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DNA methylation alterations in Werner syndrome. a Volcano plot of DMPs between WS patients and CTRs. The difference between mean DNA methylation values in WS patients and in CTRs is plotted on the x-axis, while the non-adjusted P value for ANOVA between the two groups is on the y-axis (− 1 × log10 scale). The green line corresponds to a non-adjusted P value of 0.001. b DNA methylation profile of the CpG island located in the CERS3 gene
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Background
Werner syndrome is a progeroid disorder characterized by premature age-related phenotypes. Although it is well established that autosomal recessive mutations in the WRN gene is responsible for Werner syndrome, the molecular alterations that lead to disease phenotype remain still unidentified. ResultsTo address whether epigenetic changes...
Contexts in source publication
Context 1
... identified 1125 DMPs that distinguished WS patients from CTRs (non-adjusted P value < 0.001) (Fig. 2a, Additional file 2, Table 1). Of these, 511 probes (mapping in 382 genic regions) were hypermethylated and 614 probes (mapping in 416 genic regions) were hypomethylated in WS patients compared to CTRs. Several DMPs showed large DNA methylation differences between the two groups, with 87/511 hypermethylated and 110/614 hypo- methylated ...
Context 2
... were hypermethylated and 614 probes (mapping in 416 genic regions) were hypomethylated in WS patients compared to CTRs. Several DMPs showed large DNA methylation differences between the two groups, with 87/511 hypermethylated and 110/614 hypo- methylated probes having mean methylation differences lar- ger than 0.15 [22]. The volcano plot in Fig. 2a shows many CpG sites with non-adjusted P values lower than 0.001 but having low DNA methylation differences between the groups. This behaviour might be related to the small num- ber of analysed WS ...
Context 3
... analysis checks whether an input set of genes significantly overlaps with an- notated gene sets. We found 47 genes overlapping with the annotated gene set from KEGG pathways (see the overlap column in Table 1), and 22 out of 47 of these genes were differentially expressed between WR patients and CTRs (P value < 0.05), as reported in Fig. 3 and Additional file 6: Fig- ure S2. The relationship between DNA methylation and ex- pression changes is reported in Additional file 7. Focusing on the DMRs, HS6ST1 was hypermethylated in the whole blood from WS patients and downregulated in WS fibro- blasts, while both CERS1 and CERS3 were hypermethylated in the whole blood from WS patients and upregulated in WS fibroblasts. ...
Context 4
... the alteration of the above-mentioned pathways in WS was fully supported when we correlated gene sets detected as differentially methylated and a publicly available gene expression dataset on WS fibroblasts Fig. 3 Differential expression of CERS1, CERS3, ITGA9 and ADAM12 genes based on the publicly available dataset on WS fibroblast analyses including ten WS and ten CTR [30]. Indeed, several of the differentially methylated genes belonging to the enriched pathways showed altered RNA expression in fibroblasts from WS patients compared to healthy controls (Fig. 3, Additional file 6: Figure S2). ...
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Citations
... Epigenetic alterations have been linked to aging and cancer, and recent findings have found an accelerated aging, DNA methylation episignature in patients and mice with biallelic variants in BLM [51][52][53][54] . Furthermore, loss of a different RecQ helicase protein, WRN, results in accelerated rates of DNA damage and increased DNA methylation aging in patients with Werner Syndrome who exhibit many clinical signs of accelerated aging 55,56 . To explore the impact of BLM mutations on mutational load in DNA methylation (DNAm) genes, we conducted a comprehensive analysis (Methods, Supplemental methods) 57,58 . ...
Bloom Syndrome (BSyn) is an autosomal recessive disorder caused by biallelic germline variants in BLM, which functions to maintain genomic stability. BSyn patients have poor growth, immune defects, insulin resistance, and a significantly increased risk of malignancies, most commonly hematologic. The malignancy risk in carriers of pathogenic variants in BLM (BLM variant carriers) remains understudied. Clonal hematopoiesis of indeterminate potential (CHIP) is defined by presence of somatic mutations in leukemia-related genes in blood of individuals without leukemia and is associated with increased risk of leukemia. We hypothesize that somatic mutations driving clonal expansion may be an underlying mechanism leading to increased cancer risk in BSyn patients and BLM variant carriers.
