ABSTRACT
Single-nucleotide polymorphisms (SNPs) near the ERAP2 gene are associated with various autoimmune conditions, as well as protection against lethal infections. Due to high linkage disequilibrium, numerous trait-associated SNPs are correlated with ERAP2 expression; however, their functional mechanisms remain unidentified. We show by reciprocal allelic replacement that ERAP2 expression is directly controlled by the splice region variant rs2248374. However, disease-associated variants in the downstream LNPEP gene promoter are independently associated with ERAP2 expression. Allele-specific conformation capture assays revealed long-range chromatin contacts between the gene promoters of LNPEP and ERAP2 and showed that interactions were stronger in patients carrying the alleles that increase susceptibility to autoimmune diseases. Replacing the SNPs in the LNPEP promoter by reference sequences lowered ERAP2 expression. These findings show that multiple SNPs act in concert to regulate ERAP2 expression and that disease-associated variants can convert a gene promoter region into a potent enhancer of a distal gene.
Subject(s)
Autoimmune Diseases , Polymorphism, Single Nucleotide , Humans , Polymorphism, Single Nucleotide/genetics , Genetic Predisposition to Disease/genetics , Autoimmune Diseases/genetics , Promoter Regions, Genetic/genetics , Aminopeptidases/geneticsABSTRACT
TRAF1/C5 was among the first loci shown to confer risk for inflammatory arthritis in the absence of an associated coding variant, but its genetic mechanism remains undefined. Using Immunochip data from 3,939 patients with juvenile idiopathic arthritis (JIA) and 14,412 control individuals, we identified 132 plausible common non-coding variants, reduced serially by single-nucleotide polymorphism sequencing (SNP-seq), electrophoretic mobility shift, and luciferase studies to the single variant rs7034653 in the third intron of TRAF1. Genetically manipulated experimental cells and primary monocytes from genotyped donors establish that the risk G allele reduces binding of Fos-related antigen 2 (FRA2), encoded by FOSL2, resulting in reduced TRAF1 expression and enhanced tumor necrosis factor (TNF) production. Conditioning on this JIA variant eliminated attributable risk for rheumatoid arthritis, implicating a mechanism shared across the arthritis spectrum. These findings reveal that rs7034653, FRA2, and TRAF1 mediate a pathway through which a non-coding functional variant drives risk of inflammatory arthritis in children and adults.
ABSTRACT
OBJECTIVE: Juvenile idiopathic arthritis (JIA) is the most common chronic immune-mediated joint disease among children and encompasses a heterogeneous group of immune-mediated joint disorders classified into 7 subtypes according to clinical presentation. However, phenotype overlap and biologic evidence suggest a shared mechanistic basis between subtypes. This study was undertaken to systematically investigate shared genetic underpinnings of JIA subtypes. METHODS: We performed a heterogeneity-sensitive genome-wide association study encompassing a total of 1,245 JIA cases (classified into 7 subtypes) and 9,250 controls, followed by fine-mapping of candidate causal variants at each genome-wide significant locus, functional annotation, and pathway and network analysis. We further identified candidate drug targets and drug repurposing opportunities by in silico analyses. RESULTS: In addition to the major histocompatibility complex locus, we identified 15 genome-wide significant loci shared between at least 2 JIA subtypes, including 10 novel loci. Functional annotation indicated that candidate genes at these loci were expressed in diverse immune cell types. CONCLUSION: This study identified novel genetic loci shared by JIA subtypes. Our findings identified candidate mechanisms underlying JIA subtypes and candidate targets with drug repurposing opportunities for JIA treatment.
