Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 9 de 9
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Arthritis Rheumatol ; 72(1): 125-136, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31342624

RESUMO

OBJECTIVE: T cells play a key role in the pathogenesis of early systemic sclerosis. This study was undertaken to assess the safety and efficacy of abatacept in patients with diffuse cutaneous systemic sclerosis (dcSSc). METHODS: In this 12-month, randomized, double-blind, placebo-controlled trial, participants were randomized 1:1 to receive either subcutaneous abatacept 125 mg or matching placebo, stratified by duration of dcSSc. Escape therapy was allowed at 6 months for worsening disease. The coprimary end points were change in the modified Rodnan skin thickness score (MRSS) compared to baseline and safety over 12 months. Differences in longitudinal outcomes were assessed according to treatment using linear mixed models, with outcomes censored after initiation of escape therapy. Skin tissue obtained from participants at baseline was classified into intrinsic gene expression subsets. RESULTS: Among 88 participants, the adjusted mean change in the MRSS at 12 months was -6.24 units for those receiving abatacept and -4.49 units for those receiving placebo, with an adjusted mean treatment difference of -1.75 units (P = 0.28). Outcomes for 2 secondary measures (Health Assessment Questionnaire disability index and a composite measure) were clinically and statistically significantly better with abatacept. The proportion of subjects in whom escape therapy was needed was higher in the placebo group relative to the abatacept group (36% versus 16%). In the inflammatory and normal-like skin gene expression subsets, decline in the MRSS over 12 months was clinically and significantly greater in the abatacept group versus the placebo group (P < 0.001 and P = 0.03, respectively). In the abatacept group, adverse events occurred in 35 participants versus 40 participants in the placebo group, including 2 deaths and 1 death, respectively. CONCLUSION: In this phase II trial, abatacept was well-tolerated, but change in the MRSS was not statistically significant. Secondary outcome measures, including gene expression subsets, showed evidence in support of abatacept. These data should be confirmed in a phase III trial.

2.
Ann Rheum Dis ; 2019 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-31767698

RESUMO

OBJECTIVES: Determine global skin transcriptome patterns of early diffuse systemic sclerosis (SSc) and how they differ from later disease. METHODS: Skin biopsy RNA from 48 patients in the Prospective Registry for Early Systemic Sclerosis (PRESS) cohort (mean disease duration 1.3 years) and 33 matched healthy controls was examined by next-generation RNA sequencing. Data were analysed for cell type-specific signatures and compared with similarly obtained data from 55 previously biopsied patients in Genetics versus Environment in Scleroderma Outcomes Study cohort with longer disease duration (mean 7.4 years) and their matched controls. Correlations with histological features and clinical course were also evaluated. RESULTS: SSc patients in PRESS had a high prevalence of M2 (96%) and M1 (94%) macrophage and CD8 T cell (65%), CD4 T cell (60%) and B cell (69%) signatures. Immunohistochemical staining of immune cell markers correlated with the gene expression-based immune cell signatures. The prevalence of immune cell signatures in early diffuse SSc patients was higher than in patients with longer disease duration. In the multivariable model, adaptive immune cell signatures were significantly associated with shorter disease duration, while fibroblast and macrophage cell type signatures were associated with higher modified Rodnan Skin Score (mRSS). Immune cell signatures also correlated with skin thickness progression rate prior to biopsy, but did not predict subsequent mRSS progression. CONCLUSIONS: Skin in early diffuse SSc has prominent innate and adaptive immune cell signatures. As a prominently affected end organ, these signatures reflect the preceding rate of disease progression. These findings could have implications in understanding SSc pathogenesis and clinical trial design.

