101
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Fu J, Wang Z, Lee K, Wei C, Liu Z, Zhang M, Zhou M, Cai M, Zhang W, Chuang PY, Ma'ayan A, He JC, Liu Z. Transcriptomic analysis uncovers novel synergistic mechanisms in combination therapy for lupus nephritis. Kidney Int 2018; 93:416-429. [PMID: 29102373 DOI: 10.1016/j.kint.2017.08.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/08/2017] [Accepted: 08/17/2017] [Indexed: 02/03/2023]
Abstract
A recent clinical study showed that combination therapy consisting of mycophenolate mofetil, tacrolimus and steroids was shown to be more effective in achieving complete remission in patients with severe forms of lupus nephritis than conventional therapy consisting of intravenous cyclophosphamide and steroids. To explore the underlying molecular and cellular mechanisms of increased efficacy of the combination therapy regimen, we employed a mouse model of lupus nephritis, MRL/lpr mice, and treated them with monotherapies of prednisone, mycophenolate mofetil, or tacrolimus, or with their combination. Consistent with previous clinical findings, combination therapy markedly improved renal outcome compared to the monotherapies in mice with lupus nephritis. Transcriptomic analysis of their kidneys revealed distinct molecular pathways that were differentially regulated in combination therapy versus monotherapies. Combination therapy not only provided additive immunosuppressive effects, but also induced gene expression and molecular pathways to confer enhanced renoprotection. Specifically, combination therapy inhibited TLR7 expression in the kidneys of mice with lupus nephritis; combination of tacrolimus and mycophenolate mofetil led to better stabilization of the podocyte actin cytoskeleton through the reciprocal regulation of RhoA and Rac1 activities. Combination therapy strongly suppressed the IL-6/Stat3 pathway. These findings were further validated in renal biopsy samples from patients with lupus nephritis before and after treatments with mycophenolate mofetil, tacrolimus or combination therapy. Thus, our study further supports the earlier clinical finding and further provides insights into the molecular basis for increased efficacy of combination therapy.
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Affiliation(s)
- Jia Fu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zichen Wang
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kyung Lee
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chengguo Wei
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zhengzhao Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Mingchao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Minlin Zhou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Minchao Cai
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Department of Nephrology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Weijia Zhang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Peter Y Chuang
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John Cijiang He
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA; Renal Program, James J Peters VA Medical Center, Bronx, New York, USA.
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.
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102
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Xu X, Eales JM, Akbarov A, Guo H, Becker L, Talavera D, Ashraf F, Nawaz J, Pramanik S, Bowes J, Jiang X, Dormer J, Denniff M, Antczak A, Szulinska M, Wise I, Prestes PR, Glyda M, Bogdanski P, Zukowska-Szczechowska E, Berzuini C, Woolf AS, Samani NJ, Charchar FJ, Tomaszewski M. Molecular insights into genome-wide association studies of chronic kidney disease-defining traits. Nat Commun 2018; 9:4800. [PMID: 30467309 PMCID: PMC6250666 DOI: 10.1038/s41467-018-07260-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/17/2018] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified >100 loci of chronic kidney disease-defining traits (CKD-dt). Molecular mechanisms underlying these associations remain elusive. Using 280 kidney transcriptomes and 9958 gene expression profiles from 44 non-renal tissues we uncover gene expression partners (eGenes) for 88.9% of CKD-dt GWAS loci. Through epigenomic chromatin segmentation analysis and variant effect prediction we annotate functional consequences to 74% of these loci. Our colocalisation analysis and Mendelian randomisation in >130,000 subjects demonstrate causal effects of three eGenes (NAT8B, CASP9 and MUC1) on estimated glomerular filtration rate. We identify a common alternative splice variant in MUC1 (a gene responsible for rare Mendelian form of kidney disease) and observe increased renal expression of a specific MUC1 mRNA isoform as a plausible molecular mechanism of the GWAS association signal. These data highlight the variants and genes underpinning the associations uncovered in GWAS of CKD-dt.
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Affiliation(s)
- Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - James M Eales
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Artur Akbarov
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Hui Guo
- Division of Population Health, Health Services Research and Primary Care, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Lorenz Becker
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - David Talavera
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Fehzan Ashraf
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Jabran Nawaz
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Sanjeev Pramanik
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - John Bowes
- Division of Musculoskeletal and Dermatological Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Xiao Jiang
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK
| | - John Dormer
- University Hospitals of Leicester NHS Trust, Leicester, LE1 5WW, UK
| | - Matthew Denniff
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK
| | - Andrzej Antczak
- Department of Urology and Uro-oncology, Karol Marcinkowski University of Medical Sciences, Poznan, 61-285, Poland
| | - Monika Szulinska
- Department of Internal Medicine, Metabolic Disorders and Hypertension, Karol Marcinkowski University of Medical Sciences, Poznan, 60-569, Poland
| | - Ingrid Wise
- School of Health and Life Sciences, Federation University Australia, Ballarat, 3350, VIC, Australia
| | - Priscilla R Prestes
- School of Health and Life Sciences, Federation University Australia, Ballarat, 3350, VIC, Australia
| | - Maciej Glyda
- Department of Transplantology and General Surgery, District Public Hospital, University of Zielona Góra, Poznan, 65-417, Poland
| | - Pawel Bogdanski
- Department of Obesity and Metabolic Disorders Treatment and Clinical Dietetics, Karol Marcinkowski University of Medical Sciences, Poznan, 60-569, Poland
| | | | - Carlo Berzuini
- Division of Population Health, Health Services Research and Primary Care, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Adrian S Woolf
- Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK.,NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Fadi J Charchar
- Department of Cardiovascular Sciences, University of Leicester, Leicester, LE3 9QP, UK.,School of Health and Life Sciences, Federation University Australia, Ballarat, 3350, VIC, Australia.,Department of Physiology, University of Melbourne, Melbourne, 3010, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Medicine, Biology and Health, University of Manchester, Manchester, M13 9PT, UK. .,Division of Medicine, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK.
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103
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A CRISP(e)R view on kidney organoids allows generation of an induced pluripotent stem cell-derived kidney model for drug discovery. Kidney Int 2018; 94:1099-1110. [PMID: 30072040 DOI: 10.1016/j.kint.2018.05.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 04/04/2018] [Accepted: 05/03/2018] [Indexed: 11/21/2022]
Abstract
Development of physiologically relevant cellular models with strong translatability to human pathophysiology is critical for identification and validation of novel therapeutic targets. Herein we describe a detailed protocol for generation of an advanced 3-dimensional kidney cellular model using induced pluripotent stem cells, where differentiation and maturation of kidney progenitors and podocytes can be monitored in live cells due to CRISPR/Cas9-mediated fluorescent tagging of kidney lineage markers (SIX2 and NPHS1). Utilizing these cell lines, we have refined the previously published procedures to generate a new, higher throughput protocol suitable for drug discovery. Using paraffin-embedded sectioning and whole-mount immunostaining, we demonstrated that organoids grown in suspension culture express key markers of kidney biology (WT1, ECAD, LTL, nephrin) and vasculature (CD31) within renal cortical structures with microvilli, tight junctions and podocyte foot processes visualized by electron microscopy. Additionally, the organoids resemble the adult kidney transcriptomics profile, thereby strengthening the translatability of our in vitro model. Thus, development of human nephron-like structures in vitro fills a major gap in our ability to assess the effect of potential treatment on key kidney structures, opening up a wide range of possibilities to improve clinical translation.
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104
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Zhou LT, Qiu S, Lv LL, Li ZL, Liu H, Tang RN, Ma KL, Liu BC. Integrative Bioinformatics Analysis Provides Insight into the Molecular Mechanisms of Chronic Kidney Disease. Kidney Blood Press Res 2018; 43:568-581. [PMID: 29642064 DOI: 10.1159/000488830] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/28/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Chronic kidney disease (CKD) is a worldwide public health problem. Regardless of the underlying primary disease, CKD tends to progress to end-stage kidney disease, resulting in unsatisfactory and costly treatment. Its common pathogenesis, however, remains unclear. The aim of this study was to provide an unbiased catalog of common gene-expression changes of CKD and reveal the underlying molecular mechanism using an integrative bioinformatics approach. METHODS We systematically collected over 250 Affymetrix microarray datasets from the glomerular and tubulointerstitial compartments of healthy renal tissues and those with various types of established CKD (diabetic kidney disease, hypertensive nephropathy, and glomerular nephropathy). Then, using stringent bioinformatics analysis, shared differentially expressed genes (DEGs) of CKD were obtained. These shared DEGs were further analyzed by the gene ontology (GO) and pathway enrichment analysis. Finally, the protein-protein interaction networks(PINs) were constructed to further refine our results. RESULTS Our analysis identified 176 and 50 shared DEGs in diseased glomeruli and tubules, respectively, including many transcripts that have not been previously reported to be involved in kidney disease. Enrichment analysis also showed that the glomerular and tubulointerstitial compartments underwent a wide range of unique pathological changes during chronic injury. As revealed by the GO enrichment analysis, shared DEGs in glomeruli were significantly enriched in exosomes. By constructing PINs, we identified several hub genes (e.g. OAS1, JUN, and FOS) and clusters that might play key roles in regulating the development of CKD. CONCLUSION Our study not only further reveals the unifying molecular mechanism of CKD pathogenesis but also provides a valuable resource of potential biomarkers and therapeutic targets.
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105
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Qing X, Chinenov Y, Redecha P, Madaio M, Roelofs JJ, Farber G, Issuree PD, Donlin L, Mcllwain DR, Mak TW, Blobel CP, Salmon JE. iRhom2 promotes lupus nephritis through TNF-α and EGFR signaling. J Clin Invest 2018; 128:1397-1412. [PMID: 29369823 DOI: 10.1172/jci97650] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 01/23/2018] [Indexed: 12/14/2022] Open
Abstract
Lupus nephritis (LN) often results in progressive renal dysfunction. The inactive rhomboid 2 (iRhom2) is a newly identified key regulator of A disintegrin and metalloprotease 17 (ADAM17), whose substrates, such as TNF-α and heparin-binding EGF (HB-EGF), have been implicated in the pathogenesis of chronic kidney diseases. Here, we demonstrate that deficiency of iRhom2 protects the lupus-prone Fcgr2b-/- mice from developing severe kidney damage without altering anti-double-stranded DNA (anti-dsDNA) Ab production by simultaneously blocking HB-EGF/EGFR and TNF-α signaling in the kidney tissues. Unbiased transcriptome profiling of kidneys and kidney macrophages revealed that TNF-α and HB-EGF/EGFR signaling pathways are highly upregulated in Fcgr2b-/- mice, alterations that were diminished in the absence of iRhom2. Pharmacological blockade of either TNF-α or EGFR signaling protected Fcgr2b-/- mice from severe renal damage. Finally, kidneys from LN patients showed increased iRhom2 and HB-EGF expression, with interstitial HB-EGF expression significantly associated with chronicity indices. Our data suggest that activation of iRhom2/ADAM17-dependent TNF-α and EGFR signaling plays a crucial role in mediating irreversible kidney damage in LN, thereby uncovering a target for selective and simultaneous dual inhibition of 2 major pathological pathways in the effector arm of the disease.
