1
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Ismail HS, Khalil A, Taha RA, Lasheen DS, Abou El Ella DA. Design, molecular modelling and synthesis of novel benzothiazole derivatives as BCL-2 inhibitors. Sci Rep 2023; 13:15554. [PMID: 37730790 PMCID: PMC10511702 DOI: 10.1038/s41598-023-41783-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023] Open
Abstract
Apoptosis plays a crucial role in cancer pathogenesis and drug resistance. BCL-2 family of enzymes is considered as one of the key enzymes which is involved in apoptosis. When there is disruption in the balance between anti-apoptotic and pro-apoptotic members of the BCL-2 family apoptosis is dysregulated in the affected cells. Herein, 33 novel benzothiazole-based molecules 7a-i, 8a-f, 9a-b, 12a-e, 13a-d, 14a,b, and 17a-j were designed, synthesized and tested for their BCL-2 inhibitory activity. Scaffold hopping strategy was applied in designing of the target compounds. Compounds 13c and 13d showed the highest activity with IC50 values equal to 0.471 and 0.363 µM, respectively. Molecular docking studies of the synthesized compounds showed comparable binding interactions with the lead compound. Structure activity relationship study was performed to show the effects of structural modifications on the inhibitory activities on BCL-2.
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Affiliation(s)
- Hoda S Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Amira Khalil
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, The British University in Egypt (BUE), El-Sherouk City, Cairo, 11837, Egypt.
| | - Rabah A Taha
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Deena S Lasheen
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Dalal A Abou El Ella
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt.
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2
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Sachs A, Moore E, Kosaloglu-Yalcin Z, Peters B, Sidney J, Rosenberg SA, Robbins PF, Sette A. Impact of Cysteine Residues on MHC Binding Predictions and Recognition by Tumor-Reactive T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:539-549. [PMID: 32571843 PMCID: PMC7413297 DOI: 10.4049/jimmunol.1901173] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 05/14/2020] [Indexed: 01/01/2023]
Abstract
The availability of MHC-binding prediction tools has been useful in guiding studies aimed at identifying candidate target Ags to generate reactive T cells and to characterize viral and tumor-reactive T cells. Nevertheless, prediction algorithms appear to function poorly for epitopes containing cysteine (Cys) residues, which can oxidize and form disulfide bonds with other Cys residues under oxidizing conditions, thus potentially interfering with their ability to bind to MHC molecules. Analysis of the results of HLA-A*02:01 class I binding assays carried out in the presence and absence of the reducing agent 2-ME indicated that the predicted affinity for 25% of Cys-containing epitopes was underestimated by a factor of 3 or more. Additional analyses were undertaken to evaluate the responses of human CD8+ tumor-reactive T cells against 10 Cys-containing HLA class I-restricted minimal determinants containing substitutions of α-aminobutyric acid (AABA), a cysteine analogue containing a methyl group in place of the sulfhydryl group present in Cys, for the native Cys residues. Substitutions of AABA for Cys at putative MHC anchor positions often significantly enhanced T cell recognition, whereas substitutions at non-MHC anchor positions were neutral, except for one epitope where this modification abolished T cell recognition. These findings demonstrate the need to evaluate MHC binding and T cell recognition of Cys-containing peptides under conditions that prevent Cys oxidation, and to adjust current prediction binding algorithms for HLA-A*02:01 and potentially additional class I alleles to more accurately rank peptides containing Cys anchor residues.
