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1.
Nat Commun ; 10(1): 3902, 2019 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-31467281

RESUMO

Systemic lupus erythematous (SLE) is a heterogeneous autoimmune disease in which outcomes vary among different racial groups. Here, we aim to identify SLE subgroups within a multiethnic cohort using an unsupervised clustering approach based on the American College of Rheumatology (ACR) classification criteria. We identify three patient clusters that vary according to disease severity. Methylation association analysis identifies a set of 256 differentially methylated CpGs across clusters, including 101 CpGs in genes in the Type I Interferon pathway, and we validate these associations in an external cohort. A cis-methylation quantitative trait loci analysis identifies 744 significant CpG-SNP pairs. The methylation signature is enriched for ethnic-associated CpGs suggesting that genetic and non-genetic factors may drive outcomes and ethnic-associated methylation differences. Our computational approach highlights molecular differences associated with clusters rather than single outcome measures. This work demonstrates the utility of applying integrative methods to address clinical heterogeneity in multifactorial multi-ethnic disease settings.


Assuntos
Biologia Computacional , Grupos Étnicos/genética , Genômica , Lúpus Eritematoso Sistêmico/genética , Família Multigênica , Estudos de Coortes , Metilação de DNA , Epigenômica , Feminino , Estudos de Associação Genética , Genótipo , Humanos , Masculino , Locos de Características Quantitativas , Índice de Gravidade de Doença , Estados Unidos
2.
Artigo em Inglês | MEDLINE | ID: mdl-31058460

RESUMO

OBJECTIVE: We examined quality measures for screening, diagnosis and treatment of lupus nephritis (LN) among participants of the California Lupus Epidemiology Study (CLUES) across 25 different clinical sites to identify gaps in quality of care. METHODS: Data from 250 lupus participants was analyzed across three sources (medical records, physician examination, and patient interviews). Overall performance on eight quality measures was calculated separately for participants with and without LN. We used generalized estimating equations in which the outcome was performance on measures, adjusting for participant demographics, lupus disease severity and practice characteristics. RESULTS: Of 148 patients without LN, 42% had screening labs for nephritis, 38% had lupus activity serologies and 81% had blood pressure checked every 6 months. Of 102 LN patients, 67% had a timely kidney biopsy, at least 81% had appropriate treatment and 78% achieved target blood pressure within 1 year of diagnosis. Overall performance in participants across quality measures was 54% (no LN) and 80% (LN). Significantly higher overall performance for screening measures for LN was seen at academic (63.4-73%) versus community clinics (37.9-38.4%). Similarly, among those with LN, higher performance in academic (84.1-85.2%) versus community clinics (54.8-60.2%) was observed for treatment measures. CONCLUSION: In this quality of care analysis across 25 diverse clinical settings, we found relatively high performance on measures for management of LN. However, future work should focus on bridging the gaps in lupus quality of care for patients without nephritis, particularly in community settings. This article is protected by copyright. All rights reserved.

3.
Artigo em Inglês | MEDLINE | ID: mdl-31069933

RESUMO

PURPOSE: Adverse childhood experiences (ACEs) are associated with poor adult health and immune dysregulation. The impact of ACEs on patients with autoimmune disease is unknown. We compared the prevalence of ACEs in Systemic Lupus Erythematosus (SLE) patients to population-based survey estimate and investigated relationships between ACEs and SLE outcomes. METHODS: Data derive from the California Lupus Epidemiology Study (CLUES), a sample of adult SLE patients. Participants completed a 10-item ACE questionnaire covering 3 domains (abuse, neglect, household challenges). We estimated ACEs prevalence in 269 CLUES participants compared to 2015 California Behavioral Risk Factor Surveillance System (BRFSS) geographically matched respondents, standardized (age, sex, race/ethnicity) to CLUES participant characteristics. We examined associations for patient-reported and physician-assessed health status measures with overall ACE levels and domains using multivariable linear regression, controlling for socio-demographics, nephritis, and childhood onset SLE. RESULTS: Though specific domains varied, overall ACE levels were similar for CLUES and BRFSS respondents. Among SLE patients, 63.2% had ≥1 ACE and 19.3% had ≥4. ACEs were more prevalent in those who were older, women, Latino or African American, without college degrees, and with lupus nephritis. In adjusted models, higher ACE levels and ACE domains were associated with worse patient-reported SLE activity, depression, and health status, but were not significantly associated with physician-assessed SLE activity, damage, or severity. CONCLUSIONS: Given the association between ACE levels and important patient-reported outcomes in SLE, our study reinforces the need for prevention of ACEs in childhood and for clinical interventions to promote resilience among adults who have experienced ACEs. This article is protected by copyright. All rights reserved.