Subject(s)
Arthritis, Juvenile , Arthritis, Juvenile/drug therapy , Arthritis, Juvenile/genetics , Genetic Loci , Genetic Predisposition to Disease , Genome-Wide Association Study , Humans , Polymorphism, Single NucleotideABSTRACT
Juvenile idiopathic arthritis (JIA) is an umbrella term for arthritis of unknown origin, lasting for >6 weeks with onset before 16 years of age. JIA is the most common chronic inflammatory rheumatic condition of childhood. According to the International League Against Rheumatism (ILAR) classification, seven mutually exclusive categories of JIA exist based on disease manifestations during the first 6 months of disease. Although the ILAR classification has been useful to foster research, it has been criticized mainly as it does not distinguish those forms of chronic arthritis observed in adults and in children from those that may be unique to childhood. Hence, efforts to provide a new evidence-based classification are ongoing. Similar to arthritis observed in adults, pathogenesis involves autoimmune and autoinflammatory mechanisms. The field has witnessed a remarkable improvement in therapeutic possibilities of JIA owing to the availability of new potent drugs and the possibility to perform controlled trials with support from legislative interventions and large networks availability. The goal of drug therapy in JIA is to rapidly reduce disease activity to inactive disease or clinical remission, minimize drug side effects and achieve a quality of life comparable to that of healthy peers. As JIA can influence all aspects of a child's and their family's life, researchers increasingly recognize improvement of health-related quality of life as a key treatment goal.
Subject(s)
Arthritis, Juvenile , Adult , Arthritis, Juvenile/diagnosis , Arthritis, Juvenile/drug therapy , Child , Humans , Quality of LifeABSTRACT
Chronic inflammatory arthritis in childhood is heterogeneous in presentation and course. Most forms exhibit clinical and genetic similarity to arthritis of adult onset, although at least one phenotype might be restricted to children. Nevertheless, paediatric and adult rheumatologists have historically addressed disease classification separately, yielding a juvenile idiopathic arthritis (JIA) nomenclature that exhibits no terminological overlap with adult-onset arthritis. Accumulating clinical, genetic and mechanistic data reveal the critical limitations of this strategy, necessitating a new approach to defining biological categories within JIA. In this Review, we provide an overview of the current evidence for biological subgroups of arthritis in children, delineate forms that seem contiguous with adult-onset arthritis, and consider integrative genetic and bioinformatic strategies to identify discrete entities within inflammatory arthritis across all ages.
Subject(s)
Arthritis, Juvenile/classification , Computational Biology/methods , Polymorphism, Single Nucleotide , Terminology as Topic , Arthritis, Juvenile/genetics , Arthritis, Juvenile/metabolism , Child , Humans , PhenotypeABSTRACT
OBJECTIVES: Juvenile idiopathic arthritis (JIA) is the most prevalent form of juvenile rheumatic disease. Our understanding of the genetic risk factors for this disease is limited due to low disease prevalence and extensive clinical heterogeneity. The objective of this research is to identify novel JIA susceptibility variants and link these variants to target genes, which is essential to facilitate the translation of genetic discoveries to clinical benefit. METHODS: We performed a genome-wide association study (GWAS) in 3305 patients and 9196 healthy controls, and used a Bayesian model selection approach to systematically investigate specificity and sharing of associated loci across JIA clinical subtypes. Suggestive signals were followed-up for meta-analysis with a previous GWAS (2751 cases/15 886 controls). We tested for enrichment of association signals in a broad range of functional annotations, and integrated statistical fine-mapping and experimental data to identify target genes. RESULTS: Our analysis provides evidence to support joint analysis of all JIA subtypes with the identification of five novel significant loci. Fine-mapping nominated causal single nucleotide polymorphisms with posterior inclusion probabilities ≥50% in five JIA loci. Enrichment analysis identified RELA and EBF1 as key transcription factors contributing to disease risk. Our integrative approach provided compelling evidence to prioritise target genes at six loci, highlighting mechanistic insights for the disease biology and IL6ST as a potential drug target. CONCLUSIONS: In a large JIA GWAS, we identify five novel risk loci and describe potential function of JIA association signals that will be informative for future experimental works and therapeutic strategies.
