Detailed immune profiling in pediatric Crohn’s disease using methylation cytometry

Figures & data

Figure 1. Blood immune cell type proportions in controls and Crohn’s patients at diagnosis. Panels a, c, and d compare cell type proportions between diagnosis and control. Panel b compares neutrophil to lymphocyte ratios. Univariate p-values are displayed on top, while p-values adjusted for age and sex, are displayed below. NS signifies a non-significant (>0.05) p-value.

Table 1. Study population demographic and disease characteristics.

Characteristics	Cases	Controls
Total Subjects	164	74
Total Samples	328	74
Age, mean (range)	13.8 (4.5–20.8)	12.0 (4.5–16.8)
Sex, n (%)
Male	96 (59)	40 (54)
Female	68 (41)	34 (46)
Stage at Baseline, n (%)
Stage B1	150 (91)	NA
Stage B2	14 (9)	NA
Stage at Follow-Up, n (%)
Stage B1	95 (58)	NA
Stage B2	69 (42)	NA

Figure 2. Blood immune cell type proportions in controls and Crohn’s patients at follow-up. Panels a, c, and d compare cell type proportions between controls and patients at follow-up. Panel b compares neutrophil to lymphocyte ratios. Univariate p-values are displayed on top, while p-values adjusted for age and sex, are displayed below. NS signifies a non-significant (>0.05) p-value.

Figure 3. Paired changes in cell type proportions (CTP) and neutrophil lymphocyte ratio (NLR) between diagnosis and follow-up (CTP_Follow-Up - CTP_Diagnosis). a positive difference indicates an increase in the proportion of a cell type from baseline to follow-up whereas a negative difference indicates a decrease in the proportion.

Figure 4. Neutrophil lymphocyte ratios in controls, patients at diagnosis, and patients at follow-up. Univariate p-values are displayed on top, while p-values adjusted for age and sex, are displayed below. NS signifies a non-significant (>0.05) p-value.

Table 2. Top 20 gene ontology pathways. BP denotes biological process while MF denotes molecular function.

ONTOLOGY	TERM	P-Value	FDR
BP	regulation of arginine metabolic process	9.34E–06	0.212436
BP	regulation of glutamine family amino acid metabolic process	6.9E–05	0.732867
BP	immune system process	0.000177	0.732867
BP	arginine metabolic process	0.000209	0.732867
BP	alpha-beta T cell differentiation	0.000218	0.732867
BP	regulation of cellular amine catabolic process	0.000305	0.732867
BP	negative regulation of cellular amine catabolic process	0.000305	0.732867
BP	regulation of arginine catabolic process	0.000305	0.732867
BP	negative regulation of arginine catabolic process	0.000305	0.732867
BP	release of cytochrome c from mitochondria	0.000322	0.732867
BP	cytokine production	0.000444	0.843094
BP	response to virus	0.000445	0.843094
MF	TRAIL binding	0.000624	0.855264
BP	purine nucleotide catabolic process	0.000646	0.855264
BP	adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process	0.000662	0.855264
BP	T cell differentiation	0.000672	0.855264
BP	response to oxygen-containing compound	0.000707	0.855264
BP	negative regulation of cellular amino acid metabolic process	0.00074	0.855264
BP	immune effector process	0.000802	0.855264
BP	regulation of type I interferon production	0.000834	0.855264

Figure 5. Crohn’s disease at diagnosis is associated with 397 CpG sites in blood. All 738,245 CpG sites are shown with those with an FDR < 0.05 shown in red. FDR < 0.05 shown above blue line and FDR < 0.01 shown above red line. Panel a was only adjusted for age and sex. Panel b was adjusted for age, sex, and the basic cell types deconvolved from the Houseman library. Panel c was adjusted for age, sex, neutrophils, monocytes, natural killer cells, naive B-cells, memory B-cells, naive CD4 T-cells, memory CD4 T-cells, naive CD8 T-cells, basophils, and eosinophils.

Figure 6. Genomic context and relation to CpG islands of CpGs associated with crohn’s disease.

Data availability statement

The datasets analysed during the current study are available under the National Center for Biotechnology’s Gene Expression Omnibus repository with the accession ID – GSE112611. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112611