Identification of DNA methylation-regulated differentially expressed genes in RA by integrated analysis of DNA methylation and RNA-Seq data

Zhang, Runrun; Chang, Cen; Jin, Yehua; Xu, Lingxia; Jiang, Ping; Wei, Kai; Xu, Linshuai; Guo, Shicheng; Sun, Songtao; He, Dongyi

doi:10.1186/s12967-022-03664-5

Cited by 7 publications

(4 citation statements)

References 39 publications

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“…Despite prior results by Zhang et al, the study showed that downregulated genes enriched in cytokine-cytokine receptor interaction, calcium signaling pathway, and T cell receptor signaling pathway. 22 The most striking observation to emerge from our data was identifying two coding-protein genes (PUM1 and AIRAPL) which are significantly differentially methylated and expressed genes, with a P value of <0.05, which are also found in gene ontology (GO) analysis. PUM1 is engaged in a variety of physiological processes, including the cell cycle, DNA repair, and cell renewal.…”

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confidence: 55%

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Promoter Methylation-Regulated Differentially Expressed Genes in Breast Cancer

Sindi¹,

Hamdi²,

Hassan³

et al. 2023

BCTT

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Background Breast cancer is one of the most common malignancies among women. Recent studies revealed that differentially methylated regions (DMRs) are implicated in regulating gene expression. The goal of this research was to determine which genes and pathways are dysregulated in breast cancer when their promoters are methylated in an abnormal way, leading to differential expression. Whole-genome bisulfite sequencing was applied to analyze DMRs for eight peripheral blood samples collected from five Saudi females diagnosed with stages I and II of breast cancer aligned with three normal females. Three of those patients and three normal samples were used to determine differentially expressed genes (DEG) using Illumina platform NovaSeq PE150. Results Based on ontology (GO) and KEGG pathways, the analysis indicated that DMGs and DEG are closely related to associated processes, such as ubiquitin-protein transferase activity, ubiquitin-mediated proteolysis, and oxidative phosphorylation. The findings indicated a potentially significant association between global hypomethylation and breast cancer in Saudi patients. Our results revealed 81 differentially promoter-methylated and expressed genes. The most significant differentially methylated and expressed genes found in gene ontology (GO) are pumilio RNA binding family member 1 ( PUM1 ) and zinc finger AN1-type containing 2B ( ZFAND2B ) also known as ( AIRAPL ). Conclusion The essential outcomes of this study suggested that aberrant hypermethylation at crucial genes that have significant parts in the molecular pathways of breast cancer could be used as a potential prognostic biomarker for breast cancer.

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confidence: 55%

“…Despite prior results by Zhang et al, the study showed that downregulated genes enriched in cytokine–cytokine receptor interaction, calcium signaling pathway, and T cell receptor signaling pathway. 22 …”

Section: Discussionmentioning

confidence: 99%

Promoter Methylation-Regulated Differentially Expressed Genes in Breast Cancer

Sindi¹,

Hamdi²,

Hassan³

et al. 2023

BCTT

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“…2 b). Gene was classified as methylation-controlled, when correlation of mean promoter methylation and gene expression was significant and negative, as it is commonly done [ 39 ]. In general, 2.9% of genes fulfilled these criteria.…”

