypermethylation of DOK7 occurs years before tumor diagnosis, suggesting a role as a powerful epigenetic blood-based biomarker as well as providing insights into breast cancer pathogenesis.

Advances in the molecular genetics of endometrial cancer (Review).

Abnormalities of the APC/β-catenin pathway in endometrial cancer

Loss of E‐cadherin mediated cell–cell adhesion as an early trigger of apoptosis induced by photodynamic treatment

Abstract Photodynamic treatment with different photosensitizers (PSs) can result in the specific induction of apoptosis in many cell types. It is commonly accepted that this apoptotic response depends on the mitochondrial accumulation of the PS. Accumulation in other cellular organelles, such as lysosomes or the Golgi complex, and subsequent photodamage resulting in an apoptotic process has been also described. However, the role played by cell adhesion in apoptosis induced in epithelial cells after photodynamic treatment is not well characterized. Here, we have used a murine keratinocyte line, showing a strong dependence on E‐cadherin for cell–cell adhesion and survival, to analyze the relevance of this adhesion complex in the context of zinc(II)‐phthalocyanine (ZnPc) photodynamic treatment. We report that under apoptotic conditions, ZnPc phototreatment induces a rapid disorganization of the E‐cadherin mediated cell–cell adhesion, which largely preceded both the detachment of cells from the substrate, via β‐1 integrins and the induction of apoptotic mitochondrial markers. Therefore, the alteration in E‐cadherin, α‐ and β‐catenins adhesion proteins preceded the release of cytochrome c (cyt c) from mitochondria to the cytosol and the activation of caspase 3. In addition, blocking E‐cadherin function with a specific antibody (Decma‐1) induced apoptosis in this cell system. These results strongly suggest that the E‐cadherin adhesion complex could be the primary target of ZnPc phototreatment, and that loss of E‐cadherin mediated cell adhesion after early photodamage triggers an apoptotic response. © 2005 Wiley‐Liss, Inc.

MicroRNA Expression Profiling and DNA Methylation Signature for Deregulated MicroRNA in Cutaneous T-Cell Lymphoma

S-adenosylmethionine Levels Regulate the Schwann Cell DNA Methylome

Epigenetic Inactivation of the Groucho Homologue Gene <i>TLE1</i> in Hematologic Malignancies

An undifferentiated status and the epigenetic inactivation of tumor-suppressor genes are hallmarks of transformed cells. Promoter CpG island hypermethylation of differentiating genes, however, has rarely been reported. The Groucho homologue Transducin-like Enhancer of Split 1 (TLE1) is a multitasked transcriptional corepressor that acts through the acute myelogenous leukemia 1, Wnt, and Notch signaling pathways. We have found that TLE1 undergoes promoter CpG island hypermethylation-associated inactivation in hematologic malignancies, such as diffuse large B-cell lymphoma and AML. We also observed a mutual exclusivity of the epigenetic alteration of TLE1 and the cytogenetic alteration of AML1. TLE1 reintroduction in hypermethylated leukemia/lymphoma cells causes growth inhibition in colony assays and nude mice, whereas TLE1-short hairpin RNA depletion in unmethylated cells enhances tumor growth. We also show that these effects are mediated by TLE1 transcriptional repressor activity on its target genes, such as Cyclin D1, Colony-Stimulating Factor 1 receptor, and Hairy/Enhancer of Split 1. These data suggest that TLE1 epigenetic inactivation contributes to the development of hematologic malignancies by disrupting critical differentiation and growth-suppressing pathways.

Data from KAT6B Is a Tumor Suppressor Histone H3 Lysine 23 Acetyltransferase Undergoing Genomic Loss in Small Cell Lung Cancer

&lt;div&gt;Abstract&lt;p&gt;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 development. Herein, we have identified the presence of homozygous deletions of the candidate histone acetyltransferase &lt;i&gt;KAT6B&lt;/i&gt;, and the loss of the corresponding transcript, in SCLC cell lines and primary tumors. Furthermore, we show, &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt;, that the depletion of KAT6B expression enhances cancer growth, while its restoration induces tumor suppressor–like features. Most importantly, we demonstrate that KAT6B exerts its tumor-inhibitory role through a newly defined type of histone H3 Lys23 acetyltransferase activity. &lt;i&gt;Cancer Res; 75(18); 3936–45. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

The role of ZFP57 and additional KRAB-zinc finger proteins in the maintenance of human imprinted methylation and multi-locus imprinting disturbances

Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation that is resistant to embryonic reprogramming, resulting in parental origin-specific monoallelic gene expression. A subset of individuals affected by imprinting disorders (IDs) displays multi-locus imprinting disturbances (MLID), which may result from aberrant establishment of imprinted differentially methylated regions (DMRs) in gametes or their maintenance in early embryogenesis. Here we investigated the extent of MLID in a family harbouring a ZFP57 truncating variant and characterize the interactions between human ZFP57 and the KAP1 co-repressor complex. By ectopically targeting ZFP57 to reprogrammed loci in mouse embryos using a dCas9 approach, we confirm that ZFP57 recruitment is sufficient to protect oocyte-derived methylation from reprogramming. Expression profiling in human pre-implantation embryos and oocytes reveals that unlike in mice, ZFP57 is only expressed following embryonic-genome activation, implying that other KRAB-zinc finger proteins (KZNFs) recruit KAP1 prior to blastocyst formation. Furthermore, we uncover ZNF202 and ZNF445 as additional KZNFs likely to recruit KAP1 to imprinted loci during reprogramming in the absence of ZFP57. Together, these data confirm the perplexing link between KZFPs and imprint maintenance and highlight the differences between mouse and humans in this respect.

DNA Methylation

DNA Methylation: Approaches, Methods and Applications describes the relation DNA methylation has to gene silencing in disease, and explores its promising role in treating cancer. Written by leaders in the field, this exceptional compilation of articles outlines the best techniques to use when addressing questions concerning the cytosine methylation

Towards the Human Cancer Epigenome: A First Draft of Histone Modifications

AbstractThe disruption of genomic DNA methylation patterns was the first epigeneticabnormality to be described in human cancer. This imbalance involves thepromoter CpG island hypermethylation of tumor-suppressor genes, causingtranscriptional repression, and global genomic hypomethylation, leading tochromosomal instability and reactivation of endoparasitic sequences. Therelationship between DNA methylation and histone modifications was initiallydescribed in the context of the inactivation of female X chromosomes and of thedemonstration of strong interactions between the DNA methylation machinery andchromatin modifiers. The repression of tumor-suppressor genes by promoterhypermethylation was also found to be associated with a specific histonemodification index. However, this jigsaw was missing a piece: a global view of howthe histone modification landscape was distorted in cancer cells. We have recentlydiscovered this piece of the puzzle, demonstrating that the association betweenDNA methylation and histone modification aberrations in cancer also occurs at theglobal level. In human and mouse tumors, histone H4 undergoes a loss ofmonoacetylated and trimethylated lysines 16 and 20, respectively. Mostimportantly, these alterations occur within the context of the repetitive DNAsequences that also become hypomethylated in transformed cells. The globalalterations of histone acetylation status suggest novel pathways by which histoneacetyltransferases (HATs), histone methyltransferases (HMTs), and histonedeacetylases (HDACs) may play roles as tumor-suppressor genes or oncogenes. Inthis regard, we have shown how the generation of particular fusion proteinsinvolving HATs in leukemias is associated with an erasure of the monoacetylatedlysine 16-H4 marker, whilst the loss of trimethylation at lysine 20-H4 disruptsheterochromatic domains and may reduce the response to DNA damage of cancercells.

<i>EGLN2</i> DNA methylation and expression interact with <i>HIF1A</i> to affect survival of early-stage NSCLC

Hypoxia occurs frequently in human cancers and promotes stabilization and activation of hypoxia inducible factor (HIF). HIF-1α is specific for the hypoxia response, and its degradation mediated by three enzymes EGLN1, EGLN2 and EGLN3. Although EGLNs expression has been found to be related to prognosis of many cancers, few studies examined DNA methylation in EGLNs and its relationship to prognosis of early-stage non-small cell lung cancer (NSCLC). We analyzed EGLNs DNA methylation data from tumor tissue samples of 1,230 early-stage NSCLC patients, as well as gene expression data from The Cancer Genome Atlas. The sliding windows sequential forward feature selection method and weighted random forest were used to screen out the candidate CpG probes in lung adenocarcinomas (LUAD) and lung squamous cell carcinomas patients, respectively, in both discovery and validation phases. Then Cox regression was performed to evaluate the association between DNA methylation and overall survival. Among the 34 CpG probes in EGLNs, DNA methylation at cg25923056EGLN2 was identified to be significantly associated with LUAD survival (HR = 1.02, 95% CI: 1.01-1.03, P = 9.90 × 10-5), and correlated with EGLN2 expression (r = - 0.36, P = 1.52 × 10-11). Meanwhile, EGLN2 expression was negatively correlated with HIF1A expression in tumor tissues (r = - 0.30, P = 4.78 × 10-8) and significantly (P = 0.037) interacted with HIF1A expression on overall survival. Therefore, DNA methylation of EGLN2- HIF1A is a potential marker for LUAD prognosis and these genes are potential treatment targets for further development of HIF-1α inhibitors in lung cancer therapy.

HDAC2 (histone deacetylase 2)

Review on HDAC2 (histone deacetylase 2), with data on DNA, on the protein encoded, and where the gene is implicated.