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1.
Artigo em Inglês | MEDLINE | ID: mdl-31199565

RESUMO

OBJECTIVE: To describe the clinical and serological manifestations of Sjögren's syndrome (SS) in ethnic groups of the United States. METHODS: Cross-sectional study of 648 patients with primary SS: 20 African-American (AA), 164 American Indian (AI), 426 European-American (EA) and 38 of other races evaluated in a multi-disciplinary sicca research clinic. RESULTS: AA subjects comprised 3.1% of the SS cohort, much lower than the percentage of AA in the State of Oklahoma (p=3.01xE-05), the United States (p=2.24E-13) or a lupus cohort at the same institution (p=4.26x10E-27). In contrast, the percentage of AI in the SS cohort (25.3%) was much higher than expected (p=3.17E-09 vs. SLE; p=6.36-26 vs. Oklahoma and p=8.14E-96 vs. USA population). The SS classification criteria were similar between AA and EA, but subjects of AI ancestry had lower rates of abnormal tear and salivary flow as well as anti-Ro/SSA and anti-La/SSB antibodies. Paradoxically, AI had higher levels of disease activity (mean±SD ESSDAI 3.77±4.78) in comparison to whites (2.90±4.12; p=0.011) and more extraglandular manifestations affecting mainly the articular and glandular domains. Meanwhile, AA patients were characterized by higher rates of hypergammaglobulinemia (OR 1.39, 95%CI 1.39-8.65, p=0.01), elevated ESR (OR 3.95, 95%CI 1.46-9.95, p=0.009), and parotid enlargement (OR 4.40, 95%CI 1.49-13.07, p=0.02). CONCLUSIONS: American Indians are affected at high rates with SS but present with few classical features, potentially preventing timely diagnosis. In contrast to SLE, SS is infrequent and not more severe amongst AA, but the triad of hypergammaglobulinemia, increased ESR and parotid enlargement warrants extra vigilance for lymphomagenesis. This article is protected by copyright. All rights reserved.

2.
J Am Dent Assoc ; 149(8): 666-667, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29960642
5.
Clin Exp Rheumatol ; 36 Suppl 112(3): 80-88, 2018 May-Jun.
Artigo em Inglês | MEDLINE | ID: mdl-29148407

RESUMO

OBJECTIVES: Evaluate the presence of minor salivary gland (SG) fibrosis in primary Sjögren's syndrome (pSS) as a function of disease pathology or a consequence of ageing. METHODS: Subjects with sicca symptoms attending a Sjögren's research clinic were classified by American European Consensus Group (AECG) criteria as either pSS or non-SS (nSS). Discovery (n=34 pSS, n=28 nSS) and replication (n=35 pSS, n=31 nSS) datasets were evaluated. Minor SG cross-sections from haematoxylin and eosin stained slides were imaged, digitally reconstructed and analysed for percent area fibrosis. Relationships between SG fibrosis, age, and clinical measures were evaluated using Spearman correlations. Association with SS was assessed by: ROC curve, Variable Selection Using Random Forests (VSURF) and uni- and bi-variate regression analyses. RESULTS: SS subjects had significantly more fibrotic tissue in their minor labial salivary glands (median 24.39%, range 5.12-51.67%) than nSS participants (median 16.7%, range 5.97-38.65%, p<0.0001); age did not differ between groups (average ± SD pSS 50.2 ±13.9 years, nSS 53.8±12.4 years). In both the discovery and replication data sets, multiple regression models showed that the area of minor salivary gland fibrosis predicted pSS significantly better than age alone. Age-corrected linear regression revealed that the area of minor salivary gland fibrosis positively associated with vanBijsterveld score (p=0.042) and biopsy focus score (p=0.002). ROC curve and VSURF analyses ranked fibrosis as a significantly more important variable for subject discrimination than age. CONCLUSIONS: SG fibrosis is an element of pSS pathology that is related to focus score and is not solely attributable to age.