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Affiliation(s)
| | - Yurii Chinenov
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA
| | | | - Michael Madaio
- Department of Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Joris Jth Roelofs
- Department of Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Gregory Farber
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York, USA
| | - Priya D Issuree
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA
| | - Laura Donlin
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA
| | - David R Mcllwain
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Tak W Mak
- Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Carl P Blobel
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, New York, USA.,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York, USA.,Institute for Advanced Study, Technical University Munich, Munich, Germany.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Jane E Salmon
- Program in Inflammation and Autoimmunity, and.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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106
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Shu B, Fang Y, He W, Yang J, Dai C. Identification of macrophage-related candidate genes in lupus nephritis using bioinformatics analysis. Cell Signal 2018; 46:43-51. [PMID: 29458096 DOI: 10.1016/j.cellsig.2018.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 01/02/2023]
Abstract
Lupus nephritis (LN) is a chronic autoimmune disorder. Here we try to identify the candidate genes in macrophages related to LN. We performed a systematic search in the Gene Expression Omnibus (GEO) database for microarray in human mononuclear cells and mouse macrophages of LN. The results of clustering and venn analysis of different GEO datasets showed that 8 genes were up-regulated and 2 genes down-regulated in samples from both human and mouse LN. The data from gene network and GO analysis revealed that CD38 and CCL2 were localized in the core of the network. Immunofluorescence staining showed that CD38 expression was markedly increased in macrophages from kidneys with LN. Our study identifies the gene expression profile for macrophages and demonstrated the induction of CCL2 and CD38 in macrophages from patients with LN. However, regarding the limited patient number included in this study, the results are preliminary and more studies are still needed to further decipher the macrophage-related candidate genes for the pathogenesis of LN.
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Affiliation(s)
- Bingyan Shu
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Yi Fang
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Weichun He
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Junwei Yang
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Chunsun Dai
- Center for Kidney Disease, 2nd Affiliated Hospital of Nanjing Medical University, 262 North Zhongshan Road, Nanjing, Jiangsu, China.
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107
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Abstract
High-throughput sequencing assays have become an increasingly common part of biological research across multiple fields. Even as the resulting sequences pile up in public databases, it is not always obvious how to make use of these data sets. Functional genomics offers approaches to integrate these "big" data into our understanding of rheumatic diseases. This review aims to provide a primer on thinking about big data from functional genomics in the context of rheumatology, using examples from the field's literature as well as the author's own work to illustrate the execution of functional genomics research. Study design is crucial to ensure the right samples are used to address the question of interest. In addition, sequencing assays produce a variety of data types, from gene expression to 3D chromatin structure and single-cell technologies, that can be integrated into a model of the underlying gene regulatory networks. The best approach for this analysis uses the scientific process: bioinformatic methods should be used in an iterative, hypothesis-driven manner to uncover the disease mechanism. Finally, the future of functional genomics will see big data fully integrated into rheumatology, leading to computationally trained researchers and interactive databases. The goal of this review is not to provide a manual, but to enhance the familiarity of readers with functional genomic approaches and provide a better sense of the challenges and possibilities.
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Affiliation(s)
- Deborah R Winter
- Department of Medicine, Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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108
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Liu T, Liu M, Shang P, Jin X, Liu W, Zhang Y, Li X, Ding Y, Li Y, Wen A. Investigation into the underlying molecular mechanisms of hypertensive nephrosclerosis using bioinformatics analyses. Mol Med Rep 2018; 17:4440-4448. [PMID: 29328390 PMCID: PMC5802219 DOI: 10.3892/mmr.2018.8405] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 11/24/2017] [Indexed: 12/11/2022] Open
Abstract
Hypertensive nephrosclerosis (HNS) is a major risk factor for end-stage renal disease. However, the underlying pathogenesis of HNS remains to be fully determined. The gene expression profile of GSE20602, which consists of 14 glomeruli samples from patients with HNS and 4 normal glomeruli control samples, was obtained from the Gene Expression Omnibus database. Gene ontology (GO) and pathway enrichment analyses were performed in order to investigate the functions and pathways of differentially expressed genes (DEGs). Pathway relation and co‑expression networks were constructed in order to identify key genes and signaling pathways involved in HNS. In total, 483 DEGs were identified to be associated with HNS, including 302 upregulated genes and 181 downregulated genes. Furthermore, GO analysis revealed that DEGs were significantly enriched in the small molecule metabolic process. In addition, pathway analysis also revealed that DEGs were predominantly involved in metabolic pathways. The tricarboxylic acid (TCA) cycle was identified as the hub pathway in the pathway relation network, whereas the sorbitol dehydrogenase (SORD) and cubulin (CUBN) genes were revealed to be the hub genes in the co‑expression network. The present study revealed that the SORD, CUBN and albumin genes as well as the TCA cycle and metabolic pathways are involved in the pathogenesis of HNS. The results of the present study may contribute to the determination of the molecular mechanisms underlying HNS, and provide insight into the exploration of novel targets for the diagnosis and treatment of HNS.
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Affiliation(s)
- Tianlong Liu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Minna Liu
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Peijin Shang
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Xin Jin
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Wenxing Liu
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yikai Zhang
- Department of Pharmacy, General Hospital of Shenyang Military Region, Shenyang, Liaoning 110016, P.R. China
| | - Xinfang Li
- Department of Inorganic Chemistry, School of Pharmacy, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yi Ding
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yuwen Li
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Aidong Wen
- Department of Pharmacy, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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109
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Kim Y, Shim SC. Wolves Trapped in the NETs–The Pathogenesis of Lupus Nephritis. JOURNAL OF RHEUMATIC DISEASES 2018. [DOI: 10.4078/jrd.2018.25.2.81] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Young Kim
- Division of Internal Medicine, Daejeon Veterans Hospital, Daejeon, Korea
| | - Seung Cheol Shim
- Division of Rheumatology, Department of Internal Medicine, Daejeon Rheumatoid and Degenerative Arthritis Center, Chungnam National University Hospital, Chungnam National University College of Medicine, Daejeon, Korea
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110
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Abstract
PURPOSE OF REVIEW The purpose of the study was to review the characteristics of renal macrophages and dendritic cells during homeostasis and disease, with a particular focus on lupus nephritis. RECENT FINDINGS Resident renal macrophages derive from embryonic sources and are long-lived and self-renewing; they are also replaced from the bone marrow with age. The unique characteristics of macrophages in each tissue are imposed by the microenvironment and reinforced by epigenetic modifications. In acute renal injury, inflammatory macrophages are rapidly recruited and then replaced by those with a wound healing/resolution phenotype. In lupus nephritis, dendritic cells infiltrate the kidneys and function to present antigen and organize tertiary lymphoid structures that amplify inflammation. In addition, both infiltrating and resident macrophages contribute to ongoing injury. These cells have a mixed inflammatory and alternatively activated phenotype that may reflect failed resolution, potentially leading to tissue fibrosis and irreversible damage. A further understanding of the renal inflammatory cells that mediate tissue injury and fibrosis should lead to new therapies to help preserve renal function in patients with lupus nephritis.
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Affiliation(s)
- Naomi I Maria
- Center for Autoimmunity and Musculoskeletal Diseases, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, NY, 11030, USA
| | - Anne Davidson
- Center for Autoimmunity and Musculoskeletal Diseases, Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, New York, NY, 11030, USA.
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111
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Tsai F, Homan PJ, Agrawal H, Misharin AV, Abdala-Valencia H, Haines GK, Dominguez S, Bloomfield CL, Saber R, Chang A, Mohan C, Hutcheson J, Davidson A, Budinger GRS, Bouillet P, Dorfleutner A, Stehlik C, Winter DR, Cuda CM, Perlman H. Bim suppresses the development of SLE by limiting myeloid inflammatory responses. J Exp Med 2017; 214:3753-3773. [PMID: 29114065 PMCID: PMC5716039 DOI: 10.1084/jem.20170479] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/25/2017] [Accepted: 09/06/2017] [Indexed: 12/27/2022] Open
Abstract
Tsai et al. demonstrate that loss of Bim (BCL2L11) in myeloid cells in mice (LysMCreBimfl/fl) is sufficient to induce systemic autoimmunity. Kidney macrophages in LysMCreBimfl/fl mice possess a proinflammatory transcriptional signature and signal through TRIF to cause end-stage glomerulonephritis. The Bcl-2 family is considered the guardian of the mitochondrial apoptotic pathway. We demonstrate that Bim acts as a molecular rheostat by controlling macrophage function not only in lymphoid organs but also in end organs, thereby preventing the break in tolerance. Mice lacking Bim in myeloid cells (LysMCreBimfl/fl) develop a systemic lupus erythematosus (SLE)–like disease that mirrors aged Bim−/− mice, including loss of marginal zone macrophages, splenomegaly, lymphadenopathy, autoantibodies (including anti-DNA IgG), and a type I interferon signature. LysMCreBimfl/fl mice exhibit increased mortality attributed to glomerulonephritis (GN). Moreover, the toll-like receptor signaling adaptor protein TRIF (TIR-domain–containing adapter-inducing interferon-β) is essential for GN, but not systemic autoimmunity in LysMCreBimfl/fl mice. Bim-deleted kidney macrophages exhibit a novel transcriptional lupus signature that is conserved within the gene expression profiles from whole kidney biopsies of patients with SLE. Collectively, these data suggest that the Bim may be a novel therapeutic target in the treatment of SLE.
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Affiliation(s)
- FuNien Tsai
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Philip J Homan
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Alexander V Misharin
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Hiam Abdala-Valencia
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - G Kenneth Haines
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Salina Dominguez
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Christina L Bloomfield
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Rana Saber
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Anthony Chang
- Department of Pathology, University of Chicago, Chicago, IL
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston, Houston, TX
| | | | - Anne Davidson
- The Feinstein Institute for Medical Research, Hofstra Northwell School of Medicine, Manhasset, NY
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Philippe Bouillet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Andrea Dorfleutner
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Christian Stehlik
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Deborah R Winter
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Carla M Cuda
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Harris Perlman
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL
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112
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Tangtanatakul P, Thammasate B, Jacquet A, Reantragoon R, Pisitkun T, Avihingsanon Y, Leelahavanichkul A, Hirankarn N. Transcriptomic profiling in human mesangial cells using patient-derived lupus autoantibodies identified miR-10a as a potential regulator of IL8. Sci Rep 2017; 7:14517. [PMID: 29109423 PMCID: PMC5673966 DOI: 10.1038/s41598-017-15160-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/23/2017] [Indexed: 11/09/2022] Open
Abstract
Autoantibody-mediated inflammation directed at resident kidney cells mediates lupus nephritis (LN) pathogenesis. This study investigated the role of miRNA in human mesangial cells (HMCs) stimulated with auto anti-dsDNA immunoglobulin (Ig)G antibodies. HMCs were treated with antibodies purified from active LN patients or non-specific IgG controls in the presence of normal serum. Aberrant miRNA was screened using high throughput sequencing. Anti-dsDNA IgG up-regulated 103 miRNAs and down-regulated 30 miRNAs. The miRNAs regulated genes in the cell cycle, catabolic processes, regulation of transcription and apoptosis signalling. miR-10a was highly abundant in HMCs but was specifically downregulated upon anti-dsDNA IgG induction. Interestingly, the expression of miR-10a in kidney biopsies from class III and IV LN patients (n = 26) was downregulated compared with cadaveric donor kidneys (n = 6). Functional studies highlighted the downstream regulator of miR-10a in the chemokine signalling and cell proliferation or apoptosis pathways. Luciferase assay confirmed for the first time that IL8 was a direct target of miR-10a in HMCs. In conclusion, anti-dsDNA IgG Ab down-regulated miR-10a expression in HMCs resulting in the induction of various target genes involved in HMC proliferation and chemokine expression.
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Affiliation(s)
- Pattarin Tangtanatakul
- Medical Microbiology Interdisciplinary Program, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.,Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Boonyakiat Thammasate
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Alain Jacquet
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rangsima Reantragoon
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Chulalongkorn University Systems Biology (CUSB), Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Yingyos Avihingsanon
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.,Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Asada Leelahavanichkul
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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Abstract
Acute kidney injury (AKI) is a growing global health concern, yet no treatment is currently available to prevent it or to promote kidney repair after injury. Animal models demonstrate that the macrophage is a major contributor to the inflammatory response to AKI. Emerging data from human biopsies also corroborate the presence of macrophages in AKI and their persistence in progressive chronic kidney disease. Macrophages are phagocytic innate immune cells that are important mediators of tissue homeostasis and host defense. In response to tissue injury, macrophages become activated based on specific signals from the damaged microenvironment. The activation and functional state of the macrophage depends on the stage of tissue injury and repair, reflecting a dynamic and diverse spectrum of macrophage phenotypes. In this review, we highlight our current understanding of the mechanisms by which macrophages contribute to injury and repair after AKI.
