Rheumatic Diseases of Childhood

A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes

BACKGROUND

Although genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis (JIA), we are still faced with the task of identifying the single nucleotide polymorphisms (SNPs) on the disease haplotypes that exert the biological effects that confer risk. Until we identify the risk-driving variants, identifying the genes influenced by these variants, and therefore translating genetic information to improved clinical care, will remain an insurmountable task. We used a function-based approach for identifying causal variant candidates and the target genes on JIA risk haplotypes.

METHODS

We used a massively parallel reporter assay (MPRA) in myeloid K562 cells to query the effects of 5,226 SNPs in non-coding regions on JIA risk haplotypes for their ability to alter gene expression when compared to the common allele. The assay relies on 180 bp oligonucleotide reporters ("oligos") in which the allele of interest is flanked by its cognate genomic sequence. Barcodes were added randomly by PCR to each oligo to achieve > 20 barcodes per oligo to provide a quantitative read-out of gene expression for each allele. Assays were performed in both unstimulated K562 cells and cells stimulated overnight with interferon gamma (IFNg). As proof of concept, we then used CRISPRi to demonstrate the feasibility of identifying the genes regulated by enhancers harboring expression-altering SNPs.

RESULTS

We identified 553 expression-altering SNPs in unstimulated K562 cells and an additional 490 in cells stimulated with IFNg. We further filtered the SNPs to identify those plausibly situated within functional chromatin, using open chromatin and H3K27ac ChIPseq peaks in unstimulated cells and open chromatin plus H3K4me1 in stimulated cells. These procedures yielded 42 unique SNPs (total = 84) for each set. Using CRISPRi, we demonstrated that enhancers harboring MPRA-screened variants in the TRAF1 and LNPEP/ERAP2 loci regulated multiple genes, suggesting complex influences of disease-driving variants.

CONCLUSION

Using MPRA and CRISPRi, JIA risk haplotypes can be queried to identify plausible candidates for disease-driving variants. Once these candidate variants are identified, target genes can be identified using CRISPRi informed by the 3D chromatin structures that encompass the risk haplotypes.

Causal relationship between serum metabolites and juvenile idiopathic arthritis: a mendelian randomization study

BACKGROUND

Juvenile Idiopathic Arthritis (JIA) is a condition that occurs when individuals under the age of 16 develop arthritis that lasts for more than six weeks, and the cause is unknown. The development of JIA may be linked to serum metabolites. Nevertheless, the association between JIA pathogenesis and serum metabolites is unclear, and there are discrepancies in the findings across studies.

METHODS

In this research, the association between JIA in humans and 486 serum metabolites was assessed using genetic variation data and genome-wide association study. The identification of causal relationships was accomplished through the application of univariate Mendelian randomization (MR) analysis. Various statistical methods, including inverse variance weighted and MR-Egger, were applied to achieve this objective. To ensure that the findings from the MR analysis were trustworthy, a number of assessments were carried out. To ensure the accuracy of the obtained results, a range of techniques were utilised including the Cochran Q test, examination of the MR-Egger intercept, implementation of the leave-one-out strategy, and regression analysis of linkage disequilibrium scores. In order to identify the specific metabolic pathways associated with JIA, our primary objective was to perform pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes.

RESULTS

Two-sample summary data MR analyses and sensitivity analyses showed that five metabolites were significantly causally associated with JIA, including two risk factors-kynurenine (odds ratio [OR]: 16.39, 95% confidence interval [CI]: 2.07-129.63, p = 5.11 × 10- 6) and linolenate (OR: 16.48, 95% CI: 1.32-206.22, p = 0.030)-and three protective factors-3-dehydrocarnitine (OR: 0.32, 95% CI: 0.14-0.72, p = 0.007), levulinate (4-oxovalerate) (OR: 0.40, 95% CI: 0.20-0.80, p = 0.010), and X-14,208 (phenylalanylserine) (OR: 0.68, 95% CI: 0.51-0.92, p = 0.010). Furthermore, seven metabolic pathways, including α-linolenic acid metabolism and pantothenate and CoA biosynthesis, are potentially associated with the onset and progression of JIA.

