Human conjunctival transcriptome in Acanthamoeba keratitis: An exploratory study

The host conjunctival transcriptome of 9 patients with Acanthamoeba keratitis (AK) is compared to the conjunctival transcriptome of 13 patients with keratitis and no identified pathogen. Pathway enrichment analysis identified thirty-six transcripts as most differentially expressed between patients with AK compared to patients with presumed sterile keratitis. Methods The host conjunctival transcriptome of 9 patients with Acanthamoeba keratitis (AK) is compared to the conjunctival transcriptome of 13 patients with keratitis and no identified pathogen. For the differential host gene expression analysis, sequencing reads were quality filtered and aligned to the GRCh38 human genome assembly using HISAT2 (version 2.1.0). Abundance of transcripts was calculated using the default parameters in stringtie2 (version 1.3.4d) and annotation of transcripts were based on ENSEMBL GRCh38.87. Gene count matrices were generated using the "prepDE.py" script according to the protocol found in the stringtie2 documentation.