3.
Arthritis Rheumatol ; 71(10): 1701-1710, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30920766

RESUMO

OBJECTIVE: High-throughput gene expression profiling of tissue samples from patients with systemic sclerosis (SSc) has identified 4 "intrinsic" gene expression subsets: inflammatory, fibroproliferative, normal-like, and limited. Prior methods required agglomerative clustering of many samples. In order to classify individual patients in clinical trials or for diagnostic purposes, supervised methods that can assign single samples to molecular subsets are required. We undertook this study to introduce a novel machine learning classifier as a robust accurate intrinsic subset predictor. METHODS: Three independent gene expression cohorts were curated and merged to create a data set covering 297 skin biopsy samples from 102 unique patients and controls, which was used to train a machine learning algorithm. We performed external validation using 3 independent SSc cohorts, including a gene expression data set generated by an independent laboratory on a different microarray platform. In total, 413 skin biopsy samples from 213 individuals were analyzed in the training and testing cohorts. RESULTS: Repeated cross-fold validation identified consistent and discriminative markers using multinomial elastic net, performing with an average classification accuracy of 87.1% with high sensitivity and specificity. In external validation, the classifier achieved an average accuracy of 85.4%. Reanalyzing data from a previous study, we identified subsets of patients that represent the canonical inflammatory, fibroproliferative, and normal-like subsets. CONCLUSION: We developed a highly accurate classifier for SSc molecular subsets for individual patient samples. The method can be used in SSc clinical trials to identify an intrinsic subset on individual samples. Our method provides a robust data-driven approach to aid clinical decision-making and interpretation of heterogeneous molecular information in SSc patients.

4.
Arthritis Res Ther ; 21(1): 49, 2019 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-30728065

RESUMO

BACKGROUND: Infectious agents have long been postulated to be disease triggers for systemic sclerosis (SSc), but a definitive link has not been found. Metagenomic analyses of high-throughput data allows for the unbiased identification of potential microbiome pathogens in skin biopsies of SSc patients and allows insight into the relationship with host gene expression. METHODS: We examined skin biopsies from a diverse cohort of 23 SSc patients (including lesional forearm and non-lesional back samples) by RNA-seq. Metagenomic filtering and annotation was performed using the Integrated Metagenomic Sequencing Analysis (IMSA). Associations between microbiome composition and gene expression were analyzed using single-sample gene set enrichment analysis (ssGSEA). RESULTS: We find the skin of SSc patients exhibits substantial changes in microbial composition relative to controls, characterized by sharp decreases in lipophilic taxa, such as Propionibacterium, combined with increases in a wide range of gram-negative taxa, including Burkholderia, Citrobacter, and Vibrio. CONCLUSIONS: Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression. These data provide a comprehensive portrait of the SSc skin microbiome and its association with local gene expression, which mirrors the molecular changes in lesional skin.

5.
Bioinformatics ; 35(19): 3635-3641, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-30799505

RESUMO

MOTIVATION: The accumulation of publicly available DNA methylation datasets has resulted in the need for tools to interpret the specific cellular phenotypes in bulk tissue data. Current approaches use either single differentially methylated CpG sites or differentially methylated regions that map to genes. However, these approaches may introduce biases in downstream analyses of biological interpretation, because of the variability in gene length. There is a lack of approaches to interpret DNA methylation effectively. Therefore, we have developed computational models to provide biological interpretation of relevant gene sets using DNA methylation data in the context of The Cancer Genome Atlas. RESULTS: We illustrate that Biological interpretation of DNA Methylation (BioMethyl) utilizes the complete DNA methylation data for a given cancer type to reflect corresponding gene expression profiles and performs pathway enrichment analyses, providing unique biological insight. Using breast cancer as an example, BioMethyl shows high consistency in the identification of enriched biological pathways from DNA methylation data compared to the results calculated from RNA sequencing data. We find that 12 out of 14 pathways identified by BioMethyl are shared with those by using RNA-seq data, with a Jaccard score 0.8 for estrogen receptor (ER) positive samples. For ER negative samples, three pathways are shared in the two enrichments with a slight lower similarity (Jaccard score = 0.6). Using BioMethyl, we can successfully identify those hidden biological pathways in DNA methylation data when gene expression profile is lacking. AVAILABILITY AND IMPLEMENTATION: BioMethyl R package is freely available in the GitHub repository (https://github.com/yuewangpanda/BioMethyl). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