4.
Arthritis Care Res (Hoboken) ; 71(12): 1630-1639, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30354017

RESUMO

OBJECTIVE: We examined psychometric performance of Patient-Reported Outcomes Measurement Information System (PROMIS) measures in a racially/ethnically and linguistically diverse cohort with systemic lupus erythematosus (SLE). METHODS: Data were from the California Lupus Epidemiology Study, a multiracial/multiethnic cohort of individuals with physician-confirmed SLE. The majority (n = 332) attended in-person research visits that included interviews conducted in English, Spanish, Cantonese, or Mandarin. Up to 12 PROMIS short forms were administered (depending on language availability). An additional 99 individuals completed the interview by phone only. Internal consistency was examined with Cronbach's alpha and item-total correlations. Correlations with the Short Form 36 subscales and both self-reported and physician-assessed disease activity assessed convergent validity. All analyses were repeated within each racial/ethnic group. Differences in scores by race/ethnicity were examined in bivariate analyses and by multiple regression analyses controlling for age, sex, disease duration, and disease damage and activity. RESULTS: The total sample was 30.0% white, 22.3% Hispanic, 10.9% African American, 33.7% Asian, and 3.0% other race/ethnicity. Seventy-seven percent of interviews were conducted in-person. Non-English interviews were conducted in 26.0% of the Hispanic subjects and 18.6% of the Asian subjects. Each scale demonstrated adequate reliability and validity overall and within racial/ethnic groups. Minimal floor effects were observed, but ceiling effects were noted. Missing item responses were minimal for most scales, except for items related to work. No differences were noted by mode of administration or by language of administration among Hispanics and Asians. After accounting for differences in disease status, age, and sex, few differences in mean scores between whites and other racial/ethnic groups were noted. CONCLUSION: PROMIS measures appear reliable and valid in persons with lupus across racial/ethnic groups.

5.
Lupus Sci Med ; 5(1): e000285, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30094041

RESUMO

SLE is a complex autoimmune disease that results from the interplay of genetics, epigenetics and environmental exposures. DNA methylation is an epigenetic mechanism that regulates gene expression and tissue differentiation. Among all the epigenetic modifications, DNA methylation perturbations have been the most widely studied in SLE. It mediates processes relevant to SLE, including lymphocyte development, X-chromosome inactivation and the suppression of endogenous retroviruses. The establishment of most DNA methylation marks occurs in utero; however, a small percentage of epigenetic marks are dynamic and can change throughout a person's lifetime and in relation to exposures. In this review, we discuss the current understanding of the biology of DNA methylation and its regulators, the measurement and interpretation of methylation marks, the effects of genetics on DNA methylation and the role of environmental exposures with relevance to SLE. We also summarise research findings associated with SLE disease risk and heterogeneity. The robust finding of hypomethylation of interferon-responsive genes in patients with SLE and new associations beyond interferon-responsive genes such as cell-specific methylation abnormalities are described. We also discuss methylation changes associated with lupus nephritis, autoantibody status and disease activity. Lastly, we explore future research directions, emphasising the need for longitudinal studies, cell tissue and context-specific profiling, as well as integrative approaches. With new technologies, DNA methylation perturbations could be targeted and edited, offering novel therapeutic approaches.