Assuntos
Glândulas Salivares Menores/patologia , Síndrome de Sjogren/patologia , Adulto , Fatores Etários , Idoso , Área Sob a Curva , Biópsia , Estudos de Casos e Controles , Feminino , Fibrose , Humanos , Modelos Lineares , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Valor Preditivo dos Testes , Prognóstico , Curva ROC , Glândulas Salivares Menores/imunologia , Índice de Gravidade de Doença , Síndrome de Sjogren/imunologia
7.
Autoimmunity ; 50(8): 451-457, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28988489

RESUMO

OBJECTIVE: Determine the presence and assess the extent of fatty infiltration of the minor salivary glands (SG) of primary SS patients (pSS) as compared to those with non-SS sicca (nSS). METHODS: Minor SG biopsy samples from 134 subjects with pSS (n = 72) or nSS (n = 62) were imaged. Total area and fatty replacement area for each glandular cross-section (n = 4-6 cross-sections per subject) were measured using Image J (National Institutes of Health, Bethesda, MD). The observer was blinded to subject classification status. The average area of fatty infiltration calculated per subject was evaluated by logistic regression and general linearized models (GLM) to assess relationships between fatty infiltration and clinical exam results, extent of fibrosis and age. RESULTS: The average area of fatty infiltration for subjects with pSS (median% (range) 4.97 (0.05-30.2)) was not significantly different from that of those with nSS (3.75 (0.087-41.9). Infiltration severity varied widely, and subjects with fatty replacement greater than 6% were equivalently distributed between pSS and nSS participants (χ2 p = .50). Age accounted for all apparent relationships between fatty infiltration and fibrosis or reduced saliva flow. The all-inclusive GLM for prediction of pSS versus non-SS classification including fibrosis, age, fatty replacement, and focus score was not significantly different from any desaturated model. In no iteration of the model did fatty replacement exert a significant effect on the capacity to predict pSS classification. CONCLUSIONS: Fatty infiltration is an age-associated phenomenon and not a selective feature of Sjögren's syndrome. Sicca patients who do not fulfil pSS criteria have similar rates of fatty infiltration of the minor SG.


Assuntos
Tecido Adiposo/patologia , Envelhecimento/imunologia , Envelhecimento/patologia , Glândulas Salivares Menores/imunologia , Glândulas Salivares Menores/patologia , Síndrome de Sjogren/imunologia , Síndrome de Sjogren/patologia , Adulto , Idoso , Autoanticorpos/imunologia , Biomarcadores , Biópsia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Prognóstico , Síndrome de Sjogren/metabolismo
8.
Arthritis Rheumatol ; 69(11): 2187-2192, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-28692793

RESUMO

OBJECTIVE: Sjögren's syndrome (SS) and systemic lupus erythematosus (SLE) are related by clinical and serologic manifestations as well as genetic risks. Both diseases are more commonly found in women than in men, at a ratio of ~10 to 1. Common X chromosome aneuploidies, 47,XXY and 47,XXX, are enriched among men and women, respectively, in either disease, suggesting a dose effect on the X chromosome. METHODS: We examined cohorts of SS and SLE patients by constructing intensity plots of X chromosome single-nucleotide polymorphism alleles, along with determining the karyotype of selected patients. RESULTS: Among ~2,500 women with SLE, we found 3 patients with a triple mosaic, consisting of 45,X/46,XX/47,XXX. Among ~2,100 women with SS, 1 patient had 45,X/46,XX/47,XXX, with a triplication of the distal p arm of the X chromosome in the 47,XXX cells. Neither the triple mosaic nor the partial triplication was found among the controls. In another SS cohort, we found a mother/daughter pair with partial triplication of this same region of the X chromosome. The triple mosaic occurs in ~1 in 25,000-50,000 live female births, while partial triplications are even rarer. CONCLUSION: Very rare X chromosome abnormalities are present among patients with either SS or SLE and may inform the location of a gene(s) that mediates an X dose effect, as well as critical cell types in which such an effect is operative.


