Ningappa Mylarappa, Shao Xiaojian, Ashokkumar Chethan, Xu Qingyong, Zeevi Adriana, Grundberg Elin, Pastinen Tomi, Sindhi Rakesh
Department of Transplant Surgery, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh and the University of Pittsburgh, Pittsburgh, PA.
Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada.
Transplant Direct. 2022 Oct 14;8(11):e1394. doi: 10.1097/TXD.0000000000001394. eCollection 2022 Nov.
Transcriptional regulation of liver transplant (LT) rejection may reveal novel predictive and therapeutic targets. The purpose of this article is to test the role of differential DNA methylation in children with biopsy-proven acute cellular rejection after LT.
Paired peripheral blood DNA samples were obtained before and after LT from 17 children, including 4 rejectors (Rs) and 13 nonrejectors (NRs), and assayed with MethylC capture sequencing 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 (DMRs) comprising 3 or more DMCs.
Contrasting Rs versus NRs, 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. Among DMRs, the proportion of hypomethylated DMRs increased from 61/282 (22%) in pre-LT to 103/216 (48%, < 0.0001) in post-LT samples. The highest-ranked biological processes enriched in post-LT DMCs were antigen processing and presentation via major histocompatibility complex (MHC) class I, MHC class I complex, and peptide binding ( < 7.92 × 10), respectively. Top-ranked DMRs mapped to genes that mediate B-cell receptor signaling () or regulate several immune cells ) ( < 3.75 × 10). DMRs in MHC class I genes were enriched for single nucleotide polymorphisms (SNPs), which bind transcription factors, affect gene expression and splicing, or alter peptide-binding amino acid sequences.
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.
肝移植（LT）排斥反应的转录调控可能揭示新的预测和治疗靶点。本文旨在测试差异DNA甲基化在经活检证实的LT术后儿童急性细胞排斥反应中的作用。
从17名儿童LT术前和术后获取配对的外周血DNA样本，其中包括4名排斥反应者（Rs）和13名无排斥反应者（NRs），采用甲基化捕获测序方法对免疫细胞特异性调控元件中500万个CpG进行检测。使用针对性别和年龄进行调整的广义线性回归模型鉴定差异甲基化CpG（DMC），并将其合并为包含3个或更多DMC的差异甲基化区域（DMR）。
对比Rs与NRs，我们在LT术后样本中鉴定出2238个DMC，在LT术前样本中鉴定出2620个DMC，它们分别聚集在216个和282个DMR中。与排斥反应相关的DMC在增强子中富集，在启动子中减少。在DMR中，低甲基化DMR的比例从LT术前的61/282（22%）增加到LT术后样本中的1,03/216（48%，<0.0001）。LT术后DMC中富集程度最高的生物学过程分别是通过主要组织相容性复合体（MHC）I类、MHC I类复合体和肽结合进行抗原加工和呈递（<7.92×10）。排名靠前的DMR映射到介导B细胞受体信号传导（）或调节多种免疫细胞（）的基因（<3.75×10）。MHC I类基因中的DMR富含单核苷酸多态性（SNP），这些SNP结合转录因子、影响基因表达和剪接或改变肽结合氨基酸序列。
远端调控区域的动态甲基化揭示了已知的与移植相关的MHC依赖性排斥途径，并为儿科移植亚组未来的机制评估确定了新的基因座。
