Identification of 17 novel major histocompatibility complex-A alleles in a population of Chinese-origin rhesus macaques

The natural history of model organisms: the rhesus macaque as a success story of the Anthropocene

Of all the non-human primate species studied by researchers, the rhesus macaque (Macaca mulatta) is likely the most widely used across biological disciplines. Rhesus macaques have thrived during the Anthropocene and now have the largest natural range of any non-human primate. They are highly social, exhibit marked genetic diversity, and display remarkable niche flexibility (which allows them to live in a range of habitats and survive on a variety of diets). These characteristics mean that rhesus macaques are well-suited for understanding the links between sociality, health and fitness, and also for investigating intra-specific variation, adaptation and other topics in evolutionary ecology.

A Specialist Macaque MHC Class I Molecule with HLA-B*27-like Peptide-Binding Characteristics

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.

Efficient mucosal transmissibility but limited pathogenicity of R5 SHIV SF162P3N in Chinese-origin rhesus macaques

BACKGROUND

Infection of rhesus macaques (RMs) of Indian origin with simian immunodeficiency virus or simian-HIV (SHIV) provided powerful tools to study HIV-1 transmission and disease and for testing the efficacy of novel drugs, vaccines, and prevention strategies. In developing alternative nonhuman primate AIDS models for the CCR5 (R5)-tropic SHIVSF162P3N, we characterized virus transmission and infection in Chinese-origin RMs.

METHODS

Virologic, immunologic, and pathogenic evaluations of R5 SHIVSF162P3N infection in Chinese RMs challenged intrarectally (ir) or intravaginally were performed and compared with those previously observed in Indian-origin rhesus exposed to the same inoculum dose and via similar route.

RESULTS

R5 SHIVSF162P3N transmits efficiently across mucosal surfaces in Chinese RMs. The magnitude and kinetics of early virus dissemination after ir inoculation in the Chinese macaques were similar to those observed in Indian rhesus, but a trend toward increased SHIVSF162P3N vaginal infectivity and rapid virus spread was seen in the Chinese macaques compared with the Indian-origin animals. Once infected, however, set point viremia in the ir- and intravaginal-infected Chinese rhesus was significantly lower and the animals survived longer compared with infected Indian rhesus.

CONCLUSIONS

The R5 SHIVSF162P3N/Chinese RM infection model is suitable for studies of mucosal HIV-1 transmission and protection, but the high frequency of spontaneous control of chronic viremia and reduced virulence with SHIVSF162P3N in this macaque subspecies may limit its utility in studying HIV-1 pathogenesis and in evaluating vaccines and antiretrovirals that rely on reduction in chronic viral load or AIDS development as an experimental end point.

Identification of MHC class I sequences in four species of Macaca of China

Tibetan macaques (Macaca thibetana), stump-tailed macaques (M. arctoides), Assamese macaques (M. assamensis), and northern pig-tailed macaques (M. leonina) are four major species of Macaca in China. In order to effectively use these species in biomedical research, thorough investigations of their MHC immunogenetics are required. In this study, we identified MHC class I sequences using cDNA cloning and sequencing on a cohort of six M. thibetana, three M. arctoides, three M. assamensis, and three M. leonina derived from Sichuan and Yunnan provinces of China. Eighty new alleles were identified, including 26 MHC-A alleles, 46 MHC-B alleles, and 8 MHC-I alleles. Among them, Math-A1*126:01, Math-B*190:01, Math-B*191:01, Math-B*192:01, Maar-A1*127:01, Maar-A1*129:01, and Maas-A1*128:01 represent lineages that had not been reported earlier in Macaca. Phylogenetic analyses show that no obvious separation of lineages among these species of Macaca. This study provides important information about the MHC immunogenetics for the four major species of Chinese macaques and adds value to these species as model organisms in biomedical research.

