Differentially Methylated CpG Sites Research Articles

Molecular subtypes explain lupus epigenomic heterogeneity unveiling new regulatory genetic risk variants

The heterogeneity of systemic lupus erythematosus (SLE) can be explained by epigenetic alterations that disrupt transcriptional programs mediating environmental and genetic risk. This study evaluated the epigenetic contribution to SLE heterogeneity considering molecular and serological subtypes, genetics and transcriptional status, followed by drug target discovery. We performed a stratified epigenome-wide association studies of whole blood DNA methylation from 213 SLE patients and 221 controls. Methylation quantitative trait loci analyses, cytokine and transcription factor activity - epigenetic associations and methylation-expression correlations were conducted. New drug targets were searched for based on differentially methylated genes. In a stratified approach, a total of 974 differential methylation CpG sites with dependency on molecular subtypes and autoantibody profiles were found. Mediation analyses suggested that SLE-associated SNPs in the HLA region exert their risk through DNA methylation changes. Novel genetic variants regulating DNAm in disease or in specific molecular contexts were identified. The epigenetic landscapes showed strong association with transcription factor activity and cytokine levels, conditioned by the molecular context. Epigenetic signals were enriched in known and novel drug targets for SLE. This study reveals possible genetic drivers and consequences of epigenetic variability on SLE heterogeneity and disentangles the DNAm mediation role on SLE genetic risk and novel disease-specific meQTLs. Finally, novel targets for drug development were discovered.

P-008 Sperm DNA methylation landscape in infertile men with clinical varicocele before and after treatment

Abstract Study question As varicocele leads to poor semen parameters, does it also affect sperm DNA methylation levels? Does varicocele treatment help in epigenetics restoration in the sperm? Summary answer Varicocele leads to aberrant sperm DNA methylation and varicocele treatment helps in the partial restoration of sperm DNA methylation levels. What is known already Varicocele affects 15% to 20% of the adult male population and 20% of men with varicocele are reported to be infertile. Treatment modalities for varicocele improve semen parameters, yet more than 50% of cases remain infertile. High oxidative stress (OS) has been implicated as a key factor in varicocele-associated infertility. OS during spermatogenesis may lead to aberrant epigenetic modifications in spermatozoa. In view of the crucial role of sperm epigenome in its functionality, this study aims to evaluate sperm genome-wide DNA methylation by whole-genome bisulfite sequencing (WGBS) before and after varicocele treatment in men with varicocele. Study design, size, duration This is a case-control study, which includes (n = 28) healthy fertile men and (n = 35) infertile men with clinical varicocele. Study participants were recruited from ICMR-NIRRCH and, LTMG Hospital, Mumbai. According to the inclusion and exclusion criteria, study participants were recruited from December 2020 to November 2023. Varicocele patients were followed up, and semen samples (n = 18) were recollected after 3-6 months of varicocele treatment. Participants/materials, setting, methods WGBS was used to identify differentially methylated CpG (DMC) sites in sperm of varicocele group compared to controls. 5 samples from each group were pooled for WGBS. DMCs identified with ≥25% methylation change and ≤0.05 q-value. DMCs within genes relevant to sperm function were selected for validation in the study population by pyrosequencing. Differentially methylated Genes (DMGs) were identified based on the location of DMC and used for pathway analysis using KEGG and DAVID tools. Main results and the role of chance Varicocele group had significantly lower semen parameters compared to controls, which were found to be improved after varicocele treatment. WGBS of sperm DNA was done and DMC sites were obtained in varicocele group compared to controls. A total of 6414 DMCs were obtained, of which, 3730 were hypermethylated and 2684 were hypomethylated. Based on genomic context, differential methylation was observed in introns, exons, promoters and intergenic regions. WGBS analysis gave a total of 1484 DMGs. KEGG and DAVID pathway analysis revealed that the PI3K-Akt signaling, MAPK signaling, cAMP signaling, calcium signaling, signal transduction pathway, cell adhesion molecules, and tight junction, were affected in the varicocele group. The DMGs SPATA6L, H2AX, SOD2, BCL2, NF1, PRKN, CDKN1B, BCR, P2RX7, RNF212B obtained are involved in spermatogenesis, regulation of cell cycle, apoptotic signaling pathway, cell differentiation, regulation of ROS metabolic process, response to heat, mitochondria regulation, regulation of gene expression, etc. Pyrosequencing validation of a few selected DMCs reflects the same methylation difference (hypo or hyper) as obtained by the WGBS pooled sample. Significant hypermethylation and hypomethylation were observed in the H2AX DMC and CDKN1B DMC, respectively, in the varicocele population; however, after varicocele treatments, these methylation levels seem to be restored. Limitations, reasons for caution The limitations of this study are the small number of patients and pooled sperm DNA sample WGBS analysis in the study population. However, a pooling sample strategy is considered more efficient than a random sample selection strategy, as pooling minimizes the amount of information lost below the detection threshold. Wider implications of the findings This study identified differentially methylated genes relevant to spermatogenesis and sperm functions in the case of varicocele compared to fertile controls and gave deeper insights into the possibility of epigenetic restoration after varicocele treatment. This study provides insight into the molecular aetiology of varicocele associated infertility. Trial registration number Not Applicable

