Development of a peripheral blood transcriptomic gene signature to predict bronchopulmonary dysplasia

Alvaro Moreira, Miriam Tovar, Alisha M. Smith, Grace C. Lee, Justin A. Meunier, Zoya Cheema, Axel Moreira, Caitlyn Winter, Shamimunisa B. Mustafa, Steven Seidner, Tina Findley, Joe G.N. Garcia, Bernard Thébaud, Przemko Kwinta, Sunil K. Ahuja

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Bronchopulmonary dysplasia (BPD) is the most common lung disease of extreme prematurity, yet mechanisms that associate with or identify neonates with increased susceptibility for BPD are largely unknown. Combining artificial intelligence with gene expression data is a novel approach that may assist in better understanding mechanisms underpinning chronic lung disease and in stratifying patients at greater risk for BPD. The objective of this study is to develop an early peripheral blood transcriptomic signature that can predict preterm neonates at risk for developing BPD. Secondary analysis of whole blood microarray data from 97 very low birth weight neonates on day of life 5 was performed. BPD was defined as positive pressure ventilation or oxygen requirement at 28 days of age. Participants were randomly assigned to a training (70%) and testing cohort (30%). Four gene-centric machine learning models were built, and their discriminatory abilities were compared with gestational age or birth weight. This study adheres to the transparent reporting of a multivariable prediction model for individual prognosis or diagnosis (TRIPOD) statement. Neonates with BPD (n = 62 subjects) exhibited a lower median gestational age (26.0 wk vs. 30.0 wk, P < 0.01) and birth weight (800 g vs. 1,280 g, P < 0.01) compared with non-BPD neonates. From an initial pool (33,252 genes/ patient), 4,523 genes exhibited a false discovery rate (FDR) <1%. The area under the receiver operating characteristic curve (AUC) for predicting BPD utilizing gestational age or birth weight was 87.8% and 87.2%, respectively. The machine learning models, using a combination of five genes, revealed AUCs ranging between 85.8% and 96.1%. Pathways integral to T cell development and differentiation were associated with BPD. A derived five-gene whole blood signature can accurately predict BPD in the first week of life.

Original languageEnglish (US)
Pages (from-to)L76-L87
JournalAmerican Journal of Physiology - Lung Cellular and Molecular Physiology
Volume324
Issue number1
DOIs
StatePublished - Jan 2023

Keywords

  • bioinformatics
  • bronchopulmonary dysplasia
  • machine learning
  • prediction
  • whole microarray

ASJC Scopus subject areas

  • Physiology
  • Pulmonary and Respiratory Medicine
  • Physiology (medical)
  • Cell Biology

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