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Kumar S, Gupta MK, Gupta SK, Katara P. Investigation of molecular interaction and conformational stability of disease concomitant to HLA-DRβ3. J Biomol Struct Dyn 2023; 41:8417-8431. [PMID: 36245311 DOI: 10.1080/07391102.2022.2134211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/03/2022] [Indexed: 10/24/2022]
Abstract
Human leucocyte antigen DRβ3 is associated with specific autoimmune thyroid disease and plays a vital role in the progression of Grave's disease. The available crystallographic structure of the HLA DRA, DRβ3*0101, was selected and used to generate mutation at position 57 from valine amino acid to Aspartic acid (D), Glutamic acid (E), Alanine (A), and Serine (S) amino acids by computational modeling approach. Mutant models were minimized, and stable conformation was chosen based on the lowest root mean square deviation value. Molecular docking assessed the best binding affinity of ligands C1, C2, C3, and C4 with wild-type and mutant HLA-DRβ3 models. Molecular dynamics simulation studies were executed to evaluate the stability of selected hits with wild-type and mutant dock complexes. The C3 has shown good binding affinity with wild-type and selected mutants; V57A, V57E, and V57D. Structural and molecular dynamics insights reveal the differences between wild-type and mutant-type HLA-DRβ3, which could help design novel antagonist molecules against autoimmune thyroid disorder.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanjay Kumar
- Department of Bioinformatics, University Institute of Engineering and Technology, Chhatrapati Shahu Ji Maharaj University Kanpur, Kanpur, Uttar Pradesh, India
| | - Manish Kumar Gupta
- Department of Biotechnology, Faculty of Science, Veer Bahadur Singh Purvanchal University Jaunpur, Jaunpur, Uttar Pradesh, India
| | - Sunil Kumar Gupta
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Pramod Katara
- Centre of Bioinformatics, IIDS, University of Allahabad, Allahabad, Uttar Pradesh, India
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Wiseman CL, Kharazi A, Sunkari VG, Galeas JL, Dozio V, Hashwah H, Macúchová E, Williams WV, Lacher MD. Regression of Breast Cancer Metastases Following Treatment with Irradiated SV-BR-1-GM, a GM-CSF Overexpressing Breast Cancer Cell Line: Intellectual Property and Immune Markers of Response. Recent Pat Anticancer Drug Discov 2022; 18:224-240. [PMID: 35593340 PMCID: PMC10009895 DOI: 10.2174/1574892817666220518123331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND SV-BR-1-GM, derived from a patient with grade 2 (moderately differentiated) breast cancer, is a GM-CSF-secreting breast cancer cell line with properties of antigen-presenting cells. SV-BR-1-GM and next-generation versions are covered by several pending and granted patents. METHODS We report findings from an open-label phase I, single-arm pilot study with irradiated SV-BR-1-GM cells in 3 breast and 1 ovarian cancer subjects. Inoculations were preceded by lowdose intravenous cyclophosphamide and followed by interferon-alpha2b injections into the SVBR- 1-GM inoculation sites. We assessed both cellular and humoral immune responses, and measured expression levels of SV-BR-1-GM HLA alleles. RESULTS Treatment was generally safe and well tolerated. Immune responses were elicited universally. Overall survival was more than 33 months for three of the four patients. As previously reported, one patient had prompt regression of metastases in lung, breast, and soft tissue. Following cessation of treatment, the patient relapsed widely, including in the brain. Upon retreatment, rapid tumor response was again seen, including complete regression of brain metastases. Consistent with a role of Class II HLA in contributing to SV-BR-1-GM's mechanism of action, this patient allele-matched SV-BR-1-GM at the HLA-DRB1 and HLA-DRB3 loci. We are in the process of developing next-generation SV-BR-1-GM, expressing patient-specific HLAs. Patent applications were filed in various jurisdictions. Thus far, one is granted, in Japan. CONCLUSION A whole-cell immunotherapy regimen with SV-BR-1-GM cells induced regression of metastatic breast cancer. We develop intellectual property based on SV-BR-1-GM's predicted mechanism of action to develop additional whole-cell immunotherapies for cancer patients.
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Affiliation(s)
- Charles L. Wiseman
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
| | - Alexander Kharazi
- Immunotherapy Laboratory, St. Vincent Medical Center, Los Angeles, CA, USA
| | - Vivekananda G. Sunkari
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
| | - Jacqueline L. Galeas
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
| | - Vito Dozio
- Operations Department, Biognosys AG, Wagistrasse 21, 8952, Schlieren, Switzerland
| | - Hind Hashwah
- Sales and Marketing Nebion AG, Hohlstrasse 515, 8048, Zurich, Switzerland
| | - Eva Macúchová
- Sales and Marketing Nebion AG, Hohlstrasse 515, 8048, Zurich, Switzerland
| | - William V. Williams
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
| | - Markus D. Lacher
- BriaCell Therapeutics Corporation, 2929 Arch Street, 3 Floor, Philadelphia, PA, 19104, USA
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Park MH, Lee HJ, Bok J, Kim CH, Hong ST, Park C, Kimm K, Oh B, Lee JY. Korean BAC Library Construction and Characterization of HLA-DRA, HLA-DRB3. BMB Rep 2006; 39:418-25. [PMID: 16889686 DOI: 10.5483/bmbrep.2006.39.4.418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A human bacterial artificial chromosome (BAC) library was constructed with high molecular weight DNA extracted from the blood of a male Korean. This Korean BAC library contains 100,224 clones of insert size ranging from 70 to 150 kb, with an average size of 86 kb, corresponding to a 2.9-fold redundancy of the genome. The average insert size was determined from 288 randomly selected BAC clones that were well distributed among all the chromosomes. We developed a pooling system and three-step PCR screen for the Korean BAC library to isolate desired BAC clones, and we confirmed its utility using primer pairs designed for one of the clones. The Korean BAC library and screening pools will allow PCR-based screening of the Korean genome for any gene of interest. We also determined the allele types of HLA-DRA and HLA-DRB3 of clone KB55453, located in the HLA class II region on chromosome 6p21.3. The HLA-DRA and DRB3 genes in this clone were identified as the DRA*010202 and DRB3*01010201 types, respectively. The haplotype found in this library will provide useful information in future human disease studies.
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Affiliation(s)
- Mi-Hyun Park
- Center for Genome Science, National Institute of Health, 5 Nokbun-dong, Eunpyung-gu, Seoul 122-701, Korea
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Greville WD, Kennedy A, Chapman G, Dunckley H. Novel HLA-DRB3 alleles discovered during routine sequencing based typing, DRB3*02023, DRB3*0212, DRB3*0213 and DRB3*03012. TISSUE ANTIGENS 2002; 59:232-4. [PMID: 12074717 DOI: 10.1034/j.1399-0039.2002.590311.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report the discovery of four HLA-DRB3 alleles during routine sequencing based typing (SBT); DRB3*02023, DRB3*0212, DRB3*0213 and DRB3*03012. These alleles differ from other HLA-DRB3 alleles by previously undescribed single nucleotide polymorphisms.
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Affiliation(s)
- Warwick D Greville
- Molecular Genetics Laboratory, Tissue Typing Services, Australian Red Cross Blood Service, Sydney, Australia.
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Tang TF, Lin YS, Robbins FM, Li L, Sintasath D, Coquillard G, Huang A, Heine U, Ng J, Hartzman RJ, Hurley CK. Description of fourteen new DRB alleles found in a stem cell donor registry. TISSUE ANTIGENS 2002; 59:63-5. [PMID: 11972885 DOI: 10.1034/j.1399-0039.2002.590115.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Fourteen DRB alleles, DRB1*0705, DRB1*11014, DRB1*1134, DRB1*1136, DRB1*1141, DRB1*1335, DRB1*1337, DRB1*1338, DRB1*1342, DRB1*1343, DRB1*1349, DRB1*1510, DRB3*0105, and DRB5*0103, are described. Among them, eleven are variants which differ by only one nucleotide from previously described alleles, including one silent variant (DRB1*11014). Alleles, DRB1*0705, DRB1*1335 and DRB3*0105, display unique sequence motifs that have never been observed in DRB alleles.
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Affiliation(s)
- T F Tang
- Department of Pediatrics, Georgetown University, Washington, DC, USA
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Marsh SG, Bodmer JG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Hansen JA, MacH B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for factors of the HLA system, 2000. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 2001; 28:377-424. [PMID: 11422419 DOI: 10.1046/j.1365-2370.2001.00268.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- S G Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, UK.
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Marsh SG, Bodmer JG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Hansen JA, Mach B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for factors of the HLA system, 2000. Hum Immunol 2001; 62:419-68. [PMID: 11295476 DOI: 10.1016/s0198-8859(01)00229-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- S G Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Hampstead, UK
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Marsh SG, Bodmer JG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Hansen JA, Mach B, Mayr WR, Parham P, Petersdorf EW, Sasazuki T, Schreuder GM, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for factors of the HLA system, 2000. TISSUE ANTIGENS 2001; 57:236-83. [PMID: 11285132 DOI: 10.1034/j.1399-0039.2001.057003236.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- S G Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom.
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Tang TF, Huang AY, Pappas A, Slack R, Ng J, Hartzman RJ, Hurley CK. Relative frequencies of DRB1*11 alleles and their DRB3 associations in five major population groups in a United States bone marrow registry. Hum Immunol 2000; 61:820-7. [PMID: 10980393 DOI: 10.1016/s0198-8859(00)00145-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One hundred sixty-one individuals from each of five US population groups, Caucasians (CAU), African Americans (AFA), Asians/Pacific Islanders (API), Hispanics (HIS), and Native Americans (NAT), were randomly selected from a volunteer bone marrow registry database consisting of 14,452 HLA-DRB1*11 positive individuals. This sampling provided at least an 80% probability of detecting a rare allele that occurred at 1% in the DRB1*11 positive population. Samples were typed for DRB1*11 alleles by polymerase chain reaction-sequence specific oligonucleotide probe typing (PCR-SSOP). A total of 10 DRB1*11 alleles out of 27 possible alleles were detected. The distribution and diversity of DRB1*11 alleles varied among populations although DRB1*1101 was the predominant DRB1*11 allele in all populations. Caucasians were the least diversified; only four common alleles (DRB1*1101-*1104) were observed. As well as the four common alleles, other groups also carried one or two other less frequent alleles including DRB1*1105 (API), *1106 (API), *1110 (AFA), *1114 (HIS), *1115 (NAT), and *1117 (AFA). A subset (418) of these individuals were also typed for DRB3 alleles. Most (97.6%) showed a strong association of DRB1*11 with DRB3*0202.
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Affiliation(s)
- T F Tang
- Department of Pediatrics, Georgetown University Medical Center, Washington, DC, USA
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