Identification of DNA methylation characteristics associated with metastasis and prognosis in colorectal cancer

Colorectal cancer (CRC) is prone to metastasis and recurrence after surgery, which is one of the main causes for its poor treatment and prognosis. Therefore, it is essential to identify biomarkers associated with metastasis and recurrence in CRC. DNA methylation has a regulatory role in cancer metastasis, tumor immune microenvironment (TME), and prognosis and may be one of the most valuable biomarkers for predicting CRC metastasis and prognosis. We constructed a diagnostic model and nomogram that can effectively predict CRC metastasis based on the differential methylation CpG sites (DMCs) between metastatic and non-metastatic CRC patients. Then, we identified 17 DMCs associated with progression free survival (PFS) of CRC and constructed a prognostic model. The prognosis model based on 17 DMCs can predict the PFS of CRC with medium to high accuracy. The results of immunohistochemical analysis indicated that the protein expression levels of the genes involved in prognostic DMCs were different between normal and colorectal cancer tissues. According to the results of immune-related analysis, we found that the low-risk patients had better immunotherapy response. In addition, high risk scores were negatively correlated with high tumor mutation burden (TMB) levels, and patients with low TMB levels in the high-risk group had the worst PFS. Our work shows the clinical value of DNA methylation in predicting CRC metastasis and PFS, as well as their correlation with TME, immunotherapy, and TMB, which helps understand the changes of DNA methylation in CRC metastasis and improving the treatment and prognosis of CRC.

Hypomethylation of Wnt signaling regulator genes in developmental language disorder.

Background: Developmental language disorder (DLD) is a neurodevelopmental disorder. Considering the pivotal role of epigenetics in neurodevelopment, we examined any altered DNA methylation between DLD and control subjects. Materials & methods: We looked into genome-wide methylation differences between DLD and control groups. The findings were validated by quantitative PCR (qPCR). Results: In the DLD group, differential methylation of CpG sites was observed in the Wnt signaling regulator genes APCDD1, AMOTL1, LRP5, MARK2, TMEM64, TRABD2B, VEPH1 and WNT2B. Hypomethylation of APCDD1, LRP5 and WNT2B was confirmed by qPCR. Conclusion: This is the first report associating Wnt signaling with DLD. The findings are relevant in the light of the essential role of Wnt in myelination, and of the altered myelination in DLD.

DNA-Methylation Signatures of Tobacco Smoking in a High Cardiovascular Risk Population: Modulation by the Mediterranean Diet.

Biomarkers based on DNA methylation are relevant in the field of environmental health for precision health. Although tobacco smoking is one of the factors with a strong and consistent impact on DNA methylation, there are very few studies analyzing its methylation signature in southern European populations and none examining its modulation by the Mediterranean diet at the epigenome-wide level. We examined blood methylation smoking signatures on the EPIC 850 K array in this population (n = 414 high cardiovascular risk subjects). Epigenome-wide methylation studies (EWASs) were performed analyzing differential methylation CpG sites by smoking status (never, former, and current smokers) and the modulation by adherence to a Mediterranean diet score was explored. Gene-set enrichment analysis was performed for biological and functional interpretation. The predictive value of the top differentially methylated CpGs was analyzed using receiver operative curves. We characterized the DNA methylation signature of smoking in this Mediterranean population by identifying 46 differentially methylated CpGs at the EWAS level in the whole population. The strongest association was observed at the cg21566642 (p = 2.2 × 10-32) in the 2q37.1 region. We also detected other CpGs that have been consistently reported in prior research and discovered some novel differentially methylated CpG sites in subgroup analyses. In addition, we found distinct methylation profiles based on the adherence to the Mediterranean diet. Particularly, we obtained a significant interaction between smoking and diet modulating the cg5575921 methylation in the AHRR gene. In conclusion, we have characterized biomarkers of the methylation signature of tobacco smoking in this population, and suggest that the Mediterranean diet can increase methylation of certain hypomethylated sites.

