Publications

Epigenetic loss of the PIWI/piRNA machinery in human testicular tumorigenesis

Although most cancer research has focused in mRNA, non-coding RNAs are also an essential player in tumorigenesis. In addition to the well-recognized microRNAs, recent studies have also shown that epigenetic silencing by CpG island hypermethylation of other classes of non-coding RNAs, such as transcribed ultraconserved regions (T-UCRs) or small nucleolar RNAs (snoRNAs), also occur in human neoplasia. Herein we have studied the putative existence of epigenetic aberrations in the activity of PIWI proteins, an Argonaute family protein subclass, and the small regulatory PIWI-interacting RNAs (piRNAs) in testicular cancer, as the PIWI/piRNA pathway plays a critical role in male germline development. We have observed the existence of promoter CpG island hypermethylation-associated silencing of PIWIL1, PIWIL2, PIWIL4, and TDRD1 in primary seminoma and non-seminoma testicular tumors, in addition to testicular germ cell tumor cell lines. Most importantly, these epigenetic lesions occur in a context of piRNA downregulation and loss of DNA methylation of the LINE-1 repetitive sequences, one of the target genomic loci where the PIWI/piRNA machinery acts as a caretaker in non-transformed cells.

Chromatin activity of IκBα mediates the exit from naïve pluripotency

Maintenance of pluripotency is a multifactorial process in which NF-κB is a negative regulator. Our previous work identified a chromatin role for IκBα, the master regulator of NF-κB signaling, that is critical for the proper regulation of various tissue stem cells. Here, we found that IκBα accumulates specifically in the chromatin fraction of pluripotent embryonic stem cells. IκBα depletion does not affect NF-kB-dependent transcription, but causes a profound epigenetic rewiring in pluripotent stem cells, including alterations in H3K27me3, a histone mark catalyzed by Polycomb repression complex 2. Chromatin changes induced by IκBα depletion affect a subset of pluripotency genes and are associated with altered gene transcription. At the cellular level, IκBα-deficient embryonic stem cells are arrested in a naive pluripotency state when cultured in serum/LIF conditions and fail to exit pluripotency under differentiation conditions. By constructing separation-of-function mutants, we show that the effects of IκBα in regulating stem cell pluripotency are NF-κB-independent, but mainly rely on its chromatin-related function. Taken together, our results reveal a novel mechanism by which IκBα participates in the regulation of the pluripotent state of embryonic stem cells and shed light on the interplay between inflammatory signals and the regulation of pluripotency.

Data from A Tumor Suppressor Enhancer of <i>PTEN</i> in T-cell Development and Leukemia

<div>Abstract<p>Long-range oncogenic enhancers play an important role in cancer. Yet, whether similar regulation of tumor suppressor genes is relevant remains unclear. Loss of expression of PTEN is associated with the pathogenesis of various cancers, including T-cell acute lymphoblastic leukemia (T-ALL). Here, we identify a highly conserved distal enhancer (PE) that interacts with the <i>PTEN</i> promoter in multiple hematopoietic populations, including T cells, and acts as a hub of relevant transcription factors in T-ALL. Consistently, loss of PE leads to reduced <i>PTEN</i> levels in T-ALL cells. Moreover, PE-null mice show reduced <i>Pten</i> levels in thymocytes and accelerated development of NOTCH1-induced T-ALL. Furthermore, secondary loss of PE in established leukemias leads to accelerated progression and a gene expression signature driven by <i>Pten</i> loss. Finally, we uncovered recurrent deletions encompassing PE in T-ALL, which are associated with decreased <i>PTEN</i> levels. Altogether, our results identify PE as the first long-range tumor suppressor enhancer directly implicated in cancer.</p>Significance:<p>Here, we identify a <i>PTEN</i> enhancer that is recurrently deleted in patients with T-ALL. Loss of this enhancer leads to reduced PTEN levels in T cells together with accelerated generation and progression of NOTCH1-induced leukemia <i>in vivo</i>. These results uncover long-range regulation of tumor suppressor genes as a relevant mechanism in cancer.</p><p><i>This article is highlighted in the In This Issue feature, p. 1</i></p></div>