Major histocompatibility complex class I haplotype diversity in Chinese rhesus macaques

The use of Chinese-origin rhesus macaques (Macaca mulatta) for infectious disease immunity research is increasing despite the relative lack of major histocompatibility complex (MHC) class I immunogenetics information available for this population. We determined transcript-based MHC class I haplotypes for 385 Chinese rhesus macaques from five different experimental cohorts, providing a concise representation of the full complement of MHC class I major alleles expressed by each animal. In total, 123 Mamu-A and Mamu-B haplotypes were defined in the full Chinese rhesus macaque cohort. We then performed an analysis of haplotype frequencies across the experimental cohorts of Chinese rhesus macaques, as well as a comparison against a group of 96 Indian rhesus macaques. Notably, 35 of the 51 Mamu-A and Mamu-B haplotypes observed in Indian rhesus macaques were also detected in the Chinese population, with 85% of the 385 Chinese-origin rhesus macaques expressing at least one of these class I haplotypes. This unexpected conservation of Indian rhesus macaque MHC class I haplotypes in the Chinese rhesus macaque population suggests that immunologic insights originally gleaned from studies using Indian rhesus macaques may be more applicable to Chinese rhesus macaques than previously appreciated and may provide an opportunity for studies of CD8(+) T-cell responses between populations. It may also be possible to extend these studies across multiple species of macaques, as we found evidence of shared ancestral haplotypes between Chinese rhesus and Mauritian cynomolgus macaques.

Haplotype diversity generated by ancient recombination-like events in the MHC of Indian rhesus macaques

The Mamu-A, Mamu-B, and Mamu-DRB genes of the rhesus macaque show several levels of complexity such as allelic heterogeneity (polymorphism), copy number variation, differential segregation of genes/alleles present on a haplotype (diversity) and transcription level differences. A combination of techniques was implemented to screen a large panel of pedigreed Indian rhesus macaques (1,384 individuals representing the offspring of 137 founding animals) for haplotype diversity in an efficient and inexpensive manner. This approach allowed the definition of 140 haplotypes that display a relatively low degree of region variation as reflected by the presence of only 17 A, 18 B and 22 DRB types, respectively, exhibiting a global linkage disequilibrium comparable to that in humans. This finding contrasts with the situation observed in rhesus macaques from other geographic origins and in cynomolgus monkeys from Indonesia. In these latter populations, nearly every haplotype appears to be characterised by a unique A, B and DRB region. In the Indian population, however, a reshuffling of existing segments generated “new” haplotypes. Since the recombination frequency within the core MHC of the Indian rhesus macaques is relatively low, the various haplotypes were most probably produced by recombination events that accumulated over a long evolutionary time span. This idea is in accord with the notion that Indian rhesus macaques experienced a severe reduction in population during the Pleistocene due to a bottleneck caused by geographic changes. Thus, recombination-like processes appear to be a way to expand a diminished genetic repertoire in an isolated and relatively small founder population.

Degree of Chinese ancestry affects behavioral characteristics of infant rhesus macaques (Macaca mulatta)

BACKGROUND

The use of Chinese-origin macaques in biomedical research is problematic for some scientists because of the reported behavioral and physiological differences from those of Indian origin. However, few studies have examined the effects of varying degrees of Chinese ancestry (DCA) on behavior, and they were typically based on small sample sizes and unusual rearing conditions.

METHODS

Using data from a colony-wide program, we examined whether DCA was related to behavior and temperament ratings reflecting emotionality (fearfulness, aggression, and anxiety) and activity. The 249 subjects, born and reared in an outdoor social environment, were separated from their groups for a 25-h period of indoor testing. Their DCA (range: 0.6-99.4%) was determined by analyzing the frequency of short tandem repeat alleles.

RESULTS AND CONCLUSIONS

The major effect of DCA was on fearfulness, with the more hybridized animals scoring lowest and the more pure Indian- and Chinese-origin macaques resembling each other.

Mamu-B genes and their allelic repertoires in different populations of Chinese-origin rhesus macaques

Since rhesus monkeys of Chinese origin have gained greater utilization in recent years, it is urgent to investigate the major histocompatibility complex (MHC) immunogenetics of Chinese rhesus macaques. In this study, we identified 81 Mamu-B sequences using complementary DNA cloning and sequencing on a cohort of 58 rhesus monkeys derived from three local populations of China. Twenty of these Mamu-B alleles are novel and four of them represent new lineages. Although more alleles are shared among different populations than Mamu-A locus, the Mamu-B allelic repertoires found in these three populations of Chinese macaques are largely independent, which underscores the MHC polymorphism among different populations of Chinese rhesus macaques. Our results are an important addition to the limited MHC immunogenetic information available for rhesus macaques of Chinese origin.