CONCLUSION

Five serum metabolites, including kynurenine and 3-dehydrocarnitine, may be causally associated with JIA. These results provide a theoretical framework for developing effective JIA prevention and screening strategies.

Comparison of the three-dimensional chromatin structures of adolescent and adult peripheral blood B cells: implications for the study of pediatric autoimmune diseases

Background/Purpose

Knowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture of primary human cells or whether developmental aspects of the pediatric immune system require use of pediatric samples. We undertook a systematic analysis of B cells and B cell lines to compare 3D genomic features encompassing risk loci for juvenile idiopathic arthritis (JIA), systemic lupus (SLE), and type 1 diabetes (T1D).

Methods

We isolated B cells from healthy individuals, ages 9-17. HiChIP was performed using CTCF antibody, and CTCF peaks were identified. CTCF loops within the pediatric were compared to three datasets: 1) self-called CTCF consensus peaks called within the pediatric samples, 2) ENCODE's publicly available GM12878 CTCF ChIP-seq peaks, and 3) ENCODE's primary B cell CTCF ChIPseq peaks from two adult females. Differential looping was assessed within the pediatric samples and each of the three peak datasets.

Results

The number of consensus peaks called in the pediatric samples was similar to that identified in ENCODE's GM12878 and primary B cell datasets. We observed <1% of loops that demonstrated significantly differential looping between peaks called within the pediatric samples themselves and when called using ENCODE GM12878 peaks . Significant looping differences were even less when comparing loops of the pediatric called peaks to those of the ENCODE primary B cell peaks. When querying loops found in juvenile idiopathic arthritis, type 1 diabetes, or systemic lupus erythematosus risk haplotypes, we observed significant differences in only 2.2%, 1.0%, and 1.3% loops, respectively, when comparing peaks called within the pediatric samples and ENCODE GM12878 dataset. The differences were even less apparent when comparing loops called with the pediatric vs ENCODE adult primary B cell peak datasets.The 3D chromatin architecture in B cells is similar across pediatric, adult, and EBVtransformed cell lines. This conservation of 3D structure includes regions encompassing autoimmune risk haplotypes.

Conclusion

Thus, even for pediatric autoimmune diseases, publicly available adult B cell and cell line datasets may be sufficient for assessing effects exerted in the 3D genomic space.

Dynamic tracking of functional gene modules in treated juvenile idiopathic arthritis

BACKGROUND

We have previously shown that childhood-onset rheumatic diseases show aberrant patterns of gene expression that reflect pathology-associated co-expression networks. In this study, we used novel computational approaches to examine how disease-associated networks are altered in one of the most common rheumatic diseases of childhood, juvenile idiopathic arthritis (JIA).

METHODS

Using whole blood gene expression profiles derived from children in a pediatric rheumatology clinical trial, we used a network approach to understanding the impact of therapy and the underlying biology of response/non-response to therapy.

RESULTS

We demonstrate that therapy for JIA is associated with extensive re-ordering of gene expression networks, even in children who respond inadequately to therapy. Furthermore, we observe distinct differences in the evolution of specific network properties when we compare children who have been treated successfully with those who have inadequate treatment response.

CONCLUSIONS

Despite the inherent noisiness of whole blood gene expression data, our findings demonstrate how therapeutic response might be mapped and understood in pathologically informative cells in a broad range of human inflammatory diseases.

RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states

BACKGROUND

The transcriptional complexity of mammalian cells suggests that they have broad abilities to respond to specific environmental stimuli and physiologic contexts. These abilities were not apparent a priori from the structure of mammalian genomes, but have been identified through detailed transcriptome analyses. In this study, we examined the transcriptomes of cells of the innate immune system, human neutrophils, using RNA sequencing (RNAseq).