6.
J Invest Dermatol ; 138(6): 1301-1310, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29391252

RESUMO

Fewer than half of patients with systemic sclerosis demonstrate modified Rodnan skin score improvement during mycophenolate mofetil (MMF) treatment. To understand the molecular basis for this observation, we extended our prior studies and characterized molecular and cellular changes in skin biopsies from subjects with systemic sclerosis treated with MMF. Eleven subjects completed ≥24 months of MMF therapy. Two distinct skin gene expression trajectories were observed across six of these subjects. Three of the six subjects showed attenuation of the inflammatory signature by 24 months, paralleling reductions in CCL2 mRNA expression in skin and reduced numbers of macrophages and myeloid dendritic cells in skin biopsies. MMF cessation at 24 months resulted in an increased inflammatory score, increased CCL2 mRNA and protein levels, modified Rodnan skin score rebound, and increased numbers of skin myeloid cells in these subjects. In contrast, three other subjects remained on MMF >24 months and showed a persistent decrease in inflammatory score, decreasing or stable modified Rodnan skin score, CCL2 mRNA reductions, sera CCL2 protein levels trending downward, reduction in monocyte migration, and no increase in skin myeloid cell numbers. These data summarize molecular changes during MMF therapy that suggest reduction of innate immune cell numbers, possibly by attenuating expression of chemokines, including CCL2.


Assuntos
Imunossupressores/uso terapêutico , Ácido Micofenólico/uso terapêutico , Células Mieloides/efeitos dos fármacos , Escleroderma Sistêmico/tratamento farmacológico , Adulto , Biópsia , Estudos de Casos e Controles , Contagem de Células , Quimiocina CCL2/imunologia , Quimiocina CCL2/metabolismo , Feminino , Perfilação da Expressão Gênica , Humanos , Imunossupressores/farmacologia , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Ácido Micofenólico/farmacologia , Células Mieloides/imunologia , Estudos Prospectivos , Escleroderma Sistêmico/imunologia , Escleroderma Sistêmico/patologia , Pele/citologia , Pele/efeitos dos fármacos , Pele/imunologia , Pele/patologia , Transcriptoma/efeitos dos fármacos , Transcriptoma/imunologia , Resultado do Tratamento
7.
Bioinformatics ; 34(11): 1868-1874, 2018 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-29360996

RESUMO

Motivation: Molecular subtypes of cancers and autoimmune disease, defined by transcriptomic profiling, have provided insight into disease pathogenesis, molecular heterogeneity and therapeutic responses. However, technical biases inherent to different gene expression profiling platforms present a unique problem when analyzing data generated from different studies. Currently, there is a lack of effective methods designed to eliminate platform-based bias. We present a method to normalize and classify RNA-seq data using machine learning classifiers trained on DNA microarray data and molecular subtypes in two datasets: breast invasive carcinoma (BRCA) and colorectal cancer (CRC). Results: Multiple analyses show that feature specific quantile normalization (FSQN) successfully removes platform-based bias from RNA-seq data, regardless of feature scaling or machine learning algorithm. We achieve up to 98% accuracy for BRCA data and 97% accuracy for CRC data in assigning molecular subtypes to RNA-seq data normalized using FSQN and a support vector machine trained exclusively on DNA microarray data. We find that maximum accuracy was achieved when normalizing RNA-seq datasets that contain at least 25 samples. FSQN allows comparison of RNA-seq data to existing DNA microarray datasets. Using these techniques, we can successfully leverage information from existing gene expression data in new analyses despite different platforms used for gene expression profiling. Availability and implementation: FSQN has been submitted as an R package to CRAN. All code used for this study is available on Github (https://github.com/jenniferfranks/FSQN). Contact: michael.l.whitfield@dartmouth.edu. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Perfilação da Expressão Gênica/métodos , Neoplasias/genética , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Máquina de Vetores de Suporte , Neoplasias da Mama/genética , Neoplasias do Colo/genética , Neoplasias Colorretais/genética , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Análise de Sequência de RNA/métodos , Software
8.
Arthritis Rheumatol ; 70(2): 308-316, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29073351

