Genetic and Transcriptomic Variation Linked to Neutrophil Granulocyte–Macrophage Colony-Stimulating Factor Signaling in Pediatric Crohn’s Disease

Abstract

Background: Granulocyte-macrophage colony-stimulating factor auto-antibodies (GMAbs) suppress neutrophil-extrinsic GM-CSF signaling and increase risk for stricturing behavior in Crohn's disease (CD). We aimed to define clinical, genomic, and functional associations with neutrophil-intrinsic GM-CSF signaling. Methods:Missense mutations in CSF2RA, CSF2RB, JAK2, STAT5A, and STAT5B were identified using whole-exome sequencing in 543 pediatric inflammatory bowel disease (IBD) patients. Neutrophil-intrinsic GM-CSF signaling was defined using the GM-CSF-induced STAT5 stimulation index (GMSI) in 180 pediatric IBD patients and 26 non-IBD controls. Reduced GM-CSF signaling (GMSI-Lo) was defined as the 20th percentile within the control group. Variation in neutrophil phospho-protein abundance, bacterial killing, and the global pattern of gene expression with the GMSI was determined. Results:We validated 18 potentially damaging missense mutations in CSF2RA and CSF2RB. CSF2RA A17G carriage increased from 10% in those with intact neutrophil GMSI to 32% in those with low GMSI (P = 0.02). Conflicts of interest:The authors have no financial arrangements with any company whose product figures prominently in the submitted manuscript or with a company making a competing product. Dr. Denson has received grant support from Janssen and holds a patent for the use of GM-CSF auto-antibodies as a diagnostic doi: 10.1093/ibd/izy265 Published online 13 August 2018 test in inflammatory bowel disease. Dr. Dubinsky has served as a consultant for Abbvie, Takeda, Janssen, and Pfizer and has received research support from Abbvie, Janssen, and Prometheus. Dr. Guthery has received research support in the last year from Regeneron Pharmaceuticals. Dr. Leleiko or his immediate family have equity interests in Celgene, Vericel, Ionis, Vertex, and Alnylam, and he has served as a consultant for CRICO. The remaining authors have nothing to declare. 2Denson et al from 17% in those with intact neutrophil GMSI to 35% in GMSI-Lo neutrophils (P = 0.043). Crohn's disease neutrophils with low GMSI exhibited specific alterations in phospho-protein networks and genes regulating cytokine production, wound healing, and cell survival and proliferation. Stricturing behavior increased from 7% in patients with both low GMAb and intact GMSI to 64% in patients with both elevated GMAb and low GMSI (P < 0.0001).Conclusions: Low/normal neutrophil-intrinsic GM-CSF signaling is associated with CSF2RA missense mutations, alterations in gene expression networks, and higher rates of disease complications in pediatric CD.

NOD2 modulates immune tolerance via the GM-CSF–dependent generation of CD103+dendritic cells

“…With the maintenance of this balance in mind, it may be the case that the GM-CSF signaling pathway is an outright hallmark of CD, as multiple studies have reported that mutations in the GM-CSF receptor genes CSF2RA and CSF2RB themselves represent genetic risk factors for developing the disease (21,22,55). Moreover, autoantibodies capable of neutralizing free circulating GM-CSF are increased 5-to 30-fold in CD patients, resulting in an impairment of the GM-CSF signaling pathway (56,57).…”

<p>GM-CSF: A Promising Target in Inflammation and Autoimmunity</p>

“…42 In line with a potential beneficial role of GM-CSF in IBD, GM-CSF administration can improve IBD experimentally 153 and in some patients; 152 , 154 also, high levels of circulating anti-GM-CSF autoantibodies have been found to correlate with worse CD prognosis. 155 , 156 …”

Neutrophil GM-CSF signaling in inflammatory bowel disease patients is influenced by non-coding genetic variants

“…An increase in GM-CSF auto-antibodies (GMAb) that suppress GM-CSF:STAT5 signaling has been associated with neutrophil dysfunction in pediatric and adult CD patients 4,5 . Recently, using peripheral blood samples of 543 pediatric IBD patients and whole exome sequencing (WES), we tested for association between coding variants and the GM-CSF:STAT5 signaling pathway in neutrophils, and disease complications 6 . We identified coding variants in highly conserved sites in the GM-CSF signaling genes CSF2RA , CSF2RB , JAK2 , STAT5A and STAT5B 6 .…”

“…Recently, using peripheral blood samples of 543 pediatric IBD patients and whole exome sequencing (WES), we tested for association between coding variants and the GM-CSF:STAT5 signaling pathway in neutrophils, and disease complications 6 . We identified coding variants in highly conserved sites in the GM-CSF signaling genes CSF2RA , CSF2RB , JAK2 , STAT5A and STAT5B 6 . In particular, we observed that patients with low neutrophil GM-CSF induced STAT5 stimulation index (low GMSI) carry more damaging missense mutations and have a reduced ability of neutrophils to kill Staph Aureus.…”

“…To test our hypothesis that non-coding variants are implicated in GMSI levels, we recruited CD and UC patients on the basis on their GMSI level and performed WGS to comprehensive variant identification genetic variants. We also attempted to replicate variants previously associated with neutrophil GMSI signaling in pediatric CD 6 .…”