Subject(s)
Arthritis, Juvenile , Genome-Wide Association Study , Arthritis, Juvenile/genetics , Bayes Theorem , Genetic Loci , Genetic Predisposition to Disease/genetics , Genotype , Humans , Polymorphism, Single NucleotideABSTRACT
OBJECTIVE: To ascertain the role of platelet glycoprotein Ib α-chain (GPIbα) plasma protein levels in cardiovascular, autoimmune, and autoinflammatory diseases and whether its effects are mediated by platelet count. METHODS: We performed a two-sample Mendelian randomization (MR) study, using both a cis-acting protein quantitative trait locus (cis-pQTL) and trans-pQTL near the GP1BA and BRAP genes as instruments. To assess if platelet count mediated the effect, we then performed a two-step MR study. Putative associations (GPIbα/platelet count/disease) detected by MR analyses were subsequently assessed using multiple-trait colocalization analyses. RESULTS: After correction for multiple testing (Bonferroni-corrected threshold P ≤ 2 × 10-3 ), GPIbα, instrumented by either cis-pQTL or trans-pQTL, was causally implicated with an increased risk of oligoarticular and rheumatoid factor (RF)-negative polyarticular juvenile idiopathic arthritis (JIA). These effects of GPIbα appeared to be mediated by platelet count and were supported by strong evidence of colocalization (probability of all 3 traits sharing a common causal variant ≥0.80). GPIbα instrumented by cis-pQTL did not appear to affect cardiovascular risk, although the GPIbα trans-pQTL was associated with an increased risk of cardiovascular diseases and autoimmune diseases but a decreased risk of autoinflammatory diseases, suggesting that this trans-acting instrument operates through other pathways. CONCLUSION: The role of platelets in thrombosis is well-established; however, our findings provide some novel genetic evidence that platelets may be causally implicated in the development of oligoarticular and RF-negative polyarticular JIA, and indicate that GPIbα may serve as a putative therapeutic target for these JIA subtypes.
Subject(s)
Arthritis, Juvenile/genetics , Genetic Predisposition to Disease , Platelet Glycoprotein GPIb-IX Complex/genetics , Quantitative Trait Loci , Arthritis, Juvenile/immunology , Female , Genome-Wide Association Study , Genotype , Humans , Male , Mendelian Randomization Analysis , PhenotypeABSTRACT
OBJECTIVE: The risk loci for juvenile idiopathic arthritis (JIA) consist of extended haplotypes that include functional elements in addition to canonical coding genes. As with most autoimmune diseases, the risk haplotypes for JIA are highly enriched for H3K4me1/H3K27ac histone marks, epigenetic signatures that typically identify poised or active enhancers. In this study, we test the hypothesis that genetic risk for JIA is exerted through altered enhancer-mediated gene regulation. METHODS: We mined publically available HiC and other chromatin conformation data to determine whether H3K27ac-marked regions in 25 JIA risk loci showed physical evidence of contact with gene promoters. We also used in vitro reporter assays to establish as proof-of-concept the idea that genetic variants in linkage disequilibrium with GWAS-identified tag SNPs alter enhancer function. RESULTS: All 25 loci examined showed multiple contact sites in the 4 different cell lines that we queried. These regions were characterized by HiC-defined loop structures that included 237 immune-related genes. Using in vitro assays, we found that a 657 bp, H3K4me1/H3K27-marked region within the first intron of IL2RA shows enhancer activity in reporter assays, and this activity is attenuated by SNPs on the IL2RA haplotype that we identified using whole genome sequencing of children with JIA. Similarly, we identified a 1,669 bp sequence in an intergenic region of the IL6R locus where SNPs identified in children with JIA increase enhancer function in reporter assays. CONCLUSIONS: These studies provide evidence that altered enhancer function contributes to genetic risk in JIA. Further studies to identify the specific target genes of genetically altered enhancers are warranted.
Subject(s)
Arthritis, Juvenile/genetics , Chromatin Assembly and Disassembly , Enhancer Elements, Genetic , Histones/genetics , Polymorphism, Single Nucleotide , Humans , K562 Cells , Quantitative Trait Loci , THP-1 CellsABSTRACT
OBJECTIVES: Patients with Crohn's disease often produce antibodies against flagellated intestinal bacteria. There are mixed data as to whether such antibodies are present in patients with spondyloarthritis. Our objectives were to evaluate for the presence of antibodies against intestinal organisms in children with enthesitis related arthritis (ERA). METHODS: Children with ERA and healthy controls were recruited at three sites. Sera were plated on a nitrocellulose array and incubated with labelled antibodies to human IgA and IgG. RESULTS: At UAB, patients and controls had similar antibody levels against the majority of the bacteria selected, with the exception of increased IgA antibodies among ERA patients against Prevotella oralis (1231 [IQR 750, 2566] versus 706 [IQR 428, 1106], p = .007.) These findings were partially validated at a second but not at a third site. CONCLUSIONS: ERA patients may produce increased IgA antibodies against P. oralis. The possible significance of this finding bears further exploration.
