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Updated: Jun 26, 2026
Gene Expression Profiling of Infecting Microbes Using a Digital Bar-coding Platform
Published on: January 13, 2016
Gene expression differences in infected and noninfected middle ear complementary DNA libraries
Joseph E Kerschner1, Edward Horsey, Azad Ahmed
1Department of Otolaryngology and Communications Disorders, Children's Hospital of Wisconsin, 9000 W Wisconsin Ave, Milwaukee, WI 53226, USA. kersch@mcw.edu
Objectives:
To investigate genetic differences in middle ear mucosa (MEM) with nontypeable Haemophilus influenzae (NTHi) infection. Genetic upregulation and downregulation occurs in MEM during otitis media (OM) pathogenesis. A comprehensive assessment of these genetic differences using the techniques of complementary DNA (cDNA) library creation has not been performed.
Design:
The cDNA libraries were constructed from NTHi-infected and noninfected chinchilla MEM. Random clones were picked, sequenced bidirectionally, and submitted to the National Center for Biotechnology Information (NCBI) Expressed Sequence Tags database, where they were assigned accession numbers. These numbers were used with the basic local alignment search tool (BLAST) to align clones against the nonredundant nucleotide database at NCBI.
Results:
Analysis with the Web-based statistical program FatiGO identified several biological processes with significant differences in numbers of represented genes. Processes involved in immune, stress, and wound responses were more prevalent in the NTHi-infected library. S100 calcium-binding protein A9 (S100A9); secretory leukoprotease inhibitor (SLPI); beta(2)-microglobulin (B2M); ferritin, heavy-chain polypeptide 1 (FTH1); and S100 calcium-binding protein A8 (S100A8) were expressed at significantly higher levels in the NTHi-infected library. Calcium-binding proteins S100A9 and S100A8 serve as markers for inflammation and have antibacterial effects. Secretory leukoprotease inhibitor is an antibacterial protein that inhibits stimuli-induced MUC1, MUC2, and MUC5AC production.
Conclusions:
A number of genes demonstrate changes during the pathogenesis of OM, including SLPI, which has an impact on mucin gene expression; this expression is known to be an important regulator in OM. The techniques described herein provide a framework for future investigations to more thoroughly understand molecular changes in the middle ear, which will likely be important in developing new therapeutic and intervention strategies.
Insights
This study reveals genetic changes in middle ear mucosa during nontypeable Haemophilus influenzae (NTHi) infection. Key genes involved in immune and stress responses were upregulated, offering insights into otitis media pathogenesis.
Area of Science:
- Microbiology
- Genetics
- Immunology
Background:
- Nontypeable Haemophilus influenzae (NTHi) is a common cause of otitis media (OM).
- Genetic changes in middle ear mucosa (MEM) during OM pathogenesis are not fully understood.
- Previous comprehensive assessments of genetic differences in NTHi-infected MEM are lacking.
Purpose of the Study:
- To investigate genetic differences in MEM during NTHi infection.
- To identify specific genes and biological processes affected by NTHi infection in the middle ear.
- To establish a framework for understanding molecular changes in OM.
Main Methods:
- Construction of complementary DNA (cDNA) libraries from NTHi-infected and noninfected chinchilla MEM.
- Sequencing of random cDNA clones and submission to NCBI Expressed Sequence Tags database.
- Analysis of gene expression differences using BLAST and FatiGO to identify significant biological processes.
Main Results:
- Significant differences in gene expression were identified between infected and noninfected MEM.
- Biological processes related to immune, stress, and wound responses were more prevalent in NTHi-infected MEM.
- Upregulation of genes such as S100A9, SLPI, B2M, FTH1, and S100A8 was observed in NTHi-infected MEM.
Conclusions:
- Gene expression changes, including SLPI, occur during OM pathogenesis and impact mucin production.
- Identified genes like SLPI play a role in regulating OM.
- The study provides a foundation for future research into middle ear molecular changes and therapeutic strategies for OM.
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