1
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Li O, Hackney JA, Choy DF, Chang D, Nersesian R, Staton TL, Cai F, Toghi Eshghi S. A targeted amplicon next-generation sequencing assay for tryptase genotyping to support personalized therapy in mast cell-related disorders. PLoS One 2024; 19:e0291947. [PMID: 38335181 PMCID: PMC10857577 DOI: 10.1371/journal.pone.0291947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/09/2023] [Indexed: 02/12/2024] Open
Abstract
Tryptase, the most abundant mast cell granule protein, is elevated in severe asthma patients independent of type 2 inflammation status. Higher active β tryptase allele counts are associated with higher levels of peripheral tryptase and lower clinical benefit from anti-IgE therapies. Tryptase is a therapeutic target of interest in severe asthma and chronic spontaneous urticaria. Active and inactive allele counts may enable stratification to assess response to therapies in asthmatic patient subpopulations. Tryptase gene loci TPSAB1 and TPSB2 have high levels of sequence identity, which makes genotyping a challenging task. Here, we report a targeted next-generation sequencing (NGS) assay and downstream bioinformatics analysis for determining polymorphisms at tryptase TPSAB1 and TPSB2 loci. Machine learning modeling using multiple polymorphisms in the tryptase loci was used to improve the accuracy of genotyping calls. The assay was tested and qualified on DNA extracted from whole blood of healthy donors and asthma patients, achieving accuracy of 96%, 96% and 94% for estimation of inactive α and βΙΙΙFS tryptase alleles and α duplication on TPSAB1, respectively. The reported NGS assay is a cost-effective method that is more efficient than Sanger sequencing and provides coverage to evaluate known as well as unreported tryptase polymorphisms.
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Affiliation(s)
- Olga Li
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Jason A. Hackney
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - David F. Choy
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Diana Chang
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Rhea Nersesian
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Tracy L. Staton
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Fang Cai
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
| | - Shadi Toghi Eshghi
- Genentech Research and Early Development, Genentech, Inc, South San Francisco, CA, United States of America
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2
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Guidi R, Wedeles C, Xu D, Kolmus K, Headland SE, Teng G, Guillory J, Zeng YJ, Cheung TK, Chaudhuri S, Modrusan Z, Liang Y, Horswell S, Haley B, Rutz S, Rose C, Franke Y, Kirkpatrick DS, Hackney JA, Wilson MS. Argonaute3-SF3B3 complex controls pre-mRNA splicing to restrain type 2 immunity. Cell Rep 2023; 42:113515. [PMID: 38096048 DOI: 10.1016/j.celrep.2023.113515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/28/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Argonaute (AGO) proteins execute microRNA (miRNA)-mediated gene silencing. However, it is unclear whether all 4 mammalian AGO proteins (AGO1, AGO2, AGO3, and AGO4) are required for miRNA activity. We generate Ago1, Ago3, and Ago4-deficient mice (Ago134Δ) and find AGO1/3/4 to be redundant for miRNA biogenesis, homeostasis, or function, a role that is carried out by AGO2. Instead, AGO1/3/4 regulate the expansion of type 2 immunity via precursor mRNA splicing in CD4+ T helper (Th) lymphocytes. Gain- and loss-of-function experiments demonstrate that nuclear AGO3 interacts directly with SF3B3, a component of the U2 spliceosome complex, to aid global mRNA splicing, and in particular the isoforms of the gene Nisch, resulting in a dysregulated Nisch isoform ratio. This work uncouples AGO1, AGO3, and AGO4 from miRNA-mediated RNA interference, identifies an AGO3:SF3B3 complex in the nucleus, and reveals a mechanism by which AGO proteins regulate inflammatory diseases.
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Affiliation(s)
- Riccardo Guidi
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | | | - Daqi Xu
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Krzysztof Kolmus
- OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Sarah E Headland
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Grace Teng
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Joseph Guillory
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Yi Jimmy Zeng
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Tommy K Cheung
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Yuxin Liang
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Stuart Horswell
- Bioinformatic and Biostatistics, The Francis Crick Institute, London, UK
| | - Benjamin Haley
- Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Sascha Rutz
- Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Christopher Rose
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Yvonne Franke
- Protein Sciences, Genentech, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Mark S Wilson
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA.
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3
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Hackney JA, Shivram H, Vander Heiden J, Overall C, Orozco L, Gao X, Kim E, West N, Qamra A, Chang D, Chakrabarti A, Choy DF, Combes AJ, Courau T, Fragiadakis GK, Rao AA, Ray A, Tsui J, Hu K, Kuhn NF, Krummel MF, Erle DJ, Kangelaris K, Sarma A, Lyon Z, Calfee CS, Woodruff PG, Ghale R, Mick E, Byrne A, Zha BS, Langelier C, Hendrickson CM, van der Wijst MGP, Hartoularos GC, Grant T, Bueno R, Lee DS, Greenland JR, Sun Y, Perez R, Ogorodnikov A, Ward A, Ye CJ, Ramalingam T, McBride JM, Cai F, Teterina A, Bao M, Tsai L, Rosas IO, Regev A, Kapadia SB, Bauer RN, Rosenberger CM. A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling. iScience 2023; 26:107813. [PMID: 37810211 PMCID: PMC10551843 DOI: 10.1016/j.isci.2023.107813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/12/2023] [Accepted: 08/30/2023] [Indexed: 10/10/2023] Open
Abstract
Altered myeloid inflammation and lymphopenia are hallmarks of severe infections. We identified the upregulated EN-RAGE gene program in airway and blood myeloid cells from patients with acute lung injury from SARS-CoV-2 or other causes across 7 cohorts. This program was associated with greater clinical severity and predicted future mechanical ventilation and death. EN-RAGEhi myeloid cells express features consistent with suppressor cell functionality, including low HLA-DR and high PD-L1. Sustained EN-RAGE program expression in airway and blood myeloid cells correlated with clinical severity and increasing expression of T cell dysfunction markers. IL-6 upregulated many EN-RAGE program genes in monocytes in vitro. IL-6 signaling blockade by tocilizumab in a placebo-controlled clinical trial led to rapid normalization of EN-RAGE and T cell gene expression. This identifies IL-6 as a key driver of myeloid dysregulation associated with worse clinical outcomes in COVID-19 patients and provides insights into shared pathophysiological mechanisms in non-COVID-19 ARDS.
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Affiliation(s)
- Jason A Hackney
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Haridha Shivram
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Chris Overall
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Luz Orozco
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xia Gao
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eugene Kim
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nathan West
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Aditi Qamra
- Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada
| | - Diana Chang
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - David F Choy
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexis J Combes
- University of California San Francisco, San Francisco, CA, USA
| | - Tristan Courau
- University of California San Francisco, San Francisco, CA, USA
| | | | - Arjun Arkal Rao
- University of California San Francisco, San Francisco, CA, USA
| | - Arja Ray
- University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tsui
- University of California San Francisco, San Francisco, CA, USA
| | - Kenneth Hu
- University of California San Francisco, San Francisco, CA, USA
| | - Nicholas F Kuhn
- University of California San Francisco, San Francisco, CA, USA
| | | | - David J Erle
- University of California San Francisco, San Francisco, CA, USA
| | | | - Aartik Sarma
- University of California San Francisco, San Francisco, CA, USA
| | - Zoe Lyon
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Rajani Ghale
- University of California San Francisco, San Francisco, CA, USA
| | - Eran Mick
- University of California San Francisco, San Francisco, CA, USA
| | - Ashley Byrne
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Tianna Grant
- University of California San Francisco, San Francisco, CA, USA
| | - Raymund Bueno
- University of California San Francisco, San Francisco, CA, USA
| | - David S Lee
- University of California San Francisco, San Francisco, CA, USA
| | | | - Yang Sun
- University of California San Francisco, San Francisco, CA, USA
| | - Richard Perez
- University of California San Francisco, San Francisco, CA, USA
| | | | - Alyssa Ward
- University of California San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Fang Cai
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anastasia Teterina
- Hoffman-La Roche Limited, 7070 Mississauga Road, Mississauga, ON L5N 5M8, Canada
| | - Min Bao
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Larry Tsai
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivan O Rosas
- Baylor College of Medicine, 7200 Cambridge St, Houston, TX 77030, USA
| | - Aviv Regev
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Rebecca N Bauer
- Genentech, Inc, 1 DNA Way, South San Francisco, CA 94080, USA
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4
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Shivram H, Hackney JA, Rosenberger CM, Teterina A, Qamra A, Onabajo O, McBride J, Cai F, Bao M, Tsai L, Regev A, Rosas IO, Bauer RN. Transcriptomic and proteomic assessment of tocilizumab response in a randomized controlled trial of patients hospitalized with COVID-19. iScience 2023; 26:107597. [PMID: 37664617 PMCID: PMC10470387 DOI: 10.1016/j.isci.2023.107597] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/16/2023] [Accepted: 08/08/2023] [Indexed: 09/05/2023] Open
Abstract
High interleukin (IL)-6 levels are associated with greater COVID-19 severity. IL-6 receptor blockade by tocilizumab (anti-IL6R; Actemra) is used globally for the treatment of severe COVID-19, yet a molecular understanding of the therapeutic benefit remains unclear. We characterized the immune profile and identified cellular and molecular pathways modified by tocilizumab in peripheral blood samples from patients enrolled in the COVACTA study, a phase 3, randomized, double-blind, placebo-controlled trial of the efficacy and safety of tocilizumab in hospitalized patients with severe COVID-19. We identified markers of inflammation, lymphopenia, myeloid dysregulation, and organ injury that predict disease severity and clinical outcomes. Proteomic analysis confirmed a pharmacodynamic effect for tocilizumab and identified novel pharmacodynamic biomarkers. Transcriptomic analysis revealed that tocilizumab treatment leads to faster resolution of lymphopenia and myeloid dysregulation associated with severe COVID-19, indicating greater anti-inflammatory activity relative to placebo and potentially leading to faster recovery in patients hospitalized with COVID-19.
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Affiliation(s)
| | | | | | | | - Aditi Qamra
- Hoffmann-La Roche Ltd, Mississauga, ON L5N 5M8, Canada
| | | | | | - Fang Cai
- Genentech, South San Francisco, CA 94080, USA
| | - Min Bao
- Genentech, South San Francisco, CA 94080, USA
| | - Larry Tsai
- Genentech, South San Francisco, CA 94080, USA
| | - Aviv Regev
- Genentech, South San Francisco, CA 94080, USA
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5
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Xie MM, Dai B, Hackney JA, Sun T, Zhang J, Jackman JK, Jeet S, Irizarry-Caro RA, Fu Y, Liang Y, Bender H, Shamir ER, Keir ME, Bevers J, Nakamura G, Townsend MJ, Fox DA, Scherl A, Lee WP, Martin F, Godowski PJ, Pappu R, Yi T. An agonistic anti-signal regulatory protein α antibody for chronic inflammatory diseases. Cell Rep Med 2023; 4:101130. [PMID: 37490914 PMCID: PMC10439247 DOI: 10.1016/j.xcrm.2023.101130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/23/2023] [Accepted: 06/30/2023] [Indexed: 07/27/2023]
Abstract
Signal regulatory protein (SIRPα) is an immune inhibitory receptor expressed by myeloid cells to inhibit immune cell phagocytosis, migration, and activation. Despite the progress of SIRPα and CD47 antagonist antibodies to promote anti-cancer immunity, it is not yet known whether SIRPα receptor agonism could restrain excessive autoimmune tissue inflammation. Here, we report that neutrophil- and monocyte-associated genes including SIRPA are increased in inflamed tissue biopsies from patients with rheumatoid arthritis and inflammatory bowel diseases, and elevated SIRPA is associated with treatment-refractory ulcerative colitis. We next identify an agonistic anti-SIRPα antibody that exhibits potent anti-inflammatory effects in reducing neutrophil and monocyte chemotaxis and tissue infiltration. In preclinical models of arthritis and colitis, anti-SIRPα agonistic antibody ameliorates autoimmune joint inflammation and inflammatory colitis by reducing neutrophils and monocytes in tissues. Our work provides a proof of concept for SIRPα receptor agonism for suppressing excessive innate immune activation and chronic inflammatory disease treatment.
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Affiliation(s)
- Markus M Xie
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA
| | - Bingbing Dai
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA
| | - Jason A Hackney
- Department of OMNI Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - Tianhe Sun
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Janet K Jackman
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA
| | - Surinder Jeet
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Ricardo A Irizarry-Caro
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA; Department of Human Pathobiology and OMNI Reverse Translation, Genentech, Inc., South San Francisco, CA, USA
| | - Yongyao Fu
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, CA, USA
| | - Yuxin Liang
- Department of Microchemistry, Proteomics, and Lipidomics and Next Generation Sequencing, Genentech, Inc., South San Francisco, CA, USA
| | - Hannah Bender
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Eliah R Shamir
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Mary E Keir
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech, Inc., South San Francisco, CA, USA
| | - Jack Bevers
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA
| | - Michael J Townsend
- Department of Human Pathobiology and OMNI Reverse Translation, Genentech, Inc., South San Francisco, CA, USA
| | - David A Fox
- Division of Rheumatology, Clinical Autoimmunity Center of Excellence, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alexis Scherl
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA, USA
| | - Flavius Martin
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA
| | - Paul J Godowski
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA.
| | - Rajita Pappu
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA.
| | - Tangsheng Yi
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA, USA.
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6
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Jha D, Al-Taie Z, Krek A, Eshghi ST, Fantou A, Laurent T, Tankelevich M, Cao X, Meringer H, Livanos AE, Tokuyama M, Cossarini F, Bourreille A, Josien R, Hou R, Canales-Herrerias P, Ungaro RC, Kayal M, Marion J, Polydorides AD, Ko HM, D’souza D, Merand R, Kim-Schulze S, Hackney JA, Nguyen A, McBride JM, Yuan GC, Colombel JF, Martin JC, Argmann C, Suárez-Fariñas M, Petralia F, Mehandru S. Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis. bioRxiv 2023:2023.06.02.542863. [PMID: 37333091 PMCID: PMC10274630 DOI: 10.1101/2023.06.02.542863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with sharply rising global prevalence. Dysfunctional epithelial compartment (EC) dynamics are implicated in UC pathogenesis although EC-specific studies are sparse. Applying orthogonal high-dimensional EC profiling to a Primary Cohort (PC; n=222), we detail major epithelial and immune cell perturbations in active UC. Prominently, reduced frequencies of mature BEST4+OTOP2+ absorptive and BEST2+WFDC2+ secretory epithelial enterocytes were associated with the replacement of homeostatic, resident TRDC+KLRD1+HOPX+ γδ+ T cells with RORA+CCL20+S100A4+ TH17 cells and the influx of inflammatory myeloid cells. The EC transcriptome (exemplified by S100A8, HIF1A, TREM1, CXCR1) correlated with clinical, endoscopic, and histological severity of UC in an independent validation cohort (n=649). Furthermore, therapeutic relevance of the observed cellular and transcriptomic changes was investigated in 3 additional published UC cohorts (n=23, 48 and 204 respectively) to reveal that non-response to anti-Tumor Necrosis Factor (anti-TNF) therapy was associated with EC related myeloid cell perturbations. Altogether, these data provide high resolution mapping of the EC to facilitate therapeutic decision-making and personalization of therapy in patients with UC.