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Affiliation(s)
- Sarah C Huen
- Section of Nephrology, Department of Internal Medicine, Yale University, New Haven, Connecticut 06520;
| | - Lloyd G Cantley
- Section of Nephrology, Department of Internal Medicine, Yale University, New Haven, Connecticut 06520;
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114
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Gosset C, Viglietti D, Rabant M, Vérine J, Aubert O, Glotz D, Legendre C, Taupin JL, Duong Van-Huyen JP, Loupy A, Lefaucheur C. Circulating donor-specific anti-HLA antibodies are a major factor in premature and accelerated allograft fibrosis. Kidney Int 2017; 92:729-742. [DOI: 10.1016/j.kint.2017.03.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/21/2017] [Accepted: 03/16/2017] [Indexed: 11/24/2022]
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115
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Schena FP, Nistor I, Curci C. Transcriptomics in kidney biopsy is an untapped resource for precision therapy in nephrology: a systematic review. Nephrol Dial Transplant 2017; 33:1094-1102. [DOI: 10.1093/ndt/gfx211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/03/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Ionut Nistor
- Nephrology Department, Grigore T. Popa University of Medicine and Pharmacy, Iasi, Romania
- Methods Support Team ERBP, Ghent University, Ghent, Belgium
| | - Claudia Curci
- University of Bari, Bari, Italy
- Schena Foundation, Valenzano, Italy
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116
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Poveda J, Sanz AB, Carrasco S, Ruiz-Ortega M, Cannata-Ortiz P, Sanchez-Niño MD, Ortiz A. Bcl3: a regulator of NF-κB inducible by TWEAK in acute kidney injury with anti-inflammatory and antiapoptotic properties in tubular cells. Exp Mol Med 2017; 49:e352. [PMID: 28684863 PMCID: PMC5565957 DOI: 10.1038/emm.2017.89] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/21/2016] [Accepted: 01/12/2017] [Indexed: 01/09/2023] Open
Abstract
Acute kidney injury (AKI) is characterized by tubular cell death and interstitial inflammation. TWEAK promotes experimental kidney injury and activates the transcription factor NF-κB, a key regulator of genes involved in cell survival and inflammatory response. In search of potential therapeutic targets for AKI, we compared a transcriptomics database of NF-κB-related genes from murine AKI-kidneys with a transcriptomics database of TWEAK-stimulated cultured tubular cells. Four out of twenty-four (17%) genes were significantly upregulated (false discovery rate, FDR<0.05), while nine out of twenty-four (37%) genes were significantly upregulated at FDR <0.1 in both databases. Bcl3 was the top upregulated NF-κB-related gene in experimental AKI and one of the most upregulated genes in TWEAK-stimulated tubular cells. Quantitative reverse transcription PCR (qRT-PCR), western blot and immunohistochemistry confirmed Bcl3 upregulation in both experimental conditions and localized increased Bcl3 expression to tubular cells in AKI. Transcriptomics database analysis revealed increased Bcl3 expression in numerous experimental and human kidney conditions. Furthermore, systemic TWEAK administration increased kidney Bcl3 expression. In cultured tubular cells, targeting Bcl3 by siRNA resulted in the magnification of TWEAK-induced NF-κB transcriptional activity, chemokine upregulation and Klotho downregulation, and in the sensitization to cell death induced by TWEAK/TNFα/interferon-γ. In contrast, Bcl3 overexpression decreased NF-κB transcriptional activity, inflammatory response and cell death while dampening the decrease in Klotho expression. In conclusion, Bcl3 expressed in response to TWEAK stimulation decreases TWEAK-induced inflammatory and lethal responses. Therefore, therapeutic upregulation of Bcl3 activity should be explored in kidney disease because it has advantages over chemical inhibitors of NF-κB that are known to prevent inflammatory responses but can also sensitize the cells to apoptosis.
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Affiliation(s)
- Jonay Poveda
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Ana B Sanz
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Susana Carrasco
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Marta Ruiz-Ortega
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Pablo Cannata-Ortiz
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Maria D Sanchez-Niño
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
| | - Alberto Ortiz
- Unidad de Dialisis, IIS-Fundación Jiménez Díaz, School of Medicine, Universidad Autónoma de Madrid, Fundación Renal Iñigo Álvarez de Toledo-IRSIN and REDINREN, Madrid, Spain
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Jourde-Chiche N, Whalen E, Gondouin B, Speake C, Gersuk V, Dussol B, Burtey S, Pascual V, Chaussabel D, Chiche L. Modular transcriptional repertoire analyses identify a blood neutrophil signature as a candidate biomarker for lupus nephritis. Rheumatology (Oxford) 2017; 56:477-487. [PMID: 28031441 DOI: 10.1093/rheumatology/kew439] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Indexed: 01/09/2023] Open
Abstract
Objective LN is a severe complication of SLE. Non-invasive biomarkers are needed for identifying patients at risk of a renal flare, for differentiating proliferative from non-proliferative forms and for assessing prognoses for LN. Methods We assessed the link between blood transcriptional signatures and LN using blood samples from patients with biopsy-proven LN, extra-renal SLE flares or quiescent SLE. Healthy controls, and control patients with glomerular diseases or bacterial sepsis were included. Modular repertoire analyses from microarray data were confirmed by PCR. Results A modular neutrophil signature (upregulation of module M5.15) was present in 65% of SLE patients and was strongly associated with LN. M5.15 activity was stronger in LN than in extra-renal flares (88 vs 17%). M5.15 was neither correlated to IFN modules, nor to SLEDAI or anti-dsDNA antibodies, but moderately to CS dose. M5.15 activity was associated with severity of LN, was stronger when proliferative, and decreased in patients responding to treatment. M5.15 activation was not caused by higher CS dose because it correlated only moderately to neutrophil count and was also observed among quiescent patients. Among quiescent patients, those with a past history of LN had higher M5.15 activity (50 vs 8%). M5.15 activation was present in patients with bacterial sepsis or ANCA-associated vasculitis, but not in patients with other glomerular diseases. Overall, M5.15 activation was associated with past, present or future flares of LN. Conclusion Modular neutrophil signature could be a biomarker for stratifying LN risk and for monitoring its response to treatment. Trial registration ClinicalTrials.gov, http://clinicaltrials.gov , NCT00920114.
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Affiliation(s)
- Noémie Jourde-Chiche
- Department of Nephrology, Aix-Marseille University, AP-HM, Hôpital Conception, UMR_S 1076, Vascular Research Center of Marseille, Marseille, France
| | - Elizabeth Whalen
- Systems Immunology Department, Benaroya Research Institute, Seattle
| | - Bertrand Gondouin
- Department of Nephrology, Aix-Marseille University, AP-HM, Hôpital Conception, UMR_S 1076, Vascular Research Center of Marseille, Marseille, France
| | - Cate Speake
- Systems Immunology Department, Benaroya Research Institute, Seattle
| | - Vivian Gersuk
- Systems Immunology Department, Benaroya Research Institute, Seattle
| | - Bertrand Dussol
- Department of Nephrology, Aix-Marseille University, AP-HM, Hôpital Conception, UMR_S 1076, Vascular Research Center of Marseille, Marseille, France
| | - Stephane Burtey
- Department of Nephrology, Aix-Marseille University, AP-HM, Hôpital Conception, UMR_S 1076, Vascular Research Center of Marseille, Marseille, France
| | - Virginia Pascual
- Immunology, Baylor Institute for Immunology Research, Dallas, TX, USA
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Laurent Chiche
- Department of Internal Medicine, Hôpital Européen, Marseille, France
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118
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Katewa A, Wang Y, Hackney JA, Huang T, Suto E, Ramamoorthi N, Austin CD, Bremer M, Chen JZ, Crawford JJ, Currie KS, Blomgren P, DeVoss J, DiPaolo JA, Hau J, Johnson A, Lesch J, DeForge LE, Lin Z, Liimatta M, Lubach JW, McVay S, Modrusan Z, Nguyen A, Poon C, Wang J, Liu L, Lee WP, Wong H, Young WB, Townsend MJ, Reif K. Btk-specific inhibition blocks pathogenic plasma cell signatures and myeloid cell-associated damage in IFN α-driven lupus nephritis. JCI Insight 2017; 2:e90111. [PMID: 28405610 DOI: 10.1172/jci.insight.90111] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is often associated with exaggerated B cell activation promoting plasma cell generation, immune-complex deposition in the kidney, renal infiltration of myeloid cells, and glomerular nephritis. Type-I IFNs amplify these autoimmune processes and promote severe disease. Bruton's tyrosine kinase (Btk) inhibitors are considered novel therapies for SLE. We describe the characterization of a highly selective reversible Btk inhibitor, G-744. G-744 is efficacious, and superior to blocking BAFF and Syk, in ameliorating severe lupus nephritis in both spontaneous and IFNα-accelerated lupus in NZB/W_F1 mice in therapeutic regimens. Selective Btk inhibition ablated plasmablast generation, reduced autoantibodies, and - similar to cyclophosphamide - improved renal pathology in IFNα-accelerated lupus. Employing global transcriptional profiling of spleen and kidney coupled with cross-species human modular repertoire analyses, we identify similarities in the inflammatory process between mice and humans, and we demonstrate that G-744 reduced gene expression signatures essential for splenic B cell terminal differentiation, particularly the secretory pathway, as well as renal transcriptional profiles coupled with myeloid cell-mediated pathology and glomerular plus tubulointerstitial disease in human glomerulonephritis patients. These findings reveal the mechanism through which a selective Btk inhibitor blocks murine autoimmune kidney disease, highlighting pathway activity that may translate to human SLE.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - James J Crawford
- Discovery Chemistry, at Genentech, South San Francisco, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lichuan Liu
- Clinical Pharmacology at Genentech, South San Francisco, California, USA
| | | | | | - Wendy B Young
- Discovery Chemistry, at Genentech, South San Francisco, California, USA
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119
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Parikh SV, Malvar A, Song H, Alberton V, Lococo B, Vance J, Zhang J, Yu L, Birmingham D, Rovin BH. Molecular imaging of the kidney in lupus nephritis to characterize response to treatment. Transl Res 2017; 182:1-13. [PMID: 27842222 PMCID: PMC5362303 DOI: 10.1016/j.trsl.2016.10.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/20/2016] [Accepted: 10/22/2016] [Indexed: 10/20/2022]
Abstract
The consequences of treatment for the kidney at the molecular level have not been explored in human lupus nephritis (LN). In this investigation, changes in intrarenal transcript expression were measured and correlated with response in a LN cohort that underwent serial kidney biopsies. The intrarenal transcript expression of 19 patients with proliferative LN (Class III or IV) was measured at diagnostic biopsy (Bx1) and after induction therapy was completed (Bx2) using Nanostring technology. Patients were segregated by clinical response into complete responders (n = 5, CR) or nonresponders (n = 4, NR). Transcript expression for each biopsy was compared with normal controls (n = 4), and the change in expression was compared in each responder group and between groups. Compared with controls, the CR group had 21 and 28, whereas NR had 45 and 103 differentially-expressed transcripts at Bx1 and Bx2, respectively. The profiles of these differentially-expressed genes indicated that the type I and II interferon, alternative complement and T cell signaling pathways discriminated CR from NR. Comparing the change in transcript expression from Bx1 to Bx2 revealed a 5-gene signature that differentiated NR from CR and included increased IL1RAP and FCAR in NR and increased NCAM1 in CR. In summary, molecular imaging of serial kidney biopsies from LN patients shows several immune and inflammatory pathways that are dysregulated in the kidneys during active disease that may serve as therapeutic targets to improve clinical response. This approach to LN biomarker development may facilitate personalized medicine in LN and improve long-term kidney outcomes.
