1
|
de Groot NG, Heijmans CM, van der Wiel MK, Bruijnesteijn J, Bontrop RE. The KIR repertoire of a West African chimpanzee population is characterized by limited gene, allele, and haplotype variation. Front Immunol 2023; 14:1308316. [PMID: 38149259 PMCID: PMC10750417 DOI: 10.3389/fimmu.2023.1308316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction The killer cell immunoglobulin-like receptors (KIR) play a pivotal role in modulating the NK cell responses, for instance, through interaction with major histocompatibility complex (MHC) class I molecules. Both gene systems map to different chromosomes but co-evolved during evolution. The human KIR gene family is characterized by abundant allelic polymorphism and copy number variation. In contrast, our knowledge of the KIR repertoire in chimpanzees is limited to 39 reported alleles, with no available population data. Only three genomic KIR region configurations have been mapped, and seventeen additional ones were deduced by genotyping. Methods Previously, we documented that the chimpanzee MHC class I repertoire has been skewed due to an ancient selective sweep. To understand the depth of the sweep, we set out to determine the full-length KIR transcriptome - in our MHC characterized pedigreed West African chimpanzee cohort - using SMRT sequencing (PacBio). In addition, the genomic organization of 14 KIR haplotypes was characterized by applying a Cas9-mediated enrichment approach in concert with long-read sequencing by Oxford Nanopore Technologies. Results In the cohort, we discovered 35 undescribed and 15 already recorded Patr-KIR alleles, and a novel hybrid KIR gene. Some KIR transcripts are subject to evolutionary conserved alternative splicing events. A detailed insight on the KIR region dynamics (location and order of genes) was obtained, however, only five new KIR region configurations were detected. The population data allowed to investigate the distribution of the MHC-C1 and C2-epitope specificity of the inhibitory lineage III KIR repertoire, and appears to be skewed towards C2. Discussion Although the KIR region is known to evolve fast, as observed in other primate species, our overall conclusion is that the genomic architecture and repertoire in West African chimpanzees exhibit only limited to moderate levels of variation. Hence, the ancient selective sweep that affected the chimpanzee MHC class I region may also have impacted the KIR system.
Collapse
Affiliation(s)
- Natasja G. de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Corrine M.C. Heijmans
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marit K.H. van der Wiel
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E. Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
2
|
Nieuwland JM, Nutma E, Philippens IHCHM, Böszörményi KP, Remarque EJ, Bakker J, Meijer L, Woerdman N, Fagrouch ZC, Verstrepen BE, Langermans JAM, Verschoor EJ, Windhorst AD, Bontrop RE, de Vries HE, Stammes MA, Middeldorp J. Longitudinal positron emission tomography and postmortem analysis reveals widespread neuroinflammation in SARS-CoV-2 infected rhesus macaques. J Neuroinflammation 2023; 20:179. [PMID: 37516868 PMCID: PMC10387202 DOI: 10.1186/s12974-023-02857-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/06/2023] [Accepted: 07/19/2023] [Indexed: 07/31/2023] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) patients initially develop respiratory symptoms, but they may also suffer from neurological symptoms. People with long-lasting effects after acute infections with severe respiratory syndrome coronavirus 2 (SARS-CoV-2), i.e., post-COVID syndrome or long COVID, may experience a variety of neurological manifestations. Although we do not fully understand how SARS-CoV-2 affects the brain, neuroinflammation likely plays a role. METHODS To investigate neuroinflammatory processes longitudinally after SARS-CoV-2 infection, four experimentally SARS-CoV-2 infected rhesus macaques were monitored for 7 weeks with 18-kDa translocator protein (TSPO) positron emission tomography (PET) using [18F]DPA714, together with computed tomography (CT). The baseline scan was compared to weekly PET-CTs obtained post-infection (pi). Brain tissue was collected following euthanasia (50 days pi) to correlate the PET signal with TSPO expression, and glial and endothelial cell markers. Expression of these markers was compared to brain tissue from uninfected animals of comparable age, allowing the examination of the contribution of these cells to the neuroinflammatory response following SARS-CoV-2 infection. RESULTS TSPO PET revealed an increased tracer uptake throughout the brain of all infected animals already from the first scan obtained post-infection (day 2), which increased to approximately twofold until day 30 pi. Postmortem immunohistochemical analysis of the hippocampus and pons showed TSPO expression in cells expressing ionized calcium-binding adaptor molecule 1 (IBA1), glial fibrillary acidic protein (GFAP), and collagen IV. In the hippocampus of SARS-CoV-2 infected animals the TSPO+ area and number of TSPO+ cells were significantly increased compared to control animals. This increase was not cell type specific, since both the number of IBA1+TSPO+ and GFAP+TSPO+ cells was increased, as well as the TSPO+ area within collagen IV+ blood vessels. CONCLUSIONS This study manifests [18F]DPA714 as a powerful radiotracer to visualize SARS-CoV-2 induced neuroinflammation. The increased uptake of [18F]DPA714 over time implies an active neuroinflammatory response following SARS-CoV-2 infection. This inflammatory signal coincides with an increased number of TSPO expressing cells, including glial and endothelial cells, suggesting neuroinflammation and vascular dysregulation. These results demonstrate the long-term neuroinflammatory response following a mild SARS-CoV-2 infection, which potentially precedes long-lasting neurological symptoms.
Collapse
Affiliation(s)
- Juliana M Nieuwland
- Department of Neurobiology and Aging, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288GJ, Rijswijk, The Netherlands
| | - Erik Nutma
- Department of Neurobiology and Aging, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288GJ, Rijswijk, The Netherlands
| | - Ingrid H C H M Philippens
- Department of Neurobiology and Aging, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288GJ, Rijswijk, The Netherlands
| | - Kinga P Böszörményi
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Edmond J Remarque
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Jaco Bakker
- Department of Radiology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Lisette Meijer
- Department of Radiology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Noor Woerdman
- Department of Radiology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Zahra C Fagrouch
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Babs E Verstrepen
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Jan A M Langermans
- Department of Animal Sciences, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
- Department Population Health Sciences, Unit Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ernst J Verschoor
- Department of Virology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Albert D Windhorst
- Department of Radiology and Nuclear Medicine, Tracer Center Amsterdam (TCA), Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
- Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Helga E de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Marieke A Stammes
- Department of Radiology, Biomedical Primate Research Centre (BPRC), Rijswijk, The Netherlands
| | - Jinte Middeldorp
- Department of Neurobiology and Aging, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288GJ, Rijswijk, The Netherlands.
| |
Collapse
|
3
|
de Groot NG, de Groot N, de Vos-Rouweler AJM, Louwerse A, Bruijnesteijn J, Bontrop RE. Dynamic evolution of Mhc haplotypes in cynomolgus macaques of different geographic origins. Immunogenetics 2022; 74:409-429. [PMID: 35084546 PMCID: PMC8792142 DOI: 10.1007/s00251-021-01249-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/26/2021] [Indexed: 11/05/2022]
Abstract
The major histocompatibility complex (MHC) plays a key role in immune defense, and the Mhc genes of cynomolgus macaque display a high degree of polymorphism. Based on their geographic distribution, different populations of cynomolgus macaques are recognized. Here we present the characterization of the Mhc class I and II repertoire of a large pedigreed group of cynomolgus macaques originating from the mainland north of the isthmus of Kra (N = 42). Segregation analyses resulted in the definition of 81 unreported Mafa-A/B/DRB/DQ/DP haplotypes, which include 32 previously unknown DRB regions. In addition, we report 13 newly defined Mafa-A/B/DRB/DQ/DP haplotypes in a group of cynomolgus macaques originating from the mainland south of the isthmus of Kra/Maritime Southeast Asia (N = 16). A relatively high level of sharing of Mafa-A (51%) and Mafa-B (40%) lineage groups is observed between the populations native to the north and the south of isthmus of Kra. At the allelic level, however, the Mafa-A/B haplotypes seem to be characteristic of a population. An overall comparison of all currently known data revealed that each geographic population has its own specific combinations of Mhc class I and II haplotypes. This illustrates the dynamic evolution of the cynomolgus macaque Mhc region, which was most likely generated by recombination and maintained by selection due to the differential pathogenic pressures encountered in different geographic areas.
Collapse
Affiliation(s)
- Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands.
| | - Nanine de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands
| | | | - Annet Louwerse
- Animal Science Department, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands
| | - Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, The Netherlands
| |
Collapse
|
4
|
Bontrop RE. Introducing our new Immunogenetics co-editor: Professor Andrew Brooks. Immunogenetics 2022; 74:445-446. [PMID: 35788884 DOI: 10.1007/s00251-022-01269-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ronald E Bontrop
- Biomedical Primate Research Centre, Department of Immunobiology, 2280 GH, Rijswijk, The Netherlands.
| |
Collapse
|
5
|
Philippens IHCHM, Böszörményi KP, Wubben JAM, Fagrouch ZC, van Driel N, Mayenburg AQ, Lozovagia D, Roos E, Schurink B, Bugiani M, Bontrop RE, Middeldorp J, Bogers WM, de Geus-Oei LF, Langermans JAM, Verschoor EJ, Stammes MA, Verstrepen BE. Brain Inflammation and Intracellular α-Synuclein Aggregates in Macaques after SARS-CoV-2 Infection. Viruses 2022; 14:v14040776. [PMID: 35458506 PMCID: PMC9025893 DOI: 10.3390/v14040776] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 causes acute respiratory disease, but many patients also experience neurological complications. Neuropathological changes with pronounced neuroinflammation have been described in individuals after lethal COVID-19, as well as in the CSF of hospitalized patients with neurological complications. To assess whether neuropathological changes can occur after a SARS-CoV-2 infection, leading to mild-to-moderate disease, we investigated the brains of four rhesus and four cynomolgus macaques after pulmonary disease and without overt clinical symptoms. Postmortem analysis demonstrated the infiltration of T-cells and activated microglia in the parenchyma of all infected animals, even in the absence of viral antigen or RNA. Moreover, intracellular α-synuclein aggregates were found in the brains of both macaque species. The heterogeneity of these manifestations in the brains indicates the virus’ neuropathological potential and should be considered a warning for long-term health risks, following SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Ingrid H. C. H. M. Philippens
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Kinga P. Böszörményi
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Jacqueline A. M. Wubben
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Zahra C. Fagrouch
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Nikki van Driel
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Amber Q. Mayenburg
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Diana Lozovagia
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Eva Roos
- Department of Pathology, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands; (E.R.); (B.S.); (M.B.)
| | - Bernadette Schurink
- Department of Pathology, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands; (E.R.); (B.S.); (M.B.)
| | - Marianna Bugiani
- Department of Pathology, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands; (E.R.); (B.S.); (M.B.)
