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1.
J Med Virol ; 96(4): e29587, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38587204

RESUMO

Obesity has been identified as an independent risk factor for severe outcomes in humans with coronavirus disease 2019 (COVID-19) and other infectious diseases. Here, we established a mouse model of COVID-19 using the murine betacoronavirus, mouse hepatitis virus 1 (MHV-1). C57BL/6 and C3H/HeJ mice exposed to MHV-1 developed mild and severe disease, respectively. Obese C57BL/6 mice developed clinical manifestations similar to those of lean controls. In contrast, all obese C3H/HeJ mice succumbed by 8 days postinfection, compared to a 50% mortality rate in lean controls. Notably, both lean and obese C3H/HeJ mice exposed to MHV-1 developed lung lesions consistent with severe human COVID-19, with marked evidence of diffuse alveolar damage (DAD). To identify early predictive biomarkers of worsened disease outcomes in obese C3H/HeJ mice, we sequenced RNA from whole blood 2 days postinfection and assessed changes in gene and pathway expression. Many pathways uniquely altered in obese C3H/HeJ mice postinfection aligned with those found in humans with severe COVID-19. Furthermore, we observed altered gene expression related to the unfolded protein response and lipid metabolism in infected obese mice compared to their lean counterparts, suggesting a role in the severity of disease outcomes. This study presents a novel model for studying COVID-19 and elucidating the mechanisms underlying severe disease outcomes in obese and other hosts.


Assuntos
COVID-19 , Vírus da Hepatite Murina , Humanos , Camundongos , Animais , Camundongos Endogâmicos C57BL , Camundongos Endogâmicos C3H , Vírus da Hepatite Murina/genética , COVID-19/complicações , Obesidade/complicações , Perfilação da Expressão Gênica
2.
J Rheumatol ; 2024 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-38621796

RESUMO

OBJECTIVE: This report evaluates rheumatologists' stated adherence to and agreement with the 2020 American College of Rheumatology (ACR) Guideline for the Management of Gout. METHODS: A 57-item questionnaire was administered to US rheumatologists. Stated adherence scores were based on several guideline recommendations reported to be followed by rheumatologists in practice, whereas stated agreement scores were based on whether respondents always followed the recommendations. RESULTS: All 201 rheumatologists completed the questionnaire. The mean overall stated adherence score was 11.5 (maximum: 15), whereas the mean overall stated agreement score was 7.7 (maximum: 14). Less experienced rheumatologists (≤8 years; n=49) were likely to claim adherence to more individual ACR recommendations than those with more experience (>8 years; n=152; mean stated adherence score: 12.3 vs 11.3; P ≤ 0.05). Rheumatologists who claimed to see ≤75 patients with gout in 6 months (n=66) had a mean stated adherence score of 12.1 versus 11.2 for those who claimed to have seen >75 patients (P ≤ 0.05). Approximately 78% of rheumatologists claimed to follow the guideline for initiating urate-lowering therapy (ULT), and 89% were likely to prescribe allopurinol as a first-line ULT. Claimed adherence to recommendations for dosing was lower (febuxostat, 43%; allopurinol, 39%). Rheumatologists from academic settings were more likely to prescribe an interleukin-1 inhibitor for gout flares. CONCLUSION: The self-reported practice of the surveyed US rheumatologists was generally concordant with the 2020 ACR Guideline for the Management of Gout. However, there were gaps in guideline knowledge and stated adherence among rheumatologists, mainly concerning the dosing of treatment regimens.

3.
Hum Genet ; 143(5): 703-719, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38609570

RESUMO

Systemic Lupus Erythematosus (SLE) is an autoimmune disease with heterogeneous manifestations, including neurological and psychiatric symptoms. Genetic association studies in SLE have been hampered by insufficient sample size and limited power compared to many other diseases. Multiple Sclerosis (MS) is a chronic relapsing autoimmune disease of the central nervous system (CNS) that also manifests neurological and immunological features. Here, we identify a method of leveraging large-scale genome wide association studies (GWAS) in MS to identify novel genetic risk loci in SLE. Statistical genetic comparison methods including linkage disequilibrium score regression (LDSC) and cross-phenotype association analysis (CPASSOC) to identify genetic overlap in disease pathophysiology, traditional 2-sample and novel PPI-based mendelian randomization to identify causal associations and Bayesian colocalization were applied to association studies conducted in MS to facilitate discovery in the smaller, more limited datasets available for SLE. Pathway analysis using SNP-to-gene mapping identified biological networks composed of molecular pathways with causal implications for CNS disease in SLE specifically, as well as pathways likely causal of both pathologies, providing key insights for therapeutic selection.


