Genome-wide DNA Methylation Differences Research Articles

Role of epigenetics in the clinical evolution of COVID-19 disease. Epigenome-wide association study identifies markers of severe outcome

BackgroundCOVID-19 has a wide spectrum of clinical manifestations and given its impact on morbidity and mortality, there is an unmet medical need to discover endogenous cellular and molecular biomarkers that predict the expected clinical course of the disease. Recently, epigenetics and especially DNA methylation have been pointed out as a promising tool for outcome prediction in several diseases.Methods and resultsUsing the Illumina Infinium Methylation EPIC BeadChip850K, we investigated genome-wide differences in DNA methylation in an Italian Cohort of patients with comorbidities and compared severe (n = 64) and mild (123) prognosis. Results showed that the epigenetic signature, already present at the time of Hospital admission, can significantly predict risk of severe outcomes. Further analyses provided evidence of an association between age acceleration and a severe prognosis after COVID-19 infection. The burden of Stochastic Epigenetic Mutation (SEMs) has been significantly increased in patients with poor prognosis. Results have been replicated in silico considering COVID-19 negative subjects and available previously published datasets.ConclusionsUsing original methylation data and taking advantage of already published datasets, we confirmed in the blood that epigenetics is actively involved in immune response after COVID-19 infection, allowing the identification of a specific signature able to discriminate the disease evolution. Furthermore, the study showed that epigenetic drift and age acceleration are associated with severe prognosis. All these findings prove that host epigenetics undergoes notable and specific rearrangements to respond to COVID-19 infection which can be used for a personalized, timely, and targeted management of COVID-19 patients during the first stages of hospitalization.

Patient-specific identification of genome-wide DNA-methylation differences between intracranial and extracranial melanoma metastases

Melanomas frequently metastasize to distant organs and especially intracranial metastases still represent a major clinical challenge. Epigenetic reprogramming of intracranial metastases is thought to be involved in therapy failure, but so far only little is known about patient-specific DNA-methylation differences between intra- and extracranial melanoma metastases. Hierarchical clustering of the methylomes of 24 patient-matched intra- and extracranial melanoma metastases pairs revealed that intra- and extracranial metastases of individual patients were more similar to each other than to metastases in the same tissue from other patients. Therefore, a personalized analysis of each metastases pair was done by a Hidden Markov Model to classify methylation levels of individual CpGs as decreased, unchanged or increased in the intra- compared to the extracranial metastasis. The predicted DNA-methylation alterations were highly patient-specific differing in the number and methylation states of altered CpGs. Nevertheless, four important general observations were made: (i) intracranial metastases of most patients mainly showed a reduction of DNA-methylation, (ii) cytokine signaling was most frequently affected by differential methylation in individual metastases pairs, but also MAPK, PI3K/Akt and ECM signaling were often altered, (iii) frequently affected genes were mainly involved in signaling, growth, adhesion or apoptosis, and (iv) an enrichment of functional terms related to channel and transporter activities supports previous findings for a brain-like phenotype. In addition, the derived set of 17 signaling pathway genes that distinguished intra- from extracranial metastases in more than 50% of patients included well-known oncogenes (e.g. PRKCA, DUSP6, BMP4) and several other genes known from neuronal disorders (e.g. EIF4B, SGK1, CACNG8). Moreover, associations of gene body methylation alterations with corresponding gene expression changes revealed that especially the three signaling pathway genes JAK3, MECOM, and TNXB differ strongly in their expression between patient-matched intra- and extracranial metastases. Our analysis contributes to an in-depth characterization of DNA-methylation differences between patient-matched intra- and extracranial melanoma metastases and may provide a basis for future experimental studies to identify targets for new therapeutic approaches.

Genome-Wide DNA Methylation Differences between Bos indicus and Bos taurus.

