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Ferl GZ, Barck KH, Patil J, Jemaa S, Malamut EJ, Lima A, Long JE, Cheng JH, Junttila MR, Carano RA. Automated segmentation of lungs and lung tumors in mouse micro-CT scans. iScience 2022; 25:105712. [PMID: 36582483 PMCID: PMC9792881 DOI: 10.1016/j.isci.2022.105712] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Here, we have developed an automated image processing algorithm for segmenting lungs and individual lung tumors in in vivo micro-computed tomography (micro-CT) scans of mouse models of non-small cell lung cancer and lung fibrosis. Over 3000 scans acquired across multiple studies were used to train/validate a 3D U-net lung segmentation model and a Support Vector Machine (SVM) classifier to segment individual lung tumors. The U-net lung segmentation algorithm can be used to estimate changes in soft tissue volume within lungs (primarily tumors and blood vessels), whereas the trained SVM is able to discriminate between tumors and blood vessels and identify individual tumors. The trained segmentation algorithms (1) significantly reduce time required for lung and tumor segmentation, (2) reduce bias and error associated with manual image segmentation, and (3) facilitate identification of individual lung tumors and objective assessment of changes in lung and individual tumor volumes under different experimental conditions.
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Affiliation(s)
- Gregory Z. Ferl
- Preclinical & Translational PKPD, Genentech, South San Francisco, CA 94080, USA,Department of Translational Imaging, Genentech, South San Francisco, CA 94080, USA,Corresponding author
| | - Kai H. Barck
- Department of Translational Imaging, Genentech, South San Francisco, CA 94080, USA,Corresponding author
| | - Jasmine Patil
- Genetic Science Group, Thermo Fisher Scientific, South San Francisco, CA 94080, USA
| | - Skander Jemaa
- Data, Analytics and Imaging, Product Development, Genentech, South San Francisco, CA 94080, USA
| | - Evelyn J. Malamut
- Preclinical & Translational PKPD, Genentech, South San Francisco, CA 94080, USA
| | - Anthony Lima
- Department of Translational Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jason E. Long
- ORIC Pharmaceuticals, South San Francisco, CA 94080, USA
| | - Jason H. Cheng
- Department of Translational Oncology, Genentech, South San Francisco, CA 94080, USA
| | | | - Richard A.D. Carano
- Data, Analytics and Imaging, Product Development, Genentech, South San Francisco, CA 94080, USA
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2
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Lee SH, Meilandt WJ, Xie L, Gandham VD, Ngu H, Barck KH, Rezzonico MG, Imperio J, Lalehzadeh G, Huntley MA, Stark KL, Foreman O, Carano RA, Friedman BA, Sheng M, Easton A, Bohlen CJ, Hansen DV. Trem2 restrains the enhancement of tau accumulation and neurodegeneration by β-amyloid pathology. Neuron 2021; 109:1283-1301.e6. [DOI: 10.1016/j.neuron.2021.02.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/07/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022]
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3
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Balestrini A, Joseph V, Dourado M, Reese RM, Shields SD, Rougé L, Bravo DD, Chernov-Rogan T, Austin CD, Chen H, Wang L, Villemure E, Shore DGM, Verma VA, Hu B, Chen Y, Leong L, Bjornson C, Hötzel K, Gogineni A, Lee WP, Suto E, Wu X, Liu J, Zhang J, Gandham V, Wang J, Payandeh J, Ciferri C, Estevez A, Arthur CP, Kortmann J, Wong RL, Heredia JE, Doerr J, Jung M, Vander Heiden JA, Roose-Girma M, Tam L, Barck KH, Carano RAD, Ding HT, Brillantes B, Tam C, Yang X, Gao SS, Ly JQ, Liu L, Chen L, Liederer BM, Lin JH, Magnuson S, Chen J, Hackos DH, Elstrott J, Rohou A, Safina BS, Volgraf M, Bauer RN, Riol-Blanco L. A TRPA1 inhibitor suppresses neurogenic inflammation and airway contraction for asthma treatment. J Exp Med 2021; 218:211821. [PMID: 33620419 PMCID: PMC7918756 DOI: 10.1084/jem.20201637] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/19/2020] [Accepted: 12/23/2020] [Indexed: 12/31/2022] Open
Abstract