| | - Ronald E. Bontrop
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
- Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Jinte Middeldorp
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Willy M. Bogers
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Lioe-Fee de Geus-Oei
- Department of Radiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
- Biomedical Photonic Imaging Group, University of Twente, 7522 ND Enschede, The Netherlands
| | - Jan A. M. Langermans
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
- Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands
| | - Ernst J. Verschoor
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
- Correspondence:
| | - Marieke A. Stammes
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| | - Babs E. Verstrepen
- Biomedical Primate Research Centre (BPRC), 2288 GJ Rijswijk, The Netherlands; (I.H.C.H.M.P.); (K.P.B.); (J.A.M.W.); (Z.C.F.); (N.v.D.); (A.Q.M.); (D.L.); (R.E.B.); (J.M.); (W.M.B.); (J.A.M.L.); (M.A.S.); (B.E.V.)
| |
Collapse
|
6
|
Bruijnesteijn J, de Groot N, de Vos-Rouweler AJM, de Groot NG, Bontrop RE. Comparative genetics of KIR haplotype diversity in humans and rhesus macaques: the balancing act. Immunogenetics 2022; 74:313-326. [PMID: 35291021 DOI: 10.1007/s00251-022-01259-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/01/2022] [Indexed: 12/25/2022]
Abstract
The role of natural killer (NK) cells is tightly modulated by interactions of killer cell immunoglobulin-like receptors (KIR) with their ligands of the MHC class I family. Several characteristics of the KIR gene products are conserved in primate evolution, like the receptor structures and the variegated expression pattern. At the genomic level, however, the clusters encoding the KIR family display species-specific diversity, reflected by differential gene expansions and haplotype architecture. The human KIR cluster is extensively studied in large cohorts from various populations, which revealed two KIR haplotype groups, A and B, that represent more inhibitory and more activating functional profiles, respectively. So far, genomic KIR analyses in large outbred populations of non-human primate species are lacking. In this study, we roughly quadrupled the number of rhesus macaques studied for their KIR transcriptome (n = 298). Using segregation analysis, we defined 112 unique KIR region configurations, half of which display a more inhibitory profile, whereas the other half has a more activating potential. The frequencies and functional potential of these profiles might mirror the human KIR haplotype groups. However, whereas the human group A and B KIR haplotypes are confined to largely fixed organizations, the haplotypes in macaques feature highly variable gene content. Moreover, KIR homozygosity was hardly encountered in this panel of macaques. This study exhibits highly diverse haplotype architectures in humans and macaques, which nevertheless might have an equivalent effect on the modulation of NK cell activity.
Collapse
Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands.
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ, Rijswijk, the Netherlands
- Theoretical Biology and Bioinformatics Group, Utrecht University, 3527, Utrecht, the Netherlands
| |
Collapse
|
7
|
Stammes MA, Lee JH, Meijer L, Naninck T, Doyle-Meyers LA, White AG, Borish HJ, Hartman AL, Alvarez X, Ganatra S, Kaushal D, Bohm RP, le Grand R, Scanga CA, Langermans JAM, Bontrop RE, Finch CL, Flynn JL, Calcagno C, Crozier I, Kuhn JH. Medical imaging of pulmonary disease in SARS-CoV-2-exposed non-human primates. Trends Mol Med 2022; 28:123-142. [PMID: 34955425 PMCID: PMC8648672 DOI: 10.1016/j.molmed.2021.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022]
Abstract
Chest X-ray (CXR), computed tomography (CT), and positron emission tomography-computed tomography (PET-CT) are noninvasive imaging techniques widely used in human and veterinary pulmonary research and medicine. These techniques have recently been applied in studies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-exposed non-human primates (NHPs) to complement virological assessments with meaningful translational readouts of lung disease. Our review of the literature indicates that medical imaging of SARS-CoV-2-exposed NHPs enables high-resolution qualitative and quantitative characterization of disease otherwise clinically invisible and potentially provides user-independent and unbiased evaluation of medical countermeasures (MCMs). However, we also found high variability in image acquisition and analysis protocols among studies. These findings uncover an urgent need to improve standardization and ensure direct comparability across studies.
Collapse
Affiliation(s)
- Marieke A Stammes
- Biomedical Primate Research Centre (BPRC), 2288 GJ, Rijswijk, The Netherlands.
| | - Ji Hyun Lee
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Fort Detrick, Frederick, MD 21702, USA
| | - Lisette Meijer
- Biomedical Primate Research Centre (BPRC), 2288 GJ, Rijswijk, The Netherlands
| | - Thibaut Naninck
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, 92260 Fontenay-aux-Roses, France
| | - Lara A Doyle-Meyers
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Alexander G White
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - H Jacob Borish
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Amy L Hartman
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pitt Public Health, Pittsburgh, PA 15261, USA
| | - Xavier Alvarez
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | | | - Deepak Kaushal
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Rudolf P Bohm
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Roger le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Université Paris-Saclay, Inserm, CEA, 92260 Fontenay-aux-Roses, France
| | - Charles A Scanga
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jan A M Langermans
- Biomedical Primate Research Centre (BPRC), 2288 GJ, Rijswijk, The Netherlands; Department Population Health Sciences, Division of Animals in Science and Society, Faculty of Veterinary Medicine, Utrecht University, 3584 CL, Utrecht, The Netherlands
| | - Ronald E Bontrop
- Biomedical Primate Research Centre (BPRC), 2288 GJ, Rijswijk, The Netherlands; Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Courtney L Finch
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Fort Detrick, Frederick, MD 21702, USA
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Claudia Calcagno
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Fort Detrick, Frederick, MD 21702, USA
| | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Fort Detrick, Frederick, MD 21702, USA
| |
Collapse
|
8
|
Storm L, Bruijnesteijn J, de Groot NG, Bontrop RE. The Genomic Organization of the LILR Region Remained Largely Conserved Throughout Primate Evolution: Implications for Health And Disease. Front Immunol 2021; 12:716289. [PMID: 34737739 PMCID: PMC8562567 DOI: 10.3389/fimmu.2021.716289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
The genes of the leukocyte immunoglobulin-like receptor (LILR) family map to the leukocyte receptor complex (LRC) on chromosome 19, and consist of both activating and inhibiting entities. These receptors are often involved in regulating immune responses, and are considered to play a role in health and disease. The human LILR region and evolutionary equivalents in some rodent and bird species have been thoroughly characterized. In non-human primates, the LILR region is annotated, but a thorough comparison between humans and non-human primates has not yet been documented. Therefore, it was decided to undertake a comprehensive comparison of the human and non-human primate LILR region at the genomic level. During primate evolution the organization of the LILR region remained largely conserved. One major exception, however, is provided by the common marmoset, a New World monkey species, which seems to feature a substantial contraction of the number of LILR genes in both the centromeric and the telomeric region. Furthermore, genomic analysis revealed that the killer-cell immunoglobulin-like receptor gene KIR3DX1, which maps in the LILR region, features one copy in humans and great ape species. A second copy, which might have been introduced by a duplication event, was observed in the lesser apes, and in Old and New World monkey species. The highly conserved gene organization allowed us to standardize the LILR gene nomenclature for non-human primate species, and implies that most of the receptors encoded by these genes likely fulfill highly preserved functions.
Collapse
Affiliation(s)
- Lisanne Storm
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
9
|
Bruijnesteijn J, van der Wiel M, de Groot NG, Bontrop RE. Rapid Characterization of Complex Killer Cell Immunoglobulin-Like Receptor (KIR) Regions Using Cas9 Enrichment and Nanopore Sequencing. Front Immunol 2021; 12:722181. [PMID: 34594334 PMCID: PMC8476923 DOI: 10.3389/fimmu.2021.722181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Long-read sequencing approaches have considerably improved the quality and contiguity of genome assemblies. Such platforms bear the potential to resolve even extremely complex regions, such as multigenic immune families and repetitive stretches of DNA. Deep sequencing coverage, however, is required to overcome low nucleotide accuracy, especially in regions with high homopolymer density, copy number variation, and sequence similarity, such as the MHC and KIR gene clusters of the immune system. Therefore, we have adapted a targeted enrichment protocol in combination with long-read sequencing to efficiently annotate complex KIR gene regions. Using Cas9 endonuclease activity, segments of the KIR gene cluster were enriched and sequenced on an Oxford Nanopore Technologies platform. This provided sufficient coverage to accurately resolve and phase highly complex KIR haplotypes. Our strategy eliminates PCR-induced amplification errors, facilitates rapid characterization of large and complex multigenic regions, including its epigenetic footprint, and is applicable in multiple species, even in the absence of a reference genome.
Collapse
Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marit van der Wiel
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
10
|
de Groot NG, Heijmans CMC, Bezstarosti S, Bruijnesteijn J, Haasnoot GW, Mulder A, Claas FHJ, Heidt S, Bontrop RE. Two Human Monoclonal HLA-Reactive Antibodies Cross-React with Mamu-B*008, a Rhesus Macaque MHC Allotype Associated with Control of Simian Immunodeficiency Virus Replication. J Immunol 2021; 206:1957-1965. [PMID: 33692147 DOI: 10.4049/jimmunol.2001405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/02/2021] [Indexed: 11/19/2022]
Abstract
MHC class I molecules play an important role in adaptive immune responses against intracellular pathogens. These molecules are highly polymorphic, and many allotypes have been characterized. In a transplantation setting, a mismatch between MHC allotypes may initiate an alloimmune response. Rhesus macaques (Macaca mulatta, Mamu) are valuable as a preclinical model species in transplantation research as well as to evaluate the safety and efficacy of vaccine candidates. In both lines of research, the availability of nonhuman primate MHC-reactive mAbs may enable in vitro monitoring and detection of presence of particular Mamu molecules. In this study, we screened a collection of thoroughly characterized HLA class I-specific human mAbs for cross-reactivity with rhesus macaque MHC class I allotypes. Two mAbs, OK4F9 and OK4F10, recognize an epitope that is defined by isoleucine (I) at amino acid position 142 that is present on the Indian rhesus macaque Mamu-B*008:01 allotype, which is an allotype known to be associated with elite control of SIV replication. The reactive pattern of a third mAb, MUS4H4, is more complex and includes an epitope shared on Mamu-A2*05:01 and -B*001:01-encoded Ags. This is the first description, to our knowledge, of human HLA-reactive mAbs that can recognize Mamu allotypes, and these can be useful tools for in vitro monitoring the presence of the relevant allelic products. Moreover, OK4F9 and OK4F10 can be powerful mAbs for application in SIV-related research.
