MHC class I A loci polymorphism and diversity in three Southeast Asian populations of cynomolgus macaque

Yuki F. Kita; Kazuyoshi Hosomichi; Sakae Kohara; Yasushi Itoh; Kazumasa Ogasawara; Hideaki Tsuchiya; Ryuzo Torii; Hidetoshi Inoko; Antoine Blancher; Jerzy K. Kulski; Takashi Shiina

doi:10.1007/s00251-009-0390-y

15-OR: Endogenously loaded Cynomolgus – macaque MHC class I peptides

Human Immunology ◽

10.1016/j.humimm.2007.08.021 ◽

2007 ◽

Vol 68 (1) ◽

pp. S16

Author(s):

Runying Tian ◽

Angela R. Wahl ◽

Oriana Hawkins ◽

David O’Connor ◽

William H. Hildebrand

Keyword(s):

Mhc Class I ◽

Cynomolgus Macaque ◽

Class I

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2-OR: Cynomolgus macaque MHC class I molecules present HLA-A and HLA-B like peptides

Human Immunology ◽

10.1016/j.humimm.2009.09.011 ◽

2009 ◽

Vol 70 ◽

pp. S1

Author(s):

Runying Tian ◽

Daryl Cox ◽

Danijela Mojsicovic ◽

Oriana Hawkins ◽

David Watkins ◽

...

Keyword(s):

Mhc Class I ◽

Cynomolgus Macaque ◽

Class I ◽

Mhc Class I Molecules

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HLA-dependent heterogeneity and macrophage immunoproteasome activation during lung COVID-19 disease

Journal of Translational Medicine ◽

10.1186/s12967-021-02965-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Christophe Desterke ◽

Ali G. Turhan ◽

Annelise Bennaceur-Griscelli ◽

Frank Griscelli

Keyword(s):

Single Cell ◽

Mhc Class I ◽

Class I ◽

Mhc Ii ◽

Asian Populations ◽

Mhc Class I Antigen ◽

Cell Transcriptome ◽

Single Cell Transcriptome ◽

Genomic Cluster ◽

Global Population

Abstract Background The worldwide pandemic caused by the SARS-CoV-2 virus is characterized by significant and unpredictable heterogeneity in symptoms that remains poorly understood. Methods Transcriptome and single cell transcriptome of COVID19 lung were integrated with deeplearning analysis of MHC class I immunopeptidome against SARS-COV2 proteome. Results An analysis of the transcriptomes of lung samples from COVID-19 patients revealed that activation of MHC class I antigen presentation in these tissues was correlated with the amount of SARS-CoV-2 RNA present. Similarly, a positive relationship was detected in these samples between the level of SARS-CoV-2 and the expression of a genomic cluster located in the 6p21.32 region (40 kb long, inside the MHC-II cluster) that encodes constituents of the immunoproteasome. An analysis of single-cell transcriptomes of bronchoalveolar cells highlighted the activation of the immunoproteasome in CD68 + M1 macrophages of COVID-19 patients in addition to a PSMB8-based trajectory in these cells that featured an activation of defense response during mild cases of the disease, and an impairment of alveolar clearance mechanisms during severe COVID-19. By examining the binding affinity of the SARS-CoV-2 immunopeptidome with the most common HLA-A, -B, and -C alleles worldwide, we found higher numbers of stronger presenters in type A alleles and in Asian populations, which could shed light on why this disease is now less widespread in this part of the world. Conclusions HLA-dependent heterogeneity in macrophage immunoproteasome activation during lung COVID-19 disease could have implications for efforts to predict the response to HLA-dependent SARS-CoV-2 vaccines in the global population.

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MHC class I allele diversity in cynomolgus macaques of Vietnamese origin

PeerJ ◽

10.7717/peerj.7941 ◽

2019 ◽

Vol 7 ◽

pp. e7941

Author(s):

Shuting Huang ◽

Xia Huang ◽

Shuang Li ◽

Mingjun Zhu ◽

Min Zhuo

Keyword(s):

Mhc Class I ◽

Binding Sites ◽

Macaca Fascicularis ◽

Peptide Binding ◽

Cynomolgus Macaque ◽

Class I ◽

Histocompatibility Complex ◽

Cynomolgus Macaques ◽

Mhc Alleles ◽

Potential Recombination Event

Cynomolgus macaques (Macaca fascicularis, Mafa) have been used as important experimental animal models for carrying out biomedical researches. The results of biomedical experiments strongly depend on the immunogenetic background of animals, especially on the diversity of major histocompatibility complex (MHC) alleles. However, there is much less information available on the polymorphism of MHC class I genes in cynomolgus macaques, than is currently available for humans. In this study, we have identified 40 Mafa-A and 60 Mafa-B exons 2 and 3 sequences from 30 unrelated cynomolgus macaques of Vietnamese origin. Among these alleles, 28 are novel. As for the remaining 72 known alleles, 15 alleles are shared with other cynomolgus macaque populations and 32 are identical to alleles previously reported in other macaque species. A potential recombination event was observed between Mafa-A1*091:02 and Mafa-A1*057:01. In addition, the Mafa-A1 genes were found to be more diverse than human HLA-A and the functional residues for peptide binding sites (PBS) or TCR binding sites (TBS) in Mafa-A1 have greater variability than that for non-PBS or non-TBS regions. Overall, this study provides important information on the diversity of Mafa-A and Mafa-B alleles from Vietnamese origin, which may help researchers to choose the most appropriate animals for their studies.

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Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities

10.1101/084947 ◽

2016 ◽

Cited By ~ 1

Author(s):

Julie A. Karl ◽

Michael E. Graham ◽

Roger W. Wiseman ◽

Katelyn E. Heimbruch ◽

Samantha M. Gieger ◽

...

Keyword(s):

Major Histocompatibility Complex ◽

Mhc Class I ◽

Mhc Class Ii ◽

Cynomolgus Macaque ◽

Full Length ◽

Class I ◽

Major Histocompatibility ◽

Histocompatibility Complex ◽

Cynomolgus Macaques ◽

Allele Discovery

ABSTRACTVery 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 (~1,100 bp in length), so no assembly is required to unambiguously resolve novel full-length sequences. Overall, we identified 313 total full-length transcripts in a subset of 72 cynomolgus macaques from these Chinese breeding facilities; 131 of these sequences were novel and an additional 116 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.

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