Despite the development of effective therapies, a substantial proportion of asthmatics continue to have uncontrolled symptoms, airflow limitation, and exacerbations. Transient receptor potential cation channel member A1 (TRPA1) agonists are elevated in human asthmatic airways, and in rodents, TRPA1 is involved in the induction of airway inflammation and hyperreactivity. Here, the discovery and early clinical development of GDC-0334, a highly potent, selective, and orally bioavailable TRPA1 antagonist, is described. GDC-0334 inhibited TRPA1 function on airway smooth muscle and sensory neurons, decreasing edema, dermal blood flow (DBF), cough, and allergic airway inflammation in several preclinical species. In a healthy volunteer Phase 1 study, treatment with GDC-0334 reduced TRPA1 agonist-induced DBF, pain, and itch, demonstrating GDC-0334 target engagement in humans. These data provide therapeutic rationale for evaluating TRPA1 inhibition as a clinical therapy for asthma.
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Affiliation(s)
- Alessia Balestrini
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
| | - Victory Joseph
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Michelle Dourado
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA
| | - Rebecca M Reese
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA
| | - Shannon D Shields
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA
| | - Lionel Rougé
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | - Daniel D Bravo
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, CA
| | - Tania Chernov-Rogan
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, CA
| | - Cary D Austin
- Department of Pathology, Genentech, Inc., South San Francisco, CA
| | - Huifen Chen
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Lan Wang
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Elisia Villemure
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Daniel G M Shore
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Vishal A Verma
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Baihua Hu
- Pharmaron-Beijing Co. Ltd., BDA, Beijing, People's Republic of China
| | - Yong Chen
- Pharmaron-Beijing Co. Ltd., BDA, Beijing, People's Republic of China
| | - Laurie Leong
- Department of Pathology, Genentech, Inc., South San Francisco, CA
| | - Chris Bjornson
- Department of Pathology, Genentech, Inc., South San Francisco, CA
| | - Kathy Hötzel
- Department of Pathology, Genentech, Inc., South San Francisco, CA
| | - Alvin Gogineni
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - Eric Suto
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - John Liu
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - Juan Zhang
- Department of Translational Immunology, Genentech, Inc., South San Francisco, CA
| | - Vineela Gandham
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Jianyong Wang
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, CA
| | - Jian Payandeh
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | - Alberto Estevez
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | | | - Jens Kortmann
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
| | - Ryan L Wong
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
| | - Jose E Heredia
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
| | - Jonas Doerr
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Min Jung
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA
| | | | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Lucinda Tam
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA
| | - Kai H Barck
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Richard A D Carano
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Han Ting Ding
- Department of Clinical Pharmacology, Genentech, Inc., South San Francisco, CA
| | - Bobby Brillantes
- Department of Biomolecular Resources, Genentech, Inc., South San Francisco, CA
| | - Christine Tam
- Department of Biomolecular Resources, Genentech, Inc., South San Francisco, CA
| | - Xiaoying Yang
- Department of Product Development Biometric Biostatistics, Genentech, Inc., South San Francisco, CA
| | - Simon S Gao
- Department of Clinical Imaging, Genentech, Inc., South San Francisco, CA
| | - Justin Q Ly
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA
| | - Liling Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA
| | - Liuxi Chen
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA
| | - Bianca M Liederer
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA
| | - Joseph H Lin
- Department of Early Clinical Development, Genentech, Inc., South San Francisco, CA
| | - Steven Magnuson
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Jun Chen
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., South San Francisco, CA
| | - David H Hackos
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA
| | - Justin Elstrott
- Department of Biomedical Imaging, Genentech, Inc., South San Francisco, CA
| | - Alexis Rohou