Mechanisms Linking COPD to Type 1 and 2 Diabetes Mellitus: Is There a Relationship between Diabetes and COPD?

Chronic obstructive pulmonary disease (COPD) patients frequently suffer from multiple comorbidities, resulting in poor outcomes for these patients. Diabetes is observed at a higher frequency in COPD patients than in the general population. Both type 1 and 2 diabetes mellitus are associated with pulmonary complications, and similar therapeutic strategies are proposed to treat these conditions. Epidemiological studies and disease models have increased our knowledge of these clinical associations. Several recent genome-wide association studies have identified positive genetic correlations between lung function and obesity, possibly due to alterations in genes linked to cell proliferation; embryo, skeletal, and tissue development; and regulation of gene expression. These studies suggest that genetic predisposition, in addition to weight gain, can influence lung function. Cigarette smoke exposure can also influence the differential methylation of CpG sites in genes linked to diabetes and COPD, and smoke-related single nucleotide polymorphisms are associated with resting heart rate and coronary artery disease. Despite the vast literature on clinical disease association, little direct mechanistic evidence is currently available demonstrating that either disease influences the progression of the other, but common pharmacological approaches could slow the progression of these diseases. Here, we review the clinical and scientific literature to discuss whether mechanisms beyond preexisting conditions, lifestyle, and weight gain contribute to the development of COPD associated with diabetes. Specifically, we outline environmental and genetic confounders linked with these diseases.

Computational epigenetic landscape analysis reveals association of CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1 lncRNAs in prostate cancer progression through aberrant methylation

Aberrant expression of long non-coding RNAs (lncRNAs), caused by alterations in DNA methylation, is a driving factor in several cancers. Interplay between lncRNAs’ aberrant methylation and expression in prostate cancer (PC) progression still remains largely elusive. Therefore, this study characterized the genome-wide epigenetic landscape and expression profiles of lncRNAs and their clinical impact by integrating multi-omics data implementing bioinformatics approaches. We identified 62 differentially methylated CpG-sites (DMCs) and 199 differentially expressed lncRNAs (DElncRNAs), where 32 DElncRNAs contain 32 corresponding DMCs within promoter regions. Significant negative correlation was observed between 8 DElncRNAs-DMCs pairs. 3 (cg23614229, cg23957912, and cg11052780) DMCs and 4 (CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1) DElncRNAs were identified as high-risk factors for poor prognosis of PC patients. Overexpression of hypo-methylated CACNA1G-AS1, F11-AS1, and NNT-AS1 and down-regulation of hyper-methylated MSC-AS1 significantly lower the survival of PC patients and could be a potential prognostic and therapeutic biomarker. These DElncRNAs were found to be associated with several molecular functions whose deregulation can lead to cancer. Involvement of these epigenetically deregulated DElncRNAs in cancer-related biological processes was also noticed. These findings provide new insights into the understanding of lncRNA regulation by aberrant DNA methylation which will help to clarify the epigenetic mechanisms underlying PC.

Long-term improvement of adipocyte insulin action during body weight relapse after bariatric surgery: a longitudinal cohort study.

There are few long-term mechanistic studies in adipose tissue that investigate the metabolic effects of bariatric surgery. Changes in lipogenesis may be involved in long-term weight development. To investigate the long-term effect of bariatric surgery on lipogenesis in abdominal fat cells and whether surgical treatment could induce an epigenetic memory that would maintain improved lipogenesis in spite of body weight relapse. Karolinska University Hospital in Stockholm County, Sweden. A total of 22 women with obesity living in the Stockholm area were examined before, 2, 5, and 10 years after bariatric surgery. Abdominal adipose tissue biopsies were obtained. Fat cells were isolated and spontaneous and insulin stimulated glucose incorporation into lipids were assayed. CpG-methylation profiling was performed on adipocytes using the Infinium EPIC BeadChips. Bariatric surgery was associated with improvement in adipocyte spontaneous and insulin stimulated lipogenesis, which was maintained despite some later weight regain (29 % of initial weight loss). There was also an increase in fat cell size between 2- and 10-year follow-up, albeit not to presurgery levels. There were 7729 differentially methylated CpG sites (DMS) at 2 years that showed no sign of return to baseline at either 5 or 10 years. Merging results with expression profiles identified 1259 genes with DMS which showed early response or continual change in expression in one direction after surgery. Upregulated genes with DMS were enriched in gene sets linked to cellular response to insulin stimulus (e.g., IRS1, IRS2, PDE3B, and AKT2) and regulation of lipid metabolic processes. Bariatric surgery leads to long-term improvement of lipogenesis and insulin responsiveness in subcutaneous adipocytes in women in spite of some partial body weight regain postoperatively. This may to some extent be explained by epigenetic modifications of fat cell function.