To determine whether de novo or somatic variation is increased in BSyn patients or carriers, we performed and analyzed exome sequencing on BSyn and control trios.
We discovered that both BSyn patients and carriers had increased numbers of low-frequency, putative somatic variants in CHIP genes compared to controls. Furthermore, BLM variant carriers had increased numbers of somatic variants in DNA methylation genes compared to controls. There was no statistical difference in the numbers of de novo variants in BSyn probands compared to control probands.
Our findings of increased CHIP in BSyn probands and carriers suggest that one or two germline pathogenic variants in BLM could be sufficient to increase the risk of clonal hematopoiesis. These findings warrant further studies in larger cohorts to determine the significance of CHIP as a potential biomarker of aging, cancer, cardiovascular disease, morbidity and mortality.
... AGING The models fairly accurately predicted the age of samples, but with an error of age acceleration throughout chronology (shifted above the line) and with overlap in age predictions for the patients and healthy subjects, Figure 2A and Supplementary Figure 2. This is biologically inconsistent, as arthritis significantly increases PBMC inflammaging, [37,38], Werner Syndrome is a disease of premature aging (caused by a mutation of DNA helicase) [39,40], and Down syndrome has a pathological juvenile blood phenotype with a prevalence of childhood leukemias and less mature circulating PBMCs [41]. In tests on BRCA-1 studies, the EN model had very high MAE and poor correlation with the age of the healthy subjects but produced fairly accurate predictions for the people with the BRCA-1 mutation, and cancer, Figure 2A. ...
This study shows that Elastic Net (EN) DNA methylation (DNAme) clocks have low accuracy of predictions for individuals of the same age and a low resolution between healthy and disease cohorts; caveats inherent in applying linear model to non-linear processes. We found that change in methylation of cytosines with age is, interestingly, not the determinant for their selection into the clocks. Moreover, an EN clock's selected cytosines change when non-clock cytosines are removed from the training data; as expected from optimization in a machine learning (ML) context, but inconsistently with the identification of health markers in a biological context. To address these limitations, we moved from predictions to measurement of biological age, focusing on the cytosines that on average remain invariable in their methylation through lifespan, postulated to be homeostatically vital. We established that dysregulation of such cytosines, measured as the sums of standard deviations of their methylation values, quantifies biological noise, which in our hypothesis is a biomarker of aging and disease. We term this approach a "noise barometer" - the pressure of aging and disease on an organism. These noise-detecting cytosines are particularly important as sums of SD on the entire 450K DNAme array data yield a random pattern through chronology. Testing how many cytosines of the 450K arrays become noisier with age, we found that the paradigm of DNAme noise as a biomarker of aging and disease remarkably manifests in ~1/4 of the total. In that large set even the cytosines that have on average constant methylation through age show increased SDs and can be used as noise detectors of the barometer.
... p < 0.001 and false-discovery rate (FDR)-adjusted p (q-value) < 0.05 were considered statistically significant in the univariable and multivariable analyses, respectively [26][27][28][29]. All statistical analyses were performed using the R software program (version 4.0.3; ...
Background:
Although knowledge of the genetic factors influencing kidney disease is increasing, epigenetic profiles, which are associated with chronic kidney disease (CKD), have not been fully elucidated. We sought to identify the DNA methylation status of CpG sites associated with reduced kidney function and examine whether the identified CpG sites are associated with CKD development.
Method:
We analyzed DNA methylation patterns of 440 participants in the Korean Genome and Epidemiology Study (KoGES) with estimated glomerular filtration rates (eGFRs) ≥ 60 mL/min/1.73 m2 at baseline. CKD development was defined as a decrease in the eGFR of <60 at any time during an 8-year follow-up period ("CKD prediction" analysis). In addition, among the 440 participants, 49 participants who underwent a second methylation profiling were assessed for an association between a decline in kidney function and changes in the degree of methylation of CpG sites during the 8 years ("kidney function slope" analysis).