Collapse
Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Suzanne Bezstarosti
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Geert W Haasnoot
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Arend Mulder
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Frans H J Claas
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
| |
Collapse
|
11
|
Vangenot C, Nunes JM, Doxiadis GM, Poloni ES, Bontrop RE, de Groot NG, Sanchez-Mazas A. Similar patterns of genetic diversity and linkage disequilibrium in Western chimpanzees (Pan troglodytes verus) and humans indicate highly conserved mechanisms of MHC molecular evolution. BMC Evol Biol 2020; 20:119. [PMID: 32933484 PMCID: PMC7491122 DOI: 10.1186/s12862-020-01669-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 08/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Many species are threatened with extinction as their population sizes decrease with changing environments or face novel pathogenic threats. A reduction of genetic diversity at major histocompatibility complex (MHC) genes may have dramatic effects on populations' survival, as these genes play a key role in adaptive immunity. This might be the case for chimpanzees, the MHC genes of which reveal signatures of an ancient selective sweep likely due to a viral epidemic that reduced their population size a few million years ago. To better assess how this past event affected MHC variation in chimpanzees compared to humans, we analysed several indexes of genetic diversity and linkage disequilibrium across seven MHC genes on four cohorts of chimpanzees and we compared them to those estimated at orthologous HLA genes in a large set of human populations. RESULTS Interestingly, the analyses uncovered similar patterns of both molecular diversity and linkage disequilibrium across the seven MHC genes in chimpanzees and humans. Indeed, in both species the greatest allelic richness and heterozygosity were found at loci A, B, C and DRB1, the greatest nucleotide diversity at loci DRB1, DQA1 and DQB1, and both significant global linkage disequilibrium and the greatest proportions of haplotypes in linkage disequilibrium were observed at pairs DQA1 ~ DQB1, DQA1 ~ DRB1, DQB1 ~ DRB1 and B ~ C. Our results also showed that, despite some differences among loci, the levels of genetic diversity and linkage disequilibrium observed in contemporary chimpanzees were globally similar to those estimated in small isolated human populations, in contrast to significant differences compared to large populations. CONCLUSIONS We conclude, first, that highly conserved mechanisms shaped the diversity of orthologous MHC genes in chimpanzees and humans. Furthermore, our findings support the hypothesis that an ancient demographic decline affecting the chimpanzee populations - like that ascribed to a viral epidemic - exerted a substantial effect on the molecular diversity of their MHC genes, albeit not more pronounced than that experienced by HLA genes in human populations that underwent rapid genetic drift during humans' peopling history. We thus propose a model where chimpanzees' MHC genes regenerated molecular variation through recombination/gene conversion and/or balancing selection after the selective sweep.
Collapse
Affiliation(s)
- Christelle Vangenot
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Gaby M Doxiadis
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Estella S Poloni
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288, GJ, Rijswijk, The Netherlands
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
| |
Collapse
|
12
|
Bruijnesteijn J, de Groot NG, Bontrop RE. The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates. Front Immunol 2020; 11:582804. [PMID: 33013938 PMCID: PMC7516082 DOI: 10.3389/fimmu.2020.582804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/18/2020] [Indexed: 12/26/2022] Open
Abstract
The activity and function of natural killer (NK) cells are modulated through the interactions of multiple receptor families, of which some recognize MHC class I molecules. The high level of MHC class I polymorphism requires their ligands either to interact with conserved epitopes, as is utilized by the NKG2A receptor family, or to co-evolve with the MHC class I allelic variation, which task is taken up by the killer cell immunoglobulin-like receptor (KIR) family. Multiple molecular mechanisms are responsible for the diversification of the KIR gene system, and include abundant chromosomal recombination, high mutation rates, alternative splicing, and variegated expression. The combination of these genetic mechanisms generates a compound array of diversity as is reflected by the contraction and expansion of KIR haplotypes, frequent birth of fusion genes, allelic polymorphism, structurally distinct isoforms, and variegated expression, which is in contrast to the mainly allelic nature of MHC class I polymorphism in humans. A comparison of the thoroughly studied human and macaque KIR gene repertoires demonstrates a similar evolutionarily conserved toolbox, through which selective forces drove and maintained the diversified nature of the KIR gene cluster. This hypothesis is further supported by the comparative genetics of KIR haplotypes and genes in other primate species. The complex nature of the KIR gene system has an impact upon the education, activity, and function of NK cells in coherence with an individual’s MHC class I repertoire and pathogenic encounters. Although selection operates on an individual, the continuous diversification of the KIR gene system in primates might protect populations against evolving pathogens.
Collapse
Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
13
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
14
|
Bruijnesteijn J, de Groot N, van der Wiel MKH, Otting N, de Vos-Rouweler AJM, de Groot NG, Bontrop RE. Unparalleled Rapid Evolution of KIR Genes in Rhesus and Cynomolgus Macaque Populations. J Immunol 2020; 204:1770-1786. [PMID: 32111732 DOI: 10.4049/jimmunol.1901140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/21/2020] [Indexed: 12/19/2022]
Abstract
The killer cell Ig-like receptors (KIR) modulate immune responses through interactions with MHC class I molecules. The KIR region in large cohorts of rhesus and cynomolgus macaque populations were characterized, and the experimental design enabled the definition of a considerable number of alleles (n = 576) and haplotypes, which are highly variable with regard to architecture. Although high levels of polymorphism were recorded, only a few alleles are shared between species and populations. The rapid evolution of allelic polymorphism, accumulated by point mutations, was further confirmed by the emergence of a novel KIR allele in a rhesus macaque family. In addition to allelic variation, abundant orthologous and species-specific KIR genes were identified, the latter of which are frequently generated by fusion events. The concerted action of both genetic mechanisms, in combination with differential selective pressures at the population level, resulted in the unparalleled rapid evolution of the KIR gene region in two closely related macaque species. The variation of the KIR gene repertoire at the species and population level might have an impact on the outcome of preclinical studies with macaque models.
Collapse
Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Marit K H van der Wiel
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; and .,Theoretical Biology and Bioinformatics Group, Utrecht University, 3527 Utrecht, the Netherlands
| |
Collapse
|
15
|
de Groot NG, Otting N, Maccari G, Robinson J, Hammond JA, Blancher A, Lafont BAP, Guethlein LA, Wroblewski EE, Marsh SGE, Shiina T, Walter L, Vigilant L, Parham P, O'Connor DH, Bontrop RE. Correction to: Nomenclature report 2019: major histocompatibility complex genes and alleles of great and small ape and old and new world monkey species. Immunogenetics 2019; 72:131-132. [PMID: 31745605 DOI: 10.1007/s00251-019-01146-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The original version of this article contained a spelling error in the Acknowledgments regarding the name of the funding organisation supporting GM and JAH. UKRI-BBSCR should have been UKRI-BBSRC, as is now indicated correctly below.
Collapse
Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288, GJ, Rijswijk, The Netherlands.
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288, GJ, Rijswijk, The Netherlands
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, Woking, Surrey, UK.,Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, Hampstead, London, NW3 2QG, UK
| | - James Robinson
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, Hampstead, London, NW3 2QG, UK.,UCL Cancer Institute, University College London, Royal Free Campus, Pond Street, Hampstead, London, NW3 2QG, UK
| | | | - Antoine Blancher
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (Inserm), Université Paul Sabatier (UPS), 31000, Toulouse, France.,Laboratoire d'Immunologie, CHU de Toulouse, Institut Fédératif de Biologie, Hôpital Purpan, 330 Avenue de Grande Bretagne, TSA40031, 31059, CEDEX 9, Toulouse, France
| | - Bernard A P Lafont
- Viral Immunology Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Lisbeth A Guethlein
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - Emily E Wroblewski
- Department of Anthropology, Washington University, St Louis, MO, 63130, USA
| | - Steven G E Marsh
- Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, Hampstead, London, NW3 2QG, UK.,UCL Cancer Institute, University College London, Royal Free Campus, Pond Street, Hampstead, London, NW3 2QG, UK
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Hiratsuka-shi, Kanagawa, Japan
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, 37077, Göttingen, Germany
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Peter Parham
- Department of Structural Biology and Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288, GJ, Rijswijk, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, 3584, CH, Utrecht, The Netherlands
| |
Collapse
|
16
|
Otting N, de Groot NG, Bontrop RE. Full-length MHC class II alleles in three New World monkey species. HLA 2019; 95:163-165. [PMID: 31705598 DOI: 10.1111/tan.13757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/05/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 11/28/2022]
Abstract
Thirty newly identified full-length MHC class II alleles in three New World monkey species.
Collapse
Affiliation(s)
- Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,IPD-MHC Database Nonhuman Primate Nomenclature Committee, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,IPD-MHC Database Nonhuman Primate Nomenclature Committee, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,IPD-MHC Database Nonhuman Primate Nomenclature Committee, Rijswijk, The Netherlands.,Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
17
|
Böck J, Remmele CW, Dittrich M, Müller T, Kondova I, Persengiev S, Bontrop RE, Ade CP, Kraus TFJ, Giese A, El Hajj N, Schneider E, Haaf T. Cell Type and Species-specific Patterns in Neuronal and Non-neuronal Methylomes of Human and Chimpanzee Cortices. Cereb Cortex 2019; 28:3724-3739. [PMID: 30085031 PMCID: PMC6132288 DOI: 10.1093/cercor/bhy180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/13/2018] [Indexed: 12/04/2022] Open
Abstract
Epigenetic changes have likely contributed to the large size and enhanced cognitive abilities of the human brain which evolved within the last 2 million years after the human–chimpanzee split. Using reduced representation bisulfite sequencing, we have compared the methylomes of neuronal and non-neuronal cells from 3 human and 3 chimpanzee cortices. Differentially methylated regions (DMRs) with genome-wide significance were enriched in specific genomic regions. Intraspecific methylation differences between neuronal and non-neuronal cells were approximately 3 times more abundant than interspecific methylation differences between human and chimpanzee cell types. The vast majority (>90%) of human intraspecific DMRs (including DMRs in retrotransposons) were hypomethylated in neurons, compared with glia. Intraspecific DMRs were enriched in genes associated with different neuropsychiatric disorders. Interspecific DMRs were enriched in genes showing human-specific brain histone modifications. Human–chimpanzee methylation differences were much more frequent in non-neuronal cells (n. DMRs = 666) than in neurons (n. DMRs = 96). More than 95% of interspecific DMRs in glia were hypermethylated in humans. Although without an outgroup we cannot assign whether a change in methylation occurred in the human or chimpanzee lineage, our results are consistent with a wave of methylation affecting several hundred non-neuronal genes during human brain evolution.