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Affiliation(s)
- Abraham Sachs
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1201
| | - Eugene Moore
- La Jolla Institute for Immunology, La Jolla, CA 92037; and
| | | | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037; and
| | - John Sidney
- La Jolla Institute for Immunology, La Jolla, CA 92037; and
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1201
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-1201;
| | - Alessandro Sette
- La Jolla Institute for Immunology, La Jolla, CA 92037; and
- Department of Medicine, University of California, San Diego, San Diego, CA 92122
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3
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Heijmans CMC, de Groot NG, Bontrop RE. Comparative genetics of the major histocompatibility complex in humans and nonhuman primates. Int J Immunogenet 2020; 47:243-260. [PMID: 32358905 DOI: 10.1111/iji.12490] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022]
Abstract
The major histocompatibility complex (MHC) is one of the most gene-dense regions of the mammalian genome. Multiple genes within the human MHC (HLA) show extensive polymorphism, and currently, more than 26,000 alleles divided over 39 different genes are known. Nonhuman primate (NHP) species are grouped into great and lesser apes and Old and New World monkeys, and their MHC is studied mostly because of their important role as animal models in preclinical research or in connection with conservation biology purposes. The evolutionary equivalents of many of the HLA genes are present in NHP species, and these genes may also show abundant levels of polymorphism. This review is intended to provide a comprehensive comparison relating to the organization and polymorphism of human and NHP MHC regions.
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Affiliation(s)
- Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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4
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Shortreed CG, Wiseman RW, Karl JA, Bussan HE, Baker DA, Prall TM, Haj AK, Moreno GK, Penedo MCT, O'Connor DH. Characterization of 100 extended major histocompatibility complex haplotypes in Indonesian cynomolgus macaques. Immunogenetics 2020; 72:225-239. [PMID: 32112172 PMCID: PMC7223175 DOI: 10.1007/s00251-020-01159-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/04/2020] [Indexed: 12/21/2022]
Abstract
Many medical advancements—including improvements to anti-rejection therapies in transplantation and vaccine development—rely on preclinical studies conducted in cynomolgus macaques (Macaca fascicularis). Major histocompatibility complex (MHC) class I and class II genes of cynomolgus macaques are orthologous to human leukocyte antigen complex (HLA) class I and class II genes, respectively. Both encode cell-surface proteins involved in cell recognition and rejection of non-host tissues. MHC class I and class II genes are highly polymorphic, so comprehensive genotyping requires the development of complete databases of allelic variants. Our group used PacBio circular consensus sequencing of full-length cDNA amplicons to characterize MHC class I and class II transcript sequences for a cohort of 293 Indonesian cynomolgus macaques (ICM) in a large, pedigreed breeding colony. These studies allowed us to expand the existing database of Macaca fascicularis (Mafa) alleles by identifying an additional 141 MHC class I and 61 class II transcript sequences. In addition, we defined co-segregating combinations of allelic variants as regional haplotypes for 70 Mafa-A, 78 Mafa-B, and 45 Mafa-DRB gene clusters. Finally, we defined class I and class II transcripts that are associated with 100 extended MHC haplotypes in this breeding colony by combining our genotyping analyses with short tandem repeat (STR) patterns across the MHC region. Our sequencing analyses and haplotype definitions improve the utility of these ICM for transplantation studies as well as infectious disease and vaccine research.
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Affiliation(s)
- Cecilia G Shortreed
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA.,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Hailey E Bussan
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Trent M Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Amelia K Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | | | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA. .,Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
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5
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Silver ZA, Watkins DI. The role of MHC class I gene products in SIV infection of macaques. Immunogenetics 2017; 69:511-519. [PMID: 28695289 PMCID: PMC5537376 DOI: 10.1007/s00251-017-0997-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 04/30/2017] [Indexed: 01/27/2023]
Abstract
Human immunodeficiency virus (HIV) remains among the most significant public health threats worldwide. Despite three decades of research following the discovery of HIV, a preventive vaccine remains elusive. The study of HIV elite controllers has been crucial to elaborate the genetic and immunologic determinants that underlie control of HIV replication. Coordinated studies of elite control in humans have, however, been limited by variability among infecting viral strains, host genotype, and the uncertainty of the timing and route of infection. In this review, we discuss the role of nonhuman primate (NHP) models for the elucidation of the immunologic correlates that underlie control of AIDS virus replication. We discuss the importance of major histocompatibility complex class I (MHC-I) alleles in activating CD8+ T-cell populations that promote control of both HIV and simian immunodeficiency virus (SIV) replication. Provocatively, we make the argument that T-cell subsets recognizing the HIV/SIV viral infectivity factor (Vif) protein may be crucial for control of viral replication. We hope that this review demonstrates how an in-depth understanding of the MHC-I gene products associated with elite control of HIV/SIV, and the epitopes that they present, can provide researchers with a glimpse into the protective immune responses that underlie AIDS nonprogression.