- Department of Structural Biology, Genentech, Inc., South San Francisco, CA
| | - Brian S Safina
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Matthew Volgraf
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA
| | - Rebecca N Bauer
- Department of OMNI-Biomarker Development, Genentech, Inc., South San Francisco, CA
| | - Lorena Riol-Blanco
- Department of Immunology Discovery, Genentech, Inc., South San Francisco, CA
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4
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Sengupta-Ghosh A, Dominguez SL, Xie L, Barck KH, Jiang Z, Earr T, Imperio J, Phu L, Budayeva HG, Kirkpatrick DS, Cai H, He D, Eastham-Anderson J, Ngu H, Foreman O, Hedehus M, Reichelt M, Hotzel I, Shang Y, Carano RAD, Ayalon G, Easton A. Corrigendum to "Muscle specific kinase (MuSK) activation preserves neuromuscular junctions in the diaphragm but is not sufficient to provide a functional benefit in the SOD1G93A mouse model of ALS" Neurobiology of Disease 124 (2019) 340-352. Neurobiol Dis 2019; 132:104558. [PMID: 31471201 DOI: 10.1016/j.nbd.2019.104558] [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: 10/26/2022] Open
Affiliation(s)
| | - Sara L Dominguez
- Department of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Luke Xie
- Department of Biomedical Imaging, Genentech, South San Francisco, CA, USA
| | - Kai H Barck
- Department of Biomedical Imaging, Genentech, South San Francisco, CA, USA
| | - Zhiyu Jiang
- Department of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Timothy Earr
- Department of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Jose Imperio
- Department of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Lilian Phu
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Hanna G Budayeva
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Hao Cai
- Department of Preclinical and Translational Pharmacokinetics, Genentech, South San Francisco, CA, USA
| | - Dongping He
- Biochemistry and Cellular Pharmacology Genentech, South San Francisco, CA, USA
| | | | - Hai Ngu
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Oded Foreman
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Maj Hedehus
- Department of Biomedical Imaging, Genentech, South San Francisco, CA, USA
| | - Michael Reichelt
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Isidro Hotzel
- Department of Antibody Discovery, Genentech, South San Francisco, CA, USA
| | - Yonglei Shang
- Department of Antibody Discovery, Genentech, South San Francisco, CA, USA
| | - Richard A D Carano
- Department of Biomedical Imaging, Genentech, South San Francisco, CA, USA
| | - Gai Ayalon
- Department of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Amy Easton
- Department of Neuroscience, Genentech, South San Francisco, CA, USA.
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5
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Sengupta-Ghosh A, Dominguez SL, Xie L, Barck KH, Jiang Z, Earr T, Imperio J, Phu L, Budayeva HG, Kirkpatrick DS, Cai H, Eastham-Anderson J, Ngu H, Foreman O, Hedehus M, Reichelt M, Hotzel I, Shang Y, Carano RAD, Ayalon G, Easton A. Muscle specific kinase (MuSK) activation preserves neuromuscular junctions in the diaphragm but is not sufficient to provide a functional benefit in the SOD1 G93A mouse model of ALS. Neurobiol Dis 2018; 124:340-352. [PMID: 30528255 DOI: 10.1016/j.nbd.2018.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/12/2018] [Accepted: 12/03/2018] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS), a neurodegenerative disease affecting motor neurons, is characterized by rapid decline of motor function and ultimately respiratory failure. As motor neuron death occurs late in the disease, therapeutics that prevent the initial disassembly of the neuromuscular junction may offer optimal functional benefit and delay disease progression. To test this hypothesis, we treated the SOD1G93A mouse model of ALS with an agonist antibody to muscle specific kinase (MuSK), a receptor tyrosine kinase required for the formation and maintenance of the neuromuscular junction. Chronic MuSK antibody treatment fully preserved innervation of the neuromuscular junction when compared with control-treated mice; however, no preservation of diaphragm function, motor neurons, or survival benefit was detected. These data show that anatomical preservation of neuromuscular junctions in the diaphragm via MuSK activation does not correlate with functional benefit in SOD1G93A mice, suggesting caution in employing MuSK activation as a therapeutic strategy for ALS patients.