A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples

Colorectal cancer is the fourth cause of cancer-related deaths worldwide, though detection at early stages associates with good prognosis. Thus, there is a clear demand for novel non-invasive tests for the early detection of colorectal cancer and premalignant advanced adenomas, to be used in population-wide screening programs. Aberrant DNA methylation detected in liquid biopsies, such as serum circulating cell-free DNA (cfDNA), is a promising source of non-invasive biomarkers. This study aimed to assess the feasibility of using cfDNA pooled samples to identify potential serum methylation biomarkers for the detection of advanced colorectal neoplasia (colorectal cancer or advanced adenomas) using microarray-based technology. cfDNA was extracted from serum samples from 20 individuals with no colorectal findings, 20 patients with advanced adenomas, and 20 patients with colorectal cancer (stages I and II). Two pooled samples were prepared for each pathological group using equal amounts of cfDNA from 10 individuals, sex-, age-, and recruitment hospital-matched. We measured the methylation levels of 866,836 CpG positions across the genome using the MethylationEPIC array. Pooled serum cfDNA methylation data meets the quality requirements. The proportion of detected CpG in all pools (> 99% with detection p value < 0.01) exceeded Illumina Infinium methylation data quality metrics of the number of sites detected. The differential methylation analysis revealed 1384 CpG sites (5% false discovery rate) with at least 10% difference in the methylation level between no colorectal findings controls and advanced neoplasia, the majority of which were hypomethylated. Unsupervised clustering showed that cfDNA methylation patterns can distinguish advanced neoplasia from healthy controls, as well as separate tumor tissue from healthy mucosa in an independent dataset. We also observed that advanced adenomas and stage I/II colorectal cancer methylation profiles, grouped as advanced neoplasia, are largely homogenous and clustered close together. This preliminary study shows the viability of microarray-based methylation biomarker discovery using pooled serum cfDNA samples as an alternative approach to tissue specimens. Our strategy sets an open door for deciphering new non-invasive biomarkers not only for colorectal cancer detection, but also for other types of cancers.

The transcription factor Slug represses<i>E-cadherin</i>expression and induces epithelial to mesenchymal transitions: a comparison with Snail and E47 repressors

Transcriptional repression mechanisms have emerged as one of the crucial processes for the downregulation of E-cadherin expression during development and tumour progression. Recently, several E-cadherin transcriptional repressors have been characterized (Snail, E12/E47, ZEB-1 and SIP-1) and shown to act through an interaction with proximal E-boxes of the E-cadherin promoter. We have analyzed the participation of another member of the Snail family, Slug, and observed that it also behaves as a repressor of E-cadherin expression. Stable expression of Slug in MDCK cells leads to the full repression of E-cadherin at transcriptional level and triggers a complete epithelial to mesenchymal transition. Slug-induced repression of E-cadherin is mediated by its binding to proximal E-boxes, particularly to the E-pal element of the mouse promoter. Detailed analysis of the binding affinity of different repressors to the E-pal element indicates that Slug binds with lower affinity than Snail and E47 proteins. These results, together with the known expression patterns of these factors in embryonic development and carcinoma cell lines, support the idea that the in vivo action of the different factors in E-cadherinrepression can be modulated by their relative concentrations as well as by specific cellular or tumour contexts.

Clonal evolution of a lethal prostate cancer: Integrated whole genome analysis case study

Chapter 9 Epigenetic Gene Regulation in Cancer

Supplementary Figure 4 from KAT6B Is a Tumor Suppressor Histone H3 Lysine 23 Acetyltransferase Undergoing Genomic Loss in Small Cell Lung Cancer

&lt;p&gt;Supplementary Figure 4. Effect of KAT6B shRNA-mediated depletion in the growth rate according to the XTT assay&lt;/p&gt;

Supplementary Figures 1-6 from DNA Methylation Biomarkers for Noninvasive Diagnosis of Colorectal Cancer

&lt;p&gt;PDF File - 916K, Representative pyrograms in a healthy colonic mucosa sample for the markers analyzed.&lt;/p&gt;

DNA methyltransferases control telomere length and telomere recombination in mammalian cells

Profiling of oxBS-450K 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci

DNA methylation (5-methylcytosine, 5 mC) is involved in many cellular processes and is an epigenetic mechanism primarily associated with transcriptional repression. The recent discovery that 5 mC can be oxidized to 5-hydromethylcytosine (5hmC) by TET proteins has revealed the “sixth base” of DNA and provides additional complexity to what was originally thought to be a stable repressive mark. However, our knowledge of the genome-wide distribution of 5hmC in different tissues is currently limited. Here, we sought to define loci enriched for 5hmC in the placenta genome by combining oxidative bisulphite (oxBS) treatment with high-density Illumina Infinium HumanMethylation450 methylation arrays and to compare our results with those obtained in brain. Despite identifying over 17,000 high-confidence CpG sites with consistent 5hmC enrichment, the distribution of this modification in placenta is relatively sparse when compared to cerebellum and frontal cortex. Supported by validation using allelic T4 β-glucosyltransferase assays we identify 5hmC at numerous imprinted loci, often overlapping regions associated with parent-of-origin allelic 5 mC in both placenta and brain samples. Furthermore, we observe tissue-specific monoallelic enrichment of 5hmC overlapping large clusters of imprinted snoRNAs-miRNAs processed from long noncoding RNAs (lncRNAs) within the <i>DLK1-DIO3</i> cluster on chromosome 14 and <i>SNRPN-UBE3A</i> domain on chromosome 15. Enrichment is observed solely on the transcribed alleles suggesting 5hmC is positively associated with transcription at these loci. Our study provides an extensive description of the 5hmC/5 mC landscape in placenta with our data available at www.humanimprints.net, which represents the most comprehensive resource for exploring the epigenetic profiles associated with human imprinted genes.

