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Al-Mustanjid M, Mahmud SMH, Akter F, Rahman MS, Hossen MS, Rahman MH, Moni MA. Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. INFORMATICS IN MEDICINE UNLOCKED 2022; 32:101003. [PMID: 35818398 PMCID: PMC9259025 DOI: 10.1016/j.imu.2022.101003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating since 2019, and its global dominance is rising. Evidences suggest the respiratory illness SARS-CoV-2 has a sensitive affect on causing organ damage and other complications to the patients with autoimmune diseases (AD), posing a significant risk factor. The genetic interrelationships and molecular appearances between SARS-CoV-2 and AD are yet unknown. We carried out the transcriptomic analytical framework to delve into the SARS-CoV-2 impacts on AD progression. We analyzed both gene expression microarray and RNA-Seq datasets from SARS-CoV-2 and AD affected tissues. With neighborhood-based benchmarks and multilevel network topology, we obtained dysfunctional signaling and ontological pathways, gene disease (diseasesome) association network and protein-protein interaction network (PPIN), uncovered essential shared infection recurrence connectivities with biological insights underlying between SARS-CoV-2 and AD. We found a total of 77, 21, 9, 54 common DEGs for SARS-CoV-2 and inflammatory bowel disorder (IBD), SARS-CoV-2 and rheumatoid arthritis (RA), SARS-CoV-2 and systemic lupus erythematosus (SLE) and SARS-CoV-2 and type 1 diabetes (T1D). The enclosure of these common DEGs with bimolecular networks revealed 10 hub proteins (FYN, VEGFA, CTNNB1, KDR, STAT1, B2M, CD3G, ITGAV, TGFB3). Drugs such as amlodipine besylate, vorinostat, methylprednisolone, and disulfiram have been identified as a common ground between SARS-CoV-2 and AD from drug repurposing investigation which will stimulate the optimal selection of medications in the battle against this ongoing pandemic triggered by COVID-19.
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Affiliation(s)
- Md Al-Mustanjid
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - S M Hasan Mahmud
- Department of Computer Science, American International University-Bangladesh, Dhaka, 1229, Bangladesh
| | - Farzana Akter
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Shazzadur Rahman
- Department of Computer Science & Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Sajid Hossen
- Department of Software Engineering, Faculty of Science and Information Technology, Daffodil International University, Dhaka-1207, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia-7003, Bangladesh
| | - Mohammad Ali Moni
- Department of Computer Science and Engineering, Pabna Science & Technology University, Pabna, 6600, Bangladesh
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Cheng FJ, Zhou XJ, Zhao YF, Zhao MH, Zhang H. Chemokine receptor 5 (CCR5) delta 32 polymorphism in lupus nephritis: a large case-control study and meta-analysis. Autoimmunity 2014; 47:383-8. [PMID: 24720467 DOI: 10.3109/08916934.2014.906581] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Recent animal experiments showed that CCR5-deficient lupus mice (CCR5(-/-)) were closely associated with aggravated lupus nephritis. CCR5 Δ32 variation, a nonsynonymous mutation of CCR5, resulted in altered CCR5 function. However, the CCR5 Δ32 mutation in human lupus nephritis has been rarely reported in the literature. METHODS A large case-control study that included 2010 samples from a Chinese population was conducted, followed by a meta-analysis combining the current and previously published studies to explore the effect of CCR5 Δ32 on lupus nephritis susceptibility. RESULTS Four CCR5 Δ32 heterozygote carriers were detected in lupus nephritis patients only. We detected no CCR5 Δ32 homozygotes in our study population. In the meta-analysis, including 1,092 cases and 2,229 controls, we found great heterogeneity between studies (p < 0.001, I(2)( )= 89.6%). Furthermore, stratified and sensitivity analyses suggested that ethnicity and CCR5 Δ32 allele frequency were the main origin of heterogeneity. In the subgroups without obvious heterogeneity, we observed a positive correlation between CCR5 Δ32 and lupus nephritis risk (p < 0.05). CONCLUSIONS Our study confirmed that the CCR5 Δ32 mutation is a very rare variation found in the Chinese population with Han ethnicity. However, CCR5 Δ32 might play a role in lupus nephritis susceptibility. Future replications and functional studies are needed.