6.
PLoS One ; 13(6): e0199003, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29953444

RESUMO

OBJECTIVE: African Americans, East Asians, and Hispanics with systemic lupus erythematous (SLE) are more likely to develop lupus nephritis (LN) than are SLE patients of European descent. The etiology of this difference is not clear, and this study was undertaken to investigate how genetic variants might explain this effect. METHODS: In this cross-sectional study, 1244 SLE patients from multiethnic case collections were genotyped for 817,810 single-nucleotide polymorphisms (SNPs) across the genome. Continental genetic ancestry was estimated utilizing the program ADMIXTURE. Gene-based testing and pathway analysis was performed within each ethnic group and meta-analyzed across ethnicities. We also performed candidate SNP association tests with SNPs previously established as risk alleles for SLE, LN, and chronic kidney disease (CKD). Association testing and logistic regression models were performed with LN as the outcome, adjusted for continental ancestries, sex, disease duration, and age. RESULTS: We studied 255 North European, 263 South European, 238 Hispanic, 224 African American and 264 East Asian SLE patients, of whom 606 had LN (48.7%). In genome-wide gene-based and candidate SNP analyses, we found distinct genes, pathways and established risk SNPs associated with LN for each ethnic group. Gene-based analyses showed significant associations between variation in ZNF546 (p = 1.0E-06), TRIM15 (p = 1.0E-06), and TRIMI0 (p = 1.0E-06) and LN among South Europeans, and TTC34 (p = 8.0E-06) was significantly associated with LN among Hispanics. The SNP rs8091180 in NFATC1 was associated with LN (OR 1.43, p = 3.3E-04) in the candidate SNP meta-analysis with the highest OR among African-Americans (OR 2.17, p = 0.0035). CONCLUSION: Distinct genetic factors are associated with the risk of LN in SLE patients of different ethnicities. CKD risk alleles may play a role in the development of LN in addition to SLE-associated risk variants. These findings may further explain the clinical heterogeneity of LN risk and response to therapy observed between different ethnic groups.


Assuntos
Nefrite Lúpica/etnologia , Nefrite Lúpica/genética , Modelos Genéticos , Polimorfismo de Nucleotídeo Único , Adulto , Estudos de Coortes , Feminino , Humanos , Nefrite Lúpica/epidemiologia , Masculino , Pessoa de Meia-Idade , Fatores de Risco
7.
Nat Biotechnol ; 36(1): 89-94, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29227470

RESUMO

Droplet single-cell RNA-sequencing (dscRNA-seq) has enabled rapid, massively parallel profiling of transcriptomes. However, assessing differential expression across multiple individuals has been hampered by inefficient sample processing and technical batch effects. Here we describe a computational tool, demuxlet, that harnesses natural genetic variation to determine the sample identity of each droplet containing a single cell (singlet) and detect droplets containing two cells (doublets). These capabilities enable multiplexed dscRNA-seq experiments in which cells from unrelated individuals are pooled and captured at higher throughput than in standard workflows. Using simulated data, we show that 50 single-nucleotide polymorphisms (SNPs) per cell are sufficient to assign 97% of singlets and identify 92% of doublets in pools of up to 64 individuals. Given genotyping data for each of eight pooled samples, demuxlet correctly recovers the sample identity of >99% of singlets and identifies doublets at rates consistent with previous estimates. We apply demuxlet to assess cell-type-specific changes in gene expression in 8 pooled lupus patient samples treated with interferon (IFN)-ß and perform eQTL analysis on 23 pooled samples.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Lúpus Eritematoso Sistêmico/tratamento farmacológico , Análise de Célula Única/métodos , Transcriptoma/genética , Genótipo , Humanos , Interferons/uso terapêutico , Lúpus Eritematoso Sistêmico/genética , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética
8.
Rheum Dis Clin North Am ; 43(4): 531-545, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-29061240

RESUMO

Neuropsychiatric systemic lupus erythematosus (NPSLE) encompasses a variety of phenomena. Manifestations are focal or diffuse, and correlate with disease mechanisms. Recent understanding of the contribution of blood-brain barrier dysfunction to the passage of circulating antineuronal antibodies into the brain parenchyma has shed light on pathogenesis. Correct attribution of neuropsychiatric manifestations to SLE remains a challenge, but validated attribution models will help. Diagnosis relies on characteristic clinical manifestations, SLE disease activity, antibody measurements, cerebrospinal fluid findings, specific neuroimaging findings, and exclusion of alternative etiologies. Current treatment encompasses the identification and management of the inciting event, symptomatic treatment, and anticoagulation or immunosuppression.


Assuntos
Vasculite Associada ao Lúpus do Sistema Nervoso Central/diagnóstico , Vasculite Associada ao Lúpus do Sistema Nervoso Central/terapia , Humanos , Vasculite Associada ao Lúpus do Sistema Nervoso Central/etiologia
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