Assuntos
Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Desequilíbrio de Ligação , Lúpus Eritematoso Sistêmico , Esclerose Múltipla , Polimorfismo de Nucleotídeo Único , Humanos , Lúpus Eritematoso Sistêmico/genética , Esclerose Múltipla/genética , Teorema de Bayes , Loci Gênicos , Análise da Randomização Mendeliana
4.
Ann Rheum Dis ; 83(6): 696-699, 2024 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-38637134

RESUMO

Chimeric antigen receptors (CARs) are synthetic proteins designed to direct an immune response toward a specific target and have been used in immunotherapeutic applications through the adoptive transfer of T cells genetically engineered to express CARs. This technology received early attention in oncology with particular success in treatment of B cell malignancies leading to the launch of numerous successful clinical trials and the US Food and Drug Administration approval of several CAR-T-based therapies. Many CAR-T constructs have been employed, but have always been administered following a lymphodepletion regimen. The success of CAR-T cell treatment in targeting malignant B cells has led many to consider the potential for using these regimens to delete pathogenic B cells in autoimmune diseases. Preliminary results have suggested efficacy, but the sample size remains small, controlled trials have not been done, the role of immunodepletion has not been established, the most effective CAR-T constructs have not been identified and the most appropriate patient subsets for treatment have not been established.


Assuntos
Doenças Autoimunes , Imunoterapia Adotiva , Receptores de Antígenos Quiméricos , Humanos , Doenças Autoimunes/terapia , Doenças Autoimunes/imunologia , Receptores de Antígenos Quiméricos/imunologia , Receptores de Antígenos Quiméricos/uso terapêutico , Imunoterapia Adotiva/métodos , Linfócitos T/imunologia , Linfócitos T/transplante , Receptores de Antígenos de Linfócitos T/imunologia , Receptores de Antígenos de Linfócitos T/uso terapêutico , Linfócitos B/imunologia
5.
Ann Rheum Dis ; 83(4): 417-420, 2024 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-38242638
6.
J Autoimmun ; 142: 103148, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37967495

RESUMO

BACKGROUND: Rheumatoid arthritis (RA) is a chronic autoimmune disorder that affects the joints and produces pain, swelling, and stiffness. It has a lifetime prevalence of up to 1% worldwide. An extract of Tripterygium wilfordii Hook F (TwHF), a member of the Celastraceae herbal family widely available in south China, has been used for treatment of RA since 1960s. METHODS: The current consensus practice guidance (CPG) aims to offer guidance on the application of TwHF in the clinical management of active RA. The CPG followed World Health Organisation (WHO)'s recommended process, carried out three systematic reviews to synthesize data from 19 randomised controlled trials (RCT) involving 1795 participants. We utilized Grading of Recommendations, Assessment, Development and Evaluation (GRADE) to evaluate certainty of evidence and derive recommendations. We rigorously followed The Appraisal of Guidelines for Research and Evaluation II (AGREE II) as conduct guides to minimise bias and promote transparency. RESULTS: There was no obvious difference between TwHF monotherapy and methotrexate (MTX) monotherapy on ACR20 (RCT = 2, N = 390, RR = 1.06, 95%CI 0.90-1.26, moderate certainty), ACR50 (RCT = 3, N = 419, RR = 1.03, 95%CI 0.80-1.34, moderate certainty), ACR70 (RCT = 2, N = 390, RR = 1.12, 95%CI 0.69-1.79, low certainty). TwHF monotherapy may be better than salicylazosulfapyridine monotherapy on ACR20 and the effect may be similar on ACR50 and ACR70. Seven RCTs compared MTX combined with TwHF versus MTX monotherapy, and the meta-analysis results favoured combination therapy group on ACR20 (RCT = 3, N = 470, RR = 1.44, 95%CI 1.28-1.62, moderate certainty), ACR50 (RCT = 4, N = 500, RR = 1.88, 95%CI 1.56-2.28, moderate certainty) and ACR70 (RCT = 2, N = 390, RR = 2.12, 95%CI 1.40-3.19, low certainty). We found no obvious difference between groups on critical safety outcomes, including infection (RCT = 3, N = 493, RR = 1.37, 95%CI 0.84-2.23), liver dysfunction (RCT = 5, N = 643, RR = 1.14, 95%CI 0.71-1.85), renal damage (RCT = 3, N = 450, RR = 2.20, 95%CI 0.50-9.72). CONCLUSION: Upon full review of the evidence, the guidance panel reached consensus on recommendations for the use of TwHF in people with active RA, either as monotherapy or as combination therapy with MTX.


Assuntos
Antirreumáticos , Artrite Reumatoide , Humanos , Antirreumáticos/uso terapêutico , Tripterygium , Consenso , Artrite Reumatoide/tratamento farmacológico , Metotrexato/uso terapêutico , Doença Crônica
7.
Clin Exp Rheumatol ; 42(1): 86-91, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37497724

RESUMO

OBJECTIVES: It has been suggested that gout is associated with non-alcoholic fatty liver disease (NAFLD). Our aim was to assess NAFLD in gout patients using the validated non-invasive imaging technique, transient elastography (FibroScan). METHODS: FibroScans in consecutive gout patients in a single centre from 11/1/2016 to 11/1/2021 and reviewed retrospectively. FibroScan results include the E- score (kPA), measuring liver stiffness, and controlled attenuation parameter (CAP) score (dB/m), assessing steatosis. In addition, a FIB-4 fibrosis score was calculated. RESULTS: 47 gout patients (7 females, 14.9%; 40 males, 85.1%) underwent FibroScans. The mean age was 59.8 years, the mean body mass index (BMI) was 30.95 kg/m2, and gout duration 0-49 years. Tophi were present in 11 (26.2%). Comorbidities included dyslipidaemia (86.7%), diabetes mellitus (31.1%), known liver disease (33.3%), current alcohol consumption (46.8%), ALT or AST elevations (54.4%), and hyperuricaemia (53.7%). FibroScan results revealed hepatic steatosis (CAP >238 dB/m) in 40 (85.1%) and were significantly associated with BMI (r=0.53, p=0.0001) but not age, serum urate (SU), glucose, triglycerides, ALT, AST. FibroScan also revealed fibrosis (E score >7) in 9 (19.1%); severe fibrosis (cirrhosis) in 8. Fibrosis was significantly associated with age (p=0.03) and known liver disease (p=0.003) but not BMI, SU, or comorbidities. The FIB-4 score was significantly associated with the fibrosis score (r2=0.24, p=0.0009) but not with CAP, ALT, or AST. CONCLUSIONS: Despite not being associated with common gout comorbidities, fatty liver and liver fibrosis were common in this gout cohort, suggesting FibroScan screening in gout patients to assess NAFLD, irrespective of serum transaminase levels.


Assuntos
Técnicas de Imagem por Elasticidade , Gota , Hepatopatia Gordurosa não Alcoólica , Masculino , Feminino , Humanos , Pessoa de Meia-Idade , Hepatopatia Gordurosa não Alcoólica/complicações , Hepatopatia Gordurosa não Alcoólica/diagnóstico por imagem , Hepatopatia Gordurosa não Alcoólica/epidemiologia , Técnicas de Imagem por Elasticidade/métodos , Estudos Retrospectivos , Cirrose Hepática/diagnóstico por imagem , Cirrose Hepática/epidemiologia , Cirrose Hepática/etiologia , Gota/complicações , Gota/diagnóstico por imagem , Gota/epidemiologia , Fígado/diagnóstico por imagem , Fígado/patologia
9.
Front Immunol ; 14: 1282770, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38155972

RESUMO

Introduction: B cells can have both pathogenic and protective roles in autoimmune diseases, including systemic lupus erythematosus (SLE). Deficiencies in the number or immunosuppressive function of IL-10 producing regulatory B cells (Bregs) can cause exacerbated autoimmune inflammation. However, the exact role of Bregs in lupus pathogenesis has not been elucidated. Methods: We carried out gene expression analysis by scRNA-seq to characterize differences in splenic Breg subsets and molecular profiles through stages of disease progression in lupus-prone mice. Transcriptome-based changes in Bregs from mice with active disease were confirmed by phenotypic analysis. Results: We found that a loss of marginal zone (MZ) lineage Bregs, an increase in plasmablast/plasma cell (PB-PC) lineage Bregs, and overall increases in inflammatory gene signatures were characteristic of active disease as compared to Bregs from the pre-disease stage. However, the frequencies of both MZ Bregs and PB-PCs expressing IL-10 were significantly decreased in active-disease mice. Conclusion: Overall, we have identified changes to the repertoire and transcriptional landscape of Breg subsets associated with active disease that provide insights into the role of Bregs in lupus pathogenesis. These results could inform the design of Breg-targeted therapies and interventions to restore Breg suppressive function in autoimmunity.


Assuntos
Doenças Autoimunes , Linfócitos B Reguladores , Lúpus Eritematoso Sistêmico , Animais , Camundongos , Interleucina-10/genética , Interleucina-10/metabolismo , Lúpus Eritematoso Sistêmico/genética , Análise de Sequência de RNA
10.
Genome Med ; 15(1): 84, 2023 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-37845772

RESUMO

BACKGROUND: Systemic lupus erythematosus (SLE) is known to be clinically heterogeneous. Previous efforts to characterize subsets of SLE patients based on gene expression analysis have not been reproduced because of small sample sizes or technical problems. The aim of this study was to develop a robust patient stratification system using gene expression profiling to characterize individual lupus patients. METHODS: We employed gene set variation analysis (GSVA) of informative gene modules to identify molecular endotypes of SLE patients, machine learning (ML) to classify individual patients into molecular subsets, and logistic regression to develop a composite metric estimating the scope of immunologic perturbations. SHapley Additive ExPlanations (SHAP) revealed the impact of specific features on patient sub-setting. RESULTS: Using five datasets comprising 2183 patients, eight SLE endotypes were identified. Expanded analysis of 3166 samples in 17 datasets revealed that each endotype had unique gene enrichment patterns, but not all endotypes were observed in all datasets. ML algorithms trained on 2183 patients and tested on 983 patients not used to develop the model demonstrated effective classification into one of eight endotypes. SHAP indicated a unique array of features influential in sorting individual samples into each of the endotypes. A composite molecular score was calculated for each patient and significantly correlated with standard laboratory measures. Significant differences in clinical characteristics were associated with different endotypes, with those with the least perturbed transcriptional profile manifesting lower disease severity. The more abnormal endotypes were significantly more likely to experience a severe flare over the subsequent 52 weeks while on standard-of-care medication and specific endotypes were more likely to be clinical responders to the investigational product tested in one clinical trial analyzed (tabalumab). CONCLUSIONS: Transcriptomic profiling and ML reproducibly separated lupus patients into molecular endotypes with significant differences in clinical features, outcomes, and responsiveness to therapy. Our classification approach using a composite scoring system based on underlying molecular abnormalities has both staging and prognostic relevance.


Assuntos
Lúpus Eritematoso Sistêmico , Transcriptoma , Humanos , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Lúpus Eritematoso Sistêmico/genética , Lúpus Eritematoso Sistêmico/tratamento farmacológico , Algoritmos
11.
iScience ; 26(10): 108042, 2023 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-37860757

RESUMO

Machine learning (ML) has the potential to identify subsets of patients with distinct phenotypes from gene expression data. However, phenotype prediction using ML has often relied on identifying important genes without a systems biology context. To address this, we created an interpretable ML approach based on blood transcriptomics to predict phenotype in systemic lupus erythematosus (SLE), a heterogeneous autoimmune disease. We employed a sequential grouped feature importance algorithm to assess the performance of gene sets, including immune and metabolic pathways and cell types, known to be abnormal in SLE in predicting disease activity and organ involvement. Gene sets related to interferon, tumor necrosis factor, the mitoribosome, and T cell activation were the best predictors of phenotype with excellent performance. These results suggest potential relationships between the molecular pathways identified in each model and manifestations of SLE. This ML approach to phenotype prediction can be applied to other diseases and tissues.

12.
Brief Bioinform ; 24(5)2023 09 20.
Artigo em Inglês | MEDLINE | ID: mdl-37670507

RESUMO

Because of the clinical heterogeneity among patients with systemic lupus erythematosus (SLE), developing molecular profiles that predict clinical features can be useful in creating a personalized approach to treatment. Toro-Domínguez et al. created a web tool to aid in therapeutic decision making for clinicians that predicts clinical features associated with SLE from blood transcriptomic data. Specifically, they present a machine learning model that predicts the presence of proliferative nephritis from blood transcriptomics. Here, we report use of the tool in independent datasets and found that it did not perform sufficiently well to consider replacement of the standard kidney biopsy as a diagnostic procedure.


Assuntos
Lúpus Eritematoso Sistêmico , Nefrite Lúpica , Humanos , Nefrite Lúpica/diagnóstico , Nefrite Lúpica/genética , Perfilação da Expressão Gênica , Aprendizado de Máquina , Transcriptoma
13.
RMD Open ; 9(3)2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-37709528

RESUMO

OBJECTIVES: Type I interferon (IFN) plays a role in the pathogenesis of systemic lupus erythematosus (SLE), but insufficient attention has been directed to the differences in IFN responses between ancestral populations. Here, we explored the expression of the interferon gene signatures (IGSs) in SLE patients of European ancestry (EA) and Asian ancestry (AsA). METHODS: We used gene set variation analysis with multiple IGS encompassing the response to both type 1 and type 2 IFN in isolated CD14+ monocytes, CD19+B cells, CD4+T cells and Natural Killer (NK) cells from patients with SLE stratified by self-identified ancestry. The expression of genes upstream of the IGS and influenced by lupus-associated risk alleles was also examined. Lastly, we employed machine learning (ML) models to assess the most important features classifying patients by disease activity. RESULTS: AsA patients with SLE exhibited greater enrichment in the IFN core and IFNA2 IGS compared with EA patients in all cell types examined and, in the presence and absence of autoantibodies. Overall, AsA patients with SLE demonstrated higher expression of genes upstream of the IGS than EA counterparts. ML with feature importance analysis indicated that IGS expression in NK cells, anti-dsDNA, complement levels and AsA status contributed to disease activity. CONCLUSIONS: AsA patients with SLE exhibited higher IGS than EA patients in all cell types regardless of autoantibody status, with enhanced expression of genetically associated genes upstream of the IGS potentially contributing. AsA, along with the IGS in NK cells, anti-dsDNA and complement, independently influenced SLE disease activity.


Assuntos
Interferon Tipo I , Lúpus Eritematoso Sistêmico , Humanos , Interferon Tipo I/genética , Alelos , Autoanticorpos , Células Matadoras Naturais , Lúpus Eritematoso Sistêmico/diagnóstico , Lúpus Eritematoso Sistêmico/genética
14.
Clin Immunol ; 255: 109749, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37657525

RESUMO

An investigator-initiated, multicentre, randomized, double-blind, triple-dummy, controlled trial was conducted at 14 tertiary rheumatology centers in China to evaluate the efficacy and safety of Tripterygium wilfordii Hook F (TwHF) with recombinant human TNF receptor IgGFc fusion protein (rhTNFR-Fc) in active Rheumatoid Arthritis (RA). Primary endpoint was the proportion of patients achieved a 50% improvement of American College of Rheumatology criteria (ACR50) in TwHF+rhTNFR-Fc vs. methotrexate (MTX) group at week 12. ACR50 was achieved in 57.1% (72/126), 41.3% (52/126), 23.0% (29/126), and 26.2% (33/126) patients receiving TwHF+rhTNFR-Fc, MTX + rhTNFR-Fc, TwHF and MTX monotherapy, respectively, at week 12 (TwHF+rhTNFR-Fc vs. other three groups, all p < 0.05). No statistical difference in serious adverse events or adverse events leading to discontinuation of study across all groups was documented. TwHF+rhTNFR-Fc was superior to MTX for active RA, and was more effective than MTX + rhTNFR-Fc on ACR50, with a similar safety profile. Trial registration:ClinicalTrials.govNCT03589833.

15.
iScience ; 26(9): 107487, 2023 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-37636066

RESUMO

Aberrant metabolic demand is observed in immune/inflammatory disorders, yet the role in pathogenesis remains unclear. Here, we discover that in lupus, activated B cells, including germinal center B (GCB) cells, have remarkably high glycolytic requirement for survival over T cell populations, as demonstrated by increased metabolic activity in lupus-activated B cells compared to immunization-induced cells. The augmented reliance on glucose oxidation makes GCB cells vulnerable to mitochondrial ROS-induced oxidative stress and apoptosis. Short-term glycolysis inhibition selectively reduces pathogenic activated B in lupus-prone mice, extending their lifespan, without affecting T follicular helper cells. Particularly, BCMA-expressing GCB cells rely heavily on glucose oxidation. Depleting BCMA-expressing activated B cells with APRIL-based CAR-T cells significantly prolongs the lifespan of mice with severe autoimmune disease. These results reveal that glycolysis-dependent activated B and GCB cells, especially those expressing BCMA, are potentially key lupus mediators, and could be targeted to improve disease outcomes.