Collapse
Affiliation(s)
- Julia Böck
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Christian W Remmele
- Department of Bioinformatics, Julius Maximilians University Würzburg, Würzburg Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany.,Department of Bioinformatics, Julius Maximilians University Würzburg, Würzburg Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University Würzburg, Würzburg Germany
| | - Ivanela Kondova
- Biomedical Primate Research Center, 2288 GJ Rijswijk, The Netherlands
| | | | - Ronald E Bontrop
- Biomedical Primate Research Center, 2288 GJ Rijswijk, The Netherlands
| | - Carsten P Ade
- Institute of Biochemistry and Molecular Biology, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Theo F J Kraus
- Center for Neuropathology and Prion Research, Ludwig Maximilians University Munich, Munich, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig Maximilians University Munich, Munich, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Eberhard Schneider
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| |
Collapse
|
18
|
de Groot N, Groen R, Orie V, Bruijnesteijn J, de Groot NG, Doxiadis GGM, Bontrop RE. Analysis of macaque BTN3A genes and transcripts in the extended MHC: conserved orthologs of human γδ T cell modulators. Immunogenetics 2019; 71:545-559. [PMID: 31384962 PMCID: PMC6790196 DOI: 10.1007/s00251-019-01126-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
Abstract
Butyrophilins (BTN), specifically BTN3A, play a central role in the modulation of γδ T cells, which are mainly present in gut and mucosal tissues. BTN3A1 is known, for example, to activate Vγ9Vδ2 T cells by means of a phosphoantigen interaction. In the extended HLA region, three genes are located, designated BTN3A1, BTN3A2 and BTN3A3, which were also defined in rhesus macaques. In contrast to humans, rhesus monkeys have an additional gene, BTN3A3Like, which has the features of a pseudogene. cDNA analysis of 32 Indian rhesus and 16 cynomolgus macaques originating from multiple-generation families revealed that all three genes are oligomorphic, and the deduced amino acids display limited variation. The macaque BTN3A alleles segregated together with MHC alleles, proving their location in the extended (Major Histocompatibility Complex) MHC. BTN3A nearly full-length transcripts of macaques and humans cluster tightly together in the phylogenetic tree, suggesting that the genes represent true orthologs of each other. Despite the limited level of polymorphism, 15 Mamu- and 14 Mafa-BTN3A haplotypes were defined, and, as in humans, all three BTN3A genes are transcribed in PBMCs and colon tissues. In addition to regular full-length transcripts, a high number of various alternative splicing (AS) products were observed for all BTN3A alleles, which may result in different isoforms. The comparable function of certain subsets of γδ T cells in human and non-human primates in concert with high levels of sequence conservation observed for the BTN3A transcripts presents the opportunity to study these not yet well understood molecules in macaques as a model species.
Collapse
Affiliation(s)
- Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Rens Groen
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Vaneesha Orie
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
19
|
Bruijnesteijn J, van der Wiel MKH, de Groot N, Otting N, de Vos-Rouweler AJM, Lardy NM, de Groot NG, Bontrop RE. Extensive Alternative Splicing of KIR Transcripts. Front Immunol 2018; 9:2846. [PMID: 30564240 PMCID: PMC6288254 DOI: 10.3389/fimmu.2018.02846] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/19/2018] [Indexed: 12/15/2022] Open
Abstract
The killer-cell Ig-like receptors (KIR) form a multigene entity involved in modulating immune responses through interactions with MHC class I molecules. The complexity of the KIR cluster is reflected by, for instance, abundant levels of allelic polymorphism, gene copy number variation, and stochastic expression profiles. The current transcriptome study involving human and macaque families demonstrates that KIR family members are also subjected to differential levels of alternative splicing, and this seems to be gene dependent. Alternative splicing may result in the partial or complete skipping of exons, or the partial inclusion of introns, as documented at the transcription level. This post-transcriptional process can generate multiple isoforms from a single KIR gene, which diversifies the characteristics of the encoded proteins. For example, alternative splicing could modify ligand interactions, cellular localization, signaling properties, and the number of extracellular domains of the receptor. In humans, we observed abundant splicing for KIR2DL4, and to a lesser extent in the lineage III KIR genes. All experimentally documented splice events are substantiated by in silico splicing strength predictions. To a similar extent, alternative splicing is observed in rhesus macaques, a species that shares a close evolutionary relationship with humans. Splicing profiles of Mamu-KIR1D and Mamu-KIR2DL04 displayed a great diversity, whereas Mamu-KIR3DL20 (lineage V) is consistently spliced to generate a homolog of human KIR2DL5 (lineage I). The latter case represents an example of convergent evolution. Although just a single KIR splice event is shared between humans and macaques, the splicing mechanisms are similar, and the predicted consequences are comparable. In conclusion, alternative splicing adds an additional layer of complexity to the KIR gene system in primates, and results in a wide structural and functional variety of KIR receptors and its isoforms, which may play a role in health and disease.
Collapse
Affiliation(s)
- Jesse Bruijnesteijn
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Marit K H van der Wiel
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Nanine de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Nel Otting
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | | | - Neubury M Lardy
- Department of Immunogenetics, Sanquin, Amsterdam, Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
20
|
Ballingall KT, Bontrop RE, Ellis SA, Grimholt U, Hammond JA, Ho CS, Kaufman J, Kennedy LJ, Maccari G, Miller D, Robinson J, Marsh SGE. Comparative MHC nomenclature: report from the ISAG/IUIS-VIC committee 2018. Immunogenetics 2018; 70:625-632. [PMID: 30039257 DOI: 10.1007/s00251-018-1073-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 05/25/2018] [Accepted: 07/13/2018] [Indexed: 12/24/2022]
Abstract
Significant progress has been made over the last decade in defining major histocompatibility complex (MHC) diversity at the nucleotide, allele, haplotype, diplotype, and population levels in many non-human species. Much of this progress has been driven by the increased availability and reduced costs associated with nucleotide sequencing technologies. This report provides an update on the activities of the comparative MHC nomenclature committee which is a standing committee of both the International Society for Animal Genetics (ISAG) and the International Union of Immunological Societies (IUIS) where it operates under the umbrella of the Veterinary Immunology Committee (VIC). A previous report from this committee in 2006 defined the role of the committee in providing guidance in the development of a standardized nomenclature for genes and alleles at MHC loci in non-human species. It described the establishment of the Immuno Polymorphism Database, IPD-MHC, which continues to provide public access to high quality MHC sequence data across a range of species. In this report, guidelines for the continued development of a universal MHC nomenclature framework are described, summarizing the continued development of each species section within the IPD-MHC project.
Collapse
Affiliation(s)
- Keith T Ballingall
- Moredun Research Institute, Midlothian, UK and Chair of the Comparative MHC Nomenclature Committee, Edinburgh, Scotland, UK.
| | | | | | | | | | | | | | - Lorna J Kennedy
- Centre for Integrated Genomic Medical Research, Manchester, UK
| | - Giuseppe Maccari
- The Pirbright Institute, Pirbright, Surrey, UK.,Anthony Nolan Research Institute, London, UK
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - James Robinson
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| |
Collapse
|
21
|
de Winter II, Qurkhuli T, de Groot N, de Vos-Rouweler AJM, van Hooft P, Heitkönig IMA, Prins HHT, Bontrop RE, Doxiadis GGM. Determining Mhc-DRB profiles in wild populations of three congeneric true lemur species by noninvasive methods. Immunogenetics 2018; 71:97-107. [PMID: 30324236 PMCID: PMC6327083 DOI: 10.1007/s00251-018-1085-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/10/2018] [Indexed: 12/22/2022]
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic and polygenic genomic region that plays a crucial role in immune-related diseases. Given the need for comparative studies on the variability of immunologically important genes among wild populations and species, we investigated the allelic variation of MHC class II DRB among three congeneric true lemur species: the red-fronted lemur (Eulemur rufifrons), red-bellied lemur (Eulemur rubriventer), and black lemur (Eulemur macaco). We noninvasively collected hair and faecal samples from these species across different regions in Madagascar. We assessed DRB exon 2 polymorphism with a newly developed primer set, amplifying nearly all non-synonymous codons of the antigen-binding sites. We defined 26 DRB alleles from 45 individuals (17 alleles from E. rufifrons (N = 18); 5 from E. rubriventer (N = 7); and 4 from E. macaco (N = 20). All detected alleles are novel and show high levels of nucleotide (26.8%) and non-synonymous codon polymorphism (39.4%). In these lemur species, we found neither evidence of a duplication of DRB genes nor a sharing of alleles among sympatric groups or allopatric populations of the same species. The non-sharing of alleles may be the result of a geographical separation over a long time span and/or different pathogen selection pressures. We found dN/dS rates > 1 in the functionally important antigen recognition sites, providing evidence for balancing selection. Especially for small and isolated populations, quantifying and monitoring DRB variation are recommended to establish successful conservation plans that mitigate the possible loss of immunogenetic diversity in lemurs.
Collapse
Affiliation(s)
- Iris I de Winter
- Resource Ecology Group, Wageningen University, Wageningen, The Netherlands. .,Department of Biology, Utrecht University, Utrecht, The Netherlands.
| | - Tamar Qurkhuli
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Pim van Hooft
- Resource Ecology Group, Wageningen University, Wageningen, The Netherlands
| | | | - Herbert H T Prins
- Resource Ecology Group, Wageningen University, Wageningen, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, University of Utrecht, Utrecht, The Netherlands
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| |
Collapse
|
22
|
Otting N, de Groot NG, Bontrop RE. Correction to: Limited MHC class II gene polymorphism in the West African chimpanzee is distributed maximally by haplotype diversity. Immunogenetics 2018; 70:689-691. [PMID: 30283990 DOI: 10.1007/s00251-018-1089-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The authors regret that an error was present in the Fig. 5 of the above article; some digits in the DRB allele-designations in Fig. 5 have been lost, and are incorrectly presented by only two digits. The correct allele-designations should have been four (or six) digits. The correct Figure is now presented correctly.
Collapse
Affiliation(s)
- Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288, GJ, Rijswijk, The Netherlands. .,IPD-MHC database Nonhuman Primate Nomenclature Committee, Rijswijk, The Netherlands.
