IgA and IgG antineutrophil cytoplasmic antibody engagement of Fc receptor genetic variants influences granulomatosis with polyangiitis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Authors: Kelley, James M.; Monach, Paul A.; Ji, Chuanyi; Zhou, Yebin; Wu, Jianming; Tanaka, Sumiaki; Mahr, Alfred D.; Johnson, Sharleen; McAlear, Carol; Cuthbertson, David; Carette, Simon; Davis, John C., Jr.; Dellaripa, Paul F.; Hoffman, Gary S.; Khalidi, Nader; Langford, Carol A.; Seo, Phillip; St Clair, E. William; Specks, Ulrich; Stone, John H.; Spiera, Robert F.; Ytterberg, Steven R.; Merkel, Peter A.; Edberg, Jeffrey C.; Kimberly, Robert P.
Abstract
Granulomatosis with polyangiitis (Wegener's) is a rare autoimmune neutrophil-mediated vasculitis that can cause renal disease and mucosal manifestations. Antineutrophil cytoplasmic antibodies (ANCA) are present in many patients, vary in level over time, and induce neutrophil activation through engagement with Fc receptors (FcRs). Given roles for FcRs in ANCA-mediated neutrophil activation and IgA antibodies in mucosal immunity, we hypothesized that FcR genetics and previously unappreciated IgA ANCA affect clinical presentation. We assembled a total of 673 patients and 413 controls from two multicenter cohorts, performed ELISA and immunofluorescence assays to determine IgA and IgG ANCA positivity, and used Illumina, TaqMan, or Pyrosequencing to genotype eight haplotype-tagging SNPs in the IgA FcR (FCAR) and to determine NA1/NA2 genotype of FCGR3B, the most prevalent neutrophil IgG FcR. We evaluated neutrophil activation by measuring degranulation marker CD11b with flow cytometry or neutrophil extracellcular trap formation with confocal microscopy. Functional polymorphisms in FCGR3B and FCAR differed between patient groups stratified by renal involvement. IgA ANCA were found in similar to 30% of patients and were less common in patients with severe renal disease. Neutrophil stimulation by IgA or IgG ANCA led to degranulation and neutrophil extracellcular trap formation in a FcR allele-specific manner (IgA: FCAR P = 0.008; IgG: FCGR3B P = 0.003). When stimulated with IgA and IgG ANCA together, IgG ANCA induced neutrophil activation was reduced (P = 0.0001). FcR genotypes, IgA ANCA, and IgG ANCA are potential prognostic and therapeutic targets for understanding the pathogenesis and presentation of granulomatosis with polyangiitis (Wegener's).
Detecting SNP-expression associations: A comparison of mutual information and median test with standard statistical approaches
STATISTICS IN MEDICINE
Authors: Szymczak, S.; Igl, B. -W.; Ziegler, A.
Abstract
Single nucleotide polymorphism-gene expression associations have received increasing interest. The aim of these studies is discovering a difference in the location parameters of gene expressions given genotype. Because gene expressions often are highly skewed, heavy-tailed or data of different genotypes vary in dispersion, the median is the most appropriate measure of location. In this case, model assumptions of standard statistical methods for comparing locations such as the analysis of variance (ANOVA) or the Kruskal-Wallis (KW) test are violated. Alternatives that might be more appropriate are the median test (MED) and tests based on mutual information (MI). In simulation studies these approaches and a novel MI test are compared with ANOVA and KW. Location, dispersion and skewness parameters of the gene expression distributions given genotypes are varied as well as genotype frequencies. The MED test and the novel MI-based method keep the nominal significance levels for comparing medians if gene expression data are non-normally distributed. ANOVA and KW have substantially inflated type I errors. They are, however, optimal if standard model assumptions are fulfilled. The MED test generally has larger power than MI and is therefore recommended if model assumptions of standard procedures are violated. A 300 kb region on chromosome 9p21.3, which is associated with coronary artery disease, was analyzed using the HapMap data. Only the alternative approaches were able to identify three genes (ADM, FCGR3B and ADORA1) as promising candidates to clarify the molecular mechanism of the genetic association. Copyright (C) 2009 John Wiley & Sons, Ltd.