Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis

Mikhail G Dozmorov,Michael B Centola,Robert E Hurst,Ricardo Saban,Kimberly D Kyker,Arto S Baghdayan,Nathan Shankar

doi:10.1186/1471-2105-8-s7-s2

Mikhail G Dozmorov, Michael B Centola + Show 5 more

Open Access

https://doi.org/10.1186/1471-2105-8-s7-s2

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Abstract

BackgroundTo better understand the response of urinary epithelial (urothelial) cells to Enterococcus faecalis, a uropathogen that exhibits resistance to multiple antibiotics, a genome-wide scan of gene expression was obtained as a time series from urothelial cells growing as a layered 3-dimensional culture similar to normal urothelium. We herein describe a novel means of analysis that is based on deconvolution of gene variability into technical and biological components.ResultsAnalysis of the expression of 21,521 genes from 30 minutes to 10 hours post infection, showed 9553 genes were expressed 3 standard deviations (SD) above the system zero-point noise in at least 1 time point. The asymmetric distribution of relative variances of the expressed genes was deconvoluted into technical variation (with a 6.5% relative SD) and biological variation components (>3 SD above the mode technical variability). These 1409 hypervariable (HV) genes encapsulated the effect of infection on gene expression. Pathway analysis of the HV genes revealed an orchestrated response to infection in which early events included initiation of immune response, cytoskeletal rearrangement and cell signaling followed at the end by apoptosis and shutting down cell metabolism. The number of poorly annotated genes in the earliest time points suggests heretofore unknown processes likely also are involved.ConclusionEnterococcus infection produced an orchestrated response by the host cells involving several pathways and transcription factors that potentially drive these pathways. The early time points potentially identify novel targets for enhancing the host response. These approaches combine rigorous statistical principles with a biological context and are readily applied by biologists.

Highlights

To better understand the response of urinary epithelial cells to Enterococcus faecalis, a uropathogen that exhibits resistance to multiple antibiotics, a genome-wide scan of gene expression was obtained as a time series from urothelial cells growing as a layered 3-dimensional culture similar to normal urothelium
Cell death occurs between 10 and 24 hours post infection Examination of cell layers infected with bacteria showed that little cell death occurred until 10 hours post infection, at which time cells began to die in significant numbers
The bacteria remained attached to the apical surface of the layer and no evidence for entry into cells was seen

Summary

Introduction

To better understand the response of urinary epithelial (urothelial) cells to Enterococcus faecalis, a uropathogen that exhibits resistance to multiple antibiotics, a genome-wide scan of gene expression was obtained as a time series from urothelial cells growing as a layered 3-dimensional culture similar to normal urothelium. In the case of the bladder, the highly specialized and multifunctional urothelium functions remarkably well to protect the host from urinary tract infections. Urothelial cells form a physical barrier against bacterial infection, trap bacteria in mucin and can desquamate, carrying the bacteria out of the bladder [4]. Urothelial cells mount their own immune response against pathogens [5]. The response of the urothelium to Escherichia coli has been investigated extensively at the molecular level [6,7], the response to gram positive organisms such as Enterococcus is poorly understood

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