Subject(s)
Antigens, Bacterial/blood , Antigens, Bacterial/immunology , Arthritis, Juvenile/blood , Arthritis, Juvenile/immunology , Prevotella/immunology , Arthritis, Juvenile/microbiology , Child , Crohn Disease/immunology , Crohn Disease/microbiology , Female , Humans , Immunoglobulin A/blood , Immunoglobulin G/blood , MaleABSTRACT
OBJECTIVE: Variants in the SLCO1B1 gene, encoding a hepatic methotrexate (MTX) transporter, affect clearance of high-dose MTX. We tested whether in the *14 and *15 alleles of SLCO1B1 influenced the response to low-dose MTX in juvenile idiopathic arthritis (JIA) patients. METHODS: The study included 310 JIA patients genotyped for three single nucleotide polymorphisms (SNPs) in SLCO1B1 (rs4149056, rs2306283, and rs11045819). A patient's SLCO1B1 diplotype was determined by combining the SNPs into the *1a, *1b, *4, *5, *14, and *15 alleles. Number of active joints at follow-up (visit closest to 6 months of treatment and prior to starting a tumor necrosis factor inhibitor) was used as the dependent variable in a negative binomial regression model that included active joint count at baseline as a covariate. RESULTS: The SLCO1B1*14 allele was associated with less response to MTX (P = 0.024) and the *15 allele was not associated with response to MTX (P = 0.392). CONCLUSION: SLCO1B1 alleles may be associated with poor response to MTX in JIA patients. The *14 allele has been associated with fast clearance (low exposure) after high-dose MTX in patients with leukemia. Thus, the SLCO1B1 gene may be informative for precision dosing of MTX in JIA patients. Patients carrying the *14 allele may require a higher dose than noncarriers to achieve a similar response to MTX.
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OBJECTIVE: Systemic lupus erythematosus (SLE) features high frequency of cardiovascular disease (CVD) and fluctuating complement levels. The clinical trial Atherosclerosis Prevention in Pediatric Lupus Erythematosus (APPLE) aimed to evaluate whether atorvastatin treatment reduced the progression of atherosclerosis in 221 patients with childhood-onset SLE (cSLE), using carotid intima media thickness (CIMT) as surrogates. We leveraged APPLE biorepository and trial data to investigate the relationship between complement and CVD in cSLE. METHODS: Gene copy numbers (GCNs) for total C4, C4A and C4B were measured by TaqMan-based real-time PCR and Southern blotting, and analysed with laboratory and clinical parameters through Student's t-test and χ2 analyses. Effects of total C4, C4A and C4B GCNs on the response to placebo or atorvastatin treatment and progression of CIMT were examined by regression analyses. RESULTS: At baseline, C4 protein levels strongly correlated with GCNs of total C4 (p=1.8×10-6). Each copy of C4 gene increased mean serum C4 by 3.28 mg/dL. Compared with those without hypertension (N=142), individuals with hypertension demonstrated significantly elevated serum levels for C4 and C3 at baseline and serially (C4: P=5.0×10-25; C3: P=5.84×10-20). Individuals with ≥2 C4B genes had 2.5 times the odds of having hypertension (p=0.016) and higher diastolic blood pressure (p=0.015) compared with those with C4B deficiency. At the study end, subjects with ≥2 C4B and atorvastatin treatment had significantly slower increase in CIMT compared with those treated with placebo (p=0.018). CONCLUSIONS: cSLE with hypertension had elevated serum levels of C4 and C3 and higher GCN of C4B; cSLE with ≥2 C4B genes would benefit from statins therapy to prevent atherosclerosis.