Disease risk is a persistent problem in domestic cattle farming, while economic traits are the main concern. This study aimed to reveal the epigenetic basis for differences between zebu (Bos indicus) and taurine cattle (Bos taurus) in disease, disease resistance, and economic traits, and provide a theoretical basis for the genetic improvement of domestic cattle. In this study, whole genome bisulfite sequencing (WGBS) was used to analyze the whole-genome methylation of spleen and liver samples from Yunnan zebu and Holstein cattle. In the genome-wide methylation pattern analysis, it was found that the methylation pattern of all samples was dominated by the CG type, which accounted for >94.9%. The DNA methylation levels of different functional regions and transcriptional elements in the CG background varied widely. However, the methylation levels of different samples in the same functional regions or transcriptional elements did not differ significantly. In addition, we identified a large number of differentially methylation region (DMR) in both the spleen and liver groups, of which 4713 and 4663 were annotated to functional elements, and most of them were annotated to the intronic and exonic regions of genes. GO and KEGG functional analysis of the same differentially methylation region (DMG) in the spleen and liver groups revealed that significantly enriched pathways were involved in neurological, disease, and growth functions. As a result of the results of DMR localization, we screened six genes (DNM3, INPP4B, PLD, PCYT1B, KCNN2, and SLIT3) that were tissue-specific candidates for economic traits, disease, and disease resistance in Yunnan zebu. In this study, DNA methylation was used to construct links between genotypes and phenotypes in domestic cattle, providing useful information for further screening of epigenetic molecular markers in zebu and taurine cattle.

Integrated genome-wide methylation and expression analyses provide predictors of diagnosis and early response to antidepressant in panic disorder

BackgroundWe investigated differentially methylated and expressed genes between panic disorder (PD) and healthy controls (HCs) to determine whether DNA methylation and expression level of candidate genes can be used as biomarkers for diagnosis and early response. MethodsIllumina infiniun Methylation EPIC (850 k) Beadchip for genome-wide methylation screening and mRNA sequencing was conducted in a discovery set (30 patients with PD and 30 matched HCs). The candidate gene loci methylation and expression were verified in an independent validation sample (101 PD patients and 107 HCs). ResultsIn the discovery set, there were 3613 differentially methylated cytosine phosphate guanosine sites and these differential methylation positions were located within 1938 unique genes, including 1758 hypermethylated genes, 150 hypomethylated genes, and the coexistence of hypermethylation and hypomethylation sites were found in 30 genes. There were 1111 differential transcripts in PD compared to normal controls (850 down-regulated and 261 up-regulated). Further, 212 differentially expressed genes were screened (40 up-regulated and 172 down-regulated). In the validation set, compared with HCs, there was no significant difference in DNA methylation level of Casitas B-lineage lymphoma (CBL) gene loci (cg07123846). The expression level of CBL gene in PD patients was lower (vs. HCs). After four weeks' treatment, the baseline expression level of CBL gene in the responders was higher than nonresponders. LimitationsThe sample size was limited. We only chose CBL as a candidate gene. Follow-up periods were short. ConclusionsThere are differences in genome-wide DNA methylation and mRNA expression between PD patients and HCs. The changes in expression level of CBL gene may be an important molecular marker for PD diagnosis and early response.

Genome-wide DNA methylation differences between conservation and breeding populations of Shaoxing ducks

The genome-wide DNA methylation assay was used to analyze the difference in methylation between the breeding and conservation populations of Shaoxing ducks. The methylation level of the breeding population was higher than that of the two conservation populations, and the proportion of CG methylation sites was the largest in the three populations, most of the methylation sites were located in the exon region. There were 1247 different methylation regions in the two populations (group A and B), and 927 different methylation regions in the two groups (group A and group C). The differential methylation regions of the three groups were evenly distributed in the gene and intergene regions. GO and KEGG enrichment analysis showed that the differentially expressed genes in the A and B groups were mainly involved in synaptic and cell connections and the signaling pathways were significantly enriched in cAMP and oxytocin signaling pathways. The results showed that the group C was significantly enriched in eight signaling pathways, including the cAMP signaling pathway and long-term enhancement, compared to the group A. There were thirty-five differentially methylated genes, including CACNA1C, GRIA1, GRIA2, GABBR2, PDE10A, BRAF, GRM5, CPEB3, FMn2, GABRB2, PTK2, and CNTN1. These genes were involved in the development and ovulation of ovaries and follicles and were closely related to the excellent production performance of the breeding population. In addition, ATP2B1, ATP2B2, and other genes related to eggshell quality were identified, which can be used as molecular markers to improve eggshell quality in the future.