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Affiliation(s)
- Divya Jha
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Shadi Toghi Eshghi
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Aurelie Fantou
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Thomas Laurent
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Michael Tankelevich
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuan Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Hadar Meringer
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra E Livanos
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arnaud Bourreille
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Regis Josien
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Ruixue Hou
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Pablo Canales-Herrerias
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan C. Ungaro
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maia Kayal
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Marion
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Huaibin M. Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center-New York Presbyterian Hospital, New York, New York
| | - Darwin D’souza
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphael Merand
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason A. Hackney
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Allen Nguyen
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Jacqueline M. McBride
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Jean Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome C. Martin
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Carmen Argmann
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Saurabh Mehandru
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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7
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Orozco LD, Chen HH, Cox C, Katschke KJ, Rommel Arceo, Espiritu C, Caplazi P, Nghiem SS, Chen YJ, Modrusan Z, Dressen A, Goldstein LD, Clarke C, Bhangale T, Yaspan B, Jeanne M, Townsend MJ, van Lookeren Campagne M, Hackney JA. Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration. Cell Rep 2023; 42:112298. [PMID: 36952338 DOI: 10.1016/j.celrep.2023.112298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
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8
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Sambandam A, Storm E, Tauc H, Hackney JA, Garfield D, Caplazi P, Liu J, Zhang J, Zhang H, Duggan J, Jeet S, Gierke S, Chang P, Wu X, Newman R, Tam L, Alcantar T, Wang L, Roose-Girma M, Modrusan Z, Lee WP, Jasper H, de Sauvage F, Pappu R. Obligate role for Rock1 and Rock2 in adult stem cell viability and function. Heliyon 2023; 9:e14238. [PMID: 36950615 PMCID: PMC10025895 DOI: 10.1016/j.heliyon.2023.e14238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
The ability of stem cells to rapidly proliferate and differentiate is integral to the steady-state maintenance of tissues with high turnover such as the blood and intestine. Mutations that alter these processes can cause primary immunodeficiencies, malignancies and defects in barrier function. The Rho-kinases, Rock1 and Rock2, regulate cell shape and cytoskeletal rearrangement, activities essential to mitosis. Here, we use inducible gene targeting to ablate Rock1 and Rock2 in adult mice, and identify an obligate requirement for these enzymes in the preservation of the hematopoietic and gastrointestinal systems. Hematopoietic cell progenitors devoid of Rho-kinases display cell cycle arrest, blocking the differentiation to mature blood lineages. Similarly, these mice exhibit impaired epithelial cell renewal in the small intestine, which is ultimately fatal. Our data reveal a novel role for these kinases in the proliferation and viability of stem cells and their progenitors, which is vital to maintaining the steady-state integrity of these organ systems.
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Affiliation(s)
| | - Elaine Storm
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Helen Tauc
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA, USA
| | - Jason A. Hackney
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - David Garfield
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | - Patrick Caplazi
- Department of Research Pathology, Genentech Inc., South San Francisco, CA, USA
| | - John Liu
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Hua Zhang
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Jeff Duggan
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA, USA
| | - Surinder Jeet
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Sarah Gierke
- Department of Research Pathology, Genentech Inc., South San Francisco, CA, USA
| | - Patrick Chang
- Department of Research Pathology, Genentech Inc., South San Francisco, CA, USA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Robert Newman
- Department of Research Biology, Genentech Inc., South San Francisco, CA, USA
| | - Lucinda Tam
- Department of Research Biology, Genentech Inc., South San Francisco, CA, USA
| | - Tuija Alcantar
- Department of Research Biology, Genentech Inc., South San Francisco, CA, USA
| | - Lifen Wang
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Meron Roose-Girma
- Department of Research Biology, Genentech Inc., South San Francisco, CA, USA
| | - Zora Modrusan
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Wyne P. Lee
- Department of Translational Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Heinrich Jasper
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA, USA
| | - Frederic de Sauvage
- Department of Molecular Oncology, Genentech Inc., South San Francisco, CA, USA
| | - Rajita Pappu
- Department of Immunology Discovery, Genentech Inc., South San Francisco, CA, USA
- Corresponding author.
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9
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Chavarria-Smith J, Chiu CPC, Jackman JK, Yin J, Zhang J, Hackney JA, Lin WY, Tyagi T, Sun Y, Tao J, Dunlap D, Morton WD, Ghodge SV, Maun HR, Li H, Hernandez-Barry H, Loyet KM, Chen E, Liu J, Tam C, Yaspan BL, Cai H, Balazs M, Arron JR, Li J, Wittwer AJ, Pappu R, Austin CD, Lee WP, Lazarus RA, Sudhamsu J, Koerber JT, Yi T. Dual antibody inhibition of KLK5 and KLK7 for Netherton syndrome and atopic dermatitis. Sci Transl Med 2022; 14:eabp9159. [PMID: 36516271 DOI: 10.1126/scitranslmed.abp9159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The epidermis is a barrier that prevents water loss while keeping harmful substances from penetrating the host. The impermeable cornified layer of the stratum corneum is maintained by balancing continuous turnover driven by epidermal basal cell proliferation, suprabasal cell differentiation, and corneal shedding. The epidermal desquamation process is tightly regulated by balance of the activities of serine proteases of the Kallikrein-related peptidases (KLK) family and their cognate inhibitor lymphoepithelial Kazal type-related inhibitor (LEKTI), which is encoded by the serine peptidase inhibitor Kazal type 5 gene. Imbalance of proteolytic activity caused by a deficiency of LEKTI leads to excessive desquamation due to increased activities of KLK5, KLK7, and KLK14 and results in Netherton syndrome (NS), a debilitating condition with an unmet clinical need. Increased activity of KLKs may also be pathological in other dermatoses such as atopic dermatitis (AD). Here, we describe the discovery of inhibitory antibodies against murine KLK5 and KLK7 that could compensate for the deficiency of LEKTI in NS. These antibodies are protective in mouse models of NS and AD and, when combined, promote improved skin barrier integrity and reduced inflammation. To translate these findings, we engineered a humanized bispecific antibody capable of potent inhibition of human KLK5 and KLK7. A crystal structure of KLK5 bound to the inhibitory Fab revealed that the antibody binds distal to its active site and uses a relatively unappreciated allosteric inhibition mechanism. Treatment with the bispecific anti-KLK5/7 antibody represents a promising therapy for clinical development in NS and other inflammatory dermatoses.
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Affiliation(s)
- Joseph Chavarria-Smith
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cecilia P C Chiu
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janet K Jackman
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jianping Yin
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- Department of Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wei-Yu Lin
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tulika Tyagi
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yonglian Sun
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janet Tao
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Debra Dunlap
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - William D Morton
- Confluence Discovery Technologies Inc., 4320 Duncan Ave, Suite 400, St. Louis, MO 63108, USA
| | - Swapnil V Ghodge
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Henry R Maun
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hong Li
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hilda Hernandez-Barry
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly M Loyet
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Emily Chen
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Liu
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christine Tam
- Department of Biomolecular Resources, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hao Cai
- Department of Preclinical and Translational Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mercedesz Balazs
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jing Li
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Arthur J Wittwer
- Confluence Discovery Technologies Inc., 4320 Duncan Ave, Suite 400, St. Louis, MO 63108, USA
| | - Rajita Pappu
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cary D Austin
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Robert A Lazarus
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - James T Koerber
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tangsheng Yi
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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10
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Keir ME, Fuh F, Ichikawa R, Acres M, Hackney JA, Hulme G, Carey CD, Palmer J, Jones CJ, Long AK, Jiang J, Klabunde S, Mansfield JC, Looney CM, Faubion WA, Filby A, Kirby JA, McBride J, Lamb CA. Regulation and Role of αE Integrin and Gut Homing Integrins in Migration and Retention of Intestinal Lymphocytes during Inflammatory Bowel Disease. J Immunol 2021; 207:2245-2254. [PMID: 34561227 PMCID: PMC8525869 DOI: 10.4049/jimmunol.2100220] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023]
Abstract
Adhesion molecules are upregulated in inflamed intestinal mucosa in IBD patients. Baseline β7 expression does not impact αE induction or gene expression in T cells. Phospho-SMAD3 is increased in inflamed mucosa in IBD.
Targeting interactions between α4β7 integrin and endothelial adhesion molecule MAdCAM-1 to inhibit lymphocyte migration to the gastrointestinal tract is an effective therapy in inflammatory bowel disease (IBD). Following lymphocyte entry into the mucosa, a subset of these cells expresses αEβ7 integrin, which is expressed on proinflammatory lymphocytes, to increase cell retention. The factors governing lymphocyte migration into the intestinal mucosa and αE integrin expression in healthy subjects and IBD patients remain incompletely understood. We evaluated changes in factors involved in lymphocyte migration and differentiation within tissues. Both ileal and colonic tissue from active IBD patients showed upregulation of ICAM-1, VCAM-1, and MAdCAM-1 at the gene and protein levels compared with healthy subjects and/or inactive IBD patients. β1 and β7 integrin expression on circulating lymphocytes was similar across groups. TGF-β1 treatment induced expression of αE on both β7+ and β7− T cells, suggesting that cells entering the mucosa independently of MAdCAM-1/α4β7 can become αEβ7+. ITGAE gene polymorphisms did not alter protein induction following TGF-β1 stimulation. Increased phospho-SMAD3, which is directly downstream of TGF-β, and increased TGF-β–responsive gene expression were observed in the colonic mucosa of IBD patients. Finally, in vitro stimulation experiments showed that baseline β7 expression had little effect on cytokine, chemokine, transcription factor, and effector molecule gene expression in αE+ and αE− T cells. These findings suggest cell migration to the gut mucosa may be altered in IBD and α4β7−, and α4β7+ T cells may upregulate αEβ7 in response to TGF-β once within the gut mucosa.
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Affiliation(s)
| | | | | | - Meghan Acres
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Histopathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | - Gillian Hulme
- Flow Cytometry Core Facility and Innovation, Methodology and Application Research Theme, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher D Carey
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Haematology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Jeremy Palmer
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Claire J Jones
- Department of Histopathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Anna K Long
- Department of Histopathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | | | | | - John C Mansfield
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom; and
| | | | | | - Andrew Filby
- Flow Cytometry Core Facility and Innovation, Methodology and Application Research Theme, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John A Kirby
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Christopher A Lamb
- Translational and Clinical Research Institute, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom;
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11
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Dai B, Hackney JA, Ichikawa R, Nguyen A, Elstrott J, Orozco LD, Sun KH, Modrusan Z, Gogineni A, Scherl A, Gubatan J, Habtezion A, Deswal M, Somsouk M, Faubion WA, Chai A, Sharafali Z, Hassanali A, Oh YS, Tole S, McBride J, Keir ME, Yi T. Dual targeting of lymphocyte homing and retention through α4β7 and αEβ7 inhibition in inflammatory bowel disease. Cell Rep Med 2021; 2:100381. [PMID: 34467254 PMCID: PMC8385326 DOI: 10.1016/j.xcrm.2021.100381] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 03/09/2021] [Accepted: 07/22/2021] [Indexed: 01/07/2023]
Abstract
Anti-integrins are therapeutically effective for inflammatory bowel disease, yet the relative contribution of α4β7 and αEβ7 to gut lymphocyte trafficking is not fully elucidated. Here, we evaluate the effect of α4β7 and αEβ7 blockade using a combination of murine models of gut trafficking and longitudinal gene expression analysis in etrolizumab-treated patients with Crohn's disease (CD). Dual blockade of α4β7 and αEβ7 reduces CD8+ T cell accumulation in the gut to a greater extent than blockade of either integrin alone. Anti-αEβ7 reduces epithelial:T cell interactions and promotes egress of activated T cells from the mucosa into lymphatics. Inflammatory gene expression is greater in human intestinal αEβ7+ T cells. Etrolizumab-treated patients with CD display a treatment-specific reduction in inflammatory and cytotoxic intraepithelial lymphocytes (IEL) genes. Concurrent blockade of α4β7 and αEβ7 promotes reduction of cytotoxic IELs and inflammatory T cells in the gut mucosa through a stepwise inhibition of intestinal tissue entry and retention.
