Computational gene expression modeling identifies salivary biomarker analysis that predict oral feeding readiness in the newborn

Abstract

Objective: To combine mathematical modeling of salivary gene expression microarray data and systems biology annotation with reverse-transcription quantitative polymerase chain reaction amplification to identify (phase I) and validate (phase II) salivary biomarker analysis for the prediction of oral feeding readiness in preterm infants.

Study design: Comparative whole-transcriptome microarray analysis from 12 preterm newborns pre- and postoral feeding success was used for computational modeling and systems biology analysis to identify potential salivary transcripts associated with oral feeding success (phase I). Selected gene expression biomarkers (15 from computational modeling; 6 evidence-based; and 3 reference) were evaluated by reverse-transcription quantitative polymerase chain reaction amplification on 400 salivary samples from successful (n = 200) and unsuccessful (n = 200) oral feeders (phase II). Genes, alone and in combination, were evaluated by a multivariate analysis controlling for sex and postconceptional age (PCA) to determine the probability that newborns achieved successful oral feeding.

Results: Advancing PCA (P < .001) and female sex (P = .05) positively predicted an infant's ability to feed orally. A combination of 5 genes, neuropeptide Y2 receptor (hunger signaling), adneosine-monophosphate-activated protein kinase (energy homeostasis), plexin A1 (olfactory neurogenesis), nephronophthisis 4 (visual behavior), and wingless-type MMTV integration site family, member 3 (facial development), in addition to PCA and sex, demonstrated good accuracy for determining feeding success (area under the receiver operator characteristic curve = 0.78).

Conclusions: We have identified objective and biologically relevant salivary biomarkers that noninvasively assess a newborn's developing brain, sensory, and facial development as they relate to oral feeding success. Understanding the mechanisms that underlie the development of oral feeding readiness through translational and computational methods may improve clinical decision making while decreasing morbidities and health care costs.

Figure 1

Flow chart depicting the methods of this study.

Figure 2

Area under the receiver operating characteristic curve (AUROC). The five most promising genes identified on our platform (PLXNA1, NPY2R, AMPK, NPHP4, WNT3) were combined to predict oral feeding success. Area under the curve = 0.78.

Figure 3

Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+)

Figure 4

1. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 2. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 3. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 4. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 5. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 6. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 7. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 8. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+).

Figure 4

1. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 2. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 3. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 4. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 5. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 6. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 7. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 8. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+).

Figure 4

1. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 2. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 3. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 4. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 5. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 6. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 7. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 8. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+).

Figure 4

1. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 2. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 3. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 4. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 5. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 6. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 7. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 8. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+).

Figure 4

1. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 2. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 3. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 4. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 5. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 6. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 7. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 8. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+).

Figure 4

1. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 2. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 3. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 4. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 5. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 6. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 7. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 8. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+).

Figure 4

1. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 2. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 3. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 4. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 5. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 6. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 7. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 8. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+).

Figure 4

1. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 2. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 3. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 4. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 5. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 6. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 7. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+). 8. Fitted probability of feeding success based upon PCA, sex and gene expression profiles. Probability of feeding success was favorable when NPY2R, WNT3 and NPHP4 were not expressed (NEG/−), while AMPK and PLXNA1 were expressed (POS/+).