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288, GJ, Rijswijk, The Netherlands.,IPD-MHC database Nonhuman Primate Nomenclature Committee, Rijswijk, The Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288, GJ, Rijswijk, The Netherlands.,IPD-MHC database Nonhuman Primate Nomenclature Committee, Rijswijk, The Netherlands.,Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
23
|
de Groot NG, Stevens JM, Bontrop RE. Does the MHC Confer Protection against Malaria in Bonobos? Trends Immunol 2018; 39:768-771. [DOI: 10.1016/j.it.2018.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/13/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022]
|
24
|
Maccari G, Robinson J, Bontrop RE, Otting N, de Groot NG, Ho CS, Ballingall KT, Marsh SGE, Hammond JA. IPD-MHC: nomenclature requirements for the non-human major histocompatibility complex in the next-generation sequencing era. Immunogenetics 2018; 70:619-623. [PMID: 30027299 PMCID: PMC6182402 DOI: 10.1007/s00251-018-1072-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/03/2018] [Indexed: 12/25/2022]
Abstract
The IPD-MHC Database is the official repository for non-human MHC sequences, overseen and supported by the Comparative MHC Nomenclature Committee, providing access to curated MHC data and associated analysis tools. To address the increasing amount and complexity of data being submitted, an entirely upgraded version of the IPD-MHC Database was recently released to maintain IPD-MHC as the central platform for the comparison of curated MHC data. As a consequence, a new level of nomenclature standardisation is required between the different species to enable data submission and to allow the unambiguous inter- and intra-species comparison of alleles. However, any changes must retain the flexibility demanded by the unique biology of different taxonomic groups. Here, we describe the rationale for a standardised nomenclature system and summarise the changes that have been driven by the requirements of implementing the IPD-MHC database. This modified nomenclature system is essential to maintain the current functionality of IPD-MHC and provide a scalable future-proof database organisation to fully exploit the bioinformatic tools used for analysis.
Collapse
Affiliation(s)
- Giuseppe Maccari
- The Pirbright Institute, Woking, Surrey, UK.,Anthony Nolan Research Institute, London, UK
| | - James Robinson
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | | | - Nel Otting
- Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | | | | | - Steven G E Marsh
- Anthony Nolan Research Institute, London, UK.,UCL Cancer Institute, Royal Free Campus, London, UK
| | | |
Collapse
|
25
|
Bruijnesteijn J, van der Wiel MKH, Swelsen WTN, Otting N, de Vos-Rouweler AJM, Elferink D, Doxiadis GG, Claas FHJ, Lardy NM, de Groot NG, Bontrop RE. Human and Rhesus Macaque KIR Haplotypes Defined by Their Transcriptomes. J Immunol 2018; 200:1692-1701. [PMID: 29358278 DOI: 10.4049/jimmunol.1701480] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/20/2017] [Indexed: 11/19/2022]
Abstract
The killer-cell Ig-like receptors (KIRs) play a central role in the immune recognition in infection, pregnancy, and transplantation through their interactions with MHC class I molecules. KIR genes display abundant copy number variation as well as high levels of polymorphism. As a result, it is challenging to characterize this structurally dynamic region. KIR haplotypes have been analyzed in different species using conventional characterization methods, such as Sanger sequencing and Roche/454 pyrosequencing. However, these methods are time-consuming and often failed to define complete haplotypes, or do not reach allele-level resolution. In addition, most analyses were performed on genomic DNA, and thus were lacking substantial information about transcription and its corresponding modifications. In this paper, we present a single-molecule real-time sequencing approach, using Pacific Biosciences Sequel platform to characterize the KIR transcriptomes in human and rhesus macaque (Macaca mulatta) families. This high-resolution approach allowed the identification of novel Mamu-KIR alleles, the extension of reported allele sequences, and the determination of human and macaque KIR haplotypes. In addition, multiple recombinant KIR genes were discovered, all located on contracted haplotypes, which were likely the result of chromosomal rearrangements. The relatively high number of contracted haplotypes discovered might be indicative of selection on small KIR repertoires and/or novel fusion gene products. This next-generation method provides an improved high-resolution characterization of the KIR cluster in humans and macaques, which eventually may aid in a better understanding and interpretation of KIR allele-associated diseases, as well as the immune response in transplantation and reproduction.
Collapse
Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Marit K H van der Wiel
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Wendy T N Swelsen
- Department of Immunogenetics, Sanquin, 1066 CX Amsterdam, the Netherlands
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Diënne Elferink
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; and
| | - Gaby G Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Frans H J Claas
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; and
| | - Neubury M Lardy
- Department of Immunogenetics, Sanquin, 1066 CX Amsterdam, the Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; .,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
| |
Collapse
|
26
|
Affiliation(s)
- Ronald E Bontrop
- Biomedical Primate Research Center, PO Box 3306, 2280, Rijswijk, GH, Netherlands.
| |
Collapse
|
27
|
de Groot NG, Heijmans CMC, de Ru AH, Janssen GMC, Drijfhout JW, Otting N, Vangenot C, Doxiadis GGM, Koning F, van Veelen PA, Bontrop RE. A Specialist Macaque MHC Class I Molecule with HLA-B*27-like Peptide-Binding Characteristics. J Immunol 2017; 199:3679-3690. [PMID: 29021373 DOI: 10.4049/jimmunol.1700502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022]
Abstract
In different macaque species, the MHC A2*05 gene is present in abundance, and its gene products are characterized by low cell-surface expression and a highly conserved peptide-binding cleft. We have characterized the peptide-binding motif of Mamu-A2*05:01, and elucidated the binding capacity for virus-derived peptides. The macaque A2*05 allotype prefers the basic amino acid arginine at the second position of the peptide, and hydrophobic and polar amino acids at the C-terminal end. These preferences are shared with HLA-B*27 and Mamu-B*008, molecules shown to be involved in elite control in human HIV type 1 and macaque SIV infections, respectively. In contrast, however, Mamu-A2*05 preferentially binds 8-mer peptides. Retention in the endoplasmic reticulum seems to be the cause of the lower cell-surface expression. Subsequent peptide-binding studies have illustrated that Mamu-A2*05:01 is able to bind SIV-epitopes known to evoke a strong CD8+ T cell response in the context of the Mamu-B*008 allotype in SIV-infected rhesus macaques. Thus, the macaque A2*05 gene encodes a specialized MHC class I molecule, and is most likely transported to the cell surface only when suitable peptides become available.
Collapse
Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Arnoud H de Ru
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - George M C Janssen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Christelle Vangenot
- Anthropology Unit, Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland; and
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter A van Veelen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
| |
Collapse
|
28
|
Bodmer JG, Marsh SGE, Albert E, Bodmer WF, Bontrop RE, Charron D, Dupont B, Erlich HA, Fauchet R, Mach B, Mayr WR, Parham P, Sasazuki T, Schreuder GMT, Strominger JL, Svejgaard A, Terasaki PI. Nomenclature for Factors of the
HLA System, 1996. Vox Sang 2017. [DOI: 10.1159/000461915] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
29
|
Kondova I, Braskamp G, Heidt PJ, Collignon W, Haaksma T, de Groot N, Otting N, Doxiadis G, Westmoreland SV, Vallender EJ, Bontrop RE. Spontaneous endometriosis in rhesus macaques: evidence for a genetic association with specific Mamu-A1 alleles. Primate Biol 2017; 4:117-125. [PMID: 32110699 PMCID: PMC7041536 DOI: 10.5194/pb-4-117-2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/28/2017] [Indexed: 11/11/2022] Open
Abstract
Endometriosis is a poorly understood common debilitating women's
reproductive disorder resulting from proliferative and ectopic endometrial
tissue associated with variable clinical symptoms including dysmenorrhea
(painful menstrual periods), dyspareunia (pain on intercourse), female
infertility, and an increased risk of malignant transformation. The rhesus
macaque (Macaca mulatta) develops a spontaneous endometriosis that is very
similar to that seen in women. We hypothesized that specific major
histocompatibility complex (MHC) alleles may contribute to the pathogenesis
of endometriosis. As part of a collaboration between the Biomedical Primate
Research Centre (BPRC) in the Netherlands and the New England Primate
Research Center (NEPRC) in the United States, we analyzed DNA sequences of
MHC class I (Macaca mulatta, Mamu-A1) and class II
(Mamu-DRB) alleles from rhesus macaques with endometriosis and
compared the allele frequencies with those of age-matched healthy macaques.
We demonstrate that two MHC class I alleles are overrepresented in diseased
macaques compared to controls: Mamu-A1*001, 33.3 % in BPRC
animals with endometriosis vs. 11.6 % in healthy macaques (p= 0.007),
and Mamu-A1*007, 21.9 % NEPRC rhesus macaques vs.
6.7 %, (p= 0.003). We provide evidence that select MHC class I alleles
are associated with endometriosis in rhesus macaques and suggest that the
disease pathogenesis contribution of MHC class I warrants further research.
Collapse
Affiliation(s)
- Ivanela Kondova
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Gerco Braskamp
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,deceased
| | - Peter J Heidt
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Wim Collignon
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Tom Haaksma
- Animal Science Department, Division of Pathology and Microbiology, Division of Veterinary care, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Nanine de Groot
- Department of Comparative Genetics, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Nel Otting
- Department of Comparative Genetics, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Gaby Doxiadis
- Department of Comparative Genetics, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Susan V Westmoreland
- AbbVie Bioresearch Center, Immunology, Pharmacology, Pathology and Exploratory Toxicology, Worcester, MA 01605, USA
| | - Eric J Vallender
- Department of Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS 39216, USA.,Division of Veterinary Medicine, Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Ronald E Bontrop
- Department of Comparative Genetics, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| |
Collapse
|
30
|
Sterck EHM, Bontrop RE, de Groot N, de Vos-Rouweler AJM, Doxiadis GGM. No postcopulatory selection against MHC-homozygous offspring: Evidence from a pedigreed captive rhesus macaque colony. Mol Ecol 2017; 26:3785-3793. [PMID: 28437562 DOI: 10.1111/mec.14153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 01/27/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
The heterozygosity status of polymorphic elements of the immune system, such as the major histocompatibility complex (MHC), is known to increase the potential to cope with a wider variety of pathogens. Pre- and postcopulatory processes may regulate MHC heterozygosity. In a population where mating occurs among individuals that share identical MHC haplotypes, postcopulatory selection may disfavour homozygous offspring or ones with two MHC haplotypes identical to its mother. We tested these ideas by determining the incidence of MHC-heterozygous and MHC-homozygous individuals in a pedigreed, partially consanguineous captive rhesus monkey colony. Bayesian statistics showed that when parents share MHC haplotypes, the distribution of MHC-heterozygous and MHC-homozygous individuals significantly fitted the expected Mendelian distribution, both for the complete MHC haplotypes, and for MHC class I or II genes separately. Altogether, we found in this captive colony no evidence for postcopulatory selection against MHC-homozygous individuals. However, the distribution of paternally and maternally inherited MHC haplotypes tended to differ significantly from expected. Individuals with two MHC haplotypes identical to their mother were underrepresented and offspring with MHC haplotypes identical to their father tended to be overrepresented. This suggests that postcopulatory processes affect MHC haplotype combination in offspring, but do not prevent low MHC heterozygosity.
