Constructing a Plasma Nutriproteome for Population Assessment: Analytical Considerations

Abstract

ObjectivesMicronutrient status is rarely assessed in low-income settings. Proteomics may offer a proxy by measuring plasma proteins correlated with nutrients on a single platform. However, the proteome is huge, diverse and measured in different ways. We describe an analytic framework and decision process to explore nutrient: protein (N:P) associations for micronutrient status assessment.MethodsIn plasma of 435 1st trimester women in rural Bangladesh, we compared relative protein abundance, revealed by a multiplexed slow off-rate modified aptamer assay (SomaLogic, Inc), to biochemical concentrations of vitamins A, D, E, B9, B12, Zn, Se, Cu, I, & Fe, 5 carotenoids, cholesterol and AGP. After log2-transforming protein abundance per convention, N:P relationships were summarized by simple linear regression. We assessed reliability by Pearson correlation (rp) and coefficients of variation (CV) in 20 blind duplicates. To define each plasma nutriproteome [proteins correlating at a false discovery rate < 0.05], in all samples we explored a) normalizing protein abundance to the median of our sample vs not, b) assessing correlations by rp vs Spearman rank (rs) estimators, and c) log2-transforming (log2) nutrients vs not. We compared differences in the number of proteins and N:P correlative strength (either more negative/positive by rp or rs) in each proteome when nutrient concentrations were left untransformed vs log2-transformed.ResultsIn duplicates, log2-transformed proteins that were normalized, vs not, to the sample-specific median generated higher median rp (0.92 vs. 0.87) and rs (0.87 vs. 0.85) and lower CV (4.8% vs. 11.7%). The median (IQR) size of the nutriproteomes was 147 (41–340) proteins by rp and 87 (29–639) by rs. For >50% of proteins in 13 nutriproteomes, rp was stronger than rs (in either +/− direction), favoring use of rp. Log2-transforming folate (B9), Zn & cholesterol increased proteome size by 39, 223 & 875 proteins and strengthened rp for >50% of proteins than untransformed nutrients. Other proteomes remained larger when nutrient concentrations remained untransformed.ConclusionsComparing plasma protein: nutrient associations via methods of normalization, transformation, and correlation offers a framework to guide plasma nutriproteome definition.Funding SourcesJohns Hopkins University.