Results:
In the CKD prediction analysis, methylation profiles of a total of 403,129 CpG sites were evaluated at baseline in 440 participants, and increased and decreased methylation of 268 and 189 CpG sites, respectively, were significantly correlated with the development of CKD in multivariable logistic regression. During kidney function slope analysis using follow-up methylation profiles of 49 participants, the percent methylation changes in 913 CpG sites showed a linear relationship with the percent change in eGFR during 8 years. During functional enrichment analyses for significant CpG sites found in the CKD prediction and kidney function slope analyses, we found that those CpG sites represented MAPK, PI3K/Akt, and Rap1 pathways. In addition, three CpG sites from three genes, NPHS2, CHCHD4, and AHR, were found to be significant in the CKD prediction analysis and related to a decline in kidney function.
Conclusion:
It is suggested that DNA methylation on specific genes is associated with the development of CKD and the deterioration of kidney function.
... Multiple inborn diseases resulting from disorders of genomic methylation are well characterized. A growing body of literature reports associations between DNA methylation and conditions including Parkinson's Disease (Chuang, et al., 2017) and methylation-based studies have also suggested the causative or correlative role of aberrant methylation in diverse rare inherited conditions (Guastafierro, et al., 2017;Sharp, et al., 2017;Sobreira, et al., 2017). ...
Background: Rare genetic disease studies have benefited from the era of high throughput sequencing. DNA sequencing results in genetic diagnosis of 18-40% of previously unsolved cases, while the incorporation of RNA-Seq analysis has more recently been shown to generate significant numbers of previously unattainable diagnoses. While DNA methylation remains less explored, multiple inborn diseases resulting from disorders of genomic imprinting are well characterized and a growing body of literature suggests the causative or correlative role of aberrant methylation in diverse rare inherited conditions. Complex pictures of methylation patterning are also emerging, including the association of regional, multiple specific-site or even single-site methylation, with disease. The systematic application of genomic-wide methylation-based sequencing for undiagnosed cases of rare diseases is a logical progression from current testing paradigms. Similar to the rationale previously exploited in RNA-based rare disease studies, we can assume that disease-associated or causative methylation aberrations in an individual will demonstrate significant differences from other individuals with unrelated phenotypes. Thus, aberrantly methylated sites will be outliers from a heterogeneous cohort of individuals.
Methods: Based on this rationale, we present BOREALIS: B isulfite-seq O utlie R M E thylation A t Sing L eS I te Re S olution. BOREALIS uses a beta binomial model to identify outlier methylation at single CpG site resolution from bisulfite sequencing data.
Results: Utilizing power analyses, we demonstrate that BOREALIS can identify outlier CpG methylation within a cohort of samples. Furthermore, we show that BOREALIS is tolerant to the inclusion of multiple identical outliers with sufficient cohort size and sequencing depth.
Conclusions: The method demonstrates improved performance versus standard statistical testing and is suited for single or multi-site downstream analysis.
... Interestingly, a "red flag" approach has been proposed to increase the suspicion of rare diseases facilitating the diagnosis [7,8]. Recently, several studies have highlighted the importance of investigating genome-wide DNA methylation patterns for confirming the correct diagnosis of rare Mendelian diseases, taking advantage of the fact that affected individuals have unique and specific methylation signatures [9][10][11][12]. Moreover, methylation arrays, such as the Infinium Methylation EPIC Array (450 k or 850 k), have been useful also for classifying VUS as pathogenic or benign in rare Mendelian diseases [13,14]. ...
Anderson–Fabry disease (FD) is an X-linked disease caused by a functional deficit of the α-galactosidase A enzyme. FD diagnosis relies on the clinical manifestations and research of GLA gene mutations. However, because of the lack of a clear genotype/phenotype correlation, FD diagnosis can be challenging. Recently, several studies have highlighted the importance of investigating DNA methylation patterns for confirming the correct diagnosis of different rare Mendelian diseases, but to date, no such studies have been reported for FD. Thus, in the present investigation, we analyzed for the first time the genome-wide methylation profile of a well-characterized cohort of patients with Fabry disease. We profiled the methylation status of about 850,000 CpG sites in 5 FD patients, all carrying the same mutation in the GLA gene (exon 6 c.901C>G) and presenting comparable low levels of α-Gal A activity. We found that, although the whole methylome profile did not discriminate the FD group from the unaffected one, several genes were significantly differentially methylated in Fabry patients. Thus, we provide here a proof of concept, to be tested in patients with different mutations and in a larger cohort, that the methylation state of specific genes can potentially identify Fabry patients and possibly predict organ involvement and disease evolution.
