The influence of polygenic risk scores on heritability of anti-CCP level in RA

Clinical Value of Detecting Anti-Mutated Citrullinated Vimentin, Anti-Cyclic Citrullinated Peptide, Red Cell Distribution Width and 25-Hydroxyvitamin D in the Diagnosis of Rheumatoid Arthritis

OBJECTIVES

To investigate the clinical value of detecting anti-mutated citrullinated vimentin (anti-MCV), anti-citrullinated peptide (anti-CCP), red-blood-cell distribution width (RDW), and 25-hydroxyvitamin D (25-[OH]D) in the diagnosis of rheumatoid arthritis (RA).

METHODS

We enrolled 119 patients with RA, 114 control individuals without RA (disease controls), and 40 healthy controls in our study (Han Chinese). Anti-CCP and anti-MCV were detected by enzyme-linked immunosorbent assay (ELISA), 25-(OH)D was detected by electrochemical luminescence, and RDW was calculated by erythrocyte parameters detected via the electric resistance method.

RESULTS

The serum levels of anti-CCP and anti-MCV in RA were higher than those in disease controls and healthy controls (P <.01). The areas under the curve (AUCs) of anti-MCV, anti-CCP, RDW, and 25-(OH)D were 0.857, 0.890, 0.611, and 0.569 respectively (P <.05). In various combinations of indicators, when RDW, 25-(OH)D, and anti-CCP; or RDW, 25-(OH)D, anti-CCP, and anti-MCV were connected in parallel, the sensitivity was the highest (all 94.1%). Also, when RDW, 25-(OH)D, anti-CCP, and anti-MCV were connected in series, the sensitivity was the lowest (13.4%).

CONCLUSIONS

Anti-CCP and anti-MCV are ideal indices for RA diagnosis. Also, in combination with RDW and 25-(OH)D, the diagnostic level will be improved, as well as the sensitivity and specificity, which is significant for the differential diagnosis of RA.

In Situ Humoral Immunity to Vimentin in HLA-DRB1*03+ Patients With Pulmonary Sarcoidosis

Vimentin has been implicated in pulmonary sarcoidosis as a T-cell autoantigen, particularly in the context of HLA-DRB1*03, the Vα2.3/Vβ22 T-cell receptor (TCR), and Löfgren’s syndrome. As vimentin is a known antigenic target in B-cell-mediated autoimmunity, we investigated in situ humoral anti-vimentin responses in pulmonary sarcoidosis and their relationship with HLA-DRB1*03. Sarcoid and healthy control (HC) lung biopsies were analyzed by multi-color confocal microscopy for B-cells, T-cells, proliferation, and vimentin, and compared to tonsillectomy tissue. Bronchoalveolar lavage fluid (BALF) and serum from 48 sarcoidosis patients and 15 healthy volunteers were typed for HLA-DRB1*03 and titrated for antibodies to full-length vimentin, vimentin truncations, and total IgG and IgA by ELISA. Presence of extracellular vimentin in BALF was determined by mass spectrometry and T-cell populations measured by flow cytometry. Sarcoid lung samples, especially from HLA-DRB1*03⁺ patients, contained vimentin-rich tertiary lymphoid structures and corresponding BALF was highly enriched for both IgG and IgA anti-vimentin antibody (AVA) titers. Furthermore, sarcoidosis patient BALF AVA concentrations (expressed as arbitrary units per milligram of total immunoglobulin isotype) correlated with the percentage of CD4⁺ T-cells expressing the Vα2.3/Vβ22 TCR. BALF antibody reactivity to the vimentin N-terminus was most prominent in HCs, whereas reactivity to the C-terminus (Vim_C-term) was enriched in the sarcoid lung. Specifically, HLA-DRB1*03⁺ patient BALF contained higher concentrations of anti-Vim_C-term antibodies than BALF from both HCs and HLA-DRB1*03⁻ patients. Consistent with the lung as a site of AVA production, the concentration of AVAs in BALF was dramatically higher than in matched serum samples. Overall, there was a poor correlation between BALF and serum AVA concentrations. Together, these studies reveal the presence of linked in situ recognition of vimentin by both T- and B-cells in HLA-DRB1*03⁺ sarcoidosis patients, associated with a selective humoral immune response to the vimentin C-terminus.

Validation of Polygenic Scores for QT Interval in Clinical Populations

BACKGROUND

Polygenic risk scores (PGS) enable rapid estimation of genome-wide susceptibility for traits, which may be useful in clinical settings, such as prediction of QT interval. In this study, we sought to validate PGS for QT interval in 2 real-world cohorts of European ancestry (EA) and African ancestry (AA).

