Cu-IUD usage causes significant perturbations to the cervicovaginal transcriptome
Cu-IUD treatment, with 907 DEGs identified, had a dramatic impact on gene expression (Immune activation pathways enriched in women assigned to Cu-IUD (nominal p-value < 0.1). Important pathways enriched in Cu-IUD study arm, were selected. (A) A dot plot to represent the gene set enrichment analysis (GSEA) statistics for these pathways, across the longitudinal comparisons in the three study arms. The statistical significance of the enrichment (1-ln (nominal p-value)) is shown by the size of the dots and the normalized enrichment score (NES) is represented by a blue-to-red color-gradient, blue for negative scores and red for positive scores. (B-G) Breakout enrichment line plots and leading-edge gene heatmaps for a few of these enriched pathways. (B,D,F) In the line plots, the running enrichment score (y-axis) is indicated for each gene ordered by their rank in the whole data set for that specific comparison, shown by the vertical bars below the x-axis. (C,E,G) Heatmaps for the leading-edge genes of the indicated pathways. The gene-expressions are log-transformed, further normalized by mean of baseline samples in the Cu-IUD. The color gradient goes from blue to red color in representing the lowest to the highest gene-expression across all samples in the comparison. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)Metallothioneins and Chemokines pathways' enriched in women assigned to Cu-IUD (nominal p-value < 0.1). (A-D) Breakout enrichment line plots and leading-edge gene heatmaps for the pathways shown in the fig. (A,C) In the line plots, the running enrichment score (y-axis) is indicated for each gene ordered by their rank in the whole data set for that specific comparison, shown by the vertical bars below the x-axis. (B,D) Heatmaps for the leading-edge genes of the indicated pathways. The gene-expressions are log-transformed, further normalized by mean of baseline samples in the Cu-IUD. The color gradient goes from blue to red color in representing the lowest to the highest gene-expression across all samples in the comparison. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)We also observed highly significant enrichment of gene sets comprising ISGs and innate immune signaling (Lastly, we observed widespread induction of genes in the metallothionein (MT) family in mucosal samples post Cu-IUD initiation, including eight isoforms of MT1 genes (MT1A, MT1B, MT1H, MT1M, MT1G, MT1X, MT1E, MT1F). MT1A and MT1B had the highest fold-change of all DEGs detected, at >1000-fold and 60-fold, respectively. MT2A was also significantly elevated. Similarly, genesets including metallothionein and metal stress responses were determined to be significantly enriched (