Abstract
Background Transcriptional regulation of liver transplant (LT) rejection may reveal novel predictive and therapeutic targets.
Purpose To test the role of differential DNA methylation in children with biopsy-proven acute cellular rejection (rejectors, R) after LT.
Methods Paired peripheral blood DNA samples were obtained before and after LT from 17 children, including 4R and 13 non-rejector (NR), and assayed with MethylC capture sequencing (MCC-Seq) approach covering 5 million CpGs in immune-cell specific regulatory elements. Differentially methylated CpGs (DMCs) were identified using generalized linear regression models adjusting for sex and age and merged into differentially methylated regions (DMR) comprising 3 or more DMCs.
Results Contrasting R vs NR, we identified 2238 DMCs in post-LT and 2620 DMCs in pre-LT samples, which clustered in 216 and 282 DMRs respectively. DMCs associated with R were enriched in enhancers and depleted in promoters. The proportion of hypomethylated versus hypermethylated DMRs increased from 22% to 48% (p<0.0001) in pre-LT vs. post-LT DMCs, respectively. The highest-ranked biological processes enriched in post-LT DMCs were antigen processing and presentation via MHC class I, MHC class I complex, and peptide binding (p<7.92E-17), respectively. Top-ranked DMRs mapped to genes which mediate B-cell receptor signaling (ADAP1) or regulate several immune cells (ARRB2) (p<3.75E-08). DMRs in MHC class I genes were enriched for SNPs which bind TFs, affect gene expression and splicing, or alter peptide-binding amino acid sequences.
Conclusions Dynamic methylation in distal regulatory regions reveals known transplant-relevant MHC-dependent rejection pathways, and identifies novel loci for future mechanistic evaluations in pediatric transplant subcohorts.
Competing Interest Statement
The authors have declared no competing interest.
Abbreviations
- ADAP1
- ArfGAP With Dual PH Domains 1
- ARRB2
- arrestin B2
- CTCF
- CCCTC binding transcription factor
- DMC
- differentially methylated CpG
- DMR
- differentially methylated regions
- GLM
- generalized linear regression models
- LHX6
- LIM Homeobox 6
- LT
- Liver transplantation
- MCC-Seq
- methylation capture sequencing
- MHC
- major histocompatibility complex
- mTOR
- mammalian target of rapamycin
- NR
- non-rejectors
- R
- Rejectors
- SNP
- single nucleotide polymorphism
- TF
- transcription factor
- TSS
- transcription start site