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Affiliation(s)
| | - Sara L Dominguez
- Departments of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Luke Xie
- Departments of Biomedical Imaging, Genentech, South San Francisco, CA, USA
| | - Kai H Barck
- Departments of Biomedical Imaging, Genentech, South San Francisco, CA, USA
| | - Zhiyu Jiang
- Departments of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Timothy Earr
- Departments of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Jose Imperio
- Departments of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Lilian Phu
- Departments of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Hanna G Budayeva
- Departments of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Donald S Kirkpatrick
- Departments of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Hao Cai
- Departments of Preclinical and Translational Pharmacokinetics, Genentech, South San Francisco, CA, USA
| | | | - Hai Ngu
- Departments of Pathology, Genentech, South San Francisco, CA, USA
| | - Oded Foreman
- Departments of Pathology, Genentech, South San Francisco, CA, USA
| | - Maj Hedehus
- Departments of Biomedical Imaging, Genentech, South San Francisco, CA, USA
| | - Michael Reichelt
- Departments of Pathology, Genentech, South San Francisco, CA, USA
| | - Isidro Hotzel
- Departments of Antibody Discovery, Genentech, South San Francisco, CA, USA
| | - Yonglei Shang
- Departments of Antibody Discovery, Genentech, South San Francisco, CA, USA
| | - Richard A D Carano
- Departments of Biomedical Imaging, Genentech, South San Francisco, CA, USA
| | - Gai Ayalon
- Departments of Neuroscience, Genentech, South San Francisco, CA, USA
| | - Amy Easton
- Departments of Neuroscience, Genentech, South San Francisco, CA, USA.
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6
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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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7
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Barck KH, Bou-Reslan H, Rastogi U, Sakhuja T, Long JE, Molina R, Lima A, Hamilton P, Junttila MR, Johnson L, Carano RAD. Quantification of Tumor Burden in a Genetically Engineered Mouse Model of Lung Cancer by Micro-CT and Automated Analysis. Transl Oncol 2015; 8:126-35. [PMID: 25926079 PMCID: PMC4415142 DOI: 10.1016/j.tranon.2015.03.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 01/06/2015] [Revised: 03/06/2015] [Accepted: 03/17/2015] [Indexed: 11/18/2022] Open
Abstract
Genetically engineered mouse models (GEMMs) of lung cancer closely recapitulate the human disease but suffer from the difficulty of evaluating tumor growth by conventional methods. Herein, a novel automated image analysis method for estimating the lung tumor burden from in vivo micro-computed tomography (micro-CT) data is described. The proposed tumor burden metric is the segmented soft tissue volume contained within a chest space region of interest, excluding an estimate of the heart volume. The method was validated by comparison with previously published manual analysis methods and applied in two therapeutic studies in a mutant K-ras GEMM of non-small cell lung carcinoma. Mice were imaged by micro-CT pre-treatment and stratified into four treatment groups: an antibody inhibiting vascular endothelial growth factor (anti-VEGF), chemotherapy, combination of anti-VEGF and chemotherapy, or control antibody. In the first study, post-treatment imaging was performed 4 weeks later. In the second study, mice were scanned serially on a high-throughput scanner every 2 weeks for 8 weeks during treatment. In both studies, the automated tumor burden estimates were well correlated with manual metrics (r value range: 0.83-0.93, P < .0001) and showed a similar, significant reduction in tumor growth in mice treated with anti-VEGF alone or in combination with chemotherapy. Given the fully automated nature of this technique, the proposed analysis method can provide a valuable tool in preclinical drug research for screening and randomizing animals into treatment groups and evaluating treatment efficacy in mouse models of lung cancer in a highly robust and efficient manner.