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Affiliation(s)
- Samir V Parikh
- Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Ana Malvar
- Nephrology Unit, Hospital Fernandez, Buenos Aires, Argentina
| | - Huijuan Song
- Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Valeria Alberton
- Department of Pathology, Hospital Fernandez, Buenos Aires, Argentina
| | - Bruno Lococo
- Nephrology Unit, Hospital Fernandez, Buenos Aires, Argentina
| | - Jay Vance
- Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Jianying Zhang
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Lianbo Yu
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Dan Birmingham
- Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Brad H Rovin
- Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio.
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Wei R, Gao B, Shih F, Ranger A, Dearth A, Mischak H, Siwy J, Wisniacki N, Petri M, Burkly LC. Alterations in urinary collagen peptides in lupus nephritis subjects correlate with renal dysfunction and renal histopathology. Nephrol Dial Transplant 2017; 32:1468-1477. [DOI: 10.1093/ndt/gfw446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/01/2016] [Indexed: 02/02/2023] Open
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122
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Tsai F, Perlman H, Cuda CM. The contribution of the programmed cell death machinery in innate immune cells to lupus nephritis. Clin Immunol 2016; 185:74-85. [PMID: 27780774 DOI: 10.1016/j.clim.2016.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/15/2016] [Accepted: 10/20/2016] [Indexed: 12/24/2022]
Abstract
Systemic lupus erythematosus (SLE) is a chronic multi-factorial autoimmune disease initiated by genetic and environmental factors, which in combination trigger disease onset in susceptible individuals. Damage to the kidney as a consequence of lupus nephritis (LN) is one of the most prevalent and severe outcomes, as LN affects up to 60% of SLE patients and accounts for much of SLE-associated morbidity and mortality. As remarkable strides have been made in unlocking new inflammatory mechanisms associated with signaling molecules of programmed cell death pathways, this review explores the available evidence implicating the action of these pathways specifically within dendritic cells and macrophages in the control of kidney disease. Although advancements into the underlying mechanisms responsible for inducing cell death inflammatory pathways have been made, there still exist areas of unmet need. By understanding the molecular mechanisms by which dendritic cells and macrophages contribute to LN pathogenesis, we can improve their viability as potential therapeutic targets to promote remission.
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Affiliation(s)
- FuNien Tsai
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Rheumatology, 240 East Huron Street, Room M300, Chicago, IL 60611, USA.
| | - Harris Perlman
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Rheumatology, 240 East Huron Street, Room M300, Chicago, IL 60611, USA.
| | - Carla M Cuda
- Northwestern University, Feinberg School of Medicine, Department of Medicine, Division of Rheumatology, 240 East Huron Street, Room M300, Chicago, IL 60611, USA.
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Gardet A, Chou WC, Reynolds TL, Velez DB, Fu K, Czerkowicz JM, Bajko J, Ranger AM, Allaire N, Kerns HM, Ryan S, Legault HM, Dunstan RW, Lafyatis R, Lukashev M, Viney JL, Browning JL, Rabah D. Pristane-Accelerated Autoimmune Disease in (SWR X NZB) F1 Mice Leads to Prominent Tubulointerstitial Inflammation and Human Lupus Nephritis-Like Fibrosis. PLoS One 2016; 11:e0164423. [PMID: 27760209 PMCID: PMC5070861 DOI: 10.1371/journal.pone.0164423] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/23/2016] [Indexed: 01/12/2023] Open
Abstract
Mouse models lupus nephritis (LN) have provided important insights into disease pathogenesis, although none have been able to recapitulate all features of the human disease. Using comprehensive longitudinal analyses, we characterized a novel accelerated mouse model of lupus using pristane treatment in SNF1 (SWR X NZB F1) lupus prone mice (pristane-SNF1 mice). Pristane treatment in SNF1 mice accelerated the onset and progression of proteinuria, autoantibody production, immune complex deposition and development of renal lesions. At week 14, the pristane-SNF1 model recapitulated kidney disease parameters and molecular signatures seen in spontaneous disease in 36 week-old SNF1 mice and in a traditional IFNα-accelerated NZB X NZW F1 (BWF1) model. Blood transcriptome analysis revealed interferon, plasma cell, neutrophil, T-cell and protein synthesis signatures in the pristane-SNF1 model, all known to be present in the human disease. The pristane-SNF1 model appears to be particularly useful for preclinical research, robustly exhibiting many characteristics reminiscent of human disease. These include i) a stronger upregulation of the cytosolic nucleic acid sensing pathway, which is thought to be key component of the pathogenesis of the human disease, and ii) more prominent kidney interstitial inflammation and fibrosis, which have been both associated with poor prognosis in human LN. To our knowledge, this is the only accelerated model of LN that exhibits a robust tubulointerstitial inflammatory and fibrosis response. Taken together our data show that the pristane-SNF1 model is a novel accelerated model of LN with key features similar to human disease.
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Affiliation(s)
- Agnes Gardet
- Biogen, Cambridge, Massachusetts, United States of America
- * E-mail: (DR); (AG)
| | - Wei C. Chou
- Biogen, Cambridge, Massachusetts, United States of America
| | | | - Diana B. Velez
- Biogen, Cambridge, Massachusetts, United States of America
| | - Kai Fu
- Biogen, Cambridge, Massachusetts, United States of America
| | | | - Jeffrey Bajko
- Biogen, Cambridge, Massachusetts, United States of America
| | - Ann M. Ranger
- Biogen, Cambridge, Massachusetts, United States of America
| | | | | | - Sarah Ryan
- Biogen, Cambridge, Massachusetts, United States of America
| | | | | | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, United States of America
| | | | | | - Jeffrey L. Browning
- Boston University School of Medicine, Department of Microbiology, Boston, United States of America
| | - Dania Rabah
- Biogen, Cambridge, Massachusetts, United States of America
- * E-mail: (DR); (AG)
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Chen Z, Wu H, Wang G, Feng Y. Identification of potential candidate genes for hypertensive nephropathy based on gene expression profile. BMC Nephrol 2016; 17:149. [PMID: 27756246 PMCID: PMC5069870 DOI: 10.1186/s12882-016-0366-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 10/11/2016] [Indexed: 01/18/2023] Open
Abstract
Background This study was aimed to explore the molecular mechanisms of hypertensive nephropathy (HTN). Methods Gene expression profile of GSE37460, which based on 27 healthy living donor samples (HTN group) and 15 hypertensive nephropathy samples (control group), were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between two groups were identified. STRING database was used to reveal protein-protein interaction (PPI) network of DEGs, followed by the functional enrichment analysis of the PPI network. Additionally, miRNA-DEG regulatory network was constructed to reveal the validated miRNAs targeting the DEGs. Results In total, 51 up-regulated genes and 140 down-regulated genes were obtained. In the PPI network, cytochrome P450 3A4 (CYP3A4) and angiotensin II receptor type 1 (AGTR1) had a higher degree, and CYP3A4 interacted with CYP4A11. The DEGs in the network were significantly enriched in drug metabolism, focal adhesion and arachidonic acid metabolism. Furthermore, in the miRNA-DEG regulatory network, hsa-miR-335-5p and hsa-miR-26b-5p were the two most outstanding miRNAs. AGTR1, CYP3A4 and CYP4A11 were predicted to be regulated by hsa-miR-26b-5p. Conclusion The DEGs, such as AGTR1, CYP3A4 and CYP4A11 may play critical roles in the development of HTN likely via the regulation by hsa-miR-26b-5p and taking part in some pathways.
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Affiliation(s)
- Zhi Chen
- Department of Nephrology, First Hospital of Jilin University, Jilin, 130021, China
| | - Hao Wu
- Department of Nephrology, First Hospital of Jilin University, Jilin, 130021, China
| | - Guohua Wang
- Department of Neonatology, First Hospital of Jilin University, Jilin, 130021, China
| | - Ye Feng
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, No.126 Xiantai Avenue, Jilin, 130033, China.
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125
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Ju W, Nair V, Smith S, Zhu L, Shedden K, Song PXK, Mariani LH, Eichinger FH, Berthier CC, Randolph A, Lai JYC, Zhou Y, Hawkins JJ, Bitzer M, Sampson MG, Thier M, Solier C, Duran-Pacheco GC, Duchateau-Nguyen G, Essioux L, Schott B, Formentini I, Magnone MC, Bobadilla M, Cohen CD, Bagnasco SM, Barisoni L, Lv J, Zhang H, Wang HY, Brosius FC, Gadegbeku CA, Kretzler M. Tissue transcriptome-driven identification of epidermal growth factor as a chronic kidney disease biomarker. Sci Transl Med 2016; 7:316ra193. [PMID: 26631632 DOI: 10.1126/scitranslmed.aac7071] [Citation(s) in RCA: 282] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chronic kidney disease (CKD) affects 8 to 16% people worldwide, with an increasing incidence and prevalence of end-stage kidney disease (ESKD). The effective management of CKD is confounded by the inability to identify patients at high risk of progression while in early stages of CKD. To address this challenge, a renal biopsy transcriptome-driven approach was applied to develop noninvasive prognostic biomarkers for CKD progression. Expression of intrarenal transcripts was correlated with the baseline estimated glomerular filtration rate (eGFR) in 261 patients. Proteins encoded by eGFR-associated transcripts were tested in urine for association with renal tissue injury and baseline eGFR. The ability to predict CKD progression, defined as the composite of ESKD or 40% reduction of baseline eGFR, was then determined in three independent CKD cohorts. A panel of intrarenal transcripts, including epidermal growth factor (EGF), a tubule-specific protein critical for cell differentiation and regeneration, predicted eGFR. The amount of EGF protein in urine (uEGF) showed significant correlation (P < 0.001) with intrarenal EGF mRNA, interstitial fibrosis/tubular atrophy, eGFR, and rate of eGFR loss. Prediction of the composite renal end point by age, gender, eGFR, and albuminuria was significantly (P < 0.001) improved by addition of uEGF, with an increase of the C-statistic from 0.75 to 0.87. Outcome predictions were replicated in two independent CKD cohorts. Our approach identified uEGF as an independent risk predictor of CKD progression. Addition of uEGF to standard clinical parameters improved the prediction of disease events in diverse CKD populations with a wide spectrum of causes and stages.