METHODS AND RESULTS

Two thousand nine hundred and fifteen participants of EA and 366 of AA in the MGH CAMP study (Cardiology and Metabolic Patient) were genotyped on a genome-wide array and imputed to the 1000 Genomes reference panel. An additional 820 EA and 57 AA participants in the Partners Biobank were genotyped and used for validation. PGS were created for each individual using effect estimates from association tests with QT interval obtained from prior genome-wide association studies, with variants selected based from multiple significance thresholds in the original study. In regression models, clinical variables explained ≈9% to 10% of total variation in resting QTc in EA individuals and ≈12% to 18% in AA individuals. The PGS significantly increased variation explained at most significance thresholds (P<0.001), with a trend toward increased variation explained at more stringent P value cut points in the CAMP EA cohort (P<0.05). In AA individuals, PGS provided no improvement in variation explained at any significance threshold.

CONCLUSIONS

For individuals of European descent, PGS provided a significant increase in variation in QT interval explained compared with a model with only nongenetic factors at nearly every significance level. There was no apparent benefit gained by relaxing the significance threshold from conventional genome-wide significance (P<5×10^-8).

Rationale and Design of the Brigham Cohort for psoriasis and psoriatic arthritis registry (COPPAR)

Background

Psoriasis (PsO) and psoriatic arthritis (PsA) are related conditions with poorly defined transition among them, risk factors for progression, complex treatment algorithms, and biomarkers for treatment response and long-term outcomes. We describe the development of a PsO/PsA registry at an academic medical center.

Methods

We developed a single-center PsO/PsA longitudinal disease registry including biorepository that captures relevant disease markers and treatment choices in a circumscribed population with a defined catchment area. We searched the electronic medical record for patients with visits in the last year for PsO or PsA. They formed the potentially eligible registry population. Baseline patient and provider questionnaires were developed using standardized measures, including demographics, comorbidities, medications, specific disease characteristics, functional status, quality of life, mental health, and resource use. An abbreviated set of items was collected every six month and at visits with treatment changes or disease flares. Biospecimens included blood (serum, plasma, DNA, RNA) and skin biopsy samples, with repeat collections of serum and plasma. Data from the EMR to augment the registry questionnaires are available on all patients.

Discussion

Searching the Brigham EMR system from 2013 through 2014, we found 1694 patients with PsO and 1028 with PsA. Their mean age was 55 years and 53% were female. Of these 17% had diabetes, 38% hyperlipidemia, and 45% hypertension. The median BMI was 29.6. PsA patients used more systemic prednisone, MTX, and TNF alpha inhibitors (47%, 60%, and 66%) compared to PsO patients (28%, 20% and 21%). We have collected plasma in 410 patients, DNA/RNA in 453 patients. In conclusion, we have developed a PsO/PsA registry to better define longitudinal disease characteristics, perform biomarker studies, and examine treatment trends.

High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis

BACKGROUND

Twin studies are powerful models to elucidate epigenetic modifications resulting from gene-environment interactions. Yet, commonly a limited number of clinical twin samples are available, leading to an underpowered situation afflicted with false positives and hampered by low sensitivity. We investigated genome-wide DNA methylation data from two small sets of monozygotic twins representing different phases during the progression of rheumatoid arthritis (RA) to find novel genes for further research.

METHODS

We implemented a robust statistical methodology aimed at investigating a small number of samples to identify differential methylation utilizing the comprehensive CHARM platform with whole blood cell DNA from two sets of twin pairs discordant either for ACPA (antibodies to citrullinated protein antigens)-positive RA versus ACPA-negative healthy or for ACPA-positive healthy (a pre-RA stage) versus ACPA-negative healthy. To deconvolute cell type-dependent differential methylation, we assayed the methylation patterns of sorted cells and used computational algorithms to resolve the relative contributions of different cell types and used them as covariates.

RESULTS

To identify methylation biomarkers, five healthy twin pairs discordant for ACPAs were profiled, revealing a single differentially methylated region (DMR). Seven twin pairs discordant for ACPA-positive RA revealed six significant DMRs. After deconvolution of cell type proportions, profiling of the healthy ACPA discordant twin-set revealed 17 genome-wide significant DMRs. When methylation profiles of ACPA-positive RA twin pairs were adjusted for cell type, the analysis disclosed one significant DMR, associated with the EXOSC1 gene. Additionally, the results from our methodology suggest a temporal connection of the protocadherine beta-14 gene to ACPA-positivity with clinical RA.

