Publications

54 MGMT methylation assessed by methyl-BEAMing technique is a prognostic and predictive biomarker in glioblastoma and metastatic colorectal cancer patients

DNA methylation-associated silencing of tumor-suppressor microRNAs in cancer

MicroRNAs (miRNAs) are recognized as being central players in many biological processes and cellular pathways. Their roles in disease have been highlighted first by observation of their aberrant expression profiles in human tumors, and then by in vitro and in vivo functional studies in transformed cells and model organisms. One of the most commonly observed features of miRNAs in malignancies is a defect in their production. Although several causes may be associated with this phenomenon, such as upstream oncogenic/tumor-suppressor defects and alterations in the miRNA-processing machinery, epigenetic inactivation is the prime suspect. The number of miRNAs with putative growth-inhibitory functions undergoing promoter CpG island hypermethylation in human cancer is growing fast and more detailed biological studies are necessary. The recognition of miR-124a and miR-34b/c as bona fide tumor-suppressor miRNAs undergoing DNA methylation-associated silencing in a wide spectrum of human neoplasms is a good starting point to be followed by other candidate miRNAs. Most importantly, even at this early stage, the transcriptional repression of miRNAs by hypermethylation of their corresponding promoter loci seems to be a common feature of all human tumors. This will have translational consequences for the management of the disease.

Identification of DNA hypermethylation of SOX9 in association with bladder cancer progression using CpG microarrays

CpG island arrays represent a high-throughput epigenomic discovery platform to identify global disease-specific promoter hypermethylation candidates along bladder cancer progression. DNA obtained from 10 pairs of invasive bladder tumours were profiled vs their respective normal urothelium using differential methylation hybridisation on custom-made CpG arrays (n=12 288 clones). Promoter hypermethylation of 84 clones was simultaneously shown in at least 70% of the tumours. SOX9 was selected for further validation by bisulphite genomic sequencing and methylation-specific polymerase chain reaction in bladder cancer cells (n=11) and primary bladder tumours (n=101). Hypermethylation was observed in bladder cancer cells and associated with lack of gene expression, being restored in vitro by a demethylating agent. In primary bladder tumours, SOX9 hypermethylation was present in 56.4% of the cases. Moreover, SOX9 hypermethylation was significantly associated with tumour grade and overall survival. Thus, this high-throughput epigenomic strategy has served to identify novel hypermethylated candidates in bladder cancer. In vitro analyses supported the role of methylation in silencing SOX9 gene. The association of SOX9 hypermethylation with tumour progression and clinical outcome suggests its relevant clinical implications at stratifying patients affected with bladder cancer.

Mutations in JMJD1C are involved in Rett syndrome and intellectual disability

Autism spectrum disorders are associated with defects in social response and communication that often occur in the context of intellectual disability. Rett syndrome is one example in which epilepsy, motor impairment, and motor disturbance may co-occur. Mutations in histone demethylases are known to occur in several of these syndromes. Herein, we aimed to identify whether mutations in the candidate histone demethylase JMJD1C (jumonji domain containing 1C) are implicated in these disorders.We performed the mutational and functional analysis of JMJD1C in 215 cases of autism spectrum disorders, intellectual disability, and Rett syndrome without a known genetic defect.We found seven JMJD1C variants that were not present in any control sample (~ 6,000) and caused an amino acid change involving a different functional group. From these, two de novo JMJD1C germline mutations were identified in a case of Rett syndrome and in a patient with intellectual disability. The functional study of the JMJD1C mutant Rett syndrome patient demonstrated that the altered protein had abnormal subcellular localization, diminished activity to demethylate the DNA damage-response protein MDC1, and reduced binding to MECP2. We confirmed that JMJD1C protein is widely expressed in brain regions and that its depletion compromises dendritic activity.Our findings indicate that mutations in JMJD1C contribute to the development of Rett syndrome and intellectual disability.Genet Med 18 1, 378-385.

Genetic and epigenetic defects of the RNA modification machinery in cancer

Cancer was initially considered to be an exclusively genetic disease, but an interplay of dysregulated genetic and epigenetic mechanisms is now known to contribute to the cancer phenotype. More recently, chemical modifications of RNA molecules - the so-called epitranscriptome - have been found to regulate various aspects of RNA function and homeostasis. Specific enzymes, known as RNA-modifying proteins (RMPs), are responsible for depositing, removing, and reading chemical modifications in RNA. Intensive investigations in the epitranscriptomic field in recent years, in conjunction with great technological advances, have revealed the critical role of RNA modifications in regulating numerous cellular pathways. Furthermore, growing evidence has revealed that RNA modification machinery is often altered in human cancers, highlighting the enormous potential of RMPs as pharmacological targets or diagnostic markers.