Preliminary observations of MHC class I A region polymorphism in three populations of Chinese-origin rhesus macaques

Rhesus macaques are an animal model for the study of a variety of human diseases. The Chinese rhesus macaques have been widely used in biomedical research in recent years. However, the polymorphism of major histocompatibility complex (MHC) class I A region among different local populations of Chinese rhesus macaques has never been investigated. In this study, we identified 46 Mamu-A alleles by cDNA cloning and sequencing on a cohort of 53 Chinese rhesus monkeys including Zhiming, Chuanxi, and Fujian populations, of which 5 were first reported in rhesus monkeys. The frequencies of alleles were identified for each population. The result suggests that the repertoire of allelic variants of MHC class I A region found in different populations of Chinese macaques is largely non-overlapping. The frequencies of alleles and the popular allele are also different for different populations. PCR-SSP experiment further confirms the different frequencies of two alleles, Mamu-A*026:01 and Mamu-A*022:01, in additional 99 Zhiming monkeys and 191 Chuanxi monkeys. Our findings have important practical implications in that the origin of the individuals and the genetic polymorphism of the monkeys need to be considered at the level of local populations for Chinese rhesus monkeys in biomedical research. Further immunogenetic work is needed to investigate the MHC polymorphism among different populations of Chinese rhesus macaques and to reveal the functional implication of such polymorphism and disease outcome correlations.

Nonhuman primate transplant models finally evolve: detailed immunogenetic analysis creates new models and strengthens the old

Nonhuman primate (NHP) models play a critical role in the translation of novel therapies for transplantation to the clinic. However, although MHC disparity significantly affects the outcome of transplantation, until recently, experiments using NHP models were performed without the ability to rigorously control the degree of MHC disparity in transplant cohorts. In this review, we discuss several key technical breakthroughs in the field, which have finally enabled detailed immunogenetic data to be incorporated into NHP transplantation studies. These advances have created a new gold-standard for NHP transplantation research, which incorporates detailed information regarding the degree of relatedness and the degree of MHC haplotype disparity between transplant pairs and the precise MHC alleles that both donors and recipients express. The adoption of this new standard promises to increase the rigor of NHP transplantation studies and to ensure that these experiments are optimally translatable to patient care.

Frequency of the major histocompatibility complex Mamu-A*01 allele in experimental rhesus macaques in China

BACKGROUND

In Indian rhesus macaques, the major histocompatibility complex Mamu gene, especially the Mamu-A*01 allele, plays an important role in simian immunodeficiency virus susceptibility and disease progression. The Mamu-A*01 allele is one of the protective genes mostly being studied in simian acquired immunodeficiency syndrome.

METHODS

PCR was used to amplify the Mamu-A*01 allele in 130 Chinese-origin rhesus macaques. Identification of the allele was then confirmed by sequencing and IFN-γ ELISPOT assay.

RESULTS

The Mamu-A*01 allele was detected in 3.85% (5 of 130) of the experimental Chinese-origin rhesus macaques. The sequence homology reached 99.1% in comparison with Indian rhesus macaques. A significantly large number of spots were observed in Mamu-A*01-positive monkeys when analyzed by ELISPOT with Gag181-189 epitope stimulation.

CONCLUSIONS

Our study suggests that Mamu-A*01-positive Chinese-origin rhesus monkeys are suitable for use in AIDS studies.

Functional analysis of frequently expressed Chinese rhesus macaque MHC class I molecules Mamu-A1*02601 and Mamu-B*08301 reveals HLA-A2 and HLA-A3 supertypic specificities

The Simian immunodeficiency virus (SIV)-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection and AIDS-related research, despite the potential that macaques of Chinese origin is a more relevant model. Ongoing efforts to further characterize the Chinese rhesus macaques' major histocompatibility complex (MHC) for composition and function should facilitate greater utilization of the species. Previous studies have demonstrated that Chinese-origin M. mulatta (Mamu) class I alleles are more polymorphic than their Indian counterparts, perhaps inferring a model more representative of human MHC, human leukocyte antigen (HLA). Furthermore, the Chinese rhesus macaque class I allele Mamu-A1*02201, the most frequent allele thus far identified, has recently been characterized and shown to be an HLA-B7 supertype analog, the most frequent supertype in human populations. In this study, we have characterized two additional alleles expressed with high frequency in Chinese rhesus macaques, Mamu-A1*02601 and Mamu-B*08301. Upon the development of MHC-peptide-binding assays and definition of their associated motifs, we reveal that these Mamu alleles share peptide-binding characteristics with the HLA-A2 and HLA-A3 supertypes, respectively, the next most frequent human supertypes after HLA-B7. These data suggest that Chinese rhesus macaques may indeed be a more representative model of HLA gene diversity and function as compared to the species of Indian origin and therefore a better model for investigating human immune responses.

