TY - JOUR
T1 - Gene expression pathways across multiple tissues in antineutrophil cytoplasmic antibody-associated vasculitis reveal core pathways of disease pathology
AU - Friedman, Marcia A.
AU - Choi, Dongseok
AU - Planck, Stephen
AU - Rosenbaum, James T.
AU - Sibley, Cailin
N1 - Publisher Copyright:
© 2019 Journal of Rheumatology. All rights reserved.
PY - 2019
Y1 - 2019
N2 - Objective. To identify commonalities in gene expression data across all antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) tissues thus far characterized. Methods. Gene expression data were collected from the 3 AAV tissues thus far characterized (orbit, peripheral leukocytes, and sinus brushings). These data were analyzed to identify commonly expressed genes and disease pathways. The pathways data were adjusted for multiple comparisons using a combined local false discovery rate, which estimates the probability of a false discovery of a given pathway in all 3 tissues analyzed. Results. Only 4 genes were upregulated in all 3 tissues - IL1RN, TLR2, SLC11A1, and MMP9. After multiple comparison adjustments, the network pathway analysis revealed 28 pathways associated with all 3 tissues. The most strongly associated pathway for all 3 tissues was the neutrophil degranulation pathway [multidimensional local false discovery (md-locfdr) = 1.05 × 10-12], followed by the osteoclast differentiation (md-locfdr = 3.8 × 10-05), cell surface interactions at the vascular wall (md-locfdr = 4.2 × 10-04), signaling by interleukins (md-locfdr = 6.1 × 10-04), and phagosome (md-locfdr = 0.003) pathways. There were no downregulated genes or pathways common to all 3 tissues. Conclusion. This analysis identified individual genes and pathways of disease common to all AAV tissues thus far characterized. The use of a network pathway analysis allowed us to identify pathologic mechanisms that were not readily apparent in the commonly expressed genes alone. Many of these pathways are consistent with current theories about infectious drivers and the crossroads of innate and adaptive immune mechanisms. In addition, this analysis highlights novel pathways, such as vessel wall interactions and platelet activation, which require further investigation.
AB - Objective. To identify commonalities in gene expression data across all antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) tissues thus far characterized. Methods. Gene expression data were collected from the 3 AAV tissues thus far characterized (orbit, peripheral leukocytes, and sinus brushings). These data were analyzed to identify commonly expressed genes and disease pathways. The pathways data were adjusted for multiple comparisons using a combined local false discovery rate, which estimates the probability of a false discovery of a given pathway in all 3 tissues analyzed. Results. Only 4 genes were upregulated in all 3 tissues - IL1RN, TLR2, SLC11A1, and MMP9. After multiple comparison adjustments, the network pathway analysis revealed 28 pathways associated with all 3 tissues. The most strongly associated pathway for all 3 tissues was the neutrophil degranulation pathway [multidimensional local false discovery (md-locfdr) = 1.05 × 10-12], followed by the osteoclast differentiation (md-locfdr = 3.8 × 10-05), cell surface interactions at the vascular wall (md-locfdr = 4.2 × 10-04), signaling by interleukins (md-locfdr = 6.1 × 10-04), and phagosome (md-locfdr = 0.003) pathways. There were no downregulated genes or pathways common to all 3 tissues. Conclusion. This analysis identified individual genes and pathways of disease common to all AAV tissues thus far characterized. The use of a network pathway analysis allowed us to identify pathologic mechanisms that were not readily apparent in the commonly expressed genes alone. Many of these pathways are consistent with current theories about infectious drivers and the crossroads of innate and adaptive immune mechanisms. In addition, this analysis highlights novel pathways, such as vessel wall interactions and platelet activation, which require further investigation.
KW - Antineutrophil Cytoplasmic Antibody-associated Vasculitis
KW - Gene Expression
KW - Granulomatosis With Polyangiitis
KW - Metaanalysis
KW - Microscopic Polyangiitis
KW - Vasculitis
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U2 - 10.3899/jrheum.180455
DO - 10.3899/jrheum.180455
M3 - Article
C2 - 30647166
AN - SCOPUS:85066755682
SN - 0315-162X
VL - 46
SP - 609
EP - 615
JO - Journal of Rheumatology
JF - Journal of Rheumatology
IS - 6
ER -