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Affiliation(s)
- Kai H Barck
- Department of Biomedical Imaging, Genentech, Inc, South San Francisco, CA, USA
| | - Hani Bou-Reslan
- Department of Biomedical Imaging, Genentech, Inc, South San Francisco, CA, USA
| | - Ujjawal Rastogi
- Department of Biomedical Imaging, Genentech, Inc, South San Francisco, CA, USA
| | - Timothy Sakhuja
- Department of Biomedical Imaging, Genentech, Inc, South San Francisco, CA, USA
| | - Jason E Long
- Department of Translational Oncology, Genentech, Inc, South San Francisco, CA, USA
| | - Rafael Molina
- Department of Translational Oncology, Genentech, Inc, South San Francisco, CA, USA
| | - Anthony Lima
- Department of Discovery Oncology, Genentech, Inc, South San Francisco, CA, USA
| | - Patricia Hamilton
- Department of Discovery Oncology, Genentech, Inc, South San Francisco, CA, USA
| | - Melissa R Junttila
- Department of Translational Oncology, Genentech, Inc, South San Francisco, CA, USA
| | - Leisa Johnson
- Department of Discovery Oncology, Genentech, Inc, South San Francisco, CA, USA
| | - Richard A D Carano
- Department of Biomedical Imaging, Genentech, Inc, South San Francisco, CA, USA.
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8
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Johnson L, Huseni M, Smyczek T, Lima A, Yeung S, Cheng JH, Molina R, Kan D, De Mazière A, Klumperman J, Kasman I, Zhang Y, Dennis MS, Eastham-Anderson J, Jubb AM, Hwang O, Desai R, Schmidt M, Nannini MA, Barck KH, Carano RAD, Forrest WF, Song Q, Chen DS, Naumovski L, Singh M, Ye W, Hegde PS. Anti-EGFL7 antibodies enhance stress-induced endothelial cell death and anti-VEGF efficacy. J Clin Invest 2013; 123:3997-4009. [PMID: 23945239 DOI: 10.1172/jci67892] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 06/13/2013] [Indexed: 01/13/2023] Open
Abstract
Many oncology drugs are administered at their maximally tolerated dose without the knowledge of their optimal efficacious dose range. In this study, we describe a multifaceted approach that integrated preclinical and clinical data to identify the optimal dose for an antiangiogenesis agent, anti-EGFL7. EGFL7 is an extracellular matrix-associated protein expressed in activated endothelium. Recombinant EGFL7 protein supported EC adhesion and protected ECs from stress-induced apoptosis. Anti-EGFL7 antibodies inhibited both of these key processes and augmented anti-VEGF-mediated vascular damage in various murine tumor models. In a genetically engineered mouse model of advanced non-small cell lung cancer, we found that anti-EGFL7 enhanced both the progression-free and overall survival benefits derived from anti-VEGF therapy in a dose-dependent manner. In addition, we identified a circulating progenitor cell type that was regulated by EGFL7 and evaluated the response of these cells to anti-EGFL7 treatment in both tumor-bearing mice and cancer patients from a phase I clinical trial. Importantly, these preclinical efficacy and clinical biomarker results enabled rational selection of the anti-EGFL7 dose currently being tested in phase II clinical trials.
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Affiliation(s)
- Leisa Johnson
- Genentech Inc., South San Francisco, California 94080, USA.