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Affiliation(s)
- Zachary A Silver
- Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL, USA. .,Department of Pathology, University of Miami Miller School of Medicine, Miami, FL, USA.
| | - David I Watkins
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL, USA
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6
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de Groot NG, Blokhuis JH, Otting N, Doxiadis GGM, Bontrop RE. Co-evolution of the MHC class I and KIR gene families in rhesus macaques: ancestry and plasticity. Immunol Rev 2016; 267:228-45. [PMID: 26284481 PMCID: PMC4544828 DOI: 10.1111/imr.12313] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Researchers dealing with the human leukocyte antigen (HLA) class I and killer immunoglobulin receptor (KIR) multi‐gene families in humans are often wary of the complex and seemingly different situation that is encountered regarding these gene families in Old World monkeys. For the sake of comparison, the well‐defined and thoroughly studied situation in humans has been taken as a reference. In macaques, both the major histocompatibility complex class I and KIR gene families are plastic entities that have experienced various rounds of expansion, contraction, and subsequent recombination processes. As a consequence, haplotypes in macaques display substantial diversity with regard to gene copy number variation. Additionally, for both multi‐gene families, differential levels of polymorphism (allelic variation), and expression are observed as well. A comparative genetic approach has allowed us to answer questions related to ancestry, to shed light on unique adaptations of the species’ immune system, and to provide insights into the genetic events and selective pressures that have shaped the range of these gene families.
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Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Jeroen H Blokhuis
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Nel Otting
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Gaby G M Doxiadis
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics & Refinement, BPRC, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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7
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Sidney J, Schloss J, Moore C, Lindvall M, Wriston A, Hunt DF, Shabanowitz J, DiLorenzo TP, Sette A. Characterization of the peptide binding specificity of the HLA class I alleles B*38:01 and B*39:06. Immunogenetics 2016; 68:231-6. [PMID: 26754738 PMCID: PMC4760861 DOI: 10.1007/s00251-015-0898-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 12/30/2015] [Indexed: 01/27/2023]
Abstract
B*38:01 and B*39:06 are present with phenotypic frequencies <2% in the general population, but are of interest as B*39:06 is the B allele most associated with type 1 diabetes susceptibility and 38:01 is most protective. A previous study derived putative main anchor motifs for both alleles based on peptide elution data. The present study has utilized panels of single amino acid substitution peptide libraries to derive detailed quantitative motifs accounting for both primary and secondary influences on peptide binding. From these analyses, both alleles were confirmed to utilize the canonical position 2/C-terminus main anchor spacing. B*38:01 preferentially bound peptides with the positively charged or polar residues H, R, and Q in position 2 and the large hydrophobic residues I, F, L, W, and M at the C-terminus. B*39:06 had a similar preference for R in position 2, but also well-tolerated M, Q, and K. A more dramatic contrast between the two alleles was noted at the C-terminus, where the specificity of B*39:06 was clearly for small residues, with A as most preferred, followed by G, V, S, T, and I. Detailed position-by-position and residue-by-residue coefficient values were generated from the panels to provide detailed quantitative B*38:01 and B*39:06 motifs. It is hoped that these detailed motifs will facilitate the identification of T cell epitopes recognized in the context of two class I alleles associated with dramatically different dispositions towards type 1 diabetes, offering potential avenues for the investigation of the role of CD8 T cells in this disease.
