Publications

DNA methylation is dynamic, varies throughout the life course, and its levels are influenced by lifestyle and environmental factors, as well as by genetic variation. The leading genetic variants at stroke risk loci identified to date explain roughly 1–2% of stroke heritability. Most of these single nucleotide polymorphisms are situated within a regulatory sequence marked by DNase I hypersensitivity sites, which would indicate involvement of an epigenetic mechanism. To detect epigenetic variants associated with stroke occurrence and stroke subtypes. A two-stage case–control epigenome-wide association study was designed. The discovery sample with 401 samples included 218 ischaemic stroke (IS) patients, assessed at Hospital del Mar (Barcelona, Spain) and 183 controls from the REGICOR cohort. In two independent samples (N = 226 and N = 166), we replicated 22 CpG sites differentially methylated in IS in 21 loci, including 2 CpGs in locus <i>ZFHX3</i>, which includes known genetic variants associated with stroke. The pathways associated with these loci are inflammation and angiogenesis. The meta-analysis identified 384 differentially methylated CpGs, including loci of known stroke and vascular risk genetic variants, enriched by loci involved in lipid metabolism, adipogenesis, circadian clock, and glycolysis pathways. We identified a set of 22 CpGs in 21 loci associated with IS. Our analysis suggests that DNA methylation changes may contribute to orchestrating gene expression that contributes to IS.

&lt;p&gt;(A) Immunoblotting was performed to measure protein levels in parental and resistant clones for pAKT/AKT and pERK/ERK in three independent experiments. GAPDH was used as a loading control. (B) Protein quantification was done normalizing first to GAPDH and then to total protein. Barplot represents the quantification in each of the independent experiments, parental in grey, resistant in red. Median and standard error of the mean for parental and resistant levels in the three experiments. Moderated t-test was performed to determine statistically significance (p&lt;0.05).&lt;/p&gt;

Highlights•PDX models mimic the clinical response to docetaxel in breast cancer patients•Sensitivity to docetaxel can be regained in metastatic resistant TNBC•A tumor-initiating CD49f chemoresistant population is present in TNBC•Docetaxel resistance associates with the expansion of a CD49f+ population in TNBCSummaryTaxanes are a mainstay of treatment for breast cancer, but resistance often develops followed by metastatic disease and mortality. Aiming to reveal the mechanisms underlying taxane resistance, we used breast cancer patient-derived orthoxenografts (PDX). Mimicking clinical behavior, triple-negative breast tumors (TNBCs) from PDX models were more sensitive to docetaxel than luminal tumors, but they progressively acquired resistance upon continuous drug administration. Mechanistically, we found that a CD49f+ chemoresistant population with tumor-initiating ability is present in sensitive tumors and expands during the acquisition of drug resistance. In the absence of the drug, the resistant CD49f+ population shrinks and taxane sensitivity is restored. We describe a transcriptional signature of resistance, predictive of recurrent disease after chemotherapy in TNBC. Together, these findings identify a CD49f+ population enriched in tumor-initiating ability and chemoresistance properties and evidence a drug holiday effect on the acquired resistance to docetaxel in triple-negative breast cancer.Graphical abstract