METHODS

We sequenced poly-A RNA from nine individual samples corresponding to specific phenotypes: three children with active, untreated juvenile idiopathic arthritis (JIA)(AD), three children with the same disease whose disease was inactive on medication (CRM), and three children with cystic fibrosis (CF).

RESULTS

We demonstrate that transcriptomes of neutrophils, typically considered non-specific in their responses and functions, display considerable specificity in their transcriptional repertoires dependent on the pathologic context, and included genes, gene isoforms, and long non-coding RNA transcripts. Furthermore, despite the small sample numbers, these findings demonstrate the potential of RNAseq approaches to biomarker development in rheumatic diseases.

CONCLUSIONS

These data demonstrate the capacity of cells previously considered non-specific in function to adapt their transcriptomes to specific biologic contexts. These data also provide insight into previously unrecognized pathological pathways and show considerable promise for elucidating disease and disease-state specific regulatory networks.

Trial of early aggressive therapy in polyarticular juvenile idiopathic arthritis

OBJECTIVE

To determine whether aggressive treatment initiated early in the course of rheumatoid factor (RF)-positive or RF-negative polyarticular juvenile idiopathic arthritis (JIA) can induce clinical inactive disease within 6 months.

METHODS

Between May 2007 and October 2010, a multicenter, prospective, randomized, double-blind, placebo-controlled trial of 2 aggressive treatments was conducted in 85 children ages 2-16 years with polyarticular JIA of <12 months' duration. Patients received either methotrexate (MTX) 0.5 mg/kg/week (maximum 40 mg) subcutaneously, etanercept 0.8 mg/kg/week (maximum 50 mg), and prednisolone 0.5 mg/kg/day (maximum 60 mg) tapered to 0 by 17 weeks (arm 1), or MTX (same dosage as arm 1), etanercept placebo, and prednisolone placebo (arm 2). The primary outcome measure was clinical inactive disease at 6 months. An exploratory phase determined the rate of clinical remission on medication (6 months of continuous clinical inactive disease) at 12 months.

RESULTS

By 6 months, clinical inactive disease had been achieved in 17 (40%) of 42 patients in arm 1 and 10 (23%) of 43 patients in arm 2 (χ(2) = 2.91, P = 0.088). After 12 months, clinical remission on medication was achieved in 9 patients in arm 1 and 3 patients in arm 2 (P = 0.053). There were no significant interarm differences in adverse events.

CONCLUSION

Although this study did not meet its primary end point, early aggressive therapy in this cohort of children with recent-onset polyarticular JIA resulted in clinical inactive disease by 6 months and clinical remission on medication within 12 months of treatment in substantial proportions of patients in both arms.

Juvenile idiopathic arthritis among Nigerians: a case study

Juvenile idiopathic arthritis (JIA) has rarely been reported among Black Africans. This retrospective case study was part of an audit of cases presenting to a private practice rheumatology clinic in Lagos, Nigeria. The objective of this study was to determine the clinical, laboratory, and radiographic features of patients with JIA, as well as to highlight their management. A total of 23 cases (F-16:M-7) were seen over an 8.5-year period. Polyarticular presentation was the commonest while systemic onset was the least. The mean age at presentation was 12.7 years. Most of the patients presented late with mean of 3.7 years before presentation. The knees and ankles were most commonly involved. ESR was elevated in most of the cases. Rheumatoid factor and Antinuclear antibodies were invariably negative. Treatments were with standard drugs. Although JIA is uncommonly seen in our population, the clinical and laboratory features are similar as elsewhere, though there are some differences.