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Affiliation(s)
- John Sidney
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Jennifer Schloss
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Carrie Moore
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Mikaela Lindvall
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Amanda Wriston
- Department of Chemistry, University of Virginia, Charlottesville, VA, 222904, USA
| | - Donald F Hunt
- Departments of Chemistry and Pathology, University of Virginia, Charlottesville, VA, 222904, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA, 222904, USA
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
- Department of Medicine (Division of Endocrinology), Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
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8
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Marcilla M, Alvarez I, Ramos-Fernández A, Lombardía M, Paradela A, Albar JP. Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B*27 and Mamu-B*08: Two MHC Class I Alleles Associated with Elite Control of HIV/SIV Infection. J Proteome Res 2016; 15:1059-69. [PMID: 26811146 DOI: 10.1021/acs.jproteome.5b01146] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Indian rhesus macaques are arguably the most reliable animal models in AIDS research. In this species the MHC class I allele Mamu-B*08, among others, is associated with elite control of SIV replication. A similar scenario is observed in humans where the expression of HLA-B*27 or HLA-B*57 has been linked to slow or no progression to AIDS after HIV infection. Despite having large differences in their primary structure, it has been reported that HLA-B*27 and Mamu-B*08 display peptides with sequence similarity. To fine-map the Mamu-B*08 binding motif and assess its similarities with that of HLA-B*27, we affinity purified the peptidomes bound to these MHC class I molecules and analyzed them by LC-MS, identifying several thousands of endogenous ligands. Sequence analysis of both sets of peptides revealed a degree of similarity in their binding motifs, especially at peptide position 2 (P2), where arginine was present in the vast majority of ligands of both allotypes. In addition, several differences emerged from this analysis: (i) ligands displayed by Mamu-B*08 tended to be shorter and to have lower molecular weight, (ii) Mamu-B*08 showed a higher preference for glutamine at P2 as a suboptimal binding motif, and (iii) the second major anchor position, found at PΩ, was much more restrictive in Mamu-B*08. In this regard, HLA-B*27 bound efficiently peptides with aliphatic, aromatic (including tyrosine), and basic C-terminal residues while Mamu-B*08 preferred peptides with leucine and phenylalanine in this position. Finally, in silico estimations of binding efficiency and competitive binding assays to Mamu-B*08 of several selected peptides revealed a good correlation between the characterized anchor motif and binding affinity. These results deepen our understanding of the molecular basis of the presentation of peptides by Mamu-B*08 and can contribute to the detection of novel SIV epitopes restricted by this allotype.
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Affiliation(s)
- Miguel Marcilla
- Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Iñaki Alvarez
- Immunology Unit, Department of Cell Biology, Physiology and Immunology and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain
| | - Antonio Ramos-Fernández
- Proteobotics SL, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Manuel Lombardía
- Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Alberto Paradela
- Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Juan Pablo Albar
- Proteomics Unit, Spanish National Biotechnology Centre (CSIC), Darwin 3, 28049 Madrid, Spain
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9
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Bergmann T, Moore C, Sidney J, Miller D, Tallmadge R, Harman RM, Oseroff C, Wriston A, Shabanowitz J, Hunt DF, Osterrieder N, Peters B, Antczak DF, Sette A. The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires. Immunogenetics 2015; 67:675-89. [PMID: 26399241 DOI: 10.1007/s00251-015-0872-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/14/2015] [Indexed: 11/29/2022]
Abstract
Here we describe a detailed quantitative peptide-binding motif for the common equine leukocyte antigen (ELA) class I allele Eqca-1*00101, present in roughly 25 % of Thoroughbred horses. We determined a preliminary binding motif by sequencing endogenously bound ligands. Subsequently, a positional scanning combinatorial library (PSCL) was used to further characterize binding specificity and derive a quantitative motif involving aspartic acid in position 2 and hydrophobic residues at the C-terminus. Using this motif, we selected and tested 9- and 10-mer peptides derived from the equine herpesvirus type 1 (EHV-1) proteome for their capacity to bind Eqca-1*00101. PSCL predictions were very efficient, with an receiver operating characteristic (ROC) curve performance of 0.877, and 87 peptides derived from 40 different EHV-1 proteins were identified with affinities of 500 nM or higher. Quantitative analysis revealed that Eqca-1*00101 has a narrow peptide-binding repertoire, in comparison to those of most human, non-human primate, and mouse class I alleles. Peripheral blood mononuclear cells from six EHV-1-infected, or vaccinated but uninfected, Eqca-1*00101-positive horses were used in IFN-γ enzyme-linked immunospot (ELISPOT) assays. When we screened the 87 Eqca-1*00101-binding peptides for T cell reactivity, only one Eqca-1*00101 epitope, derived from the intermediate-early protein ICP4, was identified. Thus, despite its common occurrence in several horse breeds, Eqca-1*00101 is associated with a narrow binding repertoire and a similarly narrow T cell response to an important equine viral pathogen. Intriguingly, these features are shared with other human and macaque major histocompatibility complex (MHC) molecules with a similar specificity for D in position 2 or 3 in their main anchor motif.