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Affiliation(s)
- Wenjun Ju
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Viji Nair
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shahaan Smith
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Li Zhu
- Renal Division, Department of Internal Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Kerby Shedden
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter X K Song
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura H Mariani
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Arbor Research Collaborative for Health, Ann Arbor, MI 48104, USA
| | - Felix H Eichinger
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Celine C Berthier
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ann Randolph
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer Yi-Chun Lai
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yan Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer J Hawkins
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Markus Bitzer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew G Sampson
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Martina Thier
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Corinne Solier
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Gonzalo C Duran-Pacheco
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | | | - Laurent Essioux
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Brigitte Schott
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Ivan Formentini
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Maria C Magnone
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Maria Bobadilla
- Roche Pharmaceutical Research and Early Development-Roche Innovation Center, 4070 Basel, Switzerland
| | - Clemens D Cohen
- Division of Nephrology, Institute of Physiology, University of Zurich, CH-8006 Zürich, Switzerland
| | - Serena M Bagnasco
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Laura Barisoni
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jicheng Lv
- Renal Division, Department of Internal Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Hong Zhang
- Renal Division, Department of Internal Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Hai-Yan Wang
- Renal Division, Department of Internal Medicine, Peking University First Hospital, Peking University Institute of Nephrology, Beijing 100034, China
| | - Frank C Brosius
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Crystal A Gadegbeku
- Temple Clinical Research Institute, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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126
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Poveda J, Sanz AB, Fernandez-Fernandez B, Carrasco S, Ruiz-Ortega M, Cannata-Ortiz P, Ortiz A, Sanchez-Niño MD. MXRA5 is a TGF-β1-regulated human protein with anti-inflammatory and anti-fibrotic properties. J Cell Mol Med 2016; 21:154-164. [PMID: 27599751 PMCID: PMC5192817 DOI: 10.1111/jcmm.12953] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/12/2016] [Indexed: 01/15/2023] Open
Abstract
Current therapy for chronic kidney disease (CKD) is unsatisfactory because of an insufficient understanding of its pathogenesis. Matrix remodelling-associated protein 5 (MXRA5, adlican) is a human protein of unknown function with high kidney tissue expression, not present in rodents. Given the increased expression of MXRA5 in injured tissues, including the kidneys, we have suggested that MXRA5 may modulate kidney injury. MXRA5 immunoreactivity was observed in tubular cells in human renal biopsies and in urine from CKD patients. We then explored factors regulating MXRA5 expression and MXRA5 function in cultured human proximal tubular epithelial cells and explored MXRA5 expression in kidney cancer cells and kidney tissue. The fibrogenic cytokine transforming growth factor-β1 (TGFβ1) up-regulated MXRA5 mRNA and protein expression. TGFβ1-induced MXRA5 up-regulation was prevented by either interference with TGFβ1 activation of the TGFβ receptor 1 (TGFBR1, ALK5) or by the vitamin D receptor agonist paricalcitol. By contrast, the pro-inflammatory cytokine TWEAK did not modulate MXRA5 expression. MXRA5 siRNA-induced down-regulation of constitutive MXRA5 expression resulted in higher TWEAK-induced expression of chemokines. In addition, MXRA5 down-regulation resulted in a magnified expression of genes encoding extracellular matrix proteins in response to TGFβ1. Furthermore, in clear cell renal cancer, von Hippel-Lindau (VHL) regulated MXRA5 expression. In conclusion, MXRA5 is a TGFβ1- and VHL-regulated protein and, for the first time, we identify MXRA5 functions as an anti-inflammatory and anti-fibrotic molecule. This information may yield clues to design novel therapeutic strategies in diseases characterized by inflammation and fibrosis.
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Affiliation(s)
- Jonay Poveda
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
| | - Ana B Sanz
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
| | | | - Susana Carrasco
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
| | - Marta Ruiz-Ortega
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain.,School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain
| | - Pablo Cannata-Ortiz
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
| | - Alberto Ortiz
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain.,School of Medicine, Universidad Autonoma de Madrid, Madrid, Spain.,Fundacion Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain
| | - Maria D Sanchez-Niño
- IIS-Fundacion Jimenez Diaz Universidad Autonoma de Madrid, REDINREN, Madrid, Spain
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127
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Abstract
PURPOSE OF REVIEW Despite recent developments and treatment successes, the outcome, and prognosis of patients with lupus nephritis (LuN) have not greatly changed since the 1980s. This review covers the application of new concepts to the understanding of renal inflammation and the study of new pharmacologic agents to improve patient outcomes. RECENT FINDINGS Studies have shown that the presence of anti-vimentin antibodies and T follicular helper cells in patient biopsies is associated with more severe interstitial inflammation, which has been tied to faster disease progression and onset of end-stage renal disease. Additionally, data regarding the role of serum IgE antidouble-stranded DNA antibodies in LuN by means of mediating IFN1 production by plasmacytoid dendritic cells are highlighted. Finally, a thorough review of completed and currently open clinical trials of therapeutic agents is provided. SUMMARY Current management of LuN is guided almost exclusively by glomerular involvement. Based on the data provided in this review, we argue that renal tubulointerstitial inflammation is no less important and represents an overlooked feature in the current clinical approach to patients. Tubulointerstitial inflammation is driven by both adaptive and innate immune mechanisms that are still poorly understood. Studying these pathogenic processes promises to reveal new therapeutic opportunities for those LuN patients with the worst prognosis. VIDEO ABSTRACT Alternate video abstract introduction (see Video, Supplemental Digital Content 1, with introduction by two of the authors - VL and KT). Abstract Video: http://links.lww.com/COR/A35.
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Affiliation(s)
- Kimberly Trotter
- Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637
| | - Marcus R. Clark
- Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637
| | - Vladimir M. Liarski
- Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637
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128
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Berthier CC, Kretzler M, Davidson A. A systems approach to renal inflammation in SLE. Clin Immunol 2016; 185:109-118. [PMID: 27534926 DOI: 10.1016/j.clim.2016.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 12/17/2022]
Abstract
Lupus disease and its complications including lupus nephritis (LN) are very disabling and significantly impact the quality of life and longevity of patients. Broadly immunosuppressive treatments do not always provide the expected clinical benefits and have significant side effects that contribute to patient morbidity. In the era of systems biology, new strategies are being deployed integrating diverse sources of information (molecular and clinical) so as to identify individual disease specificities and select less aggressive treatments. In this review, we summarize integrative approaches linking molecular disease profiles (mainly tissue transcriptomics) and clinical phenotypes. The main goals are to better understand the pathogenesis of lupus nephritis, to identify the risk factors for renal flare and to find the predictors of both short and long-term clinical outcome. Identification of common key drivers and additional patient-specific key drivers can open the door to improved and individualized therapy to prevent and treat LN.
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Affiliation(s)
- Celine C Berthier
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Kretzler
- Internal Medicine, Department of Nephrology, University of Michigan, Ann Arbor, MI, USA
| | - Anne Davidson
- Feinstein Institute, Center for Autoimmunity and Musculoskeletal Diseases, Manhasset, NY, USA 11030.
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129
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Grammer AC, Ryals MM, Heuer SE, Robl RD, Madamanchi S, Davis LS, Lauwerys B, Catalina MD, Lipsky PE. Drug repositioning in SLE: crowd-sourcing, literature-mining and Big Data analysis. Lupus 2016; 25:1150-70. [DOI: 10.1177/0961203316657437] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lupus patients are in need of modern drugs to treat specific manifestations of their disease effectively and safely. In the past half century, only one new treatment has been approved by the US Food and Drug Administration (FDA) for systemic lupus erythematosus (SLE). In 2014–2015, the FDA approved 71 new drugs, only one of which targeted a rheumatic disease and none of which was approved for use in SLE. Repositioning/repurposing drugs approved for other diseases using multiple approaches is one possible means to find new treatment options for lupus patients. “Big Data” analysis approaches this challenge from an unbiased standpoint whereas literature mining and crowd sourcing for candidates assessed by the CoLTs (Combined Lupus Treatment Scoring) system provide a hypothesis-based approach to rank potential therapeutic candidates for possible clinical application. Both approaches mitigate risk since the candidates assessed have largely been extensively tested in clinical trials for other indications. The usefulness of a multi-pronged approach to drug repositioning in lupus is highlighted by orthogonal confirmation of hypothesis-based drug repositioning predictions by “Big Data” analysis of differentially expressed genes from lupus patient samples. The goal is to identify novel therapies that have the potential to affect disease processes specifically. Involvement of SLE patients and the scientists that study this disease in thinking about new drugs that may be effective in lupus though crowd-sourcing sites such as LRxL-STAT ( www.linkedin.com/in/lrxlstat ) is important in stimulating the momentum needed to test these novel drug targets for efficacy in lupus rapidly in small, proof-of-concept trials conducted by LuCIN, the Lupus Clinical Investigators Network ( www.linkedin.com/in/lucinstat ).
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Affiliation(s)
- A C Grammer
- AMPEL BioSolutions and RILITE Foundation, University of Virginia Research Park, Charlottesville, VA, USA
| | - M M Ryals
- AMPEL BioSolutions and RILITE Foundation, University of Virginia Research Park, Charlottesville, VA, USA
| | - S E Heuer
- AMPEL BioSolutions and RILITE Foundation, University of Virginia Research Park, Charlottesville, VA, USA
| | - R D Robl
- AMPEL BioSolutions and RILITE Foundation, University of Virginia Research Park, Charlottesville, VA, USA
| | - S Madamanchi
- AMPEL BioSolutions and RILITE Foundation, University of Virginia Research Park, Charlottesville, VA, USA
| | - L S Davis
- Department of Internal Medicine, UTSW Medical Center at Dallas, Dallas, TX, USA
| | - B Lauwerys
- Université Catholique de Louvain, Brussels, Belgium
| | - M D Catalina
- AMPEL BioSolutions and RILITE Foundation, University of Virginia Research Park, Charlottesville, VA, USA
| | - P E Lipsky
- AMPEL BioSolutions and RILITE Foundation, University of Virginia Research Park, Charlottesville, VA, USA
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130
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Valiño-Rivas L, Gonzalez-Lafuente L, Sanz AB, Ruiz-Ortega M, Ortiz A, Sanchez-Niño MD. Non-canonical NFκB activation promotes chemokine expression in podocytes. Sci Rep 2016; 6:28857. [PMID: 27353019 PMCID: PMC4926283 DOI: 10.1038/srep28857] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 06/10/2016] [Indexed: 12/13/2022] Open
Abstract
TNF-like weak inducer of apoptosis (TWEAK) receptor Fn14 is expressed by podocytes and Fn14 deficiency protects from experimental proteinuric kidney disease. However, the downstream effectors of TWEAK/Fn14 in podocytes are poorly characterized. We have explored TWEAK activation of non-canonical NFκB signaling in cultured podocytes. In cultured podocytes, TWEAK increased the expression of the chemokines CCL21, CCL19 and RANTES in a time-dependent manner. The inhibitor of canonical NFκB activation parthenolide inhibited the CCL19 and the early RANTES responses, but not the CCL21 or late RANTES responses. In this regard, TWEAK induced non-canonical NFκB activation in podocytes, characterized by NFκB2/p100 processing to NFκB2/p52 and nuclear migration of RelB/p52. Silencing by a specific siRNA of NIK, the upstream kinase of the non-canonical NFκB pathway, prevented CCL21 upregulation but did not modulate CCL19 or RANTES expression in response to TWEAK, thus establishing CCL21 as a non-canonical NFκB target in podocytes. Increased kidney Fn14 and CCL21 expression was also observed in rat proteinuric kidney disease induced by puromycin, and was localized to podocytes. In conclusion, TWEAK activates the non-canonical NFκB pathway in podocytes, leading to upregulation of CCL21 expression. The non-canonical NFκB pathway should be explored as a potential therapeutic target in proteinuric kidney disease.
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Affiliation(s)
- Lara Valiño-Rivas
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Laura Gonzalez-Lafuente
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Ana B Sanz
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Marta Ruiz-Ortega
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Alberto Ortiz
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
| | - Maria D Sanchez-Niño
- IIS-Fundación Jiménez Díaz-Universidad Autónoma de Madrid and Fundación Renal Iñigo Alvarez de Toledo-IRSIN, Madrid, Spain.,REDINREN, Madrid, Spain
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131
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Goilav B, Putterman C, Rubinstein TB. Biomarkers for kidney involvement in pediatric lupus. Biomark Med 2016; 9:529-43. [PMID: 26079958 DOI: 10.2217/bmm.15.25] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Lupus nephritis (LN), the renal involvement in systemic lupus erythematosus, is currently diagnosed by histopathology obtained by percutaneous renal biopsy and is associated with increased morbidity and mortality in both adults and children. LN is more prevalent and severe in children, requiring aggressive and prolonged immunosuppression. The consequences of the diagnosis and its treatment have devastating long-term effects on the growth, well-being and quality of life of affected children. The paucity of reliable clinical indicators of the presence and severity of renal involvement have contributed to a halt in the reduction of progression to end-stage renal disease in recent years. Here, we discuss the recent development of biomarkers in the management of LN and their role as therapeutic targets.