Association of PDCD1 polymorphisms with childhood-onset systemic lupus erythematosus

A regulatory single nucleotide polymorphism (SNP) PD1.3G/A located on programmed cell death 1 (PDCD1) gene, was shown to be involved in susceptibility to systemic lupus erythematosus (SLE) in Swedish, European American, and Mexican cases. However, association to childhood-onset SLE has not been analyzed. The aim of this study was to investigate the association of PDCD1 polymorphisms and haplotypes with susceptibility to childhood-onset SLE in Mexican population. Three PDCD1 SNPs, PD1.3G/A, PD1.5C/T, PD1.6G/A, were analyzed in 250 childhood-onset SLE Mexican patients and 355 healthy controls in a case-control association study. Polymorphisms were genotyped by TaqMan technology. Stratification analysis was performed on the SLE cohort to investigate the SNP association with renal disorder. In addition, haplotypes were constructed with these three SNPs. The PD1.3A allele was significantly associated to childhood-onset SLE (P=0.0019, odds ratio (OR) 2.73, 95% confidence interval (95% CI) 1.35-5.56). The other PDCD1 SNPs did not show association. A total of 155 patients (62%) had nephritis, and no association was observed with PDCD1 SNPs. The ACG haplotype (PD1.3A, PD1.5C, PD1.6G) included almost all PD1.3A alleles, and it was more frequent in SLE patients (5.5%) than in controls (2.1%) (P=0.003; OR 2.73, 95% CI 1.37-5.46). The haplotype structure in Mexican controls was significantly different from those reported in Spanish and Swedish. Our results support association of the PD1.3A SNP to susceptibility of childhood-onset SLE in Mexican population and does not show association to lupus nephritis in this age group.

Damage did not independently influence mortality in childhood systemic lupus erythematosus

OBJECTIVE

To analyze clinical, laboratory and treatment features associated with death in a childhood-onset SLE population.

PATIENTS AND METHODS

Patients with childhood-onset SLE followed at the State University of Campinas, Brazil, between 1980 and 2002 were included. Data on clinical and laboratory features of the disease were collected regularly. Logistic regression was used for analyzing association between clinical and laboratory features and death. Kaplan-Meyer tests were used to estimate the survival curves.

RESULTS

Of 61 patients identified, six were lost to follow-up during the first year of disease. The mean follow-up period of the remaining 55 patients was 3.25 years (SD=1.2). Mean SLICC/ACR-DI score was 4.9 (SD=3.4). Death occurred in 12 (21.8%) of 55 patients. Direct causes of death were: infection in six (50%), stroke in four (33.3%), and renal insufficiency in two (16.7%). Five patients (41.7%) died during the first 5 years of disease due to infection. Male gender (p=0.004; OR=9.1; 95% CI=7.6-21.0), infection (p=0.001; OR=4.2; 95% CI=1.6-15.2) and nephritis (p=0.02; OR=2.3; 95% CI=1.3-5.2) were independent factors associated with death in the multivariate analysis. The global survival rate adjusted for duration of disease was 93.9% in the first year of disease, 88.9% in the second year, 80.8% in the fifth year and 48.1% in 20 years of follow-up. When comparing survival curves, male gender, the presence of infection during the course of the disease and the presence of nephritis during follow-up had a worse survival.

CONCLUSION

Male gender, the presence of infection and nephritis were independent risk factors for death in our Brazilian cohort. Damage did not independently influence survival in this study.

Rheumatic diseases in North America's indigenous peoples

OBJECTIVES

There are at least 3 million North American Indians and Eskimos in North America. The epidemiology of rheumatic diseases in Native North Americans differs from that described for the remainder of the North American population. An enhanced understanding of rheumatic diseases in these indigenous people may provide valuable clues to the cause of these disorders and improve rheumatologic care.

METHODS

The world literature was searched for all reports of rheumatic diseases in North American Indians and Eskimos. The reports were reviewed and the findings summarized by disease process.

RESULTS

Many Native American groups have high prevalence rates of rheumatoid arthritis (RA), systemic lupus erythematosus, connective tissue diseases, and spondyloarthropathies. There appears to be a correlation between the pattern of rheumatic diseases in Native North Americans and the patterns of migration and ancestry. In general, Amerind Indians have increased rates of RA and connective tissue disease, while Na-Dene Indians and Eskimos have high rates of spondyloarthropathies. The RA seen in Native Americans is generally severe, seropositive, with an early age of onset, and frequent extraarticular manifestations. Many Native American groups have very high frequencies of the RA shared epitope. The majority of Native American and Eskimo groups also have high frequencies of HLA-B27, and some of the world's highest prevalence rates of spondyloarthropathies are described in these groups. Although some groups show a marked tendency to develop either Reiter's syndrome or ankylosing spondylitis, psoriatic and enteropathic arthritis are rare.