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Affiliation(s)
- Tobias Bergmann
- Institut für Virologie, Freie Universtiät Berlin, 14163, Berlin, Germany
| | - Carrie Moore
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - John Sidney
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Rebecca Tallmadge
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Rebecca M Harman
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Carla Oseroff
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Amanda Wriston
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, 22904, USA
| | | | - Bjoern Peters
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Alessandro Sette
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA.
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10
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Macaque species susceptibility to simian immunodeficiency virus: increased incidence of SIV central nervous system disease in pigtailed macaques versus rhesus macaques. J Neurovirol 2015; 21:148-58. [PMID: 25672885 DOI: 10.1007/s13365-015-0313-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/23/2014] [Accepted: 01/05/2015] [Indexed: 12/15/2022]
Abstract
Immune pressure exerted by MHC class I-restricted cytotoxic T cells drives the development of viral escape mutations, thereby regulating HIV disease progression. Nonetheless, the relationship between host immunity and HIV central nervous system (CNS) disease remains poorly understood. The simian immunodeficiency virus (SIV) macaque model recapitulates key features of HIV infection including development of AIDS and CNS disease. To investigate cell-mediated immunity regulating SIV CNS disease progression, we compared the incidence of SIV encephalitis and the influence of MHC class I allele expression on the development of CNS disease in rhesus macaques (Macaca mulatta) versus pigtailed macaques (Macaca nemestrina). After inoculation with the immunosuppressive swarm SIV/DeltaB670 and the neurovirulent molecular clone SIV/17E-Fr, pigtailed macaques progressed more rapidly to AIDS, had higher plasma and cerebrospinal fluid (CSF) viral loads, and were more likely to progress to SIV-associated encephalitis (SIVE) compared to rhesus macaques. In addition, MHC class I alleles were neuroprotective in both species (Mamu-A*001 in rhesus macaques and Mane-A1*084:01:01 in pigtailed macaques); animals expressing these alleles were less likely to develop SIV encephalitis and correspondingly had lower viral replication in the brain. Species-specific differences in susceptibility to SIV disease demonstrated that cell mediated immune responses are critical to SIV CNS disease progression.
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11
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Cancer therapeutics: Targeting the apoptotic pathway. Crit Rev Oncol Hematol 2014; 90:200-19. [DOI: 10.1016/j.critrevonc.2013.12.012] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 12/05/2013] [Accepted: 12/12/2013] [Indexed: 01/20/2023] Open
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12
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Choudhary A, Galvin TA, Williams DK, Beren J, Bryant MA, Khan AS. Influence of naturally occurring simian foamy viruses (SFVs) on SIV disease progression in the rhesus macaque (Macaca mulatta) model. Viruses 2013; 5:1414-30. [PMID: 23744104 PMCID: PMC3717714 DOI: 10.3390/v5061414] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 05/22/2013] [Accepted: 05/30/2013] [Indexed: 01/10/2023] Open
Abstract
We have investigated the influence of naturally occurring simian foamy viruses (SFVs) on simian immunodeficiency virus (SIV) infection and disease in Indian rhesus macaques. Animals were divided into two groups based upon presence or absence of SFV; in each group, eight monkeys were injected with SIV(mac239) virus obtained from a molecular clone and four were injected with medium. Blood was collected every two weeks for evaluation of SIV infection based upon T cell-subsets, plasma viral load, development and persistence of virus-specific antibodies, and clinical changes by physical examination and hematology. Comparative analysis of SFV+/SIV+ and SFV-/SIV+ monkey groups indicated statistically significant differences in the plasma viral load between 6-28 weeks, particularly after reaching plateau at 20-28 weeks, in the CD4+ and CD8+ T-cell numbers over the entire study period (2-43 weeks), and in the survival rates evaluated at 49 weeks. There was an increase in the plasma viral load, a decreasing trend in the CD4+ T cells, and a greater number of animal deaths in the SFV+/SIV+ group. The results, although based upon a small number of animals, indicated that pre-existing SFV infection can influence SIV infection and disease outcome in the rhesus macaque model. The study highlights consideration of the SFV status in evaluating results from SIV pathogenesis and vaccine challenge studies in monkeys and indicates the potential use of the SFV/SIV monkey model to study the dynamics of SFV and HIV-1 dual infections, recently reported in humans.