DNA methylation and transcription of the FOXO3a gene are associated with ankylosing spondylitis.

To explore the association between methylation level and transcript level of Forkhead box O3a (FOXO3a) gene with ankylosing spondylitis (AS) susceptibility. Methylation levels of the FOXO3a promoter were measured in 84 AS patients and 83 healthy controls. A total of 77 patients and 66 healthy subjects were included in subsequent mRNA level testing. DNA methylation levels of 107CpG sites on 6CpG islands in the FOXO3a gene were investigated. This study indicated that CpG-4 and CpG-5 islands were markedly hypomethylated in AS patients. The methylation level of CpG-4 island in AS patients was negatively correlated with erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and Ankylosing Spondylitis Disease Activity Score (ASDAS). Moreover, FOXO3a mRNA levels were significantly decreased in AS patients and were obviously negatively correlated with the methylation levels of CpG-2 and CpG-5 islands in AS patients without treatment. The sensitivity and specificity of differential methylated CpG sites of FOXO3a were 74.7 and 85.4%, respectively. Besides, FOXO3a mRNA had a sensitivity of 80.0% and a specificity of 68.8%. DNA methylation and transcription of FOXO3a might be related to AS susceptibility and play a crucial role in the diagnosis of AS, but many open questions remain.

Genome-Wide Analysis of DNA Methylation in Cd4+ T Lymphocytes of Patients with Primary Progressive Multiple Sclerosis Indicates Involvement of This Epigenetic Process in the Disease Immunopathogenesis

The pathogenesis of multiple sclerosis (MS), a chronic disease of the CNS, includes autoimmune and neurodegenerative components. In most cases, patients develop relapsing-remitting MS (RRMS), while 10-15% of patients develop primary progressive MS (PPMS), which differs from RRMS in the mechanisms of the pathological process, some demographic, and some clinical characteristics. These differences may be explained by the epigenetic regulation of gene expression in PPMS including DNA methylation as one of the key epigenetic processes. The features of DNA methylation in various cell populations in PPMS patients remain understudied. The goal of this study is to identify differentially methylated CpG sites (DMSs) of the genome of CD4+ T lymphocytes, which characterize PPMS. The study included eight treatment-naive PPMS patients and eight healthy controls. Genome-wide analysis of DNA methylation of CD4+ T lymphocytes was performed using high-density DNA microarrays. We have identified 108 DMSs, which distinguish PPMS patients from healthy controls. In PPMS patients 81% of the DMSs are hypermethylated. More than a half of the identified DMSs are located in known genes in CpG islands and adjacent regions, which indicates a high functional significance of these DMSs in PPMS development. Analysis of the overrepresentation of DMS-containing genes in the main biological processes demonstrates their involvement in the regulation of cell adhesion to the extracellular matrix and the development of the immune response, i.e., antigen processing and presentation, and development of the immune system. Genome-wide analysis of DNA methylation in CD4+ T lymphocytes of PPMS patients indicates the involvement of this epigenetic process in the immunopathogenesis of the disease. These results may help better understand the pathogenesis of this severe form of MS.

Methylation biomarkers of polybrominated diphenyl ethers (PBDEs) and association with breast cancer risk at the time of menopause.

Exposure to polybrominated diphenyl ethers (PBDEs) may influence risk of developing post-menopausal breast cancer. Although mechanisms are poorly understood, epigenetic regulation of gene expression may play a role. To identify DNA methylation (DNAm) changes associated with PBDE serum levels and test the association of these biomarkers with breast cancer risk. We studied 397 healthy women (controls) and 133 women diagnosed with breast cancer (cases) between ages 40 and 58years who participated in the California Teachers Study. PBDE levels were measured in blood. Infinium Human Methylation EPIC Bead Chips were used to measure DNAm. Using multivariable linear regression models, differentially methylated CpG sites (DMSs) and regions (DMRs) associated with serum PBDE levels were identified using controls. For top-ranked DMSs and DMRs, targeted next-generation bisulfite sequencing was used to measure DNAm for 133 invasive breast cancer cases and 301 age-matched controls. Conditional logistic regression was used to evaluate associations between DMSs and DMRs and breast cancer risk. We identified 15 DMSs and 10 DMRs statistically significantly associated with PBDE levels (FDR<0.05). Methylation changes in a DMS at BMP8B and DMRs at TP53 and A2M-AS1 were statistically significantly (FDR<0.05) associated with breast cancer risk. We show for the first time that serum PBDE levels are associated with differential methylation and that PBDE-associated DNAm changes in blood are associated with breast cancer risk.

