The resurgence and genetic implications of New World primates in biomedical research

What we have learned from non-human primates as animal models of epilepsy

Non-human primates (NHPs) have played a crucial role in our understanding of epilepsy, given their striking similarities with humans. Through their use, we have gained a deeper understanding of the neurophysiology and pathophysiology of epileptic seizures, and they have proven invaluable allies in developing anti-seizure therapies. This review explores the history of NHPs as natural models of epilepsy, discusses the findings obtained after exposure to various chemoconvulsant drugs and focal electrical stimulation protocols that helped uncover important mechanisms related to epilepsy, examines diverse treatments to prevent and manage epilepsy, and addresses essential ethical issues in research. In this review, we aim to emphasize the important role of NHPs in epilepsy research and summarize the benefits and challenges associated with their use as models.

Identification of Specific Cell Surface Markers on Immune Cells of Squirrel Monkeys (Saimiri sciureus)

Nonhuman primates are an important experimental model for the development of targeted biological therapeutics because of their immunological closeness to humans. However, there are very few antibody reagents relevant for delineating the different immune cell subsets based on nonhuman primate antigens directly or with cross-reactivity to those in humans. Here, we report specific expression of HLA-DR, PD-1, and CD123 on different circulating immune cell subsets in the peripheral blood that included T cells (CD3+), T cells subsets (CD4+ and CD8+), B cells (CD20+), natural killer (NK) cells (CD3-CD16+), and natural killer T cells (CD3+CD16+) along with different monocyte subsets in squirrel monkey (Saimiri sciureus). We established cross-reactivity of commercial mouse antihuman monoclonal antibodies (mAbs), with these various immune cell surface markers. These findings should aid further future comprehensive understanding of the immune parameters and identification of new biomarkers to significantly improve SQM as a model for biomedical studies.

Morphometry and skeletopy of kidneys and renal vessels in Alouatta guariba clamitans (Primates: Atelidae): case reports

Various animal models are used for research; however, non-human primates are well suited for biomedical research owing to their genetic homology with humans. The objective of this research was the anatomical characterization of red howler's kidneys in view of the scarcity of information in the literature. Protocols were approved by the Committee for Ethics in the Use of Animals at the Federal Rural University of Rio de Janeiro (number 018/2017). The study was conducted at the Laboratory of Teaching and Research in Domestic and Wild Animal Morphology, Federal Rural University of Rio de Janeiro. Specimens of Alouatta guariba clamitans were collected from the Serra dos Órgãos National Park road in Rio de Janeiro and subsequently frozen. Four adult cadavers (two males and two females) were used, identified, and injected with a 10% formaldehyde solution. Later, the specimens were dissected, and measurements and topography of the kidneys and renal vessels were recorded. The kidneys of A. g. clamitans resemble a "bean seed," with a smooth surface. The longitudinal section shows two distinct regions, cortical and medullary; in addition, the kidneys are unipyramidal. The renal arteries emerged from the abdominal aorta as a single vessel posterior to the renal veins. The renal veins drained directly into the caudal vena cava as a single vessel in all specimens.

Zika Virus Infection Damages the Testes in Pubertal Common Squirrel Monkeys (Saimiri collinsi)

During the Zika virus (ZIKV) outbreak and after evidence of its sexual transmission was obtained, concerns arose about the impact of the adverse effects of ZIKV infection on human fertility. In this study, we evaluated the clinical-laboratory aspects and testicular histopathological patterns of pubertal squirrel monkeys (Saimiri collinsi) infected with ZIKV, analyzing the effects at different stages of infection. The susceptibility of S. collinsi to ZIKV infection was confirmed by laboratory tests, which detected viremia (mean 1.63 × 106 RNA copies/µL) and IgM antibody induction. Reduced fecal testosterone levels, severe testicular atrophy and prolonged orchitis were observed throughout the experiment by ultrasound. At 21 dpi, testicular damage associated with ZIKV was confirmed by histopathological and immunohistochemical (IHC) analyses. Tubular retraction, the degeneration and necrosis of somatic and germ cells in the seminiferous tubules, the proliferation of interstitial cells and an inflammatory infiltrate were observed. ZIKV antigen was identified in the same cells where tissue injuries were observed. In conclusion, squirrel monkeys were found to be susceptible to the Asian variant of ZIKV, and this model enabled the identification of multifocal lesions in the seminiferous tubules of the infected group evaluated. These findings may suggest an impact of ZIKV infection on male fertility.