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Affiliation(s)
- Anil Choudhary
- Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA; E-Mails: (A.C.); (T.A.G.); (D.K.W.)
| | - Teresa A. Galvin
- Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA; E-Mails: (A.C.); (T.A.G.); (D.K.W.)
| | - Dhanya K. Williams
- Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA; E-Mails: (A.C.); (T.A.G.); (D.K.W.)
| | - Joel Beren
- Division of Veterinary Services, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA; E-Mail:
| | - Mark A. Bryant
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD 20892, USA; E-Mail:
| | - Arifa S. Khan
- Laboratory of Retroviruses, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA; E-Mails: (A.C.); (T.A.G.); (D.K.W.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-301-827-0791; Fax: +1-301-496-1810
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13
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Mothé BR, Southwood S, Sidney J, English AM, Wriston A, Hoof I, Shabanowitz J, Hunt DF, Sette A. Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles. Immunogenetics 2013; 65:371-86. [PMID: 23417323 PMCID: PMC3633659 DOI: 10.1007/s00251-013-0686-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Accepted: 01/23/2013] [Indexed: 02/07/2023]
Abstract
Chinese rhesus macaques are of particular interest in simian immunodeficiency virus/human immunodeficiency virus (SIV/HIV) research as these animals have prolonged kinetics of disease progression to acquired immunodeficiency syndrome (AIDS), compared to their Indian counterparts, suggesting that they may be a better model for HIV. Nevertheless, the specific mechanism(s) accounting for these kinetics remains unclear. The study of major histocompatibility complex (MHC) molecules, including their MHC/peptide-binding motifs, provides valuable information for measuring cellular immune responses and deciphering outcomes of infection and vaccine efficacy. In this study, we have provided detailed characterization of six prevalent Chinese rhesus macaque MHC class I alleles, yielding a combined phenotypic frequency of 29 %. The peptide-binding specificity of two of these alleles, Mamu-A2*01:02 and Mamu-B*010:01, as well as the previously characterized allele Mamu-B*003:01 (and Indian rhesus Mamu-B*003:01), was found to be analogous to that of alleles in the HLA-B27 supertype family. Specific alleles in the HLA-B27 supertype family, including HLA-B*27:05, have been associated with long-term nonprogression to AIDS in humans. All six alleles characterized in the present study were found to have specificities analogous to HLA supertype alleles. These data contribute to the concept that Chinese rhesus macaque MHC immunogenetics is more similar to HLA than their Indian rhesus macaque counterparts and thereby warrants further studies to decipher the role of these alleles in the context of SIV infection.