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Affiliation(s)
- Beatrice Goilav
- Children's Hospital at Montefiore, Department of Pediatrics, Division of Nephrology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA
| | - Chaim Putterman
- Division of Rheumatology & Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA
| | - Tamar B Rubinstein
- Children's Hospital at Montefiore, Department of Pediatrics, Division of Rheumatology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, NY 10461, USA
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132
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Seleznik G, Seeger H, Bauer J, Fu K, Czerkowicz J, Papandile A, Poreci U, Rabah D, Ranger A, Cohen CD, Lindenmeyer M, Chen J, Edenhofer I, Anders HJ, Lech M, Wüthrich RP, Ruddle NH, Moeller MJ, Kozakowski N, Regele H, Browning JL, Heikenwalder M, Segerer S. The lymphotoxin β receptor is a potential therapeutic target in renal inflammation. Kidney Int 2016; 89:113-26. [PMID: 26398497 DOI: 10.1038/ki.2015.280] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 07/14/2015] [Accepted: 07/16/2015] [Indexed: 02/07/2023]
Abstract
Accumulation of inflammatory cells in different renal compartments is a hallmark of progressive kidney diseases including glomerulonephritis (GN). Lymphotoxin β receptor (LTβR) signaling is crucial for the formation of lymphoid tissue, and inhibition of LTβR signaling has ameliorated several non-renal inflammatory models. Therefore, we tested whether LTβR signaling could also have a role in renal injury. Renal biopsies from patients with GN were found to express both LTα and LTβ ligands, as well as LTβR. The LTβR protein and mRNA were localized to tubular epithelial cells, parietal epithelial cells, crescents, and cells of the glomerular tuft, whereas LTβ was found on lymphocytes and tubular epithelial cells. Human tubular epithelial cells, mesangial cells, and mouse parietal epithelial cells expressed both LTα and LTβ mRNA upon stimulation with TNF in vitro. Several chemokine mRNAs and proteins were expressed in response to LTβR signaling. Importantly, in a murine lupus model, LTβR blockade improved renal function without the reduction of serum autoantibody titers or glomerular immune complex deposition. Thus, a preclinical mouse model and human studies strongly suggest that LTβR signaling is involved in renal injury and may be a suitable therapeutic target in renal diseases.
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Affiliation(s)
- Gitta Seleznik
- Division of Visceral & Transplantation Surgery, Swiss Hepato-Pancreato-Biliary Center, Zurich, Switzerland; Division of Nephrology, University Hospital, Zurich, Switzerland
| | - Harald Seeger
- Division of Nephrology, University Hospital, Zurich, Switzerland; Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Judith Bauer
- Institute of Virology, Technische Universität München, Helmholz Zentrum, Munich, Germany
| | - Kai Fu
- Department of Immunobiology, Biogen, Cambridge, Massachusetts, USA
| | - Julie Czerkowicz
- Department of Immunobiology, Biogen, Cambridge, Massachusetts, USA
| | - Adrian Papandile
- Department of Immunobiology, Biogen, Cambridge, Massachusetts, USA
| | - Uriana Poreci
- Department of Immunobiology, Biogen, Cambridge, Massachusetts, USA
| | - Dania Rabah
- Department of Immunobiology, Biogen, Cambridge, Massachusetts, USA
| | - Ann Ranger
- Department of Immunobiology, Biogen, Cambridge, Massachusetts, USA
| | - Clemens D Cohen
- Division of Nephrology, University Hospital, Zurich, Switzerland; Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Maja Lindenmeyer
- Division of Nephrology, University Hospital, Zurich, Switzerland; Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Jin Chen
- Division of Nephrology, University Hospital, Zurich, Switzerland; Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Ilka Edenhofer
- Division of Nephrology, University Hospital, Zurich, Switzerland; Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Hans J Anders
- Division of Nephrology, Medizinische Klinik und Poliklinik IV, Campus Innenstadt, University of Munich-LMU, Munich, Germany
| | - Maciej Lech
- Division of Nephrology, Medizinische Klinik und Poliklinik IV, Campus Innenstadt, University of Munich-LMU, Munich, Germany
| | - Rudolf P Wüthrich
- Division of Nephrology, University Hospital, Zurich, Switzerland; Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Nancy H Ruddle
- Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Marcus J Moeller
- Department of Nephrology and Clinical Immunology, Rheinisch-Westfälische Technische Hochschule (RWTH) University Hospital Aachen, Aachen, Germany
| | | | - Heinz Regele
- Clinical Institute of Pathology, University of Vienna, Vienna, Austria
| | - Jeffrey L Browning
- Department of Immunobiology, Biogen, Cambridge, Massachusetts, USA; Department of Microbiology and Section of Rheumatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München, Helmholz Zentrum, Munich, Germany; Institute of Surgical Pathology, University Hospital, Zurich, Switzerland
| | - Stephan Segerer
- Division of Nephrology, University Hospital, Zurich, Switzerland; Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland.
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133
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Abstract
Despite marked improvements in the survival of patients with severe lupus nephritis over the past 50 years, the rate of complete clinical remission after immune suppression therapy is <50% and renal impairment still occurs in 40% of affected patients. An appreciation of the factors that lead to the development of chronic kidney disease following acute or subacute renal injury in patients with systemic lupus erythematosus is beginning to emerge. Processes that contribute to end-stage renal injury include continuing inflammation, activation of intrinsic renal cells, cell stress and hypoxia, metabolic abnormalities, aberrant tissue repair and tissue fibrosis. A deeper understanding of these processes is leading to the development of novel or adjunctive therapies that could protect the kidney from the secondary non-immune consequences of acute injury. Approaches based on a molecular-proteomic-lipidomic classification of disease should yield new information about the functional basis of disease heterogeneity so that the most effective and least toxic treatment regimens can be formulated for individual patients.
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134
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Parikh SV, Malvar A, Song H, Alberton V, Lococo B, Vance J, Zhang J, Yu L, Rovin BH. Characterising the immune profile of the kidney biopsy at lupus nephritis flare differentiates early treatment responders from non-responders. Lupus Sci Med 2015; 2:e000112. [PMID: 26629350 PMCID: PMC4654163 DOI: 10.1136/lupus-2015-000112] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/12/2015] [Accepted: 09/02/2015] [Indexed: 01/22/2023]
Abstract
Introduction The kidney biopsy is used to diagnose and guide initial therapy in patients with lupus nephritis (LN). Kidney histology does not correlate well with clinical measurements of kidney injury or predict how patients will respond to standard-of-care immunosuppression. We postulated that the gene expression profile of kidney tissue at the time of biopsy may differentiate patients who will from those who will not respond to treatment. Methods The expression of 511 immune-response genes was measured in kidney biopsies from 19 patients with proliferative LN and 4 normal controls. RNA was extracted from formalin-fixed, paraffin-embedded kidney biopsies done at flare. After induction therapy, 5 patients achieved a complete clinical response (CR), 10 had a partial response (PR) and 4 patients were non-responders (NRs). Transcript expression was compared with normal controls and between renal response groups. Results A principal component analysis showed that intrarenal transcript expression from normal kidney, CR biopsies and NR biopsies segregated from each other. The top genes responsible for CR clustering included several interferon pathway genes (STAT1, IRF1, IRF7, MX1, STAT2, JAK2), while complement genes (C1R, C1QB, C6, C9, C5, MASP2) were mainly responsible for NR clustering. Overall, 35 genes were uniquely expressed in NR compared with CR. Pathway analysis revealed that interferon signalling and complement activation pathways were upregulated in both groups, while BAFF, APRIL, nuclear factor-κB and interleukin-6 signalling were increased in CR but suppressed in NR. Conclusions These data suggest that molecular profiling of the kidney biopsy at LN flare may be useful in predicting treatment response to induction therapy.
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Affiliation(s)
- Samir V Parikh
- Division of Nephrology , The Ohio State University Wexner Medical Center , Columbus, Ohio , USA
| | - Ana Malvar
- Nephrology Unit , Hospital Fernandez , Buenos Aires , Argentina
| | - Huijuan Song
- Division of Nephrology , The Ohio State University Wexner Medical Center , Columbus, Ohio , USA
| | - Valeria Alberton
- Department of Pathology , Hospital Fernandez , Buenos Aires , Argentina
| | - Bruno Lococo
- Nephrology Unit , Hospital Fernandez , Buenos Aires , Argentina
| | - Jay Vance
- Division of Nephrology , The Ohio State University Wexner Medical Center , Columbus, Ohio , USA
| | - Jianying Zhang
- Center for Biostatistics, The Ohio State University Wexner Medical Center , Columbus, Ohio , USA
| | - Lianbo Yu
- Nephrology Unit , Hospital Fernandez , Buenos Aires , Argentina
| | - Brad H Rovin
- Division of Nephrology , The Ohio State University Wexner Medical Center , Columbus, Ohio , USA
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Costa-Reis P, Russo PA, Zhang Z, Colonna L, Maurer K, Gallucci S, Schulz SW, Kiani AN, Petri M, Sullivan KE. The Role of MicroRNAs and Human Epidermal Growth Factor Receptor 2 in Proliferative Lupus Nephritis. Arthritis Rheumatol 2015; 67:2415-26. [PMID: 26016809 DOI: 10.1002/art.39219] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 05/21/2015] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To understand the roles of microRNAs (miRNAs) in proliferative lupus nephritis (LN). METHODS A high-throughput analysis of the miRNA pattern of the kidneys of LN patients and controls was performed by molecular digital detection. Urinary miRNAs were measured by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Target gene expression in human mesangial cells was evaluated by arrays and qRT-PCR. Human epidermal growth factor receptor 2 (HER-2) was analyzed by immunohistochemistry in kidney samples from LN patients and in a murine model of lupus. Urinary levels of HER-2, monocyte chemotactic protein 1 (MCP-1), and vascular cell adhesion molecule 1 (VCAM-1) were measured by enzyme-linked immunosorbent assay. RESULTS Levels of the miRNAs miR-26a and miR-30b were decreased in the kidneys and urine of LN patients. In vitro these miRNAs controlled mesangial cell proliferation, and their expression was regulated by HER-2. HER-2 was overexpressed in lupus-prone NZM2410 mice and in the kidneys of patients with LN, but not in other mesangioproliferative glomerulonephritides. HER-2 was found to be up-regulated by interferon-α and interferon regulatory factor 1. Urinary HER-2 was increased in LN and reflected disease activity, and its levels correlated with those of 2 other recognized LN biomarkers, MCP-1 and VCAM-1. CONCLUSION The kidney miRNA pattern is broadly altered in LN, which contributes to uncontrolled cell proliferation. Levels of the miRNAs miR-26a and miR-30b are decreased in the kidneys and urine of LN patients, and they directly regulate the cell cycle in mesangial cells. The levels of these miRNAs are controlled by HER-2, which is overexpressed in NZM2410 mice and in the kidneys and urine of LN patients. HER-2, miR-26a, and miR-30b are thus potential LN biomarkers, and blocking HER-2 may be a promising new strategy to decrease cell proliferation and damage in this disease.