HPA axis dysregulation is associated with differential methylation of CpG-sites in related genes

DNA methylation shifts in Hypothalamic–pituitary–adrenal (HPA) axis related genes is reported in psychiatric disorders including hypersexual disorder. This study, comprising 20 dexamethasone suppression test (DST) non-suppressors and 73 controls, examined the association between the HPA axis dysregulation, shifts in DNA methylation of HPA axis related genes and importantly, gene expression. Individuals with cortisol level ≥ 138 nmol/l, after the low dose (0.5 mg) dexamethasone suppression test (DST) were classified as non-suppressors. Genome-wide methylation pattern, measured in whole blood using the EPIC BeadChip, investigated CpG sites located within 2000 bp of the transcriptional start site of key HPA axis genes, i.e.: CRH, CRHBP, CRHR-1, CRHR-2, FKBP5 and NR3C1. Regression models including DNA methylation M-values and the binary outcome (DST non-suppression status) were performed. Gene transcripts with an abundance of differentially methylated CpG sites were identified with binomial tests. Pearson correlations and robust linear regressions were performed between CpG methylation and gene expression in two independent cohorts. Six of 76 CpG sites were significantly hypermethylated in DST non-suppressors (nominal P < 0.05), associated with genes CRH, CRHR1, CRHR2, FKBP5 and NR3C1. NR3C1 transcript AJ877169 showed statistically significant abundance of probes differentially methylated by DST non-suppression status and correlated with DST cortisol levels. Further, methylation levels of cg07733851 and cg27122725 were positively correlated with gene expression levels of the NR3C1 gene. Methylation levels of cg08636224 (FKBP5) correlated with baseline cortisol and gene expression. Our findings revealed that DNA methylation shifts are involved in the altered mechanism of the HPA axis suggesting that new epigenetic targets should be considered behind psychiatric disorders.

Integrative Analysis of DNA Methylation and Gene Expression Profiles Identifies Colorectal Cancer-Related Diagnostic Biomarkers.

Background: Colorectal cancer (CRC) is a common human malignancy worldwide. The prognosis of patients is largely frustrated by delayed diagnosis or misdiagnosis. DNA methylation alterations have been previously proved to be involved in CRC carcinogenesis. Methods: In this study, we proposed to identify CRC-related diagnostic biomarkers by analyzing DNA methylation and gene expression profiles. TCGA-COAD datasets downloaded from the Cancer Genome Atlas (TCGA) were used as the training set to screen differential expression genes (DEGs) and methylation CpG sites (dmCpGs) in CRC samples. A logistic regression model was constructed based on hyper-methylated CpG sites which were located in downregulated genes for CRC diagnosis. Another two independent datasets from the Gene Expression Omnibus (GEO) were used as a testing set to evaluate the performance of the model in CRC diagnosis. Results: We found that CpG island methylator phenotype (CIMP) was a potential signature of poor prognosis by dividing CRC samples into CIMP and noCIMP groups based on a set of CpG sites with methylation standard deviation (sd) > 0.2 among CRC samples and low methylation levels (mean β < 0.05) in adjacent samples. Hyper-methylated CpGs tended to be more closed to CpG island (CGI) and transcription start site (TSS) relative to hypo-methylated CpGs (p-value < 0.05, Fisher exact test). A logistic regression model was finally constructed based on two hyper-methylated CpGs, which had an area under receiver operating characteristic curve of 0.98 in the training set, and 0.85 and 0.95 in the two independent testing sets. Conclusions: In conclusion, our study identified promising DNA methylation biomarkers for CRC diagnosis.