Collapse
Affiliation(s)
- E H M Sterck
- Department of Animal Ecology, Utrecht University, Utrecht, The Netherlands.,Department of Animal Science, Ethology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - R E Bontrop
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands.,Department of Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - N de Groot
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - A J M de Vos-Rouweler
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - G G M Doxiadis
- Department of Comparative Genetics & Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| |
Collapse
|
31
|
Abstract
Common chimpanzees (Pan troglodytes) experienced a selective sweep, probably caused by a SIV-like virus, which targeted their MHC class I repertoire. Based on MHC class I intron 2 data analyses, this selective sweep took place about 2-3 million years ago. As a consequence, common chimpanzees have a skewed MHC class I repertoire that is enriched for allotypes that are able to recognise conserved regions of the SIV proteome. The bonobo (Pan paniscus) shared an ancestor with common chimpanzees approximately 1.5 to 2 million years ago. To investigate whether the signature of this selective sweep is also detectable in bonobos, the MHC class I gene repertoire of two bonobo panels comprising in total 29 animals was investigated by Sanger sequencing. We identified 14 Papa-A, 20 Papa-B and 11 Papa-C alleles, of which eight, five and eight alleles, respectively, have not been reported previously. Within this pool of MHC class I variation, we recovered only 2 Papa-A, 3 Papa-B and 6 Papa-C intron 2 sequences. As compared to humans, bonobos appear to have an even more diminished MHC class I intron 2 lineage repertoire than common chimpanzees. This supports the notion that the selective sweep may have predated the speciation of common chimpanzees and bonobos. The further reduction of the MHC class I intron 2 lineage repertoire observed in bonobos as compared to the common chimpanzee may be explained by a founding effect or other subsequent selective processes.
Collapse
Affiliation(s)
- Natasja G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands.
| | - Corrine M C Heijmans
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Nel Otting
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands
| | - Zjef Pereboom
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | - Jeroen M G Stevens
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium.,Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Ronald E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics & Refinement, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH, Utrecht, The Netherlands
| |
Collapse
|
32
|
Karl JA, Graham ME, Wiseman RW, Heimbruch KE, Gieger SM, Doxiadis GGM, Bontrop RE, O'Connor DH. Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities. Immunogenetics 2017; 69:211-229. [PMID: 28078358 PMCID: PMC5352482 DOI: 10.1007/s00251-017-0969-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/03/2017] [Indexed: 10/20/2022]
Abstract
Very little is currently known about the major histocompatibility complex (MHC) region of cynomolgus macaques (Macaca fascicularis; Mafa) from Chinese breeding centers. We performed comprehensive MHC class I haplotype analysis of 100 cynomolgus macaques from two different centers, with animals from different reported original geographic origins (Vietnamese, Cambodian, and Cambodian/Indonesian mixed-origin). Many of the samples were of known relation to each other (sire, dam, and progeny sets), making it possible to characterize lineage-level haplotypes in these animals. We identified 52 Mafa-A and 74 Mafa-B haplotypes in this cohort, many of which were restricted to specific sample origins. We also characterized full-length MHC class I transcripts using Pacific Biosciences (PacBio) RS II single-molecule real-time (SMRT) sequencing. This technology allows for complete read-through of unfragmented MHC class I transcripts (~1100 bp in length), so no assembly is required to unambiguously resolve novel full-length sequences. Overall, we identified 311 total full-length transcripts in a subset of 72 cynomolgus macaques from these Chinese breeding facilities; 130 of these sequences were novel and an additional 115 extended existing short database sequences to span the complete open reading frame. This significantly expands the number of Mafa-A, Mafa-B, and Mafa-I full-length alleles in the official cynomolgus macaque MHC class I database. The PacBio technique described here represents a general method for full-length allele discovery and genotyping that can be extended to other complex immune loci such as MHC class II, killer immunoglobulin-like receptors, and Fc gamma receptors.
Collapse
Affiliation(s)
- Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Michael E Graham
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Katelyn E Heimbruch
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Samantha M Gieger
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Gaby G M Doxiadis
- 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
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, 53715, USA.
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 585 Science Drive, Madison, WI, 53711, USA.
| |
Collapse
|
33
|
Guethlein LA, Norman PJ, Heijmans CMC, de Groot NG, Hilton HG, Babrzadeh F, Abi-Rached L, Bontrop RE, Parham P. Two Orangutan Species Have Evolved Different KIR Alleles and Haplotypes. J Immunol 2017; 198:3157-3169. [PMID: 28264973 DOI: 10.4049/jimmunol.1602163] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/09/2017] [Indexed: 11/19/2022]
Abstract
The immune and reproductive functions of human NK cells are regulated by interactions of the C1 and C2 epitopes of HLA-C with C1-specific and C2-specific lineage III killer cell Ig-like receptors (KIR). This rapidly evolving and diverse system of ligands and receptors is restricted to humans and great apes. In this context, the orangutan has particular relevance because it represents an evolutionary intermediate, one having the C1 epitope and corresponding KIR but lacking the C2 epitope. Through a combination of direct sequencing, KIR genotyping, and data mining from the Great Ape Genome Project, we characterized the KIR alleles and haplotypes for panels of 10 Bornean orangutans and 19 Sumatran orangutans. The orangutan KIR haplotypes have between 5 and 10 KIR genes. The seven orangutan lineage III KIR genes all locate to the centromeric region of the KIR locus, whereas their human counterparts also populate the telomeric region. One lineage III KIR gene is Bornean specific, one is Sumatran specific, and five are shared. Of 12 KIR gene-content haplotypes, 5 are Bornean specific, 5 are Sumatran specific, and 2 are shared. The haplotypes have different combinations of genes encoding activating and inhibitory C1 receptors that can be of higher or lower affinity. All haplotypes encode an inhibitory C1 receptor, but only some haplotypes encode an activating C1 receptor. Of 130 KIR alleles, 55 are Bornean specific, 65 are Sumatran specific, and 10 are shared.
Collapse
Affiliation(s)
- Lisbeth A Guethlein
- Department of Structural Biology, Stanford University, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Paul J Norman
- Department of Structural Biology, Stanford University, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Corinne M C Heijmans
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Hugo G Hilton
- Department of Structural Biology, Stanford University, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | | | - Laurent Abi-Rached
- Department of Structural Biology, Stanford University, Stanford, CA 94305.,Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Peter Parham
- Department of Structural Biology, Stanford University, Stanford, CA 94305; .,Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| |
Collapse
|
34
|
de Groot N, Stanbury K, de Vos-Rouweler AJM, de Groot NG, Poirier N, Blancho G, de Luna C, Doxiadis GGM, Bontrop RE. A quick and robust MHC typing method for free-ranging and captive primate species. Immunogenetics 2017; 69:231-240. [PMID: 28084496 PMCID: PMC5350218 DOI: 10.1007/s00251-016-0968-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022]
Abstract
Gene products of the major histocompatibility complex (MHC) of human and non-human primates play a crucial role in adaptive immunity, and most of the relevant genes not only show a high degree of variability (polymorphism) but also copy number variation (CNV) is observed. Due to this diversity, MHC proteins influence the capability of individuals to cope with various pathogens. MHC and/or MHC-linked gene products such as odorant receptor genes are thought to influence mate choice and reproductive success. Therefore, MHC typing of wild and captive primate populations is considered to be useful in conservation biology, which is, however, often hampered by the need of invasive and time-consuming methods. All intact Mhc-DRB genes in primates appear to possess a complex and highly divergent microsatellite, DRB-STR. A panel of 154 pedigreed olive baboons (Papio anubis) was examined for their DRB content by DRB-STR analysis of genomic DNA. Using the same methodology on DNA of feces samples, DRB variability of a silvery gibbon population (Hylobates moloch) (N = 24), an endangered species, could successfully be studied. In both species, length determination of the DRB-STR resulted in the definition of unique genotyping patterns that appeared to be specific for a certain chromosome. Moreover, the different STR lengths were shown to segregate with the allelic variation of the respective gene. The results obtained expand data gained previously on DRB-STR typing in macaques, great apes, and humans and strengthen the conclusion that this protocol is applicable in molecular ecology, conservation biology, and colony management, especially of endangered primate species.
Collapse
Affiliation(s)
- N de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - K Stanbury
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - A J M de Vos-Rouweler
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N G de Groot
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - N Poirier
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - G Blancho
- Institut National de la Sante et de la Recherche Medicale (INSERM) UMR1064, Institut de Transplantation-Urologie-Nephrologie (ITUN), 30 Bd Jean Monnet, 44093, Nantes, France
| | - C de Luna
- Writtle College, Essex University, Lordship Road, Writtle, Chelmsford, Essex, CM1 3RR, UK
| | - G G M Doxiadis
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
| | - R E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.,Department of Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| |
Collapse
|
35
|
Maccari G, Robinson J, Ballingall K, Guethlein LA, Grimholt U, Kaufman J, Ho CS, de Groot NG, Flicek P, Bontrop RE, Hammond JA, Marsh SGE. IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex. Nucleic Acids Res 2016; 45:D860-D864. [PMID: 27899604 PMCID: PMC5210539 DOI: 10.1093/nar/gkw1050] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/17/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023] Open
Abstract
The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group.
Collapse
Affiliation(s)
- Giuseppe Maccari
- The Pirbright Institute, Pirbright, Woking, Surrey, GU24 0NF, UK.,Anthony Nolan Research Institute (ANRI), Royal Free Hospital, London, NW3 2QG, UK
| | - James Robinson
- Anthony Nolan Research Institute (ANRI), Royal Free Hospital, London, NW3 2QG, UK.,UCL Cancer Institute, Royal Free Campus, London, NW3 2QG, UK
| | - Keith Ballingall
- Moredun Research Institute, Pentlands Science Park, Midlothian, EH26 0PZ, UK
| | | | | | - Jim Kaufman
- University of Cambridge, Cambridge, CB2 1QP, UK
| | - Chak-Sum Ho
- Gift of Life Michigan, Ann Arbor, MI, 48108, USA
| | - Natasja G de Groot
- Biomedical Primate Research Centre, Rijswijk, 2288 GJ Rijswijk, Netherlands
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Ronald E Bontrop
- Biomedical Primate Research Centre, Rijswijk, 2288 GJ Rijswijk, Netherlands
| | - John A Hammond
- The Pirbright Institute, Pirbright, Woking, Surrey, GU24 0NF, UK
| | - Steven G E Marsh
- Anthony Nolan Research Institute (ANRI), Royal Free Hospital, London, NW3 2QG, UK .,UCL Cancer Institute, Royal Free Campus, London, NW3 2QG, UK
| |
Collapse
|
36
|
Otting N, van der Wiel MKH, de Groot N, de Vos-Rouweler AJM, de Groot NG, Doxiadis GGM, Wiseman RW, O'Connor DH, Bontrop RE. The orthologs of HLA-DQ and -DP genes display abundant levels of variability in macaque species. Immunogenetics 2016; 69:87-99. [PMID: 27771735 DOI: 10.1007/s00251-016-0954-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/12/2016] [Indexed: 11/29/2022]
Abstract
The human major histocompatibility complex (MHC) region encodes three types of class II molecules designated HLA-DR, -DQ, and -DP. Both the HLA-DQ and -DP gene region comprise a duplicated tandem of A and B genes, whereas in macaques, only one set of genes is present per region. A substantial sequencing project on the DQ and DP genes in various macaque populations resulted in the detection of previously 304 unreported full-length alleles. Phylogenetic studies showed that humans and macaques share trans-species lineages for the DQA1 and DQB1 genes, whereas the DPA1 and DPB1 lineages in macaques appear to be species-specific. Amino acid variability plot analyses revealed that each of the four genes displays more allelic variation in macaques than is encountered in humans. Moreover, the numbers of different amino acids at certain positions in the encoded proteins are higher than in humans. This phenomenon is remarkably prominent at the contact positions of the peptide-binding sites of the deduced macaque DPβ-chains. These differences in the MHC class II DP regions of macaques and humans suggest separate evolutionary mechanisms in the generation of diversity.
