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Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection.

Hassan MA, Jensen KD, Butty V, Hu K, Boedec E, Prins P, Saeij JP - PLoS Genet. (2015)

Bottom Line: However, the potential role that differences in macrophage activation phenotypes play in modulating differences in susceptibility to infectious and inflammatory disease is just emerging.We show that specific transcriptional programs, defined by distinct genomic loci, modulate macrophage activation phenotypes.Our results provide a template for discovering candidate genes that modulate macrophage-mediated complex traits.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

ABSTRACT
Macrophages display flexible activation states that range between pro-inflammatory (classical activation) and anti-inflammatory (alternative activation). These macrophage polarization states contribute to a variety of organismal phenotypes such as tissue remodeling and susceptibility to infectious and inflammatory diseases. Several macrophage- or immune-related genes have been shown to modulate infectious and inflammatory disease pathogenesis. However, the potential role that differences in macrophage activation phenotypes play in modulating differences in susceptibility to infectious and inflammatory disease is just emerging. We integrated transcriptional profiling and linkage analyses to determine the genetic basis for the differential murine macrophage response to inflammatory stimuli and to infection with the obligate intracellular parasite Toxoplasma gondii. We show that specific transcriptional programs, defined by distinct genomic loci, modulate macrophage activation phenotypes. In addition, we show that the difference between AJ and C57BL/6J macrophages in controlling Toxoplasma growth after stimulation with interferon gamma and tumor necrosis factor alpha mapped to chromosome 3, proximal to the Guanylate binding protein (Gbp) locus that is known to modulate the murine macrophage response to Toxoplasma. Using an shRNA-knockdown strategy, we show that the transcript levels of an RNA helicase, Ddx1, regulates strain differences in the amount of nitric oxide produced by macrophage after stimulation with interferon gamma and tumor necrosis factor. Our results provide a template for discovering candidate genes that modulate macrophage-mediated complex traits.

No MeSH data available.


Related in: MedlinePlus

The transcriptional response in BMDM is regulated by stimulation-specific trans-loci.Expression quantitative trait loci (eQTL) in the RI mice were mapped in A) non-stimulated, B) IFNG+TNF-stimulated, C) Toxoplasma-infected, and D) CpG-Stimulated BMDM. Each dot represents a single eQTL (transcript). Significant eQTL located ≤ 10 Mb from the start of the physical location of the corresponding gene were designated as cis mapping (diagonal lines). All other eQTL were designated as trans-mapping (vertical lines). eQTL significance was calculated after 1000 permutations and reported at genome-wide thresholds corresponding to FDR ≤ 10%. Red spots identify genes mapping to a trans-eQTL hotpot (trans-band).
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pgen.1005619.g002: The transcriptional response in BMDM is regulated by stimulation-specific trans-loci.Expression quantitative trait loci (eQTL) in the RI mice were mapped in A) non-stimulated, B) IFNG+TNF-stimulated, C) Toxoplasma-infected, and D) CpG-Stimulated BMDM. Each dot represents a single eQTL (transcript). Significant eQTL located ≤ 10 Mb from the start of the physical location of the corresponding gene were designated as cis mapping (diagonal lines). All other eQTL were designated as trans-mapping (vertical lines). eQTL significance was calculated after 1000 permutations and reported at genome-wide thresholds corresponding to FDR ≤ 10%. Red spots identify genes mapping to a trans-eQTL hotpot (trans-band).

Mentions: Next, using the FPKM values from each of the 26 RI BMDM and the corresponding AXB/BXA genetic map, we mapped the genomic loci that modulate gene expression (expression QTL, eQTL) [32] using R/qtl [57]. As previously described [25], we performed 1000 permutations to correct for multiple testing across the 934 informative genetic markers in the AXB/BXA cross. Next, we used a false discovery rate (FDR) ≤ 10%, calculated in the qvalue package [70], to correct for multiple testing on the transcripts and to nominate significant eQTL. Finally, to allow for meaningful comparisons, we only included in the downstream analyses, for each stimulation condition, eQTL for transcripts with an average FPKM ≥ 5 across the 26 RI BMDM. The linkage analyses and the subsequent filtering steps were performed separately in resting, IFNG+TNF-stimulated, CpG-stimulated, and Toxoplasma-infected BMDM and identified, 131, 367, 688 and 1008 significant eQTL, respectively, dispersed throughout the genome (Fig 2A and 2B and S1A–S1D Dataset). Thus, consistent with previous studies [24, 71], the genetic background influences macrophage gene expression profile. Importantly the different stimuli induced transcriptional programs that were modulated by distinct eQTL hotspots, which can be exploited to unravel the complex molecular networks that regulate macrophage activation states.


Transcriptional and Linkage Analyses Identify Loci that Mediate the Differential Macrophage Response to Inflammatory Stimuli and Infection.

