Figure 4. Blood gene expression signatures reflect innate and adaptive immune cell changes during early childhood.

A) The age (in months) of the Tanzanian children at blood samples B0 and B32 for which RNA sequencing was performed. Dots represent individual samples, B0 (n=21) and B32 (n=9). B) Hierarchical clustering of 2146 differentially expressed (DE) genes between B0 and B32 (1148 upregulated at B0, 1008 upregulated at B32). Significantly different genes had an fdr-adjusted p-value of <0.01 from DESeq2 and an fdr-adjusted p-value of <0.05 from the intensity-difference test, and were clustered using Euclidean distance. Each column represents an individual sample, and genes shown as rows. Enriched blood transcriptional modules (BMTs) at C) B0 and D) B32, represented as colored circles with annotations as text. Colors and connecting lines show gene-sets with related genes, and summary terms shown in text boxes. BTMs enriched from within all expressed genes (17,607) with an enrichment score greater than 1.5 or less and −0.5 and a fdr adjusted p-value of <0.01 (Kolmorogov-Smirnov test) are shown. E) A stylized representation of the Multi-Omics Factor Analysis (MOFA) modelling, which was built using 5000 most variable genes from RNA-Seq and 61 immune cell types measured by flow cytometry for 27 samples (19 B0, 8 B32), and reduces these 5061 parameters to latent factors (LF). F) The percentage of total variance (R²) in the MOFA model explained by flow cytometry or RNA-Seq data sets. G) Scatter plot showing the distribution of samples by the first 2 LF determined by MOFA modelling. Each sample shown as a circle (B0 = white, B32 = black). The percentage of total variance, and the contribution of flow and RNA to each factor are indicated in the axes labels. H) The correlation between the age in weeks for each sample and the sum of values for LF1 and LF2 (Factor sum, B0 = white, B32 = black). Linear regression fit shown by the red line, and R² and p-value from Pearson correlation are shown. The proportional loading for the 12 cell types with the strongest contribution to I) Factor 1 or K) Factor 2 are shown. The p-values (-log₁₀ fdr-adjusted) for BTMs that were significantly enriched (p-adjusted <0.05) among genes identified by J) Factor 1 and L) Factor 2, and corresponding enrichment scores. I-L) Colour and symbol representing the direction of loading or enrichment in factor space (blue = negative, red = positive).