Dynamics of Methylation Profiling in Response to Tyrosine Kinase Inhibitor Therapy in Chronic Myeloid Leukemia

BackgroundChronic myeloid leukemia (CML) is characterized by gene rearrangement event between the ABL1 gene and the BCR gene, yielding a bcr-abl fusion oncoprotein. Increasing evidence suggests that major DNA methylation change is associated with disease progression in CML. However, the impact of tyrosine kinase inhibitor (TKI) therapy on methylation in CML has never been analyzed on a genome-wide level. Accordingly, this study attempted to analyze methylation profiles in 78 CML patients prior to/after TKI therapy and its clinical relevance with respect to molecular response to TKI therapy.MethodsGenome-wide methylation microarray was performed through the latest Illumina methylation profiling microarray with 850k probes, MethylationEPIC BeadChip in a series of 78 sample pairs from 78 CML patients, collected prior to and after TKI therapy. Response to TKI therapy was determined according to the ELN recommendation as optimal responder (n=58), failure but remained in chronic phase (n=16; CP) and progression to advanced disease (n=4). Healthy control samples were obtained through NCBI (series number: GSE54939). Methylation statuses prior to and after TKI were profiled and compared according to disease phase, response to TKI therapy, and somatic mutation profiles by targeted sequencing.ResultsOverall, the methylome 867,926 CpG sites were profiled, of which 606,030 (69.8%) passed quality control, followed by normalization procedure applied.In comparison to control (23.1%), CML patients show higher proportion of methylation on CpG sites (34.2%, bonferroni corrected p-value <1e-22) prior to TKI therapy. Decrease in the percentage of methylated CpG sites was observed in CML sample following TKI therapy (30.7%, p-value < 1e-28), but not to the level in control (Figure 1). However, post TKI methylation status with advanced phase showed less decrease to 31.6%. In detail, 250,541 (41% of remained) CpG sites were differentially methylated (DM) between pre and post TKI therapy samples. Among all DM CpG sites, 113,692 CpG sites were hyper-methylated in post TKI samples, while 136,849 were hypo-methylated.Next, comparison between the subgroups categorized according to the response to TKI therapy were conducted separately in pre and post TKI therapy samples, which were classified as responsive (R), resistant (T) and progressive (P). A total of 18 and 525 CpG sites was found to be significantly different in pre and post TKI samples, respectively. It implies that TKI therapy potentiates the difference of methylation on CpG sites, and methylation changes in CpG site correlates with the response to TKI therapy. In post TKI samples, 317,579 and 0 CpG sites were identified to be DM between R:T, R:P and T:P comparisons. On each DM site, the corresponding gene was annotated. In post-TKI R:P comparison, four genes were highlighted, i.e. CTC-479C5.6, EML1, IRF4 and RPS12P15. In addition, locus 16p68.01 was found as significant locus in epigenetic change.Then, cumulative incidence analysis was performed to compare methylation status with respect to complete cytogenetic, major molecular response, MR4.5, MR5, failure, progression and overall survival. Nineteen recurrently CpG sites were reported to be associated with above 7 endpoints, recurrently. The list of associated genes are as follows: AIG1, ATAD2, ATP5F1, C11orf24, ETAA1, FAM63A, OVOL1, PRUNE, ST20, ST20-MTHFS, WDR77, WDYHV1, WNT7A, ZDHHC4, ZNF10, ZNF252P, ZNF252P-AS1, ZNF268, and ZNF891. There are five zinc finger protein genes.Finally, integrative analysis of methylation profile with somatic mutation profile was conducted. As our group had reported previously (Kim, Blood 2017), we have divided them into 5 mutation patterns, then analyzed methylation profiles accordingly. Methylation profile was significantly different both in pre- and post-TKI samples in patient with pattern 2 compared to others. Pattern 2 was defined as acquisition of new mutation or increasing variant allele frequency over TKI therapy which correlates with TKI therapy failure or progression over treatment.ConclusionThe present study suggested that methylation profile correlates with response to TKI therapy as well as progression to advanced disease over TKI therapy in CML patients. Also, correlation between somatic mutation profiles and methylation profile is also suggested in the context of TKI therapy. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

SETD4 in the Proliferation, Migration, Angiogenesis, Myogenic Differentiation and Genomic Methylation of Bone Marrow Mesenchymal Stem Cells.

Epigenetic modification is a crucial mechanism affecting the biological function of stem cells. SETD4 is a histone methyltransferase, and its biological role in bone marrow mesenchymal stem cells (BMSCs) is currently unknown. In this study, we employed CRISPR/Cas9 technology edited mouse model and found that SETD4 knockout significantly promoted the proliferation of BMSCs, impaired BMSCs migration and differentiation potentials of lineages of cardiacmyocyte and smooth muscle cell, and even the angiogenesis via paracrine of VEGF. Through Reduced Representation Bisulfite Sequencing (RRBS) method, we verified that the overall genomic methylation of BMSCs in the SETD4 knockout group only was decreased by 0.47 % compared with wild type. However, the changed genomic methylation covers a total of 96,331 differential methylated CpG sites and 8,692 differential methylation regions (DMRs), with part of them settled in promoter regions. Bioinformatic analysis revealed that differential CpG islands and DMRs in promoter impacted 270 GO functions and 34 KEGG signaling pathways, with some closely related to stem cell biology. Mechanismly, SETD4 knockout inhibited sets of monomethylases and dimethylases for histone lysine, along with significant changes in some factors including Nkx2.5, Gata4, Gli2, Grem2, E2f7, Map7, Nr2f2 and Shox2 that associated with stem cell biology. These results are the first to reveal that even though SETD4 changes the genome's overall methylation to a limited extent in BMSCs, it still affects the numerous cellular functions and signaling pathways, implying SETD4-altered genomic methylation serves a crucial molecular role in BMSCs' biological functions.