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Affiliation(s)
- Bianca R Mothé
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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14
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Zhang XH, Dai ZX, Zhang GH, Han JB, Zheng YT. Molecular characterization, balancing selection, and genomic organization of the tree shrew (Tupaia belangeri) MHC class I gene. Gene 2013; 522:147-55. [PMID: 23566832 DOI: 10.1016/j.gene.2013.03.113] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 03/20/2013] [Accepted: 03/25/2013] [Indexed: 10/27/2022]
Abstract
The major histocompatibility complex (MHC) class I genes play a pivotal role in the adaptive immune response among vertebrates. Accordingly, in numerous mammals the genomic structure and molecular characterization of MHC class I genes have been thoroughly investigated. To date, however, little is known about these genes in tree shrews, despite the increasingly popularity of its usage as an animal model. To address this deficiency, we analyzed the structure and characteristic of the tree shrew MHC class I genes (Tube-MHC I) and performed a comparative gene analysis of the tree shrew and other mammal species. We found that the full-length cDNA sequence of the tree shrew MHC class I is 1074bp in length. The deduced peptide is composed of 357 amino acids containing a leader peptide, an α1 and α2 domain, an α3 domain, a transmembrane domain and a cytoplasmic domain. Among these peptides, the cysteines, CD8(+) interaction and N-glycosylation sites are all well conserved. Furthermore, the genomic sequence of the tree shrew MHC class I gene was identified to be 3180bp in length, containing 8 exons and 7 introns. In 21 MHC class I sequences, we conducted an extensive study of nucleotide substitutions. The results indicated that in the peptide binding region (PBR) the rate of non-synonymous substitutions (dN) to synonymous substitutions (dS) was greater than 1, suggesting balancing selection at the PBR. These findings provide valuable contributions in furthering our understanding of the structure, molecular polymorphism, and function of the MHC class I genes in tree shrews, further improving their utility as an animal model in biomedical research.
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Affiliation(s)
- Xi-He Zhang
- Key laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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15
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Wiseman RW, Karl JA, Bohn PS, Nimityongskul FA, Starrett GJ, O'Connor DH. Haplessly hoping: macaque major histocompatibility complex made easy. ILAR J 2013; 54:196-210. [PMID: 24174442 PMCID: PMC3814398 DOI: 10.1093/ilar/ilt036] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Major histocompatibility complex (MHC) gene products control the repertoire of T cell responses that an individual may create against pathogens and foreign tissues. This text will review the current understanding of MHC genetics in nonhuman primates, with a focus on Mauritian-origin cynomolgus macaques (Macaca fascicularis) and Indian-origin rhesus macaques (Macaca mulatta). These closely related macaque species provide important experimental models for studies of infectious disease pathogenesis, vaccine development, and transplantation research. Recent advances resulting from the application of several cost effective, high-throughput approaches, with deep sequencing technologies have revolutionized our ability to perform MHC genotyping of large macaque cohorts. Pyrosequencing of cDNA amplicons with a Roche/454 GS Junior instrument, provides excellent resolution of MHC class I allelic variants with semi-quantitative estimates of relative levels of transcript abundance. Introduction of the Illumina MiSeq platform significantly increased the sample throughput, since the sample loading workflow is considerably less labor intensive, and each instrument run yields approximately 100-fold more sequence data. Extension of these sequencing methods from cDNA to genomic DNA amplicons further streamlines the experimental workflow and opened opportunities for retrospective MHC genotyping of banked DNA samples. To facilitate the reporting of MHC genotypes, and comparisons between groups of macaques, this text also introduces an intuitive series of abbreviated rhesus MHC haplotype designations based on a major Mamu-A or Mamu-B transcript characteristic for ancestral allele combinations. The authors believe that the use of MHC-defined macaques promises to improve the reproducibility, and predictability of results from pre-clinical studies for translation to humans.