ABSTRACT
PURPOSE OF REVIEW: We assess the implications of recent advances in the genetics of juvenile idiopathic arthritis (JIA) for the evolving understanding of inflammatory arthritis in children. RECENT FINDINGS: JIA exhibits prominent genetic associations with the human leukocyte antigen (HLA) region, extending perhaps surprisingly even to the hyperinflammatory systemic JIA category. Some HLA associations resemble those for adult-onset inflammatory arthritides, providing evidence for pathogenic continuity across the age spectrum. Genome-wide association studies have defined an increasing number of JIA-linked non-HLA loci, many again shared with adult-onset arthritis. As most risk loci contain only noncoding variants, new experimental methods such as SNP-seq and innovative big-data strategies help identify responsible causative mutations, termed functional SNPs (fSNPs). Alternately, gene hunting in multiplex families implicates new genes in monogenic childhood arthritis, including MYD88 and the intriguing innate immune gene LACC1. SUMMARY: Genetic data indicate a continuity between JIA and adult arthritis poorly reflected in current nomenclature. Advancing methodologies will help to identify new pathogenic mechanisms that inform the understanding of biologic subdivisions within JIA. Resulting insights will facilitate the application of lessons learned across the age spectrum to the treatment of arthritis in children and adults.
Subject(s)
Arthritis, Juvenile/genetics , Genetic Predisposition to Disease , Genome-Wide Association Study/methods , HLA Antigens/genetics , Polymorphism, Single Nucleotide , Humans , Risk FactorsABSTRACT
Polyarticular juvenile idiopathic arthritis (JIA) is among the most challenging of the JIA subtypes to treat. Even with current biologic therapies, the disease remains difficult to control in a substantial subset of patients, highlighting the need for new therapies. The aim of this study was to use the high dimensionality afforded by mass cytometry with phospho-specific antibodies to delineate signaling abnormalities in immune cells from treatment-naive polyarticular JIA patients. Peripheral blood mononuclear cells were isolated from 17 treatment-naive polyarticular JIA patients, 10 of the patients after achieving clinical remission, and 19 healthy controls. Samples were stimulated for 15 minutes with IL-6 or IFN-γ and analyzed by mass cytometry. Following IFN-γ stimulation, increased STAT1 and/or STAT3 phosphorylation was observed in subsets of CD4 T cells and classical monocytes from treatment-naive patients. The enhanced IFN-γ signaling was associated with increased expression of JAK1 and SOCS1 in CD4 T cells. Furthermore, substantial heterogeneity in surface marker expression was observed among the subsets of CD4 T cells and classical monocytes with increased IFN-γ responsiveness. The identification of enhanced IFN-γ signaling in CD4 T cells and classical monocytes from treatment-naive polyarticular JIA patients provides mechanistic support for investigations into therapies that attenuate IFN-γ signaling in this disease.
Subject(s)
Arthritis, Juvenile/immunology , Interferon-gamma/metabolism , Adolescent , Antirheumatic Agents/pharmacology , Antirheumatic Agents/therapeutic use , Arthritis, Juvenile/blood , Arthritis, Juvenile/drug therapy , CD4-Positive T-Lymphocytes/drug effects , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , Case-Control Studies , Child , Child, Preschool , Female , Flow Cytometry , Humans , Infant , Interferon-gamma/immunology , Male , Monocytes/drug effects , Monocytes/immunology , Monocytes/metabolism , Young AdultABSTRACT
OBJECTIVE: Juvenile idiopathic arthritis (JIA) comprises 7 heterogeneous categories of chronic childhood arthritides. Approximately 5% of children with JIA have rheumatoid factor (RF)-positive arthritis, which phenotypically resembles adult rheumatoid arthritis (RA). Our objective was to compare and contrast the genetics of RF-positive polyarticular JIA with those of RA and selected other JIA categories, to more fully understand the pathophysiologic relationships of inflammatory arthropathies. METHODS: Patients with RF-positive polyarticular JIA (n = 340) and controls (n = 14,412) were genotyped using the Immunochip array. Single-nucleotide polymorphisms were tested for association using a logistic regression model adjusting for admixture proportions. We calculated weighted genetic risk scores (wGRS) of reported RA and JIA risk loci, and we compared the ability of these wGRS to predict RF-positive polyarticular JIA. RESULTS: As expected, the HLA region was strongly associated with RF-positive polyarticular JIA (P = 5.51 × 10-31 ). Nineteen of 44 RA risk loci and 6 of 27 oligoarticular/RF-negative polyarticular JIA risk loci were associated with RF-positive polyarticular JIA (P < 0.05). The RA wGRS predicted RF-positive polyarticular JIA (area under the curve [AUC] 0.71) better than did the oligoarticular/RF-negative polyarticular JIA wGRS (AUC 0.59). The genetic profile of patients with RF-positive polyarticular JIA was more similar to that of RA patients with age at onset 16-29 years than to that of RA patients with age at onset ≥70 years. CONCLUSION: RF-positive polyarticular JIA is genetically more similar to adult RA than to the most common JIA categories and thus appears to be a childhood-onset presentation of autoantibody-positive RA. These findings suggest common disease mechanisms, which could lead to novel therapeutic targets and shared treatment strategies.