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Affiliation(s)
- Bingbing Dai
- Departments of Immunology Discovery, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A. Hackney
- OMNI Biomarker Development, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ryan Ichikawa
- Biomarker Discovery OMNI, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Allen Nguyen
- OMNI Biomarker Development, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Justin Elstrott
- Biomedical Imaging, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Luz D. Orozco
- Bioinformatics, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kai-Hui Sun
- Molecular Biology, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Molecular Biology, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alvin Gogineni
- Biomedical Imaging, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexis Scherl
- Pathology, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Gubatan
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aida Habtezion
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Monika Deswal
- University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Ma Somsouk
- University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - William A. Faubion
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Akiko Chai
- Product Development, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zaineb Sharafali
- Product Development, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Azra Hassanali
- Product Development, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Young S. Oh
- Product Development, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Swati Tole
- Product Development, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jacqueline McBride
- OMNI Biomarker Development, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mary E. Keir
- Biomarker Discovery OMNI, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tangsheng Yi
- Departments of Immunology Discovery, Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA
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12
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Isenberg D, Furie R, Jones NS, Guibord P, Galanter J, Lee C, McGregor A, Toth B, Rae J, Hwang O, Desai R, Lokku A, Ramamoorthi N, Hackney JA, Miranda P, de Souza VA, Jaller-Raad JJ, Maura Fernandes A, Garcia Salinas R, Chinn LW, Townsend MJ, Morimoto AM, Tuckwell K. Efficacy, Safety, and Pharmacodynamic Effects of the Bruton's Tyrosine Kinase Inhibitor Fenebrutinib (GDC-0853) in Systemic Lupus Erythematosus: Results of a Phase II, Randomized, Double-Blind, Placebo-Controlled Trial. Arthritis Rheumatol 2021; 73:1835-1846. [PMID: 34042314 DOI: 10.1002/art.41811] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/11/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Fenebrutinib (GDC-0853) is a noncovalent, oral, and highly selective inhibitor of Bruton's tyrosine kinase (BTK). The efficacy, safety, and pharmacodynamics of fenebrutinib in systemic lupus erythematosus (SLE) were assessed in this phase II, multicenter, randomized, placebo-controlled study. METHODS Patients who had moderately to severely active SLE while receiving background standard therapy were randomized to receive placebo, fenebrutinib 150 mg once daily, or fenebrutinib 200 mg twice daily. Glucocorticoid taper was recommended from weeks 0 to 12 and from weeks 24 to 36. The primary end point was the SLE Responder Index 4 (SRI-4) response at week 48. RESULTS Patients (n = 260) were enrolled from 44 sites in 12 countries, with the majority from Latin America, the US, and Western Europe. The SRI-4 response rates at week 48 were 51% for fenebrutinib 150 mg once daily (P = 0.37 versus placebo), 52% for fenebrutinib 200 mg twice daily (P = 0.34 versus placebo), and 44% for placebo. British Isles Lupus Assessment Group-based Combined Lupus Assessment response rates at week 48 were 53% for fenebrutinib 150 mg once daily (P = 0.086 versus placebo), 42% for fenebrutinib 200 mg twice daily (P = 0.879 versus placebo), and 41% for placebo. Safety results were similar across all arms, although serious adverse events were more frequent with fenebrutinib 200 mg twice daily. By week 48, patients treated with fenebrutinib had reduced levels of a BTK-dependent plasmablast RNA signature, anti-double-stranded DNA autoantibodies, total IgG, and IgM, as well as increased complement C4 levels, all relative to placebo. CONCLUSION While fenebrutinib had an acceptable safety profile, the primary end point, SRI-4 response, was not met despite evidence of strong pathway inhibition.
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Affiliation(s)
| | | | | | | | | | - Chin Lee
- Genentech, Inc., South San Francisco, California
| | | | - Balazs Toth
- Genentech, Inc., South San Francisco, California
| | - Julie Rae
- Genentech, Inc., South San Francisco, California
| | - Olivia Hwang
- Genentech, Inc., South San Francisco, California
| | - Rupal Desai
- Genentech, Inc., South San Francisco, California
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13
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Tauc HM, Rodriguez-Fernandez IA, Hackney JA, Pawlak M, Ronnen Oron T, Korzelius J, Moussa HF, Chaudhuri S, Modrusan Z, Edgar BA, Jasper H. Age-related changes in polycomb gene regulation disrupt lineage fidelity in intestinal stem cells. eLife 2021; 10:62250. [PMID: 33724181 PMCID: PMC7984841 DOI: 10.7554/elife.62250] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 03/15/2021] [Indexed: 01/01/2023] Open
Abstract
Tissue homeostasis requires long-term lineage fidelity of somatic stem cells. Whether and how age-related changes in somatic stem cells impact the faithful execution of lineage decisions remains largely unknown. Here, we address this question using genome-wide chromatin accessibility and transcriptome analysis as well as single-cell RNA-seq to explore stem-cell-intrinsic changes in the aging Drosophila intestine. These studies indicate that in stem cells of old flies, promoters of Polycomb (Pc) target genes become differentially accessible, resulting in the increased expression of enteroendocrine (EE) cell specification genes. Consistently, we find age-related changes in the composition of the EE progenitor cell population in aging intestines, as well as a significant increase in the proportion of EE-specified intestinal stem cells (ISCs) and progenitors in aging flies. We further confirm that Pc-mediated chromatin regulation is a critical determinant of EE cell specification in the Drosophila intestine. Pc is required to maintain expression of stem cell genes while ensuring repression of differentiation and specification genes. Our results identify Pc group proteins as central regulators of lineage identity in the intestinal epithelium and highlight the impact of age-related decline in chromatin regulation on tissue homeostasis.
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Affiliation(s)
- Helen M Tauc
- Immunology Discovery, Genentech, South San Francisco, United States
| | | | - Jason A Hackney
- OMNI Bioinformatics, Genentech, South San Francisco, United States
| | - Michal Pawlak
- Institute of Hematology and Blood Transfusion, Warsaw, Poland
| | | | - Jerome Korzelius
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Hagar F Moussa
- Department of Biomedical Engineering and Biological Design Center,Boston University, Boston, United States
| | - Subhra Chaudhuri
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, United States
| | - Zora Modrusan
- Immunology Discovery, Genentech, South San Francisco, United States.,Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, United States
| | - Bruce A Edgar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, United States
| | - Heinrich Jasper
- Immunology Discovery, Genentech, South San Francisco, United States
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14
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AhYoung AP, Eckard SC, Gogineni A, Xi H, Lin SJ, Gerhardy S, Cox C, Phung QT, Hackney JA, Katakam AK, Reichelt M, Caplazi P, Manzanillo P, Zhang J, Roose-Girma M, Tam LW, Newman RJ, Murthy A, Weimer RM, Lill JR, Lee WP, Grimbaldeston M, Kirchhofer D, van Lookeren Campagne M. Neutrophil serine protease 4 is required for mast cell-dependent vascular leakage. Commun Biol 2020; 3:687. [PMID: 33214666 PMCID: PMC7677402 DOI: 10.1038/s42003-020-01407-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/17/2020] [Indexed: 02/06/2023] Open
Abstract
Vascular leakage, or edema, is a serious complication of acute allergic reactions. Vascular leakage is triggered by the release of histamine and serotonin from granules within tissue-resident mast cells. Here, we show that expression of Neutrophil Serine Protease 4 (NSP4) during the early stages of mast cell development regulates mast cell-mediated vascular leakage. In myeloid precursors, the granulocyte-macrophage progenitors (GMPs), loss of NSP4 results in the decrease of cellular levels of histamine, serotonin and heparin/heparan sulfate. Mast cells that are derived from NSP4-deficient GMPs have abnormal secretory granule morphology and a sustained reduction in histamine and serotonin levels. Consequently, in passive cutaneous anaphylaxis and acute arthritis models, mast cell-mediated vascular leakage in the skin and joints is substantially reduced in NSP4-deficient mice. Our findings reveal that NSP4 is required for the proper storage of vasoactive amines in mast cell granules, which impacts mast cell-dependent vascular leakage in mouse models of immune complex-mediated diseases.
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Affiliation(s)
- Andrew P AhYoung
- Department of Early Discovery Biochemistry, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Sterling C Eckard
- Department of Immunology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Alvin Gogineni
- Department of Biomedical Imaging, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Hongkang Xi
- Department of Immunology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - S Jack Lin
- Department of Early Discovery Biochemistry, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Stefan Gerhardy
- Department of Early Discovery Biochemistry, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Christian Cox
- Department of Immunology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Qui T Phung
- Department of Microchemistry, Proteomics, Lipidomics, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jason A Hackney
- Department of Bioinformatics, 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Mike Reichelt
- Department of Pathology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Patrick Caplazi
- Department of Pathology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Paolo Manzanillo
- Department of Immunology, 1 DNA Way, South San Francisco, CA, 94080, USA
- Department of Inflammation and Oncology, Amgen Research, Amgen, 1120 Veterans Boulevard, South San Francisco, CA, 94080, USA
| | - Juan Zhang
- Department of Translational Immunology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Lucinda W Tam
- Department of Molecular Biology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Robert J Newman
- Department of Molecular Biology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Aditya Murthy
- Department of Cancer Immunology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Robby M Weimer
- Department of Biomedical Imaging, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jennie R Lill
- Department of Microchemistry, Proteomics, Lipidomics, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Michele Grimbaldeston
- OMNI-Biomarker Development, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Menno van Lookeren Campagne
- Department of Immunology, 1 DNA Way, South San Francisco, CA, 94080, USA.
- Department of Inflammation and Oncology, Amgen Research, Amgen, 1120 Veterans Boulevard, South San Francisco, CA, 94080, USA.
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15
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Lewis MJ, Barnes MR, Blighe K, Goldmann K, Rana S, Hackney JA, Ramamoorthi N, John CR, Watson DS, Kummerfeld SK, Hands R, Riahi S, Rocher-Ros V, Rivellese F, Humby F, Kelly S, Bombardieri M, Ng N, DiCicco M, van der Heijde D, Landewé R, van der Helm-van Mil A, Cauli A, McInnes IB, Buckley CD, Choy E, Taylor PC, Townsend MJ, Pitzalis C. Molecular Portraits of Early Rheumatoid Arthritis Identify Clinical and Treatment Response Phenotypes. Cell Rep 2020; 28:2455-2470.e5. [PMID: 31461658 PMCID: PMC6718830 DOI: 10.1016/j.celrep.2019.07.091] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 05/22/2019] [Accepted: 07/24/2019] [Indexed: 12/31/2022] Open
Abstract
There is a current imperative to unravel the hierarchy of molecular pathways that drive the transition of early to established disease in rheumatoid arthritis (RA). Herein, we report a comprehensive RNA sequencing analysis of the molecular pathways that drive early RA progression in the disease tissue (synovium), comparing matched peripheral blood RNA-seq in a large cohort of early treatment-naive patients, namely, the Pathobiology of Early Arthritis Cohort (PEAC). We developed a data exploration website (https://peac.hpc.qmul.ac.uk/) to dissect gene signatures across synovial and blood compartments, integrated with deep phenotypic profiling. We identified transcriptional subgroups in synovium linked to three distinct pathotypes: fibroblastic pauci-immune pathotype, macrophage-rich diffuse-myeloid pathotype, and a lympho-myeloid pathotype characterized by infiltration of lymphocytes and myeloid cells. This is suggestive of divergent pathogenic pathways or activation disease states. Pro-myeloid inflammatory synovial gene signatures correlated with clinical response to initial drug therapy, whereas plasma cell genes identified a poor prognosis subgroup with progressive structural damage. Deep phenotyping and RNA-seq of early rheumatoid arthritis individuals pre-treatment Synovial plasma cell gene expression predicts future progressive joint damage on X-ray Blood interferon gene signature associates with synovial B and plasma cell infiltration Interactive website enables RNA-seq and clinical data to be fully explored
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Affiliation(s)
- Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael R Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Alan Turing Institute, British Library, London NW1 2DB, UK
| | - Kevin Blighe
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Katriona Goldmann
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sharmila Rana
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jason A Hackney
- Bioinformatics and Computational Biology, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nandhini Ramamoorthi
- Biomarker Discovery OMNI, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christopher R John
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - David S Watson
- Centre for Translational Bioinformatics, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK; Alan Turing Institute, British Library, London NW1 2DB, UK; Oxford Internet Institute, University of Oxford, Oxford OX1 3JS, UK
| | - Sarah K Kummerfeld
- Bioinformatics and Computational Biology, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rebecca Hands
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sudeh Riahi
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Vidalba Rocher-Ros
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Felice Rivellese
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Frances Humby
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Stephen Kelly
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michele Bombardieri
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Nora Ng
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Maria DiCicco
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Robert Landewé
- Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, the Netherlands
| | | | - Alberto Cauli
- Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy
| | - Iain B McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK
| | - Christopher D Buckley
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK; Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences and the Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Ernest Choy
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Peter C Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences and the Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Michael J Townsend
- Biomarker Discovery OMNI, Genentech Research & Early Development, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
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16
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Maun HR, Jackman JK, Choy DF, Loyet KM, Staton TL, Jia G, Dressen A, Hackney JA, Bremer M, Walters BT, Vij R, Chen X, Trivedi NN, Morando A, Lipari MT, Franke Y, Wu X, Zhang J, Liu J, Wu P, Chang D, Orozco LD, Christensen E, Wong M, Corpuz R, Hang JQ, Lutman J, Sukumaran S, Wu Y, Ubhayakar S, Liang X, Schwartz LB, Babina M, Woodruff PG, Fahy JV, Ahuja R, Caughey GH, Kusi A, Dennis MS, Eigenbrot C, Kirchhofer D, Austin CD, Wu LC, Koerber JT, Lee WP, Yaspan BL, Alatsis KR, Arron JR, Lazarus RA, Yi T. An Allosteric Anti-tryptase Antibody for the Treatment of Mast Cell-Mediated Severe Asthma. Cell 2020; 179:417-431.e19. [PMID: 31585081 DOI: 10.1016/j.cell.2019.09.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 07/09/2019] [Accepted: 09/05/2019] [Indexed: 12/18/2022]
Abstract
Severe asthma patients with low type 2 inflammation derive less clinical benefit from therapies targeting type 2 cytokines and represent an unmet need. We show that mast cell tryptase is elevated in severe asthma patients independent of type 2 biomarker status. Active β-tryptase allele count correlates with blood tryptase levels, and asthma patients carrying more active alleles benefit less from anti-IgE treatment. We generated a noncompetitive inhibitory antibody against human β-tryptase, which dissociates active tetramers into inactive monomers. A 2.15 Å crystal structure of a β-tryptase/antibody complex coupled with biochemical studies reveal the molecular basis for allosteric destabilization of small and large interfaces required for tetramerization. This anti-tryptase antibody potently blocks tryptase enzymatic activity in a humanized mouse model, reducing IgE-mediated systemic anaphylaxis, and inhibits airway tryptase in Ascaris-sensitized cynomolgus monkeys with favorable pharmacokinetics. These data provide a foundation for developing anti-tryptase as a clinical therapy for severe asthma.
