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Randomized Controlled Trial
. 2018 Nov;142(5):1479-1488.e12.
doi: 10.1016/j.jaci.2017.11.059. Epub 2018 Mar 2.

Systems Biology and in Vitro Validation Identifies Family With Sequence Similarity 129 Member A (FAM129A) as an Asthma Steroid Response Modulator

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Free PMC article
Randomized Controlled Trial

Systems Biology and in Vitro Validation Identifies Family With Sequence Similarity 129 Member A (FAM129A) as an Asthma Steroid Response Modulator

Michael J McGeachie et al. J Allergy Clin Immunol. .
Free PMC article

Abstract

Background: Variation in response to the most commonly used class of asthma controller medication, inhaled corticosteroids, presents a serious challenge in asthma management, particularly for steroid-resistant patients with little or no response to treatment.

Objective: We applied a systems biology approach to primary clinical and genomic data to identify and validate genes that modulate steroid response in asthmatic children.

Methods: We selected 104 inhaled corticosteroid-treated asthmatic non-Hispanic white children and determined a steroid responsiveness endophenotype (SRE) using observations of 6 clinical measures over 4 years. We modeled each subject's cellular steroid response using data from a previously published study of immortalized lymphoblastoid cell lines under dexamethasone (DEX) and sham treatment. We integrated SRE with immortalized lymphoblastoid cell line DEX responses and genotypes to build a genome-scale network using the Reverse Engineering, Forward Simulation modeling framework, identifying 7 genes modulating SRE.

Results: Three of these genes were functionally validated by using a stable nuclear factor κ-light-chain-enhancer of activated B cells luciferase reporter in A549 human lung epithelial cells, IL-1β cytokine stimulation, and DEX treatment. By using small interfering RNA transfection, knockdown of family with sequence similarity 129 member A (FAM129A) produced a reduction in steroid treatment response (P < .001).

Conclusion: With this systems-based approach, we have shown that FAM129A is associated with variation in clinical asthma steroid responsiveness and that FAM129A modulates steroid responsiveness in lung epithelial cells.

Keywords: FAM129A; Inhaled corticosteroids; Reverse Engineering, Forward Simulation modeling; genomics; steroid response endophenotype; systems biology.

Conflict of interest statement

Statement of Competing Interests: BH, KR, BC, and IK are employed by GNS Healthcare which developed the REFS methodology.

Figures

Figure 1
Figure 1
Study Design Diagram. We used 104 participants of the CAMP clinical trial all randomized to the budesonide ICS treatment arm. Each was assessed along 6 longitudinal measures of steroid treatment for the duration of the original CAMP trial (4 years) to obtain their Steroid Responsiveness Endophenotype (SRE) value, measuring the effectiveness of ICS therapy at managing asthma. These subjects further provided blood samples which were immortalized and treated with both a steroid, Dexamethasone, and a sham treatment. LCL DEX response and genome-wide SNPs from these participants were used in the REFS network modeling framework to identify a number of genes that interacted with SRE. Three of these seven genes were validated in lung epithelial cell lines, and FAM129A was shown to be significantly associated with IL1B under steroid treatment.
Figure 2
Figure 2
Interaction network of Gene-SNP-phenotype associations for SRE. A plot of the interaction network SRE subgraph taken from the second ensemble of 256 REFs networks. Vertex type is indicated by: red star = SRE,. blue circle = gene, and green square = SNP. In the network, genes are seen to play a major role, and SNPs a minor role. The size of symbols is proportional to the number of edges incident on the vertex. The sizes of SRE and SNPs are exaggerated by factor of 3 and 2 respectively for readability. Vertices are located using multidimensional scaling of the network shortest path matrix using the R igraph layout_with_multidimentional function.
Figure 3
Figure 3
Gene neighborhoods from the second REFS Interaction Network. Vertex type is indicated by: red star = SRE, circle = gene. Neighborhoods, indicated by colored outlines, were determined as described in Methods. Symbol size is proportional to the number of all interaction network edges incident on the vertex, some of which may not be shown. The figure was plotted using the Kamada-Kawai layout algorithm. SRE appears in a central location as a result of the neighborhood and layout selection.
Figure 4
Figure 4
Neighborhood of the FAM129A gene, a direct neighbor of SRE. This shows that action of FAM129A on SRE is likely mediated by a number of genes including AGO2 and RAD21. Edge width is proportional to, and edges are labeled with, the proportion of the 256 ensemble networks that contain the edge. Vertex type is indicated by: red star = SRE, circle = gene. The FAM129A neighborhood, indicated by the colored outline, was determined as described in Methods. Symbol size is proportional to the number of all interaction network edges incident on the vertex, some of which may not be shown. The figure was plotted using the same layout as Figure 2.
Figure 5
Figure 5
Effects of FAM129A on NFκB activation and anti-inflammation effect of glucocorticoid. (A) A549/NFκB-Luc cells were transfected with non-targeting (NT) siRNA or siRNA targeting FAM129A, and 88 h later mRNA levels of FAM129A gene were measured using qPCR and normalized to the level in control siRNA transfected cells. (B) A549/NFκB-Luc cells were transfected with siRNA as in (A). 72 h after transfection, cells were treated with 5 ng/mL IL1β for 16h. The luciferase (Luc) activity was measured and normalized with the amount of total protein. The Luc level was shown relative to that of untreated NT siRNA transfected cells. (C) In the same experiment as shown in (B), additional groups of cells were treated with 5 ng/mL IL1β+100 nM DEX and the Luc level normalized with that upon 5 ng/mL IL1β treatment to determine the percentage values shown. **, P<0.01; ***, P<0.005.

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