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Affiliation(s)
- Fa-Juan Cheng
- Renal Division, Department of Medicine, Peking University First Hospital , Beijing , China
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Sarkar SA, Lee CE, Victorino F, Nguyen TT, Walters JA, Burrack A, Eberlein J, Hildemann SK, Homann D. Expression and regulation of chemokines in murine and human type 1 diabetes. Diabetes 2012; 61:436-46. [PMID: 22210319 PMCID: PMC3266427 DOI: 10.2337/db11-0853] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
More than one-half of the ~50 human chemokines have been associated with or implicated in the pathogenesis of type 1 diabetes, yet their actual expression patterns in the islet environment of type 1 diabetic patients remain, at present, poorly defined. Here, we have integrated a human islet culture system, murine models of virus-induced and spontaneous type 1 diabetes, and the histopathological examination of pancreata from diabetic organ donors with the goal of providing a foundation for the informed selection of potential therapeutic targets within the chemokine/receptor family. Chemokine (C-C motif) ligand (CCL) 5 (CCL5), CCL8, CCL22, chemokine (C-X-C motif) ligand (CXCL) 9 (CXCL9), CXCL10, and chemokine (C-X3-C motif) ligand (CX3CL) 1 (CX3CL1) were the major chemokines transcribed (in an inducible nitric oxide synthase-dependent but not nuclear factor-κB-dependent fashion) and translated by human islet cells in response to in vitro inflammatory stimuli. CXCL10 was identified as the dominant chemokine expressed in vivo in the islet environment of prediabetic animals and type 1 diabetic patients, whereas CCL5, CCL8, CXCL9, and CX3CL1 proteins were present at lower levels in the islets of both species. Of importance, additional expression of the same chemokines in human acinar tissues emphasizes an underappreciated involvement of the exocrine pancreas in the natural course of type 1 diabetes that will require consideration for additional type 1 diabetes pathogenesis and immune intervention studies.
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Affiliation(s)
- Suparna A. Sarkar
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
| | - Catherine E. Lee
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
| | - Francisco Victorino
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
- Integrated Department of Immunology, University of Colorado Denver and National Jewish Health, Denver, Colorado
| | - Tom T. Nguyen
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
| | - Jay A. Walters
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
| | - Adam Burrack
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
- Integrated Department of Immunology, University of Colorado Denver and National Jewish Health, Denver, Colorado
| | - Jens Eberlein
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
| | | | - Dirk Homann
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, Colorado
- Integrated Department of Immunology, University of Colorado Denver and National Jewish Health, Denver, Colorado
- Department of Anesthesiology, University of Colorado Denver, Aurora, Colorado
- Corresponding author: Dirk Homann,
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Smyth DJ, Plagnol V, Walker NM, Cooper JD, Downes K, Yang JHM, Howson JMM, Stevens H, McManus R, Wijmenga C, Heap GA, Dubois PC, Clayton DG, Hunt KA, van Heel DA, Todd JA. Shared and distinct genetic variants in type 1 diabetes and celiac disease. N Engl J Med 2008; 359:2767-77. [PMID: 19073967 PMCID: PMC2840835 DOI: 10.1056/nejmoa0807917] [Citation(s) in RCA: 555] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Two inflammatory disorders, type 1 diabetes and celiac disease, cosegregate in populations, suggesting a common genetic origin. Since both diseases are associated with the HLA class II genes on chromosome 6p21, we tested whether non-HLA loci are shared. METHODS We evaluated the association between type 1 diabetes and eight loci related to the risk of celiac disease by genotyping and statistical analyses of DNA samples from 8064 patients with type 1 diabetes, 9339 control subjects, and 2828 families providing 3064 parent-child trios (consisting of an affected child and both biologic parents). We also investigated 18 loci associated with type 1 diabetes in 2560 patients with celiac disease and 9339 control subjects. RESULTS Three celiac disease loci--RGS1 on chromosome 1q31, IL18RAP on chromosome 2q12, and TAGAP on chromosome 6q25--were associated with type 1 diabetes (P<1.00x10(-4)). The 32-bp insertion-deletion variant on chromosome 3p21 was newly identified as a type 1 diabetes locus (P=1.81x10(-8)) and was also associated with celiac disease, along