New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling

P1‐132: INFLUENCE OF <i>BDNF</i> VAL66MET POLYMORPHISM ON HIPPOCAMPAL SUBFIELDS: MET CARRIERS DISPLAY GREATER SUBICULUM VOLUMES

Current evidence supports the involvement of brain-derived neurotrophic factor (BDNF) Val66Met polymorphisms in psychiatric and neurodegenerative disorders, including Alzheimer disease (AD) [1]. Previous studies of the association of this genotype with whole hippocampal volume included patients of a variety of disorders [2-3]. However, the impact of BDNF Val66Met polymorphisms on the volumes of the hippocampal subfields in cognitively unimpaired individuals remains to be elucidated. Therefore, the aim of the present study is to evaluate the impact of Val66Met polymorphism on hippocampal subfield volumes in cognitively unimpaired participants. BDNF Val66Met polymorphisms were determined in a sample of 430 cognitively unimpaired late/middle-aged participants from the ALFA (ALzheimer & FAmilies study [4]). Participants underwent a brain 3D-T1-weighted MRI scan and volumes of the hippocampal subfields were determined using Freesurfer (v6.0). The dominant, recessive, codominant and additive effects of the Val66Met genotype on the hippocampal subfield volumes were assessed using general linear models corrected by age, gender, education, number of APOE-e4 alleles and total intracranial volume. We additionally evaluated whether the association between age and hippocampal subfields was modified by BDNF Val66Met genotypes. p-values below 0.05 (FDR-corrected) were considered as statistically significant. Characteristics of the study participants, and differences in hippocampal subfield volumes between Val66Met genotypes are shown in Table 1 and Figure 1, respectively. Association analysis revealed that BDNF Met carriers showed statistically significant larger bilateral volumes of the subiculum under dominant and additive models (bd =20.5, pd=0.003; ba = 19.4, pa = 0.013) [Tables 2-3]. No significant results after FDR-correction were found under recessive and codominant models [Tables 4-5]. Furthermore, subfield volume reductions with aging were not significantly moderated by the Val66Met status.

Unexpected thermodynamic signature for the interaction of hydroxymethylated DNA with MeCP2

[Introduction to molecular biology of endometrial cancer].

Supplementary Figure 3 from KAT6B Is a Tumor Suppressor Histone H3 Lysine 23 Acetyltransferase Undergoing Genomic Loss in Small Cell Lung Cancer

&lt;p&gt;Supplementary Figure 3. Expression of KAT6B isoforms in SCLC cell lines.&lt;/p&gt;

Supplementary Table 2 from CD137 (4-1BB) Costimulation Modifies DNA Methylation in CD8&lt;sup&gt;+&lt;/sup&gt; T Cell–Relevant Genes

&lt;p&gt;DNA methylation array results with 6B4 antiCD137 mAb&lt;/p&gt;

Proteins that bind methylated DNA and human cancer: reading the wrong words

DNA methylation and the machinery involved in epigenetic regulation are key elements in the maintenance of cellular homeostasis. Epigenetic mechanisms are involved in embryonic development and the establishment of tissue-specific expression, X-chromosome inactivation and imprinting patterns, and maintenance of chromosome stability. The balance between all the enzymes and factors involved in DNA methylation and its interpretation by different groups of nuclear factors is crucial for normal cell behaviour. In cancer and other diseases, misregulation of epigenetic marks is a common feature, also including DNA methylation and histone post-translational modifications. In this scenario, it is worth mentioning a family of proteins characterized by the presence of a methyl-CpG-binding domain (MBDs) that are involved in interpreting the information encoded by DNA methylation and the recruitment of the enzymes responsible for establishing a silenced state of the chromatin. The generation of novel aberrantly hypermethylated regions during cancer development and progression makes MBD proteins interesting targets for their biological and clinical implications.

E47 phosphorylation by p38 MAPK promotes MyoD/E47 association and muscle-specific gene transcription

Dynamic epigenetic age mosaicism in the human atherosclerotic artery

Accelerated epigenetic ageing, a promising marker of disease risk, has been detected in peripheral blood cells of atherosclerotic patients, but evidence in the vascular wall is lacking. Understanding the trends of epigenetic ageing in the atheroma may provide insights into mechanisms of atherogenesis or identify targets for molecular therapy. We surveyed DNA methylation age in two human artery samples: a set of donor-matched, paired atherosclerotic and healthy aortic portions, and a set of carotid artery atheromas. The well-characterized pan-tissue Horvath epigenetic clock was used, together with the Weidner whole-blood-specific clock as validation. For the first time, we document dynamic DNA methylation age mosaicism of the vascular wall that is atherosclerosis-related, switches from acceleration to deceleration with chronological ageing, and is consistent in human aorta and carotid atheroma. At CpG level, the Horvath epigenetic clock showed modest differential methylation between atherosclerotic and healthy aortic portions, weak association with atheroma histological grade and no clear evidence for participation in atherosclerosis-related cellular pathways. Our data suggest caution when assigning a unidirectional DNA methylation age change to the atherosclerotic arterial wall. Also, the results support previous conclusions that epigenetic ageing reflects non-disease-specific cellular alterations.

