Integration of proteomics with prospective birth cohort to elucidate early life origins of cardiometabolic diseases: rationale, study design, lab assay, and quality control.

Abstract

There is growing evidence that the plasma proteome provides insights into personal health status at different stages of life. However, limited data are available on high-throughput proteomic studies in pediatric populations, especially, using prospective birth cohorts. We launched a proteomics study in 990 children from a US predominantly urban, low-income, multi-ethnic prospective Boston Birth Cohort (BBC, referred as "BBC proteomics study"), which aimed to leverage proteomics to investigate the biological pathways underlying the link between preterm birth and child long-term cardiometabolic health. The objective of this paper is to describe the rationale, study design, proteomic assay and quality control steps for the BBC proteomics study in a subset of children with available proteomic profiling. Using the OLINK^® Explore 3072 platform, proteomic profiling was performed in cord plasma at birth and in postnatal plasma collected during early childhood. Quality control (QC) steps were performed, including calculation of coefficient of variation (CV), missingness rates per sample or per protein, principal component analyses to identify clustering and outliers, and correlation analyses among the duplicates to indicate reproducibility. A total of 2,941 proteins from eight OLINK panels were successfully measured at both time points. Almost 100% of samples passed lab-prespecified QC. Approximately 89% of proteins were detected in > 50% samples; 79.6% had intra-CV < 15% and 79.9% of had inter-CV < 30%. Four samples were identified as outliers due to high missingness rates. Our data also demonstrated that this assay had a good reproducibility with correlation coefficient (r) > 0.65 in most of the duplicates, although we also identified potential batch effects. In conclusion, our data suggests that this high-throughput proteomic profiling is feasible and reproducible in archived plasma samples, including cord blood. We anticipated that successful completion of this proteomics study will help identify novel predictive biomarkers and therapeutic targets so that high-risk newborns can be identified, and effective interventions can be initiated during the earliest developmental window when they may have the greatest life-long benefit.