Hassan MA, Jensen KD, Butty V, Hu K, Boedec E, Prins P, Saeij JP - PLoS Genet. (2015)

The transcriptional response in BMDM is regulated by stimulation-specific trans-loci.Expression quantitative trait loci (eQTL) in the RI mice were mapped in A) non-stimulated, B) IFNG+TNF-stimulated, C) Toxoplasma-infected, and D) CpG-Stimulated BMDM. Each dot represents a single eQTL (transcript). Significant eQTL located ≤ 10 Mb from the start of the physical location of the corresponding gene were designated as cis mapping (diagonal lines). All other eQTL were designated as trans-mapping (vertical lines). eQTL significance was calculated after 1000 permutations and reported at genome-wide thresholds corresponding to FDR ≤ 10%. Red spots identify genes mapping to a trans-eQTL hotpot (trans-band).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4625001&req=5

pgen.1005619.g002: The transcriptional response in BMDM is regulated by stimulation-specific trans-loci.Expression quantitative trait loci (eQTL) in the RI mice were mapped in A) non-stimulated, B) IFNG+TNF-stimulated, C) Toxoplasma-infected, and D) CpG-Stimulated BMDM. Each dot represents a single eQTL (transcript). Significant eQTL located ≤ 10 Mb from the start of the physical location of the corresponding gene were designated as cis mapping (diagonal lines). All other eQTL were designated as trans-mapping (vertical lines). eQTL significance was calculated after 1000 permutations and reported at genome-wide thresholds corresponding to FDR ≤ 10%. Red spots identify genes mapping to a trans-eQTL hotpot (trans-band).
Mentions: Next, using the FPKM values from each of the 26 RI BMDM and the corresponding AXB/BXA genetic map, we mapped the genomic loci that modulate gene expression (expression QTL, eQTL) [32] using R/qtl [57]. As previously described [25], we performed 1000 permutations to correct for multiple testing across the 934 informative genetic markers in the AXB/BXA cross. Next, we used a false discovery rate (FDR) ≤ 10%, calculated in the qvalue package [70], to correct for multiple testing on the transcripts and to nominate significant eQTL. Finally, to allow for meaningful comparisons, we only included in the downstream analyses, for each stimulation condition, eQTL for transcripts with an average FPKM ≥ 5 across the 26 RI BMDM. The linkage analyses and the subsequent filtering steps were performed separately in resting, IFNG+TNF-stimulated, CpG-stimulated, and Toxoplasma-infected BMDM and identified, 131, 367, 688 and 1008 significant eQTL, respectively, dispersed throughout the genome (Fig 2A and 2B and S1A–S1D Dataset). Thus, consistent with previous studies [24, 71], the genetic background influences macrophage gene expression profile. Importantly the different stimuli induced transcriptional programs that were modulated by distinct eQTL hotspots, which can be exploited to unravel the complex molecular networks that regulate macrophage activation states.

Bottom Line: However, the potential role that differences in macrophage activation phenotypes play in modulating differences in susceptibility to infectious and inflammatory disease is just emerging.We show that specific transcriptional programs, defined by distinct genomic loci, modulate macrophage activation phenotypes.Our results provide a template for discovering candidate genes that modulate macrophage-mediated complex traits.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Centre for Molecular Parasitology, University of Glasgow, Glasgow, United Kingdom; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

ABSTRACT
Macrophages display flexible activation states that range between pro-inflammatory (classical activation) and anti-inflammatory (alternative activation). These macrophage polarization states contribute to a variety of organismal phenotypes such as tissue remodeling and susceptibility to infectious and inflammatory diseases. Several macrophage- or immune-related genes have been shown to modulate infectious and inflammatory disease pathogenesis. However, the potential role that differences in macrophage activation phenotypes play in modulating differences in susceptibility to infectious and inflammatory disease is just emerging. We integrated transcriptional profiling and linkage analyses to determine the genetic basis for the differential murine macrophage response to inflammatory stimuli and to infection with the obligate intracellular parasite Toxoplasma gondii. We show that specific transcriptional programs, defined by distinct genomic loci, modulate macrophage activation phenotypes. In addition, we show that the difference between AJ and C57BL/6J macrophages in controlling Toxoplasma growth after stimulation with interferon gamma and tumor necrosis factor alpha mapped to chromosome 3, proximal to the Guanylate binding protein (Gbp) locus that is known to modulate the murine macrophage response to Toxoplasma. Using an shRNA-knockdown strategy, we show that the transcript levels of an RNA helicase, Ddx1, regulates strain differences in the amount of nitric oxide produced by macrophage after stimulation with interferon gamma and tumor necrosis factor. Our results provide a template for discovering candidate genes that modulate macrophage-mediated complex traits.

No MeSH data available.


Related in: MedlinePlus