Data from Identification of PMF1 Methylation in Association with Bladder Cancer Progression

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Polyamines are important regulators of cell growth and death. The polyamine modulated factor-1 (PMF-1) is involved in polyamine homeostasis. After identifying an enriched CpG island encompassing the PMF1 promoter, we aimed at evaluating the clinical relevance of PMF1 methylation in bladder cancer.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; The epigenetic silencing of PMF1 by hypermethylation was tested in bladder cancer cells (&lt;i&gt;n&lt;/i&gt; = 11) after azacytidine treatment. PMF1 methylation status was evaluated in 507 bladder tumors and 118 urinary specimens of bladder cancer patients and controls. PMF1 protein expression was analyzed by immunohistochemistry on tissue arrays containing bladder tumors for which PMF1 methylation was assessed (&lt;i&gt;n&lt;/i&gt; = 218).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; PMF1 hypermethylation was associated with gene expression loss, being restored &lt;i&gt;in vitro&lt;/i&gt; by a demethylating agent. An initial set of 101 primary frozen bladder tumors served to identify PMF1 hypermethylation in 88.1% of the cases. An independent set of 406 paraffin-embedded tumors also revealed a high PMF1 methylation rate (77.6%). PMF1 methylation was significantly associated with increasing stage (&lt;i&gt;P&lt;/i&gt; = 0.025). Immunohistochemical analyses revealed that PMF1 methylation was associated with cytoplasmic PMF1 expression loss (&lt;i&gt;P&lt;/i&gt; = 0.032). PMF1 protein expression patterns were significantly associated with stage (&lt;i&gt;P&lt;/i&gt; &lt; 0.001), grade (&lt;i&gt;P&lt;/i&gt; &lt; 0.001), and poor overall survival using univariate (&lt;i&gt;P&lt;/i&gt; &lt; 0.001) and multivariate (&lt;i&gt;P&lt;/i&gt; = 0.011) analyses. Moreover, PMF1 methylation in urinary specimens distinguished bladder cancer patients from controls (area under the curve = 0.800).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; PMF1 was identified to be epigenetically modified in bladder cancer. The association of PMF1 methylation with tumor progression and its diagnostic ability using urinary specimens support including PMF1 assessment for the clinical management of bladder cancer patients.&lt;/p&gt;&lt;/div&gt;

Figure S5 from Single-cell Multiomics Analysis of Myelodysplastic Syndromes and Clinical Response to Hypomethylating Therapy

&lt;p&gt;Impact of AZA treatment on cell populations according to response status&lt;/p&gt;

Data from Single-cell Multiomics Analysis of Myelodysplastic Syndromes and Clinical Response to Hypomethylating Therapy

&lt;div&gt;Abstract&lt;p&gt;Alterations in epigenetic marks, such as DNA methylation, represent a hallmark of cancer that has been successfully exploited for therapy in myeloid malignancies. Hypomethylating agents (HMA), such as azacitidine, have become standard-of-care therapy to treat myelodysplastic syndromes (MDS), myeloid neoplasms that can evolve into acute myeloid leukemia. However, our capacity to identify who will respond to HMAs, and the duration of response, remains limited. To shed light on this question, we have leveraged the unprecedented analytic power of single-cell technologies to simultaneously map the genome and immunoproteome of MDS samples throughout clinical evolution. We were able to chart the architecture and evolution of molecular clones in precious paired bone marrow MDS samples at diagnosis and posttreatment to show that a combined imbalance of specific cell lineages with diverse mutational profiles is associated with the clinical response of patients with MDS to hypomethylating therapy.&lt;/p&gt;Significance:&lt;p&gt;MDS are myeloid clonal hemopathies with a low 5-year survival rate, and approximately half of the cases do not respond to standard HMA therapy. Our innovative single-cell multiomics approach offers valuable biological insights and potential biomarkers associated with the demethylating agent efficacy. It also identifies vulnerabilities that can be targeted using personalized combinations of small drugs and antibodies.&lt;/p&gt;&lt;/div&gt;

Dormant hypermethylated tumour suppressor genes: questions and answers

Abstract The epigenetic inactivation of tumour suppressor genes by promoter CpG island methylation is nowadays one of the hottest topics in cancer research. However, there are still several important open questions: Can we use CpG island hypermethylation to classify tumours according to their clinical behaviour and chemosensitivity? How do we prove that our hypermethylated gene is important for cancer development and/or progression? Which enzymes are directly responsible for the CpG island hypermethylation of tumour suppressor genes? How is the chromatin structure and molecular environment in and around the hypermethylated CpG islands? Can we wake up these dormant hypermethylated tumour suppressor genes in an epigenetic therapy of cancer? Some answers are provided in this review, but other questions remain unsolved, awaiting the eager epigenetic researcher. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.