Subject(s)
Arthritis, Juvenile/genetics , Arthritis, Rheumatoid/genetics , Autoantibodies/genetics , Genetic Profile , Rheumatoid Factor/genetics , Adolescent , Adult , Arthritis, Juvenile/immunology , Arthritis, Rheumatoid/immunology , Child , Female , Genotype , Humans , Logistic Models , Male , Phenotype , Polymorphism, Single Nucleotide , Rheumatoid Factor/immunologyABSTRACT
Current classification of primary inflammatory arthritis begins from the assumption that adults and children are different. No form of juvenile idiopathic arthritis bears the same name as an adult arthritis, a nomenclature gap with implications for both clinical care and research. Recent genetic data have raised questions regarding this adult/pediatric divide, revealing instead broad patterns that span the age spectrum. Combining these genetic patterns with demographic and clinical data, we propose that inflammatory arthritis can be segregated into 4 main clusters, largely irrespective of pediatric or adult onset: seropositive, seronegative (likely including a distinct group that usually begins in early childhood), spondyloarthritis, and systemic. Each of these broad clusters is internally heterogeneous, highlighting the need for further study to resolve etiologically discrete entities. Eliminating divisions based on arbitrary age cutoffs will enhance opportunities for collaboration between adult and pediatric rheumatologists, thereby helping to promote the understanding and treatment of arthritis.
Subject(s)
Arthritis/classification , Adult , Arthritis/genetics , Child , Child, Preschool , Diagnosis, Differential , Female , Genetic Predisposition to Disease , Humans , MaleABSTRACT
OBJECTIVE: Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease and has a strong genomic component. To date, JIA genetic association studies have had limited sample sizes, used heterogeneous patient populations, or included only candidate regions. The aim of this study was to identify new associations between JIA patients with oligoarticular disease and those with IgM rheumatoid factor (RF)-negative polyarticular disease, which are clinically similar and the most prevalent JIA disease subtypes. METHODS: Three cohorts comprising 2,751 patients with oligoarticular or RF-negative polyarticular JIA were genotyped using the Affymetrix Genome-Wide SNP Array 6.0 or the Illumina HumanCoreExome-12+ Array. Overall, 15,886 local and out-of-study controls, typed on these platforms or the Illumina HumanOmni2.5, were used for association analyses. High-quality single-nucleotide polymorphisms (SNPs) were used for imputation to 1000 Genomes prior to SNP association analysis. RESULTS: Meta-analysis showed evidence of association (P < 1 × 10-6 ) at 9 regions: PRR9_LOR (P = 5.12 × 10-8 ), ILDR1_CD86 (P = 6.73 × 10-8 ), WDFY4 (P = 1.79 × 10-7 ), PTH1R (P = 1.87 × 10-7 ), RNF215 (P = 3.09 × 10-7 ), AHI1_LINC00271 (P = 3.48 × 10-7 ), JAK1 (P = 4.18 × 10-7 ), LINC00951 (P = 5.80 × 10-7 ), and HBP1 (P = 7.29 × 10-7 ). Of these, PRR9_LOR, ILDR1_CD86, RNF215, LINC00951, and HBP1 were shown, for the first time, to be autoimmune disease susceptibility loci. Furthermore, associated SNPs included cis expression quantitative trait loci for WDFY4, CCDC12, MTP18, SF3A1, AHI1, COG5, HBP1, and GPR22. CONCLUSION: This study provides evidence of both unique JIA risk loci and risk loci overlapping between JIA and other autoimmune diseases. These newly associated SNPs are shown to influence gene expression, and their bounding regions tie into molecular pathways of immunologic relevance. Thus, they likely represent regions that contribute to the pathology of oligoarticular JIA and RF-negative polyarticular JIA.
