Richard Ahn

Association Analysis of the Extended MHC Region in Celiac Disease Implicates Multiple Independent Susceptibility Loci

Celiac disease is a common autoimmune disease caused by sensitivity to the dietary protein gluten. Forty loci have been implicated in the disease. All disease loci have been characterized as low-penetrance, with the exception of the high-risk genotypes in the HLA-DQA1 and HLA-DQB1 genes, which are necessary but not sufficient to cause the disease. The very strong effects from the known HLA loci and the genetically complex nature of the major histocompatibility complex (MHC) have precluded a thorough investigation of the region. The purpose of this study was to test the hypothesis that additional celiac disease loci exist within the extended MHC (xMHC). A set of 1898 SNPs was analyzed for association across the 7.6 Mb xMHC region in 1668 confirmed celiac disease cases and 517 unaffected controls. Conditional recursive partitioning was used to create an informative indicator of the known HLA-DQA1 and HLA-DQB1 high-risk genotypes that was included in the association analysis to account for their effects. A linkage disequilibrium-based grouping procedure was utilized to estimate the number of independent celiac disease loci present in the xMHC after accounting for the known effects. There was significant statistical evidence for four new independent celiac disease loci within the classic MHC region. This study is the first comprehensive association analysis of the xMHC in celiac disease that specifically accounts for the known HLA disease genotypes and the genetic complexity of the region.

Genome-Wide Association Study of Celiac Disease in North America Confirms FRMD4B as New Celiac Locus

We performed a genome-wide association study (GWAS) of 1550 North American celiac disease cases and 3084 controls. Twelve SNPs, distributed across four regions (3p21.31, 4q27, 6q15, 6q25), were significantly associated with disease (p-value <1.0×10−7), and a further seven SNPs, across four additional regions (1q24.3, 10p15.1, 6q22.31, 17q21.32) had suggestive evidence (1.0×10−7 < p-value < 1.0×10−6). This study replicated a previous suggestive association within FRMD4B (3p14.1), confirming it as a celiac disease locus. All four regions with significant associations and two regions with suggestive results (1q24.3, 10p15.1) were known disease loci. The 6q22.31 and 10p11.23 regions were not replicated. A total of 410 SNPs distributed across the eight significant and suggestive regions were tested for association with dermatitis herpetiformis and microscopic colitis. Preliminary, suggestive statistical evidence for association with the two traits was found at chromosomes 3p21.31, 6q15, 6q25, 1q24.3 and 10p11.23, with future studies being required to validate the reported associations.

Meta-analysis of the TNFAIP3 region in psoriasis reveals a risk haplotype that is distinct from other autoimmune diseases

Tumor necrosis factor alpha-inducible protein 3 (TNFAIP3) encodes a ubiquitin-modifying protein, A20, that is a critical regulator of inflammatory responses. TNFAIP3 polymorphisms are associated with the susceptibility to multiple autoimmune diseases (AIDs) including psoriasis, systemic lupus erythematosus, rheumatoid arthritis, systemic sclerosis and celiac disease. In order to refine the TNFAIP3 association signal in psoriasis and identify candidate causal variants, we performed imputation and meta-analysis of the TNFAIP3 region in five European ancestry cohorts totaling 4704 psoriasis cases and 7805 controls. We identified 49 variants whose significance exceeded a corrected Bonferroni threshold, with the top variant being rs582757 (P=6.07 × 10−12, odds ratio (OR)=1.23). Conditional analysis revealed a suggestive independent association at rs6918329 (Pcond=7.22 × 10−5, OR=1.15). Functional annotation of the top variants identified several with a strong evidence of regulatory potential and several within long noncoding RNAs. Analysis of TNFAIP3 haplotypes revealed that the psoriasis risk haplotype is distinct from other AIDs. Overall, our findings identify novel candidate causal variants of TNFAIP3 in psoriasis and highlight the complex genetic architecture of this locus in autoimmune susceptibility.

