Combination of the fetal urinary metabolome and peptidome for the prediction of postnatal renal outcome in fetuses with PUV

J Proteomics. 2018 Jul 30;184:1-9. doi: 10.1016/j.jprot.2018.06.012. Epub 2018 Jun 19.

Abstract

Most of biomarker panels, extracted from single omics traits, still need improvement since they display a gray zone where prediction is uncertain. Here we verified whether a combination of omics traits, fetal urinary metabolites and peptides analyzed in the same sample, improved prediction of postnatal renal function in fetuses with posterior urethral valves (PUV) compared to individual omics traits. Using CE-MS, we explored the urinary metabolome of 13 PUV fetuses with end stage renal disease (ESRD) and 12 PUV fetuses without postnatal ESRD at 2 years postnatally. This allowed the selection of 24 differentially abundant metabolite features which were modelled into predictive classifiers, alone or in combination with 12 peptides previously identified as predictive of ESRD. Validation in 35 new fetuses showed that the combination of peptides and metabolites significantly outperformed the 24 metabolite features with increased AUC (0.987 vs 0.905), net reclassification improvement (36%) and better sensitivity accuracy (86% vs 60%). In addition, the two trait combination tended to improve, but without reaching statistical significance, the already high performances of the 12 peptide biomarkers (AUC 0.967, accuracy 80%). In conclusion, this study demonstrates the potential of cumulating different omics traits in biomarker research where single omics traits fall short.

Significance: Although increasingly proposed in disease-diagnosis and -prognosis because of their improved efficacy over single markers, panels of body fluid biomarkers based on single omics analysis still fail to display perfect accuracy, probably due to biological variability. Here, we hypothesized that combination of different omics traits allowed to better capture this biological variability. As proof of concept, we studied the added value of fetal urine metabolites and peptides using CE-MS, starting from the same urine sample, to predict postnatal renal outcome in fetuses with posterior urethral valves. We observed that the prognostic power of combined metabolite and peptide markers was clearly higher than that of metabolites alone and slightly, but non-significantly, improved compared to the peptides alone. To our knowledge, this report is the first to demonstrate that combining multiomics traits extracted from (fetal) urine samples displays clear promise for kidney disease stratification.

Keywords: Antenatal medicine; Metabolites; Peptides; Prognosis accuracy; Urinary biomarkers.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biomarkers / urine
  • Female
  • Fetal Diseases / diagnosis
  • Fetal Diseases / urine
  • Fetus / metabolism
  • Humans
  • Infant, Newborn
  • Infant, Newborn, Diseases / diagnosis*
  • Infant, Newborn, Diseases / urine
  • Kidney Failure, Chronic / congenital*
  • Kidney Failure, Chronic / diagnosis*
  • Kidney Failure, Chronic / urine
  • Male
  • Metabolome / physiology*
  • Peptide Fragments / analysis
  • Peptide Fragments / urine*
  • Predictive Value of Tests
  • Pregnancy
  • Pregnancy Outcome
  • Prenatal Diagnosis / methods*
  • Prognosis
  • Proteome / analysis
  • Proteome / metabolism
  • Retrospective Studies
  • Urethral Stricture / congenital
  • Urethral Stricture / diagnosis
  • Urethral Stricture / urine
  • Urinalysis / methods

Substances

  • Biomarkers
  • Peptide Fragments
  • Proteome