Publications

Introduction: Central Nervous System (CNS) involvement in Diffuse Large B Cell Lymphoma (DLBCL) is a rare complication associated with bad prognosis. The CNS Prognostic Index identifies patients in high risk of CNS relapse; however, its specificity is limited and not accurate. Biomarkers that can predict CNS relapse are still missing. For that reason, we aimed to characterize the transcriptomic, genomic and epigenomic hallmarks of systemic tumors at diagnosis of patients that will relapse in the CNS. Methods: We conducted a retrospective study including 38 patients with nodal DLBCL that relapsed within the first two years after diagnosis: 12 with CNS relapse and 26 with systemic relapse. As controls, we included 21 patients that did not relapse. DNA and RNA were extracted from tumors at diagnosis. Immune infiltration was evaluated using the nCounter PanCancer Immune Profiling Panel (Nanostring); COO was determined using the Lymph2Cx assay. Transcriptomic profiles were generated by bulk RNA sequencing; mutational analysis was performed using a custom targeted NGS panel. Methylation profiles were described using the Illumina Infinium MethylationEPIC Array 850K (Figure 1A). Results: Immune cell composition was similar between groups; however, several genes were overexpressed at diagnosis in patients with CNS relapse. Genes related to chemokine signaling as CCL14, IL7R, and CCR6; adhesion like VCAM1 and ITGA4; and immune checkpoints as BTLA were upregulated in the CNS relapse group in comparison to patients without relapse (Figure 1B). Among these, the ITGA4 gene was also found to be overexpressed in the CNS relapse group when compared to both systemic and no relapse groups together (Figure 1C). No differences in COO were observed between groups. Whole transcriptomic data showed enrichment in genesets related to proliferation and survival in CNS relapse group in comparison to all others (Figure 1D). Patients with CNS relapse had increased mutation load and frequency in PIM1, IGLL5 and KMT2D genes. A total of 343 CpG sites were differentially methylated in CNS relapse group in comparison to No CNS relapse, involving 211 genes (Figure 1E). Keywords: Diagnostic and Prognostic Biomarkers, Extranodal non-Hodgkin lymphoma, Genomics, Epigenomics, and Other -Omics No conflicts of interests pertinent to the abstract.

ApoE ε4 carriers, specially the homozygous ones, are at increased risk for developing Alzheimer's Disease (AD). Healthy late-middle aged APOE4 carriers show alterations in brain regions known to be affected by AD. Conversely, there is controversy on whether, at these ages, asymptomatic APOE4 carriers display reduced hippocampal volumes, even though this is a characteristic feature by the time AD symptoms occur. In this work, we aimed at determining APOE4-associated structural changes in cognitively healthy late-middle age subjects in the whole brain and, specifically, in the hippocampus. A total of 238 subjects aged 45-65 were enrolled (107 noncarriers, 100 heterozygous and 31 homozygous) from the ALFA project. 3D-T1 weighted MRIs underwent VBM8-SPM (p<0.001) and Freesurfer (p<0.001) analyses for ε4 allele additive effects after correcting for intracranial volume, age and sex. Additionally, the hippocampal formation was further segmented into 8 subfields using Freesurfer which were subsequently analyzed (p<0.05). The VBM analysis revealed a cluster of ApoE ε4-associated volumetric decrease in the right hippocampus. Cortical thickness was bilaterally reduced in the precuneus, orbitofrontal and cingulate cortices as well as in small temporal, parietal and frontal regions. No between group differences could be detected in neither of the hippocampal subfields.