End-of-Life Quality-of-Care Measures for Nursing Homes: Place of Death and Hospice

OBJECTIVE The Centers for Medicare and Medicaid Services (CMS) publishes a web-based quality report card for nursing homes. The quality measures (QMs) do not assess quality of end-of-life (EOL) care, which affects a large proportion of residents. This study developed prototype EOL QMs that can be calculated from data sources available for all nursing homes nationally. METHODS The study included approximately 1.5 million decedents residing in 16,000 nursing homes during 2003-2007, nationally. Minimum Data Set (MDS) data were linked to Medicare enrollment files, hospital claims, and hospice claims. Random effect logistic models were estimated to develop risk-adjustment models predicting two outcome measures (place of death [POD] and hospice enrollment), which were then used to construct two EOL QMs. The distributional properties of the QMs were investigated. RESULTS The QMs exhibited moderate stability over time. They were more stable in identifying quality outliers among the larger nursing homes and in identifying poor-quality outliers than high-quality outliers. CONCLUSIONS This study offers two QMs specialized to EOL care in nursing homes that can be calculated from data that are readily available and could be incorporated in the Nursing Home Compare (NHC) report card. Further work to validate the QMs is required.

Inhibitory KIR3DL1 alleles are associated with psoriasis.

DEAR EDITOR, Genetic association studies have implicated over 40 genetic loci in the pathogenesis of psoriasis, with the largest signal observed at the major histocompatibility complex (MHC) class I locus for human leucocyte antigen (HLA)-C. However, recent data also suggest a lesser but significant pathogenic role for HLA-B. Although both of these molecules participate in adaptive immunity through antigen presentation, they can also regulate the innate immune response through interaction with killer cell immunoglobulin-like receptors (KIRs) expressed on the surface of both natural killer cells and a subset of T cells. KIRs form a family of receptors encoded by a cluster of 14 genes on chromosome 19q13 4. They may encode activating or inhibitory receptors that bind the Bw4 motif on HLA-B or the C1/C2 motif on HLA-C. Previous studies have shown that the presence of activating KIR3DS1 and KIR2DS1 mutations is associated with increased susceptibility to psoriasis and psoriatic arthritis. These results are consistent with a model wherein expression of activating KIRs increases the risk of developing immune-mediated diseases. However, whether decreased expression of inhibitory KIRs is also associated with increased risk of psoriasis has not been fully explored. The inhibitory KIR3DL1 is among the most polymorphic of all KIR loci (http://www.ebi.ac.uk/ipd/kir/stats.html). Cellsurface expression of KIR3DL1 varies greatly between alleles, and alleles can be classified into three allotypes: KIR3DL1*NULL (no cell-surface expression: *004 and *019), KIR3DL1*LOW (low expression: *005, *007 and *053) and KIR3DL1*HIGH (high expression: *001, *002, *008, *009, *015, *020, *029 and *035). The ligand for KIR3DL1 is the Bw4 epitope present on several HLA-B molecules such as HLA-B*57, HLAB*27 and HLA-A*24. To investigate the association of KIR3DL1 and HLA-Bw4 with psoriasis, we carried out genotyping of KIR3DL1 and HLA-B in a cohort of 314 subjects (203 with psoriasis and 111 healthy controls) of European descent recruited from the U.S.A. Diagnosis of psoriasis was established by a dermatologist. The average age of onset of psoriasis was 19 years, 54% of patients were female, and approximately 23% were diagnosed with psoriatic arthritis. Controls were healthy volunteers without a history of autoimmune disease; their average age was 39 0 years and 51 4% were female. KIR3DL1 typing was performed by sequencing exons 3, 4, 5 and 9 of KIR3DL1. The primers and polymerase chain reaction (PCR) conditions are shown in Table S1 (see Supporting Information). KIR3DL1 alleles were called from the sequencing data using Assign software (Conexio Genomics, Fremantle, Australia). HLA typing of cases was performed as previously described. HLA typing of controls was performed with the PCR sequence-based typing method recommended by the 13th International Histocompatibility Workshop (http:// www.ihwg.org). HLA sequences were analysed using Assign software. In a minority of cases with missing HLA-B typing (n = 18), HLA-B genotypes were imputed with genome-wide association data (Appendix S1; see Supporting Information).

Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin

Human skin consists of multiple cell types, including epithelial, immune, and stromal cells. Transcriptomic analyses have previously been performed from bulk skin samples or from epithelial and immune cells expanded in cell culture. However, transcriptomic analysis of bulk skin tends to drown out expression signals from relatively rare cells while cell culture methods may significantly alter cellular phenotypes and gene expression profiles. To identify distinct transcriptomic profiles of multiple cell populations without substantially altering cell phenotypes, we employed a fluorescence activated cell sorting method to isolate keratinocytes, dendritic cells, CD4+ T effector cells, and CD8+ T effector cells from healthy skin samples, followed by RNA-seq of each cell population. Principal components analysis revealed distinct clustering of cell types across samples, while differential expression and coexpression network analyses revealed transcriptional profiles of individual cell populations distinct from bulk skin, most strikingly in the least abundant CD8+ T effector population. Our work provides a high resolution view of cutaneous cellular gene expression and suggests that transcriptomic profiling of bulk skin may inadequately capture the contribution of less abundant cell types.

A Case Study of Fixed-Effects and Random-Effects Meta-Analysis Models for Genome-Wide Association Studies in Celiac Disease

Background/Aims: Amongst the many approaches to genome-wide association study (GWAS) meta-analysis (MA), the most popular methods are based on fixed-effects (FE) modeling because it tends to be the statistically most powerful approach in the absence of heterogeneity. However, FE-based MA ignores the potential heterogeneity that may exist between studies. The purpose of our analysis was to test whether results from random effects (RE)-based methods that account for heterogeneity differed significantly from the results that were originally published. Methods: We reanalyzed two GWAS FE-based MAs of celiac disease with RE-based methods: (1) a two-stage GWAS MA that includes 9,451 celiac disease cases and 16,434 controls from 12 collections and (2) a single-stage GWAS MA using a custom dense genotyping platform to capture low-frequency and rare variants in 12,041 cases and 12,228 controls from 7 collections. Results: We present evidence that SNPs at loci that were previously reported to be genome-wide significant (GWS; p < 5 × 10-8) in either the two-stage GWAS MA or the single-stage GWAS MA were not GWS when heterogeneity was accounted for by an RE MA method. Conclusion: This case study highlights the strengths of RE MA methods in the presence of heterogeneity and of pooled FE methods.

RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways

It has long been recognized that anatomic location is an important feature for defining distinct subtypes of plaque psoriasis. However, little is known about the molecular differences between scalp, palmoplantar, and conventional plaque psoriasis. To investigate the molecular heterogeneity of these psoriasis subtypes, we performed RNA-seq and flow cytometry on skin samples from individuals with scalp, palmoplantar, and conventional plaque psoriasis, along with samples from healthy control patients. We performed differential expression analysis and network analysis using weighted gene coexpression network analysis (WGCNA). Our analysis revealed a core set of 763 differentially expressed genes common to all sub-types of psoriasis. In contrast, we identified 605, 632, and 262 genes uniquely differentially expressed in conventional, scalp, and palmoplantar psoriasis, respectively. WGCNA and pathway analysis revealed biological processes for the core genes as well as subtype-specific genes. Flow cytometry analysis revealed a shared increase in the percentage of CD4+ T regulatory cells in all psoriasis subtypes relative to controls, whereas distinct psoriasis subtypes displayed differences in IL-17A, IFN-gamma, and IL-22 production. This work reveals the molecular heterogeneity of plaque psoriasis and identifies subtype-specific signaling pathways that will aid in the development of therapy that is appropriate for each subtype of plaque psoriasis.

Dietary modifications in atopic dermatitis: patient-reported outcomes

Abstract Background: Patients with atopic dermatitis (AD) commonly turn to dietary modifications to manage their skin condition. Objectives: To investigate patient-reported outcomes and perceptions regarding the role of diet in AD. Methods: One hundred and sixty nine AD patients were surveyed in this cross-sectional study. The 61-question survey asked about dietary modifications, perceptions and outcomes. Results: Eighty seven percent of participants reported a trial of dietary exclusion. The most common were junk foods (68%), dairy (49.7%) and gluten (49%). The best improvement in skin was reported when removing white flour products (37 of 69, 53.6%), gluten (37 of 72, 51.4%) and nightshades (18 of 35, 51.4%). 79.9% of participants reported adding items to their diet. The most common were vegetables (62.2%), fish oil (59.3%) and fruits (57.8%). The best improvement in skin was noted when adding vegetables (40 of 84, 47.6%), organic foods (17 of 43, 39.5%) and fish oil (28 of 80, 35%). Although 93.5% of patients believed it was important that physicians discuss with them the role of diet in managing skin disease, only 32.5% had consulted their dermatologist. Conclusions: Since dietary modifications are extremely common, the role of diet in AD and potential nutritional benefits and risks need to be properly discussed with patients.

Additional file 4: of Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs

List of GO and Broad MSigDB terms enriched for in the top correlated modules of PPvPT. The full list of GO and Broad MSigDB terms enriched for (p â ¤ 0.005) in the sienna3 and lightyellow modules of PPvPT. (XLS 83 kb)