The conjunctival transcriptome in Ethiopians after trichiasis surgery: associations with the development of eyelid contour abnormalities and the effect of oral doxycycline treatment

Abstract

Background: Surgery to correct trichiasis is a key component of the World Health Organisation trachoma control strategy, however unfavourable outcomes such as eyelid contour abnormalities (ECA) following surgery are relatively common. This study aimed to understand the transcriptional changes associated with the early development of ECA and the impact of doxycycline, which has anti-inflammatory and anti-fibrotic properties, upon these transcription patterns. Methods: One thousand Ethiopians undergoing trichiasis surgery were enrolled in a randomised controlled trial following informed consent. Equal groups of randomly assigned individuals were orally administered with 100mg/day of doxycycline (n=499) or placebo (n=501) for 28 days. Conjunctival swabs were collected immediately prior to surgery and at one- and six-months post-surgery. 3’ mRNA sequencing was performed on paired baseline and one-month samples from 48 individuals; 12 in each treatment/ECA outcome group. qPCR validation was then performed for 46 genes of interest in 145 individuals who developed ECA at one month and 145 matched controls, using samples from baseline, one and six months. Results: All treatment/outcome groups upregulated genes associated with wound healing pathways at one month relative to baseline, however no individual differences were detected between groups. The summed expression of a highly coexpressed cluster of pro-fibrotic genes was higher in patients that developed ECA in the placebo group relative to controls. qPCR validation revealed that all genes in this cluster and a number of other pro-inflammatory genes were strongly associated with ECA, however these associations were not modulated by trial arm. Conclusions: The development of post-operative ECA is associated with overexpression of pro-inflammatory and pro-fibrotic genes including growth factors, matrix metalloproteinases, collagens and extracellular matrix proteins. There was no evidence that doxycycline modulated the association between gene expression and ECA.

Atlas of ACE2 gene expression reveals novel insights into transmission of SARS-CoV-2

“…Transcriptome data from 191 RNA-seq experiments (whole transcriptome shotgun sequencing) was collected from publicly available sources. Briefly, human data was from the GTEx (Genotype-Tissue Expression) project [ 34 ], ENCODE (ENCyclopedia Of DNA Elements) project [ 35 , 36 ], and [ 37 ]; bat data was from [ 38 ]; pangolin data was from [ 39 ] and [ 40 ]; cat data was from 99 Lives Cat Genome Sequencing Initiative project; dog data was from [ 41 , 42 ] and [ 43 ]; ferret and rabbit data was from [ 44 ]; hamster and goat data was from [ 45 ]; cow data was from [ 46 ]; pig data was from [ 47 ]; and tiger data was from [ 48 ]. Detailed information on data sources, including the accession numbers and tissues for each species, was listed in Supplementary Table S2.…”

High expression of SARS-CoV2 viral entry-related proteins in human limbal stem cells

“…Given the importance of the eye transcription factor PAX6 in orchestrating ocular gene expression, we hypothesized that PAX6 might play a role in regulating SARS-CoV2 entry protein expression by human limbal epithelial cells. To test this hypothesis, utilizing publicly available RNA-seq results (GSE135455) [ 27 ], we first examined the correlation between PAX6, TMPRSS2, and ACE2 mRNA expression in conjunctival swabs collected from 48 human patients. The analyses revealed a moderate negative correlation between PAX6 and TMPRSS2 mRNA expression (r = −0.58, p = 2e-5), while no significant correlation was observed between PAX6 and ACE2 expression (r = −0.26, p = 0.074) ( Supplementary Fig.…”