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Affiliation(s)
- Henry R Maun
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janet K Jackman
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - David F Choy
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly M Loyet
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tracy L Staton
- Department of OMNI Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Guiquan Jia
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Amy Dressen
- Department of Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Meire Bremer
- Department of OMNI Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin T Walters
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rajesh Vij
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiaocheng Chen
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Neil N Trivedi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Ashley Morando
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Michael T Lipari
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yvonne Franke
- Depratment of Biomolecular Resources, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Liu
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ping Wu
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Diana Chang
- Department of Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Luz D Orozco
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Erin Christensen
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Manda Wong
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Racquel Corpuz
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Julie Q Hang
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jeff Lutman
- Department of Preclinical and Translational Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Siddharth Sukumaran
- Department of Preclinical and Translational Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yan Wu
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Savita Ubhayakar
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiaorong Liang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lawrence B Schwartz
- Department of Internal Medicine, Division of Rheumatology, Allergy and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Magda Babina
- Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Prescott G Woodruff
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John V Fahy
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rahul Ahuja
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - George H Caughey
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Aija Kusi
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mark S Dennis
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Charles Eigenbrot
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cary D Austin
- Department of Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lawren C Wu
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - James T Koerber
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kathila R Alatsis
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Robert A Lazarus
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Tangsheng Yi
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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17
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Corzo CA, Varfolomeev E, Setiadi AF, Francis R, Klabunde S, Senger K, Sujatha-Bhaskar S, Drobnick J, Do S, Suto E, Huang Z, Eastham-Anderson J, Katewa A, Pang J, Domeyer M, Dela Cruz C, Paler-Martinez A, Lau VWC, Hadadianpour A, Ramirez-Carrozi V, Sun Y, Bao K, Xu D, Hunley E, Brightbill HD, Warming S, Roose-Girma M, Wong A, Tam L, Emson CL, Crawford JJ, Young WB, Pappu R, McKenzie BS, Asghari V, Vucic D, Hackney JA, Austin CD, Lee WP, Lekkerkerker A, Ghilardi N, Bryan MC, Kiefer JR, Townsend MJ, Zarrin AA. The kinase IRAK4 promotes endosomal TLR and immune complex signaling in B cells and plasmacytoid dendritic cells. Sci Signal 2020; 13:13/634/eaaz1053. [PMID: 32487715 DOI: 10.1126/scisignal.aaz1053] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The dysregulation of multiple signaling pathways, including those through endosomal Toll-like receptors (TLRs), Fc gamma receptors (FcγR), and antigen receptors in B cells (BCR), promote an autoinflammatory loop in systemic lupus erythematosus (SLE). Here, we used selective small-molecule inhibitors to assess the regulatory roles of interleukin-1 receptor (IL-1R)-associated kinase 4 (IRAK4) and Bruton's tyrosine kinase (BTK) in these pathways. The inhibition of IRAK4 repressed SLE immune complex- and TLR7-mediated activation of human plasmacytoid dendritic cells (pDCs). Correspondingly, the expression of interferon (IFN)-responsive genes (IRGs) in cells and in mice was positively regulated by the kinase activity of IRAK4. Both IRAK4 and BTK inhibition reduced the TLR7-mediated differentiation of human memory B cells into plasmablasts. TLR7-dependent inflammatory responses were differentially regulated by IRAK4 and BTK by cell type: In pDCs, IRAK4 positively regulated NF-κB and MAPK signaling, whereas in B cells, NF-κB and MAPK pathways were regulated by both BTK and IRAK4. In the pristane-induced lupus mouse model, inhibition of IRAK4 reduced the expression of IRGs during disease onset. Mice engineered to express kinase-deficient IRAK4 were protected from both chemical (pristane-induced) and genetic (NZB/W_F1 hybrid) models of lupus development. Our findings suggest that kinase inhibitors of IRAK4 might be a therapeutic in patients with SLE.
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Affiliation(s)
- Cesar A Corzo
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | | | - Ross Francis
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sha Klabunde
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kate Senger
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Joy Drobnick
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steven Do
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eric Suto
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zhiyu Huang
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Arna Katewa
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jodie Pang
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Melanie Domeyer
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | | | - Vivian W C Lau
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | | | - Yonglian Sun
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Katherine Bao
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Daqi Xu
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Emily Hunley
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Soren Warming
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Alfred Wong
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lucinda Tam
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Claire L Emson
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - James J Crawford
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wendy B Young
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rajita Pappu
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brent S McKenzie
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vida Asghari
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Domagoj Vucic
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cary D Austin
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Nico Ghilardi
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Marian C Bryan
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - James R Kiefer
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Ali A Zarrin
- Research, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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18
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Cohen S, Tuckwell K, Katsumoto TR, Zhao R, Galanter J, Lee C, Rae J, Toth B, Ramamoorthi N, Hackney JA, Berman A, Damjanov N, Fedkov D, Jeka S, Chinn LW, Townsend MJ, Morimoto AM, Genovese MC. Fenebrutinib versus Placebo or Adalimumab in Rheumatoid Arthritis: A Randomized, Double-Blind, Phase II Trial (ANDES Study). Arthritis Rheumatol 2020; 72:1435-1446. [PMID: 32270926 PMCID: PMC7496340 DOI: 10.1002/art.41275] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/26/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To evaluate fenebrutinib, an oral and highly selective non-covalent inhibitor of Bruton's tyrosine kinase (BTK), in patients with active rheumatoid arthritis (RA). METHODS Patients with RA and inadequate response to methotrexate (cohort 1, n=480) were randomized to fenebrutinib (50 mg once daily, 150 mg once daily, 200 mg twice daily), 40 mg adalimumab every other week, or placebo. Patients with RA and inadequate response to tumor necrosis factor inhibitors (cohort 2, n=98) received fenebrutinib (200 mg twice daily) or placebo. Both cohorts continued methotrexate therapy. RESULTS In cohort 1, American College of Rheumatology scores (ACR50) at week 12 were similar for fenebrutinib 50 mg once daily and placebo, and higher for fenebrutinib 150 mg once daily (28%) and 200 mg twice daily (35%) than placebo (15%) (p=0.017; p=0.0003). Fenebrutinib 200 mg twice daily and adalimumab (36%) were comparable (p=0.81). In cohort 2, more patients achieved ACR50 with fenebrutinib 200 mg twice daily (25%) than placebo (12%) (p=0.072). The most common adverse events for fenebrutinib included nausea, headache, anemia, and upper respiratory tract infections. Fenebrutinib had significant effects on myeloid and B cell biomarkers (CCL4 and rheumatoid factor). Fenebrutinib and adalimumab caused overlapping as well as distinct changes in B cell and myeloid biomarkers. CONCLUSION Fenebrutinib demonstrated efficacy comparable to adalimumab in patients with an inadequate response to methotrexate, and safety consistent with existing immunomodulatory therapies for RA. These data support targeting both B and myeloid cells via this novel mechanism for potential efficacy in the treatment of RA.
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Affiliation(s)
| | | | | | - Rui Zhao
- Genentech, Inc.South San FranciscoCalifornia
| | | | - Chin Lee
- Genentech, Inc.South San FranciscoCalifornia
| | - Julie Rae
- Genentech, Inc.South San FranciscoCalifornia
| | - Balazs Toth
- Genentech, Inc.South San FranciscoCalifornia
| | | | | | | | | | | | - Slawomir Jeka
- Collegium Medicum Jan Biziel University Hospital no 2BydgoszczPoland
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19
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Orozco LD, Chen HH, Cox C, Katschke KJ, Arceo R, Espiritu C, Caplazi P, Nghiem SS, Chen YJ, Modrusan Z, Dressen A, Goldstein LD, Clarke C, Bhangale T, Yaspan B, Jeanne M, Townsend MJ, van Lookeren Campagne M, Hackney JA. Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration. Cell Rep 2020; 30:1246-1259.e6. [PMID: 31995762 DOI: 10.1016/j.celrep.2019.12.082] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/04/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of vision loss. To better understand disease pathogenesis and identify causal genes in GWAS loci for AMD risk, we present a comprehensive database of human retina and retinal pigment epithelium (RPE). Our database comprises macular and non-macular RNA sequencing (RNA-seq) profiles from 129 donors, a genome-wide expression quantitative trait loci (eQTL) dataset that includes macula-specific retina and RPE/choroid, and single-nucleus RNA-seq (NucSeq) from human retina and RPE with subtype resolution from more than 100,000 cells. Using NucSeq, we find enriched expression of AMD candidate genes in RPE cells. We identify 15 putative causal genes for AMD on the basis of co-localization of genetic association signals for AMD risk and eye eQTL, including the genes TSPAN10 and TRPM1. These results demonstrate the value of our human eye database for elucidating genetic pathways and potential therapeutic targets for ocular diseases.
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Affiliation(s)
- Luz D Orozco
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Hsu-Hsin Chen
- Department of Biomarker Discovery OMNI, Genentech, South San Francisco, CA 94080, USA
| | - Christian Cox
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Kenneth J Katschke
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Rommel Arceo
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Carmina Espiritu
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Patrick Caplazi
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | | | - Ying-Jiun Chen
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Amy Dressen
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Leonard D Goldstein
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA; Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Christine Clarke
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Brian Yaspan
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Marion Jeanne
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Michael J Townsend
- Department of Biomarker Discovery OMNI, Genentech, South San Francisco, CA 94080, USA.
| | | | - Jason A Hackney
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA.
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20
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Maun HR, Jackman JK, Choy DF, Loyet KM, Staton TL, Jia G, Dressen A, Hackney JA, Bremer M, Walters BT, Vij R, Chen X, Trivedi NN, Morando A, Lipari MT, Franke Y, Wu X, Zhang J, Liu J, Wu P, Chang D, Orozco LD, Christensen E, Wong M, Corpuz R, Hang JQ, Lutman J, Sukumaran S, Wu Y, Ubhayakar S, Liang X, Schwartz LB, Babina M, Woodruff PG, Fahy JV, Ahuja R, Caughey GH, Kusi A, Dennis MS, Eigenbrot C, Kirchhofer D, Austin CD, Wu LC, Koerber JT, Lee WP, Yaspan BL, Alatsis KR, Arron JR, Lazarus RA, Yi T. An Allosteric Anti-tryptase Antibody for the Treatment of Mast Cell-Mediated Severe Asthma. Cell 2020; 180:406. [PMID: 31978350 DOI: 10.1016/j.cell.2020.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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21
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Lliso-Ribera G, Humby F, Lewis M, Nerviani A, Mauro D, Rivellese F, Kelly S, Hands R, Bene F, Ramamoorthi N, Hackney JA, Cauli A, Choy EH, Filer A, Taylor PC, McInnes I, Townsend MJ, Pitzalis C. Synovial tissue signatures enhance clinical classification and prognostic/treatment response algorithms in early inflammatory arthritis and predict requirement for subsequent biological therapy: results from the pathobiology of early arthritis cohort (PEAC). Ann Rheum Dis 2019; 78. [PMID: 31582377 PMCID: PMC6900253 DOI: 10.1136/annrheumdis-2019-215751+10.1136/annrheumdis-2019-215751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
OBJECTIVE To establish whether synovial pathobiology improves current clinical classification and prognostic algorithms in early inflammatory arthritis and identify predictors of subsequent biological therapy requirement. METHODS 200 treatment-naïve patients with early arthritis were classified as fulfilling RA1987 American College of Rheumatology (ACR) criteria (RA1987) or as undifferentiated arthritis (UA) and patients with UA further classified into those fulfilling RA2010 ACR/European League Against Rheumatism (EULAR) criteria. Treatment requirements at 12 months (Conventional Synthetic Disease Modifying Antirheumatic Drugs (csDMARDs) vs biologics vs no-csDMARDs treatment) were determined. Synovial tissue was retrieved by minimally invasive, ultrasound-guided biopsy and underwent processing for immunohistochemical (IHC) and molecular characterisation. Samples were analysed for macrophage, plasma-cell and B-cells and T-cells markers, pathotype classification (lympho-myeloid, diffuse-myeloid or pauci-immune) by IHC and gene expression profiling by Nanostring. RESULTS 128/200 patients were classified as RA1987, 25 as RA2010 and 47 as UA. Patients classified as RA1987 criteria had significantly higher levels of disease activity, histological synovitis, degree of immune cell infiltration and differential upregulation of genes involved in B and T cell activation/function compared with RA2010 or UA, which shared similar clinical and pathobiological features. At 12-month follow-up, a significantly higher proportion of patients classified as lympho-myeloid pathotype required biological therapy. Performance of a clinical prediction model for biological therapy requirement was improved by the integration of synovial pathobiological markers from 78.8% to 89%-90%. CONCLUSION The capacity to refine early clinical classification criteria through synovial pathobiological markers offers the potential to predict disease outcome and stratify therapeutic intervention to patients most in need.
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Affiliation(s)
- Gloria Lliso-Ribera
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Frances Humby
- Centre for Experimental Medicine and Rheumatology, Barts and the London School of Medicine and Dentistry, London, UK
| | - Myles Lewis
- Queen Mary University of London—Charterhouse Square Campus, London, UK
| | - Alessandra Nerviani
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Daniele Mauro
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Felice Rivellese
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | | | - Rebecca Hands
- Experimental Medicine and Rheumatology, Queen Marys University of London, London, UK
| | - Fabiola Bene
- Queen Mary University of London—Charterhouse Square Campus, London, UK
| | - Nandhini Ramamoorthi
- Biomarker Discovery OMNI, Genentech Research & Early Development, San Francisco, California, USA
| | - Jason A Hackney
- ITGR Biomarker Discovery Group, Genentech, South San Francisco, California, USA
| | - Alberto Cauli
- Rheumatology and Rheumatology Unit, University of Cagliari and AOU University Clinic of Cagliari, Monserrato, Italy
| | - Ernest H Choy
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Andrew Filer
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Peter C Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Michael J Townsend
- ITGR Biomarker Discovery Group, Genentech, South San Francisco, California, USA
| | - Costantino Pitzalis
- Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
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22
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Lliso-Ribera G, Humby F, Lewis M, Nerviani A, Mauro D, Rivellese F, Kelly S, Hands R, Bene F, Ramamoorthi N, Hackney JA, Cauli A, Choy EH, Filer A, Taylor PC, McInnes I, Townsend MJ, Pitzalis C. Synovial tissue signatures enhance clinical classification and prognostic/treatment response algorithms in early inflammatory arthritis and predict requirement for subsequent biological therapy: results from the pathobiology of early arthritis cohort (PEAC). Ann Rheum Dis 2019. [PMID: 31582377 DOI: 10.1136/annrheumdis-2019-215751 10.1136/annrheumdis-2019-215751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To establish whether synovial pathobiology improves current clinical classification and prognostic algorithms in early inflammatory arthritis and identify predictors of subsequent biological therapy requirement. METHODS 200 treatment-naïve patients with early arthritis were classified as fulfilling RA1987 American College of Rheumatology (ACR) criteria (RA1987) or as undifferentiated arthritis (UA) and patients with UA further classified into those fulfilling RA2010 ACR/European League Against Rheumatism (EULAR) criteria. Treatment requirements at 12 months (Conventional Synthetic Disease Modifying Antirheumatic Drugs (csDMARDs) vs biologics vs no-csDMARDs treatment) were determined. Synovial tissue was retrieved by minimally invasive, ultrasound-guided biopsy and underwent processing for immunohistochemical (IHC) and molecular characterisation. Samples were analysed for macrophage, plasma-cell and B-cells and T-cells markers, pathotype classification (lympho-myeloid, diffuse-myeloid or pauci-immune) by IHC and gene expression profiling by Nanostring. RESULTS 128/200 patients were classified as RA1987, 25 as RA2010 and 47 as UA. Patients classified as RA1987 criteria had significantly higher levels of disease activity, histological synovitis, degree of immune cell infiltration and differential upregulation of genes involved in B and T cell activation/function compared with RA2010 or UA, which shared similar clinical and pathobiological features. At 12-month follow-up, a significantly higher proportion of patients classified as lympho-myeloid pathotype required biological therapy. Performance of a clinical prediction model for biological therapy requirement was improved by the integration of synovial pathobiological markers from 78.8% to 89%-90%. CONCLUSION The capacity to refine early clinical classification criteria through synovial pathobiological markers offers the potential to predict disease outcome and stratify therapeutic intervention to patients most in need.