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Affiliation(s)
- Patrícia Costa-Reis
- The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, and University of Lisbon, Lisbon, Portugal
| | - Pierre A Russo
- The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Zhe Zhang
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lucrezia Colonna
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly Maurer
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stefania Gallucci
- The Children's Hospital of Philadelphia and Temple University, Philadelphia, Pennsylvania
| | | | - Adnan N Kiani
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michelle Petri
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kathleen E Sullivan
- The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia
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Krasoudaki E, Banos A, Stagakis E, Loupasakis K, Drakos E, Sinatkas V, Zampoulaki A, Papagianni A, Iliopoulos D, Boumpas DT, Bertsias GK. Micro-RNA analysis of renal biopsies in human lupus nephritis demonstrates up-regulated miR-422a driving reduction of kallikrein-related peptidase 4. Nephrol Dial Transplant 2015; 31:1676-86. [DOI: 10.1093/ndt/gfv374] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022] Open
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Mariani LH, Kretzler M. Pro: 'The usefulness of biomarkers in glomerular diseases'. The problem: moving from syndrome to mechanism--individual patient variability in disease presentation, course and response to therapy. Nephrol Dial Transplant 2015; 30:892-8. [PMID: 25994659 DOI: 10.1093/ndt/gfv108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The diagnosis and treatment decisions in glomerular disease are principally based on renal pathology and nonspecific clinical laboratory measurements such as serum creatinine and urine protein. Using these classification approaches, patients have marked variability in rate of progression and response to therapy, exposing a significant number of patients to toxicity without benefit. Additionally, clinical trials are at risk of not being able to detect an efficacious therapy in relevant subgroups as patients with shared clinical-pathologic diagnoses have heterogeneous underlying pathobiology. To change this treatment paradigm, biomarkers that reflect the molecular mechanisms underlying the clinical-pathologic diagnoses are needed. Recent progress to identify such biomarkers has been aided by advances in molecular profiling, large-scale data generation and multi-scalar data integration, including prospectively collected clinical data. This article reviews the evolving success stories in glomerular disease biomarkers across the genotype-phenotype continuum and highlights opportunities to transition to precision medicine in glomerular disease.
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Affiliation(s)
- Laura H Mariani
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, MI, USA Arbor Research Collaborative for Health, Ann Arbor, MI, USA
| | - Matthias Kretzler
- Department of Internal Medicine/Nephrology, University of Michigan, Ann Arbor, MI, USA Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
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El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Müller T, Blin G, Heringa J, Nikolski M, Wessels LFA, Klau GW. xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics 2015; 31:3147-55. [PMID: 26023104 DOI: 10.1093/bioinformatics/btv316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/18/2015] [Indexed: 01/18/2023] Open
Abstract
MOTIVATION Integrative network analysis methods provide robust interpretations of differential high-throughput molecular profile measurements. They are often used in a biomedical context-to generate novel hypotheses about the underlying cellular processes or to derive biomarkers for classification and subtyping. The underlying molecular profiles are frequently measured and validated on animal or cellular models. Therefore the results are not immediately transferable to human. In particular, this is also the case in a study of the recently discovered interleukin-17 producing helper T cells (Th17), which are fundamental for anti-microbial immunity but also known to contribute to autoimmune diseases. RESULTS We propose a mathematical model for finding active subnetwork modules that are conserved between two species. These are sets of genes, one for each species, which (i) induce a connected subnetwork in a species-specific interaction network, (ii) show overall differential behavior and (iii) contain a large number of orthologous genes. We propose a flexible notion of conservation, which turns out to be crucial for the quality of the resulting modules in terms of biological interpretability. We propose an algorithm that finds provably optimal or near-optimal conserved active modules in our model. We apply our algorithm to understand the mechanisms underlying Th17 T cell differentiation in both mouse and human. As a main biological result, we find that the key regulation of Th17 differentiation is conserved between human and mouse. AVAILABILITY AND IMPLEMENTATION xHeinz, an implementation of our algorithm, as well as all input data and results, are available at http://software.cwi.nl/xheinz and as a Galaxy service at http://services.cbib.u-bordeaux2.fr/galaxy in CBiB Tools. CONTACT gunnar.klau@cwi.nl SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mohammed El-Kebir
- Life Sciences, Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU, VU University Amsterdam, The Netherlands, Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Hayssam Soueidan
- Computational Cancer Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thomas Hume
- Univ. Bordeaux, CBiB, 33000 Bordeaux, France, Univ. Bordeaux, CNRS/LaBRI, 33405 Talence, France
| | - Daniela Beisser
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen
| | - Marcus Dittrich
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany, Institute of Human Genetics, University of Würzburg, Würzburg, Germany and
| | - Tobias Müller
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Jaap Heringa
- Centre for Integrative Bioinformatics VU, VU University Amsterdam, The Netherlands
| | - Macha Nikolski
- Univ. Bordeaux, CBiB, 33000 Bordeaux, France, Univ. Bordeaux, CNRS/LaBRI, 33405 Talence, France
| | - Lodewyk F A Wessels
- Computational Cancer Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gunnar W Klau
- Life Sciences, Centrum Wiskunde & Informatica (CWI), Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU, VU University Amsterdam, The Netherlands, Erable Team, INRIA, Lyon, France
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Cuaranta-Monroy I, Kiss M, Simandi Z, Nagy L. Genomewide effects of peroxisome proliferator-activated receptor gamma in macrophages and dendritic cells--revealing complexity through systems biology. Eur J Clin Invest 2015; 45:964-75. [PMID: 26251129 DOI: 10.1111/eci.12491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/01/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Systems biology approaches have become indispensable tools in biomedical and basic research. These data integrating bioinformatic methods gained prominence after high-throughput technologies became available to investigate complex cellular processes, such as transcriptional regulation and protein-protein interactions, on a scale that had not been studied before. Immunology is one of the medical fields that systems biology impacted profoundly due to the plasticity of cell types involved and the accessibility of a wide range of experimental models. MATERIALS AND METHODS In this review, we summarize the most important recent genomewide studies exploring the function of peroxisome proliferator-activated receptor γ in macrophages and dendritic cells. PPARγ ChIP-seq experiments were performed in adipocytes derived from embryonic stem cells to complement the existing data sets and to provide comparators to macrophage data. Finally, lists of regulated genes generated from such experiments were analysed with bioinformatics and system biology approaches. RESULTS We show that genomewide studies utilizing high-throughput data acquisition methods made it possible to gain deeper insights into the role of PPARγ in these immune cell types. We also demonstrate that analysis and visualization of data using network-based approaches can be used to identify novel genes and functions regulated by the receptor. CONCLUSIONS The example of PPARγ in macrophages and dendritic cells highlights the crucial importance of systems biology approaches in establishing novel cellular functions for long-known signaling pathways.
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Affiliation(s)
- Ixchelt Cuaranta-Monroy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Faculty of Medicine, Debrecen, Hungary
| | - Mate Kiss
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Faculty of Medicine, Debrecen, Hungary
| | - Zoltan Simandi
- Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA
| | - Laszlo Nagy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Faculty of Medicine, Debrecen, Hungary.,Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, FL, USA.,MTA-DE 'Lendulet' Immunogenomics Research Group, Debrecen, Hungary
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141
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Clark MR, Trotter K, Chang A. The Pathogenesis and Therapeutic Implications of Tubulointerstitial Inflammation in Human Lupus Nephritis. Semin Nephrol 2015; 35:455-64. [PMID: 26573548 PMCID: PMC4653081 DOI: 10.1016/j.semnephrol.2015.08.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nephritis is a common complication of systemic lupus erythematosus for which current therapies often prove inadequate. Current lupus nephritis classification systems emphasize glomerular acuity and scarring. However, tubulointerstitial inflammation (TII) and scarring are much better predictors of progression to renal failure. It now is becoming clear that the immunologic features, and probable underlying mechanisms, are very different in lupus glomerulonephritis and TII at the time of biopsy. Although glomerulonephritis is a manifestation of systemic autoimmunity, TII is associated with local in situ adaptive immune cell networks predicted to amplify local inflammation and tissue damage. In addition, poorly defined networks of innate immune cells and effectors likely contribute to the severity of local inflammation. Defining these in situ immune mechanisms should lead to a better understanding of prognostically meaningful lupus nephritis subsets and show novel therapeutic opportunities.
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Affiliation(s)
- Marcus R Clark
- Department of Medicine, University of Chicago, Chicago, IL; Department of Pathology, University of Chicago, Chicago, IL; Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL.
| | | | - Anthony Chang
- Department of Pathology, University of Chicago, Chicago, IL
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Hu Q, Yang C, Wang Q, Zeng H, Qin W. Demethylzeylasteral (T-96) Treatment Ameliorates Mice Lupus Nephritis Accompanied by Inhibiting Activation of NF-κB Pathway. PLoS One 2015. [PMID: 26208003 PMCID: PMC4514757 DOI: 10.1371/journal.pone.0133724] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Inflammation plays a vital role in the pathogenesis in lupus nephritis (LN), which is largely attributable to the activation of nuclear factor kappa B (NF-κB) signal pathway. NF-κB up-regulates pro-inflammatory mediators, such as TNF-α, cyclo-oxygenase-2 (COX-2) and ICAM-1, and promotes macrophage infiltration into renal tissue, further inducing the progression of LN. Over the past 30 years, research has demonstrated that Tripterygium wilfordii Hook F (TWHF) possesses potent anti-inflammatory and immunosuppressive activities, and that demethylzeylasteral (T-96), an extract of TWHF, may be one of the responsible compounds. Here, we investigate the pharmacodynamic role and therapeutic mechanism by which T-96 suppresses inflammation and reduces renal pathology in the lupus-prone MRL/lpr mice. Methods Forty-eight MRL/lpr mice were equally randomly divided into 6 groups (1.2, 0.6 or 0.3 mg/10g T-96, 0.022 pills/10g kang lang chuang san (one of Traditional Chinese herb as positive control), 0.125 mg/10g prednisone and 0.1 ml/10g normal saline as the LN disease control group). Also, eight WT C57BL/6 mice were used as normal control. After treatment by gavage with 0.10 ml/10g/day volumes for 8 weeks, all mice were sacrificed and renal tissues were collected. The amount of 24 h proteinuria and the levels of anti-dsDNA antibody in serum were assessed respectively at weeks 0, 4 and 8. Inflammation, cytokines and NF-κB levels were assessed by histological examinations, immunohistochemical analyses and Western blot analyses. Results In comparison with untreated MRL/lpr mice, mice treated with 1.2 and 0.6 mg/10g of T-96 showed a significant improvement in 24 h proteinuria and the levels of anti-dsDNA antibody in serum. In addition, T-96 reduced the secretion of pro-inflammatory mediators such as TNF-α, COX-2 and ICAM-1, and the infiltration of macrophages in renal tissue. Moreover, T-96 significantly suppressed phosphorylations of cytoplasmic IKK and nuclear p65. Conclusion This study suggests that T-96 exhibits reno-protective effects in LN accompanied by inhibiting the activation of NF-κB, reducing the downstream pro-inflammatory mediators and thus restricting macrophage infiltration. Because of these potent properties, T-96 should be considered as a promising therapeutic drug for LN.
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Affiliation(s)
- Qiongyi Hu
- Department of Dermatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, P.R. China
| | - Chunxin Yang
- Department of Pharmaceutical Chemistry, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, P.R. China
- * E-mail: (CXY); (QW)
| | - Qiang Wang
- Department of Dermatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, P.R. China
- * E-mail: (CXY); (QW)
| | - Haiying Zeng
- Department of Pathology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, P.R. China
| | - Wanzhang Qin
- Department of Dermatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, P.R. China
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Bates MA, Brandenberger C, Langohr I, Kumagai K, Harkema JR, Holian A, Pestka JJ. Silica Triggers Inflammation and Ectopic Lymphoid Neogenesis in the Lungs in Parallel with Accelerated Onset of Systemic Autoimmunity and Glomerulonephritis in the Lupus-Prone NZBWF1 Mouse. PLoS One 2015; 10:e0125481. [PMID: 25978333 PMCID: PMC4433215 DOI: 10.1371/journal.pone.0125481] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/18/2015] [Indexed: 01/02/2023] Open
Abstract
Genetic predisposition and environmental factors influence the development of human autoimmune disease. Occupational exposure to crystalline silica (cSiO2) has been etiologically linked to increased incidence of autoimmunity, including systemic lupus erythematosus (SLE), but the underlying mechanisms are poorly understood. The purpose of this study was to test the hypothesis that early repeated short-term cSiO2 exposure will modulate both latency and severity of autoimmunity in the lupus-prone female NZBWF1 mouse. Weekly intranasal exposure to cSiO2 (0.25 and 1.0 mg) for 4 wk beginning at 9 wk of age both reduced latency and increased intensity of glomerulonephritis. cSiO2 elicited robust inflammatory responses in the lungs as evidenced by extensive perivascular and peribronchial lymphoplasmacytic infiltration consisting of IgG-producing plasma cells, and CD45R+ and CD3+ lymphocytes that were highly suggestive of ectopic lymphoid tissue (ELT). In addition, there were elevated concentrations of immunoglobulins and the cytokines MCP-1, TNF-α and IL-6 in bronchoalveolar lavage fluid. cSiO2-associated kidney and lung effects paralleled dose-dependent elevations of autoantibodies and proinflammatory cytokines in plasma. Taken together, cSiO2-induced pulmonary inflammation and ectopic lymphoid neogenesis in the NZBWF1 mouse corresponded closely to systemic inflammatory and autoimmune responses as well as the early initiation of pathological outcomes in the kidney. These findings suggest that following airway exposure to crystalline silica, in mice genetically prone to SLE, the lung serves as a platform for triggering systemic autoimmunity and glomerulonephritis.
