Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources

Abstract

BackgroundGene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on single studies. Using the program Pointillist, we performed meta-analysis of transcription-profiling data from six independent studies of infections with mammary gland pathogens, including samples from cattle challenged in vivo with S. aureus, E. coli, and S. uberis, samples from goats challenged in vivo with S. aureus, as well as cattle macrophages and ovine dendritic cells infected in vitro with S. aureus. We combined different time points from those studies, testing different responses to mastitis infection: overall (common signature), early stage, late stage, and cattle-specific.ResultsIngenuity Pathway Analysis of affected genes showed that the four meta-analysis combinations share biological functions and pathways (e.g. protein ubiquitination and polyamine regulation) which are intrinsic to the general disease response. In the overall response, pathways related to immune response and inflammation, as well as biological functions related to lipid metabolism were altered. This latter observation is consistent with the milk fat content depression commonly observed during mastitis infection. Complementarities between early and late stage responses were found, with a prominence of metabolic and stress signals in the early stage and of the immune response related to the lipid metabolism in the late stage; both mechanisms apparently modulated by few genes, including XBP1 and SREBF1.The cattle-specific response was characterized by alteration of the immune response and by modification of lipid metabolism. Comparison of E. coli and S. aureus infections in cattle in vivo revealed that affected genes showing opposite regulation had the same altered biological functions and provided evidence that E. coli caused a stronger host response.ConclusionsThis meta-analysis approach reinforces previous findings but also reveals several novel themes, including the involvement of genes, biological functions, and pathways that were not identified in individual studies. As such, it provides an interesting proof of principle for future studies combining information from diverse heterogeneous sources.

Response of the goat mammary gland to infection with Staphylococcus aureus revealed by gene expression profiling in milk somatic and white blood cells

“…Meta-analysis approaches are used to combine or integrate information from independent studies to overcome low statistical power in studies and identify common results to increase confidence in the generality of information [22]. In the present study meta-analysis was used to combine information across samples and time-points, which identified 17 differentially expressed genes (Figure 5) which are involved in five pathways.…”

“…The application of these approaches for dairy ruminants transcriptome profiling has identified genes, pathways and regulatory networks activated in mammary tissues during experimental infection by various pathogens, including E. coli , S. aureus and S. uberis [10,17-21]. The meta-analysis of transcription-profiling data from six independent studies of the mammary gland infected with different pathogens identified common signatures of infection among species and that were characteristic of early vs late stage responses [22]. …”

A proteomic perspective on the changes in milk proteins due to high somatic cell count

“…The ratios of common proteins and immune-related proteins between samples at different SCC levels (SCC1 = <10 5 cells/mL; SCC2 = 2.5 × 10 5 cells/mL; SCC3 = 4 × 10 5 cells/mL; SCC4 = 7.5 × 10 5 cells/mL; SCC5 = 10 6 cells/mL) from cows with mastitis (Moyes et al, 2009;Huang et al, 2014). These changes in concentration of cellular function proteins were related to the immune response to mastitis infection (Genini et al, 2011). Because the complement regulatory protein CD59 can protect the mammary gland from overactivated complement medi- Figure 3.…”

Escherichia coli- and Staphylococcus aureus-induced mastitis differentially modulate transcriptional responses in neighbouring uninfected bovine mammary gland quarters

“…A direct comparison of the induced transcriptional responses identified in these studies is difficult because of differences in the experimental design and the microarray platforms used. However, meta-analyses of such transcriptional studies have recently been reported [8,9]. The meta-analysis reported by Genini et al [8] identified a common transcriptional response in the mammary glands of several species to different pathogens and identified several new pathways not previously identified in the individual studies.…”

“…However, meta-analyses of such transcriptional studies have recently been reported [8,9]. The meta-analysis reported by Genini et al [8] identified a common transcriptional response in the mammary glands of several species to different pathogens and identified several new pathways not previously identified in the individual studies. However, a considerable amount of information was excluded from this meta-analysis because of the limited overlap of probes included on the microarrays used in the original studies.…”