FIG 4.

Innate immune defenses against CDI are upregulated following treatment with lead drugs. Following antibiotic pretreatment, mice were infected with C. difficile spores and administered lead drugs or the vehicle control PBS. Uninfected, but antibiotic-pretreated, mice (ABX) and untouched (naive) mice served as controls (Table 1). Thirty hours postinfection, cecal tissue was harvested for total RNA isolation and subjected to RNA-seq analysis. Data represent RNA pooled from 5 mice/group. (A) Hierarchical clustering of 5,894 transcripts representing unique genes altered by >4-fold in one or more groups compared to untreated, naive controls (see Table S1 in the supplemental material). Bright orange represents the highest values (standardized counts per million), white represents the lowest values, and black represents median values. (B) Heat map displaying gene expression differences for select genes of functional interest profiled by RNA-seq. Data shown are log₂ fold change (treatment groups versus naive controls) in expression plotted using the color scale shown. (C) Venn diagram of 4,557 genes with a 4-fold change in expression induced by drug treatment in comparison to that of the PBS-treated group. (D and E) Enriched pathways of the top upregulated transcripts and upstream targets listed by significance [−log₁₀ (P)] based on IPA. (F) Correlation between RNA-seq and qRT-PCR expression levels was determined for 20 select genes.