CONCLUSIONS

The excess rheumatic disease seen in this population is most likely genetic in origin. Because of the combination of high rates of rheumatic disease and relative genetic homogeneity, Native North Americans represent a singular opportunity to study genetic contributions to rheumatic disease. For clinicians, the index of suspicion for rheumatic diseases in North American Indians and Eskimos should be high, and the severe disease and sometimes atypical presentations kept in mind.

Isolated digital swelling as the initial presentation of juvenile rheumatoid arthritis

Juvenile rheumatoid arthritis (JRA) is an inflammatory condition that affects children under 16 years of age. The cases of 7 patients with isolated finger swelling as the initial manifestation of JRA are reviewed. In these children, the diagnosis was significantly delayed (t-test, p < .0076) for up to 14 months (mean, 8 months) when compared to a mean of 3.4 months in the JRA patients with a typical onset. Of the patients with the initial presentation of isolated digital swelling, +/7 (57%) had disease that became polyarticular, whereas only 15% of the patients with the initial presentation of large-joint disease experienced progression to polyarticular disease (Fisher's exact test, p < .0307). This presentation of JRA should be recognized so that appropriate management can be instituted promptly.

Epidemiology of chronic arthritis in childhood

This study was performed to review reports of the descriptive epidemiology of chronic arthritis in childhood and to analyze the factors that may explain differences in its reported frequency. Articles were retrieved by searching MEDLINE and EMBASE under the following index terms: juvenile rheumatoid arthritis (JRA), juvenile chronic arthritis (JCA), spondyloarthropathy, epidemiology, prevalence, and incidence. For reports published between 1977 to 1982, the Index Medicus was used. All original articles that provided prevalence or incidence rates, population size, or number of cases, were reviewed and entered into the analysis. Variables analyzed were disease prevalence and incidence. Modifier variables investigated were diagnostic criteria, source population, geographic origin of the report (Europe or North America), duration of the study, and race of the population studied. Diagnostic criteria had no effect on reported prevalence or incidence rates. Prevalence per 100,000 at risk obtained from population studies (132, 95% CI: 119, 145) was significantly higher than values derived from practitioner- (26, 95% CI: 23, 29) or clinic-based studies (12, 95% CI: 10, 15) (P = .02). North American clinic-based studies had higher prevalence values compared with European reports (32, 95% CI: 26, 38 versus 8, 95% CI: 5, 11, P = .009). None of the factors analyzed accounted for the variability in reported incidence rates. An effect of race was detected only in the distribution of patients among onset subsets. Thus, the percentage of patients with pauciarticular JRA was highest in series of North American and European caucasian patients (58, 95% CI: 56, 60) compared with series of East Indian (25, 95% CI: 20, 31), native North American Indian (26, 95% CI: 15, 37), or other races (31, 95% CI: 28, 35) (P = .001). In contrast, the percentage of patients with polyarticular JRA was lowest in the former (27, 95% CI: 25, 28) compared with the other racial groups (East Indian, 61, 95% CI: 55, 66; native North American Indian, 64, 95% CI: 53, 76; other races, 34, 95% CI: 30, 38) (P = .004). Although an effect of source population on reported prevalence was confirmed, the effect of geographic origin suggests that environmental or ethnic differences also may influence the prevalence of chronic arthritis in children. Differences in the percentages of patients with pauciarticular and polyarticular JRA may reflect racial differences in the prevalence of these conditions.

A pilot trial of oral type II collagen in the treatment of juvenile rheumatoid arthritis

OBJECTIVE

To evaluate the efficacy of oral chicken type II collagen (CCII) in the treatment of juvenile rheumatoid arthritis (JRA).