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Affiliation(s)
- Melissa A. Bates
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, United States of America
- Center for Integrative Toxicology, Michigan State University, East Lansing, Michigan, United States of America
| | - Christina Brandenberger
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan, United States of America
- Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany
| | - Ingeborg Langohr
- Department of Pathobiological Studies, School of Veterinary Medicine, Louisiana State University, Baton Rogue, Louisiana, United States of America
| | - Kazuyoshi Kumagai
- Center for Integrative Toxicology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan, United States of America
| | - Jack R. Harkema
- Center for Integrative Toxicology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan, United States of America
| | - Andrij Holian
- Center for Environmental Health Sciences, University of Montana, Missoula, Montana, United States of America
| | - James J. Pestka
- Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, United States of America
- Center for Integrative Toxicology, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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Kim KJ, Lee S, Kim WU. Applications of systems approaches in the study of rheumatic diseases. Korean J Intern Med 2015; 30:148-60. [PMID: 25750554 PMCID: PMC4351319 DOI: 10.3904/kjim.2015.30.2.148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/23/2014] [Indexed: 12/27/2022] Open
Abstract
The complex interaction of molecules within a biological system constitutes a functional module. These modules are then acted upon by both internal and external factors, such as genetic and environmental stresses, which under certain conditions can manifest as complex disease phenotypes. Recent advances in high-throughput biological analyses, in combination with improved computational methods for data enrichment, functional annotation, and network visualization, have enabled a much deeper understanding of the mechanisms underlying important biological processes by identifying functional modules that are temporally and spatially perturbed in the context of disease development. Systems biology approaches such as these have produced compelling observations that would be impossible to replicate using classical methodologies, with greater insights expected as both the technology and methods improve in the coming years. Here, we examine the use of systems biology and network analysis in the study of a wide range of rheumatic diseases to better understand the underlying molecular and clinical features.
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Affiliation(s)
- Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Saseong Lee
- POSTECH-CATHOLIC BioMedical Engineering Institute, The Catholic University of Korea, Seoul, Korea
| | - Wan-Uk Kim
- POSTECH-CATHOLIC BioMedical Engineering Institute, The Catholic University of Korea, Seoul, Korea
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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145
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Daikh DI. Animal models of lupus. Rheumatology (Oxford) 2015. [DOI: 10.1016/b978-0-323-09138-1.00129-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Liu N, Shi J, Xiao Y, Yasue M, Takei Y, Sanefuji H, Tsujimoto G, Hirasawa A. Effects of a Tricaprylin Emulsion on Anti-glomerular Basement Membrane Glomerulonephritis in Rats: In Vivo and in Silico Studies. Biol Pharm Bull 2015; 38:1175-84. [DOI: 10.1248/bpb.b15-00124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ning Liu
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Junfeng Shi
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Ying Xiao
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Misato Yasue
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Yoshinori Takei
- Department of Nanobio Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University
| | | | - Gozoh Tsujimoto
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University
| | - Akira Hirasawa
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University
- Institute for Integrated Medical Sciences, Tokyo Women’s Medical University
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Sahu R, Bethunaickan R, Singh S, Davidson A. Structure and function of renal macrophages and dendritic cells from lupus-prone mice. Arthritis Rheumatol 2014; 66:1596-607. [PMID: 24866269 DOI: 10.1002/art.38410] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 02/11/2014] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To characterize renal macrophages and dendritic cells (DCs) in 2 murine models of lupus nephritis. METHODS We used a bead-based enrichment step followed by cell sorting to isolate populations of interest from young mice and nephritic mice. Cell morphology was examined by microscopy. Arginase and nitrite production was examined using biochemical assays. The antigen-presenting functions of the cells were determined using mixed lymphocyte reactions. Selected cytokine, chemokine, and Toll-like receptor (TLR) profiles were examined using real-time quantitative polymerase chain reaction. RESULTS We identified 2 populations of macrophages and 3 populations of DCs in both of our murine models of lupus (NZB/NZW and [NZW × BXSB]F1 mice). F4/80(high) macrophages, which were resident in normal kidneys and found to be increased in number during nephritis, did not produce either arginase or nitrite upon cytokine stimulation and acquired a mixed proinflammatory and antiinflammatory functional phenotype during nephritis that resembles the constitutively activated phenotype of gut F4/80(high) macrophages. The various cell types differed in their expression of chemokine receptors and TLRs, consistent with variability in their renal location. Resident renal CD103+ DCs were the best antigen-presenting cells and could easily be distinguished from CD11c(high) myeloid DCs that accumulated in large numbers during nephritis. CONCLUSION Our study highlights the heterogeneity of the macrophage/DC infiltrate in chronic lupus nephritis and provides an initial phenotypic and functional analysis of the different cellular components that can now be used to define the role of each cell subset in nephritis progression or amelioration. Of note, the dominant macrophage population that accumulates during nephritis has an acquired phenotype that is neither M1 nor M2 and may reflect failure of resolution of inflammation.
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Affiliation(s)
- Ranjit Sahu
- Feinstein Institute for Medical Research, Manhasset, New York
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Bethunaickan R, Berthier CC, Zhang W, Eksi R, Li HD, Guan Y, Kretzler M, Davidson A. Identification of stage-specific genes associated with lupus nephritis and response to remission induction in (NZB × NZW)F1 and NZM2410 mice. Arthritis Rheumatol 2014; 66:2246-2258. [PMID: 24757019 PMCID: PMC4554534 DOI: 10.1002/art.38679] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 04/17/2014] [Indexed: 11/10/2022]
Abstract
OBJECTIVE To elucidate the molecular mechanisms involved in renal inflammation during the progression, remission, and relapse of nephritis in murine lupus models using transcriptome analysis. METHODS Kidneys from (NZB × NZW)F1 (NZB/NZW) and NZM2410 mice were harvested at intervals during the disease course or after remission induction. Genome-wide expression profiles were obtained from microarray analysis of perfused kidneys. Real-time polymerase chain reaction (PCR) analysis for selected genes was used to validate the microarray data. Comparisons between groups using SAM, and unbiased analysis of the entire data set using singular value decomposition and self-organizing maps were performed. RESULTS Few changes in the renal molecular profile were detected in prenephritic kidneys, but a significant shift in gene expression, reflecting inflammatory cell infiltration and complement activation, occurred at proteinuria onset. Subsequent changes in gene expression predominantly affected mitochondrial dysfunction and metabolic stress pathways. Endothelial cell activation, tissue remodeling, and tubular damage were the major pathways associated with loss of renal function. Remission induction reversed most, but not all, of the inflammatory changes, and progression toward relapse was associated with recurrence of inflammation, mitochondrial dysfunction, and metabolic stress signatures. CONCLUSION Immune cell infiltration and activation is associated with proteinuria onset and is reversed by immunosuppressive therapy, but disease progression is associated with renal hypoxia and metabolic stress. Optimal therapy for lupus nephritis may therefore need to target both immune and nonimmune disease mechanisms. In addition, the overlap of a substantial subset of molecular markers with those expressed in the kidneys of lupus patients suggests potential new biomarkers and therapeutic targets.
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Affiliation(s)
- Ramalingam Bethunaickan
- Center for Autoimmunity and Musculoskeletal Diseases, Feinstein Institute for Medical Research, Manhasset, New York, NY 11030
| | - Celine C. Berthier
- Department of Internal Medicine, Nephrology, University of Michigan, Ann Arbor, MI 48109
| | - Weijia Zhang
- Department of Medicine, Mount Sinai Medical Center, New York, NY 10029
| | | | - Hong-Dong Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
| | - Matthias Kretzler
- Department of Internal Medicine, Nephrology, University of Michigan, Ann Arbor, MI 48109
| | - Anne Davidson
- Center for Autoimmunity and Musculoskeletal Diseases, Feinstein Institute for Medical Research, Manhasset, New York, NY 11030
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149
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Kahlenberg JM, Kaplan MJ. Reply. Arthritis Rheumatol 2014; 66:2311-2. [DOI: 10.1002/art.38677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Mariana J. Kaplan
- National Institute of Arthritis and Musculoskeletal and Skin Disorders, NIH; Bethesda MD
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150
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Martini S, Nair V, Keller BJ, Eichinger F, Hawkins JJ, Randolph A, Böger CA, Gadegbeku CA, Fox CS, Cohen CD, Kretzler M. Integrative biology identifies shared transcriptional networks in CKD. J Am Soc Nephrol 2014; 25:2559-72. [PMID: 24925724 DOI: 10.1681/asn.2013080906] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A previous meta-analysis of genome-wide association data by the Cohorts for Heart and Aging Research in Genomic Epidemiology and CKDGen consortia identified 16 loci associated with eGFR. To define how each of these single-nucleotide polymorphisms (SNPs) could affect renal function, we integrated GFR-associated loci with regulatory pathways, producing a molecular map of CKD. In kidney biopsy specimens from 157 European subjects representing nine different CKDs, renal transcript levels for 18 genes in proximity to the SNPs significantly correlated with GFR. These 18 genes were mapped into their biologic context by testing coregulated transcripts for enriched pathways. A network of 97 pathways linked by shared genes was constructed and characterized. Of these pathways, 56 pathways were reported previously to be associated with CKD; 41 pathways without prior association with CKD were ranked on the basis of the number of candidate genes connected to the respective pathways. All pathways aggregated into a network of two main clusters comprising inflammation- and metabolism-related pathways, with the NRF2-mediated oxidative stress response pathway serving as the hub between the two clusters. In all, 78 pathways and 95% of the connections among those pathways were verified in an independent North American biopsy cohort. Disease-specific analyses showed that most pathways are shared between sets of three diseases, with closest interconnection between lupus nephritis, IgA nephritis, and diabetic nephropathy. Taken together, the network integrates candidate genes from genome-wide association studies into their functional context, revealing interactions and defining established and novel biologic mechanisms of renal impairment in renal diseases.
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Affiliation(s)
- Sebastian Martini
- Departments of Internal Medicine, Nephrology, and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Viji Nair
- Departments of Internal Medicine, Nephrology, and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Benjamin J Keller
- Department of Computer Science, Eastern Michigan University, Ypsilanti, Michigan
| | - Felix Eichinger
- Departments of Internal Medicine, Nephrology, and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Jennifer J Hawkins
- Departments of Internal Medicine, Nephrology, and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Ann Randolph
- Departments of Internal Medicine, Nephrology, and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Carsten A Böger
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Crystal A Gadegbeku
- Department of Medicine, Section of Nephrology and Kidney Transplantation, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Caroline S Fox
- Division of Intramural Research and Laboratory for Population and Metabolic Health, National Heart, Lung, and Blood Institute, Framingham, Massachusetts; Department of Endocrinology, Brigham and Women's Hospital, Boston, Massachusetts; and
| | - Clemens D Cohen
- Institute of Physiology, University of Zürich, Zürich, Switzerland
| | - Matthias Kretzler
- Departments of Internal Medicine, Nephrology, and Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan;
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