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9
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Singh M, Couto SS, Forrest WF, Lima A, Cheng JH, Molina R, Long JE, Hamilton P, McNutt A, Kasman I, Nannini MA, Reslan HB, Cao TC, Ho CCK, Barck KH, Carano RAD, Foreman O, Eastham-Anderson J, Jubb AM, Ferrara N, Johnson L. Anti-VEGF antibody therapy does not promote metastasis in genetically engineered mouse tumour models. J Pathol 2012; 227:417-30. [PMID: 22611036 DOI: 10.1002/path.4053] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/05/2012] [Accepted: 05/10/2012] [Indexed: 12/15/2022]
Abstract
Resistance to anti-angiogenic therapy can occur via several potential mechanisms. Unexpectedly, recent studies showed that short-term inhibition of either VEGF or VEGFR enhanced tumour invasiveness and metastatic spread in preclinical models. In an effort to evaluate the translational relevance of these findings, we examined the consequences of long-term anti-VEGF monoclonal antibody therapy in several well-validated genetically engineered mouse tumour models of either neuroendocrine or epithelial origin. Anti-VEGF therapy decreased tumour burden and increased overall survival, either as a single agent or in combination with chemotherapy, in all four models examined. Importantly, neither short- nor long-term exposure to anti-VEGF therapy altered the incidence of metastasis in any of these autochthonous models, consistent with retrospective analyses of clinical trials. In contrast, we observed that sunitinib treatment recapitulated previously reported effects on tumour invasiveness and metastasis in a pancreatic neuroendocrine tumour (PNET) model. Consistent with these results, sunitinib treatment resulted in an up-regulation of the hypoxia marker GLUT1 in PNETs, whereas anti-VEGF did not. These results indicate that anti-VEGF mediates anti-tumour effects and therapeutic benefits without a paradoxical increase in metastasis. Moreover, these data underscore the concept that drugs targeting VEGF ligands and receptors may affect tumour metastasis in a context-dependent manner and are mechanistically distinct from one another.
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Affiliation(s)
- Mallika Singh
- Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.
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10
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Carlsson F, Kim J, Dumitru C, Barck KH, Carano RAD, Sun M, Diehl L, Brown EJ. Host-detrimental role of Esx-1-mediated inflammasome activation in mycobacterial infection. PLoS Pathog 2010; 6:e1000895. [PMID: 20463815 PMCID: PMC2865529 DOI: 10.1371/journal.ppat.1000895] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 04/05/2010] [Indexed: 11/19/2022] Open
Abstract
The Esx-1 (type VII) secretion system is a major virulence determinant of pathogenic mycobacteria, including Mycobacterium marinum. However, the molecular events and host-pathogen interactions underlying Esx-1-mediated virulence in vivo remain unclear. Here we address this problem in a non-lethal mouse model of M. marinum infection that allows detailed quantitative analysis of disease progression. M. marinum established local infection in mouse tails, with Esx-1-dependent formation of caseating granulomas similar to those formed in human tuberculosis, and bone deterioration reminiscent of skeletal tuberculosis. Analysis of tails infected with wild type or Esx-1-deficient bacteria showed that Esx-1 enhanced generation of proinflammatory cytokines, including the secreted form of IL-1β, suggesting that Esx-1 promotes inflammasome activation in vivo. In vitro experiments indicated that Esx-1-dependent inflammasome activation required the host NLRP3 and ASC proteins. Infection of wild type and ASC-deficient mice demonstrated that Esx-1-dependent inflammasome activation exacerbated disease without restricting bacterial growth, indicating a host-detrimental role of this inflammatory pathway in mycobacterial infection. These findings define an immunoregulatory role for Esx-1 in a specific host-pathogen interaction in vivo, and indicate that the Esx-1 secretion system promotes disease and inflammation through its ability to activate the inflammasome. With ∼2 million people dying from tuberculosis every year, Mycobacterium tuberculosis represents the single most important bacterial pathogen globally. We use the closely related Mycobacterium marinum to study fundamental aspects of mycobacterial pathogenesis, likely to extend to human tuberculosis. The Esx-1 (type VII) secretion system is a major virulence determinant of pathogenic mycobacteria, including M. tuberculosis and M. marinum. However, a molecular explanation for Esx-1-mediated virulence in vivo has been lacking. Here we address this problem in a non-lethal mouse model of M. marinum infection that allows quantitative analysis of disease progression. M. marinum established local infection with important features of human tuberculosis, including formation of granulomas with caseating centers. Using a combination of bacterial and host mutants, we show that Esx-1-mediated activation of the host inflammasome increases inflammation without restricting bacterial growth, suggesting that activation of the inflammasome during mycobacterial infection is a manifestation of bacterial virulence rather than a manifestation of host response. These findings define a biological role for Esx-1 in a specific host-pathogen interaction in vivo, and imply that the Esx-1 secretion system has evolved specifically to promote host pathology.