METHODS

Ten patients with active JRA were treated with CCII for 12 weeks. Efficacy parameters, which included swollen and tender joint count and score, grip strength, 50-foot walking time, duration of morning stiffness, and patient and physician global scores of disease severity, were assessed monthly.

RESULTS

All patients completed the full course of therapy. Eight patients had reductions in both swollen and tender joint counts after 3 months of CCII. The mean changes from baseline in swollen and tender joint counts for the 8 responders at the end of the study were -61% and -54%, respectively. Mean values for other efficacy parameters also showed improvement from baseline. There were no adverse events that were considered to be treatment related.

CONCLUSION

Oral CCII may be a safe and effective therapy for JRA, and its use in this disease warrants further investigation.

Rheumatoid arthritis and connective tissue disorders: juvenile chronic arthritis

That juvenile chronic arthritis (JCA) occurs in tropical countries there is no doubt. The spectrum of differential diagnoses is wider than in temperate regions. The disease tends to be more severe irrespective of the type of onset, and there is a high incidence of positive rheumatoid factor. Many cases present with advanced disease. There is a need for the establishment of clinics devoted specifically to the detection, documentation, and treatment of JCA.

Measurement of health status in children with juvenile rheumatoid arthritis

OBJECTIVE

To develop and validate a self- or parent-administered instrument for measuring functional status in children with juvenile rheumatoid arthritis (JRA).

METHODS

We adapted the Stanford Health Assessment Questionnaire (HAQ) for use in children ages 1-19 years, by adding several new questions, such that for each functional area, there was at least 1 question relevant to children of all ages. The face validity of the instrument was evaluated by a group of 20 health professionals and parents of 22 healthy children. The questionnaire was then administered to parents of 72 JRA patients (mean age 9.1 years, onset type systemic in 16, polyarticular in 21, pauciarticular in 35).

RESULTS

The instrument showed excellent internal reliability (Cronbach's alpha = 0.94), with a mean inter-item correlation of 0.6. The convergent validity was demonstrated by strong correlations of the Disability Index (average of scores on all functional areas) with Steinbrocker functional class (Kendall's tau b = 0.77, P < 0.0001), number of involved joints (Kendall's tau b = 0.67, P < 0.0001), and morning stiffness (Kendall's tau b = 0.54, P < 0.0001). Spearman's correlation coefficient between Disability Index scores from questionnaires administered to parents and those from questionnaires administered to older children (> 8 years) was 0.84 (n = 29; P < 0.001), showing that parents can accurately report for their children. The test-retest reliability, studied at a 2-week interval, revealed virtually identical Disability Index scores measured on the 2 occasions (0.96 versus 0.96; P > 0.9 by paired t-test; Spearman's correlation coefficient = 0.8, P < 0.002).

CONCLUSION

The Childhood HAQ, which takes less than 10 minutes to complete, is a valid, reliable, and sensitive instrument for measuring functional status in children with JRA.

Pediatric rheumatic diseases

The rheumatic diseases of childhood are a relatively common and extraordinarily diverse group of illnesses; nevertheless, they are at least distantly related by similarities of immunodysregulation. These pathophysiologic relationships are reflected in affected children in similarities of historical, physical, and laboratory data as well as therapeutic intervention.

Back pain in children and teenagers

Controversial opinions have been published concerning the frequency of LBP among children and adolescents. Studies from orthopaedics or neurosurgical departments have reported low figures for prevalence of specific LBP due to serious disorders. Field surveys, on the contrary, have shown that cumulative life prevalence of non-specific LBP in children and teenagers can be comparable to the prevalence data for adult populations. Some specific diagnoses are more common or characteristic of children complaining of LBP. Age, gender, sports activities and family history of LBP have been found to be significantly associated with an increased prevalence in non-specific LBP among children. Low back pain among children and teenagers is common and should be recognized. This chapter provides guidelines for a clinical approach and differential diagnoses. Most back pain in these age groups is benign and should be treated as such.