Systems biology of malaria explored with nonhuman primates

"The Primate Malarias" book has been a uniquely important resource for multiple generations of scientists, since its debut in 1971, and remains pertinent to the present day. Indeed, nonhuman primates (NHPs) have been instrumental for major breakthroughs in basic and pre-clinical research on malaria for over 50 years. Research involving NHPs have provided critical insights and data that have been essential for malaria research on many parasite species, drugs, vaccines, pathogenesis, and transmission, leading to improved clinical care and advancing research goals for malaria control, elimination, and eradication. Whilst most malaria scientists over the decades have been studying Plasmodium falciparum, with NHP infections, in clinical studies with humans, or using in vitro culture or rodent model systems, others have been dedicated to advancing research on Plasmodium vivax, as well as on phylogenetically related simian species, including Plasmodium cynomolgi, Plasmodium coatneyi, and Plasmodium knowlesi. In-depth study of these four phylogenetically related species over the years has spawned the design of NHP longitudinal infection strategies for gathering information about ongoing infections, which can be related to human infections. These Plasmodium-NHP infection model systems are reviewed here, with emphasis on modern systems biological approaches to studying longitudinal infections, pathogenesis, immunity, and vaccines. Recent discoveries capitalizing on NHP longitudinal infections include an advanced understanding of chronic infections, relapses, anaemia, and immune memory. With quickly emerging new technological advances, more in-depth research and mechanistic discoveries can be anticipated on these and additional critical topics, including hypnozoite biology, antigenic variation, gametocyte transmission, bone marrow dysfunction, and loss of uninfected RBCs. New strategies and insights published by the Malaria Host-Pathogen Interaction Center (MaHPIC) are recapped here along with a vision that stresses the importance of educating future experts well trained in utilizing NHP infection model systems for the pursuit of innovative, effective interventions against malaria.

Molecular characterisation of parvorder Platyrrhini IgG sub-classes

Non-human primates (NHP) are essential in modern biomedical research; New World monkeys (NWM) are mainly used as an experimental model regarding human malaria as they provide useful information about the parasite's biology and an induced immune response. It is known that a vaccine candidate's efficacy is mediated by a protection-inducing antibody response (IgG). Not enough information is available concerning IgG subclasses' molecular characteristics regarding NHP from parvorder Platyrrhini. Understanding the nature of the humoral immune response and characterising the IgG subclasses' profile will provide valuable information about the immunomodulator mechanisms of vaccines evaluated using an NHP animal model. This article has characterised IgG subclasses in NWM (i.e. genera Aotus, Cebus, Ateles and Alouatta) based on the amplification, cloning and sequencing of the immunoglobulin heavy constant gamma (IGHG) gene's CH1 to CH3 regions. The resulting sequences enabled elucidating IGHG gene organisation; two IgG variants were found in the Aotus and Ateles monkey group and three IgG variants in the Cebus and Alouatta group. The sequences were highly conserved in Platyrrhini and had a similar structure to that reported for monkeys from parvorder Catarrhini. Such information will help in developing tools for a detailed characterisation of the humoral immune response in an NWM experimental animal model.

