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Kletzl H, Marquet A, Günther A, Tang W, Heuberger J, Groeneveld GJ, Birkhoff W, Mercuri E, Lochmüller H, Wood C, Fischer D, Gerlach I, Heinig K, Bugawan T, Dziadek S, Kinch R, Czech C, Khwaja O. The oral splicing modifier RG7800 increases full length survival of motor neuron 2 mRNA and survival of motor neuron protein: Results from trials in healthy adults and patients with spinal muscular atrophy. Neuromuscul Disord 2018; 29:21-29. [PMID: 30553700 DOI: 10.1016/j.nmd.2018.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 06/22/2018] [Revised: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 11/15/2022]
Abstract
Spinal muscular atrophy (SMA) is a rare genetic and progressively debilitating neuromuscular disease. It is the leading genetic cause of death among infants. In SMA, low levels of survival of motor neuron (SMN) protein lead to motor neuron death and muscle atrophy as the SMN protein is critical to motor neuron survival. SMA is caused by mutations in, or deletion of, the SMN1 gene. A second SMN gene, SMN2, produces only low levels of functional SMN protein due to alternative splicing which excludes exon 7 from most transcripts, generating truncated, rapidly degraded SMN protein. Patients with SMA rely on limited expression of functional SMN full-length protein from the SMN2 gene, but insufficient levels are generated. RG7800 is an oral, selective SMN2 splicing modifier designed to modulate alternative splicing of SMN2 to increase the levels of functional SMN protein. In two trials, oral administration of RG7800 increased in blood full-length SMN2 mRNA expression in healthy adults and SMN protein levels in SMA patients by up to two-fold, which is expected to provide clinical benefit.
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Affiliation(s)
- Heidemarie Kletzl
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland.
| | - Anne Marquet
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Andreas Günther
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Wakana Tang
- Research, Genomics & Oncology, Roche Molecular Systems, Inc., Pleasanton, USA
| | | | | | | | | | - Hanns Lochmüller
- Medical Center-University of Freiburg, Freiburg, Germany; Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK; Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada and Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | - Claire Wood
- John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Dirk Fischer
- Universitäts-Kinderspital beider Basel, Basel, Switzerland; University Clinic of Internal Medicine, Kantonsspital Baselland, Bruderholz, Switzerland
| | - Irene Gerlach
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Katja Heinig
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Teodorica Bugawan
- Research, Genomics & Oncology, Roche Molecular Systems, Inc., Pleasanton, USA
| | - Sebastian Dziadek
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Russell Kinch
- Roche Innovation Center, Hoffmann-La Roche Ltd., Welwyn, UK
| | - Christian Czech
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Omar Khwaja
- Roche Innovation Center, Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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Czech C, Tang W, Bugawan T, Mano C, Horn C, Iglesias VA, Fröhner S, Zaworski PG, Paushkin S, Chen K, Kremer T. Biomarker for Spinal Muscular Atrophy: Expression of SMN in Peripheral Blood of SMA Patients and Healthy Controls. PLoS One 2015; 10:e0139950. [PMID: 26468953 PMCID: PMC4607439 DOI: 10.1371/journal.pone.0139950] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [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: 05/13/2015] [Accepted: 09/17/2015] [Indexed: 11/24/2022] Open
Abstract
Spinal muscular atrophy is caused by a functional deletion of SMN1 on Chromosome 5, which leads to a progressive loss of motor function in affected patients. SMA patients have at least one copy of a similar gene, SMN2, which produces functional SMN protein, although in reduced quantities. The severity of SMA is variable, partially due to differences in SMN2 copy numbers. Here, we report the results of a biomarker study characterizing SMA patients of varying disease severity. SMN copy number, mRNA and Protein levels in whole blood of patients were measured and compared against a cohort of healthy controls. The results show differential regulation of expression of SMN2 in peripheral blood between patients and healthy subjects.
