Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data

• Published in: Clinical epigenetics 2023-06, Vol.15 (1), p.96-13, Article 96
• Main Authors: Yu, Jeffrey C Y, Zeng, Yixiao, Zhao, Kaiqiong, Lu, Tianyuan, Oros Klein, Kathleen, Colmegna, Inés, Lora, Maximilien, Bhatnagar, Sahir R, Leask, Andrew, Greenwood, Celia M T, Hudson, Marie
• Format: Article
• Language: English
• Subjects: Agreements; Binomial distribution; Bisulfite; CD4 antigen; Chromosomes; Connective tissues; CpG Islands; Differentially methylated regions; Disease; DNA fingerprinting; DNA Methylation; DNA sequencing; Epigenetics; Extracellular matrix; Female; Genes; Genetic research; Genomes; Genomics; Glycosaminoglycans; Health maintenance organizations; Humans; Lymphocytes T; Methods; Methylation; Pathogenesis; Rankings; Regions; Scleroderma; Scleroderma (Disease); Scleroderma, Systemic - genetics; Smoothing; Sulfites; Systemic scleroderma; Systemic sclerosis; T cells; Whole genome bisulfite sequencing; Whole Genome Sequencing - methods
• ISSN: 1868-7083; 1868-7075; 1868-7083; 1868-7075
• DOI: 10.1186/s13148-023-01513-w

Abnormal DNA methylation is thought to contribute to the onset and progression of systemic sclerosis. Currently, the most comprehensive assay for profiling DNA methylation is whole-genome bisulfite sequencing (WGBS), but its precision depends on read depth and it may be subject to sequencing errors. SOMNiBUS, a method for regional analysis, attempts to overcome some of these limitations. Using SOMNiBUS, we re-analyzed WGBS data previously analyzed using bumphunter, an approach that initially fits single CpG associations, to contrast DNA methylation estimates by both methods. Purified CD4+ T lymphocytes of 9 SSc and 4 control females were sequenced using WGBS. We separated the resulting sequencing data into regions with dense CpG data, and differentially methylated regions (DMRs) were inferred with the SOMNiBUS region-level test, adjusted for age. Pathway enrichment analysis was performed with ingenuity pathway analysis (IPA). We compared the results obtained by SOMNiBUS and bumphunter. Of 8268 CpG regions of ≥ 60 CpGs eligible for analysis with SOMNiBUS, we identified 131 DMRs and 125 differentially methylated genes (DMGs; p-values less than Bonferroni-corrected threshold of 6.05-06 controlling family-wise error rate at 0.05; 1.6% of the regions). In comparison, bumphunter identified 821,929 CpG regions, 599 DMRs (of which none had ≥ 60 CpGs) and 340 DMGs (q-value of 0.05; 0.04% of all regions). The top ranked gene identified by SOMNiBUS was FLT4, a lymphangiogenic orchestrator, and the top ranked gene on chromosome X was CHST7, known to catalyze the sulfation of glycosaminoglycans in the extracellular matrix. The top networks identified by IPA included connective tissue disorders. SOMNiBUS is a complementary method of analyzing WGBS data that enhances biological insights into SSc and provides novel avenues of investigation into its pathogenesis.