ATRT-04. Clinical and (epi)genetic characterisation of patients with atypical teratoid/rhabdoid tumor (ATRT) and extracranial malignant rhabdoid tumor conceived following assisted reproduction technologies (ART)

Abstract INTRODUCTION: Anecdotal case reports suggest an association between assisted reproduction technologies (ART) and malignant rhabdoid tumors (MRT). We performed a multi-institutional retrospective analysis of the EU-RHAB database, complemented by additional cases outside of EU-RHAB to compile clinical, (epi)genetic characteristics and outcome data of children with MRT following ART. METHODS: Data of 14 patients (from 311 patients with MRT) from 9 countries were analyzed (2010-2018). Tumors and matching blood samples were examined for SMARCB1 mutations using FISH, MLPA and sequencing. Molecular subgroups were determined using DNA methylation arrays and correlated with a validation cohort (n=22, tumor samples of MRT; n=39 blood samples of patients small for gestational age). RESULTS: The median age at diagnosis of the 13 girls and 1 boy was 9 months (0 – 66). 8 patients with ATRT, 3 with extracranial, extrarenal-, 1 with renal rhabdoid tumor and 2 with synchronous tumors were identified. Distant metastases at diagnosis were present in 6 patients. A germline mutation (GLM) was detected in 5 patients. In 11 tumors complete data on SMARCB1 mutational status were available. DNA methylation subgrouping was available in 10 tumors and 6 blood samples. A female predominance was noted as compared to the EU-RHAB cohort with MRT born without ART (n=213, p=0.009). A total of 8 patients received gross total resection, n=12 patients received conventional chemotherapy (EU-RHAB=9, Head Start II=2, IRS III=1). Radiotherapy was applied to 6 patients. 10 patients achieved CR, and 5 remain in continuing CR. Significant genome-wide DNA methylation differences (including imprinted genes) between patients born after ART and patients born without ART could not be demonstrated. CONCLUSIONS: Long-term survival is achievable in patients who develop MRT after ART, even in cases with GLM, metastatic disease at diagnosis, or relapse. Larger epidemiological studies are needed to confirm a potential association between MRT and ART.

Genome-Wide DNA Methylation Patterns of Muscle and Tail-Fat in DairyMeade Sheep and Mongolian Sheep.

Simple SummaryDNA methylation is an important epigenetic modification and plays an important role in the regulation of gene expression. The study of DNA methylation will help to explore the effects of epigenetic modifications, other than DNA sequence variation, on biological phenotypes and physiological functions, promoting the revolution of livestock selection and breeding practices. DairyMeade sheep (thin-tailed) and Mongolian sheep (fat-tailed) have large differences in their dairy and meat production performances, as well as their tail phenotype, thus providing us with good materials for genomic DNA methylation studies. The below results provided a genome-wide DNA methylation landscape of muscle and tail-fat tissues between DairyMeade sheep and Mongolian sheep and a series of differentiated methylation regions (DMRs) in which CAMK2D may play a crucial role in fat metabolism and meat quality traits. These results may help us to understand how DNA methylation affects the economic traits of domestic animals like sheep.This study aimed to explore the genome-wide DNA methylation differences between muscle and tail-fat tissues of DairyMeade sheep (thin-tailed, lean carcass) and Mongolian sheep (fat-tailed, fat-deposited carcass). Whole-genome bisulfite sequencing (WGBS) was conducted and the global DNA methylation dynamics were mapped. Generally, CGs had a higher DNA methylation level than CHHs and CHGs, and tail-fat tissues had higher CG methylation levels than muscle tissues. For DNA repeat elements, SINE had the highest methylation level, while Simple had the lowest. When dividing the gene promoter region into small bins (200 bp per bin), the bins near the transcription start site (±200 bp) had the highest CG count per bin but the lowest DNA methylation levels. A series of DMRs were identified in muscle and tail-fat tissues between the two breeds. Among them, the introns of gene CAMK2D (calcium/calmodulin-dependent protein kinase II δ) demonstrated significant DNA methylation level differences between the two breeds in both muscle and tail-fat tissues, and it may play a crucial role in fat metabolism and meat quality traits. This study may provide basic datasets and references for further epigenetic modification studies during sheep genetic improvement.

Supplement to Genome-wide DNA Methylation Differences in Non-functioning Pituitary Adenomas With and Without Postsurgical Progression

Supplement to Genome-wide DNA Methylation Differences in Non-functioning Pituitary Adenomas With and Without Postsurgical Progression

DNA methylation analysis of cord blood samples in neonates born to gestational diabetes mothers diagnosed before 24 gestational weeks

IntroductionGenome-wide methylation analyses of gestational diabetes mellitus (GDM) diagnosed after 24 gestational weeks (late GDM (L-GDM)) using cord blood have been reported. However, epigenetic changes in neonates born to mothers...