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Affiliation(s)
- Christian Czech
- Roche Pharmaceutical Research & Early Development, Neuroscience, Roche Innovation Center Basel F. Hoffmann –La Roche, Basel
- * E-mail:
| | - Wakana Tang
- Research - Genomics & Oncology, Roche Molecular Systems, Inc., Pleasanton, CA, United States of America
| | - Teodorica Bugawan
- Research - Genomics & Oncology, Roche Molecular Systems, Inc., Pleasanton, CA, United States of America
| | - Calvin Mano
- Research - Genomics & Oncology, Roche Molecular Systems, Inc., Pleasanton, CA, United States of America
| | - Carsten Horn
- Roche Pharmaceutical Research & Early Development, Neuroscience, Roche Innovation Center Basel F. Hoffmann –La Roche, Basel
| | - Victor Alejandro Iglesias
- Roche Pharmaceutical Research & Early Development, Neuroscience, Roche Innovation Center Basel F. Hoffmann –La Roche, Basel
| | | | | | | | - Karen Chen
- SMA Foundation, New York, NY, United States of America
| | - Thomas Kremer
- Roche Pharmaceutical Research & Early Development, Neuroscience, Roche Innovation Center Basel F. Hoffmann –La Roche, Basel
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Simpson M, Brady H, Yin X, Seifert J, Barriga K, Hoffman M, Bugawan T, Barón AE, Sokol RJ, Eisenbarth G, Erlich H, Rewers M, Norris JM. No association of vitamin D intake or 25-hydroxyvitamin D levels in childhood with risk of islet autoimmunity and type 1 diabetes: the Diabetes Autoimmunity Study in the Young (DAISY). Diabetologia 2011; 54:2779-88. [PMID: 21858504 PMCID: PMC3478880 DOI: 10.1007/s00125-011-2278-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 07/25/2011] [Indexed: 12/19/2022]
Abstract
AIMS/HYPOTHESIS The aim of the study was to investigate the association between vitamin D intake and status and the risk of islet autoimmunity (IA) and subsequent type 1 diabetes in children at increased risk of type 1 diabetes. METHODS The Diabetes Autoimmunity Study in the Young (DAISY) in Denver, CO, USA, has been following children at increased risk of diabetes since 1993. As of February 2011, 198 children developed IA during follow-up of 2,644 DAISY children. Vitamin D intake and plasma 25-hydroxyvitamin D [25(OH)D] were measured longitudinally. Proportional hazards regression analyses of time to IA, or type 1 diabetes in IA-positive children, were conducted, with vitamin D intake and 25(OH)D as time-varying covariates. HRs were calculated for a standard deviation difference in exposure, with adjustment for confounders. RESULTS Intake of vitamin D was not associated with the risk of IA (adjusted HR 1.13; 95% CI 0.95, 1.35; p = 0.18) nor progression to diabetes in IA-positive children (adjusted HR 1.30; 95% CI 0.91, 1.86; p = 0.15). Moreover, 25(OH)D level was not associated with the risk of IA (adjusted HR 1.12; 95% CI 0.88, 1.43; p = 0.36), nor progression to diabetes in IA-positive children (adjusted HR 0.91; 95% CI 0.68, 1.22; p = 0.54). In the 128 children in whom we measured 25(OH)D at 9 months of age, 25(OH)D was not associated with risk of IA (n = 30 IA-positive children) (adjusted HR 1.02; 95% CI 0.96, 1.07; p = 0.58). CONCLUSIONS/INTERPRETATION Neither vitamin D intake nor 25(OH)D levels throughout childhood were associated with the risk of IA or progression to type 1 diabetes in our population.
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Affiliation(s)
- M. Simpson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, 13001 East 17th Place, Campus Box B119, Aurora, CO 80045, USA
| | - H. Brady
- University of Colorado Boulder, Boulder, CO, USA
| | - X. Yin
- Colorado School of Public Health, Department of Biostatistics and Informatics, University of Colorado, Aurora, CO, USA
| | - J. Seifert
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, 13001 East 17th Place, Campus Box B119, Aurora, CO 80045, USA
| | - K. Barriga
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - M. Hoffman
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - T. Bugawan
- Roche Molecular Systems Inc., Alameda, CA, USA
| | - A. E. Barón
- Colorado School of Public Health, Department of Biostatistics and Informatics, University of Colorado, Aurora, CO, USA
| | - R. J. Sokol
- The Children’s Hospital of Denver, Aurora, CO, USA
| | - G. Eisenbarth
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - H. Erlich
- Roche Molecular Systems Inc., Alameda, CA, USA
| | - M. Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - J. M. Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, 13001 East 17th Place, Campus Box B119, Aurora, CO 80045, USA
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Bugawan T, Isoda W, Mano C, Blair A, Mallal S, Thorborn D, Erlich H. 163-P: HLA-B*5701 Taqman assay for abacavir sensitivity; application to PREDICT-1 trials. Hum Immunol 2008. [DOI: 10.1016/j.humimm.2008.08.182] [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: 10/21/2022]
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Hollenbach J, Bugawan T, Sudman M, Thomson G, Thompson S, Ryan M, Langefeld C, Erlich H, Glass D. 177-P: Association of HLA-DR-DQ haplotypes with juvenile idiopathic arthritis (JIA). Hum Immunol 2008. [DOI: 10.1016/j.humimm.2008.08.196] [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: 10/21/2022]
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Rhodes SL, Erlich H, Im KA, Wang J, Li J, Bugawan T, Jeffers L, Tong X, Su X, Rosen HR, Yee LJ, Liang TJ, Yang H. Associations between the human MHC and sustained virologic response in the treatment of chronic hepatitis C virus infection. Genes Immun 2008; 9:328-33. [PMID: 18418397 DOI: 10.1038/gene.2008.21] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The human major histocompatability complex (MHC) genes encode the human leukocyte antigens, which are important in antigen presentation and regulation of CD8+ and CD4+ T cells. Response to therapies in hepatitis C virus (HCV) infection is highly variable (30-80%) and lower response rates have been reported among African Americans (AA; approximately 30%) compared to Caucasian Americans (CA; approximately 50%) infected with genotype-1 viruses. We evaluated whether MHC gene variants were associated with response to therapy and racial differences in AA and CA sustained virologic response (SVR) rates. We genotyped alleles at 8 MHC loci: 3 class I (A, B and C) and 5 class II (DRB1, DQA1, DQB1, DPA1 and DPB1) loci in 373 individuals (179 AA and 194 CA) with genotype-1 HCV infections, who were treated with peginterferon-alpha-2a and ribavirin. We observed carriage of A(*)02 (RR=1.33(1.08-1.64); P=0.008), B(*)58 (RR=1.84(1.24-2.73); P=0.002) and DPB1(*)1701 (RR=1.57(1.09-2.26); P=0.015) to be associated with SVR after adjustment for other predictors of response. In analysis of AA and CA subgroups separately, we observed potential, though not statistically significant, differences in these MHC associations. Variation in the immunogenetic background of HCV-infected individuals might account for some observed variation in viral-specific immunity and courses of disease. In this regard, future studies examining broader patient populations are warranted.