with PTPN2 on chromosome 18p11 and CTLA4 on chromosome 2q33, bringing the total number of loci with evidence of a shared association to seven, including SH2B3 on chromosome 12q24. The effects of the IL18RAP and TAGAP alleles confer protection in type 1 diabetes and susceptibility in celiac disease. Loci with distinct effects in the two diseases included INS on chromosome 11p15, IL2RA on chromosome 10p15, and PTPN22 on chromosome 1p13 in type 1 diabetes and IL12A on 3q25 and LPP on 3q28 in celiac disease. CONCLUSIONS A genetic susceptibility to both type 1 diabetes and celiac disease shares common alleles. These data suggest that common biologic mechanisms, such as autoimmunity-related tissue damage and intolerance to dietary antigens, may be etiologic features of both diseases.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antigens, CD/genetics
- Autoimmunity/genetics
- CTLA-4 Antigen
- Celiac Disease/genetics
- Celiac Disease/immunology
- Child
- Child, Preschool
- Cytoskeletal Proteins/genetics
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/immunology
- Female
- Genetic Linkage
- Genetic Predisposition to Disease
- Humans
- Infant
- Interleukin-12 Subunit p35/genetics
- Interleukin-18 Receptor beta Subunit/genetics
- Interleukin-2 Receptor alpha Subunit/genetics
- Intracellular Signaling Peptides and Proteins
- LIM Domain Proteins
- Male
- Middle Aged
- Polymorphism, Single Nucleotide
- Protein Tyrosine Phosphatase, Non-Receptor Type 2/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 22/genetics
- Proteins/genetics
- RGS Proteins/genetics
- Receptors, CCR5/genetics
- Young Adult
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Affiliation(s)
- Deborah J Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Vincent Plagnol
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Neil M Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Jason D Cooper
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Kate Downes
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Jennie HM Yang
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Joanna MM Howson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Helen Stevens
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Ross McManus
- Department of Clinical Medicine, Institute of Molecular Medicine, Trinity College Dublin, Dublin, Ireland
| | - Cisca Wijmenga
- Genetics Department, University Medical Center and Groningen University, Groningen, 9700 RB Groningen, The Netherlands
| | - Graham A. Heap
- Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Newark Street, London, E1 2AT, UK
| | - Patrick C. Dubois
- Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Newark Street, London, E1 2AT, UK
| | - David G. Clayton
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Karen A Hunt
- Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Newark Street, London, E1 2AT, UK
| | - David A van Heel
- Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Newark Street, London, E1 2AT, UK
| | - John A Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
- Correspondence to Prof. John Todd Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK Phone 01223 762101 FAX 01223 762103
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Balistreri CR, Caruso C, Grimaldi MP, Listì F, Vasto S, Orlando V, Campagna AM, Lio D, Candore G. CCR5 receptor: biologic and genetic implications in age-related diseases. Ann N Y Acad Sci 2007; 1100:162-72. [PMID: 17460174 DOI: 10.1196/annals.1395.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The CC chemokine receptor 5 (CCR5) is a member of CC-chemokine receptor family. CCR5 has the characteristic structure of a seven transmembrane G protein-coupled receptor (GPCR), which regulates trafficking and effector functions of memory/effector Th1 cells, macrophages, NK cells, and immature dendritic cells. CCR5 and its ligands are important molecules in viral pathogenesis. CCR5 represents the co-receptor for macrophage (M) and dual (T cell and M)-tropic immunodeficiency viruses. Recent evidence has also demonstrated the role of CCR5 in a variety of human diseases, ranging from infectious and inflammatory diseases to cancer. In this article, we describe the involvement of CCR5 in two age-related diseases, atherosclerosis and Alzheimer's disease, suggesting a possible role of chemokine system on these diseases' pathophysiology. Finally, we review the data on the probable association between CCR5Delta32 deletion and cardiovascular diseases and Alzheimer's disease.
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Affiliation(s)
- Carmela Rita Balistreri
- Gruppo di Studio sull'Immunosenescenza, Dipartimento di Biopatologia e Metodologie Biomediche, Corso Tukory 211, 90134 Palermo, Italy.