&lt;p&gt;Supplementary Figure 6. Immunohistochemistry studies for KAT6B and acetylated K23-H3 staining according to KAT6B deletion status&lt;/p&gt;

Rett syndrome (RTT) is a severe neurodevelopmental disease caused almost exclusively by mutations to the MeCP2 gene. This disease may be regarded as a synaptopathy, with impairments affecting synaptic plasticity, inhibitory and excitatory transmission and network excitability. The complete understanding of the mechanisms behind how the transcription factor MeCP2 so profoundly affects the mammalian brain are yet to be determined. What is known, is that MeCP2 involvement in activity-dependent expression programs is a critical link between this protein and proper neuronal activity, which allows the correct maturation of connections in the brain. By using RNA-sequencing analysis, we found several immediate-early genes (IEGs, key mediators of activity-dependent responses) directly bound by MeCP2 at the chromatin level and upregulated in the hippocampus and prefrontal cortex of the Mecp2-KO mouse. Quantification of the IEGs response to stimulus both in vivo and in vitro detected an aberrant expression pattern in MeCP2-deficient neurons. Furthermore, altered IEGs levels were found in RTT patient's peripheral blood and brain regions of post-mortem samples, correlating with impaired expression of downstream myelination-related genes. Altogether, these data indicate that proper IEGs expression is crucial for correct synaptic development and that MeCP2 has a key role in the regulation of IEGs.

BackgroundPatients with ulcerative colitis and Crohn's colonic disease are at increased risk of developing colorectal cancer (CRC). The aim of the study was to analyze the methylation status of selected genes as a risk marker for CRC in inflammatory bowel disease (IBD) patients.

Abstract N6-methyladenosine (m 6 A) is an RNA modification that governs multiple aspects of RNA metabolism, including splicing, translation, stability, decay, and the processing of marked transcripts. Although accumulating evidence suggests that the m 6 A writer METTL16 is involved in leukemia, the molecular pathway(s) by which it contributes to leukemogenesis remain unexplored. In this study, we shed light on a novel molecular mechanism whereby METTL16 plays a role in acute myeloid leukemia (AML) progression through an m 6 A-dependent manner. Our investigations revealed that METTL16 is overexpressed in primary AML cells. Genetic depletion of METTL16 or its pharmacological inhibition strongly affected the proliferation of AML cells, eventually triggering apoptosis. Transcriptome-wide analysis identified mRNA of MAX Dimerization Protein 4 (MXD4), a MYC pathway regulator, as a downstream target of METTL16. Mechanistically, we showed that METTL16 controls the stability of MXD4 mRNA, resulting in a reduction in MXD4 protein levels that indirectly activates the MYC-MAX axis, essential for leukemogenesis. Strikingly, the suppression of MXD4 rescued the expression levels of MYC target genes, restoring AML cell survival. Our findings unveil a novel METTL16-MXD4 oncogenic axis crucial for AML progression, establishing small-molecule inhibition of METTL16 as a potential therapeutic approach in leukemia and providing a new strategy to target MYC activity in cancer.

Additional file 2: Table S1. Discovery stage of the EWAS on acute myocardial infarction (REGICOR-1 sample). Model 1 was adjusted for estimated cell counts and two surrogate variables. Model 2 was further adjusted for smoking status. Model 3 was additionally adjusted for diabetes, hypercholesterolemia and hypertension. Coefficients, standard errors and p-values are given for each model before and after the correction of the inflation using the bacon R package. Suggestive significant associations (p-value&lt;10-5) are in bold. The total number of suggestive significant associations in each model is given. Table S2. Meta-analyses of the results from the discovery (REGICOR-1) and the validation stage (REGICOR-2). Model 1 was adjusted for estimated cell counts and two surrogate variables. Model 2 was further adjusted for smoking status. Model 3 was additionally adjusted for diabetes, hypercholesterolemia and hypertension. Coefficients, standard errors and p-values of REGICOR-1 are those corrected with the bacon R package. Significant associations (p-value&lt;6.17 × 10-8) are highlighted in bold. The total number of significant associations in each model is given. Table S3. Meta-analysis of the results from the follow-up association studies performed in the samples with incident cases of cardiovascular (CVD) and coronary heart disease (CHD). Model 1 was adjusted for age, estimated cell counts and two surrogate variables (plus ethnicity in WHI and sex in FOS). Model 2 was further adjusted for smoking status. Model 3 was additionally adjusted for diabetes, hypercholesterolaemia and hypertension. Significant associations (4.17 × 10-3) found in the fixed-effects meta-analysis are highlighted in bold. The total number of significant associations in each model is given. Table S4. Utility of the methylation risk scores (MRS): association with cardiovascular (CVD) or coronary (CHD) incidence and assessment of their predictive capacity. MRSs were based on the results from model 1 of incident CHD and CVD. Analyses of the association with the CVD or CHD incidence were adjusted for age, sex, total cholesterol and HDL-C levels, diabetes, smoking status, systolic blood pressure, and hypertensive treatment, which are the cardiovascular risk factors considered in the Framingham risk function. Analysis of the improvement in the predictive capacity of the Framingham function was performed with and without the corresponding MRS. Table S5. Results of the Wald ratio method applied to determine the causality between the identified CpGs and coronary heart disease or myocardial infarction.