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Affiliation(s)
- S L Rhodes
- Cedars Sinai Medical Center, Los Angeles, CA, USA
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Moonsamy PV, Blair A, Bonella P, Hoglund B, Sali P, Hodge A, Post J, Noble J, Bugawan T, Erlich H. HLA and SNP co-amplification and multiplex assays for estimating Type 1 diabetes genetic risk. Hum Immunol 2004. [DOI: 10.1016/j.humimm.2004.07.058] [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: 11/29/2022]
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Cruz TD, Valdes AM, Santiago A, Frazer de Llado T, Raffel LJ, Zeidler A, Rotter JI, Erlich HA, Rewers M, Bugawan T, Noble JA. DPB1 alleles are associated with type 1 diabetes susceptibility in multiple ethnic groups. Diabetes 2004; 53:2158-63. [PMID: 15277401 DOI: 10.2337/diabetes.53.8.2158] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genetic associations between type 1 diabetes and alleles at the HLA class II locus DPB1 have been previously reported. Observed associations could be due to variation in the DPB1 locus itself or to linkage disequilibrium (LD) between DPB1 alleles and other susceptibility loci. One measure of whether the association of an allele with a disease reflects a true effect of the locus or is simply due to LD is the observation of that association in multiple ethnic groups. Previous type 1 diabetes associations have been reported for DPB1*0301 and DPB1*0202 (predisposing) and for DPB1*0402 (protective). In this study, results are reported from testing these associations in three different sample sets: 1) Puerto Rican case and control subjects, 2) Mexican-American simplex families, and 3) high-risk (DR3/DR4) individuals with and without an affected relative. DPB1*0301 was associated in all three groups, even after accounting for LD with DRB1-DQB1. DPB1*0202 and DPB1*0402 were positively and negatively associated, respectively, in two of the three populations. These results suggest that the observed DPB1 associations, especially that of the DPB1*0301 allele, with type 1 diabetes are likely to be true associations. This supports the concept that multiple genes in the HLA region can affect type 1 diabetes susceptibility.
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Affiliation(s)
- Thomas D Cruz
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
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Petrone A, Battelino T, Krzisnik C, Bugawan T, Erlich H, Di Mario U, Pozzilli P, Buzzetti R. Similar incidence of type 1 diabetes in two ethnically different populations (Italy and Slovenia) is sustained by similar HLA susceptible/protective haplotype frequencies. Tissue Antigens 2002; 60:244-53. [PMID: 12445307 DOI: 10.1034/j.1399-0039.2002.600306.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The incidence of type 1 diabetes (T1DM) seems to depend in part on the population frequencies of susceptible and protective HLA haplotypes. The present study aimed to (i): characterize the genetic susceptibility to T1DM in the Slovenian population, (ii) test the general hypothesis that T1DM incidence is related to the frequencies of susceptible/protective haplotypes, (iii) compare allele, haplotype and genotype frequencies in Slovenians and Italians that represent two white populations with a similar incidence of T1DM (7.9/100,000/year and 8.1/100,000/year, respectively). The haplotype found most frequently among Slovenian T1DM patients was DRB1*0301-DQA1*0501-DQB1*0201 (53%). The DR4-DQA1*0301-DQB1*0302 haplotypes conferring susceptibility to T1DM were those bearing DRB1*0401 (OR = 12), DRB1*0404 (OR = 4.7) and DRB1*0402 (OR = 4.5). Negative associations with the disease were found for the following haplotypes: DRB1*1501-DQA1*0102-DQB1*0602, DRB1*1301-DQA1*0102-DQB1*0603, DRB1*1101/1104-DQA1*0501-DQB1*0301, and DRB1*1401-DQA1*0101-DQB1*0503. Our findings indicate that the low frequencies of susceptible genotypes, in particular, DR3-DQA1*0501-DQB1*0201/DR4-DQA1*0301-DQB1*0302, together with a high frequency of protective haplotypes, could in part explain the low incidence of T1DM in the Slovenian population. The combined frequencies of susceptible genotypes were similar in the two populations (Slovenia = 19.2%, Italy = 17.6%), and the 95% confidence limits of the OR values for each genotype in the two populations overlapped, indicating no significant differences between the values. We conclude that the similar incidences of T1DM in Italian and Slovenian populations are in part a reflection of similar frequencies of HLA susceptible/protective haplotypes.
