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.
Key Findings
Results
Differential gene expression analysis identified distinct transcriptomic profiles for mild HIE versus moderate or severe HIE, with very little overlap between the two groups.
981 differentially expressed genes were identified in mild HIE and 622 genes in moderate or severe HIE (false discovery rate <0.05)
Only 37 genes (3.0%) were shared between mild HIE and moderate or severe HIE gene sets
Analysis used whole-blood RNA next-generation sequencing from 112 full-term infants
73 infants had HIE (40 mild, 29 moderate, 4 severe) and 39 were healthy controls
Results
In mild HIE, the processing of capped intron-containing pre-mRNA was downregulated as the most significantly enriched pathway.
The pathway showed a z score of -0.68 (P < .001)
This pathway enrichment was specific to mild HIE and not the dominant finding in moderate or severe HIE
Pathway analysis characterized the biological mechanisms underlying differential expression by HIE severity
Results
In moderate or severe HIE, autoimmune thyroid disease signaling showed the highest pathway significance.
Autoimmune thyroid disease signaling pathway reached P < .001
A z score was not determined for this pathway
This pathway was the most significant finding in moderate or severe HIE, contrasting with the pre-mRNA processing pathway dominant in mild HIE
Results
Transcriptomic disturbances substantially attenuated by 72 hours after birth, particularly in mild HIE, with gene expression profiles converging toward control levels.
Temporal changes in gene expression were evaluated over the first 72 hours compared with matched healthy controls
The convergence toward control levels was especially pronounced in mild HIE
This temporal attenuation suggests the early postnatal period is a critical window for transcriptomic-based risk stratification
Methods
Whole-blood gene expression at birth distinguished infants with mild HIE from both healthy controls and infants with moderate or severe encephalopathy.
The study was a case-control design combining data from the COMET pilot randomized clinical trial (October 31, 2019, to April 28, 2023) and two prospective observational studies
Six tertiary neonatal intensive care units in the United Kingdom and Italy participated
Eligible infants were full-term (gestational age ≥36 weeks; birth weight ≥1.8 kg)
Median birth weight was 3.3 kg (IQR, 3.0–3.6 kg) for moderate or severe HIE, 3.3 kg (IQR, 3.1–3.5 kg) for mild HIE, and 3.4 kg (IQR, 3.0–3.6 kg) for controls
Results
The study population had balanced demographic characteristics across HIE severity groups and controls.
19 infants with mild HIE (47.5%) and 20 infants with moderate or severe HIE (61.0%) were female; 23 control infants (59.0%) were female
Median gestational age was 40.0 weeks (IQR, 39.0–40.6 weeks) for mild HIE, 39.3 weeks (IQR, 39.0–41.0 weeks) for moderate HIE, and 39.4 weeks (IQR, 39.0–40.4 weeks) for severe HIE
Data were analyzed from October 2025 to February 2026
What This Means
This research suggests that analyzing gene activity in a newborn's blood at the time of birth can help identify how severely a baby's brain has been affected by oxygen deprivation (a condition called hypoxic-ischemic encephalopathy, or HIE). The study looked at 112 full-term newborns across six hospitals in the UK and Italy — some with mild HIE, some with moderate or severe HIE, and some healthy — and found that babies with different levels of brain injury showed very different patterns of gene activity, with only about 3% of affected genes overlapping between the mild and more severe groups. Mild HIE was associated with changes in how cells process genetic instructions (pre-mRNA processing), while more severe HIE was linked to immune signaling pathways.
Importantly, these gene expression differences were detectable right at birth, during the narrow time window when treatments like therapeutic cooling can still be effective. By 72 hours after birth, the gene activity patterns had largely returned toward normal levels — especially in babies with mild HIE — meaning the early timepoint is particularly valuable for assessment. This is significant because mild HIE is difficult to diagnose clinically and can lead to either undertreating babies who need help or overtreating those who do not.
This research suggests that whole-blood gene expression testing at birth could one day serve as a tool to better classify the severity of newborn brain injury and help doctors make more informed decisions about which babies should receive neuroprotective treatments. The findings support the potential of this approach for risk stratification during a period when both accurate diagnosis and timely intervention are critically important.