Analysis of the Epigenetic Signature of Cell Reprogramming by Computational DNA Methylation Profiles

Background: DNA methylation plays an important role in the reprogramming process. Understanding the underlying molecular mechanism of reprogramming is crucial for answering fundamental questions regarding the transition of cell identity. Methods: In this study, based on the genome-wide DNA methylation data from different cell lines, comparative methylation profiles were proposed to identify the epigenetic signature of cell reprogramming. Results: The density profile of CpG methylation showed that pluripotent cells are more polarized than Human Dermal Fibroblasts (HDF) cells. The heterogeneity of iPS has a greater deviation in the DNA hypermethylation pattern. The result of regional distribution showed that the differential CpG sites between pluripotent cells and HDFs tend to accumulate in the gene body and CpG shelf regions, whereas the internal differential methylation CpG sites (DMCs) of three types of pluripotent cells tend to accumulate in the TSS1500 region. Furthermore, a series of endogenous markers of cell reprogramming were identified based on the integrative analysis, including focal adhesion, pluripotency maintenance and transcription regulation. The calcium signaling pathway was detected as one of the signatures between NT cells and iPS cells. Finally, the regional bias of DNA methylation for key pluripotency factors was discussed. Our studies provide new insight into the barrier identification of cell reprogramming. Conclusion: Our studies analyzed some epigenetic markers and barriers of nuclear reprogramming, hoping to provide new insight into understanding the underlying molecular mechanism of reprogramming.

A Novel Promoter CpG-Based Signature for Long-Term Survival Prediction of Breast Cancer Patients.

DNA methylation has been reported as one of the most critical epigenetic aberrations during the tumorigenesis and development of breast cancer (BC). This study explored a novel promoter CpG-based signature for long-term survival prediction of BC patients. We used The Cancer Genome Atlas (TCGA) data as training set, and results were validated in an independent dataset from Gene Expression Omnibus (GEO). First, the differential methylation CpG sites were screened in TCGA dataset, of which the candidate promoter CpG sites were preliminarily identified with the univariate Cox regression analysis and the least absolute shrinkage and selection operator regression analysis. Second, the signature was constructed with stepwise regression analysis and multivariate Cox proportional hazards model, which was validated with the survival analysis of two cohorts each from TCGA and GEO databases. The 10-year receiver operating characteristic curves of risk score presented an area under the curve of over 0.7 for both cohorts. A nomogram was also constructed and released. Moreover, Gene Set Enrichment Analysis was performed to identify the more active pathways in high-risk patients. The CpG sites–target gene correlations and differential methylation regions were further explored. In conclusion, the promoter CpG-based signature exhibited good prognostic prediction efficacy in the long-term overall survival of BC patients.

Pan-cancer analysis of differential DNA methylation patterns

BackgroundDNA methylation is a key epigenetic regulator contributing to cancer development. To understand the role of DNA methylation in tumorigenesis, it is important to investigate and compare differential methylation (DM) patterns between normal and case samples across different cancer types. However, current pan-cancer analyses call DM separately for each cancer, which suffers from lower statistical power and fails to provide a comprehensive view for patterns across cancers.MethodsIn this work, we propose a rigorous statistical model, PanDM, to jointly characterize DM patterns across diverse cancer types. PanDM uses the hidden correlations in the combined dataset to improve statistical power through joint modeling. PanDM takes summary statistics from separate analyses as input and performs methylation site clustering, differential methylation detection, and pan-cancer pattern discovery. We demonstrate the favorable performance of PanDM using simulation data. We apply our model to 12 cancer methylome data collected from The Cancer Genome Atlas (TCGA) project. We further conduct ontology- and pathway-enrichment analyses to gain new biological insights into the pan-cancer DM patterns learned by PanDM.ResultsPanDM outperforms two types of separate analyses in the power of DM calling in the simulation study. Application of PanDM to TCGA data reveals 37 pan-cancer DM patterns in the 12 cancer methylomes, including both common and cancer-type-specific patterns. These 37 patterns are in turn used to group cancer types. Functional ontology and biological pathways enriched in the non-common patterns not only underpin the cancer-type-specific etiology and pathogenesis but also unveil the common environmental risk factors shared by multiple cancer types. Moreover, we also identify PanDM-specific DM CpG sites that the common strategy fails to detect.ConclusionsPanDM is a powerful tool that provides a systematic way to investigate aberrant methylation patterns across multiple cancer types. Results from real data analyses suggest a novel angle for us to understand the common and specific DM patterns in different cancers. Moreover, as PanDM works on the summary statistics for each cancer type, the same framework can in principle be applied to pan-cancer analyses of other functional genomic profiles. We implement PanDM as an R package, which is freely available at http://www.sta.cuhk.edu.hk/YWei/PanDM.html.