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Affiliation(s)
- A Petrone
- Endocrinologia, Dipartimento di Scienze Cliniche, University La Sapienza, Rome, Italy
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Fries JF, Wolfe F, Apple R, Erlich H, Bugawan T, Holmes T, Bruce B. HLA-DRB1 genotype associations in 793 white patients from a rheumatoid arthritis inception cohort: frequency, severity, and treatment bias. Arthritis Rheum 2002; 46:2320-9. [PMID: 12355479 DOI: 10.1002/art.10485] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE The HLA-DRB1 "shared epitope" (SE) genotypes are associated with rheumatoid arthritis (RA), but it remains controversial whether the association is with incidence, severity, or both, whether there are associations in seronegative patients, and whether different DRB1 alleles that contain the SE have similar effects on RA susceptibility and/or severity. The present study was undertaken to study these issues in a large cohort of patients with RA. METHODS White patients with RA of <6 months' duration (n = 793) were enrolled in an inception cohort. HLA-DRB1 typing was performed, and patients were categorized into 21 DRB1 genotype groups. The disability index of the Health Assessment Questionnaire was the primary outcome measure. RESULTS DRB1 associations in seronegative RA patients closely resembled those in controls. Of seropositive patients, 21% had 2 copies of the epitope, 52% had 1 copy, and 27% had none. However, not all genotypes with 1 copy were associated with increased susceptibility; for example, frequencies of DRB1*0404/X and *01/X did not differ from those in controls. Absolute differences between seropositive RA patients and controls were greatest for DRB1*0401 homozygosity (3.8% versus 0.8%, respectively) and *0401/0404 heterozygosity (4.7% versus 1.0%). DRB1*0404 was increased in frequency in seropositive RA but, unlike *0401, an increased frequency was seen only with 2 epitope copies. The relatively rare DRB1*10 had an unexpected association with seropositive RA, being present in 1.7% of seropositive RA patients and 0.7% of controls, and also showed a trend toward association with greater disease severity. The presence of 2 epitope copies was associated with increased frequency of seropositivity and younger age at disease onset, not with disease severity. Treatment indication bias was substantial and may have accounted for some of these effects. HLA-DRB1*0401/0404 was found much more frequently in men and in patients with a lower age at disease onset, and there was a trend toward a higher frequency of *0404/0401 in women. CONCLUSION This large inception cohort study confirms previously identified major associations and provides additional insights. Only one dominant association was found: *0401, which differs from other SE alleles in a single Lys-for-Arg substitution. The association of the rare DRB1*10 allele has not previously been postulated. Sex associations were confirmed. Associations with seronegative RA were not seen. Not all genotypes containing an SE copy showed increased susceptibility to RA. The association of SE genotypes found in this study related to disease susceptibility rather than severity.
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Affiliation(s)
- James F Fries
- Stanford University School of Medicine, Palo Alto, California, USA
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11
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Jawaheer D, Li W, Graham RR, Chen W, Damle A, Xiao X, Monteiro J, Khalili H, Lee A, Lundsten R, Begovich A, Bugawan T, Erlich H, Elder JT, Criswell LA, Seldin MF, Amos CI, Behrens TW, Gregersen PK. Dissecting the genetic complexity of the association between human leukocyte antigens and rheumatoid arthritis. Am J Hum Genet 2002; 71:585-94. [PMID: 12181776 PMCID: PMC449696 DOI: 10.1086/342407] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.3] [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] [Received: 04/23/2002] [Accepted: 06/14/2002] [Indexed: 11/03/2022] Open
Abstract
Rheumatoid arthritis (RA) is an inflammatory disease with a complex genetic component. An association between RA and the human leukocyte antigen (HLA) complex has long been observed in many different populations, and most studies have focused on a direct role for the HLA-DRB1 "shared epitope" in disease susceptibility. We have performed an extensive haplotype analysis, using 54 markers distributed across the entire HLA complex, in a set of 469 multicase families with RA. The results show that, in addition to associations with the DRB1 alleles, at least two additional genetic effects are present within the major histocompatibility complex. One of these lies within a 497-kb region in the central portion of the HLA complex, an interval that excludes DRB1. This genetic risk factor is present on a segment of a highly conserved ancestral A1-B8-DRB1*03 (8.1) haplotype. Additional risk genes may also be present in the HLA class I region in a subset of DRB1*0404 haplotypes. These data emphasize the importance of defining haplotypes when trying to understand the HLA associations with disease, and they clearly demonstrate that such associations with RA are complex and cannot be completely explained by the DRB1 locus.