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Affiliation(s)
- Gloria Lliso-Ribera
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Frances Humby
- Centre for Experimental Medicine and Rheumatology, Barts and the London School of Medicine and Dentistry, London, UK
| | - Myles Lewis
- Queen Mary University of London-Charterhouse Square Campus, London, UK
| | - Alessandra Nerviani
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Daniele Mauro
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Felice Rivellese
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | | | - Rebecca Hands
- Experimental Medicine and Rheumatology, Queen Marys University of London, London, UK
| | - Fabiola Bene
- Queen Mary University of London-Charterhouse Square Campus, London, UK
| | - Nandhini Ramamoorthi
- Biomarker Discovery OMNI, Genentech Research & Early Development, San Francisco, California, USA
| | - Jason A Hackney
- ITGR Biomarker Discovery Group, Genentech, South San Francisco, California, USA
| | - Alberto Cauli
- Rheumatology and Rheumatology Unit, University of Cagliari and AOU University Clinic of Cagliari, Monserrato, Italy
| | - Ernest H Choy
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Andrew Filer
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Peter C Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Michael J Townsend
- ITGR Biomarker Discovery Group, Genentech, South San Francisco, California, USA
| | - Costantino Pitzalis
- Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
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23
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Lliso-Ribera G, Humby F, Lewis M, Nerviani A, Mauro D, Rivellese F, Kelly S, Hands R, Bene F, Ramamoorthi N, Hackney JA, Cauli A, Choy EH, Filer A, Taylor PC, McInnes I, Townsend MJ, Pitzalis C. Synovial tissue signatures enhance clinical classification and prognostic/treatment response algorithms in early inflammatory arthritis and predict requirement for subsequent biological therapy: results from the pathobiology of early arthritis cohort (PEAC). Ann Rheum Dis 2019; 78:1642-1652. [PMID: 31582377 PMCID: PMC6900253 DOI: 10.1136/annrheumdis-2019-215751] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 01/20/2023]
Abstract
OBJECTIVE To establish whether synovial pathobiology improves current clinical classification and prognostic algorithms in early inflammatory arthritis and identify predictors of subsequent biological therapy requirement. METHODS 200 treatment-naïve patients with early arthritis were classified as fulfilling RA1987 American College of Rheumatology (ACR) criteria (RA1987) or as undifferentiated arthritis (UA) and patients with UA further classified into those fulfilling RA2010 ACR/European League Against Rheumatism (EULAR) criteria. Treatment requirements at 12 months (Conventional Synthetic Disease Modifying Antirheumatic Drugs (csDMARDs) vs biologics vs no-csDMARDs treatment) were determined. Synovial tissue was retrieved by minimally invasive, ultrasound-guided biopsy and underwent processing for immunohistochemical (IHC) and molecular characterisation. Samples were analysed for macrophage, plasma-cell and B-cells and T-cells markers, pathotype classification (lympho-myeloid, diffuse-myeloid or pauci-immune) by IHC and gene expression profiling by Nanostring. RESULTS 128/200 patients were classified as RA1987, 25 as RA2010 and 47 as UA. Patients classified as RA1987 criteria had significantly higher levels of disease activity, histological synovitis, degree of immune cell infiltration and differential upregulation of genes involved in B and T cell activation/function compared with RA2010 or UA, which shared similar clinical and pathobiological features. At 12-month follow-up, a significantly higher proportion of patients classified as lympho-myeloid pathotype required biological therapy. Performance of a clinical prediction model for biological therapy requirement was improved by the integration of synovial pathobiological markers from 78.8% to 89%-90%. CONCLUSION The capacity to refine early clinical classification criteria through synovial pathobiological markers offers the potential to predict disease outcome and stratify therapeutic intervention to patients most in need.
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Affiliation(s)
- Gloria Lliso-Ribera
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Frances Humby
- Centre for Experimental Medicine and Rheumatology, Barts and the London School of Medicine and Dentistry, London, UK
| | - Myles Lewis
- Queen Mary University of London-Charterhouse Square Campus, London, UK
| | - Alessandra Nerviani
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Daniele Mauro
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | - Felice Rivellese
- Centre of Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
| | | | - Rebecca Hands
- Experimental Medicine and Rheumatology, Queen Marys University of London, London, UK
| | - Fabiola Bene
- Queen Mary University of London-Charterhouse Square Campus, London, UK
| | - Nandhini Ramamoorthi
- Biomarker Discovery OMNI, Genentech Research & Early Development, San Francisco, California, USA
| | - Jason A Hackney
- ITGR Biomarker Discovery Group, Genentech, South San Francisco, California, USA
| | - Alberto Cauli
- Rheumatology and Rheumatology Unit, University of Cagliari and AOU University Clinic of Cagliari, Monserrato, Italy
| | - Ernest H Choy
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Andrew Filer
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Peter C Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Michael J Townsend
- ITGR Biomarker Discovery Group, Genentech, South San Francisco, California, USA
| | - Costantino Pitzalis
- Experimental Medicine and Rheumatology, William Harvey Research Institute, London, UK
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24
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Austin CD, Mouchess M, Suto E, Chan S, Dai B, Santell L, Tam C, Hackney JA, Cao Y, Luan P, Darwish M, He D, Haller S, Eastham‐Anderson J, Franke Y, Lu Y, Blanchette C, Lee WP, Lazarus RA, Yi T. A Rationally Engineered Hyperactive Actin‐Resistant DNase1‐Fc Fusion Protein Ameliorates Autoimmune Glomerulonephritis. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.802.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Maria Mouchess
- Discovery ImmunologyGenentech, Inc.South San FranciscoCA
| | - Eric Suto
- Translational ImmunologyGenentech, Inc.South San FranciscoCA
| | - Sara Chan
- PathologyGenentech, Inc.South San FranciscoCA
| | - Bingbing Dai
- Discovery ImmunologyGenentech, Inc.South San FranciscoCA
| | - Lydia Santell
- Early Discovery BiochemistryGenentech, Inc.South San FranciscoCA
| | - Christine Tam
- Protein Chemistry and Structural BiologyGenentech, Inc.South San FranciscoCA
| | | | - Yi Cao
- BioinformaticsGenentech, Inc.South San FranciscoCA
| | - Peng Luan
- Antibody EngineeringGenentech, Inc.South San FranciscoCA
| | - Martine Darwish
- Protein Chemistry and Structural BiologyGenentech, Inc.South San FranciscoCA
| | - Dongping He
- Biochemical and Cellular PharmacologyGenentech, Inc.South San FranciscoCA
| | | | | | | | - Yanmei Lu
- Biochemical and Cellular PharmacologyGenentech, Inc.South San FranciscoCA
| | | | - Wyne P. Lee
- Translational ImmunologyGenentech, Inc.South San FranciscoCA
| | | | - Tangsheng Yi
- Discovery ImmunologyGenentech, Inc.South San FranciscoCA
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25
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Humby F, Lewis M, Ramamoorthi N, Hackney JA, Barnes MR, Bombardieri M, Setiadi AF, Kelly S, Bene F, DiCicco M, Riahi S, Rocher V, Ng N, Lazarou I, Hands R, van der Heijde D, Landewé RBM, van der Helm-van Mil A, Cauli A, McInnes I, Buckley CD, Choy EH, Taylor PC, Townsend MJ, Pitzalis C. Synovial cellular and molecular signatures stratify clinical response to csDMARD therapy and predict radiographic progression in early rheumatoid arthritis patients. Ann Rheum Dis 2019; 78:761-772. [PMID: 30878974 PMCID: PMC6579551 DOI: 10.1136/annrheumdis-2018-214539] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 02/06/2019] [Accepted: 02/14/2019] [Indexed: 12/21/2022]
Abstract
Objectives To unravel the hierarchy of cellular/molecular pathways in the disease tissue of early, treatment-naïve rheumatoid arthritis (RA) patients and determine their relationship with clinical phenotypes and treatment response/outcomes longitudinally. Methods 144 consecutive treatment-naïve early RA patients (<12 months symptoms duration) underwent ultrasound-guided synovial biopsy before and 6 months after disease-modifying antirheumatic drug (DMARD) initiation. Synovial biopsies were analysed for cellular (immunohistology) and molecular (NanoString) characteristics and results compared with clinical and imaging outcomes. Differential gene expression analysis and logistic regression were applied to define variables correlating with treatment response and predicting radiographic progression. Results Cellular and molecular analyses of synovial tissue demonstrated for the first time in early RA the presence of three pathology groups: (1) lympho-myeloid dominated by the presence of B cells in addition to myeloid cells; (2) diffuse-myeloid with myeloid lineage predominance but poor in B cells nd (3) pauci-immune characterised by scanty immune cells and prevalent stromal cells. Longitudinal correlation of molecular signatures demonstrated that elevation of myeloid- and lymphoid-associated gene expression strongly correlated with disease activity, acute phase reactants and DMARD response at 6 months. Furthermore, elevation of synovial lymphoid-associated genes correlated with autoantibody positivity and elevation of osteoclast-targeting genes predicting radiographic joint damage progression at 12 months. Patients with predominant pauci-immune pathology showed less severe disease activity and radiographic progression. Conclusions We demonstrate at disease presentation, prior to pathology modulation by therapy, the presence of specific cellular/molecular synovial signatures that delineate disease severity/progression and therapeutic response and may pave the way to more precise definition of RA taxonomy, therapeutic targeting and improved outcomes.
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Affiliation(s)
- Frances Humby
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Myles Lewis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | | | - Jason A Hackney
- Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, USA
| | - Michael R Barnes
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK.,Centre for Translational Bioinformatics, William Harvey Research Institute, London, UK
| | - Michele Bombardieri
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - A Francesca Setiadi
- Biomarker Discovery OMNI, Genentech Inc, South San Francisco, California, USA
| | - Stephen Kelly
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Fabiola Bene
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Maria DiCicco
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Sudeh Riahi
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Vidalba Rocher
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Nora Ng
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Ilias Lazarou
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Rebecca Hands
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | | | - Robert B M Landewé
- Amsterdam Rheumatology Center, AMC, Amsterdam, Netherlands.,Department of Rheumatology, Zuyderland MC, Heerlen, Netherlands
| | | | | | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | | | - Ernest H Choy
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Peter C Taylor
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Kennedy Institute of Rheumatology, Oxford, UK
| | - Michael J Townsend
- Biomarker Discovery OMNI, Genentech Inc, South San Francisco, California, USA
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
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Samie M, Lim J, Verschueren E, Baughman JM, Peng I, Wong A, Kwon Y, Senbabaoglu Y, Hackney JA, Keir M, Mckenzie B, Kirkpatrick DS, van Lookeren Campagne M, Murthy A. Selective autophagy of the adaptor TRIF regulates innate inflammatory signaling. Nat Immunol 2018; 19:246-254. [PMID: 29358708 DOI: 10.1038/s41590-017-0042-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/15/2017] [Indexed: 12/17/2022]
Abstract
Defective autophagy is linked to diseases such as rheumatoid arthritis, lupus and inflammatory bowel disease (IBD). However, the mechanisms by which autophagy limits inflammation remain poorly understood. Here we found that loss of the autophagy-related gene Atg16l1 promoted accumulation of the adaptor TRIF and downstream signaling in macrophages. Multiplex proteomic profiling identified SQSTM1 and Tax1BP1 as selective autophagy-related receptors that mediated the turnover of TRIF. Knockdown of Tax1bp1 increased production of the cytokines IFN-β and IL-1β. Mice lacking Atg16l1 in myeloid cells succumbed to lipopolysaccharide-mediated sepsis but enhanced their clearance of intestinal Salmonella typhimurium in an interferon receptor-dependent manner. Human macrophages with the Crohn's disease-associated Atg16l1 variant T300A exhibited more production of IFN-β and IL-1β. An elevated interferon-response gene signature was observed in patients with IBD who were resistant to treatment with an antibody to the cytokine TNF. These findings identify selective autophagy as a key regulator of signaling via the innate immune system.
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Affiliation(s)
- Mohammad Samie
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Junghyun Lim
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Erik Verschueren
- Department of Microchemistry, Proteomics & Lipidomics, Genentech, South San Francisco, CA, USA
| | - Joshua M Baughman
- Department of Microchemistry, Proteomics & Lipidomics, Genentech, South San Francisco, CA, USA
| | - Ivan Peng
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Aaron Wong
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Youngsu Kwon
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Yasin Senbabaoglu
- Department of Bioinformatics & Computational Biology, Genentech, South San Francisco, CA, USA
| | - Jason A Hackney
- Department of Bioinformatics & Computational Biology, Genentech, South San Francisco, CA, USA
| | - Mary Keir
- Biomarker Discovery OMNI, Genentech, South San Francisco, CA, USA
| | - Brent Mckenzie
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics & Lipidomics, Genentech, South San Francisco, CA, USA
| | | | - Aditya Murthy
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA.