Follistatin treatment modifies DNA methylation of the CDX2 gene in bovine preimplantation embryos.

CDX2 plays a crucial role in the formation and maintenance of the trophectoderm epithelium in preimplantation embryos. Follistatin supplementation during the first 72 hr of in vitro culture triggers a significant increase in blastocyst rates, CDX2 expression, and trophectoderm cell numbers. However, the underlying epigenetic mechanisms by which follistatin upregulates CDX2 expression are not known. Here, we investigated whether stimulatory effects of follistatin are linked to alterations in DNA methylation within key regulatory regions of the CDX2 gene. In vitro-fertilized (IVF) zygotes were cultured with or without 10 ng/ml of recombinant human follistatin for 72 hr, then cultured without follistatin until Day 7. The bisulfite-sequencing analysis revealed differential methylation (DM) at specific CpG sites within the CDX2 promoter and intron 1 following follistatin treatment. These DM CpG sites include five hypomethylated sites at positions -1384, -1283, -297, -163, and -23, and four hypermethylated sites at positions -1501, -250, -243, and +20 in the promoter region. There were five hypomethylated sites at positions +3060, +3105, +3219, +3270, and +3545 in intron 1. Analysis of transcription factor binding sites using MatInspector combined with a literature search revealed a potential association between differentially methylated CpG sites and putative binding sites for key transcription factors involved in regulating CDX2 expression. The hypomethylated sites are putative binding sites for FXR, STAF, OCT1, KLF, AP2 family, and P53 protein, whereas the hypermethylated sites are putative binding sites for NRSF. Collectively, our results suggest that follistatin may increase CDX2 expression in early bovine embryos, at least in part, by modulating DNA methylation at key regulatory regions.

Molecular Characterization of Human Lymph Node Stromal Cells During the Earliest Phases of Rheumatoid Arthritis.

Rheumatoid arthritis (RA) is a progressive, destructive autoimmune arthritis. Break of tolerance and formation of autoantibodies occur years before arthritis. Adaptive immunity is initiated in lymphoid tissue where lymph node stromal cells (LNSCs) play a crucial role in shaping the immune response and maintaining peripheral tolerance. Here we performed the first epigenomic characterization of LNSCs during health and early RA, by analyzing their transcriptome and DNA methylome in LNSCs isolated from lymph node needle biopsies obtained from healthy controls (HC), autoantibody positive RA-risk individuals and patients with established RA. Of interest, LNSCs from RA-risk individuals and RA patients revealed a common significantly differential expressed gene signature compared with HC LNSCs. Pathway analysis of this common signature showed, among others, significant enrichment of pathways affecting the extracellular matrix (ECM), cholesterol biosynthesis and immune system. In a gel contraction assay LNSCs from RA-risk individuals and RA patients showed impaired collagen contraction compared to healthy LNSCs. In RA LNSCs a significant enrichment was observed for genes involved in cytokine signaling, hemostasis and packaging of telomere ends. In contrast, in RA-risk LNSCs pathways in cancer (cell cycle related genes) were differentially expressed compared with HC, which could be validated in vitro using a proliferation assay, which indicated a slower proliferation rate. DNA methylation analyses revealed common and specific differentially methylated CpG sites (DMS) in LNSC from RA patients and RA-risk individuals compared with HC. Intriguingly, shared DMS were all associated with antigen processing and presentation. This data point toward alterations in cytoskeleton and antigen-processing and presentation in LNSC from RA-risk individuals and RA patients. Further studies are required to investigate the consequence of this LNSC abnormality on LNSC-mediated immunomodulation.