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Affiliation(s)
- Damini Jawaheer
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Wentian Li
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Robert R. Graham
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Wei Chen
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Aarti Damle
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Xiangli Xiao
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Joanita Monteiro
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Houman Khalili
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Annette Lee
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Robert Lundsten
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Ann Begovich
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Teodorica Bugawan
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Henry Erlich
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - James T. Elder
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Lindsey A. Criswell
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Michael F. Seldin
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Christopher I. Amos
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Timothy W. Behrens
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
| | - Peter K. Gregersen
- Center for Genomics and Human Genetics, North Shore–Long Island Jewish Research Institute, Manhasset, New York; Center for Immunology, University of Minnesota, Minneapolis; Departments of Epidemiology and Biomathematics, University of Texas, M. D. Anderson Cancer Center, Houston; Roche Molecular Systems, Berkeley, CA; Departments of Dermatology and Radiation Oncology, University of Michigan, Ann Arbor; The Rosalind Russell Medical Research Center for Arthritis, Department of Medicine, Division of Rheumatology, University of California at San Francisco, San Francisco; and Department of Biological Chemistry, University of California at Davis, Davis
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12
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Verge CF, Vardi P, Babu S, Bao F, Erlich HA, Bugawan T, Tiosano D, Yu L, Eisenbarth GS, Fain PR. Evidence for oligogenic inheritance of type 1 diabetes in a large Bedouin Arab family. J Clin Invest 1998; 102:1569-75. [PMID: 9788970 PMCID: PMC509007 DOI: 10.1172/jci3379] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [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] [Indexed: 12/18/2022] Open
Abstract
Based on a genomic search for linkage, a locus contributing to type 1 diabetes in a large Bedouin Arab family (19 affected relatives) maps to the long arm of chromosome 10 (10q25; nonparametric linkage = 4.99; P = 0.00004). All affected relatives carry one or two high-risk HLA-DR3 haplotypes that are rarely found in other family members. One chromosome 10 haplotype, the B haplotype, was transmitted from a heterozygous parent to 13 of 13 affected offspring compared to 10 of 23 unaffected siblings. Recombination events occurring on this haplotype place the susceptibility locus in an 8-cM interval between markers D10S1750 and D10S1773. Two adjacent markers, D10S592 and D10S554, showed evidence of linkage disequilibrium with the disease locus. A 273-bp allele at D10S592 was transmitted to 8 of 10 affected offspring compared to 3 of 14 unaffected siblings, and a 151-bp allele at D10S554 was transmitted to 15 of 15 affected offspring compared with 10 of 24 unaffected siblings. D10S554 and D10S592 and the closest flanking markers are contained in a 1,240-kb yeast artificial chromosome, a region small enough to proceed with positional cloning.
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Affiliation(s)
- C F Verge
- Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, Denver, Colorado 80262-0001, USA
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13
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Beck HP, Felger I, Barker M, Bugawan T, Genton B, Alexander N, Jazwinska E, Erlich H, Alpers M. Evidence of HLA class II association with antibody response against the malaria vaccine SPF66 in a naturally exposed population. Am J Trop Med Hyg 1995; 53:284-8. [PMID: 7573714] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The antibody response against the malaria vaccine SPf66 and against circumsporozoite (CS) protein has been tested in immune adults from a malaria endemic area in Papua New Guinea. All individuals were genotyped for the HLA class II DQB1 and DRB1 loci, and the humoral response was analyzed with respect to the identified class II alleles. At each locus, only three alleles were frequent, namely DRB1*11, *15, and *16, and DQB1*0301, *0502, and *0601. Antibodies against SPf66 and CS protein were found in 84% and 79% of the individuals, respectively. A strong negative association was detected between the humoral response against SPf66 and DRB1*15 and DQB1*0601. A positive association of the response was observed with DRB1*11 and DQB1*0301. After analysis with a multiple regression model in which all alleles were included simultaneously, only DRB1*15 remained significantly associated with low antibody responses. This suggests that nonresponders may be expected after immunization with SPf66 in certain populations.