... With the development of molecular biology, the regulation of epigenetic changes in gene expression and disease progression has received more and more attention (8). DNA methylation, which is an important key epigenetic trait, involves the addition of a methyl group to the cytosine of CpG dinucleotides and is associated with many biological processes, including X-chromosome inactivation, genomic imprinting, aging, and canceration (9). According to recent studies, epigenetic changes by DNA methylation were dynamic, individual, and highly important in inflammatory processes, and influencing mechanisms of DNA methylation such as DNA methyltransferases activity could directly affect the RA development and might be a very promising therapeutic target for RA (10,11). ...
Abnormal vitamin D metabolism is involved in the pathogenesis of rheumatoid arthritis (RA). In this study, we evaluated the association of single nucleotide polymorphisms (SNPs) and methylation levels in vitamin D metabolic pathway genes with RA susceptibility. Ten SNPs in vitamin D metabolic pathway genes (CYP2R1, CYP24A1, VDR, CYP27B1) were genotyped in 477 RA patients and 496 controls by improved multiple ligase detection reaction (iMLDR). The methylation levels of the promoter regions of these genes were detected in 122 RA patients and 123 controls using Illumina Hiseq platform. We found that the CYP2R1 rs1993116 GA genotype, CYP27B1 rs4646536 GA genotype, rs4646536 A allele frequencies were significantly increased in RA patients when compared to controls. The decreased risk of rs1993116, rs4646536 was found under the dominant mode in RA patients. However, no significant association was found between CYP2R1 rs7936142, rs12794714, CYP24A1 rs2762934, rs6068816, rs2296239, rs2296241, VDR rs11574129, rs3847987 polymorphism, and RA susceptibility. The VDR, CYP27B1 methylation levels in RA patients were significantly lower than those in controls, while CYP2R1, CYP24A1 methylation levels were not associated with RA. There were no statistical associations between CYP2R1, CYP24A1, VDR, CYP27B1 methylation levels and their respective genotype in RA patients. In addition, plasma 25OHD level in RA patients was significantly lower than that in healthy controls. In summary, our results showed that CYP2R1, CYP27B1 genetic variations were associated with the genetic background of RA, while altered VDR, CYP27B1 methylation levels were related to the risk of RA.
... Studies reported the control of gene expression by epigenetic which involves DNA methylation of cytosine in a CpG dinucleotide (Guastafierro et al., 2017). It has been shown that hypermethylation in cytochrome 450 gene promoter leads to suppression of vitamin D levels (Zhu et al., 2013). ...
The CYP2R1 gene expresses the enzyme 25-hydroxylase, involved in the synthesis of major circulating vitamin D metabolite 25-hydroxyvitaminD [25(OH)D]. CYP2R1 gene variants have been reported to be associated with altered 25(OH)D level and associated with the development of active disease including tuberculosis (TB). The aim of the present study was to understand the association of rs10741657 (G/A) and rs2060793(A/G) CYP2R1 gene polymorphisms with tuberculosis susceptibility/protection in 104 Healthy controls (HCs) and 105 pulmonary tuberculosis (PTB) patients and to understand the influence of gene variants on 25(OH)D levels in South Indian population. Genotyping was performed by polymerase chain reaction trailed by restriction fragment length polymorphism (PCR-RFLP) method. Plasma samples were used for 25(OH)D level estimation by ELISA method. In rs10741657, under a dominant model (GG vs AG + AA), “AG” and “AA” genotypes as well as in rs2060793 under an overdominant model (GA vs GG + AA), “GA” genotype were significantly associated with protection to pulmonary tuberculosis. Based on sex, rs10741657 “AG” was significantly associated with protection and “GG” was significantly associated with susceptibility to TB in males. A sufficient vitamin D level was found with rs10741657 “AA” and “AG” genotypes and “GG” genotype associated with 81.8% of vitamin D deficiency in PTB individuals. In conclusion, rs10741657 “AG” and “AA” genotypes were associated with higher 25(OH)D levels and protection to TB. The lower 25(OH)D levels associated with rs10741657 “GG” genotype individuals may be recommended for higher vitamin D supplementation for better outcome from the disease. Further studies with large sample size are needed to confirm this study finding.