Assuntos
Cromossomos Humanos X/genética , Lúpus Eritematoso Sistêmico/genética , Mosaicismo/estatística & dados numéricos , Aberrações dos Cromossomos Sexuais/estatística & dados numéricos , Síndrome de Sjogren/genética , Alelos , Teorema de Bayes , Feminino , Dosagem de Genes , Humanos , Cariótipo , Lúpus Eritematoso Sistêmico/epidemiologia , Polimorfismo de Nucleotídeo Único , Transtornos do Cromossomo Sexual no Desenvolvimento Sexual/epidemiologia , Transtornos do Cromossomo Sexual no Desenvolvimento Sexual/genética , Síndrome de Sjogren/epidemiologia , Trissomia/genética , Síndrome de Turner/epidemiologia , Síndrome de Turner/genética
9.
PLoS Genet ; 13(6): e1006820, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28640813

RESUMO

Sjögren's syndrome (SS) is a common, autoimmune exocrinopathy distinguished by keratoconjunctivitis sicca and xerostomia. Patients frequently develop serious complications including lymphoma, pulmonary dysfunction, neuropathy, vasculitis, and debilitating fatigue. Dysregulation of type I interferon (IFN) pathway is a prominent feature of SS and is correlated with increased autoantibody titers and disease severity. To identify genetic determinants of IFN pathway dysregulation in SS, we performed cis-expression quantitative trait locus (eQTL) analyses focusing on differentially expressed type I IFN-inducible transcripts identified through a transcriptome profiling study. Multiple cis-eQTLs were associated with transcript levels of 2'-5'-oligoadenylate synthetase 1 (OAS1) peaking at rs10774671 (PeQTL = 6.05 × 10-14). Association of rs10774671 with SS susceptibility was identified and confirmed through meta-analysis of two independent cohorts (Pmeta = 2.59 × 10-9; odds ratio = 0.75; 95% confidence interval = 0.66-0.86). The risk allele of rs10774671 shifts splicing of OAS1 from production of the p46 isoform to multiple alternative transcripts, including p42, p48, and p44. We found that the isoforms were differentially expressed within each genotype in controls and patients with and without autoantibodies. Furthermore, our results showed that the three alternatively spliced isoforms lacked translational response to type I IFN stimulation. The p48 and p44 isoforms also had impaired protein expression governed by the 3' end of the transcripts. The SS risk allele of rs10774671 has been shown by others to be associated with reduced OAS1 enzymatic activity and ability to clear viral infections, as well as reduced responsiveness to IFN treatment. Our results establish OAS1 as a risk locus for SS and support a potential role for defective viral clearance due to altered IFN response as a genetic pathophysiological basis of this complex autoimmune disease.


Assuntos
2',5'-Oligoadenilato Sintetase/genética , Interferon Tipo I/genética , Locos de Características Quantitativas/genética , Síndrome de Sjogren/genética , 2',5'-Oligoadenilato Sintetase/biossíntese , Alelos , Processamento Alternativo/genética , Feminino , Regulação da Expressão Gênica , Estudos de Associação Genética , Predisposição Genética para Doença , Humanos , Interferon Tipo I/metabolismo , Masculino , Síndrome de Sjogren/metabolismo , Síndrome de Sjogren/patologia , Viroses/genética , Viroses/virologia
10.
PLoS One ; 12(2): e0170249, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28166540