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Affiliation(s)
- H P Beck
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
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14
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Kim J, Namchuk M, Bugawan T, Fu Q, Jaffe M, Shi Y, Aanstoot HJ, Turck CW, Erlich H, Lennon V, Baekkeskov S. Higher autoantibody levels and recognition of a linear NH2-terminal epitope in the autoantigen GAD65, distinguish stiff-man syndrome from insulin-dependent diabetes mellitus. J Exp Med 1994; 180:595-606. [PMID: 7519242 PMCID: PMC2191592 DOI: 10.1084/jem.180.2.595] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The smaller form of the GABA-synthesizing enzyme glutamic acid decarboxylase (GAD65) is a major autoantigen in two human diseases that affect its principal sites of expression. Thus, destruction of pancreatic beta cells, which results in insulin-dependent diabetes mellitus (IDDM), and impairment of GABA-ergic synaptic transmission in Stiff-Man syndrome (SMS) are both characterized by circulating autoantibodies to GAD65. Anti-GAD65 autoantibodies in IDDM are predominantly directed to conformational epitopes. Here we report the characterization of humoral autoimmune responses to GAD65 in 35 SMS patients, of whom 13 (37%) also had IDDM. All SMS patients immunoprecipitated native GAD65 and the main titers were orders of magnitude higher than in IDDM patients. Furthermore, in contrast to the situation in IDDM, autoantibodies in 35 of 35 (100%) of SMS patients recognized denatured GAD65 on Western blots. Two major patterns of epitope specificity were identified on Western blots. The first pattern, detected in 25 of 35 SMS patients (71%), of whom 11 had IDDM (44%), was predominantly reactive with a linear NH2-terminal epitope residing in the first eight amino acids of GAD65. Nine of nine individuals who were HLA-haplotyped in this group carried an IDDM susceptibility haplotype and HLA-DR3, DQw2 was particularly abundant. The second pattern, detected in 10 of 35 patients (29%) of whom two had IDDM (20%), included reactivity with the NH2-terminal epitope plus strong reactivity with one or more additional epitope(s) residing COOH-terminal to amino acid 101. The second epitope pattern may represent epitope spreading in the GAD65 molecule, but may also include some cases of epitope recognition associated with IDDM resistant HLA-haplotypes. The principal NH2-terminal linear epitope in GAD65 distinguishes the reactivity of SMS and IDDM autoantibodies and may be a determinant of pathogenicity for GABA-ergic neurons. The greater magnitude and distinct specificity of the humoral response to GAD65 in SMS may reflect a biased involvement of the T helper cell type 2 (Th2) subset of CD4+ T cells and antibody responses, whereas IDDM is likely mediated by the Th1 subset of CD4+ T cells and cytotoxic T cell responses.
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Affiliation(s)
- J Kim
- Department of Medicine, University of California San Francisco 94143
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15
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Pugliese A, Bugawan T, Moromisato R, Awdeh ZL, Alper CA, Jackson RA, Erlich HA, Eisenbarth GS. Two subsets of HLA-DQA1 alleles mark phenotypic variation in levels of insulin autoantibodies in first degree relatives at risk for insulin-dependent diabetes. J Clin Invest 1994; 93:2447-52. [PMID: 8200980 PMCID: PMC294453 DOI: 10.1172/jci117253] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [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: 01/29/2023] Open
Abstract
Levels of insulin autoantibodies (IAA) vary among different first degree relatives of insulin-dependent diabetes mellitus patients, suggesting genetic regulation. We previously reported elevated IAA among DR4-positive at risk relatives. In this study, 72/82 at risk relatives were IAA positive, of whom 75% (54/72) carried DR4 versus 20% (2/10) of IAA-negative relatives (P = 0.0004). However, 69% (18/26) of DR4-negative relatives were IAA positive. Since DR4 did not account for all IAA positivity, we analyzed DQA1 and DQB1 alleles. Homozygosity for DQA1 alleles deriving from the evolutionary lineage 4 (*0401, *0501, *0601) was associated with low IAA levels, while lineage 1-3 alleles (*0101, *0102, *0103, *0201, *0301) correlated with higher levels. Most (93%, 65/70) relatives with lineage 1-3 alleles were IAA positive (mean = 360 +/- 63 SEM nU/ml). Only 7/12 relatives homozygous for lineage 4 alleles were IAA-positive, with lower levels than relatives with lineage 1-3 alleles (mean = 55 +/- 15 SEM nU/ml, P < 0.0001; 7/12 vs 65/70, P = 0.004). The amino acid sequences of lineage 1-3 alleles uniquely share glutamic acid (E) and phenylalanine (F) at positions 40 and 51 (EF alleles). Lineage 4 alleles have glycine (G) and leucine (L) at those positions (GL alleles). 90% (65/72) of IAA-positive relatives had an EF allele, while only 75% (54/72) had DR4 (P = 0.01). Homozygosity for GL alleles (often DQA1 *0501 on DR3 haplotypes) correlated with little or no humoral response to insulin. Thus, HLA-DQB1 GL alleles, or other genes on haplotypes (e.g., DR3) that carry these DQA1 alleles, may confer recessive low responsiveness to insulin.