Additional file 11: Table S8. of N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration

Clinico-pathological features of the fourth CRC patient cohort. (XLSX 10 kb)

Epigenetic and genetic alterations of <i>APC</i> and <i>CDH1</i> genes in lobular breast cancer: Relationships with abnormal E‐cadherin and catenin expression and microsatellite instability

Abstract The causes and functional consequences of E‐cadherin (E‐CD) loss in breast cancer are poorly understood. E‐CD loss might act in concert with alterations in the APC/β‐catenin pathway to permit oncogenic β‐catenin signaling. To test this hypothesis, we have analyzed the presence of genetic and epigenetic alterations affecting E‐CD ( CDH1 ), APC and β‐catenin ( CTNNB1 ) genes and the immunohistochemical expression of E‐CD, β‐ and γ‐catenin in a series of 46 infiltrating lobular breast carcinomas (ILCs). Since 80% of ILCs featured complete loss of E‐CD expression, we analyzed the molecular alterations responsible for E‐CD inactivation in these tumors. We found that 10 of 46 (22%) cases harbored mutations in CDH1 , including 1 case with 2 different mutations (1 of which was germline). CDH1 was also inactivated by loss of heterozygosity (LOH; 30/41, 73%) and promoter hypermethylation (19/46, 41%). Interestingly, LOH and mutations were also detected in the corresponding in situ lesions of the ILCs, implying that these alterations are early events in lobular cancer tumorogenesis. Additionally, the presence of a polymorphism in the CDH1 promoter was found to be inversely correlated with CDH1 mutations, but not with E‐CD levels. We next examined whether alterations in the APC/β‐catenin pathway also occurred in the same series of ILCs. Although no CTNNB1 or APC mutations were detected, promoter methylation (25/46, 52%) and LOH (7/30, 23%) of APC were found. Moreover, methylation of APC and CDH1 occurred concordantly. However, β‐ and γ‐catenin were severely reduced or absent in 90% of these tumors, implying that alterations in CDH1 and APC genes do not promote β‐catenin accumulation in ILC. These molecular alterations were not associated with microsatellite instability. In summary, several different mechanisms (mutations, LOH, methylation) are involved in the frequent CDH1 inactivation in invasive and in situ lobular breast cancer. The same tumors also show genetic and epigenetic alterations of APC gene. However, altered CDH1 and APC genes do not promote β‐catenin accumulation in this tumor type. © 2003 Wiley‐Liss, Inc.

MeCP2: the long trip from a chromatin protein to neurological disorders

Additional file 2 of Genetically predicted telomere length and Alzheimer’s disease endophenotypes: a Mendelian randomization study

Additional file 2: Supplementary Table 1. Linear regression estimates for cognition outcomes in the entire sample. All models are adjusted for covariates: age, sex, education, and APOE status. Supplementary Table 2. Linear regression estimates for neuroimaging outcomes (i.e., Alzheimer’s disease and aging signatures) outcome in the entire sample. All models are adjusted for covariates: age, sex, education, and APOE status. Supplementary Table 3. Linear regression estimates for CSF biomarkers outcomes in the entire sample. All models are adjusted for covariates: age, sex, education, and APOE status. Supplementary Table 4. Linear regression estimates for cognition outcomes in APOE-ɛ4 carriers. All models are adjusted for covariates: age, sex, and education. Supplementary Table 5. Linear regression estimates for neuroimaging outcomes (i.e., Alzheimer’s disease and aging signatures) in APOE-ɛ4 carriers. All models are adjusted for covariates: age, sex, and education. Supplementary Table 6. Linear regression estimates for CSF biomarkers outcomes in APOE-ɛ4 carriers. All models are adjusted for covariates: age, sex, and education. Supplementary Table 7. Linear regression estimates for cognition outcomes in APOE-ɛ4 non-carriers. All models are adjusted for covariates: age, sex, and education. Supplementary Table 8. Linear regression estimates for neuroimaging outcomes (i.e., Alzheimer’s disease and aging signatures) in APOE-ɛ4 non-carriers. All models are adjusted for covariates: age, sex, and education. Supplementary Table 9. Linear regression estimates for CSF biomarkers outcomes in APOE-ɛ4 carriers. All models are adjusted for covariates: age, sex, and education. Supplementary Table 10. Linear regression estimates for cognition outcomes among individuals at high genetic predisposition to AD. All models are adjusted for covariates: age, sex, and education. Supplementary Table 11. Linear regression estimates for neuroimaging outcomes (i.e., Alzheimer’s disease and aging signatures) among individuals at high genetic predisposition to AD. All models are adjusted for covariates: age, sex, and education. Supplementary Table 12. Linear regression estimates for CSF biomarkers outcomes (i.e., Alzheimer’s disease and aging signatures) among individuals at high genetic predisposition to AD. All models are adjusted for covariates: age, sex, and education. Supplementary Table 13. Linear regression estimates for cognition outcomes among individuals at low genetic predisposition to AD. All models are adjusted for covariates: age, sex, and education. Supplementary Table 14. Linear regression estimates for neuroimaging outcomes (i.e., Alzheimer’s disease and aging signatures) among individuals at low genetic predisposition to AD. All models are adjusted for covariates: age, sex, and education. Supplementary Table 15. Linear regression estimates for CSF biomarkers outcomes among individuals at low genetic predisposition to AD. All models are adjusted for covariates: age, sex, and education.