Genome-Wide DNA Methylation Differences between Conservation and Breeding Populations of Shaoxing Ducks

Genome-Wide DNA Methylation Differences between Conservation and Breeding Populations of Shaoxing Ducks

872Novel approach to estimating sex differences unconfounded by familial factors from studying male-female twin pairs

Abstract Focus of Presentation Males and females differ substantially in their exposures and outcomes across the life-course. Previous research into sex differences has been limited by an inability to account for inter-individual differences in genetic factors and in their early-life environment. Studying within male-female twin pair differences offers a unique opportunity to address these weaknesses that has not yet been exploited. Findings We studied linked health administrative data for 28,054 newborn Brazilian male-female twin pairs. Using random-effects logistic regression, we found that males had 1.61 (95% CI: 1.38– 1.90, P<0.001) times higher risk of early neonatal mortality (first 6 days of life) compared with their female co-twins, after adjusting empirically for birthweight and matching for gestational age and, by design, for unmeasured familial factors including on average 50% of genetic factors. From analysing within-pair differences in genome-wide DNA methylation in blood samples for 55 Australian adolescent male-female twin pairs, we found that 1,227 DNA methylation sites were more methylated in females while only 157 sites were more methylated in males (P<10-6). We also found weak evidence suggesting that males have older DNA-methylation-based biological age than females (P=0.2). Conclusions/Implications Sex differences not explained by familial confounders exist for neonatal mortality in newborns and for DNA methylation in blood during adolescence. Key messages Analysing the within-pair differences of male-female twin pairs brings novel and important strengths to the study of sex differences, helping mitigate bias from uncontrolled familial confounding caused by genetic and environmental factors.

An epigenome-wide DNA methylation study of patients with COVID-19.

In the early 2000s, emerging SARS‐CoV‐2, which is highly pathogenic, posed a great threat to public health. During COVID‐19, epigenetic regulation is deemed to be an important part of the pathophysiology and illness severity. Using the Illumina Infinium Methylation EPIC BeadChip (850 K), we investigated genome‐wide differences in DNA methylation between healthy subjects and COVID‐19 patients with different disease severities. We conducted a combined analysis and selected 35 “marker” genes that could indicate a SARS‐CoV‐2 infection, including 12 (ATHL1, CHN2, CHST15, CPLX2, CRHR2, DCAKD, GNAI2, HECW1, HYAL1, MIR510, PDE11A, and SMG6) situated in the promoter region. The functions and pathways of differentially methylated genes were enriched in biological processes, signal transduction, and the immune system. In the “Severe versus Mild” group, differentially methylated genes, after eliminating duplicates, were used for PPI analyses. The four hub genes (GNG7, GNAS, PRKCZ, and PRKAG2) that had the highest degree of nodes were identified and among them, GNG7 and GNAS genes expressions were also downregulated in the severe group in sequencing results. Above all, the results suggest that GNG7 and GNAS may play a non‐ignorable role in the progression of COVID‐19. In conclusion, the identified key genes and related pathways in the current study can be used to study the molecular mechanisms of COVID‐19 and may provide possibilities for specific treatments.

Genome-wide DNA methylation analysis in Chinese Chenghua and Yorkshire pigs

BackgroundThe Chinese Chenghua pig (CHP) is a typical Chinese domestic fatty pig breed with superior meat quality characteristics, while the Yorkshire pig (YP) has the characteristics of fast growth and a high rate of lean meat. Long term natural selection and artificial selection resulted in great phenotypic differences between the two breeds, including growth, development, production performance, meat quality, and coat color. However, genome-wide DNA methylation differences between CHP and YP remain unclear.ResultsDNA methylation data were generated for muscle tissues of CHP and YP using reduced representation bisulfite sequencing (RRBS). In this study, a total of 2,416,211 CpG sites were identified. Besides, the genome-wide DNA methylation analysis revealed 722 differentially methylated regions (DMRs) and 466 differentially methylated genes (DMGs) in pairwise CHP vs. YP comparison. Six key genomic regions (Sus scrofa chromosome (SSC)1:253.47–274.23 Mb, SSC6:148.71–169.49 Mb, SSC7:0.25–9.86 Mb, SSC12:43.06–61.49 Mb, SSC14:126.43–140.95 Mb, and SSC18:49.17–54.54 Mb) containing multiple DMRs were identified, and differences of methylation patterns in these regions may be related to phenotypic differences between CHP and YP. Based on the functional analysis of DMGs, 8 DMGs (ADCY1, AGBL4, EXOC2, FUBP3, PAPPA2, PIK3R1, MGMT and MYH8) were considered as important candidate genes associated with muscle development and meat quality traits in pigs.ConclusionsThis study explored the difference in meat quality between CHP and YP from the epigenetic point of view, which has important reference significance for the local pork industry and pork food processing.