RESUMO

OBJECTIVES: To assess the association of smoking habits with the clinical, serological, and histopathological manifestations of Sjögren's syndrome (SS) and non-Sjögren's sicca (non-SS sicca). METHODS: Cross-sectional case-control study of 1288 patients with sicca symptoms (587 SS and 701 non-SS sicca) evaluated in a multi-disciplinary research clinic. Smoking patterns were obtained from questionnaire data and disease-related clinical and laboratory data were compared between current, past, ever, and never smokers. RESULTS: Current smoking rates were 4.6% for SS patients compared to 14.1% in non-SS sicca (p = 5.17x10E-09), 18% in a local lupus cohort (p = 1.13x10E-14) and 16.8% in the community (p = 4.12x10E-15). Current smoking was protective against SS classification (OR 0.35, 95%CI 0.22-0.56, FDR q = 1.9E10-05), focal lymphocytic sialadenitis (OR 0.26, 95%CI 0.15-0.44, FDR q = 1.52x10E-06), focus score ≥1 (OR 0.22, 95%CI 0.13-0.39, FDR q = 1.43x10E-07), and anti-Ro/SSA(+) (OR 0.36, 95%CI 0.2-0.64, FDR q = 0.0009); ever smoking was protective against the same features and against anti-La/SSB(+) (OR 0.52, 95%CI 0.39-0.70, FDR q = 5.82x10E-05). Duration of smoking was inversely correlated with SS even after controlling for socioeconomic status, BMI, alcohol and caffeine consumption. CONCLUSIONS: Current tobacco smoking is negatively and independently associated with SS, protecting against disease-associated humoral and cellular autoimmunity. The overall smoking rate amongst SS patients is significantly lower than in matched populations and the effects of smoking are proportional to exposure duration. In spite of the protective effects of tobacco on SS manifestations, it is associated with other serious comorbidities such as lung disease, cardiovascular risk and malignancy, and should thus be strongly discouraged in patients with sicca.


Assuntos
Síndrome de Sjogren/sangue , Síndrome de Sjogren/patologia , Fumar , Adulto , Idoso , Autoanticorpos/sangue , Biomarcadores , Biópsia , Estudos de Casos e Controles , Estudos Transversais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Razão de Chances , Fatores de Risco , Síndrome de Sjogren/diagnóstico , Fumar/efeitos adversos
12.
Am J Otolaryngol ; 37(6): 502-506, 2016 Nov - Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27968958

RESUMO

OBJECTIVE: Requirements of an NCI contract examining a novel treatment for leukoplakia were to compare standard bi-dimensional measurement of oral lesions to examine for correlation with Response Evaluation Criteria in Solid Tumors (RECIST) criteria, and to examine the feasibility of digital image analysis for automated measurements. STUDY DESIGN: Retrospective review. METHODS: We examined 13 patients by bi-dimensional measurement and compared these measurements to 1) RECIST criteria, 2) scalar digital measurements using a standardized measuring device within the photograph, and 3) pixel number. RESULTS: RECIST criteria correlated (r-squared=0.8535, p<0.0001) with bi-dimensional measurements. Digitized measures in photographs correlated with bi-dimensional measurements (r-squared=0.6661, p=0.0007), but were time consuming. There was minimal to no correlation between pixel number in Adobe Photoshop and the other measures. CONCLUSION: Bi-dimensional measurement of oral leukoplakia and RECIST criteria are highly correlated. Digital photography measurements, though highly correlative, are very cumbersome. We recommend bi-dimensional or longest length measurement and a simple photograph as standard of documentation for leukoplakia lesions.


Assuntos
Leucoplasia Oral/patologia , Humanos , Leucoplasia Oral/diagnóstico por imagem , Leucoplasia Oral/tratamento farmacológico , PPAR gama/antagonistas & inibidores , Fotografação , Reprodutibilidade dos Testes , Estudos Retrospectivos , Carga Tumoral
14.
Clin Immunol ; 168: 25-29, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-27109640

RESUMO

Primary Sjögren's syndrome (pSS) has a strong female bias. We evaluated an X chromosome dose effect by analyzing 47,XXY (Klinefelter's syndrome, 1 in 500 live male births) among subjects with pSS. 47,XXY was determined by examination of fluorescence intensity of single nucleotide polymorphisms from the X and Y chromosomes. Among 136 pSS men there were 4 with 47,XXY. This was significantly different from healthy controls (1 of 1254 had 47,XXY, p=0.0012 by Fisher's exact test) as well men with rheumatoid arthritis (0 of 363 with 47,XXY), but not different compared to men with systemic lupus erythematosus (SLE) (4 of 136 versus 8 of 306, Fisher's exact test p=NS). These results are consistent with the hypothesis that the number of X chromosomes is critical for the female bias of pSS, a property that may be shared with SLE but not RA.