Epigenetic biomarkers for human cancer: The time is now

IκBα controls dormancy induction in Hematopoietic stem cell development via retinoic acid

Summary Recent findings are challenging the classical hematopoietic model in which long-term hematopoietic stem cells (LT-HSC) are the base of the hematopoietic system. Clonal dynamics analysis of the hematopoietic system indicate that LT-HSC are not the main contributors of normal hemapoiesis in physiological conditions and the hematopoietic system is mainly maintained by multipotent progenitors (MPPs, hereafter HPC) and LT-HSCs are mostly in a non-active state. The first HSCs emerge from the aorta-gonad and mesonephros (AGM) region along with hematopoietic progenitors (HPC) within hematopoietic clusters. Molecular pathways that determine the HSC fate instead of HPC are still unknown, although inflammatory signaling, including NF-κB has been implicated in the development of HSCs. Here, we identify a chromatin binding function for IκBα (also known as the inhibitor of NF-κB) that is Polycomb repression complex 2 (PRC2)-dependent and specifically determines dormant vs proliferating HSCs from the onset of their emergence in the AGM. We find a specific reduction of LT-HSCs in the IκBα knockout new-born pups. This defect is manifested at the FL stage already, and traceable to the first emerging HSCs in the E11.5 AGM, without affecting the general HPC population. IκBα deficient LT-HSCs express dormancy signature genes, are less proliferative and can robustly respond to activation stimuli such as in vitro culture and serial transplantation. At the molecular level, we find decreased PRC2-dependent H3K27me3 at the promoters of several retinoic acid signaling elements in the IκBα - deficient aortic endothelium and E14.5 FL LT-HSCs. Additionally, IκBα binding itself is found in the promoters of retinoic acid receptors rarα in the AGM, and rarγ in the LT-HSC of FL. Overall, we demonstrate that the retinoic acid pathway is over-activated in the hematopoietic clusters of IκBα-deficient AGMs leading to premature dormancy of LT-HSCs that persists in the FL LT-HSCs.

Epigenetic mechanisms during ageing and neurogenesis as novel therapeutic avenues in human brain disorders

Ageing is the main risk factor for human neurological disorders. Among the diverse molecular pathways that govern ageing, epigenetics can guide age-associated decline in part by regulating gene expression and also through the modulation of genomic instability and high-order chromatin architecture. Epigenetic mechanisms are involved in the regulation of neural differentiation as well as in functional processes related to memory consolidation, learning or cognition during healthy lifespan. On the other side of the coin, many neurodegenerative diseases are associated with epigenetic dysregulation. The reversible nature of epigenetic factors and, especially, their role as mediators between the genome and the environment make them exciting candidates as therapeutic targets. Rather than providing a broad description of the pathways epigenetically deregulated in human neurological disorders, in this review, we have focused on the potential use of epigenetic enzymes as druggable targets to ameliorate neural decline during normal ageing and especially in neurological disorders. We will firstly discuss recent progress that supports a key role of epigenetic regulation during healthy ageing with an emphasis on the role of epigenetic regulation in adult neurogenesis. Then, we will focus on epigenetic alterations associated with ageing-related human disorders of the central nervous system. We will discuss examples in the context of psychiatric disorders, including schizophrenia and posttraumatic stress disorders, and also dementia or Alzheimer's disease as the most frequent neurodegenerative disease. Finally, methodological limitations and future perspectives are discussed.