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Affiliation(s)
- A Pugliese
- Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, Denver 80262
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Zangenberg G, Huang M, Bugawan T, Arnheim N, Erlich H. Detection of new HLA-DPB1 alleles generated by interallelic gene conversion using PCR amplification of DPB1 second exon sequences from sperm. Hum Immunol 1994. [DOI: 10.1016/0198-8859(94)91733-7] [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: 10/27/2022]
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17
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Abstract
Stiff-man syndrome (SMS) is a rare disorder of the central nervous system of probable autoimmune origin. Patients with SMS often have other autoimmune diseases, in particular type I (insulin-dependent) diabetes mellitus (IDDM). Approximately 60% of patients with SMS have high titers of autoantibodies against the enzyme glutamic acid decarboxylase. Similar to SMS, the majority of patients with IDDM have autoantibodies against glutamic acid decarboxylase at or before diabetes onset, although usually at a lower titer and with a different reaction pattern than patients with SMS. To investigate the immunogenetic basis of SMS, we HLA-typed 18 patients with the disease. Seventy-two percent carried the DQB1*0201 allele (13 of 18, P = 0.02 vs. 18 of 48 controls), indicating that SMS is associated with this allele. DQB1*0201 is also a susceptibility allele for IDDM and other autoimmune diseases. Patients with SMS carried the IDDM-protective DQB1*0602 allele and other sequence-related DQB1*06 alleles with the same frequency observed in controls. In contrast, these alleles are rarely found in IDDM. Five of 8 (62.5%) SMS patients lacking a DQB1*06 allele were diabetic in contrast to only 2 of 10 (20%) with a DQB1*06 allele (P = 0.08), suggesting that the presence of DQB1*0602 or other DQB1*06 alleles may be associated with a reduced prevalence of diabetes among patients with SMS.
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Affiliation(s)
- A Pugliese
- Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, Denver 80262
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18
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Erlich H, Bugawan T, Begovich A, Scharf S. Analysis of HLA class II polymorphism using polymerase chain reaction. Arch Pathol Lab Med 1993; 117:482-5. [PMID: 8489336] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A simple, rapid, and precise method of typing HLA class II polymorphism would be valuable in the areas of disease susceptibility, tissue transplantation, individual identification, and anthropological genetics. Herein, we describe a method of analyzing class II sequence polymorphism based on polymerase chain reaction (PCR) amplification and hybridization with oligonucleotide probes. Many more DNA-defined alleles at the class II loci have been identified than can be distinguished by conventional serologic typing. Consequently, matching transplant donors and recipients by PCR/oligonucleotide typing should reduce graft rejection and graft-vs-host disease. Also, the ability to identify alleles conferring genetic predisposition to specific diseases (eg, insulin-dependent diabetes mellitus) is significantly enhanced by distinguishing the many alleles or "subtypes" within a serologic type (eg, DR4). One valuable property of sequence-based HLA typing strategies, like oligonucleotide probe hybridization, is that they reveal how and where two alleles differ, not simply that they can be operationally distinguished. The nature and location of HLA polymorphisms appears to be critical in disease association studies and are important in tissue typing for transplantation. New alleles at the DRB1, DPB1, and DQB1 loci are likely to be identified as this technology is applied to more and more samples, particularly in nonwhite ethnic groups. A new allele is uncovered as an unusual pattern of probe binding and then confirmed by sequencing. This pattern is observed because class II polymorphism is localized to specific regions and virtually all "new" alleles represent "shuffled" combinations of polymorphic sequences found in previously known alleles. Since these polymorphisms are in the region of probe binding, these new alleles can be detected without increasing the probe panel. Obviously, any new allele with a new polymorphic sequence in a region for which typing probes are not available would not be revealed by oligonucleotide typing. With the PCR primers and probes described here, 7 DQ alpha 1 alleles, 15 DQ beta 1 alleles, 18 DPB1 alleles, and 32 DRB1 alleles are distinguished. Additional primers and/or probes can, of course, increase the allelic discrimination of PCR/oligonucleotide probe typing. These horseradish peroxidase-labeled oligonucleotide probes are stable (> 2 years when stored at 4 degrees C) and the typing system is simple and robust. Although this dot blot/oligonucleotide hybridization procedure is a powerful and precise method of HLA class II typing, the complexity of the procedure increases as the number of probes required for analysis increases.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- H Erlich
- Department of Human Genetics, Roche Molecular Systems Inc, Alameda, Calif. 94501
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Erlich HA, Zeidler A, Chang J, Shaw S, Raffel LJ, Klitz W, Beshkov Y, Costin G, Pressman S, Bugawan T. HLA class II alleles and susceptibility and resistance to insulin dependent diabetes mellitus in Mexican-American families. Nat Genet 1993; 3:358-64. [PMID: 7981758 DOI: 10.1038/ng0493-358] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.1] [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: 01/28/2023]
Abstract
The role of HLA class II alleles in genetic predisposition to insulin dependent diabetes mellitus (IDDM) was examined by PCR/oligonucleotide probe typing of 42 Mexican-American IDDM families derived from Hispanic Caucasians and Native Americans. All high risk haplotypes (HLA-DR3 and DR4) were of European origin while the most strongly protective haplotype (DRB1*1402) was Native American. Of the 16 DR-DQ DR4 haplotypes identified, only those bearing DQB1*0302 conferred risk; the DRB1 allele, however, also markedly influenced IDDM risk. The general pattern of neutral and protective haplotypes indicates that the presence of Asp-57 in the HLA-DQ beta chain does not confer IDDM protection per se and indicates that both DRB1 and DQB1 influence IDDM susceptibility as well as protection.