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Affiliation(s)
- Fredric Carlsson
- Department of Microbial Pathogenesis, Genentech Inc., South San Francisco, California, United States of America
- * E-mail: (FC); (EJB)
| | - Janice Kim
- Department of Translational Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Calin Dumitru
- Department of Translational Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Kai H. Barck
- Department of Biomedical Imaging, Genentech Inc., South San Francisco, California, United States of America
| | - Richard A. D. Carano
- Department of Biomedical Imaging, Genentech Inc., South San Francisco, California, United States of America
| | - Mei Sun
- Department of Pathology, Genentech Inc., South San Francisco, California, United States of America
| | - Lauri Diehl
- Department of Pathology, Genentech Inc., South San Francisco, California, United States of America
| | - Eric J. Brown
- Department of Microbial Pathogenesis, Genentech Inc., South San Francisco, California, United States of America
- * E-mail: (FC); (EJB)
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11
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Barck KH, Willis B, Ross J, French DM, Filvaroff EH, Carano RAD. Viable tumor tissue detection in murine metastatic breast cancer by whole-body MRI and multispectral analysis. Magn Reson Med 2009; 62:1423-30. [DOI: 10.1002/mrm.22109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Berry LR, Barck KH, Go MA, Ross J, Wu X, Williams SP, Gogineni A, Cole MJ, Van Bruggen N, Fuh G, Peale F, Ferrara N, Ross S, Schwall RH, Carano RAD. Quantification of viable tumor microvascular characteristics by multispectral analysis. Magn Reson Med 2008; 60:64-72. [PMID: 18421695 DOI: 10.1002/mrm.21470] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tumor heterogeneity complicates the quantification of tumor microvascular characteristics assessed by dynamic contrast-enhanced MRI (DCE-MRI). To address this issue a novel approach was developed that combines DCE-MRI with diffusion-based multispectral (MS) analysis to quantify the microvascular characteristics of specific tumor tissue populations. Diffusion-based MS segmentation (feature space: apparent diffusion coefficient, T(2) and proton density) was performed to identify tumor tissue populations and the DCE-MRI characteristics were determined for each tissue class. The ability of this MS DCE-MRI technique to detect microvascular changes due to treatment with an antibody (G6-31) to vascular endothelial growth factor-A (VEGF) was evaluated in a tumor xenograft mouse model. Anti-VEGF treatment resulted in a significant reduction in K(trans) for the MS viable tumor tissue class (-0.0034 +/- 0.0022 min(-1), P < 0.01) at 24 hr posttreatment that differ significantly from the change observed in the control group (0.0002 +/- 0.0025 min(-1)). Viable tumor K(trans) for the anti-VEGF group was also reduced 62% relative to the pretreatment values (P < 0.01). Necrotic tissue classes were found to add only noise to DCE-MRI estimates. This approach provides a means to measure physiological parameters within the viable tumor and address the issue of tumor heterogeneity that complicates DCE-MRI analysis.