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Affiliation(s)
- Roger W. Wiseman
- Address correspondence and reprint requests to Dr. Roger Wiseman, Wisconsin National Primate Research Center, University of Wisconsin-Madison, 555 Science Drive, Madison, WI 53711 or email
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16
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Moore C, Sidney J, English AM, Wriston A, Hunt DF, Shabanowitz J, Southwood S, Bradley K, Lafont BAP, Mothé BR, Sette A. Identification of the peptide-binding motif recognized by the pigtail macaque class I MHC molecule Mane-A1*082:01 (Mane A*0301). Immunogenetics 2012; 64:461-8. [PMID: 22278177 PMCID: PMC3626442 DOI: 10.1007/s00251-012-0600-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 01/13/2012] [Indexed: 11/29/2022]
Abstract
Rhesus and pigtail macaques have proven to be valuable animal models for several important human diseases, including HIV, where they exhibit similar pathology and disease progression. Because rhesus macaques have been extensively characterized in terms of their major histocompatibility complex (MHC) class I alleles, their demand has soared, making them increasingly difficult to obtain for research purposes. This problem has been exacerbated by a continued export ban in place since 1978. Pigtail macaques represent a potential alternative animal model. However, because their MHC class I alleles have not been characterized in detail, their use has been hindered. To address this, in the present study, we have characterized the peptide binding specificity of the pigtail macaque class I allele Mane-A1*082:01 (formerly known as Mane A*0301), representative of the second most common MHC class I antigen detected across several cohorts. The motif was defined on the basis of binding studies utilizing purified MHC protein and panels of single amino acid substitution analog peptides, as well as sequences of peptide ligands eluted from Mane-A1*082:01. Based on these analyses, Mane-A1*082:01 was found to recognize a motif with H in position 2 and the aromatic residues F and Y, or the hydrophobic/aliphatic residue M, at the C-terminus. Finally, analysis of the binding of a combinatorial peptide library allowed the generation of a detailed quantitative motif that proved effective in the prediction of a set of high-affinity binders derived from chimeric SIV/HIV, an important model virus for studying HIV infection in humans.
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Affiliation(s)
- Carrie Moore
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - A. Michelle English
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Amanda Wriston
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Donald F. Hunt
- Department of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22908, USA
| | - Scott Southwood
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Kate Bradley
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Bernard A. P. Lafont
- Non-Human Primate Immunogenetics and Cellular Immunology Unit, Laboratory of Molecular Microbiology, NIAID/NIH, Bethesda, MD 20892, USA
| | - Bianca R. Mothé
- Department of Biological Sciences, California State University–San Marcos, San Marcos, CA 92069, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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17
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Sette A, Sidney J, Southwood S, Moore C, Berry J, Dow C, Bradley K, Hoof I, Lewis MG, Hildebrand WH, McMurtrey CP, Wilson NA, Watkins DI, Mothé BR. A shared MHC supertype motif emerges by convergent evolution in macaques and mice, but is totally absent in human MHC molecules. Immunogenetics 2012; 64:421-34. [PMID: 22322672 PMCID: PMC3349854 DOI: 10.1007/s00251-011-0598-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/25/2011] [Indexed: 02/07/2023]
Abstract
The SIV-infected rhesus macaque (Macaca mulatta) is the most established model of AIDS disease systems, providing insight into pathogenesis and a model system for testing novel vaccines. The understanding of cellular immune responses based on the identification and study of Major Histocompatibility Complex (MHC) molecules, including their MHC:peptide-binding motif, provides valuable information to decipher outcomes of infection and vaccine efficacy. Detailed characterization of Mamu-B*039:01, a common allele expressed in Chinese rhesus macaques, revealed a unique MHC:peptide-binding preference consisting of glycine at the second position. Peptides containing a glycine at the second position were shown to be antigenic from animals positive for Mamu-B*039:01. A similar motif was previously described for the Dd mouse MHC allele, but for none of the human HLA molecules for which a motif is known. Further investigation showed that one additional macaque allele, present in Indian rhesus macaques, Mamu-B*052:01, shares this same motif. These “G2” alleles were associated with the presence of specific residues in their B pocket. This pocket structure was found in 6% of macaque sequences but none of 950 human HLA class I alleles. Evolutionary studies using the “G2” alleles points to common ancestry for the macaque sequences, while convergent evolution is suggested when murine and macaque sequences are considered. This is the first detailed characterization of the pocket residues yielding this specific motif in nonhuman primates and mice, revealing a new supertype motif not present in humans.
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Affiliation(s)
- Alessandro Sette
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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