&lt;p&gt;Integration of all MDS patient samples and distribution of cell surface markers across cell populations&lt;/p&gt;

Summary Hematopoietic stem cells (HSCs) develop within a short time window from the hemogenic endothelium in the aorta- gonads-and mesonephros (AGM) region during embryonic development. The first HSCs reside within Intra-aortic hematopoietic clusters (IAHC) along with hematopoietic progenitors (HPC). The signalling mechanisms that divert HSCs from HPCs are unknown. Notch signaling is essential for arterial specification, IAHC formation and HSC activity, but current studies on how Notch drives these different fates are inconsistent. To determine the role of Notch in the specification of hemogenic endothelium, HSC and/or HPCs, we extensively analyzed Notch dynamics in the period of HSC generation. We defined the expression pattern of Notch signalling molecules at the gene and protein level and established a molecular mechanism that reconcile previous studies demonstrating the loss of HSC activity in NOTCH1, JAG1 and RBPJ null mutants, the enhanced HSC generation by blocking specific Notch activities or the abrogation of emerging HSCs by high Notch activation. We now demonstrate that Notch activity is highest in a subset of Gfi1+ hemogenic endothelial cells and is gradually lost with HSC maturation. We uncover that the HSC phenotype is maintained through loss of Notch activity due to increasing levels of NOTCH1 and JAG1 interactions on the surface of the same cell ( cis ) that renders the NOTCH1 receptor from being activated. Forcing activation of the NOTCH1 receptor in IAHC cells activates a hematopoietic differentiation program and supports a cis -inhibitory function for JAG1 and NOTCH1. Furthermore, we demonstrate that this cis -inhibitory interaction is enabled by RADICAL FRINGE (RFNG), a glycosyltransferase that enhances the affinity of NOTCH1 to JAG1 in cis . Finally, our results indicate that NOTCH1-JAG1 cis -inhibition is necessary for preserving the HSC phenotype in the hematopoietic clusters of the aorta.

No abstract is provided for this article.

&lt;p&gt;Supplementary Table 1. List of antibodies and primer sets used in the study.&lt;/p&gt;

DNA methylation biomarkers for noninvasive diagnosis of colorectal cancer (CRC) and precursor lesions have been extensively studied. Different panels have been reported attempting to improve current protocols in clinical practice, although no definite biomarkers have been established. In the present study, we have examined patient biopsies starting from a comprehensive analysis of DNA methylation differences between paired normal and tumor samples in known cancer-related genes aiming to select the best performing candidates informative for CRC diagnosis in stool samples. Five selected markers were considered for subsequent analyses in independent biologic cohorts and in silico data sets. Among the five selected genes, three of them (AGTR1, WNT2 and SLIT2) were validated in stool DNA of affected patients with a detection sensitivity of 78% [95% confidence interval (CI), 56%-89%]. As a reference, DNA methylation of VIM and SEPT9 was evaluated in a subset of stool samples yielding sensitivities of 55% and 20%, respectively. Moreover, our panel may complement histologic and endoscopic diagnosis of inflammatory bowel disease (IBD)-associated neoplasia, as it was also efficient detecting aberrant DNA methylation in non-neoplastic tissue samples from affected patients. This novel panel of specific methylation markers can be useful for early diagnosis of CRC using stool DNA and may help in the follow-up of high-risk patients with IBD.