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Affiliation(s)
- Leanne R Berry
- Department of Translational Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
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13
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Katschke KJ, Helmy KY, Steffek M, Xi H, Yin J, Lee WP, Gribling P, Barck KH, Carano RAD, Taylor RE, Rangell L, Diehl L, Hass PE, Wiesmann C, van Lookeren Campagne M. A novel inhibitor of the alternative pathway of complement reverses inflammation and bone destruction in experimental arthritis. ACTA ACUST UNITED AC 2007; 204:1319-25. [PMID: 17548523 PMCID: PMC2118595 DOI: 10.1084/jem.20070432] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [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] [Indexed: 01/12/2023]
Abstract
Complement is an important component of the innate and adaptive immune response, yet complement split products generated through activation of each of the three complement pathways (classical, alternative, and lectin) can cause inflammation and tissue destruction. Previous studies have shown that complement activation through the alternative, but not classical, pathway is required to initiate antibody-induced arthritis in mice, but it is unclear if the alternative pathway (AP) plays a role in established disease. Previously, we have shown that human complement receptor of the immunoglobulin superfamily (CRIg) is a selective inhibitor of the AP of complement. Here, we present the crystal structure of murine CRIg and, using mutants, provide evidence that the structural requirements for inhibition of the AP are conserved in human and mouse. A soluble form of CRIg reversed inflammation and bone loss in two experimental models of arthritis by inhibiting the AP of complement in the joint. Our data indicate that the AP of complement is not only required for disease induction, but also disease progression. The extracellular domain of CRIg thus provides a novel tool to study the effects of inhibiting the AP of complement in established disease and constitutes a promising therapeutic with selectivity for a single complement pathway.
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14
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Barck KH, Lee WP, Diehl LJ, Ross J, Gribling P, Zhang Y, Nguyen K, van Bruggen N, Hurst S, Carano RAD. Quantification of cortical bone loss and repair for therapeutic evaluation in collagen-induced arthritis, by micro-computed tomography and automated image analysis. ACTA ACUST UNITED AC 2004; 50:3377-86. [PMID: 15476252 DOI: 10.1002/art.20557] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [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: 11/07/2022]
Abstract
OBJECTIVE Ex vivo and in vivo micro-computed tomography (micro-CT) combined with a novel image analysis algorithm were used to quantify cortical bone loss and periosteal new bone formation for therapeutic evaluation in a murine model of collagen-induced arthritis. METHODS An automated algorithm was created to locate 5 metatarsophalangeal and 3 metacarpophalangeal joints in 3-dimensional micro-CT images of mouse paws for evaluation of joint cortical bone volume (JCBV) within close proximity of the joints as well as cortical bone mineral density and periosteal new bone formation within the paws. For validation, automated estimates of JCBV were compared with radiographic visual scores (RVS) in 4 treatment groups (n = 9 per group): rat anti-mouse CD11a monoclonal antibody, methotrexate (MTX), anti-CD11a plus MTX, and saline only. In a separate study, serial images of hind limbs were evaluated in 2 treatment groups: murine tumor necrosis factor receptor II-Fc fusion protein (mTNFRII; n = 10) and control antibody (n = 7). RESULTS Automated estimates of the JCBV were significantly correlated with the RVS (hind paws R = -0.94, front paws R = -0.81, combined R = -0.87). The anti-CD11a group had significantly higher JCBV compared with controls. In the serial study, the automated estimate of JCBV detected significant treatment effects in the mTNFRII-Fc group compared with controls. Cortical bone mineral density was significantly higher in all treatment groups compared with controls. CONCLUSION Micro-CT combined with a novel image analysis technique (estimation of JCBV) provides a fully automated means to quantify bone destruction in a mouse model of rheumatoid arthritis.
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MESH Headings
- Algorithms
- Animals
- Arthritis, Experimental/chemically induced
- Arthritis, Experimental/diagnostic imaging
- Arthritis, Experimental/pathology
- Arthritis, Experimental/therapy
- Arthritis, Rheumatoid/chemically induced
- Arthritis, Rheumatoid/diagnostic imaging
- Arthritis, Rheumatoid/pathology
- Arthritis, Rheumatoid/therapy
- Autoantibodies/therapeutic use
- Bone Density
- CD11a Antigen/administration & dosage
- CD11a Antigen/immunology
- Collagen
- Male
- Methotrexate/administration & dosage
- Methotrexate/therapeutic use
- Mice
- Mice, Inbred DBA
- Osteogenesis
- Tomography, X-Ray Computed/methods
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Affiliation(s)
- Kai H Barck
- Genentech, Inc., South San Francisco, California 94080, USA
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