Dynamic molecular changes during the first week of human life follow a robust developmental trajectory

Abstract

Systems biology can unravel complex biology but has not been extensively applied to human newborns, a group highly vulnerable to a wide range of diseases. We optimized methods to extract transcriptomic, proteomic, metabolomic, cytokine/chemokine, and single cell immune phenotyping data from <1 ml of blood, a volume readily obtained from newborns. Indexing to baseline and applying innovative integrative computational methods reveals dramatic changes along a remarkably stable developmental trajectory over the first week of life. This is most evident in changes of interferon and complement pathways, as well as neutrophil-associated signaling. Validated across two independent cohorts of newborns from West Africa and Australasia, a robust and common trajectory emerges, suggesting a purposeful rather than random developmental path. Systems biology and innovative data integration can provide fresh insights into the molecular ontogeny of the first week of life, a dynamic developmental phase that is key for health and disease.

Fig. 1

Sample processing overview. Thirty newborns were recruited in The Gambia, with each newborn providing a peripheral blood sample on DOL0 and subsets of ten newborns each providing a second peripheral blood sample at either DOL1, 3 or 7, resulting in a total of 60 blood samples. Newborn peripheral venous blood was drawn directly into heparinized collection tubes. Aliquots (200 μl) were removed for transcriptomic analysis. Plasma was then harvested from the remaining whole blood after a spin, and cryopreserved for cytokine, proteomic and metabolomic analyses. The remaining cellular fraction was diluted with phosphate-buffered saline (PBS) to replace the volume of plasma removed, and 100 μl aliquots from this mixture were processed for single-cell immunophenotyping by flow cytometry. With a starting volume of 1 ml, this standard operating protocol still left the cellular fraction contained in 400 µl of starting blood volume that could be used for other analyses. DOL: day of life

Fig. 2

Indexing cellular and soluble immune markers revealed developmental progression over the first week of life. a, b Principal component analysis was used to plot cellular composition (a) and plasma cytokines/chemokine concentration (b) for each sample; this highlighted the substantial variability between participants and lack of defined clustering by DOL due to higher influence of individual variance over ontogeny. c, d Accounting for repeat measures from the same individual across different sampling days compared to DOL0 (indexing to DOL0) revealed sample clustering by DOL between samples. e, f Normalized cell counts showing developmental trajectories for cell populations that significantly changed (e) or did not change (f) over the first week of life. g, h Normalized plasma cytokine/chemokine concentrations showing developmental trajectories for cytokines/chemokines that significantly changed (g) or did not change (h) over the first week of life. Boxplots display medians with lower and upper hinges representing first and third quartiles. Whiskers reach the highest and lowest values, no more than 1.5× interquartile range from the hinge. ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05, Kruskal−Wallis test, Benjamini−Hochberg adjusted p values. DOL: day of life

Fig. 3

Transcriptomic, proteomic, and metabolomic analyses identified a robust trajectory of differentially expressed genes, proteins, and metabolites over the first week of life. a Up- and downregulated differentially expressed genes were plotted by DOL (vs. DOL0) and numbers of genes are listed above each point except for downregulated genes at DOL1 vs. DOL0, where the number was zero. b, c Up- and downregulated differentially expressed proteins and metabolites, respectively, plotted by DOL compared to DOL0, with numbers of differentially expressed proteins or metabolites listed above each point. d Zero-order interaction networks for genes differentially expressed at DOL3 vs. DOL0 and DOL7 vs. DOL0. Within networks, upregulated nodes are displayed in red and downregulated nodes in blue. DOL: day of life

Fig. 4

Integration of multiple data types via NetworkAnalyst molecular interaction networks provided novel biological insights. Minimum-connected networks for DOL3 vs. DOL0 (a) and DOL7 vs. DOL0 (b), respectively, containing all three individual data types, where nodes derived from the transcriptome are shown in blue, nodes from the metabolome in red, and nodes from the proteome in green. Novel nodes, which are nodes that only appeared after integrating the three data types but are not present in the individual minimum network, are shown in orange. DOL: day of life

Fig. 5

DIABLO uncovered biologically relevant features by integrating information across data types. Schematic representation of two contrasting integration approaches using multivariate techniques: a shows that DIABLO selects features jointly across data types, resulting in the identification of features with strong associations across data types. Conversely, as shown in b, ensembles of multivariate models, constructed independently of each other, result in a selection of features that are poorly associated across data types. This is visualized in correlation heatmaps of the selected features and corresponding networks, with dense subgraphs, or network modules, encircled. In particular, the network modules identified in (a) include a number of features selected from all data types. This is not the case in b. The minimal set of features selected by DIABLO across data types as shown in c could discriminate between DOL and distinct sets of these features separated DOL0 from all other DOLs (DIABLO component 1) and DOL1, 3, and 7 from each other (DIABLO component 2). Features identified by DIABLO (blue bars) were largely distinct from those identified by more traditional single-OMICs multivariate approaches (red bars; overlaps in gray); shown in d using an UpSet plot. Moreover, features identified by DIABLO were more strongly enriched for known biological (functional) pathways; shown in e using an UpSet plot (blue vs. red bars). Horizontal bars are mapped to the number of elements in each set of features being compared. Vertical bars correspond to the number of elements in the intersections when carrying out various set comparisons. DIABLO: Data Integration Analysis for Biomarker discovery using Latent cOmponents, DOL: day of life

Fig. 6

Independent validation and data meta-integration of the robust developmental trajectory during the first week of life. Generalizability of the multivariate integrative model (DIABLO) depicted in Fig. 5 based on data from Gambian newborns was evaluated by assessing its ability to classify DOL from OMICs profiles in a new set of validation samples collected from newborns from a second site (Papua New Guinea (PNG)). a Pathway enrichments of Molecular Interaction Networks Integration, DIABLO and MMRN identified congruent functional pathways of the first week of life. b The dashed line corresponds to the 95% confidence level ellipses for the scores obtained from the Gambia training data. Samples from the PNG site generally resided within the correct ellipse, demonstrating good agreement between actual DOL and DOL as predicted by the model. Similar figures were generated for other OMICs data (Supplementary Figure 10). c This agreement was quantified using area under the receiver operator characteristics curve (AUROC) analysis comparing DOL0 (red), 1 (blue), 3 (green), and 7 (purple) individually vs. all other DOLs combined. d shows zero-order interaction networks for DOL7 vs. DOL0 containing nodes for transcriptome (blue), proteome (green), metabolome (red), and DIABLO-selected features (purple). Genes involved in the interferon and complement pathways and neutrophil degranulation are highlighted by the orange boxes. e−g Relative abundance of a selected subset of markers identified by DIABLO are shown for each DOL for both the Gambian cohort, on which the model was trained, and the validation cohort from PNG. The cells (flow cytometry; FC), plasma cytokines (Luminex assay; CYT) and plasma proteins (mass-spectrometry proteomics; PROT), transcripts (RNA-Seq; RNA), and metabolites (mass-spectrometry metabolomics; META) identified by DIABLO were associated with interferon signaling (e), neutrophil recruitment and activation (f), and complement pathways (g). The differences observed between DOLs in the Gambia cohort were generally replicated in the PNG cohort. Boxplots display medians with lower and upper hinges representing first and third quartiles; whiskers reach the highest and lowest values no more than 1.5× interquartile range from the hinge ****p ≤ 0.0001, ***p ≤ 0.001, **p ≤ 0.01, *p ≤ 0.05, ns p > 0.05, by ANOVA. DIABLO: Data Integration Analysis for Biomarker discovery using Latent cOmponents, DOL: day of life, MMRN: multiscale, multifactorial response network