RESUMO

OBJECTIVE: To assess the safety and efficacy of treatment with belimumab in patients with early diffuse cutaneous systemic sclerosis (dcSSc) treated with background mycophenolate mofetil (MMF). METHODS: In this 52-week, investigator-initiated, single-center, double-blind, placebo-controlled, pilot study, 20 patients with dcSSc recently started on MMF were randomized 1:1 to additionally receive belimumab at 10 mg/kg intravenously or placebo. We assessed safety, efficacy, and differential gene expression. RESULTS: In the belimumab group, the median modified Rodnan skin thickness score (MRSS) decreased from 27 (interquartile range [IQR] 26.5, 31) to 18 (IQR 11, 23) (P = 0.039). In the placebo group, the median MRSS decreased from 28 (IQR 22, 28) to 21 (IQR 14, 25) (P = 0.023). The median change in MRSS was -10 (IQR -13, -9) in the belimumab group and -3.0 (IQR -15, -1) in the placebo group (P = 0.411). There were no significant differences between the groups in the number of adverse events (AEs). A significant decrease in expression of B cell signaling and profibrotic genes and pathways was observed in patients with improved MRSS in the belimumab group but not in the placebo group. CONCLUSION: Patients in both treatment groups experienced significant improvements in MRSS. The median difference was greater in the belimumab group but did not achieve statistical significance in this small pilot study. AEs were similar between the groups. Changes in gene expression were consistent with mechanism of action and showed that clinical response to treatment with belimumab is associated with a significant decrease in profibrotic genes and pathways. Additional studies are needed to determine the role of belimumab in the treatment of dcSSc.


Assuntos
Anticorpos Monoclonais Humanizados/uso terapêutico , Imunossupressores/uso terapêutico , Esclerodermia Difusa/tratamento farmacológico , Adulto , Idoso , Anticorpos Monoclonais Humanizados/efeitos adversos , Método Duplo-Cego , Feminino , Expressão Gênica/efeitos dos fármacos , Humanos , Imunossupressores/efeitos adversos , Masculino , Pessoa de Meia-Idade , Ácido Micofenólico/uso terapêutico , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Projetos Piloto , Esclerodermia Difusa/genética , Índice de Gravidade de Doença , Pele/patologia , Resultado do Tratamento , Escala Visual Analógica
9.
Biol Reprod ; 88(6): 146, 2013 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-23595904

RESUMO

Kisspeptin stimulates gonadotropin-releasing hormone (GnRH) neurons via the kisspeptin receptor, Kiss1r. In rodents, estrogen-responsive kisspeptin neurons in the rostral hypothalamus have been postulated to mediate estrogen-induced positive feedback induction of the preovulatory luteinizing hormone (LH) surge. However, conflicting evidence exists regarding the ability of mice lacking Kiss1r to display LH surges in response to exogenous hormones. Whether the discrepancy reflects different mouse strains used and/or utilization of different surge-induction paradigms is unknown. Here, we tested multiple hormonal paradigms in one Kiss1r knockout (KO) model to see which paradigms, if any, could generate circadian-timed LH surges. Kiss1r KO and wild-type (WT) females were ovariectomized, given sex steroids in various modes, and assessed several days later for LH levels in the morning or evening (when surges occur). Serum LH levels were very low in all morning animals, regardless of genotype or hormonal paradigm. In each paradigm, virtually all WT females displayed clear LH surges in the evening, whereas none of the KO females demonstrated LH surges. The lack of LH surges in KO mice reflects a lack of GnRH secretion rather than diminished pituitary responsiveness from a lifetime lack of GnRH exposure because KO mice responded to GnRH priming with robust LH secretion. Moreover, high cfos-GnRH coexpression was detected in WT females in the evening, whereas low cfos-GnRH coexpression was present in KO females at all time points. Our findings conclusively demonstrate that WT females consistently display LH surges under multiple hormonal paradigms, whereas Kiss1r KO mice do not, indicating that kisspeptin-Kiss1r signaling is mandatory for GnRH/LH surge induction.


Assuntos
Retroalimentação Fisiológica/fisiologia , Hormônio Liberador de Gonadotropina/metabolismo , Hipotálamo/metabolismo , Hormônio Luteinizante/metabolismo , Receptores Acoplados a Proteínas-G/metabolismo , Animais , Ritmo Circadiano/genética , Estradiol/farmacologia , Retroalimentação Fisiológica/efeitos dos fármacos , Feminino , Hipotálamo/efeitos dos fármacos , Hormônio Luteinizante/sangue , Camundongos , Camundongos Knockout , Neurônios/efeitos dos fármacos , Neurônios/metabolismo , Ovariectomia , Progesterona/farmacologia , Receptores Acoplados a Proteínas-G/genética , Receptores de Kisspeptina-1 , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/genética
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA