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Falkenstein DK, Jarvis JN. Systemic lupus erythematosus in American Indian/Alaska natives: Incorporating our new understanding of the biology of trauma. Semin Arthritis Rheum 2023; 63:152245. [PMID: 37595507 DOI: 10.1016/j.semarthrit.2023.152245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/07/2023] [Accepted: 07/17/2023] [Indexed: 08/20/2023]
Abstract
OBJECTIVE To review the literature regarding systemic lupus erythematosus (SLE) in American Indian/Alaska Native (AI/AN) people and relate prevalence and/or disease severity to our emerging understanding of the biology of trauma and toxic stress. METHODS We conducted a search and review of the literature using search terms "lupus and American Indians" "ACEs and disease outcome" "Biology of Adversity" "lupus and ACE scores," " lupus and childhood abuse." These search criteria were entered into Google Scholar and articles retrieved from PubMed, NBCI. This approach yielded a small numbers of papers used throughout this review. We excluded articles that were not published in a peer reviewed journals, as well as editorial commentaries. RESULTS In the AI/AN population, SLE shows high prevalence rates and severe disease manifestations, comparable to the African American population. AI/AN populations also have high rates of childhood trauma. Toxic stress and trauma such as those catalogued in the Adverse Childhood Experiences (ACE) study have broad-reaching immunologic and epigenetic effects that are likely to be relevant to our understanding of SLE in AI/AN people. CONCLUSIONS AI/AN people have high rates of SLE. These high rates are likely to be driven by many complex factors, not all of which are genetic. Future research is needed to establish (or refute) a causal connection between the biology of adversity and SLE in socially marginalized and historically traumatized populations.
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Affiliation(s)
- Danielle K Falkenstein
- Medical Student, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, USA; Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, USA.
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Karasawa R, Yudoh K, Sato T, Tanaka M, Sabbagh SE, Flegel WA, Mammen AL, Jarvis JN, Rider LG. Association of anti-TPM4 autoantibodies with vasculopathic cutaneous manifestations in juvenile dermatomyositis. Rheumatology (Oxford) 2023; 62:3757-3762. [PMID: 37144941 PMCID: PMC10629777 DOI: 10.1093/rheumatology/kead203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 05/06/2023] Open
Abstract
OBJECTIVES AECAs are detected in multiple forms of vasculitis or vasculopathy, including JDM. High levels of tropomyosin alpha-4 chain (TPM4) gene expression in cutaneous lesions and TPM4 protein expression in some endothelial cells (ECs) have been proven. Furthermore, the presence of autoantibodies to tropomyosin proteins have been discovered in DM. We therefore investigated whether anti-TPM4 autoantibodies are an AECA in JDM and are correlated with clinical features of JDM. METHODS The expression of TPM4 protein in cultured normal human dermal microvascular ECs was investigated by Western blotting. Plasma samples from 63 children with JDM, 50 children with polyarticular JIA (pJIA) and 40 healthy children (HC) were tested for the presence of anti-TPM4 autoantibodies using an ELISA. Clinical features were compared between JDM patients with and without anti-TPM4 autoantibodies. RESULTS Autoantibodies to TPM4 were detected in the plasma of 30% of JDM, 2% of pJIA (P < 0.0001) and 0% of HC (P < 0.0001). In JDM, anti-TPM4 autoantibodies were associated with the presence of cutaneous ulcers (53%; P = 0.02), shawl sign rash (47%; P = 0.03), mucous membrane lesions (84%; P = 0.04) and subcutaneous edema (42%; P < 0.05). Anti-TPM4 autoantibodies significantly correlated with the use of intravenous steroids and IVIG therapy in JDM (both P = 0.01). The total number of medications received was higher in patients with anti-TPM4 autoantibodies (P = 0.02). CONCLUSION Anti-TPM4 autoantibodies are detected frequently in children with JDM and are novel myositis-associated autoantibodies. Their presence correlates with vasculopathic and other cutaneous manifestations of JDM that may be indicative of more refractory disease.
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Affiliation(s)
- Rie Karasawa
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kazuo Yudoh
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Toshiko Sato
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Megumi Tanaka
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Sara E Sabbagh
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
- Division of Rheumatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Willy A Flegel
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Andrew L Mammen
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James N Jarvis
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, MD, USA
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Jiang K, Fu Y, Kelly JA, Gaffney PM, Holmes LC, Jarvis JN. Comparison of the three-dimensional chromatin structures of adolescent and adult peripheral blood B cells: implications for the study of pediatric autoimmune diseases. bioRxiv 2023:2023.09.11.557171. [PMID: 37745336 PMCID: PMC10515843 DOI: 10.1101/2023.09.11.557171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background/Purpose Knowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture of primary human cells or whether developmental aspects of the pediatric immune system require use of pediatric samples. We undertook a systematic analysis of B cells and B cell lines to compare 3D genomic features encompassing risk loci for juvenile idiopathic arthritis (JIA), systemic lupus (SLE), and type 1 diabetes (T1D). Methods We isolated B cells from healthy individuals, ages 9-17. HiChIP was performed using CTCF antibody, and CTCF peaks were identified. CTCF loops within the pediatric were compared to three datasets: 1) self-called CTCF consensus peaks called within the pediatric samples, 2) ENCODE's publicly available GM12878 CTCF ChIP-seq peaks, and 3) ENCODE's primary B cell CTCF ChIPseq peaks from two adult females. Differential looping was assessed within the pediatric samples and each of the three peak datasets. Results The number of consensus peaks called in the pediatric samples was similar to that identified in ENCODE's GM12878 and primary B cell datasets. We observed <1% of loops that demonstrated significantly differential looping between peaks called within the pediatric samples themselves and when called using ENCODE GM12878 peaks . Significant looping differences were even less when comparing loops of the pediatric called peaks to those of the ENCODE primary B cell peaks. When querying loops found in juvenile idiopathic arthritis, type 1 diabetes, or systemic lupus erythematosus risk haplotypes, we observed significant differences in only 2.2%, 1.0%, and 1.3% loops, respectively, when comparing peaks called within the pediatric samples and ENCODE GM12878 dataset. The differences were even less apparent when comparing loops called with the pediatric vs ENCODE adult primary B cell peak datasets.The 3D chromatin architecture in B cells is similar across pediatric, adult, and EBVtransformed cell lines. This conservation of 3D structure includes regions encompassing autoimmune risk haplotypes. Conclusion Thus, even for pediatric autoimmune diseases, publicly available adult B cell and cell line datasets may be sufficient for assessing effects exerted in the 3D genomic space.
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Affiliation(s)
- Kaiyu Jiang
- Department of Pediatrics, University of Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Jennifer A. Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Patrick M. Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Lucy C. Holmes
- Department of Pediatrics, University of Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - James N. Jarvis
- Department of Pediatrics, University of Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
- Genetics, Genomics and Bioinformatics Program, University of Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
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Crinzi EA, Haley EK, Poppenberg KE, Jiang K, Tutino VM, Jarvis JN. Analysis of chromatin data supports a role for CD14+ monocytes/macrophages in mediating genetic risk for juvenile idiopathic arthritis. Front Immunol 2022; 13:913555. [PMID: 36248892 PMCID: PMC9559786 DOI: 10.3389/fimmu.2022.913555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionGenome wide association studies (GWAS) have identified multiple regions that confer genetic risk for the polyarticular/oligoarticular forms of juvenile idiopathic arthritis (JIA). However, genome-wide scans do not identify the cells impacted by genetic polymorphisms on the risk haplotypes or the genes impacted by those variants. We have shown that genetic variants driving JIA risk are likely to affect both innate and adaptive immune functions. We provide additional evidence that JIA risk variants impact innate immunity.Materials and methodsWe queried publicly available H3K4me1/H3K27ac ChIP-seq data in CD14+ monocytes to determine whether the linkage disequilibrium (LD) blocks incorporating the SNPs that tag JIA risk loci showed enrichment for these epigenetic marks. We also queried monocyte/macrophage GROseq data, a functional readout of active enhancers. We defined the topologically associated domains (TADs) encompassing enhancers on the risk haplotypes and identified genes within those TADs expressed in monocytes. We performed ontology analyses of these genes to identify cellular processes that may be impacted by these variants. We also used whole blood RNAseq data from the Genotype-Tissue Expression (GTEx) data base to determine whether SNPs lying within monocyte GROseq peaks influence plausible target genes within the TADs encompassing the JIA risk haplotypes.ResultsThe LD blocks encompassing the JIA genetic risk regions were enriched for H3K4me1/H3K27ac ChIPseq peaks (p=0.00021 and p=0.022) when compared to genome background. Eleven and sixteen JIA were enriched for resting and activated macrophage GROseq peaks, respectively risk regions (p=0.04385 and p=0.00004). We identified 321 expressed genes within the TADs encompassing the JIA haplotypes in human monocytes. Ontological analysis of these genes showed enrichment for multiple immune functions. Finally, we found that SNPs lying within the GROseq peaks are strongly associated with expression levels of plausible target genes in human whole blood.ConclusionsThese findings support the idea that both innate and adaptive immunity are impacted by JIA genetic risk variants.
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Affiliation(s)
- Elizabeth A. Crinzi
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
| | - Emma K. Haley
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
| | - Kerry E. Poppenberg
- Canon Stroke and Vascular Center, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
| | - Kaiyu Jiang
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
| | - Vincent M. Tutino
- Canon Stroke and Vascular Center, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
- Department of Neurosurgery, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
| | - James N. Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
- Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY, United States
- *Correspondence: James N. Jarvis,
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Falkenstein DK, Jarvis JN. Health inequities in the rheumatic diseases of childhood. Curr Opin Rheumatol 2022; 34:262-266. [PMID: 35797523 DOI: 10.1097/bor.0000000000000893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW To describe differences in disease manifestations and outcomes in pediatric rheumatic diseases as they occur in non-European-descended populations in North America. RECENT FINDINGS Differences in disease prevalence, clinical phenotypes, disease course, and outcomes have been described across the spectrum of pediatric-onset rheumatic diseases. Although these differences are commonly explained by differences in genetic risk or access to tertiary healthcare facilities, our emerging understanding of the immunobiology of historical/ongoing trauma suggest a more complex explanation for these observed differences. SUMMARY Health inequities as observed in pediatric rheumatic diseases are likely to emerge from a complex interplay between social and biological factors. The important contribution of historical and repetitive trauma deserves further exploration.
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Affiliation(s)
| | - James N Jarvis
- Department of Pediatrics
- Genetics, Genomics, & Bioinformatics Program, University at Buffalo, Buffalo, New York, USA
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Karasawa R, Yudoh K, Sato T, Tanaka M, Tamaki M, Sabbagh SE, O’Hanlon TP, Noroozi-Farhadi P, Targoff IN, Flegel WA, Mammen AL, Miller FW, Hicar MD, Rider LG, Jarvis JN. Association of anti-HSC70 autoantibodies with cutaneous ulceration and severe disease in juvenile dermatomyositis. Rheumatology (Oxford) 2022; 61:2969-2977. [PMID: 34791087 PMCID: PMC9258543 DOI: 10.1093/rheumatology/keab846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/06/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES JDM is an inflammatory myopathy characterized by prominent vasculopathy. AECAs are frequently detected in inflammatory and autoimmune diseases. We sought to determine whether AECAs correlate with clinical features of JDM, and thus serve as biomarkers to guide therapy or predict outcome. METHODS Plasma samples from 63 patients with JDM, 49 patients with polyarticular JIA and 40 juvenile healthy controls were used to detect anti-heat shock cognate 71 kDa protein (HSC70) autoantibodies, a newly identified AECA, in ELISA assays. Clinical features were compared between JDM patients with and without anti-HSC70 autoantibodies. RESULTS Anti-HSC70 autoantibodies were detected in 35% of patients with JDM, in 0% of patients with JIA (P < 0.0001) and in 0% of healthy donors (P < 0.0001). Both the presence of cutaneous ulcers (59% vs 17%, P < 0.002) and the use of wheelchairs and/or assistive devices (64% vs 27%, P < 0.007) were strongly associated with anti-HSC70 autoantibodies in JDM. High scores on the severity of myositis damage measures at the time of measurement of anti-HSC70 autoantibodies and an increased number of hospitalizations were also associated with anti-HSC70 autoantibodies. Intravenous immunoglobulin therapy was used more often in anti-HSC70 autoantibody-positive patients. CONCLUSION Anti-HCS70 autoantibodies are detected frequently in children with JDM and are novel myositis-associated autoantibodies correlating with disease severity.
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Affiliation(s)
- Rie Karasawa
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kazuo Yudoh
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Toshiko Sato
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Megumi Tanaka
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Mayumi Tamaki
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Sara E Sabbagh
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD
- Division of Rheumatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Terrance P O’Hanlon
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Bethesda, MD
| | - Payam Noroozi-Farhadi
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Bethesda, MD
| | - Ira N Targoff
- Oklahoma City VA Health Care System, University of Oklahoma Health Sciences Center, and Oklahoma Medical Research Foundation, Oklahoma City, OK
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD
| | - Andrew L Mammen
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health (NIH), Bethesda, MD
| | - Frederick W Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Bethesda, MD
| | - Mark D Hicar
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health (NIH), Bethesda, MD
| | - James N Jarvis
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences
- Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
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Tutino VM, Kuo CC, Avasthi N, Rai HH, Waqas M, Siddiqui AH, Jarvis JN, Poppenberg KE. Chromatin architecture around stroke haplotypes provides evidence that genetic risk is conferred through vascular cells. Epigenomics 2022; 14:243-259. [PMID: 35184600 DOI: 10.2217/epi-2021-0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Introduction: Genome-wide association studies (GWAS) have identified numerous stroke-associated SNPs. To understand how SNPs affect gene expression related to increased stroke risk, we studied epigenetic landscapes surrounding 26 common, validated stroke-associated loci. Methods: We mapped the SNPs to linkage disequilibrium (LD) blocks and examined H3K27ac, H3K4me1, H3K9ac, and H3K4me3 histone marks and transcription-factor binding-sites in pathologically relevant cell types (hematopoietic and vascular cells). Hi-C data were used to identify topologically associated domains (TADs) encompassing the LD blocks and overlapping genes. Results: Fibroblasts, smooth muscle, and endothelial cells showed significant enrichment for enhancer-associated marks within stroke-associated LD blocks. Genes within encompassing TADs reflected vessel homeostasis, cellular turnover, and enzymatic activity. Conclusions: Stroke-associated genetic variants confer risk predominantly through vascular cells rather than hematopoietic cell types.
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Affiliation(s)
- Vincent M Tutino
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA.,Department of Pathology & Anatomical Sciences, University at Buffalo, Buffalo, NY 14203, USA.,Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, NY 14203, USA
| | - Cathleen C Kuo
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA
| | - Naval Avasthi
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14203, USA
| | - Hamid H Rai
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Muhammad Waqas
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Adnan H Siddiqui
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA.,Department of Radiology, University at Buffalo, Buffalo, NY 14203, USA
| | - James N Jarvis
- Department of Pediatrics, Department of Pathology & Anatomical Sciences, University at Buffalo, Buffalo, NY 14203, USA.,Genetics, Genomics, & Bioinformatics Program, University at Buffalo, Buffalo, NY 14203, USA
| | - Kerry E Poppenberg
- Canon Stroke & Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
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Poppenberg KE, Zebraski HR, Avasthi N, Waqas M, Siddiqui AH, Jarvis JN, Tutino VM. Epigenetic landscapes of intracranial aneurysm risk haplotypes implicate enhancer function of endothelial cells and fibroblasts in dysregulated gene expression. BMC Med Genomics 2021; 14:162. [PMID: 34134708 PMCID: PMC8210394 DOI: 10.1186/s12920-021-01007-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified many single nucleotide polymorphisms (SNPs) associated with increased risk for intracranial aneurysm (IA). However, how such variants affect gene expression within IA is poorly understood. We used publicly-available ChIP-Seq data to study chromatin landscapes surrounding risk loci to determine whether IA-associated SNPs affect functional elements that regulate gene expression in cell types comprising IA tissue. METHODS We mapped 16 significant IA-associated SNPs to linkage disequilibrium (LD) blocks within human genome. Using ChIP-Seq data, we examined these regions for presence of H3K4me1, H3K27ac, and H3K9ac histone marks (typically associated with latent/active enhancers). This analysis was conducted in several cell types that are present in IA tissue (endothelial cells, smooth muscle cells, fibroblasts, macrophages, monocytes, neutrophils, T cells, B cells, NK cells). In cell types with significant histone enrichment, we used HiC data to investigate topologically associated domains (TADs) encompassing the LD blocks to identify genes that may be affected by IA-associated variants. Bioinformatics were performed to determine the biological significance of these genes. Genes within HiC-defined TADs were also compared to differentially expressed genes from RNA-seq/microarray studies of IA tissues. RESULTS We found that endothelial cells and fibroblasts, rather than smooth muscle or immune cells, have significant enrichment for enhancer marks on IA risk haplotypes (p < 0.05). Bioinformatics demonstrated that genes within TADs subsuming these regions are associated with structural extracellular matrix components and enzymatic activity. The majority of histone marked TADs (83% fibroblasts [IMR90], 77% HUVEC) encompassed at least one differentially expressed gene from IA tissue studies. CONCLUSIONS These findings provide evidence that genetic variants associated with IA risk act on endothelial cells and fibroblasts. There is strong circumstantial evidence that this may be mediated through altered enhancer function, as genes in TADs encompassing enhancer marks have also been shown to be differentially expressed in IA tissue. These genes are largely related to organization and regulation of the extracellular matrix. This study builds upon our previous (Poppenberg et al., BMC Med Genomics, 2019) by including a more diverse set of data from additional cell types and by identifying potential affected genes (i.e. those in TADs).
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Affiliation(s)
- Kerry E Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - Haley R Zebraski
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | - Naval Avasthi
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | - Muhammad Waqas
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - Adnan H Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Vincent M Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA. .,Department of Neurosurgery, University at Buffalo, Buffalo, NY, USA. .,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA. .,Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY, USA. .,Department of Mechanical and Aerospace Engineering, University at Buffalo, Buffalo, NY, USA.
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Tutino VM, Zebraski HR, Rajabzadeh-Oghaz H, Waqas M, Jarvis JN, Bach K, Mokin M, Snyder KV, Siddiqui AH, Poppenberg KE. Identification of Circulating Gene Expression Signatures of Intracranial Aneurysm in Peripheral Blood Mononuclear Cells. Diagnostics (Basel) 2021; 11:diagnostics11061092. [PMID: 34203780 PMCID: PMC8232768 DOI: 10.3390/diagnostics11061092] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/18/2022] Open
Abstract
Peripheral blood mononuclear cells (PBMCs) play an important role in the inflammation that accompanies intracranial aneurysm (IA) pathophysiology. We hypothesized that PBMCs have different transcriptional profiles in patients harboring IAs as compared to IA-free controls, which could be the basis for potential blood-based biomarkers for the disease. To test this, we isolated PBMC RNA from whole blood of 52 subjects (24 with IA, 28 without) and performed next-generation RNA sequencing to obtain their transcriptomes. In a randomly assigned discovery cohort of n = 39 patients, we performed differential expression analysis to define an IA-associated signature of 54 genes (q < 0.05 and an absolute fold-change ≥ 1.3). In the withheld validation dataset, these genes could delineate patients with IAs from controls, as the majority of them still had the same direction of expression difference. Bioinformatics analyses by gene ontology enrichment analysis and Ingenuity Pathway Analysis (IPA) demonstrated enrichment of structural regulation processes, intracellular signaling function, regulation of ion transport, and cell adhesion. IPA analysis showed that these processes were likely coordinated through NF-kB, cytokine signaling, growth factors, and TNF activity. Correlation analysis with aneurysm size and risk assessment metrics showed that 4/54 genes were associated with rupture risk. These findings highlight the potential to develop predictive biomarkers from PBMCs to identify patients harboring IAs.
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Affiliation(s)
- Vincent M. Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, NY 14203, USA
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
- Department of Mechanical and Aerospace Engineering, University at Buffalo, Buffalo, NY 14228, USA
- Correspondence: ; Tel.: +1-(716)-829-5400; Fax: +1-(716)-854-1850
| | - Haley R. Zebraski
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY 14228, USA;
| | - Hamidreza Rajabzadeh-Oghaz
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Muhammad Waqas
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - James N. Jarvis
- Department of Pediatrics, University at Buffalo, Buffalo, NY 14203, USA;
| | - Konrad Bach
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33620, USA; (K.B.); (M.M.)
| | - Maxim Mokin
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33620, USA; (K.B.); (M.M.)
| | - Kenneth V. Snyder
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
| | - Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Buffalo, NY 14203, USA; (H.R.-O.); (M.W.); (K.V.S.); (A.H.S.); (K.E.P.)
- Department of Neurosurgery, University at Buffalo, Buffalo, NY 14203, USA
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10
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Poppenberg KE, Tutino VM, Tarbell E, Jarvis JN. Broadening our understanding of genetic risk for scleroderma/systemic sclerosis by querying the chromatin architecture surrounding the risk haplotypes. BMC Med Genomics 2021; 14:114. [PMID: 33894768 PMCID: PMC8066847 DOI: 10.1186/s12920-021-00964-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/14/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genetic variants in the human leukocyte antigen (HLA) locus contribute to the risk for developing scleroderma/systemic sclerosis (SSc). However, there are other replicated loci that also contribute to genetic risk for SSc, and it is unknown whether genetic risk in these non-HLA loci acts primarily on the vasculature, immune system, fibroblasts, or other relevant cell types. We used the Cistrome database to investigate the epigenetic landscapes surrounding 11 replicated SSc associated loci to determine whether SNPs in these loci may affect regulatory elements and whether they are likely to impact a specific cell type. METHODS We mapped 11 replicated SNPs to haplotypes and sought to determine whether there was significant enrichment for H3K27ac and H3K4me1 marks, epigenetic signatures of enhancer function, on these haplotypes. We queried pathologically relevant cell types: B cells, endothelial cells, fibroblasts, monocytes, and T cells. We then identified the topologically associated domains (TADs) that encompass the SSc risk haplotypes in primary T cells to identify the full range of genes that may be influenced by SSc causal SNPs. We used gene ontology analyses of the genes within the TADs to gain insight into immunologic functions that might be affected by SSc causal SNPs. RESULTS The SSc-associated haplotypes were enriched (p value < 0.01) for H3K4me1/H3K27ac marks in monocytes. Enrichment of one of the two histone marks was found in B cells, fibroblasts, and T cells. No enrichment was identified in endothelial cells. Ontological analyses of genes within the TADs encompassing the risk haplotypes showed enrichment for regulation of transcription, protein binding, activation of T lymphocytes, and proliferation of immune cells. CONCLUSIONS The 11 non-HLA SSc risk haplotypes queried are highly enriched for H3K4me1/H3K27ac-marked regulatory elements in a broad range of immune cells and fibroblasts. Furthermore, in immune cells, the risk haplotypes belong to larger chromatin structures encompassing genes that regulate a wide array of immune processes associated with SSc pathogenesis. Though importance of the vasculature in the pathobiology of SSc is widely accepted, we were unable to find evidence for genetic influences on endothelial cell function in these regions.
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Affiliation(s)
- Kerry E Poppenberg
- Canon Stroke and Vascular Research Center, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Vincent M Tutino
- Canon Stroke and Vascular Research Center, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | - Evan Tarbell
- Quantitative Systems Pharmacology, Enhanced Pharmacodynamics, LLC, Buffalo, NY, USA
| | - James N Jarvis
- Quantitative Systems Pharmacology, Enhanced Pharmacodynamics, LLC, Buffalo, NY, USA. .,Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. .,Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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11
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Poppenberg KE, Li L, Waqas M, Paliwal N, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H, Tutino VM. Whole blood transcriptome biomarkers of unruptured intracranial aneurysm. PLoS One 2020; 15:e0241838. [PMID: 33156839 PMCID: PMC7647097 DOI: 10.1371/journal.pone.0241838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The rupture of an intracranial aneurysm (IA) causes devastating subarachnoid hemorrhages, yet most IAs remain undiscovered until they rupture. Recently, we found an IA RNA expression signature of circulating neutrophils, and used transcriptome data to build predictive models for unruptured IAs. In this study, we evaluate the feasibility of using whole blood transcriptomes to predict the presence of unruptured IAs. METHODS We subjected RNA from peripheral whole blood of 67 patients (34 with unruptured IA, 33 without IA) to next-generation RNA sequencing. Model genes were identified using the least absolute shrinkage and selection operator (LASSO) in a random training cohort (n = 47). These genes were used to train a Gaussian Support Vector Machine (gSVM) model to distinguish patients with IA. The model was applied to an independent testing cohort (n = 20) to evaluate performance by receiver operating characteristic (ROC) curve. Gene ontology and pathway analyses investigated the underlying biology of the model genes. RESULTS We identified 18 genes that could distinguish IA patients in a training cohort with 85% accuracy. This SVM model also had 85% accuracy in the testing cohort, with an area under the ROC curve of 0.91. Bioinformatics reflected activation and recruitment of leukocytes, activation of macrophages, and inflammatory response, suggesting that the biomarker captures important processes in IA pathogenesis. CONCLUSIONS Circulating whole blood transcriptomes can detect the presence of unruptured IAs. Pending additional testing in larger cohorts, this could serve as a foundation to develop a simple blood-based test to facilitate screening and early detection of IAs.
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Affiliation(s)
- Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
| | - Lu Li
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York, United States of America
| | - Muhammad Waqas
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
| | - Nikhil Paliwal
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, United States of America
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, New York, United States of America
| | - James N. Jarvis
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, New York, United States of America
- Department of Pediatrics, University at Buffalo, Buffalo, New York, United States of America
| | - Yijun Sun
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, New York, United States of America
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, United States of America
| | - Kenneth V. Snyder
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, Buffalo, New York, United States of America
- Department of Neurology, University at Buffalo, Buffalo, New York, United States of America
| | - Elad I. Levy
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, Buffalo, New York, United States of America
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, Buffalo, New York, United States of America
| | - John Kolega
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Hui Meng
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, New York, United States of America
| | - Vincent M. Tutino
- Canon Stroke and Vascular Research Center, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, Buffalo, New York, United States of America
- Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York, United States of America
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12
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Poppenberg KE, Tutino VM, Li L, Waqas M, June A, Chaves L, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H. Classification models using circulating neutrophil transcripts can detect unruptured intracranial aneurysm. J Transl Med 2020; 18:392. [PMID: 33059716 PMCID: PMC7565814 DOI: 10.1186/s12967-020-02550-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/27/2020] [Indexed: 12/14/2022] Open
Abstract
Background Intracranial aneurysms (IAs) are dangerous because of their potential to rupture. We previously found significant RNA expression differences in circulating neutrophils between patients with and without unruptured IAs and trained machine learning models to predict presence of IA using 40 neutrophil transcriptomes. Here, we aim to develop a predictive model for unruptured IA using neutrophil transcriptomes from a larger population and more robust machine learning methods. Methods Neutrophil RNA extracted from the blood of 134 patients (55 with IA, 79 IA-free controls) was subjected to next-generation RNA sequencing. In a randomly-selected training cohort (n = 94), the Least Absolute Shrinkage and Selection Operator (LASSO) selected transcripts, from which we constructed prediction models via 4 well-established supervised machine-learning algorithms (K-Nearest Neighbors, Random Forest, and Support Vector Machines with Gaussian and cubic kernels). We tested the models in the remaining samples (n = 40) and assessed model performance by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (RT-qPCR) of 9 IA-associated genes was used to verify gene expression in a subset of 49 neutrophil RNA samples. We also examined the potential influence of demographics and comorbidities on model prediction. Results Feature selection using LASSO in the training cohort identified 37 IA-associated transcripts. Models trained using these transcripts had a maximum accuracy of 90% in the testing cohort. The testing performance across all methods had an average area under ROC curve (AUC) = 0.97, an improvement over our previous models. The Random Forest model performed best across both training and testing cohorts. RT-qPCR confirmed expression differences in 7 of 9 genes tested. Gene ontology and IPA network analyses performed on the 37 model genes reflected dysregulated inflammation, cell signaling, and apoptosis processes. In our data, demographics and comorbidities did not affect model performance. Conclusions We improved upon our previous IA prediction models based on circulating neutrophil transcriptomes by increasing sample size and by implementing LASSO and more robust machine learning methods. Future studies are needed to validate these models in larger cohorts and further investigate effect of covariates.
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Affiliation(s)
- Kerry E Poppenberg
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Vincent M Tutino
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Biomedical Engineering, University of Buffalo, Buffalo, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Lu Li
- Department of Computer Science and Engineering, University of Buffalo, Buffalo, USA
| | - Muhammad Waqas
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Armond June
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Lee Chaves
- Department of Internal Medicine, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - James N Jarvis
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Yijun Sun
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Kenneth V Snyder
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Elad I Levy
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Adnan H Siddiqui
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA.,Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - John Kolega
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA.,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA
| | - Hui Meng
- Canon Stroke and Vascular Research Center, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14214, USA. .,Department of Biomedical Engineering, University of Buffalo, Buffalo, USA. .,Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, Buffalo, USA. .,Department of Mechanical & Aerospace Engineering, University At Buffalo, Buffalo, NY, USA.
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13
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Leeme TB, Mine M, Lechiile K, Mulenga F, Mosepele M, Mphoyakgosi T, Muthoga C, Ngidi J, Nkomo B, Ramaabya D, Tau M, Tenforde MW, Hayes R, Jarvis JN. Utility of CD4 count measurement in the era of universal antiretroviral therapy: an analysis of routine laboratory data in Botswana. HIV Med 2020; 22:1-10. [PMID: 32876378 DOI: 10.1111/hiv.12951] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 07/14/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVES National guidelines in Botswana recommend baseline CD4 count measurement and both CD4 and HIV viral load (VL) monitoring post-antiretroviral therapy (ART) initiation. We evaluated the utility of CD4 count measurement in Botswana in the era of universal ART. METHODS CD4 and VL data were analysed for HIV-infected adults undergoing CD4 count measurement in 2015-2017 at the Botswana Harvard HIV-Reference Laboratory. We determined (1) the proportion of individuals with advanced HIV disease (CD4 count < 200 cells/µL) at initial CD4 assessment, (2) the proportion with an initial CD4 count ≥ 200 cells/µL experiencing a subsequent decline in CD4 count to < 200 cells/µL, and (3) the proportion of these immunologically failing individuals who had virological failure. Logistic regression modelling examined factors associated with advanced HIV disease. CD4 count trajectories were assessed using locally weighted scatterplot smoothing (LOWESS) regression. RESULTS Twenty-five per cent (3571/14 423) of individuals with an initial CD4 assessment during the study period had advanced HIV disease at baseline. Older age [≥ 35 years; adjusted odds ratio (aOR) 1.9; 95% confidence interval (CI) 1.8-2.1] and male sex were associated with advanced HIV disease. Fifty per cent (7163/14 423) of individuals had at least two CD4 counts during the study period. Of those with an initial CD4 count ≥ 200 cells/µL, 4% (180/5061) experienced a decline in CD4 count to < 200 cells/µL; the majority of CD4 count declines were in virologically suppressed individuals and transient. CONCLUSIONS One-quarter of HIV-positive individuals in Botswana still present with advanced HIV disease, highlighting the importance of baseline CD4 count measurement to identify this at-risk population. Few with a baseline CD4 count ≥ 200 cells/µL experienced a drop below 200 cells/µL, suggesting limited utility for ongoing CD4 monitoring.
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Affiliation(s)
- T B Leeme
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - M Mine
- National Health Laboratory, Gaborone, Botswana
| | - K Lechiile
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - F Mulenga
- National Health Laboratory, Gaborone, Botswana
| | - M Mosepele
- Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | | | - C Muthoga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Botswana-UPenn Partnership, Gaborone
| | - J Ngidi
- National Health Laboratory, Gaborone, Botswana
| | - B Nkomo
- Ministry of Health and Wellness, Gaborone, Botswana
| | - D Ramaabya
- Ministry of Health and Wellness, Gaborone, Botswana
| | - M Tau
- Ministry of Health and Wellness, Gaborone, Botswana
| | | | - R Hayes
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - J N Jarvis
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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14
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Jiang K, Kessler H, Park Y, Sudman M, Thompson SD, Jarvis JN. Broadening our understanding of the genetics of Juvenile Idiopathic Arthritis (JIA): Interrogation of three dimensional chromatin structures and genetic regulatory elements within JIA-associated risk loci. PLoS One 2020; 15:e0235857. [PMID: 32730263 PMCID: PMC7392255 DOI: 10.1371/journal.pone.0235857] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022] Open
Abstract
Objective The risk loci for juvenile idiopathic arthritis (JIA) consist of extended haplotypes that include functional elements in addition to canonical coding genes. As with most autoimmune diseases, the risk haplotypes for JIA are highly enriched for H3K4me1/H3K27ac histone marks, epigenetic signatures that typically identify poised or active enhancers. In this study, we test the hypothesis that genetic risk for JIA is exerted through altered enhancer-mediated gene regulation. Methods We mined publically available HiC and other chromatin conformation data to determine whether H3K27ac-marked regions in 25 JIA risk loci showed physical evidence of contact with gene promoters. We also used in vitro reporter assays to establish as proof-of-concept the idea that genetic variants in linkage disequilibrium with GWAS-identified tag SNPs alter enhancer function. Results All 25 loci examined showed multiple contact sites in the 4 different cell lines that we queried. These regions were characterized by HiC-defined loop structures that included 237 immune-related genes. Using in vitro assays, we found that a 657 bp, H3K4me1/H3K27-marked region within the first intron of IL2RA shows enhancer activity in reporter assays, and this activity is attenuated by SNPs on the IL2RA haplotype that we identified using whole genome sequencing of children with JIA. Similarly, we identified a 1,669 bp sequence in an intergenic region of the IL6R locus where SNPs identified in children with JIA increase enhancer function in reporter assays. Conclusions These studies provide evidence that altered enhancer function contributes to genetic risk in JIA. Further studies to identify the specific target genes of genetically altered enhancers are warranted.
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Affiliation(s)
- Kaiyu Jiang
- Department of Pediatrics, Pediatric Rheumatology Research, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of America
| | - Haeja Kessler
- Department of Pediatrics, Pediatric Rheumatology Research, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of America
| | - Yungki Park
- Department of Biochemistry, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of America
- Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of Americass
| | - Marc Sudman
- Center for Autoimmune Genetics & Epigenetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Susan D. Thompson
- Center for Autoimmune Genetics & Epigenetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - James N. Jarvis
- Department of Pediatrics, Pediatric Rheumatology Research, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of America
- Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of Americass
- * E-mail:
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15
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Alexander JJ, Jacob A, Chang A, Quigg RJ, Jarvis JN. Double negative T cells, a potential biomarker for systemic lupus erythematosus. Precis Clin Med 2020; 3:34-43. [PMID: 32257532 PMCID: PMC7093895 DOI: 10.1093/pcmedi/pbaa001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/17/2019] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease that is a challenge to diagnose and treat. There is an urgent need for biomarkers to help define organ involvement, and more effective therapies. A unique population of T cells, the CD3+CD4−CD8− (DNeg) cells, is significantly increased in lupus patients. Twenty-seven cases (53%) of pediatric SLE patients had elevated DNeg cells in their peripheral blood, which correlated with kidney function (R2 = 0.54). Significant infiltration of DNeg cells was observed in both adult and pediatric lupus kidneys by immunofluorescence. For the first time, this study provides direct evidence that DNeg cells facilitate kidney injury in preclinical 8-week-old MRL/lpr lupus mice. In lupus mice, the increase in DNeg cells tracked with worsening disease and correlated with kidney function (R2 = 0.85). Our results show that DNeg cells per se can cause kidney dysfunction, increase in number with increase in disease pathology, and could serve as a potential biomarker.
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Affiliation(s)
- Jessy J Alexander
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA.,Departments of Medicine, Pediatrics, Jacobs School of Medicine and Biomedical Sciences and Genetics, Genomics, & Bioinformatics Program, University at Buffalo, Buffalo, NY 14203, USA
| | - Alexander Jacob
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA.,Departments of Medicine, Pediatrics, Jacobs School of Medicine and Biomedical Sciences and Genetics, Genomics, & Bioinformatics Program, University at Buffalo, Buffalo, NY 14203, USA
| | - Anthony Chang
- Departments of Medicine, Pediatrics, Jacobs School of Medicine and Biomedical Sciences and Genetics, Genomics, & Bioinformatics Program, University at Buffalo, Buffalo, NY 14203, USA
| | - Richard J Quigg
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA.,Departments of Medicine, Pediatrics, Jacobs School of Medicine and Biomedical Sciences and Genetics, Genomics, & Bioinformatics Program, University at Buffalo, Buffalo, NY 14203, USA
| | - James N Jarvis
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
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16
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Poppenberg KE, Jiang K, Li L, Sun Y, Meng H, Wallace CA, Hennon T, Jarvis JN. The feasibility of developing biomarkers from peripheral blood mononuclear cell RNAseq data in children with juvenile idiopathic arthritis using machine learning approaches. Arthritis Res Ther 2019; 21:230. [PMID: 31706344 PMCID: PMC6842535 DOI: 10.1186/s13075-019-2010-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/23/2019] [Indexed: 01/09/2023] Open
Abstract
Background The response to treatment for juvenile idiopathic arthritis (JIA) can be staged using clinical features. However, objective laboratory biomarkers of remission are still lacking. In this study, we used machine learning to predict JIA activity from transcriptomes from peripheral blood mononuclear cells (PBMCs). We included samples from children with Native American ancestry to determine whether the model maintained validity in an ethnically heterogeneous population. Methods Our dataset consisted of 50 samples, 23 from children in remission and 27 from children with an active disease on therapy. Nine of these samples were from children with mixed European/Native American ancestry. We used 4 different machine learning methods to create predictive models in 2 populations: the whole dataset and then the samples from children with exclusively European ancestry. Results In both populations, models were able to predict JIA status well, with training accuracies > 74% and testing accuracies > 78%. Performance was better in the whole dataset model. We note a high degree of overlap between genes identified in both populations. Using ingenuity pathway analysis, genes from the whole dataset associated with cell-to-cell signaling and interactions, cell morphology, organismal injury and abnormalities, and protein synthesis. Conclusions This study demonstrates it is feasible to use machine learning in conjunction with RNA sequencing of PBMCs to predict JIA stage. Thus, developing objective biomarkers from easy to obtain clinical samples remains an achievable goal.
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Affiliation(s)
- Kerry E Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Kaiyu Jiang
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Lu Li
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, NY, USA
| | - Yijun Sun
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo, Buffalo, NY, USA.,Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY, USA
| | - Hui Meng
- Canon Stroke and Vascular Research Center, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA.,Department of Neurosurgery, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, State University of New York, Buffalo, NY, USA.,Department of Mechanical & Aerospace Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Carol A Wallace
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Teresa Hennon
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA. .,Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo, Buffalo, NY, USA. .,Pediatric Rheumatology Research, Clinical & Translational Research Center, 875 Ellicott Street, Buffalo, NY, 14203, USA.
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Poppenberg KE, Jiang K, Tso MK, Snyder KV, Siddiqui AH, Kolega J, Jarvis JN, Meng H, Tutino VM. Epigenetic landscapes suggest that genetic risk for intracranial aneurysm operates on the endothelium. BMC Med Genomics 2019; 12:149. [PMID: 31666072 PMCID: PMC6821037 DOI: 10.1186/s12920-019-0591-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genetics play an important role in intracranial aneurysm (IA) pathophysiology. Genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) that are linked to IA but how they affect disease pathobiology remains poorly understood. We used Encyclopedia of DNA Elements (ENCODE) data to investigate the epigenetic landscapes surrounding genetic risk loci to determine if IA-associated SNPs affect functional elements that regulate gene expression and if those SNPs are most likely to impact a specific type of cells. METHODS We mapped 16 highly significant IA-associated SNPs to linkage disequilibrium (LD) blocks within the human genome. Within these regions, we examined the presence of H3K4me1 and H3K27ac histone marks and CCCTC-binding factor (CTCF) and transcription-factor binding sites using chromatin immunoprecipitation-sequencing (ChIP-Seq) data. This analysis was conducted in several cell types relevant to endothelial (human umbilical vein endothelial cells [HUVECs]) and inflammatory (monocytes, neutrophils, and peripheral blood mononuclear cells [PBMCs]) biology. Gene ontology analysis was performed on genes within extended IA-risk regions to understand which biological processes could be affected by IA-risk SNPs. We also evaluated recently published data that showed differential methylation and differential ribonucleic acid (RNA) expression in IA to investigate the correlation between differentially regulated elements and the IA-risk LD blocks. RESULTS The IA-associated LD blocks were statistically significantly enriched for H3K4me1 and/or H3K27ac marks (markers of enhancer function) in endothelial cells but not in immune cells. The IA-associated LD blocks also contained more binding sites for CTCF in endothelial cells than monocytes, although not statistically significant. Differentially methylated regions of DNA identified in IA tissue were also present in several IA-risk LD blocks, suggesting SNPs could affect this epigenetic machinery. Gene ontology analysis supports that genes affected by IA-risk SNPs are associated with extracellular matrix reorganization and endopeptidase activity. CONCLUSION These findings suggest that known genetic alterations linked to IA risk act on endothelial cell function. These alterations do not correlate with IA-associated gene expression signatures of circulating blood cells, which suggests that such signatures are a secondary response reflecting the presence of IA rather than indicating risk for IA.
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Affiliation(s)
- Kerry E Poppenberg
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Michael K Tso
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Kenneth V Snyder
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Radiology, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Adnan H Siddiqui
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Radiology, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - John Kolega
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - James N Jarvis
- Genetics, Genomics, and Bioinformatics Program, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Pediatrics, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Hui Meng
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA.,Department of Biomedical Engineering, University at Buffalo, Buffalo, NY, USA.,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, NY, USA
| | - Vincent M Tutino
- Clinical and Translational Research Center, Canon Stroke and Vascular Research Center, 875 Ellicott Street, 14203, Buffalo, NY, USA. .,Department of Neurosurgery, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. .,Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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Jiang K, Karasawa R, Hu Z, Chen Y, Holmes L, O’Neil KM, Jarvis JN. Plasma exosomes from children with juvenile dermatomyositis are taken up by human aortic endothelial cells and are associated with altered gene expression in those cells. Pediatr Rheumatol Online J 2019; 17:41. [PMID: 31299993 PMCID: PMC6626431 DOI: 10.1186/s12969-019-0347-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/03/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The pathology of juvenile dermatomyositis (JDM) is characterized by prominent vessel wall and perivascular inflammation. This feature of the disease has remained unexplained and under-investigated. We have hypothesized that plasma exosomes, which play an important role in inter-cellular communication, may play a role in the vascular injury associated with JDM. OBJECTIVE To characterize the circulating exosomes of children with JDM and determine whether the small RNA cargoes within those exosomes are capable of altering transcriptional programs within endothelial cells. DESIGN/METHODS We purified exosomes from plasma samples of children with active, untreated JDM (n = 6) and healthy controls (n = 9). We characterized the small RNA cargoes in JDM and control exosomes by RNA sequencing using the Illumina HiSeq 2500 platform. We then incubated isolated exosomes from healthy controls and children with JDM with cultured human aortic endothelial cells (HAEC) for 24 h. Fluorescence microscopy was used to confirm that both control and JDM exosomes were taken up by HAEC. RNA was then purified from HAEC that had been incubated with either control or JDM exosomes and sequenced on the Illumina platform. Differential expression of mRNAs from HAEC incubated with control or JDM exosomes was ascertained using standard computational methods. Finally, we assessed the degree to which differential gene expression in HAEC could be attributed to the different small RNA cargoes in JDM vs control exosomes using conventional and novel analytic methods. RESULTS We identified 10 small RNA molecules that showed differential abundance when we compared JDM and healthy control exosomes. Fluorescence microscopy of labeled exosomes confirmed that both JDM and control exosomes were taken up by HAEC. Differential gene expression analysis revealed 59 genes that showed differential expression between HAEC incubated with JDM exosomes vs HAEC incubated with exosomes from controls. Statistical analysis of gene expression data demonstrated that multiple miRNAs exerted transcriptional control on multiple genes with HAEC. CONCLUSIONS Plasma exosomes from children with active, untreated JDM are taken up by HAEC and are associated with alterations in gene expression in those cells. These findings provide new insight into potential mechanisms leading to the targeting of vascular tissue by the immune system in JDM.
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Affiliation(s)
- Kaiyu Jiang
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY USA
| | - Rie Karasawa
- Department of Frontier Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Zihua Hu
- Center for Computational Research, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY USA
| | - Yanmin Chen
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY USA
| | - Lucy Holmes
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY USA
| | - Kathleen M. O’Neil
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN USA
| | - James N. Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY USA
- Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY USA
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19
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Tutino VM, Poppenberg KE, Li L, Shallwani H, Jiang K, Jarvis JN, Sun Y, Snyder KV, Levy EI, Siddiqui AH, Kolega J, Meng H. Biomarkers from circulating neutrophil transcriptomes have potential to detect unruptured intracranial aneurysms. J Transl Med 2018; 16:373. [PMID: 30593281 PMCID: PMC6310942 DOI: 10.1186/s12967-018-1749-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/17/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Intracranial aneurysms (IAs) are dangerous because of their potential to rupture and cause deadly subarachnoid hemorrhages. Previously, we found significant RNA expression differences in circulating neutrophils between patients with unruptured IAs and aneurysm-free controls. Searching for circulating biomarkers for unruptured IAs, we tested the feasibility of developing classification algorithms that use neutrophil RNA expression levels from blood samples to predict the presence of an IA. METHODS Neutrophil RNA extracted from blood samples from 40 patients (20 with angiography-confirmed unruptured IA, 20 angiography-confirmed IA-free controls) was subjected to next-generation RNA sequencing to obtain neutrophil transcriptomes. In a randomly-selected training cohort of 30 of the 40 samples (15 with IA, 15 controls), we performed differential expression analysis. Significantly differentially expressed transcripts (false discovery rate < 0.05, fold change ≥ 1.5) were used to construct prediction models for IA using four well-known supervised machine-learning approaches (diagonal linear discriminant analysis, cosine nearest neighbors, nearest shrunken centroids, and support vector machines). These models were tested in a testing cohort of the remaining 10 neutrophil samples from the 40 patients (5 with IA, 5 controls), and model performance was assessed by receiver-operating-characteristic (ROC) curves. Real-time quantitative polymerase chain reaction (PCR) was used to corroborate expression differences of a subset of model transcripts in neutrophil samples from a new, separate validation cohort of 10 patients (5 with IA, 5 controls). RESULTS The training cohort yielded 26 highly significantly differentially expressed neutrophil transcripts. Models using these transcripts identified IA patients in the testing cohort with accuracy ranging from 0.60 to 0.90. The best performing model was the diagonal linear discriminant analysis classifier (area under the ROC curve = 0.80 and accuracy = 0.90). Six of seven differentially expressed genes we tested were confirmed by quantitative PCR using isolated neutrophils from the separate validation cohort. CONCLUSIONS Our findings demonstrate the potential of machine-learning methods to classify IA cases and create predictive models for unruptured IAs using circulating neutrophil transcriptome data. Future studies are needed to replicate these findings in larger cohorts.
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Affiliation(s)
- Vincent M. Tutino
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY USA
| | - Kerry E. Poppenberg
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY USA
| | - Lu Li
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, NY USA
| | - Hussain Shallwani
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY USA
| | - James N. Jarvis
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY USA
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Yijun Sun
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, NY USA
| | - Kenneth V. Snyder
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Elad I. Levy
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Adnan H. Siddiqui
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Radiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - John Kolega
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
| | - Hui Meng
- Canon Stroke and Vascular Research Center, University at Buffalo, Clinical and Translational Research Center, 875 Ellicott Street, Buffalo, NY 14214 USA
- Department of Biomedical Engineering, University at Buffalo, Buffalo, NY USA
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY USA
- Department of Mechanical & Aerospace Engineering, University at Buffalo, Buffalo, NY USA
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20
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Kessler H, Jiang K, Jarvis JN. Using Chromatin Architecture to Understand the Genetics and Transcriptomics of Juvenile Idiopathic Arthritis. Front Immunol 2018; 9:2964. [PMID: 30619322 PMCID: PMC6302745 DOI: 10.3389/fimmu.2018.02964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
The presence of abnormal gene expression signatures is a well-described feature of the oligoarticular and polyarticular forms of juvenile idiopathic arthritis. In this review, we discuss how new insights into genetic risk for JIA and the three dimensional architecture of the genome may be used to develop a better understanding of the mechanisms driving these gene expression patterns.
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Affiliation(s)
- Haeja Kessler
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
| | - Kaiyu Jiang
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States.,Genetics, Genomics, and Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, United States
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21
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Karasawa R, Tamaki M, Sato T, Tanaka M, Nawa M, Yudoh K, Jarvis JN. Multiple target autoantigens on endothelial cells identified in juvenile dermatomyositis using proteomics. Rheumatology (Oxford) 2018; 57:671-676. [PMID: 29361142 DOI: 10.1093/rheumatology/kex468] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 12/15/2022] Open
Abstract
Objective Although generally classified within the group of inflammatory myopathies, JDM displays many pathological features of vasculitis. Previous work has shown that AECA are abundant in other forms of vasculitis. We therefore investigated whether such antibodies might also be detected in JDM. Methods We screened plasma from children with JDM for the presence of AECA by western blotting and 2D gel electrophoresis (2DE) using proteins extracted from human aortic endothelial cells as the substrate. We performed mass spectrometry to identify candidate antigens from 2DE gels and used ELISA to confirm the presence of specific antibodies. Results We identified 22 candidate target autoantigens for AECA probed with JDM plasma. Interestingly, 17 of these 22 target antigens were proteins associated with antigen processing and protein trafficking. ELISA confirmed the presence of antibodies to heat shock cognate 71 kDa protein in JDM plasma, particularly in children with active, untreated disease. Conclusion Children with JDM express antibodies to autoantigens in endothelial cells. The clinical and pathological significance of such autoantibodies require further investigation.
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Affiliation(s)
- Rie Karasawa
- Department of Frontier Medicine, St Marianna University School of Medicine, Kawasak, Japani
| | - Mayumi Tamaki
- Department of Frontier Medicine, St Marianna University School of Medicine, Kawasak, Japani
| | - Toshiko Sato
- Department of Frontier Medicine, St Marianna University School of Medicine, Kawasak, Japani
| | - Megumi Tanaka
- Department of Frontier Medicine, St Marianna University School of Medicine, Kawasak, Japani
| | - Makiko Nawa
- Institute of Nanken-Kyoten and RCC, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazuo Yudoh
- Department of Frontier Medicine, St Marianna University School of Medicine, Kawasak, Japani
| | - James N Jarvis
- Department of Pediatrics and Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, NY, USA.,Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences University at Buffalo, Buffalo, NY, USA
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22
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Jiang K, Wong L, Chen Y, Xing X, Li D, Wang T, Jarvis JN. Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. J Reprod Immunol 2018; 128:2-8. [PMID: 29800761 PMCID: PMC6086739 DOI: 10.1016/j.jri.2018.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 04/27/2018] [Accepted: 05/10/2018] [Indexed: 11/23/2022]
Abstract
The studies proposed here were undertaken to test the hypothesis that, under specific circumstances (e.g., a strong enough inflammatory stimulus), genes that are repressed at the maternal-fetal interface via DNA methylation might be de-methylated, allowing either a maternal immune response to the semi-allogenic fetus or the onset of early labor. Chorionic trophoblasts (CT) were isolated from fetal membranes, followed by incubation with medium from LPS-activated PBMC or resting PBMC medium for 2 h. RNA and DNA were isolated from the cells for RNA-seq and DNA methylation studies. Two hrs after being exposed to conditioned medium from LPS-activated PBMC, CT showed differential expression of 114 genes, all but 2 of which showed higher expression in the stimulated cells than is the unstimulated cells. We also identified 318 differentially methylated regions (DMRs) that associated with 306 genes (155 protein coding genes) in the two groups, but the observed methylation changes had negligible impact on the observed transcriptional changes in CT. CT display complex patterns of transcription in response to inflammation. DNA methylation does not appear to be an important regulator of the observed transcriptional changes.
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Affiliation(s)
- Kaiyu Jiang
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Laiping Wong
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Yanmin Chen
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Xiaoyun Xing
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Ave, St. Louis, MO, 63108, USA
| | - Daofeng Li
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Ave, St. Louis, MO, 63108, USA
| | - Ting Wang
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4515 McKinley Ave, St. Louis, MO, 63108, USA
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA; Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
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23
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Kheir JM, Guthridge CJ, Johnston JR, Adams LJ, Rasmussen A, Gross TF, Munroe ME, Bourn RL, Sivils KL, Guthridge JM, Weisman MH, Wallace DJ, Anaya JM, Rojas Villarraga A, Jarvis JN, Harley JB, James JA. Unique clinical characteristics, autoantibodies and medication use in Native American patients with systemic lupus erythematosus. Lupus Sci Med 2018. [PMID: 29531773 PMCID: PMC5844376 DOI: 10.1136/lupus-2017-000247] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Objective Systemic lupus erythematosus (SLE) is a systemic autoimmune disease with varied morbidity and mortality. We assessed clinical presentations, autoantibody specificities and therapeutic interventions in Native American (NA) patients with SLE. Methods Patients with SLE meeting 1997 American College of Rheumatology classification criteria (n=3148) were enrolled between 1992 and 2010 in the multiethnic, cross-sectional Lupus Family Registry and Repository. Clinical, demographic and therapeutic information were extracted from medical records using a standardised form and formalised training. Autoantibodies were assessed by indirect immunofluorescence (antinuclear antibodies (ANA) and antidouble-stranded DNA), precipitin (ENA) and ELISA (IgG and IgM anticardiolipins). Results NA patients met SLE classification at a younger age (29.89±12.3 years) than European Americans (EA; 32.02±12.87, P=0.0157) and a similar age to African-Americans (AAs) and Hispanics (HIS). More NA patients had concurrent rheumatic diseases or symptoms, such as Raynaud’s phenomenon, interstitial lung disease, Sjӧgren’s syndrome and systemic sclerosis. Compared with EAs, NAs were more likely to have high-titre ANA (≥1:3240; P<0.0001) and had more SLE-associated autoantibodies. Autoantibodies with unknown specificities were more common in NAs (41%) compared with other racial/ethnic groups in this collection (AA: 24%, P=0.0006; EA: 17%, P<0.0001; HIS: 23%, P=0.0050). Fewer NA patients used hydroxychloroquine (68%) compared with others (AA: 74%, P=0.0308; EA: 79%, P=0.0001, HIS: 77%, P=0.0173); this was influenced by lower hydroxychloroquine use in NA patients from Latin America (32%). NA patients had higher rates of methotrexate use (28%) compared with AA (18%, P=0.0006) and HIS patients (14%, P=0.0003), higher azathioprine use (38%) compared with EA patients (30%, P=0.0105) and higher mycophenolate mofetil use (26%) compared with EA (17%, P=0.0012) and HIS patients (11%, P<0.0001). Conclusions NA patients are diagnosed with SLE earlier in life and present worse concurrent rheumatic disease symptoms than EA patients. NA patients also are more likely to have expanded autoantibody profiles and precipitins of unknown specificities.
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Affiliation(s)
- Joseph M Kheir
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Carla J Guthridge
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Jonathon R Johnston
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Oklahoma State University Health Sciences Center, Tulsa, Oklahoma, USA
| | - Lucas J Adams
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Astrid Rasmussen
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Timothy F Gross
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Melissa E Munroe
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Rebecka L Bourn
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kathy L Sivils
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Joel M Guthridge
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Michael H Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Daniel J Wallace
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | | | - James N Jarvis
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Judith A James
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.,Department of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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24
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Tutino VM, Poppenberg KE, Jiang K, Jarvis JN, Sun Y, Sonig A, Siddiqui AH, Snyder KV, Levy EI, Kolega J, Meng H. Circulating neutrophil transcriptome may reveal intracranial aneurysm signature. PLoS One 2018; 13:e0191407. [PMID: 29342213 PMCID: PMC5771622 DOI: 10.1371/journal.pone.0191407] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/04/2018] [Indexed: 12/30/2022] Open
Abstract
Background Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs. Methods Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls. Samples from the two groups were paired based on demographics and comorbidities. RNA was extracted from isolated neutrophils and subjected to next-generation RNA sequencing to obtain differential expressions for identification of an IA-associated signature. Bioinformatics analyses, including gene set enrichment analysis and Ingenuity Pathway Analysis, were used to investigate the biological function of all differentially expressed transcripts. Results Transcriptome profiling identified 258 differentially expressed transcripts in patients with and without IAs. Expression differences were consistent with peripheral neutrophil activation. An IA-associated RNA expression signature was identified in 82 transcripts (p<0.05, fold-change ≥2). This signature was able to separate patients with and without IAs on hierarchical clustering. Furthermore, in an independent, unpaired, replication cohort of patients with IAs (n = 5) and controls (n = 5), the 82 transcripts separated 9 of 10 patients into their respective groups. Conclusion Preliminary findings show that RNA expression from circulating neutrophils carries an IA-associated signature. These findings highlight a potential to use predictive biomarkers from peripheral blood samples to identify patients with IAs.
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Affiliation(s)
- Vincent M. Tutino
- Toshiba Stroke and Vascular Research Center; University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Kerry E. Poppenberg
- Toshiba Stroke and Vascular Research Center; University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Kaiyu Jiang
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - James N. Jarvis
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Pediatrics, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Yijun Sun
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Ashish Sonig
- Toshiba Stroke and Vascular Research Center; University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Adnan H. Siddiqui
- Toshiba Stroke and Vascular Research Center; University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Kenneth V. Snyder
- Toshiba Stroke and Vascular Research Center; University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Neurology, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Elad I. Levy
- Toshiba Stroke and Vascular Research Center; University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Radiology, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - John Kolega
- Toshiba Stroke and Vascular Research Center; University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Pathology and Anatomical Sciences, University at Buffalo, State University of New York, Buffalo, New York, United States of America
| | - Hui Meng
- Toshiba Stroke and Vascular Research Center; University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Neurosurgery, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- Department of Mechanical & Aerospace Engineering, University at Buffalo, State University of New York, Buffalo, New York, United States of America
- * E-mail:
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Zhu L, Jiang K, Webber K, Wong L, Liu T, Chen Y, Jarvis JN. Chromatin landscapes and genetic risk for juvenile idiopathic arthritis. Arthritis Res Ther 2017; 19:57. [PMID: 28288683 PMCID: PMC5348874 DOI: 10.1186/s13075-017-1260-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/13/2017] [Indexed: 02/07/2023] Open
Abstract
Background The transcriptomes of peripheral blood cells in children with juvenile idiopathic arthritis (JIA) have distinct transcriptional aberrations that suggest impairment of transcriptional regulation. To gain a better understanding of this phenomenon, we studied known JIA genetic risk loci, the majority of which are located in non-coding regions, where transcription is regulated and coordinated on a genome-wide basis. We examined human neutrophils and CD4 primary T cells to identify genes and functional elements located within those risk loci. Methods We analyzed RNA sequencing (RNA-Seq) data, H3K27ac and H3K4me1 chromatin immunoprecipitation-sequencing (ChIP-Seq) data, and previously published chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) data to characterize the chromatin landscapes within the known JIA-associated risk loci. Results In both neutrophils and primary CD4+ T cells, the majority of the JIA-associated linkage disequilibrium (LD) blocks contained H3K27ac and/or H3K4me1 marks. These LD blocks were also binding sites for a small group of transcription factors, particularly in neutrophils. Furthermore, these regions showed abundant intronic and intergenic transcription in neutrophils. In neutrophils, none of the genes that were differentially expressed between untreated patients with JIA and healthy children were located within the JIA-risk LD blocks. In CD4+ T cells, multiple genes, including HLA-DQA1, HLA-DQB2, TRAF1, and IRF1 were associated with the long-distance interacting regions within the LD regions as determined from ChIA-PET data. Conclusions These findings suggest that genetic risk contributes to the aberrant transcriptional control observed in JIA. Furthermore, these findings demonstrate the challenges of identifying the actual causal variants within complex genomic/chromatin landscapes. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1260-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisha Zhu
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Kaiyu Jiang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Karstin Webber
- Graduate Program in Biological Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Laiping Wong
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.,Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yanmin Chen
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. .,Genetics, Genomics, & Bioinformatics Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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Hui-Yuen JS, Zhu L, Wong LP, Jiang K, Chen Y, Liu T, Jarvis JN. Chromatin landscapes and genetic risk in systemic lupus. Arthritis Res Ther 2016; 18:281. [PMID: 27906046 PMCID: PMC5134118 DOI: 10.1186/s13075-016-1169-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/02/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a multi-system, complex disease in which the environment interacts with inherited genes to produce broad phenotypes with inter-individual variability. Of 46 single nucleotide polymorphisms (SNPs) shown to confer genetic risk for SLE in recent genome-wide association studies, 30 lie within noncoding regions of the human genome. We therefore sought to identify and describe the functional elements (aside from genes) located within these regions of interest. METHODS We used chromatin immunoprecipitation followed by sequencing to identify epigenetic marks associated with enhancer function in adult neutrophils to determine whether enhancer-associated histone marks were enriched within the linkage disequilibrium (LD) blocks encompassing the 46 SNPs of interest. We also interrogated available data in Roadmap Epigenomics for CD4+ T cells and CD19+ B cells to identify these same elements in lymphoid cells. RESULTS All three cell types demonstrated enrichment of enhancer-associated histone marks compared with genomic background within LD blocks encoded by SLE-associated SNPs. In addition, within the promoter regions of these LD blocks, all three cell types demonstrated enrichment for transcription factor binding sites above genomic background. In CD19+ B cells, all but one of the LD blocks of interest were also enriched for enhancer-associated histone marks. CONCLUSIONS Much of the genetic risk for SLE lies within or near genomic regions of disease-relevant cells that are enriched for epigenetic marks associated with enhancer function. Elucidating the specific roles of these noncoding elements within these cell-type-specific genomes will be crucial to our understanding of SLE pathogenesis.
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Affiliation(s)
- Joyce S. Hui-Yuen
- Division of Pediatric Rheumatology, Steven and Alexandra Cohen Children’s Medical Center, 1991 Marcus Avenue, Suite M100, Lake Success, NY 11042 USA
- Department of Pediatrics, Hofstra-Northwell School of Medicine, Hempstead, NY 11549 USA
| | - Lisha Zhu
- Department of Biochemistry, University at Buffalo, Buffalo, NY 14203 USA
| | - Lai Ping Wong
- Department of Pediatrics, University at Buffalo, Buffalo, NY 14203 USA
| | - Kaiyu Jiang
- Department of Pediatrics, University at Buffalo, Buffalo, NY 14203 USA
| | - Yanmin Chen
- Department of Pediatrics, University at Buffalo, Buffalo, NY 14203 USA
| | - Tao Liu
- Department of Biochemistry, and Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY 14203 USA
| | - James N. Jarvis
- Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY 14203 USA
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27
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Abstract
Juvenile dermatomyositis is a complex illness characterized by vascular/perivascular inflammation, primarily in the skin and muscles. In this review, we discuss how proteomic and genomic technologies have expanded our understanding of the immune pathogenesis of this disease. We will also discuss further directions that the field may take to use existing and developing technologies to further our understanding of this often-perplexing disease.
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Affiliation(s)
- Rie Karasawa
- Department of Pediatrics and Genetics, Genomics & Bioinformatics Program, University at Buffalo
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28
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Fotis L, Shaikh N, Baszis K, French A, Tarr P, Grevich S, Lee P, Ringold S, Leroux B, Leahey H, Yuasa M, Foster J, Sokolove J, Lahey L, Robinson W, Newsom J, Stevens A, Karasawa R, Tamaki M, Tanaka M, Sato T, Yudoh K, Jarvis JN, Moncrieffe H, Bennett MF, Tsoras M, Luyrink L, Xu H, Prahalad S, Morris P, Dare J, Nigrovic PA, Rosenkranz M, Becker M, O’Neil KM, Griffin T, Lovell DJ, Grom AA, Medvedovic M, Thompson SD, Zhu L, Jiang K, Wong L, Buck MJ, Chen Y, Moncrieffe H, Brungs L, Liu T, Wang T, Jarvis JN, Alsaeid K, Alfailakawi J, Alenezi H, Alsaeed H, Beukelman T, Natter M, Ilowite N, Mieszkalski K, Burrell G, Best B, Bristow H, Carr S, Dennos A, Kaufmann R, Kimura Y, Schanberg L, Blier PR, Boneparth A, Wenderfer SE, Moorthy LN, Radhakrishna SM, Sagcal-Gironella ACP, von Scheven E, Gedik KC, Siddique S, Aguiar CL, Erkan D, Cohen E, Lee Y, Dossett M, Mehta D, Davis R, Gilbert M, Goilav B, Meidan E, Hsu J, Boneparth A, Chua A, Ardoin S, Wenderfer SE, Von Scheven E, Ruth NM, Hui-Yuen J, Gedik KC, Bermudez L, Cook A, Imundo L, Starr A, Eichenfield A, Askanase A, Janow G, Schanberg LE, Setoguchi S, Hasselblad V, Mellins ED, Schneider R, Kimura Y, Kimura Y, Grevich S, Beukelman T, Morgan E, Graham TB, Ibarra M, Ruas YS, Klein-Gitelman M, Onel K, Prahalad S, Punaro M, Ringold S, Toib D, Van Mater H, Weiss JE, Weiss PF, Mieszkalski K, Schanberg LE, Kwok TSH, Bisaillon J, Smith C, Brosseau L, Stinson J, Huber AM, Duffy CM, April KT, Lewandowski LB, Scott C, Li SC, Torok KS, Rabinovich CE, Hong SD, Becker ML, Dedeoglu F, Ibarra MF, Ferguson PJ, Fuhbrigge RC, Stewart KG, Pope E, Laxer RM, Mason TG, Higgins GC, Li X, Punaro MG, Tomlinson G, Pullenayegum E, Matelski J, Schanberg L, Feldman BM, Manthiram K, Correa H, Edwards K, Oberle EJ, Bayer M, Co DO, Baris HE, Chiu Y, Huber A, Kim S, Oberle EJ, Beukelman T, Orandi AB, Baszis KW, Dharnidharka V, Hoeltzel MF, Reed A, Huber A, Tomlinson G, Pullenayegum E, Matelski J, Goh YI, Schanberg L, Feldman BM, Schnabel A, Range U, Hahn G, Siepmann T, Berner R, Hedrich CM, Stevens B, Torok KS, Li S, Hershey N, Curran M, Higgins G, Moore K, Rabinovich E, Stevens AM, Stinson J, Connelly M, Huber A, Luca N, Spiegel L, Tsimicalis A, Luca S, Tajuddin N, Berard R, Barsalou J, Campillo S, Dancey P, Duffy C, Feldman B, Johnson N, McGrath P, Shiff N, Tse S, Tucker L, Victor C, Stinson J, Lalloo C, Harris L, Cafazzo J, Spiegel L, Feldman B, Luca N, Laxer R, Bullock DR, Vehe RK, Zhang L, Correll CK, Ganguli S, Shenberger M, Korumilli R, Gottlieb B, Rodriguez M, de Ranieri D, Onel K, Wagner-Weiner L, Tesher M, Wojcicki ER, Maletta KL, Co DO, Malloy M, Thomson S, Olson JC, Wenderfer SE, Gilbert M, Hsu J, Sule S, Rubinstein TB, Goilav B, Okamura DM, Chua A, Greenbaum LA, Lane JC, von Scheven E, Ardoin SP, Ruth NM, Woo JMP, Malloy MM, Jegers JA, Hahn DJ, Hintermeyer MK, Martinetti SM, Heckel GR, Roth-Wojcicki EL, Co DO. Proceedings of the 2016 Childhood Arthritis and Rheumatology Research Alliance (CARRA) Scientific Meeting : Toronto, Canada. 14-17 April 2016. Pediatr Rheumatol Online J 2016; 14 Suppl 1:41. [PMID: 27409414 PMCID: PMC4943514 DOI: 10.1186/s12969-016-0098-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
P1 Serologic evidence of gut-driven systemic inflammation in juvenile idiopathic arthritis Lampros Fotis, Nur Shaikh, Kevin Baszis, Anthony French, Phillip Tarr P2 Oral health and anti-citrullinated peptide antibodies (ACPA) in juvenile idiopathic arthritis Sriharsha Grevich, Peggy Lee, Sarah Ringold, Brian Leroux, Hannah Leahey, Megan Yuasa, Jessica Foster, Jeremy Sokolove, Lauren Lahey, William Robinson, Joshua Newsom, Anne Stevens P3 Novel autoantigens for endothelial cell antibodies in pediatric rheumatic diseases identified by proteomics Rie Karasawa, Mayumi Tamaki, Megumi Tanaka, Toshiko Sato, Kazuo Yudoh, James N. Jarvis P4 Transcriptional profiling reveals monocyte signature associated with JIA patient poor response to methotrexate Halima Moncrieffe, Mark F. Bennett, Monica Tsoras, Lorie Luyrink, Huan Xu, Sampath Prahalad, Paula Morris, Jason Dare, Peter A. Nigrovic, Margalit Rosenkranz, Mara Becker, Kathleen M. O’Neil, Thomas Griffin, Daniel J. Lovell, Alexei A. Grom, Mario Medvedovic, Susan D. Thompson P5 A multi-dimensional genomic map for polyarticular juvenile idiopathic arthritis Lisha Zhu, Kaiyu Jiang, Laiping Wong, Michael J Buck, Yanmin Chen, Halima Moncrieffe, Laura Brungs, Tao Liu, Ting Wang, James N Jarvis P6 Tocilizumab for treatment of children with refractory JIA Khaled Alsaeid, Jasim Alfailakawi, Hamid Alenezi, Hazim Alsaeed P7 Clinical characteristics of the initial patients enrolled in the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Registry Tim Beukelman, Marc Natter, Norm Ilowite, Kelly Mieszkalski, Grendel Burrell, Brian Best, Helen Bristow, Shannon Carr, Anne Dennos, Rachel Kaufmann, Yukiko Kimura, Laura Schanberg P8 Comparative performance of small and large clinical centers in a comprehensive pediatric rheumatology disease registry Peter R Blier P9 Clinical characteristics of children with membranous lupus nephritis: The Childhood Arthritis and Rheumatology Research Alliance Legacy Registry Alexis Boneparth, Scott E. Wenderfer, L. Nandini Moorthy, Suhas M. Radhakrishna, Anna Carmela P. Sagcal-Gironella, Emily von Scheven P10 Rituximab use in pediatric lupus anticoagulant hypoprothrombinemia syndrome - a two center experience Kader Cetin Gedik, Salma Siddique, Cassyanne L. Aguiar, Doruk Erkan P11 Predictors of complementary and alternative medicine use and response in children with musculoskeletal conditions Ezra Cohen, Yvonne Lee, Michelle Dossett, Darshan Mehta, Roger Davis P12 Comparison of pediatric rheumatology and nephrology survey results for the treatment of refractory proliferative lupus nephritis and renal flare in juvenile SLE Mileka Gilbert, Beatrice Goilav, Esra Meidan, Joyce Hsu, Alexis Boneparth, Anabelle Chua, Stacy Ardoin, Scott E. Wenderfer, Emily Von Scheven, Natasha M. Ruth P13 Transitioning lupus patients from pediatric to adult rheumatology Joyce Hui-Yuen, Kader Cetin Gedik, Liza Bermudez, Ashlea Cook, Lisa Imundo, Amy Starr, Andrew Eichenfield, Anca Askanase P14 The systemic juvenile idiopathic arthritis cohort of the Childhood Arthritis & Rheumatology Research Alliance Registry Ginger Janow, Laura E. Schanberg, Soko Setoguchi, Victor Hasselblad, Elizabeth D. Mellins, Rayfel Schneider, Yukiko Kimura, The CARRA Legacy Registry Investigators P15 Results of the pilot study of the Childhood Arthritis and Rheumatology Research Alliance (CARRA) consensus treatment plans for new-onset systemic juvenile idiopathic arthritis Yukiko Kimura, Sriharsha Grevich, Timothy Beukelman, Esi Morgan, T Brent Graham, Maria Ibarra, Yonit Sterba Ruas, Marisa Klein-Gitelman, Karen Onel, Sampath Prahalad, Marilynn Punaro, Sarah Ringold, Dana Toib, Heather Van Mater, Jennifer E. Weiss, Pamela F. Weiss, Kelly Mieszkalski, Laura E. Schanberg P16 A systemic review of pain relief modalities in juvenile idiopathic arthritis: First step in developing a novel decision support intervention Timothy S. H. Kwok, Jacinthe Bisaillon, Christine Smith, Lucie Brosseau, Jennifer Stinson, Adam M. Huber, Ciaran M. Duffy, Karine Toupin April P17 Barriers and facilitators to care retention for pediatric systemic lupus erythematous patients in South Africa: A qualitative study Laura B Lewandowski, Christiaan Scott P18 Evaluating the feasibility of conducting comparative effectiveness studies in juvenile Localized Scleroderma (jLS) Suzanne C. Li, Kathryn S. Torok, C. Egla Rabinovich, Sandy D. Hong, Mara L Becker, Fatma Dedeoglu, Maria F. Ibarra, Polly J Ferguson, Rob C. Fuhbrigge, Katie G. Stewart, Elena Pope, Ronald M. Laxer, Thomas G. Mason, Gloria C. Higgins, Xiaohu Li, Marilynn G. Punaro, George Tomlinson, Eleanor Pullenayegum, John Matelski, Laura Schanberg, Brian M. Feldman P19 Tonsillar histology in patients with periodic fever, aphthous stomatitis, pharyngitis, adenitis (PFAPA) syndrome Kalpana Manthiram, Hernan Correa, Kathryn Edwards P20 Clinical course of juvenile dermatomyositis presenting as skin predominant disease Edward J. Oberle, Michelle Bayer, Dominic O. Co, Hatice Ezgi Baris, Yvonne Chiu, Adam Huber, Susan Kim P21 A Survey of musculoskeletal ultrasound practices of pediatric rheumatologists in North America Edward J Oberle, Timothy Beukelman P22 Assessment, classification and treatment of calcinosis as a complication of juvenile dermatomyositis: A survey of pediatric rheumatologists by the Childhood Arthritis and Rheumatology Research Alliance Amir B. Orandi, Kevin W. Baszis, Vikas Dharnidharka, Mark F. Hoeltzel, for the CARRA JDM Committee P23 CARRA dermatomyositis CTP pilot study Ann Reed, Adam Huber, George Tomlinson, Eleanor Pullenayegum, John Matelski, Y. Ingrid Goh, Laura Schanberg, Brian M. Feldman P24 Unexpectedly high incidences and prolonged disease activity in children with chronic non-bacterial osteomyelitis (CNO) as compared to bacterial osteomyelitis Anja Schnabel, Ursula Range, Gabriele Hahn, Timo Siepmann, Reinhard Berner, Christian Michael Hedrich P25 Juvenile systemic sclerosis cohort within the Childhood Arthritis and Rheumatology Research Alliance (CARRA) Legacy Registry: Follow up characteristics Brandi Stevens, Kathryn S. Torok, Suzanne Li, Nicole Hershey, Megan Curran, Gloria Higgins, Katharine Moore, Egla Rabinovich, Anne M. Stevens, for the CARRA Registry Investigators P26 Development and usability testing of an iPad and desktop psycho-educational game for children with Juvenile Idiopathic Arthritis and their parents Jennifer Stinson, Mark Connelly, Adam Huber, Nadia Luca, Lynn Spiegel, Argerie Tsimicalis, Stephanie Luca, Naweed Tajuddin, Roberta Berard, Julia Barsalou, Sarah Campillo, Paul Dancey, Ciaran Duffy, Brian Feldman, Nicole Johnson, Patrick McGrath, Natalie Shiff, Shirley Tse, Lori Tucker, Charles Victor P27 iCanCopeTM: User-centred design and development of a smartphone app to support self-management for youth with arthritis pain Jennifer Stinson, Chitra Lalloo, Lauren Harris, Joseph Cafazzo, Lynn Spiegel, Brian Feldman, Nadia Luca, Ronald Laxer P28 Accessing pediatric rheumatology care: Despite barriers, few parents prefer telemedicine Danielle R. Bullock, Richard K. Vehe, Lei Zhang, Colleen K. Correll1 P29 Exploration of factors contributing to time to achieve clinically inactive disease (CID) in juvenile idiopathic arthritis (JIA): A preliminary report Suhas Ganguli, Max Shenberger, Ritesh Korumilli, Beth Gottlieb P30 Pediatric rheumatology referral patterns: Presenting complaints of new patients at a large, urban academic center Martha Rodriguez, Deirdre de Ranieri, Karen Onel, Linda Wagner-Weiner, Melissa Tesher P31 Quality improvement (QI) initiatives in childhood systemic lupus erythematosus (cSLE) Elizabeth Roth Wojcicki, Kristyn L. Maletta, Dominic O. Co, Marsha Malloy, Sarah Thomson, Judyann C. Olson P32 Proliferative lupus nephritis in juvenile SLE: Support from the pediatric nephrology community for the definitions of responsiveness and flare in the 2012 consensus treatment plans Scott E. Wenderfer, Mileka Gilbert, Joyce Hsu, Sangeeta Sule, Tamar B. Rubinstein, Beatrice Goilav, Daryl M. Okamura, Annabelle Chua, Laurence A. Greenbaum, Jerome C. Lane, Emily von Scheven, Stacy P. Ardoin, Natasha M. Ruth P33 The steroid taper app: Making of a mobile app Jennifer M. P. Woo, Marsha M. Malloy, James A. Jegers, Dustin J. Hahn, Mary K. Hintermeyer, Stacey M. Martinetti, Gretchen R. Heckel, Elizabeth L. Roth-Wojcicki, Dominic O. Co
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Affiliation(s)
- Lampros Fotis
- Washington University School of Medicine, St Louis, Missouri USA
| | - Nur Shaikh
- Washington University School of Medicine, St Louis, Missouri USA
| | - Kevin Baszis
- Washington University School of Medicine, St Louis, Missouri USA
| | - Anthony French
- Washington University School of Medicine, St Louis, Missouri USA
| | - Phillip Tarr
- Washington University School of Medicine, St Louis, Missouri USA
| | - Sriharsha Grevich
- Department of Pediatrics, Division of Rheumatology, University of Washington, Seattle, WA USA
| | - Peggy Lee
- Department of Oral Medicine, University of Washington, Seattle, WA USA
| | - Sarah Ringold
- Department of Rheumatology, Seattle Children’s Hospital, Seattle, WA USA
| | - Brian Leroux
- Department of Oral Health Sciences, University of Washington, Seattle, WA USA
| | | | | | | | - Jeremy Sokolove
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA USA
| | - Lauren Lahey
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA USA
| | - William Robinson
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA USA
| | | | - Anne Stevens
- Department of Pediatrics, Division of Rheumatology, University of Washington, Seattle, WA USA ,Seattle Children’s Research Institute, Seattle, WA USA
| | - Rie Karasawa
- St. Marianna University School of Medicine, Kawasaki, Japan
| | - Mayumi Tamaki
- St. Marianna University School of Medicine, Kawasaki, Japan
| | - Megumi Tanaka
- St. Marianna University School of Medicine, Kawasaki, Japan
| | - Toshiko Sato
- St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kazuo Yudoh
- St. Marianna University School of Medicine, Kawasaki, Japan
| | - James N. Jarvis
- University at Buffalo, State University of New York, Buffalo, NY USA
| | - Halima Moncrieffe
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,University of Cincinnati, Cincinnati, OH USA
| | | | - Monica Tsoras
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Lorie Luyrink
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Huan Xu
- University of Cincinnati, Cincinnati, OH USA
| | | | - Paula Morris
- Arkansas Children’s Hospital Research Institute, Little Rock, AR USA
| | - Jason Dare
- Arkansas Children’s Hospital Research Institute, Little Rock, AR USA
| | | | | | - Mara Becker
- Children’s Mercy Hospital, Kansas City, MO USA
| | | | | | - Daniel J. Lovell
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Alexei A. Grom
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | | | - Susan D. Thompson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,University of Cincinnati, Cincinnati, OH USA
| | - Lisha Zhu
- University at Buffalo, The State University of New York, Buffalo, NY USA
| | - Kaiyu Jiang
- University at Buffalo, The State University of New York, Buffalo, NY USA
| | - Laiping Wong
- University at Buffalo, The State University of New York, Buffalo, NY USA
| | - Michael J Buck
- University at Buffalo, The State University of New York, Buffalo, NY USA
| | - Yanmin Chen
- University at Buffalo, The State University of New York, Buffalo, NY USA
| | | | | | - Tao Liu
- University at Buffalo, The State University of New York, Buffalo, NY USA
| | - Ting Wang
- Washington University, St. Louis, MO USA
| | - James N Jarvis
- University at Buffalo, The State University of New York, Buffalo, NY USA
| | - Khaled Alsaeid
- Department of Pediatrics, Kuwait University, Kuwait City, Kuwait ,Mubarak Hospital, Jabriya, Kuwait
| | | | | | | | - Tim Beukelman
- University of Alabama at Birmingham, Birmingham, AL USA
| | - Marc Natter
- Tufts University, Medford, MA USA ,Harvard University, Boston, MA USA
| | - Norm Ilowite
- The Children’s Hospital at Montefiore, Bronx, NY USA
| | | | | | | | | | | | | | | | - Yukiko Kimura
- Hackensack University Medical Center, Hackensack, NJ USA
| | | | - Peter R. Blier
- Baystate Children’s Hospital, Springfield, MA USA ,Tufts University School of Medicine, Boston, MA USA
| | - Alexis Boneparth
- Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ USA
| | | | | | | | | | | | | | - Salma Siddique
- Hospital for Special Surgery-Weill Cornell Medical Center, New York, NY USA
| | | | - Doruk Erkan
- Hospital for Special Surgery-Weill Cornell Medical Center, New York, NY USA
| | - Ezra Cohen
- Boston Children’s Hospital, Boston, MA USA
| | - Yvonne Lee
- Brigham and Women’s Hospital, Boston, MA USA
| | | | | | | | - Mileka Gilbert
- Medical University of South Carolina, Charleston, SC USA
| | | | | | - Joyce Hsu
- Stanford University, Stanford, CA USA
| | | | | | - Stacy Ardoin
- Nationwide Children’s Hospital, Columbus, OH USA
| | | | | | | | - Joyce Hui-Yuen
- Division of Pediatric Rheumatology, Cohen Children’s Medical Center, New Hyde Park, NY USA
| | - Kader Cetin Gedik
- Division of Pediatric Rheumatology, Cohen Children’s Medical Center, New Hyde Park, NY USA
| | - Liza Bermudez
- Division of Pediatric Rheumatology, Morgan Stanley Children’s Hospital of New York-Presbyterian, Columbia University Medical Center, New York, NY USA
| | - Ashlea Cook
- Division of Pediatric Rheumatology, Morgan Stanley Children’s Hospital of New York-Presbyterian, Columbia University Medical Center, New York, NY USA
| | - Lisa Imundo
- Division of Adult Rheumatology, Columbia University Medical Center, New York, NY USA
| | - Amy Starr
- Division of Pediatric Rheumatology, Morgan Stanley Children’s Hospital of New York-Presbyterian, Columbia University Medical Center, New York, NY USA
| | - Andrew Eichenfield
- Division of Pediatric Rheumatology, Morgan Stanley Children’s Hospital of New York-Presbyterian, Columbia University Medical Center, New York, NY USA
| | - Anca Askanase
- Division of Adult Rheumatology, Columbia University Medical Center, New York, NY USA
| | - Ginger Janow
- Pediatrics, Joseph M Sanzari Children’s Hospital, Hackensack, NJ USA
| | - Laura E. Schanberg
- Pediatrics, Duke University, Durham, NC USA ,Duke Clinical Research Institute, Durham, NC USA
| | | | | | | | - Rayfel Schneider
- Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Yukiko Kimura
- Pediatrics, Joseph M Sanzari Children’s Hospital, Hackensack, NJ USA
| | | | - Yukiko Kimura
- Hackensack University Medical Center, Hackensack, NJ USA
| | | | | | - Esi Morgan
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | | | | | | | | | - Karen Onel
- Comer Children’s Hospital of Chicago, Chicago, IL USA
| | | | | | | | - Dana Toib
- St. Christopher’s Hospital for Children, Philadelphia, PA USA
| | | | | | | | | | | | - Timothy S. H. Kwok
- Undergraduate Medical Education, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Jacinthe Bisaillon
- School of Nursing Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario Canada
| | - Christine Smith
- School of Epidemiology, Public Health and Preventive Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Lucie Brosseau
- School of Rehabilitation Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario Canada
| | - Jennifer Stinson
- Hospital for Sick Children, Lawrence S. Bloomberg Faculty of Nursing University of Toronto, Toronto, Ontario Canada
| | - Adam M. Huber
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia Canada
| | - Ciaran M. Duffy
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Children’s Hospital of Eastern Ontario Research Institute, Ottawa, Ontario Canada
| | - Karine Toupin April
- Department of Pediatrics, Children’s Hospital of Eastern Ontario Research Institute, Faculty of Medicine, School of Rehabilitation Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario Canada
| | - Laura B. Lewandowski
- Pediatric Rheumatology, Duke University Medical Center, Durham, NC USA ,Duke Global Health Institute, Duke University, Durham, NC USA ,Paediatric Rheumatology, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa ,National Institute of Arthritis, Musculoskeletal, and Skin Diseases, NIH, Bethesda, MD USA
| | - Christiaan Scott
- Paediatric Rheumatology, Red Cross War Memorial Children’s Hospital and University of Cape Town, Cape Town, South Africa
| | - Suzanne C. Li
- Hackensack University Medical Center, Hackensack, NJ USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xiaohu Li
- Stevens Institute of Technology, Hoboken, NJ USA
| | | | | | | | | | | | | | - Kalpana Manthiram
- Division of Pediatric Infectious Diseases, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Hernan Correa
- Department of Pathology, Immunology, and Microbiology, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Kathryn Edwards
- Division of Pediatric Infectious Diseases, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Edward J. Oberle
- Nationwide Children’s Hospital, The Ohio State University, Columbus, OH USA
| | - Michelle Bayer
- Children’s Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI USA
| | - Dominic O. Co
- Children’s Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI USA
| | | | - Yvonne Chiu
- Children’s Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, WI USA
| | - Adam Huber
- IWK Health Centre, Dalhousie University, Halifax, NS Canada
| | - Susan Kim
- Boston Children’s Hospital, Boston, MA USA ,Harvard Medical School, Boston, MA USA
| | - Edward J. Oberle
- Nationwide Children’s Hospital, Columbus, OH USA ,The Ohio State University, Columbus, OH USA
| | | | - Amir B. Orandi
- St. Louis Children’s Hospital, Washington University School of Medicine, St. Louis, MO USA
| | - Kevin W. Baszis
- St. Louis Children’s Hospital, Washington University School of Medicine, St. Louis, MO USA
| | - Vikas Dharnidharka
- St. Louis Children’s Hospital, Washington University School of Medicine, St. Louis, MO USA
| | - Mark F. Hoeltzel
- Mott Children’s Hospital, University of Michigan Medical School, Ann Arbor, MI USA
| | | | | | - Adam Huber
- Dalhousie University, Halifax, NS Canada
| | | | | | | | | | | | | | - Anja Schnabel
- Pediatric Rheumatology and Immunology, Children’s Hospital Dresden, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ursula Range
- Institute for Medical Informatics and Biometry, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gabriele Hahn
- Department of Radiology, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Timo Siepmann
- Division of Health Care Sciences, Center for Clinical Research and Management Education, Dresden International University, Dresden, Germany
| | - Reinhard Berner
- Pediatric Rheumatology and Immunology, Children’s Hospital Dresden, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Christian Michael Hedrich
- Pediatric Rheumatology and Immunology, Children’s Hospital Dresden, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Brandi Stevens
- Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA USA
| | | | - Suzanne Li
- Hackensack University Medical Center, Hackensack, NJ USA
| | - Nicole Hershey
- Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA USA
| | - Megan Curran
- Northwestern University Feinberg School of Medicine, Chicago, IL USA
| | | | | | | | - Anne M. Stevens
- Seattle Children’s Research Institute, University of Washington, Seattle, WA USA
| | | | - Jennifer Stinson
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Mark Connelly
- University of Kansas Medical Center, Kansas City, MO USA
| | - Adam Huber
- IWK Health Centre, Halifax, Nova Scotia Canada
| | - Nadia Luca
- Alberta Children’s Hospital, Calgary, Alberta Canada
| | - Lynn Spiegel
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | - Stephanie Luca
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Naweed Tajuddin
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | | | | | - Paul Dancey
- Memorial University of Newfoundland, Newfoundland, Canada
| | - Ciaran Duffy
- Children’s Hospital of Eastern Ontario, Ottawa, Canada
| | - Brian Feldman
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | | | | | | | - Shirley Tse
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Lori Tucker
- British Columbia Children’s Hospital, Vancouver, British Columbia Canada
| | | | | | | | - Lauren Harris
- The Hospital for Sick Children, Toronto, Canada ,University of Toronto, Toronto, Canada ,Centre for Global eHealth Innovation, Toronto, Canada
| | | | | | | | - Nadia Luca
- Alberta Children’s Hospital, Calgary, Alberta Canada
| | | | - Danielle R. Bullock
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Minnesota Masonic Children’s Hospital, Minneapolis, MN USA
| | - Richard K. Vehe
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Minnesota Masonic Children’s Hospital, Minneapolis, MN USA
| | - Lei Zhang
- Clinical and Translational Sciences Institute, University of Minnesota, Minneapolis, MN USA
| | - Colleen K. Correll
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Minnesota Masonic Children’s Hospital, Minneapolis, MN USA
| | - Suhas Ganguli
- Pediatric Rheumatology, Cohen Children’s Medical Center, New York, NY 11040 USA
| | - Max Shenberger
- Pediatric Rheumatology, Cohen Children’s Medical Center, New York, NY 11040 USA
| | - Ritesh Korumilli
- Pediatrics, Flushing Hospital Medical Center, New York, NY 11355 USA
| | - Beth Gottlieb
- Pediatric Rheumatology, Cohen Children’s Medical Center, New York, NY 11040 USA
| | - Martha Rodriguez
- University of Chicago Medicine Comer Children’s Hospital, Chicago, IL USA
| | - Deirdre de Ranieri
- University of Chicago Medicine Comer Children’s Hospital, Chicago, IL USA
| | - Karen Onel
- University of Chicago Medicine Comer Children’s Hospital, Chicago, IL USA
| | | | - Melissa Tesher
- University of Chicago Medicine Comer Children’s Hospital, Chicago, IL USA
| | | | | | | | | | | | | | | | - Mileka Gilbert
- Medical University of South Carolina, Charleston, SC USA
| | - Joyce Hsu
- Stanford University, Stanford, CA USA
| | - Sangeeta Sule
- Johns Hopkins Children’s Hospital, Baltimore, MD USA
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Mahajan SD, Tutino VM, Redae Y, Meng H, Siddiqui A, Woodruff TM, Jarvis JN, Hennon T, Schwartz S, Quigg RJ, Alexander JJ. C5a induces caspase-dependent apoptosis in brain vascular endothelial cells in experimental lupus. Immunology 2016; 148:407-19. [PMID: 27213693 DOI: 10.1111/imm.12619] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/06/2016] [Accepted: 05/10/2016] [Indexed: 12/18/2022] Open
Abstract
Blood-brain barrier (BBB) dysfunction complicates central nervous system lupus, an important aspect of systemic lupus erythematosus. To gain insight into the underlying mechanism, vascular corrosion casts of brain were generated from the lupus mouse model, MRL/lpr mice and the MRL/MpJ congenic controls. Scanning electron microscopy of the casts showed loss of vascular endothelial cells in lupus mice compared with controls. Immunostaining revealed a significant increase in caspase 3 expression in the brain vascular endothelial cells, which suggests that apoptosis could be an important mechanism causing cell loss, and thereby loss of BBB integrity. Complement activation occurs in lupus resulting in increased generation of circulating C5a, which caused the endothelial layer to become 'leaky'. In this study, we show that C5a and lupus serum induced apoptosis in cultured human brain microvascular endothelial cells (HBMVECs), whereas selective C5a receptor 1 (C5aR1) antagonist reduced apoptosis in these cells, demonstrating C5a/C5aR1-dependence. Gene expression of initiator caspases, caspase 1 and caspase 8, and pro-apoptotic proteins death-associated protein kinase 1, Fas-associated protein (FADD), cell death-inducing DNA fragmentation factor 45 000 MW subunit A-like effector B (CIDEB) and BCL2-associated X protein were increased in HBMVECs treated with lupus serum or C5a, indicating that both the intrinsic and extrinsic apoptotic pathways could be critical mediators of brain endothelial cell apoptosis in this setting. Overall, our findings suggest that C5a/C5aR1 signalling induces apoptosis through activation of FADD, caspase 8/3 and CIDEB in brain endothelial cells in lupus. Further elucidation of the underlying apoptotic mechanisms mediating the reduced endothelial cell number is important in establishing the potential therapeutic effectiveness of C5aR1 inhibition that could prevent and/or reduce BBB alterations and preserve the physiological function of BBB in central nervous system lupus.
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Affiliation(s)
| | - Vincent M Tutino
- Toshiba Vascular Stroke Center, Biomedical Engineering Department, University at Buffalo, Buffalo, NY, USA
| | - Yonas Redae
- Department of Medicine, University at Buffalo, Buffalo, NY, USA
| | - Hui Meng
- Toshiba Vascular Stroke Center, Biomedical Engineering Department, University at Buffalo, Buffalo, NY, USA
| | - Adnan Siddiqui
- Toshiba Vascular Stroke Center, Biomedical Engineering Department, University at Buffalo, Buffalo, NY, USA
| | - Trent M Woodruff
- School of Biomedical Sciences, University of Queensland, St Lucia, QLD, Australia
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Teresa Hennon
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | | | - Richard J Quigg
- Department of Medicine, University at Buffalo, Buffalo, NY, USA
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30
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Jiang K, Wong L, Sawle AD, Frank MB, Chen Y, Wallace CA, Jarvis JN. Whole blood expression profiling from the TREAT trial: insights for the pathogenesis of polyarticular juvenile idiopathic arthritis. Arthritis Res Ther 2016; 18:157. [PMID: 27388672 PMCID: PMC4936089 DOI: 10.1186/s13075-016-1059-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/22/2016] [Indexed: 12/22/2022] Open
Abstract
Background The Trial of Early Aggressive Therapy in Juvenile Idiopathic Arthritis (TREAT trial) was accompanied by a once-in-a-generation sample collection for translational research. In this paper, we report the results of whole blood gene expression analyses and genomic data-mining designed to cast light on the immunopathogenesis of polyarticular juvenile idiopathic arthritis (JIA). Methods TREAT samples and samples from an independent cohort were analyzed on Affymetrix microarrays and compared to healthy controls. Data from the independent cohort were used to validate the TREAT data. Pathways analysis was used to characterize gene expression profiles. Furthermore, we correlated differential gene expression with new information about functional regulatory elements within the genome to develop models of aberrant gene expression in JIA. Results There was a strong concordance in gene expression between TREAT samples and the independent cohort. In addition, rheumatoid factor (RF)-positive and RF-negative patients showed only small differences on whole blood expression profiles. Analysis of the combined samples showed 158 genes represented by 176 probes that showed differential expression between TREAT subjects at baseline and healthy controls. None of the differentially expressed genes were encoded within linkage disequilibrium blocks containing single nucleotide polymorphisms known to be associated with risk for JIA. Functional analysis of these genes showed functional associations with multiple processes associated with innate and adaptive immunity, and appeared to reflect overall suppression of STAT1–3/interferon response factor-mediated pathways. Conclusions Despite their limitations, whole blood expression profiles clearly distinguish children with polyarticular JIA from healthy controls. Whole blood expression profiles identify several immunologic pathways of biologic relevance that will need to be pursued in homogeneous cell populations in order to clarify mechanisms of pathogenesis. Trial registration ClinicalTrials.gov registry #NCT00443430, originally registered 2 March 2007 and last updated 30 May 2013.
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Affiliation(s)
- Kaiyu Jiang
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Clinical & Translational Research Center, 875 Ellicott St., Buffalo, NY, USA
| | - Laiping Wong
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Clinical & Translational Research Center, 875 Ellicott St., Buffalo, NY, USA
| | - Ashley D Sawle
- Irving Cancer institute, Columbia University College of Physicians and Surgeons, 1130 Saint Nicholas Ave., New York, NY, 10032, USA
| | - M Barton Frank
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 800 NE 13th St., Oklahoma City, OK, 73104, USA
| | - Yanmin Chen
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Clinical & Translational Research Center, 875 Ellicott St., Buffalo, NY, USA
| | - Carol A Wallace
- Division of Rheumatology, Seattle Children's Hospital and Research Institute, 4800 Sand Point Way NE, MA.7.110, Seattle, WA, 98105, USA.,Genetics, Genomics, and Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Clinical & Translational Research Center, 875 Ellicott St., Buffalo, NY, USA. .,Genetics, Genomics, and Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
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31
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Hu Z, Jiang K, Frank MB, Chen Y, Jarvis JN. Complexity and Specificity of the Neutrophil Transcriptomes in Juvenile Idiopathic Arthritis. Sci Rep 2016; 6:27453. [PMID: 27271962 PMCID: PMC4895221 DOI: 10.1038/srep27453] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 05/19/2016] [Indexed: 12/17/2022] Open
Abstract
NIH projects such as ENCODE and Roadmap Epigenomics have revealed surprising complexity in the transcriptomes of mammalian cells. In this study, we explored transcriptional complexity in human neutrophils, cells generally regarded as nonspecific in their functions and responses. We studied distinct human disease phenotypes and found that, at the gene, gene isoform, and miRNA level, neutrophils exhibit considerable specificity in their transcriptomes. Thus, even cells whose responses are considered non-specific show tailoring of their transcriptional repertoire toward specific physiologic or pathologic contexts. We also found that miRNAs had a global impact on neutrophil transcriptome and are associated with innate immunity in juvenile idiopathic arthritis (JIA). These findings have important implications for our understanding of the link between genes, non-coding transcripts and disease phenotypes.
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Affiliation(s)
- Zihua Hu
- Center for Computational Research, New York State Center of Excellence in Bioinformatics &Life Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA.,Department of Ophthalmology, Department of Biostatistics, Department of Medicine, State University of New York at Buffalo, Buffalo, NY 14260, USA.,SUNY Eye Institute, Buffalo, NY 14260, USA
| | - Kaiyu Jiang
- Department of Pediatrics, Division of Allergy/Immunology/Rheumatology, University at Buffalo, Buffalo, NY 14203, USA
| | - Mark Barton Frank
- Arthritis &Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Yanmin Chen
- Department of Pediatrics, Division of Allergy/Immunology/Rheumatology, University at Buffalo, Buffalo, NY 14203, USA
| | - James N Jarvis
- Department of Pediatrics, Division of Allergy/Immunology/Rheumatology, University at Buffalo, Buffalo, NY 14203, USA.,Graduate Program in Genetics, Genomics, &Bioinformatics, University at Buffalo, Buffalo, NY 14203, USA
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32
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Chaney JM, Gamwell KL, Baraldi AN, Ramsey RR, Cushing CC, Mullins AJ, Gillaspy SR, Jarvis JN, Mullins LL. Parent Perceptions of Illness Uncertainty and Child Depressive Symptoms in Juvenile Rheumatic Diseases: Examining Caregiver Demand and Parent Distress as Mediators. J Pediatr Psychol 2016; 41:941-51. [DOI: 10.1093/jpepsy/jsw004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
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Du N, Jiang K, Sawle AD, Frank MB, Wallace CA, Zhang A, Jarvis JN. Dynamic tracking of functional gene modules in treated juvenile idiopathic arthritis. Genome Med 2015; 7:109. [PMID: 26497493 PMCID: PMC4619406 DOI: 10.1186/s13073-015-0227-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 10/01/2015] [Indexed: 12/25/2022] Open
Abstract
Background We have previously shown that childhood-onset rheumatic diseases show aberrant patterns of gene expression that reflect pathology-associated co-expression networks. In this study, we used novel computational approaches to examine how disease-associated networks are altered in one of the most common rheumatic diseases of childhood, juvenile idiopathic arthritis (JIA). Methods Using whole blood gene expression profiles derived from children in a pediatric rheumatology clinical trial, we used a network approach to understanding the impact of therapy and the underlying biology of response/non-response to therapy. Results We demonstrate that therapy for JIA is associated with extensive re-ordering of gene expression networks, even in children who respond inadequately to therapy. Furthermore, we observe distinct differences in the evolution of specific network properties when we compare children who have been treated successfully with those who have inadequate treatment response. Conclusions Despite the inherent noisiness of whole blood gene expression data, our findings demonstrate how therapeutic response might be mapped and understood in pathologically informative cells in a broad range of human inflammatory diseases.
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Affiliation(s)
- Nan Du
- Department of Computer Sciences and Engineering, University at Buffalo, Buffalo, NY, USA.
| | - Kaiyu Jiang
- Department of Pediatrics, Rheumatology Research, University at Buffalo School of Medicine, Buffalo, NY, USA.
| | - Ashley D Sawle
- The Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
| | - Mark Barton Frank
- Oklahoma Medical Research Foundation, Clinical Immunology Program, Oklahoma City, OK, USA.
| | - Carol A Wallace
- Department of Pediatrics, University of Washington, Seattle, WA, USA.
| | - Aidong Zhang
- Department of Computer Sciences and Engineering, University at Buffalo, Buffalo, NY, USA.
| | - James N Jarvis
- Department of Pediatrics, Rheumatology Research, University at Buffalo School of Medicine, Buffalo, NY, USA. .,Genetics, Genomics, and Bioinformatics Program, University at Buffalo, Buffalo, NY, USA. .,Pediatric Rheumatology Research, University at Buffalo Clinical & Translational Research Center, 875 Ellicott St, Buffalo, NY, 14203, USA.
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34
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Jiang K, Zhu L, Buck MJ, Chen Y, Carrier B, Liu T, Jarvis JN. Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells. Arthritis Rheumatol 2015; 67:1966-77. [PMID: 25833190 DOI: 10.1002/art.39135] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 03/24/2015] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Juvenile idiopathic arthritis (JIA) is considered a complex disease in which the environment interacts with inherited genes to produce a phenotype that shows broad interindividual variability. Twenty-four regions of genetic risk for JIA were identified in a recent genome-wide association study (GWAS); however, as is typical of the results of GWAS, most of the regions of genetic risk (22 of 24) were in noncoding regions of the genome. This study was undertaken to identify functional elements (other than genes) that might be located within the regions of genetic risk. METHODS We used paired-end RNA sequencing to identify noncoding RNAs (ncRNAs) located within 5 kb of disease-associated single-nucleotide polymorphisms (SNPs). In addition, we used chromatin immunoprecipitation (ChIP) followed by sequencing to identify epigenetic marks associated with enhancer function (H3K4me1 and H3K27ac) in human neutrophils to determine whether enhancer-associated histone marks were enriched in the linkage disequilibrium blocks that encompassed the 22 SNPs identified in the GWAS. RESULTS In human neutrophils, we identified H3K4me1 and/or H3K27ac marks in 15 of the 22 regions previously identified as risk loci for JIA. In CD4+ T cells, 18 regions had H3K4me1 and/or H3K27ac marks. In addition, we identified ncRNA transcripts at the rs4705862 and rs6894249 loci in human neutrophils. CONCLUSION Much of the genetic risk for JIA lies within or adjacent to regions of neutrophil and CD4+ T cell genomes that carry epigenetic marks associated with enhancer function and/or ncRNA transcripts. These findings are consistent with the hypothesis that JIA is fundamentally a disorder of gene regulation that includes both the innate and the adaptive immune system. Elucidating the specific roles of these noncoding elements within leukocyte genomes will be critical to our understanding of JIA pathogenesis.
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Affiliation(s)
| | - Lisha Zhu
- University at Buffalo, Buffalo, New York
| | | | | | | | - Tao Liu
- University at Buffalo, Buffalo, New York
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35
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Tenforde MW, Longley N, Meya DB, Boulware DR, Meintjes G, Goercke I, Harrison TS, Jarvis JN. Poor specificity of urinary cryptococcal antigen testing: Reply to Drain et al. Prevalence of cryptococcal antigenuria at initial HIV diagnosis in KwaZulu-Natal. HIV Med 2015; 19:e47-e48. [PMID: 26347456 DOI: 10.1111/hiv.12319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2015] [Indexed: 01/01/2023]
Affiliation(s)
- M W Tenforde
- Botswana-UPenn Partnership, Gaborone, Botswana.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - N Longley
- Centre for Infection, St. George's University of London, London, UK
| | - D B Meya
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.,Infectious Disease Institute Collect of Health Sciences, Makerere University, Kampala, Uganda
| | - D R Boulware
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - G Meintjes
- Institute of Infectious Disease and Molecular Medicine and Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - I Goercke
- University of Botswana, Gaborone, Botswana
| | - T S Harrison
- Centre for Infection, St. George's University of London, London, UK
| | - J N Jarvis
- Botswana-UPenn Partnership, Gaborone, Botswana.,Faculty of Infectious Diseases and Tropical Medicine, London School of Hygiene and Tropical Medicine, London, UK.,Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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36
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Jiang K, Sun X, Chen Y, Shen Y, Jarvis JN. RNA sequencing from human neutrophils reveals distinct transcriptional differences associated with chronic inflammatory states. BMC Med Genomics 2015; 8:55. [PMID: 26310571 PMCID: PMC4551565 DOI: 10.1186/s12920-015-0128-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 08/11/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The transcriptional complexity of mammalian cells suggests that they have broad abilities to respond to specific environmental stimuli and physiologic contexts. These abilities were not apparent a priori from the structure of mammalian genomes, but have been identified through detailed transcriptome analyses. In this study, we examined the transcriptomes of cells of the innate immune system, human neutrophils, using RNA sequencing (RNAseq). METHODS We sequenced poly-A RNA from nine individual samples corresponding to specific phenotypes: three children with active, untreated juvenile idiopathic arthritis (JIA)(AD), three children with the same disease whose disease was inactive on medication (CRM), and three children with cystic fibrosis (CF). RESULTS We demonstrate that transcriptomes of neutrophils, typically considered non-specific in their responses and functions, display considerable specificity in their transcriptional repertoires dependent on the pathologic context, and included genes, gene isoforms, and long non-coding RNA transcripts. Furthermore, despite the small sample numbers, these findings demonstrate the potential of RNAseq approaches to biomarker development in rheumatic diseases. CONCLUSIONS These data demonstrate the capacity of cells previously considered non-specific in function to adapt their transcriptomes to specific biologic contexts. These data also provide insight into previously unrecognized pathological pathways and show considerable promise for elucidating disease and disease-state specific regulatory networks.
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Affiliation(s)
- Kaiyu Jiang
- Department of Pediatrics, State University of New York at Buffalo School of Medicine, Buffalo, NY, USA.
| | - Xiaoyun Sun
- JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY, USA.
| | - Yanmin Chen
- Department of Pediatrics, State University of New York at Buffalo School of Medicine, Buffalo, NY, USA.
| | - Yufeng Shen
- JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY, USA. .,Departments of Systems Biology and Biomedical Informatics, Columbia University Medical Center, New York, NY, USA.
| | - James N Jarvis
- Department of Pediatrics, State University of New York at Buffalo School of Medicine, Buffalo, NY, USA.
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37
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Mahajan SD, Parikh NU, Woodruff TM, Jarvis JN, Lopez M, Hennon T, Cunningham P, Quigg RJ, Schwartz SA, Alexander JJ. C5a alters blood-brain barrier integrity in a human in vitro model of systemic lupus erythematosus. Immunology 2015; 146:130-43. [PMID: 26059553 DOI: 10.1111/imm.12489] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/27/2015] [Accepted: 06/01/2015] [Indexed: 12/23/2022] Open
Abstract
The blood-brain barrier (BBB) plays a crucial role in brain homeostasis, thereby maintaining the brain environment precise for optimal neuronal function. Its dysfunction is an intriguing complication of systemic lupus erythematosus (SLE). SLE is a systemic autoimmune disorder where neurological complications occur in 5-50% of cases and is associated with impaired BBB integrity. Complement activation occurs in SLE and is an important part of the clinical profile. Our earlier studies demonstrated that C5a generated by complement activation caused the loss of brain endothelial layer integrity in rodents. The goal of the current study was to determine the translational potential of these studies to a human system. To assess this, we used a two dimensional in vitro BBB model constructed using primary human brain microvascular endothelial cells and astroglial cells, which closely emulates the in vivo BBB allowing the assessment of BBB integrity. Increased permeability monitored by changes in transendothelial electrical resistance and cytoskeletal remodelling caused by actin fiber rearrangement were observed when the cells were exposed to lupus serum and C5a, similar to the observations in mice. In addition, our data show that C5a/C5aR1 signalling alters nuclear factor-κB translocation into nucleus and regulates the expression of the tight junction proteins, claudin-5 and zonula occludens 1 in this setting. Our results demonstrate for the first time that C5a regulates BBB integrity in a neuroinflammatory setting where it affects both endothelial and astroglial cells. In addition, we also demonstrate that our previous findings in a mouse model, were emulated in human cells in vitro, bringing the studies one step closer to understanding the translational potential of C5a/C5aR1 blockade as a promising therapeutic strategy in SLE and other neurodegenerative diseases.
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Affiliation(s)
| | - Neil U Parikh
- Department of Medicine, University at Buffalo, Buffalo, NY, USA
| | - Trent M Woodruff
- School of Biomedical Sciences, University of Queensland, St. Lucia, QLD, Australia
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Molly Lopez
- Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Teresa Hennon
- Department of Medicine, University at Buffalo, Buffalo, NY, USA
| | | | - Richard J Quigg
- Department of Medicine, University at Buffalo, Buffalo, NY, USA
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Bonner MS, Ramsey RR, Ryan JL, Fedele DA, Mullins LL, Wagner JL, Jarvis JN, Chaney JM. Examination of parent-child adjustment in juvenile rheumatic diseases using depression-specific indices of parent and youth functioning. J Child Health Care 2015; 19:63-72. [PMID: 23939726 DOI: 10.1177/1367493513496910] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Studies demonstrate a link between parental distress, youth illness appraisals, and depression symptoms in youth with juvenile rheumatic diseases. However, the exclusive use of broadband (i.e. general) measures of parental distress in these studies has resulted in conceptual and clinical imprecision regarding the parent-child adjustment process. Our aim was to reanalyze previously published data (i.e. Wagner et al., 2003) using a depression-specific scale derived from the general adult distress measure in the original study. Parents completed the Brief Symptom Inventory (BSI), youth completed the Child Depression Inventory (CDI), and the Illness Intrusiveness Scale (IIS-C). Thirteen Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) depression-specific items from the BSI comprised the parent measure of Depressive Symptoms Scale (DS). Consistent with Wagner et al. (2003), adult DS scores were associated with youth CDI scores. However, youth illness appraisals had unique effects on the parent-child depression relation. Elevated youth perceptions of illness intrusiveness amplified the negative effect of parent depressive symptoms on youth depressive symptoms; decreased illness intrusiveness buffered the negative effect of parent depression. The empirical and clinical implications of assessing parent and youth adjustment in a domain-specific manner are discussed.
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Jiang K, Sawle AD, Frank MB, Chen Y, Wallace CA, Jarvis JN. Whole blood gene expression profiling predicts therapeutic response at six months in patients with polyarticular juvenile idiopathic arthritis. Arthritis Rheumatol 2014; 66:1363-71. [PMID: 24782192 PMCID: PMC4077198 DOI: 10.1002/art.38341] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 12/26/2013] [Indexed: 01/12/2023]
Abstract
Objective To determine whether gene expression profiles identified in peripheral whole blood samples could be used to determine therapeutic outcome in a cohort of children with newly diagnosed polyarticular juvenile idiopathic arthritis (JIA). Methods Whole blood samples from the Trial of Early Aggressive Therapy (TREAT) in JIA patients were analyzed on Illumina microarrays, and differential gene expression was compared to expression in healthy controls. Microarray results were validated by real-time quantitative polymerase chain reaction in an independent cohort of samples. Pathway analysis software was used to characterize gene expression profiles. Support vector machines were used to develop predictive models for different patient classes. Results Differential gene expression profiles for rheumatoid factor (RF)–positive and RF-negative patients were remarkably similar. Pathway analysis revealed a broad range of affected pathways, consistent with current mechanistic theories. Modeling showed that the prognosis at 6 months was strongly linked to gene expression at presentation, irrespective of treatment. Conclusion Gene expression is linked to therapeutic outcome, and gene expression in the peripheral blood may be a suitable target for a prognostic test.
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Affiliation(s)
- Kaiyu Jiang
- Columbia University Medical Center, New York, New York
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Ryan JL, Mullins LL, Ramsey RR, Bonner MS, Jarvis JN, Gillaspy SR, Chaney JM. Caregiver demand and parent distress in juvenile rheumatic disease: the mediating effect of parent attitude toward illness. J Clin Psychol Med Settings 2014; 20:351-60. [PMID: 23613109 DOI: 10.1007/s10880-013-9365-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Parents of youth with juvenile rheumatic diseases (JRD) often take on illness management responsibilities that can become burdensome, potentially resulting in poor parent adjustment outcomes. However, not all caregivers will experience increased distress as a result of variability in stress appraisals. The current study examined the role of parent illness attitudes in the relation between perceived caregiver demand and parental distress. Youth (N = 70) ages 7-18 years diagnosed with a JRD and their parents were recruited from a pediatric rheumatology clinic. Parents completed measures of caregiver demand, parental distress, and illness attitudes. Hierarchical regression revealed a relationship between caregiver demand and parental distress. A significant relationship was also found between caregiver demand and parent illness attitudes, as well as parent illness attitudes and parental distress. Thus, parent illness attitudes mediated the relationship between caregiver demand and parental distress. Techniques aimed at altering negative illness attitudes may help parents cope with their caregiving responsibilities.
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Affiliation(s)
- Jamie L Ryan
- Department of Psychology, Oklahoma State University, 116 North Murray Hall, Stillwater, OK 74078, USA.
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Jarvis JN, Jiang K, Liu T, Buck M, Carrier B, Chen Y. A174: JIA-Associated SNPs From Non-Coding Regions Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils. Arthritis Rheumatol 2014. [DOI: 10.1002/art.38600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Tao Liu
- University at Buffalo; Buffalo NY
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Jiang K, Hu Z, Chen Y, Jarvis JN. A176: Deep Sequencing Reveals Differential Small RNA Expression in Serum Exosomes of Children With Juvenile Idiopathic Arthritis. Arthritis Rheumatol 2014. [DOI: 10.1002/art.38602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Zihua Hu
- University at Buffalo; Buffalo NY
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Abstract
Rheumatoid arthritis and juvenile rheumatoid arthritis are histopathologically similar diseases characterized by chronic inflammation of the synovium. The pathogenesis of these diseases is unknown, but the emergence of gene expression profiling provides considerable promise that some of the complex, interconnected immunopathologic events underlying these diseases will soon be better understood. This review will summarize the potential use of gene expression profiling as a diagnostic or prognostic modality, and the potential benefits or limits of such uses. It will conclude with a short discussion of the potential for using gene expression profiling to identify novel targets of therapy in rheumatoid arthritis and related diseases.
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Affiliation(s)
- James N Jarvis
- University of Oklahoma College of Medicine, Department of Pediatrics, Rheumatology Section, Oklahoma City, OK 73104, USA.
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Bicanic TA, Jarvis JN, Loyse A, Harrison TS. Starting ART following cryptococcal meningitis:The optimal time has yet to be defined. South Afr J HIV Med 2013. [DOI: 10.4102/sajhivmed.v14i3.61] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Ever since the public sector rollout of antiretroviral therapy (ART) in 2004, the question of the optimal time to start ART following diagnosis of an opportunistic infection has aroused controversy among South African HIV clinicians and researchers.
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Abstract
Introduction The attainment of remission has become an important end point for clinical trials in juvenile idiopathic arthritis (JIA), although we do not yet have a full understanding of what remission is at the cell and molecular level. Methods Two independent cohorts of patients with JIA and healthy child controls were studied. RNA was prepared separately from peripheral blood mononuclear cells (PBMC) and granulocytes to identify differentially expressed genes using whole genome microarrays. Expression profiling results for selected genes were confirmed by quantitative, real-time polymerase chain reaction (RT-PCR). Results We found that remission in JIA induced by either methotrexate (MTX) or MTX plus a TNF inhibitor (etanercept, Et) (MTX + Et) is characterized by numerous differences in gene expression in peripheral blood mononuclear cells and in granulocytes compared with healthy control children; that is, remission is not a restoration of immunologic normalcy. Network analysis of the differentially expressed genes demonstrated that the steroid hormone receptor superfamily member hepatocyte nuclear factor 4 alpha (HNF4α) is a hub in several of the gene networks that distinguished children with arthritis from controls. Confocal microscopy revealed that HNF4a is present in both T lymphocytes and granulocytes, suggesting a previously unsuspected role for this transcription factor in regulating leukocyte function and therapeutic response in JIA. Conclusions These findings provide a framework from which to understand therapeutic response in JIA and, furthermore, may be used to develop strategies to increase the frequency with which remission is achieved in adult forms of rheumatoid arthritis.
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Fedele DA, Ryan JL, Ramsey RR, Grant DM, Bonner MS, Stermer SP, Mullins LL, Jarvis JN, Chaney JM. Utility of the Illness Intrusiveness Scale in parents of children diagnosed with juvenile rheumatic diseases. Rehabil Psychol 2012; 57:73-80. [PMID: 22369119 DOI: 10.1037/a0027003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To examine the factor structure and convergent validity of the Illness Intrusiveness Scale--Parent Version in mother and fathers of children and adolescents ages 7 to 18 (M = 13.56 years, SD = 2.67) diagnosed with a juvenile rheumatic disease. DESIGN Parents of 122 children and adolescents (82 girls, 40 boys) completed the Illness Intrusiveness Scale-Parent Version, and both parents and children and adolescents completed measures of functional disability, general distress, and illness uncertainty. An exploratory factor analysis was conducted on the Illness Intrusiveness Scale--Parent Version to identify the factor structure. The factors were then compared with parent- and child-report measures of functional disability, general distress, and uncertainty. Finally, analyses were conducted to determine whether the magnitude of the correlations was significantly different between factors for parents and children and adolescents. RESULTS The Illness Intrusiveness Scale--Parent Version was found to have a two-factor structure. The Relationships/Personal Development factor contained items related to self-fulfillment and interactions with others, and the Instrumental factor contained items related to health and work. These factors were found to have good internal consistency and were significantly correlated with measures of parent-reported functional disability and parent- and youth-reported distress and uncertainty. The magnitude of these correlations was also found to differ depending on informant and outcome measure. CONCLUSION The Illness Intrusiveness Scale--Parent Version appears to be a valid measure for use in parents of children with juvenile rheumatic disease.
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Affiliation(s)
| | - Jamie L Ryan
- Department of Psychology, Oklahoma State University
| | | | | | | | | | | | - James N Jarvis
- Department of Pediatrics, Oklahoma University Health Sciences Center
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Abstract
Studies in model organisms and humans have begun to reveal the complexity of the transcriptome. In addition to serving as passive templates from which genes are translated, RNA molecules are active, functional elements of the cell whose products can detect, interact with, and modify other transcripts. Gene expression profiling is the method most commonly used thus far to enrich our understanding of the molecular basis of rheumatoid arthritis in adults and juvenile idiopathic arthritis in children. The feasibility of this approach for patient classification (for example, active versus inactive disease, disease subsets) and improving prognosis (for example, response to therapy) has been demonstrated over the past 7 years. Mechanistic understanding of disease-related differences in gene expression must be interpreted in the context of interactions with transcriptional regulatory molecules and epigenetic alterations of the genome. Ongoing work regarding such functional complexities in the human genome will likely bring both insight and surprise to our understanding of rheumatoid arthritis.
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Affiliation(s)
- James N Jarvis
- Department of Pediatrics, Pediatric Rheumatology Research, Basic Science Education Building #235A, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma 73104, USA.
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Ryan JL, Ramsey RR, Fedele DA, Mullins LL, Chaney JM, Jarvis JN. A longitudinal examination of the parent–child distress relationship in children with juvenile rheumatic disease. Rehabil Psychol 2010; 55:286-91. [DOI: 10.1037/a0020182] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jiang K, Krous LC, Knowlton N, Chen Y, Frank MB, Cadwell C, Centola M, Jarvis JN. Ablation of Stat3 by siRNA alters gene expression profiles in JEG-3 cells: a systems biology approach. Placenta 2009; 30:806-15. [PMID: 19616846 DOI: 10.1016/j.placenta.2009.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/19/2009] [Accepted: 06/23/2009] [Indexed: 01/27/2023]
Abstract
Control of inflammation at the maternal-fetal interface is a critical element in mammalian pregnancy. Previous work from our laboratory has shown that Stat3 may be a placental mediator involved in maintaining immunologic homeostasis at the maternal-fetal interface. The aim of the current study is to further elucidate the role of Stat3 in response to inflammation. As ablation of Stat3 in mice results in embryonic lethality, we evaluated the role of Stat3 in vitro using an siRNA approach. Trophoblast-like JEG-3 cells were transfected with an siRNA construct specific to Stat3. Experimental and control cells were exposed to conditioned medium from PHA-activated peripheral blood mononuclear cells and incubated for 45 min. Cells were then collected and RNA isolated for transcriptional profiling using human Affymetrix U133 plus 2.0 GeneChips. Differences in gene expression between control and Stat3-ablated cells were evaluated using conventional statistical methods. Fifty-two genes were detected as up-regulated in conditioned medium in both mock transfected and in Stat3 siRNA transfected JEG-3 cells. Two genes (EPAS1 and RASGEF1B) were up-regulated only in cells transfected with negative control siRNA, while 36 genes were up-regulated only in cells transfected with Stat3 siRNA. Sixty genes were differentially expressed between Stat3 siRNA transfected cells relative to mock transfected cells both in basal and conditioned medium. These included 31 genes up-regulated with Stat3 siRNA transfected cells and 29 genes down-regulated with Stat3 siRNA. Eleven genes were differentially expressed only in basal medium. Seven of these were up-regulated in the presence of Stat3 siRNA and four were down-regulated. Nine genes were differentially expressed only in conditioned medium. Six of these were up-regulated and three down-regulated in the presence of Stat3 siRNA. Off-target effects were excluded in a second set of experiments in which Stat3 mRNA was targeted at a different site and quantitative real-time PCR performed on selected genes derived from the microarray analysis. While some of the genes that showed differential expression between Stat3-ablated cells and mock transfected controls were genes typically associated with immune response (e.g., CCR7 and IRAK1), in silico modeling of the microarray data also revealed complex networks of signaling molecules and molecules associated with cellular metabolism previously seen in transcription factor ablation in model organisms. We conclude thus: Stat3 controls a specific gene set in trophoblast-like JEG-3 cells. While some differentially expressed genes and in silico models of their functions are consistent with the hypothesis that Stat3 plays a role in regulating inflammation, Stat3-mediated response to inflammation appears to also involve complex homeostatic adaptations of a non-immunologic nature.
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Affiliation(s)
- K Jiang
- Department of Pediatrics, Pediatric Rheumatology Research, University of Oklahoma College of Medicine, Oklahoma City, OK 73104, USA.
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Jarvis JN, Jiang K, Frank MB, Knowlton N, Aggarwal A, Wallace CA, McKee R, Chaser B, Tung C, Smith LB, McGhee JL, Chen Y, Osban J, O'Neil KM, Centola M. Gene expression profiling in neutrophils from children with polyarticular juvenile idiopathic arthritis. ACTA ACUST UNITED AC 2009; 60:1488-95. [PMID: 19404961 DOI: 10.1002/art.24450] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE We have previously reported a defect in neutrophil activation in children with polyarticular juvenile idiopathic arthritis (JIA). The current study was undertaken to determine whether gene expression abnormalities persist in JIA in remission and to use systems biology analysis to elucidate pathologic pathways in polyarticular JIA. METHODS We performed gene expression profiling on neutrophils from children with polyarticular JIA. Children were grouped according to disease status. We studied 14 children with active disease who were taking medication, 8 children with clinical remission of disease who were taking medication (CRM status), and 6 children with clinical remission of disease who were not taking medication (CR status). We also studied 13 healthy children whose age ranges overlapped those of the patients. RESULTS Neutrophil abnormalities persisted in children with polyarticular JIA even after disease remission was achieved. Children with active disease and those with CRM status showed no differences in expression of specific genes, although they could be separated on cluster analysis. A comparison of children with CR status and healthy control children revealed networks of pro- and antiinflammatory genes that suggested that remission is a state of homeostasis and balance rather than a return to normal immune function. Furthermore, gene overexpression in patients with CR status supports the hypothesis that neutrophils play a role in regulating adaptive immunity in this disease. CONCLUSION Neutrophil gene profiling in polyarticular JIA suggests important roles for neutrophils in disease pathogenesis. These findings suggest the presence of complex interactions between innate and adaptive immunity, that are not easily modeled in conventional, linear, reductionist systems.
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Affiliation(s)
- James N Jarvis
- Pediatric Rheumatology Research, College of Medicine, Children's Hospital of Oklahoma, University of Oklahoma, Oklahoma City, OK 73013, USA.
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