Whole genome methylation and transcriptome analyses to identify risk for cerebral palsy (CP) in extremely low gestational age neonates (ELGAN)

Abstract

Preterm birth remains the leading identifiable risk factor for cerebral palsy (CP), a devastating form of motor impairment due to developmental brain injury occurring around the time of birth. We performed genome wide methylation and whole transcriptome analyses to elucidate the early pathogenesis of CP in extremely low gestational age neonates (ELGANs). We evaluated peripheral blood cell specimens collected during a randomized trial of erythropoietin for neuroprotection in the ELGAN (PENUT Trial, NCT# 01378273). DNA methylation data were generated from 94 PENUT subjects (n = 47 CP vs. n = 47 Control) on day 1 and 14 of life. Gene expression data were generated from a subset of 56 subjects. Only one differentially methylated region was identified for the day 1 to 14 change between CP versus no CP, without evidence for differential gene expression of the associated gene RNA Pseudouridine Synthase Domain Containing 2. iPathwayGuide meta-analyses identified a relevant upregulation of JAK1 expression in the setting of decreased methylation that was observed in control subjects but not CP subjects. Evaluation of whole transcriptome data identified several top pathways of potential clinical relevance including thermogenesis, ferroptossis, ribosomal activity and other neurodegenerative conditions that differentiated CP from controls.

Figure 1

Significant DMR on chromosome 15 for the interaction (day 1 to 14 change) in CP vs Control. Methylation decreases in CP babies on day 14 (pink) compared to day 1 (blue), whereas appears stable in Control babies (red and green). Individual CpG numbers (denoted by green vertical bars) are listed as follows: cg09167084; cg18988510; cg12754238; cg20139049; cg17356999; cg15454857; cg21874278; cg14760714; cg12307764; cg18013830; cg00066468. Figure generated with the Bioconductor Gviz package (version 1.28.3).

Figure 2

Venn diagram of differentially expressed genes between day 1 and 14 that are unique in CP (yellow) compared to control (blue) ELGANs. Figure generated using the CRAN package gplots (version 3.0.1.1).

Figure 3

iPathwayGuide meta-analysis of DNA methylation and gene expression data identified 2 genes (highlighted in white) unique to CP, and 4 genes (black box) unique to Controls, that demonstrated evidence of differential methylation and gene expression. Figure generated using Advaita Bio’s iPathway Guide (https://www.advaitabio.com/ipathwayguide).