Transcriptional profiling specifies the pathogen-specific human host response to infectious keratitis

Front Cell Infect Microbiol. 2024 Jan 11:13:1285676. doi: 10.3389/fcimb.2023.1285676. eCollection 2023.

Abstract

Purpose: Corneal infections are a leading cause of visual impairment and blindness worldwide. Here we applied high-resolution transcriptomic profiling to assess the general and pathogen-specific molecular and cellular mechanisms during human corneal infection.

Methods: Clinical diagnoses of herpes simplex virus (HSV) (n=5) and bacterial/fungal (n=5) keratitis were confirmed by histology. Healthy corneas (n=7) and keratoconus (n=4) samples served as controls. Formalin-fixed, paraffin-embedded (FFPE) human corneal specimens were analyzed using the 3' RNA sequencing method Massive Analysis of cDNA Ends (MACE RNA-seq). The cellular host response was investigated using comprehensive bioinformatic deconvolution (xCell and CYBERSORTx) analyses and by integration with published single cell RNA-seq data of the human cornea.

Results: Our analysis identified 216 and 561 genes, that were specifically overexpressed in viral or bacterial/fungal keratitis, respectively, and allowed to distinguish the two etiologies. The virus-specific host response was driven by adaptive immunity and associated molecular signaling pathways, whereas the bacterial/fungal-specific host response mainly involved innate immunity signaling pathways and cell types. We identified several genes and pathways involved in the host response to infectious keratitis, including CXCL9, CXCR3, and MMP9 for viral, and S100A8/A9, MMP9, and the IL17 pathway for bacterial/fungal keratitis.

Conclusions: High-resolution molecular profiling provides new insights into the human corneal host response to viral and bacterial/fungal infection. Pathogen-specific molecular profiles may provide the foundation for novel diagnostic biomarker and therapeutic approaches that target inflammation-induced damage to corneal host cells with the goal to improve the outcome of infectious keratitis.

Keywords: FFPE (formalin fixed paraffin embedded); RNA sequencing; bacterial keratitis; host response; human corneal tissue; infectious keratitis; keratoplasty; viral keratitis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cornea / microbiology
  • Cornea / pathology
  • Corneal Ulcer*
  • Eye Infections, Bacterial*
  • Eye Infections, Fungal*
  • Humans
  • Inflammation / pathology
  • Keratitis* / diagnosis
  • Keratitis* / genetics
  • Matrix Metalloproteinase 9

Substances

  • Matrix Metalloproteinase 9

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research is funded by a grant from the Ernst-und-Berta-Grimmke-Stiftung (Germany) to PK and by a grant from the Freunde der Universitäts-Augenklinik Freiburg e.V. Foundation (Germany) to TL. We acknowledge support by the Open Access Publication Fund of the University of Freiburg.