Whole-Blood Gene Expression and Hypoxic-Ischemic Encephalopathy at Birth

Importance: Mild hypoxic-ischemic encephalopathy (HIE) spans a broad spectrum of neurological dysfunction, making early identification challenging and leading to undertreatment or overtreatment. Objectives: To investigate whether whole-blood gene expression at birth is associated with HIE severity (mild, moderate, or severe), to characterize pathways underlying differential expression, and to evaluate temporal changes over the first 72 hours compared with matched healthy controls. Design, Setting, and Participants: This case-control study combines data from the COMET (Cooling in Mild Encephalopathy) pilot randomized clinical trial from October 31, 2019, to April 28, 2023, recruiting infants with mild HIE and data from 2 prospective observational studies (January 1, 2017, to June 1, 2019, and September 30, 2019, to September 30, 2025) enrolling infants with moderate or severe HIE and healthy control infants. The settings include 6 tertiary neonatal intensive care units in the United Kingdom and Italy, and the participants were full-term infants (gestational age, ≥36 weeks; birth weight, ≥1.8 kg) with mild, moderate, or severe HIE and healthy control infants. Data were analyzed from October 2025 to February 2026. Exposure: Whole-blood RNA next-generation sequencing. Main Outcomes and Measures: Measures were gene-level counts and pathway enrichment statistics. Primary outcomes were gene expression differences by HIE severity and the temporal evolution of transcriptomic profiles compared with controls. Results: A total of 112 full-term infants were included: 73 with HIE (40 with mild HIE, 29 with moderate HIE, and 4 with severe HIE; 19 infants with mild HIE [47.5%] and 20 infants with moderate or severe HIE [61.0%] were female) and 39 healthy control infants (23 female infants [59.0%]). The median birth weight was 3.3 kg (IQR, 3.0-3.6 kg) for infants with moderate or severe HIE, 3.3 kg (IQR, 3.1-3.5 kg) for infants with mild HIE, and 3.4 kg (IQR, 3.0-3.6 kg) for controls. The median gestational age was 40.0 weeks (IQR, 39.0-40.6 weeks) for infants with mild HIE, 39.3 weeks (IQR, 39.0-41.0 weeks) for infants with moderate HIE, and 39.4 weeks (IQR, 39.0-40.4 weeks) for infants with severe HIE. Differential expression analysis identified 981 genes in mild HIE and 622 genes in moderate or severe HIE (false discovery rate <0.05), with 37 genes (3.0%) shared. In mild HIE, the processing of capped intron-containing pre-mRNA was downregulated (z score, -0.68; P < .001), whereas in moderate or severe HIE, autoimmune thyroid disease signaling showed the highest significance (z score not determined; P < .001). By 72 hours, transcriptomic disturbances had substantially attenuated, particularly in mild HIE, with gene expression profiles converging toward control levels. Conclusions and Relevance: In this case-control study of infants with HIE, whole-blood gene expression at birth was associated with HIE severity, distinguishing infants with mild HIE from both controls and those with moderate or severe encephalopathy, supporting its role in risk stratification during the period when neuroprotective interventions remain possible and clinical diagnosis may still be challenging.