16.
Arthritis Res Ther ; 25(1): 128, 2023 07 25.
Artigo em Inglês | MEDLINE | ID: mdl-37491293

RESUMO

OBJECTIVES: The objective of this systematic review was to assess the effects of interleukin-1ß (IL-1ß) inhibitors on gout flares. METHODS: Studies published between 2011 and 2022 that evaluated the effects of IL-1ß inhibitors in adult patients experiencing gout flares were eligible for inclusion. Outcomes including pain, frequency and intensity of gout flares, inflammation, and safety were assessed. Five electronic databases (Pubmed/Medline, Embase, Biosis/Ovid, Web of Science and Cochrane Library) were searched. Two independent reviewers performed study screening, data extraction and risk of bias assessments (Cochrane Risk of Bias Tool 2 for randomised controlled trials [RCTs] and Downs and Black for non-RCTs). Data are reported as a narrative synthesis. RESULTS: Fourteen studies (10 RCTs) met the inclusion criteria, with canakinumab, anakinra, and rilonacept being the three included IL-1ß inhibitors. A total of 4367 patients with a history of gout were included from the 14 studies (N = 3446, RCTs; N = 159, retrospective studies [with a history of gout]; N = 762, post hoc analysis [with a history of gout]). In the RCTs, canakinumab and rilonacept were reported to have a better response compared to an active comparator for resolving pain, while anakinra appeared to be not inferior to an active comparator for resolving pain. Furthermore, canakinumab and rilonacept reduced the frequency of gout flares compared to the comparators. All three medications were mostly well-tolerated compared to their comparators. CONCLUSION: IL-1ß inhibitors may be a beneficial and safe medication for patients experiencing gout flares for whom current standard therapies are unsuitable. REVIEW PROTOCOL REGISTRATION: PROSPERO ID: CRD42021267670.


Assuntos
Artrite Gotosa , Gota , Adulto , Humanos , Inibidores de Interleucina , Interleucina-1beta , Proteína Antagonista do Receptor de Interleucina 1/uso terapêutico , Gota/tratamento farmacológico , Artrite Gotosa/tratamento farmacológico
17.
Sci Rep ; 13(1): 5339, 2023 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-37005464

RESUMO

Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder with a prominent genetic component. Individuals of Asian-Ancestry (AsA) disproportionately experience more severe SLE compared to individuals of European-Ancestry (EA), including increased renal involvement and tissue damage. However, the mechanisms underlying elevated severity in the AsA population remain unclear. Here, we utilized available gene expression data and genotype data based on all non-HLA SNP associations in EA and AsA SLE patients detected using the Immunochip genotyping array. We identified 2778 ancestry-specific and 327 trans-ancestry SLE-risk polymorphisms. Genetic associations were examined using connectivity mapping and gene signatures based on predicted biological pathways and were used to interrogate gene expression datasets. SLE-associated pathways in AsA patients included elevated oxidative stress, altered metabolism and mitochondrial dysfunction, whereas SLE-associated pathways in EA patients included a robust interferon response (type I and II) related to enhanced cytosolic nucleic acid sensing and signaling. An independent dataset derived from summary genome-wide association data in an AsA cohort was interrogated and identified similar molecular pathways. Finally, gene expression data from AsA SLE patients corroborated the molecular pathways predicted by SNP associations. Identifying ancestry-related molecular pathways predicted by genetic SLE risk may help to disentangle the population differences in clinical severity that impact AsA and EA individuals with SLE.


