A genome-wide DNA methylation signature for SETD1B-related syndrome

Abstract

SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identified SETD1B VUS (variant of uncertain significance) in two patients.

Fig. 1

The volcano plot of the methylation difference between patients with certain pathogenic variation in SETD1B and healthy individuals (group analysis). The y-axis represents a negative log₁₀ of adj. P-values_M; the x-axis represents the different beta values between patients and controls. Each dot on the plot represents a single CpG site. The horizontal, dotted line represents the statistical significance threshold (adj. P-values_M = 0.05). The vertical, dotted lines show the effect-size threshold (− 0.1 and 0.1). CpGs with adj. P-value_M lesser than 0.05 and an absolute beta difference higher than 0.1 are highlighted in green

Fig. 2

SETD1B-related DNAm signature. Unsupervised hierarchical clustering of 3340 CpG sites identified in the SETD1B group analysis (DNAm of patients with certain pathogenic aberration/variation in SETD1B compared to that in healthy controls). C represents controls; aberrations/variations are annotated to patients. Note that the data was obtained from two batches

Fig. 3

Multidimensional scaling (MDS) of 502 individuals with neurodevelopmental disorders. Red dots represent eight patients with SETD1B-related DNAm signature of the current study, blue dots represent controls of the current study, and green dots represent patients with other disorders

Fig. 4

Genomic distribution of the significant differentially methylated CpG sites identified in group analysis according to the genomic annotations of the epic array. The light blue bars (EPIC) represent all the informative probes included in the data (777,148 CpGs) and the dark blue bars the CpGs identified in the group analysis (TOP; 3340 CpGs). The numbers on the top of the bars represent the percentage distribution of CpGs for each category. All categories are listed in the supplemental information—Infinium Methylation EPIC Manifest Column Headings®. This comparison demonstrates the enrichment in the body (between the ATG and stop codon), DHS–DNase I hypersensitivity site, RDMR–reprogramming-specific differentially methylated region, promoter-associated, and promoter-associated cell-type specific

Fig. 5

Unsuperviesed hierarchical clustering of the 697 CpG sites identified in KDM2B group analysis. C–represents controls, aberrations/variations annotated to patients. The data was obtained from two batches

Fig. 6

Comparison between deleted regions in patients with a microdeletion of 12q24.31. The light blue bars represent the deleted regions for individual patients. Numbers 1, 2, 3, 4, and 5 represent patients 1_del12q24.31, 2_del12q24.31, 3_del12q24.31, 4_del12q24.31, and 5_del12q24.31, respectively. The red frames highlight genes SETD1B and KDM2B. Note: microdeletion of patient 5_del12q24.31 has not been fully displayed on the plot and does not overlap KDM2B and SETD1B