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27
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Brightbill HD, Suto E, Blaquiere N, Ramamoorthi N, Sujatha-Bhaskar S, Gogol EB, Castanedo GM, Jackson BT, Kwon YC, Haller S, Lesch J, Bents K, Everett C, Kohli PB, Linge S, Christian L, Barrett K, Jaochico A, Berezhkovskiy LM, Fan PW, Modrusan Z, Veliz K, Townsend MJ, DeVoss J, Johnson AR, Godemann R, Lee WP, Austin CD, McKenzie BS, Hackney JA, Crawford JJ, Staben ST, Alaoui Ismaili MH, Wu LC, Ghilardi N. NF-κB inducing kinase is a therapeutic target for systemic lupus erythematosus. Nat Commun 2018; 9:179. [PMID: 29330524 PMCID: PMC5766581 DOI: 10.1038/s41467-017-02672-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/18/2017] [Indexed: 02/06/2023] Open
Abstract
NF-κB-inducing kinase (NIK) mediates non-canonical NF-κB signaling downstream of multiple TNF family members, including BAFF, TWEAK, CD40, and OX40, which are implicated in the pathogenesis of systemic lupus erythematosus (SLE). Here, we show that experimental lupus in NZB/W F1 mice can be treated with a highly selective and potent NIK small molecule inhibitor. Both in vitro as well as in vivo, NIK inhibition recapitulates the pharmacological effects of BAFF blockade, which is clinically efficacious in SLE. Furthermore, NIK inhibition also affects T cell parameters in the spleen and proinflammatory gene expression in the kidney, which may be attributable to inhibition of OX40 and TWEAK signaling, respectively. As a consequence, NIK inhibition results in improved survival, reduced renal pathology, and lower proteinuria scores. Collectively, our data suggest that NIK inhibition is a potential therapeutic approach for SLE.
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Affiliation(s)
- Hans D Brightbill
- Department of Immunology Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Eric Suto
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Nicole Blaquiere
- Department of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Nandhini Ramamoorthi
- Department of Biomarker Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Swathi Sujatha-Bhaskar
- Department of Immunology Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Emily B Gogol
- Department of Immunology Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Georgette M Castanedo
- Department of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Benjamin T Jackson
- Department of Immunology Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Youngsu C Kwon
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Susan Haller
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Justin Lesch
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Karin Bents
- Evotec, Inc., Essener Bogen 7, Hamburg, 22419, Germany
| | - Christine Everett
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Pawan Bir Kohli
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Sandra Linge
- Evotec, Inc., Essener Bogen 7, Hamburg, 22419, Germany
| | - Laura Christian
- Department of Immunology Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Kathy Barrett
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Allan Jaochico
- Department of Drug Metabolism and Pharmacokinetics, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Leonid M Berezhkovskiy
- Department of Drug Metabolism and Pharmacokinetics, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Peter W Fan
- Department of Drug Metabolism and Pharmacokinetics, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Kelli Veliz
- Department of Laboratory Animal Resources, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Michael J Townsend
- Department of Biomarker Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Jason DeVoss
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Adam R Johnson
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | | | - Wyne P Lee
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Cary D Austin
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Brent S McKenzie
- Department of Translational Immunology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Jason A Hackney
- Department of Bioinformatics and Computational Biology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - James J Crawford
- Department of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Steven T Staben
- Department of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Moulay H Alaoui Ismaili
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Lawren C Wu
- Department of Immunology Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA
| | - Nico Ghilardi
- Department of Immunology Discovery, Genentech, 1 DNA Way, South San Francisco, CA-94080, USA.
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28
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Martinez-Martin N, Ramani SR, Hackney JA, Tom I, Wranik BJ, Chan M, Wu J, Paluch MT, Takeda K, Hass PE, Clark H, Gonzalez LC. Corrigendum: The extracellular interactome of the human adenovirus family reveals diverse strategies for immunomodulation. Nat Commun 2017; 8:16150. [PMID: 28825416 PMCID: PMC5601198 DOI: 10.1038/ncomms16150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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29
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Brightbill HD, Suto E, Blaquiere N, Ramamoorthi N, Sujatha-Bhaskar S, Gogol E, Castanedo G, Jackson B, Haller S, Lesch J, Bents K, Everett C, Kohli PB, Linge S, Christian L, Barrett K, Jaochico A, Berezhkovskiy LM, Fan PW, Veliz K, Townsend M, DeVoss J, Johnson A, Godemann R, Lee WP, Austin CD, McKenzie B, Hackney JA, Crawford JJ, Staben S, Ismaili MHA, Wu LC, Ghilardi N. Selective inhibition of NF-kB inducing kinase (NIK) is therapeutically efficacious in IFNα-accelerated lupus nephritis prone mice. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.217.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Systemic lupus erythematosus (SLE) is often considered a disease driven by autoreactive B cells and anti-nuclear antibodies. However, therapeutic targeting of B cells, for example through BAFF blockade, has been only partially effective in SLE. NF-kB Inducing Kinase (NIK) mediates non-canonical NF-kB signaling downstream of disease relevant TNF family members, such as BAFF, TWEAK, CD40, and OX40. We hypothesized that NIK inhibition might be more efficacious than BAFF blockade in lupus, and therefore generated a highly selective and potent small molecule inhibitor (SMI) of NIK to test this hypothesis. In cellular assays, this molecule inhibits non-canonical NF-kB signaling downstream of multiple TNFRSF family members. In order to differentiate the effects of NIK inhibition and BAFF blockade in vivo, we compared NIK inhibition with BAFF blockade in the context of NZB/W F1 lupus prone mice. As predicted, NIK inhibition recapitulated the pharmacological effects of BAFF blockade. Furthermore, NIK inhibition, but not BAFF blockade, affected T cell parameters in the spleen and pro-inflammatory gene expression in the kidney, the latter of which is partly attributable to TWEAK signaling. Finally, NIK inhibition resulted in improved survival, ameliorated renal pathology, and lower proteinuria scores. Collectively, our data suggest that NIK inhibition affects multiple disease-relevant pathways and may therefore have superior efficacy compared to BAFF inhibition in SLE.
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30
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Senger K, Pham VC, Varfolomeev E, Hackney JA, Corzo CA, Collier J, Lau VWC, Huang Z, Hamidzhadeh K, Caplazi P, Peng I, Setiadi AF, Francis R, Paler-Martinez A, Kwon YC, Ramirez-Carrozzi V, Sun Y, Grigg PW, Roose-Girma M, Jeet S, Barck KH, Pham A, Ota N, Ha C, Stinson J, Guillory J, Tam L, Modrusan Z, Emson C, McKenzie BS, Townsend MJ, Carano RAD, Warming S, Vucic D, DeVoss J, Lee WP, Lill JR, Zarrin AA. The kinase TPL2 activates ERK and p38 signaling to promote neutrophilic inflammation. Sci Signal 2017; 10:10/475/eaah4273. [PMID: 28420753 DOI: 10.1126/scisignal.aah4273] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Tumor progression locus 2 (TPL2; also known as MAP3K8) is a mitogen-activated protein kinase (MAPK) kinase kinase (MAP3K) that phosphorylates the MAPK kinases MEK1 and MEK2 (MEK1/2), which, in turn, activate the MAPKs extracellular signal-regulated kinase 1 (ERK1) and ERK2 (ERK1/2) in macrophages stimulated through the interleukin-1 receptor (IL-1R), Toll-like receptors (TLRs), or the tumor necrosis factor receptor (TNFR). We describe a conserved and critical role for TPL2 in mediating the effector functions of neutrophils through the activation of the p38 MAPK signaling pathway. Gene expression profiling and functional studies of neutrophils and monocytes revealed a MEK1/2-independent branch point downstream of TPL2 in neutrophils. Biochemical analyses identified the MAPK kinases MEK3 and MEK6 and the MAPKs p38α and p38δ as downstream effectors of TPL2 in these cells. Genetic ablation of the catalytic activity of TPL2 or therapeutic intervention with a TPL2-specific inhibitor reduced the production of inflammatory mediators by neutrophils in response to stimulation with the TLR4 agonist lipopolysaccharide (LPS) in vitro, as well as in rodent models of inflammatory disease. Together, these data suggest that TPL2 is a drug target that activates not only MEK1/2-dependent but also MEK3/6-dependent signaling to promote inflammatory responses.
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Affiliation(s)
- Kate Senger
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Victoria C Pham
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eugene Varfolomeev
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cesar A Corzo
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jenna Collier
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Vivian W C Lau
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zhiyu Huang
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kajal Hamidzhadeh
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Patrick Caplazi
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivan Peng
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - A Francesca Setiadi
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ross Francis
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Youngsu C Kwon
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Yonglian Sun
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Patricia W Grigg
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Merone Roose-Girma
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Surinder Jeet
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kai H Barck
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anna Pham
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Naruhisa Ota
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Connie Ha
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jeremy Stinson
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph Guillory
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lucinda Tam
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Claire Emson
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brent S McKenzie
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Michael J Townsend
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Richard A D Carano
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Søren Warming
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Domagoj Vucic
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason DeVoss
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jennie R Lill
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ali A Zarrin
- Genentech Research, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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31
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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: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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32
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Vander Lugt B, Riddell J, Khan AA, Hackney JA, Lesch J, DeVoss J, Weirauch MT, Singh H, Mellman I. Transcriptional determinants of tolerogenic and immunogenic states during dendritic cell maturation. J Cell Biol 2017; 216:779-792. [PMID: 28130292 PMCID: PMC5350508 DOI: 10.1083/jcb.201512012] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 10/21/2016] [Accepted: 12/30/2016] [Indexed: 11/22/2022] Open
Abstract
Dendritic cells promote either immunosuppressive or immunogenic T cell responses, but the transcriptional and epigenetic programs regulating these functions are unclear. Vander Lugt et al. dissect the distinct programs underlying the immunogenic and tolerogenic mature states of dendritic cells in vitro. Dendritic cells (DCs) promote either tolerogenic or immunogenic T cell responses, the latter upon sensing microbes. Using an in vitro system, we analyzed transcriptional determinants that enable mature DCs to direct these opposing T cell outcomes. In the absence of microbial products, the transcription factor interferon regulatory factor 4 (IRF4) promotes regulatory T cell (Treg) generation by enhancing expression of genes required for antigen presentation along with those for T cell tolerance. IRF4-deficient DCs were impaired for Treg generation in vivo. When exposed to microbial stimuli, DCs activated nuclear factor (NF)-κB, which induced expression of a proinflammatory cytokine module that, along with the antigen presentation module, promoted the generation of effector T cells. NF-κB was, however, dispensable for Treg development. Chromatin profiling revealed transcriptional motifs associated with the divergent DC programs. Thus, DCs modulate their ability to prime tolerogenic or immunogenic T cells by expressing a core antigen presentation module that is overlaid by distinctive regulatory modules to promote either tolerance or immunity.
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Affiliation(s)
- Bryan Vander Lugt
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080
| | - Jeremy Riddell
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Aly A Khan
- Institute for Systems and Genomics Biology, The University of Chicago, Chicago, IL 60637.,Department of Human Genetics, The University of Chicago, Chicago, IL 60637
| | - Jason A Hackney
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080
| | - Justin Lesch
- Department Translational Immunology, Genentech, South San Francisco, CA 94080
| | - Jason DeVoss
- Department Translational Immunology, Genentech, South San Francisco, CA 94080
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Harinder Singh
- Center for Systems Immunology, Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Ira Mellman
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080
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33
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Kolumam G, Wu X, Lee WP, Hackney JA, Zavala-Solorio J, Gandham V, Danilenko DM, Arora P, Wang X, Ouyang W. IL-22R Ligands IL-20, IL-22, and IL-24 Promote Wound Healing in Diabetic db/db Mice. PLoS One 2017; 12:e0170639. [PMID: 28125663 PMCID: PMC5268431 DOI: 10.1371/journal.pone.0170639] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 11/30/2016] [Indexed: 12/21/2022] Open
Abstract
Diabetic foot ulcers (DFU) are one of the major complications in type II diabetes patients and can result in amputation and morbidity. Although multiple approaches are used clinically to help wound closure, many patients still lack adequate treatment. Here we show that IL-20 subfamily cytokines are upregulated during normal wound healing. While there is a redundant role for each individual cytokine in this subfamily in wound healing, mice deficient in IL-22R, the common receptor chain for IL-20, IL-22, and IL-24, display a significant delay in wound healing. Furthermore, IL-20, IL-22 and IL-24 are all able to promote wound healing in type II diabetic db/db mice. Mechanistically, when compared to other growth factors such as VEGF and PDGF that accelerate wound healing in this model, IL-22 uniquely induced genes involved in reepithelialization, tissue remodeling and innate host defense mechanisms from wounded skin. Interestingly, IL-22 treatment showed superior efficacy compared to PDGF or VEGF in an infectious diabetic wound model. Taken together, our data suggest that IL-20 subfamily cytokines, particularly IL-20, IL-22, and IL-24, might provide therapeutic benefit for patients with DFU.
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Affiliation(s)
- Ganesh Kolumam
- Department of Biomedical Imaging, Genentech, South San Francisco, California, United States of America
| | - Xiumin Wu
- Department of Immunology, Genentech, South San Francisco, California, United States of America
| | - Wyne P. Lee
- Department of Immunology, Genentech, South San Francisco, California, United States of America
| | - Jason A. Hackney
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, California, United States of America
| | - Jose Zavala-Solorio
- Department of Molecular Biology, Genentech, South San Francisco, California, United States of America
| | - Vineela Gandham
- Department of Biomedical Imaging, Genentech, South San Francisco, California, United States of America
| | - Dimitry M. Danilenko
- Department of Safety Assessment Pathology, Genentech, South San Francisco, California, United States of America
| | - Puneet Arora
- Department of Early Clinical Development, Genentech, South San Francisco, California, United States of America
| | - Xiaoting Wang
- Department of Immunology, Genentech, South San Francisco, California, United States of America
| | - Wenjun Ouyang
- Department of Immunology, Genentech, South San Francisco, California, United States of America
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34
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Affiliation(s)
- Mary E Keir
- Genentech Research and Early Development, South San Francisco, California
| | - Gaik W Tew
- Genentech Research and Early Development, South San Francisco, California
| | - Jason A Hackney
- Genentech Research and Early Development, South San Francisco, California
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35
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Martinez-Martin N, Ramani SR, Hackney JA, Tom I, Wranik BJ, Chan M, Wu J, Paluch MT, Takeda K, Hass PE, Clark H, Gonzalez LC. The extracellular interactome of the human adenovirus family reveals diverse strategies for immunomodulation. Nat Commun 2016; 7:11473. [PMID: 27145901 PMCID: PMC4858740 DOI: 10.1038/ncomms11473] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/30/2016] [Indexed: 01/06/2023] Open
Abstract
Viruses encode secreted and cell-surface expressed proteins essential to modulate host immune defenses and establish productive infections. However, to date there has been no systematic study of the extracellular interactome of any human virus. Here we utilize the E3 proteins, diverse and rapidly evolving transmembrane-containing proteins encoded by human adenoviruses, as a model system to survey the extracellular immunomodulatory landscape. From a large-scale protein interaction screen against a microarray of more than 1,500 human proteins, we find and validate 51 previously unidentified virus–host interactions. Our results uncover conserved strategies as well as substantial diversity and multifunctionality in host targeting within and between viral species. Prominent modulation of the leukocyte immunoglobulin-like and signalling lymphocyte activation molecule families and a number of inhibitory receptors were identified as hubs for viral perturbation, suggesting unrecognized immunoregulatory strategies. We describe a virus–host extracellular interaction map of unprecedented scale that provides new insights into viral immunomodulation. Viruses interact with their hosts via secreted and membrane-bound proteins to affect host immune responses and virulence. Here the authors contribute to our understanding of this relationship with an extracellular interaction map of human and adenoviral E3 immunomodulatory proteins.