Assuntos
Artrite Reumatoide/genética , Síndrome de Klinefelter/genética , Lúpus Eritematoso Sistêmico/genética , Síndrome de Sjogren/genética , Cromossomos Humanos X/genética , Cromossomos Humanos Y/genética , Feminino , Frequência do Gene , Genótipo , Humanos , Masculino , Polimorfismo de Nucleotídeo Único
15.
Rheumatology (Oxford) ; 55(7): 1195-201, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-26998859

RESUMO

OBJECTIVE: The diagnosis of SS is often difficult and many patients are symptomatic for years with other diagnoses before confirmation of SS. Our aim was to determine whether overlapping clinical and serologic features with RA and SLE may in part drive the misdiagnoses. METHODS: A total of 1175 sicca patients were evaluated in a multidisciplinary clinic and classified as having SS based on the American-European Consensus Group Criteria. They were interrogated for a past history of suspicion or diagnosis of RA, SLE or SSc. These diseases were confirmed or ruled out by applying the corresponding classification criteria if the patients responded affirmatively. RESULTS: Of these, 524 (44.6%) subjects reported previous diagnosis or suspicion of RA, SLE or SSc, which was confirmed in 130 (24.8%) but excluded in 394 (75.2%) subjects. Of those previously diagnosed with another illness, 183 (34.9%) met the criteria for primary SS. RF was present in 70/191 patients with previous diagnosis of RA compared with 445/845 without a prior RA diagnosis (P = 3.38E-05), while 128/146 with a diagnosis of SLE had positive ANA compared with 622/881 without the diagnosis (P = 8.77E-06). Age also influenced former diagnoses: people with suspected RA were older than those without the diagnosis (P = 5.89E-06), while patients with SLE suspicion were younger (P = 0.0003). Interestingly, the previous diagnoses did not significantly delay a final classification of SS. CONCLUSION: Among subjects classified as SS, the presence of a positive ANA or RF was associated with a previous, apparently erroneous diagnosis of SLE or RA, respectively.


Assuntos
Artrite Reumatoide/diagnóstico , Erros de Diagnóstico , Lúpus Eritematoso Sistêmico/diagnóstico , Síndrome de Sjogren/diagnóstico , Idoso , Anticorpos Antinucleares/sangue , Diagnóstico Diferencial , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Fator Reumatoide/sangue , Síndrome de Sjogren/sangue
16.
Arthritis Rheumatol ; 68(5): 1290-1300, 2016 05.
Artigo em Inglês | MEDLINE | ID: mdl-26713507

RESUMO

OBJECTIVE: More than 80% of autoimmune disease predominantly affects females, but the mechanism for this female bias is poorly understood. We suspected that an X chromosome dose effect accounts for this, and we undertook this study to test our hypothesis that trisomy X (47,XXX; occurring in ∼1 in 1,000 live female births) would be increased in patients with female-predominant diseases (systemic lupus erythematosus [SLE], primary Sjögren's syndrome [SS], primary biliary cirrhosis, and rheumatoid arthritis [RA]) compared to patients with diseases without female predominance (sarcoidosis) and compared to controls. METHODS: All subjects in this study were female. We identified subjects with 47,XXX using aggregate data from single-nucleotide polymorphism arrays, and, when possible, we confirmed the presence of 47,XXX using fluorescence in situ hybridization or quantitative polymerase chain reaction. RESULTS: We found 47,XXX in 7 of 2,826 SLE patients and in 3 of 1,033 SS patients, but in only 2 of 7,074 controls (odds ratio in the SLE and primary SS groups 8.78 [95% confidence interval 1.67-86.79], P = 0.003 and odds ratio 10.29 [95% confidence interval 1.18-123.47], P = 0.02, respectively). One in 404 women with SLE and 1 in 344 women with SS had 47,XXX. There was an excess of 47,XXX among SLE and SS patients. CONCLUSION: The estimated prevalence of SLE and SS in women with 47,XXX was ∼2.5 and ∼2.9 times higher, respectively, than that in women with 46,XX and ∼25 and ∼41 times higher, respectively, than that in men with 46,XY. No statistically significant increase of 47,XXX was observed in other female-biased diseases (primary biliary cirrhosis or RA), supporting the idea of multiple pathways to sex bias in autoimmunity.