... Most syndromes caused by variants in a single gene are associated with one episignature specific to that disorder [4,39,40,46,48,50,[57][58][59][60]. Sometimes, however, there is an overlap between the episignatures of two syndromes. ...
Mendelian neurodevelopmental disorders customarily present with complex and overlapping symptoms, complicating the clinical diagnosis. Individuals with a growing number of the so-called rare disorders exhibit unique, disorder-specific DNA methylation patterns, consequent to the underlying gene defects. Besides providing insights to the pathophysiology and molecular biology of these disorders, we can use these epigenetic patterns as functional biomarkers for the screening and diagnosis of these conditions. This review summarizes our current understanding of DNA methylation episignatures in rare disorders and describes the underlying technology and analytical approaches. We discuss the computational parameters, including statistical and machine learning methods, used for the screening and classification of genetic variants of uncertain clinical significance. Describing the rationale and principles applied to the specific computational models that are used to develop and adapt the DNA methylation episignatures for the diagnosis of rare disorders, we highlight the opportunities and challenges in this emerging branch of diagnostic medicine.
... Scientists have found that the PI3K/ AKT signaling pathway is central in the development of cancers and is related to CERS1. 14,15 Thus, we hypothesized that CERS1 might have tumor-regulation effects through the PI3K/AKT signaling pathway. ...
To explore the role and mechanism of CERS1 in hypophysoma and investigate whether CERS1 overexpression can change the autophagy process of hypophysoma, and then to explore whether CERS1’s effect was regulated by the PI3K/AKT signaling pathway. Western blot and RT-PCR were used to analyze the expression or mRNA level of CERS1 at different tissues or cell lines. Afterwards, the occurrence and development of hypophysoma in vivo and in vitro, respectively, was observed by using CERS1 overexpression by lentivirus. Finally, MK-2206 and LY294002 were applied to discuss whether the role of CERS1 was regulated by the PI3K/AKT signaling pathway. Results show that the CERS1 expression and mRNA level in tumor or AtT-20 cells were decreased. CERS1 over-expressed by lentivirus could inhibit hypophysoma development in vivo and in vitro by reducing tumor volume and weight, weakening tumor proliferation and invasion, and enhancing apoptosis. In addition, shCERS1 could reverse the process. The above results indicate that CERS1 is possibly able to enhance autophagy in hypophysoma through the PI3K/AKT signaling pathway.
... The second case form Clinical Epigenetics [31] uses the Infinium Human Methylation 850 K BeadChip arrays to verify whether epigenetic changes are associated with Werner syndrome phenotype. As the operation of the workflow mentioned above, step by step we selected beta value to conduct differential methylation analyses, and input the detection p-value 0.01 as a threshold to filter out unreliable probes, and chose "TRUE" to remove all probes from X and Y chromosomes. ...
Background
DNA methylation in the human genome is acknowledged to be widely associated with biological processes and complex diseases. The Illumina Infinium methylation arrays have been approved as one of the most efficient and universal technologies to investigate the whole genome changes of methylation patterns. As methylation arrays may still be the dominant method for detecting methylation in the anticipated future, it is crucial to develop a reliable workflow to analysis methylation array data.
Results
In this study, we develop a web service MADA for the whole process of methylation arrays data analysis, which includes the steps of a comprehensive differential methylation analysis pipeline: pre-processing (data loading, quality control, data filtering, and normalization), batch effect correction, differential methylation analysis, and downstream analysis. In addition, we provide the visualization of pre-processing, differentially methylated probes or regions, gene ontology, pathway and cluster analysis results. Moreover, a customization function for users to define their own workflow is also provided in MADA.
Conclusions
With the analysis of two case studies, we have shown that MADA can complete the whole procedure of methylation array data analysis. MADA provides a graphical user interface and enables users with no computational skills and limited bioinformatics background to carry on complicated methylation array data analysis. The web server is available at: http://120.24.94.89:8080/MADA