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Affiliation(s)
- Nadia Martinez-Martin
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Sree R Ramani
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Jason A Hackney
- Department of Bioinformatics and Computational Biology, Genentech, 455 East Grand Avenue, South San Francisco, California 94080, USA
| | - Irene Tom
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Bernd J Wranik
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Michelle Chan
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Johnny Wu
- Department of Bioinformatics and Computational Biology, Genentech, 455 East Grand Avenue, South San Francisco, California 94080, USA
| | - Maciej T Paluch
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Kentaro Takeda
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Philip E Hass
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
| | - Hilary Clark
- Department of Bioinformatics and Computational Biology, Genentech, 455 East Grand Avenue, South San Francisco, California 94080, USA
| | - Lino C Gonzalez
- Department of Protein Chemistry, Genentech, 470 East Grand Avenue, South San Francisco, California 94080, USA
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Bueno R, Stawiski EW, Goldstein LD, Durinck S, De Rienzo A, Modrusan Z, Gnad F, Nguyen TT, Jaiswal BS, Chirieac LR, Sciaranghella D, Dao N, Gustafson CE, Munir KJ, Hackney JA, Chaudhuri A, Gupta R, Guillory J, Toy K, Ha C, Chen YJ, Stinson J, Chaudhuri S, Zhang N, Wu TD, Sugarbaker DJ, de Sauvage FJ, Richards WG, Seshagiri S. Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations. Nat Genet 2016; 48:407-16. [PMID: 26928227 DOI: 10.1038/ng.3520] [Citation(s) in RCA: 600] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/04/2016] [Indexed: 02/06/2023]
Abstract
We analyzed transcriptomes (n = 211), whole exomes (n = 99) and targeted exomes (n = 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we identified four distinct molecular subtypes: sarcomatoid, epithelioid, biphasic-epithelioid (biphasic-E) and biphasic-sarcomatoid (biphasic-S). Through exome analysis, we found BAP1, NF2, TP53, SETD2, DDX3X, ULK2, RYR2, CFAP45, SETDB1 and DDX51 to be significantly mutated (q-score ≥ 0.8) in MPMs. We identified recurrent mutations in several genes, including SF3B1 (∼2%; 4/216) and TRAF7 (∼2%; 5/216). SF3B1-mutant samples showed a splicing profile distinct from that of wild-type tumors. TRAF7 alterations occurred primarily in the WD40 domain and were, except in one case, mutually exclusive with NF2 alterations. We found recurrent gene fusions and splice alterations to be frequent mechanisms for inactivation of NF2, BAP1 and SETD2. Through integrated analyses, we identified alterations in Hippo, mTOR, histone methylation, RNA helicase and p53 signaling pathways in MPMs.
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Affiliation(s)
- Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eric W Stawiski
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Leonard D Goldstein
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Steffen Durinck
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA.,Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Assunta De Rienzo
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Florian Gnad
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Lucian R Chirieac
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniele Sciaranghella
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nhien Dao
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Corinne E Gustafson
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kiara J Munir
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jason A Hackney
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Amitabha Chaudhuri
- Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India
| | - Ravi Gupta
- Bioinformatics Department, MedGenome Labs, Pvt., Ltd., Narayana Health City, Bangalore, India
| | - Joseph Guillory
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Karen Toy
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Connie Ha
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Ying-Jiun Chen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Jeremy Stinson
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Na Zhang
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thomas D Wu
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - David J Sugarbaker
- Division of Thoracic Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Frederic J de Sauvage
- Molecular Oncology Department, Genentech, Inc., South San Francisco, California, USA
| | - William G Richards
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
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Tew GW, Hackney JA, Gibbons D, Lamb CA, Luca D, Egen JG, Diehl L, Eastham Anderson J, Vermeire S, Mansfield JC, Feagan BG, Panes J, Baumgart DC, Schreiber S, Dotan I, Sandborn WJ, Kirby JA, Irving PM, De Hertogh G, Van Assche GA, Rutgeerts P, O'Byrne S, Hayday A, Keir ME. Association Between Response to Etrolizumab and Expression of Integrin αE and Granzyme A in Colon Biopsies of Patients With Ulcerative Colitis. Gastroenterology 2016; 150:477-87.e9. [PMID: 26522261 DOI: 10.1053/j.gastro.2015.10.041] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 10/05/2015] [Accepted: 10/22/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Etrolizumab is a humanized monoclonal antibody against the β7 integrin subunit that has shown efficacy vs placebo in patients with moderate to severely active ulcerative colitis (UC). Patients with colon tissues that expressed high levels of the integrin αE gene (ITGAE) appeared to have the best response. We compared differences in colonic expression of ITGAE and other genes between patients who achieved clinical remission with etrolizumab vs those who did. METHODS We performed a retrospective analysis of data collected from 110 patients with UC who participated in a phase 2 placebo-controlled trial of etrolizumab, as well as from 21 patients with UC or without inflammatory bowel disease (controls) enrolled in an observational study at a separate site. Colon biopsies were collected from patients in both studies and analyzed by immunohistochemistry and gene expression profiling. Mononuclear cells were isolated and analyzed by flow cytometry. We identified biomarkers associated with response to etrolizumab. In the placebo-controlled trial, clinical remission was defined as total Mayo Clinic Score ≤2, with no individual subscore >1, and mucosal healing was defined as endoscopic score ≤1. RESULTS Colon tissues collected at baseline from patients who had a clinical response to etrolizumab expressed higher levels of T-cell-associated genes than patients who did not respond (P < .05). Colonic CD4(+) integrin αE(+) cells from patients with UC expressed higher levels of granzyme A messenger RNA (GZMA mRNA) than CD4(+) αE(-) cells (P < .0001); granzyme A and integrin αE protein were detected in the same cells. Of patients receiving 100 mg etrolizumab, a higher proportion of those with high levels of GZMA mRNA (41%) or ITGAE mRNA (38%) than those with low levels of GZMA (6%) or ITGAE mRNA (13%) achieved clinical remission (P < .05) and mucosal healing (41% GZMA(high) vs 19% GZMA(low) and 44% ITGAE(high) vs 19% ITGAE(low)). Compared with ITGAE(low) and GZMA(low) patients, patients with ITGAE(high) and GZMA(high) had higher baseline numbers of epithelial crypt-associated integrin αE(+) cells (P < .01 for both), but a smaller number of crypt-associated integrin αE(+) cells after etrolizumab treatment (P < .05 for both). After 10 weeks of etrolizumab treatment, expression of genes associated with T-cell activation and genes encoding inflammatory cytokines decreased by 40%-80% from baseline (P < .05) in patients with colon tissues expressing high levels of GZMA at baseline. CONCLUSIONS Levels of GZMA and ITGAE mRNAs in colon tissues can identify patients with UC who are most likely to benefit from etrolizumab; expression levels decrease with etrolizumab administration in biomarker(high) patients. Larger, prospective studies of markers are needed to assess their clinical value.
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Affiliation(s)
- Gaik W Tew
- Genentech Research and Early Development, South San Francisco, California
| | - Jason A Hackney
- Genentech Research and Early Development, South San Francisco, California
| | | | | | - Diana Luca
- Genentech Research and Early Development, South San Francisco, California
| | - Jackson G Egen
- Genentech Research and Early Development, South San Francisco, California
| | - Lauri Diehl
- Genentech Research and Early Development, South San Francisco, California
| | | | | | | | | | - Julian Panes
- Hospital Clinic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Barcelona, Spain
| | | | - Stefan Schreiber
- Department of Medicine I, University Hospital Schleswig-Holstein, Christian Albrechts University, Kiel, Germany
| | - Iris Dotan
- Inflammatory Bowel Disease Center, Department of Gastroenterology and Liver Diseases, Tel Aviv Medical Center and Sackler Faculty of Medicine, Tel Aviv, Israel
| | | | - John A Kirby
- Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | - Gert A Van Assche
- University of Leuven, Leuven, Belgium; University of Toronto, Toronto, Ontario, Canada
| | | | - Sharon O'Byrne
- Genentech Research and Early Development, South San Francisco, California
| | | | - Mary E Keir
- Genentech Research and Early Development, South San Francisco, California.
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Xi H, Katschke KJ, Li Y, Truong T, Lee WP, Diehl L, Rangell L, Tao J, Arceo R, Eastham-Anderson J, Hackney JA, Iglesias A, Cote-Sierra J, Elstrott J, Weimer RM, van Lookeren Campagne M. IL-33 amplifies an innate immune response in the degenerating retina. J Exp Med 2016; 213:189-207. [PMID: 26755704 PMCID: PMC4749925 DOI: 10.1084/jem.20150894] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/07/2015] [Indexed: 01/12/2023] Open
Abstract
Xi et al. demonstrate that IL-33 is a key regulator of retinal inflammation and degeneration. Age-related macular degeneration (AMD), a leading cause of vision impairment in the ageing population, is characterized by irreversible loss of retinal pigment epithelial (RPE) cells and photoreceptors and can be associated with choroidal neovascularization. Mononuclear phagocytes are often present in AMD lesions, but the processes that direct myeloid cell recruitment remain unclear. Here, we identify IL-33 as a key regulator of inflammation and photoreceptor degeneration after retina stress or injury. IL-33+ Müller cells were more abundant and IL-33 cytokine was elevated in advanced AMD cases compared with age-matched controls with no AMD. In rodents, retina stress resulted in release of bioactive IL-33 that in turn increased inflammatory chemokine and cytokine expression in activated Müller cells. Deletion of ST2, the IL-33 receptor α chain, or treatment with a soluble IL-33 decoy receptor significantly reduced release of inflammatory mediators from Müller cells, inhibited accumulation of mononuclear phagocytes in the outer retina, and protected photoreceptor rods and cones after a retina insult. This study demonstrates a central role for IL-33 in regulating mononuclear phagocyte recruitment to the photoreceptor layer and positions IL-33 signaling as a potential therapeutic target in macular degenerative diseases.
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Affiliation(s)
- Hongkang Xi
- Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Kenneth J Katschke
- Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Yun Li
- Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Tom Truong
- Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Wyne P Lee
- Department of Immunology, Genentech, Inc., South San Francisco, CA 94080
| | - Lauri Diehl
- Department of Pathology, Genentech, Inc., South San Francisco, CA 94080
| | - Linda Rangell
- Department of Pathology, Genentech, Inc., South San Francisco, CA 94080
| | - Jianhua Tao
- Department of Pathology, Genentech, Inc., South San Francisco, CA 94080
| | - Rommel Arceo
- Department of Pathology, Genentech, Inc., South San Francisco, CA 94080
| | | | - Jason A Hackney
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080
| | - Antonio Iglesias
- Roche Pharmaceutical Research and Early Development, Pharmacological Sciences, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Javier Cote-Sierra
- Roche Pharmaceutical Research and Early Development, Pharmacological Sciences, Roche Innovation Center Basel, CH-4070 Basel, Switzerland
| | - Justin Elstrott
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA 94080
| | - Robby M Weimer
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA 94080
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Dennis G, Holweg CTJ, Kummerfeld SK, Choy DF, Setiadi AF, Hackney JA, Haverty PM, Gilbert H, Lin WY, Diehl L, Fischer S, Song A, Musselman D, Klearman M, Gabay C, Kavanaugh A, Endres J, Fox DA, Martin F, Townsend MJ. Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics. Arthritis Res Ther 2014; 16:R90. [PMID: 25167216 PMCID: PMC4060385 DOI: 10.1186/ar4555] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 02/25/2014] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Rheumatoid arthritis (RA) is a complex and clinically heterogeneous autoimmune disease. Currently, the relationship between pathogenic molecular drivers of disease in RA and therapeutic response is poorly understood. METHODS We analyzed synovial tissue samples from two RA cohorts of 49 and 20 patients using a combination of global gene expression, histologic and cellular analyses, and analysis of gene expression data from two further publicly available RA cohorts. To identify candidate serum biomarkers that correspond to differential synovial biology and clinical response to targeted therapies, we performed pre-treatment biomarker analysis compared with therapeutic outcome at week 24 in serum samples from 198 patients from the ADACTA (ADalimumab ACTemrA) phase 4 trial of tocilizumab (anti-IL-6R) monotherapy versus adalimumab (anti-TNFα) monotherapy. RESULTS We documented evidence for four major phenotypes of RA synovium - lymphoid, myeloid, low inflammatory, and fibroid - each with distinct underlying gene expression signatures. We observed that baseline synovial myeloid, but not lymphoid, gene signature expression was higher in patients with good compared with poor European league against rheumatism (EULAR) clinical response to anti-TNFα therapy at week 16 (P =0.011). We observed that high baseline serum soluble intercellular adhesion molecule 1 (sICAM1), associated with the myeloid phenotype, and high serum C-X-C motif chemokine 13 (CXCL13), associated with the lymphoid phenotype, had differential relationships with clinical response to anti-TNFα compared with anti-IL6R treatment. sICAM1-high/CXCL13-low patients showed the highest week 24 American College of Rheumatology (ACR) 50 response rate to anti-TNFα treatment as compared with sICAM1-low/CXCL13-high patients (42% versus 13%, respectively, P =0.05) while anti-IL-6R patients showed the opposite relationship with these biomarker subgroups (ACR50 20% versus 69%, P =0.004). CONCLUSIONS These data demonstrate that underlying molecular and cellular heterogeneity in RA impacts clinical outcome to therapies targeting different biological pathways, with patients with the myeloid phenotype exhibiting the most robust response to anti-TNFα. These data suggest a path to identify and validate serum biomarkers that predict response to targeted therapies in rheumatoid arthritis and possibly other autoimmune diseases. TRIAL REGISTRATION ClinicalTrials.gov NCT01119859
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Vander Lugt B, Khan AA, Hackney JA, Agrawal S, Lesch J, Zhou M, Lee WP, Park S, Xu M, DeVoss J, Spooner CJ, Chalouni C, Delamarre L, Mellman I, Singh H. Transcriptional programming of dendritic cells for enhanced MHC class II antigen presentation. Nat Immunol 2013; 15:161-7. [DOI: 10.1038/ni.2795] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/20/2013] [Indexed: 12/14/2022]
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Huntley MA, Larson JL, Chaivorapol C, Becker G, Lawrence M, Hackney JA, Kaminker JS. ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses. ACTA ACUST UNITED AC 2013; 29:3220-1. [PMID: 24078713 DOI: 10.1093/bioinformatics/btt551] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API. AVAILABILITY The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html. Installation instructions and usage documentation can also be found at the above URL.