Assuntos
Artrite Reumatoide/epidemiologia , Cirrose Hepática Biliar/epidemiologia , Lúpus Eritematoso Sistêmico/epidemiologia , Transtornos do Cromossomo Sexual no Desenvolvimento Sexual/epidemiologia , Síndrome de Sjogren/epidemiologia , Doenças Autoimunes/epidemiologia , Estudos de Casos e Controles , Cromossomos Humanos X , Feminino , Dosagem de Genes , Humanos , Hibridização in Situ Fluorescente , Prevalência , Sarcoidose/epidemiologia , Aberrações dos Cromossomos Sexuais , Distribuição por Sexo , Trissomia
17.
Arthritis Rheumatol ; 68(3): 724-9, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26636433

RESUMO

OBJECTIVE: Autoantibodies reactive with Ro52 (tripartite motif-containing protein 21 [TRIM21]) are detected in 70% of patients with primary Sjögren's syndrome (SS). TRIM21 belongs to a 34-member C-IV family of TRIM proteins. Although autoantibodies against other TRIM proteins within the C-IV family have been detected in the sera of patients with primary SS, their clinical relevance remains unclear. This study was undertaken to investigate the frequency of anti-TRIM38 in patients with primary SS and evaluate its association with various clinical measures of the disease. METHODS: Serum samples from patients with primary SS (n = 235) and controls (n = 50) were analyzed for reactivity with in vitro-transcribed and -translated (35) S-methionine-labeled TRIM38 protein. The associations of anti-TRIM38 with various laboratory and clinical measures of primary SS were evaluated. Reactivity of anti-TRIM38 with different structural domains of TRIM38 was analyzed. Affinity-purified anti-TRIM38 antibodies were used to immunoprecipitate TRIM21. RESULTS: TRIM38-reactive autoantibodies were detected in the sera of 24 of the 235 patients with primary SS and 2 of the 50 controls. Anti-TRIM38 positivity was significantly associated with the presence of anti-Ro60, anti-Ro52, anti-La, rheumatoid factor, and hypergammaglobulinemia. Clinically, anti-TRIM38 was associated with significantly higher ocular surface staining scores, lower Schirmer's test scores, and minor labial salivary gland biopsy focus scores of ≥3.0. Anti-TRIM38 antibodies mainly recognized the cortactin-binding protein 2 (CortBP-2; amino acids 128-238) and the B30.2/SPRY (amino acids 268-465) domains on TRIM38. Affinity-purified antibodies to TRIM38-CortBP-2 and TRIM38-B30.2/SPRY domains reacted with TRIM21. CONCLUSION: Our data demonstrate that anti-TRIM38 specificity arising in a subset of patients with primary SS is associated with increased severity of the disease.