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Affiliation(s)
- H A Erlich
- Department of Human Genetics, Roche Molecular Systems, Inc., Alameda, California 94501
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20
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Erlich H, Bugawan T, Begovich AB, Scharf S, Griffith R, Saiki R, Higuchi R, Walsh PS. HLA-DR, DQ and DP typing using PCR amplification and immobilized probes. Eur J Immunogenet 1991; 18:33-55. [PMID: 2069944 DOI: 10.1111/j.1744-313x.1991.tb00005.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A simple, rapid, and precise method of typing HLA class II polymorphism would be valuable in the areas of disease susceptibility, tissue transplantation, individual identification and anthropological genetics. Here we describe a method of analysing class II sequence polymorphism based on polymerase chain reaction (PCR) amplification and hybridization with oligonucleotide probes. One valuable property of sequence-based HLA typing strategies, like oligonucleotide probe hybridization, is that they reveal how and where two alleles differ, not simply that they can be operationally distinguished. The nature and location of HLA polymorphisms appears to be critical in disease association studies and are likely to be important in tissue typing for transplantation. New alleles at the DRB1, DPB1 and DQB1 loci are likely to be identified as this technology is applied to more and more samples, particularly in non-Caucasian ethnic groups. A new allele is uncovered as an unusual pattern of probe binding and then confirmed by sequencing. This pattern is observed because class II polymorphism is localized to specific regions and virtually all 'new' alleles have polymorphisms in the region of probe binding. Obviously, any new allele with a new polymorphic sequence in a region for which typing probes are not available would not be revealed by oligonucleotide typing. With the PCR primers and probes described here, 7 DQA1 alleles, 15 DQB1 alleles, 18 DPB1 alleles, and 32 DRB1 alleles are distinguished. Additional primers and/or probes can, of course, increase the allelic discrimination of oligonucleotide dot blot typing. These horseradish peroxidase (HRP)-labelled oligonucleotide probes are stable (greater than 2 years when stored at 4 degrees C) and the typing system is simple and robust. Over 500 samples from the CEPH pedigrees (unpublished data; A. B. Begovich, et al., manuscript in preparation) and greater than 1000 unrelated samples have been typed by this procedure. Although this dot blot/oligonucleotide hybridization procedure is a powerful and precise method of HLA class II typing, the complexity of the procedure increases as the number of probes required for analysis increases. The reverse dot blot method, based on an array of immobilized probes, allows the typing of individual samples in one single hybridization reaction. In this approach, a panel of unlabelled oligonucleotides are immobilized to a nylon membrane. The PCR product is labelled during the amplification reaction by using biotinylated primers and hybridized to the membrane. The presence of bound PCR product specifically hybridized to a given probe is detected using streptavidin-HRP conjugates and either chromogenic or chemiluminescent substrates.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- H Erlich
- Department of Human Genetics, Cetus Corp., Emeryville, California 94608
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Angelini G, Bugawan T, Delfino L, Erlich H, Ferrara G. HLA-DP typing by DNA amplification and hybridization with allele-specific oligonucleotide. Hum Immunol 1988. [DOI: 10.1016/0198-8859(88)90094-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Erlich H, Lee JS, Petersen JW, Bugawan T, DeMars R. Molecular analysis of HLA class I and class II antigen loss mutants reveals a homozygous deletion of the DR, DQ, and part of the DP region: implications for class II gene order. Hum Immunol 1986; 16:205-19. [PMID: 3459724 DOI: 10.1016/0198-8859(86)90049-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The mutant human B-lymphoblastoid cell lines, 721.174 and 721.180, previously reported to exhibit greatly reduced expression of human HLA class I and II antigens (DeMars et al., Hum Immunol 11:77, 1984), were analyzed by Southern blotting using class II cDNA and genomic clones as hybridization probes. All genomic sequences complementary to DR alpha, DR beta, DQ alpha, and DQ beta probes were absent from these mutants. DZ alpha genomic sequences were deleted as were the DP alpha 1 and DP beta 1 loci but the DP beta 2 and most, if not all, of the DP alpha 2 locus were retained. However, no RNA transcripts for either DP alpha 2 or DP beta 2 could be detected. The mapping of the deletion breakpoint within the DP cluster allows the orientation of the loci in the DP region with respect to the centromere as follows: centromere, DP beta 2, DP beta 1, DP alpha 1, (DQ, DR). In addition, the analysis of a set of DR-, DQ-, DP+ homozygous deletion mutants (721.82, 721.84, and 721.101) reveals a deletion breakpoint between the DQ alpha 1/DQ beta 1 loci and the DQ alpha 2/DQ beta 2 loci. These mutants retain DZ alpha genomic sequences, tentatively mapping the DZ alpha locus between the DQ and the DP region. The residual ability of the DR-, DQ-, DP- mutants (174 and 180)* to stimulate allogeneic and autologous lymphoproliferative responses must be attributed to expression of as yet unidentified class II antigens, or to non-class II antigens.
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