Genome-Wide DNA Methylation Differences in Patients With Non-Functioning Pituitary Adenomas With or Without Postsurgical Intervention

Background: More than half of all surgically treated patients with non-functioning pituitary adenomas (NFPA) experience tumor progression during their follow-up, with some of these adenomas exhibiting locally aggressive behavior. Tumor progression is strongly associated with excess morbidity and mortality. Tumor control is, therefore, of vital importance for the patient outcome. There is no reliable method to predict tumor behavior after the initial surgical treatment. The aim of this study was therefore to study associations between DNA methylation patterns and tumor progression in patients with NFPA. Methods: In a case-controlled trial, 43 patients operated for NFPA with immunohistochemical characteristics of gonadotroph subtype were selected. Cases included patients who needed reintervention due to tumor progression (Reintervention group, n = 26), and controls had residual tumor without tumor progression during at least five years of follow-up (Radiologically stable group, n = 17). Genome-wide methylation analysis of the tumor tissue from each patient was performed on the Infinium MethylationEPIC BeadChip platform. Results: Principal component analysis (PCA) showed that clinical course was a strong contributor to the difference in DNA methylation profiles between the two groups. Also, unsupervised hierarchical clustering of the top 5,000 most variable CpG sites revealed three methylation profiles corresponding to, (1) the Reintervention group, (2) the Radiologically stable group, and (3) a mix of the two groups. Although the overall average methylation levels in the two groups did not differ (P = 0.16), 142,521 Differentially Methylated Positions (DMPs) were identified. Of these, 650 showed a difference in beta value methylation larger than 0.2. Interestingly, among the genes harboring the most significantly DMPs was GABRA1, and among the genes containing the largest number of DMPs were GATA2, NUP93, and LGALS1. In addition, the three most hypomethylated and the three most hypermethylated DMPs were all significantly (P <0.05) independently associated with tumor progression free survival (Log-rank test, data not shown). Conclusion: In this novel explorative study, we found a methylation pattern associated with postoperative tumor progression requiring reintervention in patients with NFPA. Among the differently methylated genes we identified, some have previously been described to be involved in pituitary adenoma differentiation or cancer development. Our study is a step towards deciphering epigenetic mechanisms involved in tumor progression and finding epigenetic signatures that might be used to predict postoperative tumor progression in NFPAs.

Individuals Diagnosed with Binge-Eating Disorder Have DNA Hypomethylated Sites in Genes of the Metabolic System: A Pilot Study.

Binge-eating disorder, recently accepted as a diagnostic category, is differentiated from bulimia nervosa in that the former shows the presence of binge-eating episodes and the absence of compensatory behavior. Epigenetics is a conjunct of mechanisms (like DNA methylation) that regulate gene expression, which are dependent on environmental changes. Analysis of DNA methylation in eating disorders shows that it is reduced. The present study aimed to analyze the genome-wide DNA methylation differences between individuals diagnosed with BED and BN. A total of 46 individuals were analyzed using the Infinium Methylation EPIC array. We found 11 differentially methylated sites between BED- and BN-diagnosed individuals, with genome-wide significance. Most of the associations were found in genes related to metabolic processes (ST3GAL4, PRKAG2, and FRK), which are hypomethylated genes in BED. Cg04781532, located in the body of the PRKAG2 gene (protein kinase AMP-activated non-catalytic subunit gamma 2), was hypomethylated in individuals with BED. Agonists of PRKAG2, which is the subunit of AMPK (AMP-activated protein kinase), are proposed to treat obesity, BED, and BN. The present study contributes important insights into the effect that BED could have on PRKAG2 activation.

Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination.

Phenotypic differences between sexes are often mediated by differential expression and alternative splicing of genes. However, the mechanisms that regulate these expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, paternal genome elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. Planococcus citri has no sex chromosomes and both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P.citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. Here, we therefore decided to explore genome-wide differences in DNA methylation between male and female P.citri using whole-genome bisulphite sequencing. We identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifest as more uniform low levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq, we identify extensive sex-specific gene expression and alternative splicing, but we find no correlation with cis-acting DNA methylation.

Common Features of the DNA Methylation Landscape of Human Naïve and Memory CD4, CD8 T Cells and B Cells

Epigenetic mechanisms including DNA methylation are critical drivers of immune cell lineage differentiation and activation. However, there has been limited coordinated investigation of common pathways in distinct cell types for immunological processes such as immune memory. Further, it remains unclear if the genesis of memory in both CD4 and CD8 lineages proceeds via a linear course of differentiation or progresses in a circular ‘on-off-on’ sequence, which is epigenetically driven. Here, we scanned genome-wide differences in DNA methylation among CD4 and CD8 naive and memory cells states and combined this data with similar data on naive and memory B cell states. Our findings, overall, are consistent with the literature describing the DNA methylome as a major driver of individual central and effector T cell memory states as well as in memory B cells. We observed unusually large differences in DNA methylation in thousands of CpG sites in hundreds of genes associated with the development of memory in each lineage, contributing considerably to our knowledge of the loci regulated during lymphocyte memory generation. Our data similarly describe considerable overlap in genes with altered DNA methylation in the T cell lineage, with primarily a loss of DNA methylation in over 125,000 CpGs significantly associated with the generation of central memory in both CD4 and CD8 cells Furthermore, our analyses revealed specific CpG dinucleotides in both CD4 and CD8 cells whose methylation pattern is consistent with the circular model of memory generation. Finally, as evidence of common pathways in the generation of immune memory we highlight 22 gene loci, including several within the promoter region of the AIM2 gene, with dramatically altered DNA methylation in all three memory lineages.

Differential DNA methylation in familial hypercholesterolemia.

BackgroundFamilial hypercholesterolemia (FH) is a monogenic disorder characterized by elevated low-density lipoprotein cholesterol (LDL-C). A FH causing genetic variant in LDLR, APOB, or PCSK9 is not identified in 12–60% of clinical FH patients (FH mutation-negative patients). We aimed to assess whether altered DNA methylation might be associated with FH in this latter groupMethodsIn this study we included 78 FH mutation-negative patients and 58 FH mutation-positive patients with a pathogenic LDLR variant. All patients were male, not using lipid lowering therapies and had LDL-C levels >6 mmol/L and triglyceride levels <3•5 mmol/L. DNA methylation was measured with the Infinium Methylation EPIC 850 K beadchip assay. Multiple linear regression analyses were used to explore DNA methylation differences between the two groups in genes related to lipid metabolism. A gradient boosting machine learning model was applied to investigate accumulated genome-wide differences between the two groups.FindingsCandidate gene analysis revealed one significantly hypomethylated CpG site in CPT1A (cg00574958) in FH mutation-negative patients, while no differences in methylation in other lipid genes were observed. The machine learning model did distinguish the two groups with a mean Area Under the Curve (AUC)±SD of 0•80±0•17 and provided two CpG sites (cg26426080 and cg11478607) in genes with a possible link to lipid metabolism (PRDM16 and GSTT1).InterpretationFH mutation-negative patients are characterized by accumulated genome wide DNA methylation differences, but not by major DNA methylation alterations in known lipid genes compared to FH mutation-positive patients.FundingZonMW grant (VIDI no. 016.156.445)

Abstract 160: Identifying differential methylation patterns of benign and tumor prostate tissue in African American and European American prostate cancer patients