Assuntos
Autoanticorpos/sangue , Proteínas de Transporte/imunologia , Índice de Gravidade de Doença , Síndrome de Sjogren/imunologia , Feminino , Humanos , Hipergamaglobulinemia/imunologia , Imunoprecipitação , Masculino , Metionina , Pessoa de Meia-Idade , Fator Reumatoide/sangue , Ribonucleoproteínas/imunologia , Síndrome de Sjogren/fisiopatologia , Radioisótopos de Enxofre
19.
Proteomics ; 15(20): 3553-65, 2015 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26058579

RESUMO

Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism (e.g. human), revealing insights into the molecular functions conferred by these communities. Compared to conventional proteomics, metaproteomics presents unique data analysis challenges, including the use of large protein databases derived from hundreds or thousands of organisms, as well as numerous processing steps to ensure high data quality. These challenges limit the use of metaproteomics for many researchers. In response, we have developed an accessible and flexible metaproteomics workflow within the Galaxy bioinformatics framework. Via analysis of human oral tissue exudate samples, we have established a modular Galaxy-based workflow that automates a reduction method for searching large sequence databases, enabling comprehensive identification of host proteins (human) as well as "meta-proteins" from the nonhost organisms. Downstream, automated processing steps enable basic local alignment search tool analysis and evaluation/visualization of peptide sequence match quality, maximizing confidence in results. Outputted results are compatible with tools for taxonomic and functional characterization (e.g. Unipept, MEGAN5). Galaxy also allows for the sharing of complete workflows with others, promoting reproducibility and also providing a template for further modification and enhancement. Our results provide a blueprint for establishing Galaxy as a solution for metaproteomic data analysis. All MS data have been deposited in the ProteomeXchange with identifier PXD001655 (http://proteomecentral.proteomexchange.org/dataset/PXD001655).


Assuntos
Microbiota/genética , Proteoma/genética , Proteômica , Sequência de Aminoácidos/genética , Biologia Computacional , Bases de Dados de Proteínas , Humanos , Boca/microbiologia , Análise de Sequência de Proteína , Software
20.
Hum Mol Genet ; 24(2): 582-96, 2015 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-25205108

RESUMO

Exploiting genotyping, DNA sequencing, imputation and trans-ancestral mapping, we used Bayesian and frequentist approaches to model the IRF5-TNPO3 locus association, now implicated in two immunotherapies and seven autoimmune diseases. Specifically, in systemic lupus erythematosus (SLE), we resolved separate associations in the IRF5 promoter (all ancestries) and with an extended European haplotype. We captured 3230 IRF5-TNPO3 high-quality, common variants across 5 ethnicities in 8395 SLE cases and 7367 controls. The genetic effect from the IRF5 promoter can be explained by any one of four variants in 5.7 kb (P-valuemeta = 6 × 10(-49); OR = 1.38-1.97). The second genetic effect spanned an 85.5-kb, 24-variant haplotype that included the genes IRF5 and TNPO3 (P-valuesEU = 10(-27)-10(-32), OR = 1.7-1.81). Many variants at the IRF5 locus with previously assigned biological function are not members of either final credible set of potential causal variants identified herein. In addition to the known biologically functional variants, we demonstrated that the risk allele of rs4728142, a variant in the promoter among the lowest frequentist probability and highest Bayesian posterior probability, was correlated with IRF5 expression and differentially binds the transcription factor ZBTB3. Our analytical strategy provides a novel framework for future studies aimed at dissecting etiological genetic effects. Finally, both SLE elements of the statistical model appear to operate in Sjögren's syndrome and systemic sclerosis whereas only the IRF5-TNPO3 gene-spanning haplotype is associated with primary biliary cirrhosis, demonstrating the nuance of similarity and difference in autoimmune disease risk mechanisms at IRF5-TNPO3.


Assuntos
Fatores Reguladores de Interferon/genética , Lúpus Eritematoso Sistêmico/genética , beta Carioferinas/genética , Doenças Autoimunes/genética , Teorema de Bayes , Estudos de Casos e Controles , Estudos de Coortes , Proteínas de Ligação a DNA/genética , Haplótipos , Humanos , Masculino , Polimorfismo de Nucleotídeo Único , Regiões Promotoras Genéticas
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