Abstract Introduction: The major clinical problem for HER2 breast cancer target therapies is the acquisition of resistance. Trastuzumab has been used for the treatment of HER2-positive early stage and metastatic breast cancers. Notoriously, up to 62% patients that respond to the initial treatment develop resistance within a year. Different cellular and molecular alterations may contribute to the development of Trastuzumab resistance, including epigenetic changes. The aim of our study has been the evaluation of epigenetic differences between Trastuzumab-sensitive and -resistant breast cancer cell lines to determine whether they might be used as potential biomarkers to help in the treatment assessment and monitoring. Experimental procedures: To understand the epigenetic changes that may be associated with Trastuzumab resistance we compared the DNA methylation status of ∼450000 CpG sites from a DNA methylation microarray performed in Trastuzumab-sensitive and resistant cells. To identify the differentially methylated CpGs we considered differences between methylation groups of ≥60%. The functions associated to genes were analysed using the Gene Ontology and were used to select a small number of candidate genes. Their differences in promoter methylation status were validated by expression techniques (qPCR) and subsequently confirmed by demethylation agent (5-aza-DC) treatment followed by qPCR. The Trastuzumab resistant HER2-positive cell line (SKTR) had been previously developed in our laboratory by exposing SKBr3 cells to Trastuzumab, starting with 1μM for three months of exposure and increasing up to 2 μM for a 12 months period. Summary of the new, unpublished data: The DNA methylation microarray data showed that different 5’-CpG island sites had altered methylation profile when comparing Trastuzumab-resistant (SKTR) and -sensible SKBr3 cells. We selected 4 candidate genes with a hypermethylation profile in -resistant vs. -sensible cells: TGFβ1 (Transforming Growth Factor Beta 1), BCL6 (B-Cell CLL/Lymphoma 6), KILLIN (P53-Regulated DNA Replication Inhibitor) and CTSZ (Cathepsin Z). The hypermethylation of these four candidate genes in SKTR was in agreement with their expression downregulation observed by PCR analysis. SKTR treatment with the demethylation agent 5-aza-2’-deoxycytidine restored the expression levels of all four genes to the levels of Trastuzumab-sensitive cells. Although previously related to breast cancer, TGFβ1, BCL6, KILLIN and CTSZ have not earlier been associated with the development of Trastuzumab resistance in breast cancer or in other cancer types and may be further studied as potential biomarkers. Conclusions: These results provide a basis for future studies to validate the hypermethylation status of these genes as a predictive or monitoring biomarker of Trastuzumab resistance in HER2+ breast cancer patients. Citation Format: Sonia Palomeras, Angel Diaz-Lagares, Sarrats Ariadna, Crujeiras Ana Belen, Giro-Perafita Ariadna, Juan Sandoval, Marc Rabionet, Manel Esteller, Teresa Puig. Epigenetic silencing of TGFβ1, BCL6, KILLIN and CTSZ is related to trastuzumab resistance in HER2-positive breast cancer models. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2130A.

Epithelial ovarian cancer (EOC) is the fifth leading cause of death in women diagnosed with gynecologic malignancies. The low survival rate is because of its advanced-stage diagnosis and either intrinsic or acquired resistance to standard platinum-based chemotherapy. So, the development of effective innovative therapeutic strategies to overcome cisplatin resistance remains a high priority.To investigate new treatments in in vivo models reproducing EOCs tumor growth, we generated a preclinical model of ovarian cancer after orthotopic implantation of a primary serous tumor in nude mice. Further, matched model of acquired cisplatin-resistant tumor version was successfully derived in mice. Effectiveness of lurbinectedin (PM01183) treatment, a novel marine-derived DNA minor groove covalent binder, was assessed in both preclinical models as a single and a combined-cisplatin agent.Orthotopically perpetuated tumor grafts mimic the histopathological characteristics of primary patients' tumors and they also recapitulate in mice characteristic features of tumor response to cisplatin treatments. We showed that single lurbinectedin or cisplatin-combined therapies were effective in treating cisplatin-sensitive and cisplatin-resistant preclinical ovarian tumor models. Furthermore, the strongest in vivo synergistic effect was observed for combined treatments, especially in cisplatin-resistant tumors. Lurbinectedin tumor growth inhibition was associated with reduced proliferation, increased rate of aberrant mitosis, and subsequent induced apoptosis.Taken together, preclinical orthotopic ovarian tumor grafts are useful tools for drug development, providing hard evidence that lurbinectedin might be a useful therapy in the treatment of EOC by overcoming cisplatin resistance.

&lt;p&gt;Panel of proteins tested in the immunoblotting or immunofluorescence experiments.&lt;/p&gt;

Abstract Dynamic post-transcriptional RNA modifications are crucial regulators of RNA metabolism and cell fate. Recent advances in sequencing, combined with antibody, enzymatic, or chemical approaches, have enabled transcriptome-wide mapping of these modifications. While prevalent in tRNAs and rRNAs, a growing number of modifications also adorn lower-abundance mRNA transcripts. Global mapping efforts, particularly for N 6 -methyladenosine (m 6 A), uncovered the affected mechanisms governing RNA metabolism, shedding light on novel, modification-dependent, modes of gene regulation. N 6 -isopentenyladenosine (i 6 A) is a conserved tRNA modification involved in translation fidelity and efficiency. i 6 A depletion is linked to mitochondrial defects and human diseases. Current i 6 A detection methods are low-throughput, and its lack of base-pairing effects makes sequencing-based identification challenging. Here we developed a novel and robust mapping technique, i 6 A-seq, a method that utilizes antibody-mediated enrichment and iodine chemical labeling to generate a reverse transcription signature, enabling transcriptome-wide i 6 A detection. Our global mapping revealed hundreds of i 6 A sites in human and mouse mRNA, indicating its presence in this RNA species, with conserved isopentenylome features. These sites exhibit a typical consensus sequence, primarily in coding transcripts (CDS), preferentially within lysine codons. Consistent with its role in tRNA, tRNA-isopentenyltransferase (TRIT1) also appears to install i 6 A in mRNA. Manipulation of TRIT1 revealed that i 6 A regulates the expression of a subset of genes through mRNA decay, specifically those isopentenylated at the CDS and translated on ER-bound ribosomes. Importantly, DIS3 like 3’-5’ exoribonuclease 2 (DIS3L2), an RNA exoribonuclease known to regulate ER-translated mRNA, was identified as the first i 6 A reader protein. Our findings introduce i 6 A as a new modified nucleotide that decorates mRNA, allowing us to decipher its regulatory roles in gene expression. This study not only establishes the presence and location of i 6 A in mRNA, but also uncovers its first functional mechanism. Similar to the knowledge accumulated on m 6 A, this work paves the way for further discoveries with potential relevance for understanding gene regulation, disease diagnosis, and therapy.

Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disease, characterized by severe hypomethylation in pericentromeric regions of chromosomes (1, 16 and 9), marked immunodeficiency and facial anomalies. The majority of ICF patients present mutations in the DNMT3B gene, affecting the DNA methyltransferase activity of the protein. In the present study, we have used the Infinium 450K DNA methylation array to evaluate the methylation level of 450,000 CpGs in lymphoblastoid cell lines and untrasformed fibroblasts derived from ICF patients and healthy donors. Our results demonstrate that ICF-specific DNMT3B variants A603T/STP807ins and V699G/R54X cause global DNA hypomethylation compared to wild-type protein. We identified 181 novel differentially methylated positions (DMPs) including subtelomeric and intrachromosomic regions, outside the classical ICF-related pericentromeric hypomethylated positions. Interestingly, these sites were mainly located in intergenic regions and inside the CpG islands. Among the identified hypomethylated CpG-island associated genes, we confirmed the overexpression of three selected genes, BOLL, SYCP2 and NCRNA00221, in ICF compared to healthy controls, which are supposed to be expressed in germ line and silenced in somatic tissues.In conclusion, this study contributes in clarifying the direct relationship between DNA methylation defect and gene expression impairment in ICF syndrome, identifying novel direct target genes of DNMT3B. A high percentage of the DMPs are located in the subtelomeric regions, indicating a specific role of DNMT3B in methylating these chromosomal sites. Therefore, we provide further evidence that hypomethylation in specific non-pericentromeric regions of chromosomes might be involved in the molecular pathogenesis of ICF syndrome. The detection of DNA hypomethylation at BOLL, SYCP2 and NCRNA00221 may pave the way for the development of specific clinical biomarkers with the aim to facilitate the identification of ICF patients.

Promoter hypermethylation is responsible for gene inactivation during carcinogenesis. It has been proposed that there is some degree of specificity in the set of genes that become altered by this mechanism in distinct tumor types. To understand whether promoter hypermethylation may differentiate the site of origin, 49 lung adenocarcinomas from 31 lung primaries and 18 metastases from colorectal primaries, respectively, were tested for the presence of this alteration in the APC, CDH1, DAPK, GSTP1, MLH1, MGMT, P14, P16, RARbeta2, RASSF1, sFRP1 and WIF-1 genes. A distinct profile was apparent for the 2 groups of lung tumors and the frequencies of promoter hypermethylation at sFRP1 and WIF-1, 2 genes involved in Wnt signaling, and at CDH1 were significantly higher in colorectal metastases than in lung primaries, whereas methylation of the APC promoter was significantly more common in lung primary adenocarcinomas. Some tumors showed concomitant APC, sFRP1 and WIF-1 gene inactivation, indicating that multiple DNA methylation events must have occurred to definitively down-regulate the signaling through Wnt. However, promoter hypermethylation at the APC and CDH1 genes tended to be mutually exclusive (Fisher's exact test, p = 0.006), suggesting a similar role in carcinogenesis. In conclusion, we propose that inactivation by promoter hypermethylation at the APC, CDH1, sFRP1 and WIF-1 genes may contribute to the discrimination of lung primary adenocarcinomas from colorectal metastasis to the lung, and report the simultaneous presence of methylation at the promoters of multiple genes involved in the Wnt signaling. This may have biological consequences for carcinogenesis.

&lt;p&gt;'Supplementary Methods'&lt;/p&gt;

&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;

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.