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Overbergh L, Gysemans C, Mathieu C. Quantification of chemokines by real-time reverse transcriptase PCR: applications in type 1 diabetes. Expert Rev Mol Diagn 2007; 6:51-64. [PMID: 16359267 DOI: 10.1586/14737159.6.1.51] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Type 1 diabetes is a T-cell mediated autoimmune disease, characterized by the destruction of insulin-producing pancreatic beta-cells. This review will discuss the role of chemokines in the recruitment of immune cells leading to the pathology of this disease. There will be a focus on the quantification of chemokines and chemokine receptors by the recently developed real-time reverse transcriptase PCR technique. Today, this technique is in widespread use for analysis of chemokines in cells, tissues and tissue biopsies. The minute amount of tissue needed for analysis, as well as the very high sensitivity of this method, make it the method of choice for analysis of chemokines, which are often expressed at very low levels in target tissues. However, validation and optimization of the technique is of crucial importance for obtaining reliable results.
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Affiliation(s)
- Lut Overbergh
- Laboratory for Experimental Medicine & Endocrinology (LEGENDO), University Hospital Gasthuisberg, Catholic University of Leuven, Leuven, Belgium.
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Zhernakova A, Alizadeh BZ, Eerligh P, Hanifi-Moghaddam P, Schloot NC, Diosdado B, Wijmenga C, Roep BO, Koeleman BPC. Genetic variants of RANTES are associated with serum RANTES level and protection for type 1 diabetes. Genes Immun 2006; 7:544-9. [PMID: 16855620 DOI: 10.1038/sj.gene.6364326] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RANTES (regulated on activation, normal T-cell expressed and secreted) is a T-helper type 1 (Th1) chemokine that promotes T-cell activation and proliferation. RANTES is genetically associated with asthma, sarcoidosis and multiple sclerosis. The concentration of RANTES is increased at inflammation sites in different autoimmune diseases. Type 1 diabetes (T1D) is a Th1-mediated disease with complex genetic predisposition. We tested RANTES as a candidate gene for association with T1D using three single-nucleotide polymorphism (SNP) variants (rs4251719, rs2306630 and rs2107538) to capture haplotype information. The minor alleles of all SNPs were transmitted less frequently to T1D offspring (transmission rates 37.3% (P=0.002), 38.7% (P=0.007) and 41.0% (P=0.01)) and were less frequently present in patients compared to controls (P=0.009, 0.03 and 0.04, respectively). A similar protective effect was observed for the haplotype carrying three minor alleles (transmission disequilibrium test (TDT): P=0.003; odds ratio (OR)=0.55; confidence interval (CI): 0.37-0.83; case/control: P=0.03; OR=0.74; CI: 0.55-0.98). Both patients and controls carrying the protective haplotype express significantly lower serum levels of RANTES compared to non-carriers. Subsequently, we tested a cohort of 310 celiac disease patients, but failed to detect association. RANTES SNPs are significantly associated with RANTES serum concentration and development of T1D. The rs4251719*A-rs2306630*A-rs2107538*A haplotype associated with low RANTES production confers protection from T1D. Our data imply that RANTES is associated with T1D both genetically and functionally, and contributes to diabetes-prone Th1 cytokine profile.
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Affiliation(s)
- A Zhernakova
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
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Ribeiro S, Horuk R. The clinical potential of chemokine receptor antagonists. Pharmacol Ther 2005; 107:44-58. [PMID: 15894378 DOI: 10.1016/j.pharmthera.2005.01.004] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Accepted: 01/18/2005] [Indexed: 11/19/2022]
Abstract
Chemokines belong to a family of chemotactic cytokines that direct the migration of immune cells towards sites of inflammation. They mediate their biological effects by binding to cell surface receptors, which belong to the G protein-coupled receptor superfamily. Since chemokines and their receptors have been implicated in the pathophysiology of a number of autoinflammatory diseases, chemokine receptor antagonists could prove to be useful therapeutics to target these diseases. Here, we review the role of chemokines in autoimmunity, concentrating mainly on the chemokine receptors CCR1 and CCR5, and discuss the potential utility of antagonists that target these 2 receptors as they progress through the clinic.
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Affiliation(s)
- Sofia Ribeiro
- Department of Molecular Pharmacology, Berlex Biosciences, 2600 Hilltop Drive, Richmond, CA 94804, USA
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