Assuntos
Predisposição Genética para Doença , Lúpus Eritematoso Sistêmico , Humanos , Estudo de Associação Genômica Ampla , Polimorfismo de Nucleotídeo Único , Lúpus Eritematoso Sistêmico/genética , Genótipo , Estudos de Casos e Controles
18.
Front Immunol ; 14: 1147526, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36936908

RESUMO

Introduction: Pathologic inflammation is a major driver of kidney damage in lupus nephritis (LN), but the immune mechanisms of disease progression and risk factors for end organ damage are poorly understood. Methods: To characterize molecular profiles through the development of LN, we carried out gene expression analysis of microdissected kidneys from lupus-prone NZM2328 mice. We examined male mice and the congenic NZM2328.R27 strain as a means to define mechanisms associated with resistance to chronic nephritis. Gene expression profiles in lupus mice were compared with those in human LN. Results: NZM2328 mice exhibited progress from acute to transitional and then to chronic glomerulonephritis (GN). Each stage manifested a unique molecular profile. Neither male mice nor R27 mice progressed past the acute GN stage, with the former exhibiting minimal immune infiltration and the latter enrichment of immunoregulatory gene signatures in conjunction with robust kidney tubule cell profiles indicative of resistance to cellular damage. The gene expression profiles of human LN were similar to those noted in the NZM2328 mouse suggesting comparable stages of LN progression. Conclusions: Overall, this work provides a comprehensive examination of the immune processes involved in progression of murine LN and thus contributes to our understanding of the risk factors for end-stage renal disease. In addition, this work presents a foundation for improved classification of LN and illustrates the applicability of murine models to identify the stages of human disease.


Assuntos
Glomerulonefrite , Falência Renal Crônica , Nefrite Lúpica , Humanos , Camundongos , Masculino , Animais , Rim/patologia , Glomerulonefrite/patologia , Inflamação , Falência Renal Crônica/patologia , Doença Crônica
19.
Int J Mol Sci ; 24(5)2023 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-36902333

RESUMO

The persistent impact of the COVID-19 pandemic and heterogeneity in disease manifestations point to a need for innovative approaches to identify drivers of immune pathology and predict whether infected patients will present with mild/moderate or severe disease. We have developed a novel iterative machine learning pipeline that utilizes gene enrichment profiles from blood transcriptome data to stratify COVID-19 patients based on disease severity and differentiate severe COVID cases from other patients with acute hypoxic respiratory failure. The pattern of gene module enrichment in COVID-19 patients overall reflected broad cellular expansion and metabolic dysfunction, whereas increased neutrophils, activated B cells, T-cell lymphopenia, and proinflammatory cytokine production were specific to severe COVID patients. Using this pipeline, we also identified small blood gene signatures indicative of COVID-19 diagnosis and severity that could be used as biomarker panels in the clinical setting.


Assuntos
COVID-19 , Humanos , Transcriptoma , SARS-CoV-2 , Pandemias , Teste para COVID-19 , Aprendizado de Máquina
20.
Sci Rep ; 13(1): 5141, 2023 03 29.
Artigo em Inglês | MEDLINE | ID: mdl-36991079

RESUMO

Regulation of intron retention (IR), a form of alternative splicing, is a newly recognized checkpoint in gene expression. Since there are numerous abnormalities in gene expression in the prototypic autoimmune disease systemic lupus erythematosus (SLE), we sought to determine whether IR was intact in patients with this disease. We, therefore, studied global gene expression and IR patterns of lymphocytes in SLE patients. We analyzed RNA-seq data from peripheral blood T cell samples from 14 patients suffering from systemic lupus erythematosus (SLE) and 4 healthy controls and a second, independent data set of RNA-seq data from B cells from16 SLE patients and 4 healthy controls. We identified intron retention levels from 26,372 well annotated genes as well as differential gene expression and tested for differences between cases and controls using unbiased hierarchical clustering and principal component analysis. We followed with gene-disease enrichment analysis and gene-ontology enrichment analysis. Finally, we then tested for significant differences in intron retention between cases and controls both globally and with respect to specific genes. Overall decreased IR was found in T cells from one cohort and B cells from another cohort of patients with SLE and was associated with increased expression of numerous genes, including those encoding spliceosome components. Different introns within the same gene displayed both up- and down-regulated retention profiles indicating a complex regulatory mechanism. These results indicate that decreased IR in immune cells is characteristic of patients with active SLE and may contribute to the abnormal expression of specific genes in this autoimmune disease.


Assuntos
Lúpus Eritematoso Sistêmico , Linfócitos T , Humanos , Íntrons/genética , Linfócitos T/metabolismo , Linfócitos B
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