Collapse
Affiliation(s)
- Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.
| | - Marit K H van der Wiel
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Annemiek J M de Vos-Rouweler
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | - Roger W Wiseman
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ronald E Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre (BPRC), Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands.,Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
37
|
Otting N, van der Wiel MKH, Doxiadis GGM, Bontrop RE. Fifty-one full-length major histocompatibility complex class II alleles in the olive baboon (Papio anubis). HLA 2016; 88:270-271. [PMID: 27696785 DOI: 10.1111/tan.12906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 09/06/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 11/28/2022]
Abstract
Here we report 51 novel major histocompatibility complex (MHC) class II alleles in a group of related olive baboons.
Collapse
Affiliation(s)
- N Otting
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Rijswijk, the Netherlands.
| | - M K H van der Wiel
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Rijswijk, the Netherlands
| | - G G M Doxiadis
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Rijswijk, the Netherlands
| | - R E Bontrop
- Biomedical Primate Research Centre, Department of Comparative Genetics and Refinement, Rijswijk, the Netherlands.,Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| |
Collapse
|
38
|
Robinson J, Maccari G, Bontrop RE, Ho CS(S, Grimholt U, Kaufman J, Guethlein LA, Ballingall K, Marsh SG, Hammond JA. P013 Development of the IPD-MHC database. Hum Immunol 2016. [DOI: 10.1016/j.humimm.2016.07.078] [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: 11/30/2022]
|
39
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
40
|
de Groot NG, Heijmans CMC, van der Wiel MKH, Blokhuis JH, Mulder A, Guethlein LA, Doxiadis GGM, Claas FHJ, Parham P, Bontrop RE. Complex MHC Class I Gene Transcription Profiles and Their Functional Impact in Orangutans. J Immunol 2015; 196:750-8. [PMID: 26685209 DOI: 10.4049/jimmunol.1500820] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 11/13/2015] [Indexed: 11/19/2022]
Abstract
MHC haplotypes of humans and the African great ape species have one copy of the MHC-A, -B, and -C genes. In contrast, MHC haplotypes of orangutans, the Asian great ape species, exhibit variation in the number of gene copies. An in-depth analysis of the MHC class I gene repertoire in the two orangutan species, Pongo abelii and Pongo pygmaeus, is presented in this article. This analysis involved Sanger and next-generation sequencing methodologies, revealing diverse and complicated transcription profiles for orangutan MHC-A, -B, and -C. Thirty-five previously unreported MHC class I alleles are described. The data demonstrate that each orangutan MHC haplotype has one copy of the MHC-A gene, and that the MHC-B region has been subject to duplication, giving rise to at least three MHC-B genes. The MHC-B*03 and -B*08 lineages of alleles each account for a separate MHC-B gene. All MHC-B*08 allotypes have the C1-epitope motif recognized by killer cell Ig-like receptor. At least one other MHC-B gene is present, pointing to MHC-B alleles that are not B*03 or B*08. The MHC-C gene is present only on some haplotypes, and each MHC-C allotype has the C1-epitope. The transcription profiles demonstrate that MHC-A alleles are highly transcribed, whereas MHC-C alleles, when present, are transcribed at very low levels. The MHC-B alleles are transcribed to a variable extent and over a wide range. For those orangutan MHC class I allotypes that are detected by human monoclonal anti-HLA class I Abs, the level of cell-surface expression of proteins correlates with the level of transcription of the allele.
Collapse
Affiliation(s)
- Natasja G de Groot
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands;
| | - Corrine M C Heijmans
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Marit K H van der Wiel
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Jeroen H Blokhuis
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Arend Mulder
- Immunohaematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Gaby G M Doxiadis
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands
| | - Frans H J Claas
- Immunohaematology and Blood Transfusion, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; and
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ronald E Bontrop
- Comparative Genetics and Refinement, Biomedical Primate Research Centre, 2288 GJ Rijswijk, the Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, the Netherlands
| |
Collapse
|
41
|
van der Wiel MKH, Otting N, Zeijdel LM, Doxiadis GGM, Bontrop RE. Novel DRA alleles extracted from seven macaque cohorts. ACTA ACUST UNITED AC 2015; 85:146-8. [PMID: 25626611 PMCID: PMC5024057 DOI: 10.1111/tan.12510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/14/2014] [Indexed: 11/27/2022]
Abstract
In this document, we report the detection of 37 DRA alleles in macaque cohorts.
Collapse
Affiliation(s)
- M K H van der Wiel
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | | | | | | |
Collapse
|
42
|
de Groot N, Doxiadis GGM, Otting N, de Vos-Rouweler AJM, Bontrop RE. Differential recombination dynamics within the MHC of macaque species. Immunogenetics 2014; 66:535-44. [PMID: 24934118 PMCID: PMC4156779 DOI: 10.1007/s00251-014-0783-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 05/21/2014] [Indexed: 10/27/2022]
Abstract
A panel of 15 carefully selected microsatellites (short tandem repeats, STRs) has allowed us to study segregation and haplotype stability in various macaque species. The STRs span the major histocompatibility complex (MHC) region and map in more detail from the centromeric part of the Mhc-A to the DR region. Two large panels of Indian rhesus and Indonesian/Indochinese cynomolgus macaques have been subjected to pedigree analysis, allowing the definition of 161 and 36 different haplotypes and the physical mapping of 10 and 5 recombination sites, respectively. Although most recombination sites within the studied section of the Indian rhesus monkey MHC are situated between the Mhc-A and Mhc-B regions, the resulting recombination rate for this genomic segment is low and similar to that in humans. In contrast, in Indonesian/Indochinese macaques, two recombination sites, which appear to be absent in rhesus macaques, map between the class III and II regions. As a result, the mean recombination frequency of the core MHC, Mhc-A to class II, is higher in Indonesian/Indochinese cynomolgus than in Indian rhesus macaques, but as such is comparable to that in humans. The present communication demonstrates that the dynamics of recombination 'hot/cold spots' in the MHC, as well as their frequencies, may differ substantially between highly related macaque species.
Collapse
Affiliation(s)
- Nanine de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ, Rijswijk, The Netherlands
| | | | | | | | | |
Collapse
|
43
|
Verstrepen BE, Verschoor EJ, Fagrouch ZC, Mooij P, de Groot NG, Bontrop RE, Bogers WM, Heeney JL, Koopman G. Strong vaccine-induced CD8 T-cell responses have cytolytic function in a chimpanzee clearing HCV infection. PLoS One 2014; 9:e95103. [PMID: 24740375 PMCID: PMC3989318 DOI: 10.1371/journal.pone.0095103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/22/2014] [Indexed: 12/16/2022] Open
Abstract
A single correlate of effective vaccine protection against chronic HCV infection has yet to be defined. In this study, we analyzed T-cell responses in four chimpanzees, immunized with core-E1-E2-NS3 and subsequently infected with HCV1b. Viral clearance was observed in one animal, while the other three became chronically infected. In the animal that cleared infection, NS3-specific CD8 T-cell responses were observed to be more potent in terms of frequency and polyfunctionality of cytokine producing cells. Unique to this animal was the presence of killing-competent CD8 T-cells, specific for NS31258–1272, being presented by the chimpanzee MHC class I molecule Patr-A*03∶01, and a high affinity recognition of this epitope. In the animals that became chronically infected, T-cells were able to produce cytokines against the same peptide but no cytolysis could be detected. In conclusion, in the animal that was able to clear HCV infection not only cytokine production was observed but also cytolytic potential against specific MHC class I/peptide-combinations.
Collapse
Affiliation(s)
- Babs E. Verstrepen
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ernst J. Verschoor
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Zahra C. Fagrouch
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Petra Mooij
- Department of Virology, 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
| | - Willy M. Bogers
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Jonathan L. Heeney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
- * E-mail:
| |
Collapse
|
44
|
Schneider E, El Hajj N, Richter S, Roche-Santiago J, Nanda I, Schempp W, Riederer P, Navarro B, Bontrop RE, Kondova I, Scholz CJ, Haaf T. Widespread differences in cortex DNA methylation of the "language gene" CNTNAP2 between humans and chimpanzees. Epigenetics 2014; 9:533-45. [PMID: 24434791 PMCID: PMC4121364 DOI: 10.4161/epi.27689] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
CNTNAP2, one of the largest genes in the human genome, has been linked to human-specific language abilities and neurodevelopmental disorders. Our hypothesis is that epigenetic rather than genetic changes have accelerated the evolution of the human brain. To compare the cortex DNA methylation patterns of human and chimpanzee CNTNAP2 at ultra-high resolution, we combined methylated DNA immunoprecipitation (MeDIP) with NimbleGen tiling arrays for the orthologous gene and flanking sequences. Approximately 1.59 Mb of the 2.51 Mb target region could be aligned and analyzed with a customized algorithm in both species. More than one fifth (0.34 Mb) of the analyzed sequence throughout the entire gene displayed significant methylation differences between six human and five chimpanzee cortices. One of the most striking interspecies differences with 28% methylation in human and 59% in chimpanzee cortex (by bisulfite pyrosequencing) lies in a region 300 bp upstream of human SNP rs7794745 which has been associated with autism and parent-of-origin effects. Quantitative real-time RT PCR revealed that the protein-coding splice variant CNTNAP2-201 is 1.6-fold upregulated in human cortex, compared with the chimpanzee. Transcripts CNTNAP2-001, -002, and -003 did not show skewed allelic expression, which argues against CNTNAP2 imprinting, at least in adult human brain. Collectively, our results suggest widespread cortex DNA methylation changes in CNTNAP2 since the human-chimpanzee split, supporting a role for CNTNAP2 fine-regulation in human-specific language and communication traits.