Section: Resultsmentioning

confidence: 99%

DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment

Baluszek

Kober

Rusetska

et al. 2023

acta neuropathol commun

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Chordomas are rare tumors of notochord remnants, occurring mainly in the sacrum and skull base. Despite of their unusually slow growth, chordomas are highly invasive and the involvement of adjacent critical structures causes treatment challenges. Due to the low incidence, the molecular pathogenesis of this entity remains largely unknown. This study aimed to investigate DNA methylation abnormalities and their impact on gene expression profiles in skull base chordomas. 32 tumor and 4 normal nucleus pulposus samples were subjected to DNA methylation and gene expression profiling with methylation microarrays and RNA sequencing. Genome-wide DNA methylation analysis revealed two distinct clusters for chordoma (termed subtypes C and I) with different patterns of aberrant DNA methylation. C Chordomas were characterized by general hypomethylation with hypermethylation of CpG islands, while I chordomas were generally hypermethylated. These differences were reflected by distinct distribution of differentially methylated probes (DMPs). Differentially methylated regions (DMRs) were identified, indicating aberrant methylation in known tumor-related genes in booth chordoma subtypes and regions encoding small RNAs in subtype C chordomas. Correlation between methylation and expression was observed in a minority of genes. Upregulation of TBXT in chordomas appeared to be related to lower methylation of tumor-specific DMR in gene promoter. Gene expression-based clusters of tumor samples did not overlap with DNA methylation-based subtypes. Nevertheless, they differ in transcriptomic profile that shows immune infiltration in I chordomas and up-regulation of cell cycle in C chordomas. Immune enrichment in chordomas I was confirmed with 3 independent deconvolution methods and immunohistochemistry. Copy number analysis showed higher chromosomal instability in C chordomas. Nine out of eight had deletion of CDKN2A/B loci and downregulation of genes encoded in related chromosomal band. No significant difference in patients’ survival was observed between tumor subtypes, however, shorter survival was observed in patients with higher number of copy number alterations.

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“…Prior research on a genome-wide scale has suggested alterations in the DNAm profiles in autoimmune disease patients (13). Several investigations have demonstrated that a characteristic trait of autoimmune diseases, including systemic lupus erythematosus, multiple sclerosis, and chronic spontaneous urticaria, is global hypomethylation (14).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide DNA methylation pattern in whole blood of patients with Hashimoto thyroiditis

Zhou,

Liu,

Chen

et al. 2023

Front. Endocrinol.

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BackgroundHashimoto thyroiditis (HT), a prevalent autoimmune disorder, is not yet thoroughly understood, especially when it comes to the influence of epigenetics in its pathogenesis. The primary goal of this research was to probe the DNAm profile across the genome in the whole blood derived from patients suffering from HT.MethodUsing the Illumina 850K BeadChip, we conducted a genome-wide DNAm assessment on 10 matched pairs of HT sufferers and healthy individuals. Genes with differential methylation (DMGs) were identified and underwent functional annotation via the databases of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. The transcriptional significance of potential epigenetic biomarker genes was corroborated through qRT-PCR.ResultsThe DNAm profiling across the genome indicated an overall reduction in methylation in HT subjects in comparison with their healthy counterparts. We detected 283 DMPs (adjusted P < 0.05 and |Δβ| > 0.1), among which 152 exhibited hypomethylation and 131 demonstrated hypermethylation. Further analysis exposed a noteworthy concentration of hypermethylated DMPs in the 3´UTR, North Shore, and CpG islands, while there was a significant decrease in the Open Sea (all P < 0.001). The 283 DMPs were broadly distributed from chromosome 1 to 22, with chromosome 6 harboring the most DMPs (n = 51) and chromosome 12 carrying the most DMGs (n = 15). The SLFN12 gene, which presented with extreme hypomethylation in its promoter DMPs among HT patients, was identified as the epigenetic marker gene. Consequently, the SLFN12 mRNA expression was markedly upregulated in HT, displaying a negative relationship with its methylation levels. The area under curve (AUC) value for the SLFN12 gene among HT patients was 0.85 (sensitivity: 0.7, specificity: 0.7), a significant difference compared with healthy controls. The methylation levels of all DMPs in SLFN12 gene were negatively correlated with TSH and one CpG site (cg24470734) was positively assocciated with FT4.ConclusionThis investigation presents an initial comprehensive DNAm blueprint for individuals with HT, which permits clear differentiation between HT subjects and normal controls through an epigenetic lens. The SLFN12 gene plays a pivotal role in the onset of HT, suggesting that the methylation status of this gene could serve as a potential epigenetic indicator for HT.

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Identification of DNA methylation-regulated differentially expressed genes in RA by integrated analysis of DNA methylation and RNA-Seq data

Cited by 7 publications

References 39 publications

Promoter Methylation-Regulated Differentially Expressed Genes in Breast Cancer

Promoter Methylation-Regulated Differentially Expressed Genes in Breast Cancer

DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment

Genome-wide DNA methylation pattern in whole blood of patients with Hashimoto thyroiditis

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