CONCLUSIONS

Our biostatistical methodology, optimized for a low-sample twin design, revealed non-genetically linked genes associated with two distinct phases of RA. Functional evidence is still lacking but the results reinforce further study of epigenetic modifications influencing the progression of RA. Our study design and methodology may prove generally useful in twin studies.

Recent Advances in Defining the Genetic Basis of Rheumatoid Arthritis

Rheumatoid arthritis (RA) is the most common inflammatory arthritis and exhibits genetic overlap with other autoimmune and inflammatory disorders. Although predominant associations with the HLA-DRB1 locus have been known for decades, recent data have revealed additional insight into the likely causative variants within HLA-DRB1 as well as within other HLA loci that contribute to disease risk. In addition, more than 100 common variants in non-HLA loci have been implicated in disease susceptibility. Genetic factors are involved not only in the development of RA, but also with various disease subphenotypes, including production and circulating levels of autoantibodies and joint destruction. The major current challenge is to integrate these new data into a precise understanding of disease pathogenesis, including the critical cell types and molecular networks involved as well as interactions with environmental factors. We predict that delineating the functional effects of genetic variants is likely to drive new diagnostic and therapeutic approaches to the disease.

Family history of rheumatoid arthritis: an old concept with new developments

Family history of rheumatoid arthritis (RA) is a proxy for an individual's genetic and, in part, environmental risk of developing RA, and is a well-recognized predictor of disease onset. Although family history of RA is an old concept, the degree of familial aggregation of RA, whether it differs by age, sex, or serology, and what value it has for clinical decisions once a diagnosis of RA has been made remain unclear. New data have been emerging in parallel to substantial progress made in genetic association studies. In this Review, we describe the various ways that familial aggregation has been measured, and how the findings from these studies, whether they are based on twins, cohorts of first-degree relatives, or genetic data, correspond to each other and aid understanding of the aetiology of RA. In addition, we review the potential usefulness of family history of RA from a clinical point of view, demonstrating that, in the era of big data and genomics, family history still has a role in directing clinical decision-making and research.

The genetics of human autoimmune disease: A perspective on progress in the field and future directions

Progress in defining the genetics of autoimmune disease has been dramatically enhanced by large scale genetic studies. Genome-wide approaches, examining hundreds or for some diseases thousands of cases and controls, have been implemented using high throughput genotyping and appropriate algorithms to provide a wealth of data over the last decade. These studies have identified hundreds of non-HLA loci as well as further defining HLA variations that predispose to different autoimmune diseases. These studies to identify genetic risk loci are also complemented by progress in gene expression studies including definition of expression quantitative trait loci (eQTL), various alterations in chromatin structure including histone marks, DNase I sensitivity, repressed chromatin regions as well as transcript factor binding sites. Integration of this information can partially explain why particular variations can alter proclivity to autoimmune phenotypes. Despite our incomplete knowledge base with only partial definition of hereditary factors and possible functional connections, this progress has and will continue to facilitate a better understanding of critical pathways and critical changes in immunoregulation. Advances in defining and understanding functional variants potentially can lead to both novel therapeutics and personalized medicine in which therapeutic approaches are chosen based on particular molecular phenotypes and genomic alterations.

Anti-CCP antibody levels are not associated with MS: results from a case-control study

Citrullinated proteins have been suggested to play a critical role in the pathogenesis of multiple sclerosis (MS). Anticyclic citrullinated peptide (anti-CCP) antibody is used in the early diagnosis of rheumatoid arthritis (RA). The objective of this study was to investigate the presence of anti-CCP antibody in patients with MS compared to RA patients and healthy controls. Fifty patients with MS (38 females, 12 males; mean age 36.72 ± 8.82 years), 52 patients with RA (40 females, 12 males; mean age 40.87 ± 10.17 years), and 50 healthy controls (32 females, 18 males; mean age 38.22 ± 11.59 years) were included in this study. The levels of serum anti-CCP antibody were measured using an enzyme-linked immunosorbent assay (ELISA). The results of the study showed that anti-CCP antibody levels were significantly higher in RA patients versus MS or healthy controls (P < 0.001). Moreover, anti-CCP antibody was positive in 43 (83%) patients with RA, while it was negative in all MS patients as well as in all healthy controls. Also, no significant correlation was found between the anti-CCP levels and EDSS scores (r = −0.250). In conclusion, the results of this study did not support a positive association between serum anti-CCP antibody and MS.