[Polymorphism of MHC-DPB1 gene exon 2 in rhesus macaques (Macaca mulatta)]

Rhesus macaque (Macaca mulatta) has long been used as an experimental model animal for biomedical research and was under the key state protection (class II) from Chinese government. In order to facilitate the use of Chinese rhesus macaques in biomedical research and their protection based on better understanding of the major mistocompability complex (MHC) genes in these macaques, the exon 2 of Mamu-DPB1 genes were determined in 106 wild rhesus macaques using DGGE, cloning and sequencing. A total of 21 Mamu-DPB1 alleles were obtained, of which 15 alleles were novel sequences that had not been documented previously. Mamu-DPB1 30 was the most frequent allele in the whole large population comprising all 106 rhesus macaque individuals (0.1120) and in Xiaojin population (0.1120), Mamu-DPB1 04 in Heishui (0.1702), -DPB1 32 in Bazhong (0.1613), -DPB1 30 in Hanyuan (0.1120), and -DPB1 04 in Jiulong (0.1139). The alignment of the amino acids sequences showed that 12 variable sites were species-specific, of which 9 sites occurred in the putative amino acids sequences of the 15 novel Mamu-DPB1 alleles. Trans-species polymorphism was observed on the phylogenetic tree based on the DPB1 alleles of rhesus macaques and cynomolgus (Macaca fascicularis). In addition, these results also demonstrated that significant genetic differentiation has occurred between Chinese and Indian rhesus macaque population.

The most common Chinese rhesus macaque MHC class I molecule shares peptide binding repertoire with the HLA-B7 supertype

Of the two rhesus macaque subspecies used for AIDS studies, the Simian immunodeficiency virus-infected Indian rhesus macaque (Macaca mulatta) is the most established model of HIV infection, providing both insight into pathogenesis and a system for testing novel vaccines. Despite the Chinese rhesus macaque potentially being a more relevant model for AIDS outcomes than the Indian rhesus macaque, the Chinese-origin rhesus macaques have not been well-characterized for their major histocompatibility complex (MHC) composition and function, reducing their greater utilization. In this study, we characterized a total of 50 unique Chinese rhesus macaques from several varying origins for their entire MHC class I allele composition and identified a total of 58 unique complete MHC class I sequences. Only nine of the sequences had been associated with Indian rhesus macaques, and 28/58 (48.3%) of the sequences identified were novel. From all MHC alleles detected, we prioritized Mamu-A1*02201 for functional characterization based on its higher frequency of expression. Upon the development of MHC/peptide binding assays and definition of its associated motif, we revealed that this allele shares peptide binding characteristics with the HLA-B7 supertype, the most frequent supertype in human populations. These studies provide the first functional characterization of an MHC class I molecule in the context of Chinese rhesus macaques and the first instance of HLA-B7 analogy for rhesus macaques.

Induction of balance and breadth in the immune response is beneficial for the control of SIVmac239 replication in rhesus monkeys

OBJECTIVES

The aim of this study was to induce cellular and humoral responses with enhanced breadth and more balanced magnitude as a possible approach for an effective HIV vaccine.

METHODS

All nine of the SIVmac239 genes (gag, pol, env, nef, vif, vpx, vpr, rev and tat) were optimized for mammalian expression, synthesized and cloned into recombinant adenovirus type 5 (Ad5). These vectors were used as a vaccine regimen, and the immunogenicity and immune protection of this regimen was assessed in murine and macaques.

RESULTS

A vaccine regimen including all nine genes of the SIVmac239 virus was developed, and it was demonstrated that in contrast to single antigen vaccination, the total SIV antigen regimen more effectively elicited the balanced and broad immune responses in murine and macaques. Moreover, the responses afforded effective immune control against infection and replication of the highly pathogenic SIVmac239.

CONCLUSIONS

Induction of balance and breadth in the immune response is beneficial in controlling SIVmac239 replication in rhesus monkeys. This study provides insight for the future development of an effective HIV vaccine.