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Affiliation(s)
- Melanie A Huntley
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA and Department of Statistics, University of California at Davis, Davis, CA 95616, USA
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Hogan VE, Holweg CTJ, Choy DF, Kummerfeld SK, Hackney JA, Teng YKO, Townsend MJ, vanLaar JM. Pretreatment synovial transcriptional profile is associated with early and late clinical response in rheumatoid arthritis patients treated with rituximab. Ann Rheum Dis 2012; 71:1888-94. [DOI: 10.1136/annrheumdis-2011-201115] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
ObjectivePersonalised healthcare is contingent on the identification of biomarkers that represent disease relevant pathways and predict drug response. The authors aimed to develop a gene expression signature in synovial tissue that could enrich clinical response of rheumatoid arthritis (RA) patients to rituximab.MethodsThe authors studied synovial gene expression using high-throughput quantitative real-time-PCR in 20 RA patients who underwent arthroscopy before and after treatment with rituximab. Several objective approaches were used to explore patterns in the data and to find genes associated with changes in disease activity due to treatment.ResultsThis analysis revealed two patient populations associated with distinct clinical, laboratory and histological features and, importantly, showed enrichment for response (60% non-responders vs 90% responders). A composite baseline gene score (GS) correlated with change in disease activity score (ΔDAS) between baseline and month 3 (r=0.74, p=0.0002), but also with ΔDAS at later time-points (month 9, r=0.54, p=0.016; month 15, r=0.45, p=0.06; month 21, r=0.72, p=0.003). Notably, the GS significantly correlated with baseline erythrocyte sedimentation rate (r=0.69, p=0.0008), but not with other DAS components. The GS genes represented T cell, macrophage, remodelling and interferon-α biology. Responders demonstrated higher expression of macrophage and T cell genes, while non-responders showed higher expression of interferon-α and remodelling genes.ConclusionsThis study reveals a baseline synovial GS that correlates with early and late clinical responses to rituximab. The GS biology suggests that T cells and macrophages are important for response to B cell depleting therapy, while expression of remodelling and interferon-α genes correlates with poor response.
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Pidasheva S, Trifari S, Phillips A, Hackney JA, Ma Y, Smith A, Sohn SJ, Spits H, Little RD, Behrens TW, Honigberg L, Ghilardi N, Clark HF. Functional studies on the IBD susceptibility gene IL23R implicate reduced receptor function in the protective genetic variant R381Q. PLoS One 2011; 6:e25038. [PMID: 22022372 PMCID: PMC3192060 DOI: 10.1371/journal.pone.0025038] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 08/26/2011] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) in several populations have demonstrated significant association of the IL23R gene with IBD (Crohn's disease (CD) and ulcerative colitis (UC)) and psoriasis, suggesting that perturbation of the IL-23 signaling pathway is relevant to the pathophysiology of these diseases. One particular variant, R381Q (rs11209026), confers strong protection against development of CD. We investigated the effects of this variant in primary T cells from healthy donors carrying IL23R(R381) and IL23R(Q381) haplotypes. Using a proprietary anti-IL23R antibody, ELISA, flow cytometry, phosphoflow and real-time RT-PCR methods, we examined IL23R expression and STAT3 phosphorylation and activation in response to IL-23. IL23R(Q381) was associated with reduced STAT3 phosphorylation upon stimulation with IL-23 and decreased number of IL-23 responsive T-cells. We also observed slightly reduced levels of proinflammatory cytokine secretion in IL23R(Q381) positive donors. Our study shows conclusively that IL23R(Q381) is a loss-of-function allele, further strengthening the implication from GWAS results that the IL-23 pathway is pathogenic in human disease. This data provides an explanation for the protective role of R381Q in CD and may lead to the development of improved therapeutics for autoimmune disorders like CD.
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Affiliation(s)
- Svetlana Pidasheva
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, United States of America
- Department of Immunology, Genentech Inc, South San Francisco, California, United States of America
- * E-mail: (SP) (SP); (HFC) (HC)
| | - Sara Trifari
- Department of Immunology, Genentech Inc, South San Francisco, California, United States of America
| | - Anne Phillips
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, United States of America
| | - Jason A. Hackney
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, United States of America
| | - Yan Ma
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, United States of America
| | - Ashley Smith
- ITGR Early Development, Genentech Inc, South San Francisco, California, United States of America
| | - Sue J. Sohn
- Department of Immunology, Genentech Inc, South San Francisco, California, United States of America
| | - Hergen Spits
- Department of Immunology, Genentech Inc, South San Francisco, California, United States of America
| | | | - Timothy W. Behrens
- ITGR Biomarker Discovery Group, Genentech Inc, South San Francisco, California, United States of America
| | - Lee Honigberg
- ITGR Early Development, Genentech Inc, South San Francisco, California, United States of America
| | - Nico Ghilardi
- Department of Immunology, Genentech Inc, South San Francisco, California, United States of America
- Department of Molecular Biology, Genentech Inc, South San Francisco, California, United States of America
| | - Hilary F. Clark
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, California, United States of America
- Department of Immunology, Genentech Inc, South San Francisco, California, United States of America
- * E-mail: (SP) (SP); (HFC) (HC)
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Ehrenkaufer GM, Hackney JA, Singh U. A developmentally regulated Myb domain protein regulates expression of a subset of stage-specific genes in Entamoeba histolytica. Cell Microbiol 2009; 11:898-910. [PMID: 19239479 DOI: 10.1111/j.1462-5822.2009.01300.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Conversion between a cyst and trophozoite stage is essential to disease transmission and pathogenesis in the parasitic protist Entamoeba histolytica. A transcriptomic analysis of E. histolytica cysts and trophozoites has recently been accomplished, but the molecular basis of the regulation of encystation is not known. We have now identified a developmentally regulated Myb protein (belonging to the SHAQKY family of Myb proteins), which controls expression of a subset of amoebic stage-specific genes. Overexpression of the nuclear localized Myb protein resulted in a transcriptome that overlapped significantly with the expression profile of amoebic cysts. Analysis of promoters from genes regulated by the Myb protein identified a CCCCCC promoter motif to which amoebic nuclear protein(s) bind in a sequence-specific manner. Chromatin immunoprecipitation demonstrated that the E. histolytica Myb protein binds to promoters of genes which contain the CCCCCC motif and which are regulated by the Myb protein. This work is the first identification of a transcription factor, which regulates expression of a subset of stage-specific genes in E. histolytica. Identification of transcriptional regulatory networks that control developmental pathways will provide novel insights into the biology of this important human pathogen.
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Affiliation(s)
- Gretchen M Ehrenkaufer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5107, USA
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Hackney JA, Misaghi S, Senger K, Garris C, Sun Y, Lorenzo MN, Zarrin AA. DNA targets of AID evolutionary link between antibody somatic hypermutation and class switch recombination. Adv Immunol 2009; 101:163-89. [PMID: 19231595 DOI: 10.1016/s0065-2776(08)01005-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As part of the adaptive immune response, B cells alter their functional immunoglobulin (Ig) receptor genes through somatic hypermutation (SHM) and/or class switch recombination (CSR) via processes that are initiated by activation induced cytidine deaminase (AID). These genetic modifications are targeted at specific sequences known as Variable (V) and Switch (S) regions. Here, we analyze and review the properties and function of AID target sequences across species and compare them with non-Ig sequences, including known translocation hotspots. We describe properties of the S sequences, and discuss species and isotypic differences among S regions. Common properties of SHM and CSR target sequences suggest that evolution of S regions might involve the duplication and selection of SHM hotspots.
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Affiliation(s)
- Jason A Hackney
- Genentech, Immunology Discovery Group, South San Francisco, California 94080, USA
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Hackney JA, Ehrenkaufer GM, Singh U. Identification of putative transcriptional regulatory networks in Entamoeba histolytica using Bayesian inference. Nucleic Acids Res 2007; 35:2141-52. [PMID: 17355990 PMCID: PMC1874630 DOI: 10.1093/nar/gkm028] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Few transcriptional regulatory networks have been described in non-model organisms. In Entamoeba histolytica seminal aspects of pathogenesis are transcriptionally controlled, however, little is known about transcriptional regulatory networks that effect gene expression in this parasite. We used expression data from two microarray experiments, cis-regulatory motif elucidation, and a naïve Bayesian classifier to identify genome-wide transcriptional regulatory patterns in E. histolytica. Our algorithm identified promoter motifs that accurately predicted the gene expression level of 68% of genes under trophozoite conditions. We identified a promoter motif (A/TAAACCCT) associated with high gene expression, which is highly enriched in promoters of ribosomal protein genes and tRNA synthetases. Additionally, we identified three promoter motifs (GAATGATG, AACTATTTAAACATC/TC and TGAACTTATAAACATC) associated with low gene expression. The promoters of a large gene family were highly enriched for these motifs, and in these genes the presence of ⩾2 motifs predicted low baseline gene expression and transcriptional activation by heat shock. We demonstrate that amebic nuclear protein(s) bind specifically to four of the motifs identified herein. Our analysis suggests that transcriptional regulatory networks can be identified using limited expression data. Thus, this approach is applicable to the multitude of systems for which microarray and genome sequence data are emerging.
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Affiliation(s)
- Jason A. Hackney
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA and Department of Internal Medicine, Division of Infectious Diseases, and Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Gretchen M. Ehrenkaufer
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA and Department of Internal Medicine, Division of Infectious Diseases, and Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Upinder Singh
- Department of Microbiology and Immunology, Stanford University, Stanford, California, USA and Department of Internal Medicine, Division of Infectious Diseases, and Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
- *To whom correspondence should be addressed.
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Ehrenkaufer GM, Haque R, Hackney JA, Eichinger DJ, Singh U. Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite. Cell Microbiol 2007; 9:1426-44. [PMID: 17250591 DOI: 10.1111/j.1462-5822.2006.00882.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Developmental switching between life-cycle stages is a common feature among many pathogenic organisms. The protozoan parasite Entamoeba histolytica converts between cysts (essential for disease transmission) and trophozoites (responsible for tissue invasion). Identification of genes involved in the developmental pathway has been severely hindered by the inability to generate E. histolytica cysts in vitro. Using parasite strains derived from recent human infections and whole-genome transcriptional profiling, we determined that 1439 genes (approximately 15% of annotated genes) were potentially developmentally regulated. Genes enriched in cysts (672 in total) included cysteine proteinases and transmembrane protein kinases, which may be involved in signal transduction. Genes enriched in trophozoites (767 in total) included genes typically thought of as important in tissue invasion by trophozoites, including the Gal/GalNAc lectin light subunit and cysteine protease 1. Putative regulators of differentiation including possible G-protein coupled receptors, signal transduction proteins and transcription factors were identified. A number of E. histolytica stage-specific genes were also developmentally regulated in the reptilian parasite E. invadens, indicating that they likely have conserved functions in Entamoeba development. These advances lay the groundwork for dissection of the molecular signals that initiate stage conversion and development of novel diagnostic and therapeutic measures targeting E. histolytica cysts.
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Affiliation(s)
- Gretchen M Ehrenkaufer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Abstract
Elucidation of the molecular mechanisms that are responsible for regulating the most basic properties of stem cells, self-renewal, and differentiation remains a major challenge in hematopoietic stem cell biology. We have taken a functional genomics approach towards revealing these mechanisms. Previous studies of the fetal liver genetic program led to the development of Stem Cell Database (SCDb, http://stemcell.princeton.edu), a resource for the stem cell community. These studies have been expanded to include the microenvironmental component of hematopoiesis and are the focus herein. In our efforts to study the microenvironmental component we have identified a stromal cell line, AFT024, which serves as a surrogate stem cell niche. The line provides a milieu that facilitates the maintenance of transplantable mouse and human stem cells as well as the generation of large populations of committed progenitors. In a manner mirroring the work done with the SCDb, we provide an online resource, Stromal Cell Database, StroCDB (http://stromalcell.princeton.edu), that is a compendium of information and data derived from biological and molecular studies of this surrogate niche. These include bioinformatic analyses of over 6000 clones derived from a subtracted library enriched for messages expressed in AFT024 as well as data derived from custom expression arrays developed from this library. Herein we describe these efforts and provide a guide for navigating the database and mining the information contained within.
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Affiliation(s)
- Jason A Hackney
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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Abstract
Mechanisms regulating self-renewal and cell fate decisions in mammalian stem cells are poorly understood. We determined global gene expression profiles for mouse and human hematopoietic stem cells and other stages of the hematopoietic hierarchy. Murine and human hematopoietic stem cells share a number of expressed gene products, which define key conserved regulatory pathways in this developmental system. Moreover, in the mouse, a portion of the genetic program of hematopoietic stem cells is shared with embryonic and neural stem cells. This overlapping set of gene products represents a molecular signature of stem cells.
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Affiliation(s)
- Natalia B Ivanova
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Hackney JA, Charbord P, Brunk BP, Stoeckert CJ, Lemischka IR, Moore KA. A molecular profile of a hematopoietic stem cell niche. Proc Natl Acad Sci U S A 2002; 99:13061-6. [PMID: 12226475 PMCID: PMC130586 DOI: 10.1073/pnas.192124499] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2002] [Indexed: 11/18/2022] Open
Abstract
The hematopoietic microenvironment provides a complex molecular milieu that regulates the self-renewal and differentiation activities of stem cells. We have characterized a stem cell supportive stromal cell line, AFT024, that was derived from murine fetal liver. Highly purified in vivo transplantable mouse stem cells are maintained in AFT024 cultures at input levels, whereas other primitive progenitors are expanded. In addition, human stem cells are very effectively supported by AFT024. We suggest that the AFT024 cell line represents a component of an in vivo stem cell niche. To determine the molecular signals elaborated in this niche, we undertook a functional genomics approach that combines extensive sequence mining of a subtracted cDNA library, high-density array hybridization and in-depth bioinformatic analyses. The data have been assembled into a biological process oriented database, and represent a molecular profile of a candidate stem cell niche.
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Affiliation(s)
- Jason A Hackney
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544; Laboratoire d'Hematopoièse, Faculté de Médecine, Université de Tours, 37041 Tours Cedex 1, France
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