Subject(s)
Arthritis, Juvenile/genetics , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Vesicular Transport/genetics , B7-2 Antigen/genetics , Child , Child, Preschool , Female , Genetic Predisposition to Disease , Genome-Wide Association Study , High Mobility Group Proteins/genetics , Humans , Infant , Intracellular Signaling Peptides and Proteins/genetics , Janus Kinase 1/genetics , Male , Mitochondrial Proteins/genetics , Polymorphism, Single Nucleotide , Proteins/genetics , Quantitative Trait Loci/genetics , RNA Splicing Factors/genetics , Receptor, Parathyroid Hormone, Type 1/genetics , Receptors, Cell Surface/genetics , Receptors, G-Protein-Coupled/genetics , Repressor Proteins/geneticsABSTRACT
Objective: The mechanisms that determine the efficacy or inefficacy of MTX in JIA are ill-defined. The objective of this study was to identify a gene expression transcriptional signature associated with poor response to MTX in patients with JIA. Methods: RNA sequencing was used to measure gene expression in peripheral blood mononuclear cells collected from 47 patients with JIA prior to MTX treatment and 14 age-matched controls. Differentially expressed baseline genes between responders and non-responders were evaluated. Biological differences between all JIA patients and controls were explored by constructing a signature of differentially expressed genes. Unsupervised clustering and pathway analysis was performed. Results: A signature of 99 differentially expressed genes (Bonferroni-corrected P < 0.05) capturing the biological differences between all JIA patients and controls was identified. Unsupervised clustering of samples based on this list of 99 genes produced subgroups enriched for MTX response status. Comparing this gene signature with reference signatures from sorted cell populations revealed high concordance between the expression signatures of monocytes and of MTX non-responders. CXCL8 (IL-8) was the most significantly differentially expressed gene transcript comparing all JIA patients with controls (Bonferroni-corrected P = 4.12 × 10-10). Conclusion: Variability in clinical response to MTX in JIA patients is associated with differences in gene transcripts modulated in monocytes. These gene expression profiles may provide a basis for biomarkers predictive of treatment response.
Subject(s)
Antirheumatic Agents/therapeutic use , Arthritis, Juvenile/drug therapy , Arthritis, Juvenile/genetics , Methotrexate/therapeutic use , Transcription, Genetic , Adolescent , Case-Control Studies , Child , Cluster Analysis , Female , Gene Expression Profiling/methods , Humans , Male , Monocytes/metabolism , Sequence Analysis, RNA/methods , Severity of Illness Index , Transcriptome , Treatment FailureABSTRACT
While biobanks have become more prevalent, little is known about adolescents' views of key governance issues. We conducted semi-structured interviews with adolescents between 15 and 17 years old to solicit their views. All interviews were audiotaped and transcribed. Two investigators coded the transcripts and resolved any discrepancies through consensus. We conducted 18 interviews before reaching data saturation. Four participants (22%) had previously heard of a biobank. Many participants had misunderstandings about biobanks, some of which persisted after education. Participants believed that enrolling in a biobank would benefit others through scientific research. Many study participants were unable to identify risks of biobank participation. Thirteen participants (72%) were willing to enroll in a biobank and only one (6%) initially was not. Participants believed that if they were unable to provide assent when enrolled, then they should be re-contacted at the age of majority and their data should not be shared until that time. Participants emphasized the importance of being aware of their enrollment and the possibility of disagreeing with their parents. Participants' misunderstanding of biobanks suggests that assent may not be adequately informed without additional education. While adolescents had positive attitudes toward biobanks, they emphasized the importance of awareness of and involvement in the decision to enroll.