Abstract This study aims to identify biological features and processes underlying disparities in prostate cancer (PCa) between African American (AA) and European American (EA) men using DNA methylation (DNAm). Changes in genome-wide DNAm accompany tumor development and progression. Differences in genome-wide DNAm across ancestry groups may be an important mechanism to understand the higher incidence and poorer prognosis among AA men. We collected paired tumor and histologically benign tissue from formalin fixed and paraffin embedded (FFPE) blocks from 150 prostate cancer patients (75 AA, 75 EA) at the University of Chicago. DNA was extracted and genome-wide DNAm was measured at ~850,000 CpG sites in benign and tumor tissue using the Illumina Infinium MethylationEpic BeadChip. After CpG and sample-level QC and normalization, we conducted differential methylation analyses, comparing tumor and benign tissue within each ancestry group, adjusting for batch, age, and tissue pair. We then used Gene Set Enrichment Analysis (GSEA) to examine enrichment of GO and Hallmark terms. 682,694 CpGs passed QC filtering. For AA and EA, CpGs hyper-methylated in cancer tissue were enriched in CpG islands while hypo-methylated CpGs were enriched in open seas. We identified 39,768 and 25,405 tumor-associated CpGs in AA and EA respectively (p&amp;lt;5 × 10-8 and absolute change in methylation 0.25). Of these, 23,068 CpGs were common to both sets. In AA, a higher proportion of tumor-associated CpGs were hypo-methylated compared to EA (40.5% vs 18.6%, p&amp;lt;2 × 10-16). A larger proportion tumor-associated CpGs annotated to non-CpG islands in AA compared to EA (67.7% vs 62%) (p=2 × 10-16). We also observed an increased proportion of differentially methylated CpGs in promoter regions in EA compared with AA. Consistent with prior studies, among the common, tumor-associated CpGs, we observed differential methylation of GSTP1 and APC, both involved in PCa development. We observed enrichment in 6 genesets in both AA and EA, including the epithelial mesenchymal transition and estrogen response. In AA we observed additional enrichment in 2 genesets including hedgehog signaling (FDR&amp;lt;0.05). Comparing the ancestry groups, adjusting for age and batch, we found 219 differentially methylated CpGs between AA and EA in tumor and 151 in benign tissue. Overall, we identified higher frequencies of differential methylation and more differentially methylated genes in AA compared with EA; despite slightly more favorable clinical features in the AA in our sample. We also found differential methylation by ancestry within each tissue type. These results suggest the existence of epigenetic alterations unique to AA and EA that may contribute to the biological basis of PCa disparities. Moving forward we will refine our analyses, adjusting for cell type proportion and further examining the differentially methylated pathways. Citation Format: Meytal B. Chernoff, Kathryn Demanelis, Marc Gillard, Dayana Delgado, Donald J. Vander Griend, Brandon L. Pierce. Identifying differential methylation patterns of benign and tumor prostate tissue in African American and European American prostate cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 160.

Genome-wide DNA methylation differences in nucleus accumbens of smokers vs. nonsmokers.

Numerous DNA methylation (DNAm) biomarkers of cigarette smoking have been identified in peripheral blood studies, but because of tissue specificity, blood-based studies may not detect brain-specific smoking-related DNAm differences that may provide greater insight as neurobiological indicators of smoking and its exposure effects. We report the first epigenome-wide association study (EWAS) of smoking in human postmortem brain, focusing on nucleus accumbens (NAc) as a key brain region in developing and reinforcing addiction. Illumina HumanMethylation EPIC array data from 221 decedents (120 European American [23% current smokers], 101 African American [26% current smokers]) were analyzed. DNAm by smoking (current vs. nonsmoking) was tested within each ancestry group using robust linear regression models adjusted for age, sex, cell-type proportion, DNAm-derived negative control principal components (PCs), and genotype-derived PCs. The resulting ancestry-specific results were combined via meta-analysis. We extended our NAc findings, using published smoking EWAS results in blood, to identify DNAm smoking effects that are unique (tissue-specific) vs. shared between tissues (tissue-shared). We identified seven CpGs (false discovery rate < 0.05), of which three CpGs are located near genes previously indicated with blood-based smoking DNAm biomarkers: ZIC1, ZCCHC24, and PRKDC. The other four CpGs are novel for smoking-related DNAm changes: ABLIM3, APCDD1L, MTMR6, and CTCF. None of the seven smoking-related CpGs in NAc are driven by genetic variants that share association signals with predisposing genetic risk variants for smoking, suggesting that the DNAm changes reflect consequences of smoking. Our results provide the first evidence for smoking-related DNAm changes in human NAc, highlighting CpGs that were undetected as peripheral biomarkers and may reflect brain-specific responses to smoking exposure.