Collapse
Affiliation(s)
- Eberhard Schneider
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| | - Nady El Hajj
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| | - Steven Richter
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| | | | - Indrajit Nanda
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| | - Werner Schempp
- Institute for Human Genetics; University of Freiburg; Freiburg, Germany
| | - Peter Riederer
- Clinical Neurochemistry Laboratory; Department of Psychiatry; University Hospital; Würzburg, Germany
| | - Bianca Navarro
- Institute of Legal Medicine; University Medical Center; Mainz, Germany
| | | | - Ivanela Kondova
- Biomedical Primate Research Center; Rijswijk, The Netherlands
| | - Claus Jürgen Scholz
- Laboratory for Microarray Applications; IZKF; Julius Maximilians University; Würzburg, Germany
| | - Thomas Haaf
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| |
Collapse
|
45
|
de Groot NG, Bontrop RE. The HIV-1 pandemic: does the selective sweep in chimpanzees mirror humankind's future? Retrovirology 2013; 10:53. [PMID: 23705941 PMCID: PMC3667106 DOI: 10.1186/1742-4690-10-53] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 04/04/2013] [Indexed: 12/31/2022] Open
Abstract
An HIV-1 infection progresses in most human individuals sooner or later into AIDS, a devastating disease that kills more than a million people worldwide on an annual basis. Nonetheless, certain HIV-1-infected persons appear to act as long-term non-progressors, and elite control is associated with the presence of particular MHC class I allotypes such as HLA-B*27 or -B*57. The HIV-1 pandemic in humans arose from the cross-species transmission of SIVcpz originating from chimpanzees. Chimpanzees, however, appear to be relatively resistant to developing AIDS after HIV-1/SIVcpz infection. Mounting evidence illustrates that, in the distant past, chimpanzees experienced a selective sweep resulting in a severe reduction of their MHC class I repertoire. This was most likely caused by an HIV-1/SIV-like retrovirus, suggesting that chimpanzees may have experienced long-lasting host-virus relationships with SIV-like viruses. Hence, if natural selection is allowed to follow its course, prospects for the human population may look grim, thus underscoring the desperate need for an effective vaccine.
Collapse
Affiliation(s)
- Natasja G de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288 GJ Rijswijk, The Netherlands.
| | | |
Collapse
|
46
|
Verstrepen BE, de Groot NG, Groothuismink ZMA, Verschoor EJ, de Groen RA, Bogers WM, Janssen HLA, Mooij P, Bontrop RE, Koopman G, Boonstra A. Evaluation of IL-28B polymorphisms and serum IP-10 in hepatitis C infected chimpanzees. PLoS One 2012; 7:e46645. [PMID: 23118858 PMCID: PMC3484116 DOI: 10.1371/journal.pone.0046645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 09/04/2012] [Indexed: 12/18/2022] Open
Abstract
In humans, clearance of hepatitis C virus (HCV) infection is associated with genetic variation near the IL-28B gene and the induction of interferon-stimulated genes, like IP-10. Also in chimpanzees spontaneous clearance of HCV is observed. To study whether similar correlations exist in these animals, a direct comparison of IP-10 and IL-28B polymorphism between chimpanzees and patients was performed. All chimpanzees studied were monomorphic for the human IL-28B SNPs which are associated with spontaneous and treatment induced HCV clearance in humans. As a result, these particular SNPs cannot be used for clinical association studies in chimpanzees. Although these human SNPs were absent in chimpanzees, gene variation in this region was present however, no correlation was observed between different SNP-genotypes and HCV outcome. Strikingly, IP-10 levels in chimpanzees correlated with HCV-RNA load and γGT, while such correlations were not observed in humans. The correlation between IP-10, γGT and virus load in chimpanzees was not found in patients and may be due to the lack of lifestyle-related confounding factors in chimpanzees. Direct comparison of IP-10 and IL-28B polymorphism between chimpanzees and patients in relation to HCV infection, illustrates that the IFN-pathways are important during HCV infection in both species. The Genbank EMBL accession numbers assigned to chimpanzees specific sequences near the IL-28B gene are HE599784 and HE599785.
Collapse
Affiliation(s)
- Babs E. Verstrepen
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Natasja G. de Groot
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Zwier M. A. Groothuismink
- Department of Gastroenterology and Hepatology, Erasmus MC University Hospital, Rotterdam, The Netherlands
| | - Ernst J. Verschoor
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Rik A. de Groen
- Department of Gastroenterology and Hepatology, Erasmus MC University Hospital, Rotterdam, The Netherlands
| | - Willy M. Bogers
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Harry L. A. Janssen
- Department of Gastroenterology and Hepatology, Erasmus MC University Hospital, Rotterdam, The Netherlands
| | - Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Ronald E. Bontrop
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Andre Boonstra
- Department of Gastroenterology and Hepatology, Erasmus MC University Hospital, Rotterdam, The Netherlands
| |
Collapse
|
47
|
Koopman G, Beenhakker N, Nieuwenhuis I, Doxiadis G, Mooij P, Drijfhout JW, Koestler J, Hanke T, Bontrop RE, Wagner R, Bogers WM, Melief CJ. SIVconsv DNA prime - TLR7/IFNα adjuvanted long peptide boost induces potent CD4+ Ab responses and protects against high dose intrarectal SIV challenge. Retrovirology 2012. [PMCID: PMC3441700 DOI: 10.1186/1742-4690-9-s2-p29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
48
|
Abstract
The HLA region shows diversity concerning the number and content of DRB genes present per haplotype. Similar observations are made for the equivalent regions in other primate species. To elucidate the evolutionary history of the various HLA-DRB genes, a large panel of intron sequences obtained from humans, chimpanzees, rhesus macaques, and common marmosets has been subjected to phylogenetic analyses. Special attention was paid to the presence and absence of particular transposable elements and/or to their segments. The sharing of different parts of the same long interspersed nuclear element-2 (LINE2, L2) and various Alu insertions by the species studied demonstrates that one precursor gene must have been duplicated several times before the Old World monkey (OWM) and hominid (HOM) divergence. At least four ancestral DRB gene families appear to have been present before the radiation of OWM and HOM, and one of these even predates the speciation of Old and New World primates. Two of these families represent the pseudogenes DRB6/DRB2 and DRB7, which have been locked in the genomes of various primate species over long evolutionary time spans. Furthermore, all phylogenies of different intron segments show consistently that, apart from the pseudogenes, only DRB5 genes are shared by OWM and HOM, and they demonstrate the common history of certain DRB genes/lineages of humans and chimpanzees. In contrast, the evolutionary history of some other DRB loci is difficult to decipher, thus illustrating the complex history of the evolution of DRB genes due to a combination of mutations and recombination-like events. The selected approach allowed us to shed light on the ancestral DRB gene pool in primates and on the evolutionary relationship of the various HLA-DRB genes.
Collapse
Affiliation(s)
- Gaby G M Doxiadis
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | | | | | | |
Collapse
|
49
|
Otting N, de Groot N, de Vos-Rouweler AJM, Louwerse A, Doxiadis GGM, Bontrop RE. Multilocus definition of MHC haplotypes in pedigreed cynomolgus macaques (Macaca fascicularis). Immunogenetics 2012; 64:755-65. [PMID: 22772814 PMCID: PMC3438390 DOI: 10.1007/s00251-012-0632-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/06/2012] [Indexed: 12/20/2022]
Abstract
Cynomolgus macaques (Macaca fascicularis) are used widely in biomedical research, and the genetics of their MHC (Mhc-Mafa) has become the focus of considerable attention in recent years. The cohort of Indonesian pedigreed macaques that we present here was typed for Mafa-A, -B, and -DR, by sequencing, as described in earlier studies. Additionally, the DRB region of these animals was characterised by microsatellite analyses. In this study, full-length sequencing of Mafa-DPA/B and -DQA/B in these animals was performed. A total of 75 different alleles were observed; 22 of which have not previously been reported, plus 18 extended exon 2 alleles that were already known. Furthermore, two microsatellites, D6S2854 and D6S2859, were used to characterise the complex Mafa-A region. Sequencing and segregation analyses revealed that the length patterns of these microsatellites are unique for each Mafa-A haplotype. In this work, we present a pedigreed colony of approximately 120 cynomolgus macaques; all of which are typed for the most significant polymorphic MHC class I and class II markers. Offspring of these pedigreed animals are easily characterised for their MHC by microsatellite analyses on the Mafa-A and -DRB regions, which makes the cumbersome sequencing analyses redundant.
Collapse
Affiliation(s)
- Nel Otting
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Lange Kleiweg 161, 2288GJ, Rijswijk, The Netherlands.
| | | | | | | | | | | |
Collapse
|
50
|
Schneider E, Mayer S, El Hajj N, Jensen LR, Kuss AW, Zischler H, Kondova I, Bontrop RE, Navarro B, Fuchs E, Zechner U, Haaf T. Methylation and expression analyses of the 7q autism susceptibility locus genes MEST , COPG2, and TSGA14 in human and anthropoid primate cortices. Cytogenet Genome Res 2012; 136:278-87. [PMID: 22456293 DOI: 10.1159/000337298] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2012] [Indexed: 12/11/2022] Open
Abstract
The autism susceptibility locus on human chromosome 7q32 contains the maternally imprinted MEST and the non-imprinted COPG2 and TSGA14 genes. Autism is a disorder of the 'social brain' that has been proposed to be due to an overbalance of paternally expressed genes. To study regulation of the 7q32 locus during anthropoid primate evolution, we analyzed the methylation and expression patterns of MEST, COPG2, and TSGA14 in human, chimpanzee, Old World monkey (baboon and rhesus macaque), and New World monkey (marmoset) cortices. In all human and anthropoid primate cortices, the MEST promoter was hemimethylated, as expected for a differentially methylated imprinting control region, whereas the COPG2 and TSGA14 promoters were completely demethylated, typical for transcriptionally active non-imprinted genes. The MEST gene also showed comparable mRNA expression levels in all analyzed species. In contrast, COPG2 expression was downregulated in the human cortex compared to chimpanzee, Old and New World monkeys. TSGA14 either showed no differential regulation in the human brain compared to chimpanzee and marmoset or a slight upregulation compared to baboon. The human-specific downregulation supports a role for COPG2 in the development of a 'social brain'. Promoter methylation patterns appear to be more stable during evolution than gene expression patterns, suggesting that other mechanisms may be more important for inter-primate differences in gene expression.
Collapse
Affiliation(s)
- E Schneider
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|