Marmosets: Welfare, Ethical Use, and IACUC/Regulatory Considerations

Use of marmosets in biomedical research has increased dramatically in recent years due, in large part, to their suitability for transgenic applications and utility as models for neuroscience investigations. This increased use includes the establishment of new colonies and involvement of people new to marmoset research. To facilitate the use of the marmoset as a research model, we provide an overview of issues surrounding the ethics and regulations associated with captive marmoset research, including discussion of the history of marmosets in research, current uses of marmosets, ethical considerations related to marmoset use, issues related to importation of animals, and recommendations for regulatory oversight of gene-edited marmosets. To understand the main concerns that oversight bodies have regarding captive biomedical research with marmosets, we developed a brief, 15-question survey that was then sent electronically to academic and biomedical research institutions worldwide that were believed to house colonies of marmosets intended for biomedical research. The survey included general questions regarding the individual respondent's colony, status of research use of the colony and institutional oversight of both the colony itself and the research use of the colony. We received completed surveys from a total of 18 institutions from North America, Europe, and Asia. Overall, there appeared to be no clear difference in regulatory oversight body concerns between countries/regions. One difference that we were able to appreciate was that while biomedical research with marmosets was noted to be either stable or decreasing in Europe, use was clearly increasing elsewhere.

Utility of Common Marmoset (Callithrix jacchus) Embryonic Stem Cells in Liver Disease Modeling, Tissue Engineering and Drug Metabolism

The incidence of liver disease is increasing significantly worldwide and, as a result, there is a pressing need to develop new technologies and applications for end-stage liver diseases. For many of them, orthotopic liver transplantation is the only viable therapeutic option. Stem cells that are capable of differentiating into all liver cell types and could closely mimic human liver disease are extremely valuable for disease modeling, tissue regeneration and repair, and for drug metabolism studies to develop novel therapeutic treatments. Despite the extensive research efforts, positive results from rodent models have not translated meaningfully into realistic preclinical models and therapies. The common marmoset Callithrix jacchus has emerged as a viable non-human primate model to study various human diseases because of its distinct features and close physiologic, genetic and metabolic similarities to humans. C. jacchus embryonic stem cells (cjESC) and recently generated cjESC-derived hepatocyte-like cells (cjESC-HLCs) could fill the gaps in disease modeling, liver regeneration and metabolic studies. They are extremely useful for cell therapy to regenerate and repair damaged liver tissues in vivo as they could efficiently engraft into the liver parenchyma. For in vitro studies, they would be advantageous for drug design and metabolism in developing novel drugs and cell-based therapies. Specifically, they express both phase I and II metabolic enzymes that share similar substrate specificities, inhibition and induction characteristics, and drug metabolism as their human counterparts. In addition, cjESCs and cjESC-HLCs are advantageous for investigations on emerging research areas, including blastocyst complementation to generate entire livers, and bioengineering of discarded livers to regenerate whole livers for transplantation.

High Angular Resolution Diffusion MRI Reveals Conserved and Deviant Programs in the Paths that Guide Human Cortical Circuitry

Diffusion magnetic resonance (MR) tractography represents a novel opportunity to investigate conserved and deviant developmental programs between humans and other species such as mice. To that end, we acquired high angular resolution diffusion MR scans of mice [embryonic day (E) 10.5 to postnatal week 4] and human brains [gestational week (GW) 17-30] at successive stages of fetal development to investigate potential evolutionary changes in radial organization and emerging pathways between humans and mice. We compare radial glial development as well as commissural development (e.g., corpus callosum), primarily because our findings can be integrated with previous work. We also compare corpus callosal growth trajectories across primates (i.e., humans and rhesus macaques) and rodents (i.e., mice). One major finding is that the developing cortex of humans is predominated by pathways likely associated with a radial glial organization at GW 17-20, which is not as evident in age-matched mice (E 16.5, 17.5). Another finding is that, early in development, the corpus callosum follows a similar developmental timetable in primates (i.e., macaques and humans) as in mice. However, the corpus callosum grows for an extended period of time in primates compared with rodents. Taken together, these findings highlight deviant developmental programs underlying the emergence of cortical pathways in the human brain.

Igh locus structure and evolution in Platyrrhines: new insights from a genomic perspective

Non-human primates have been used as animal models because of their phylogenetic closeness to humans. However, the genetic differences between humans and non-human primates must be considered to select the appropriate animal models. Recently, New World monkeys (Platyrrhines) have generated a higher interest in biomedical research, especially in assessing vaccine safety and immunogenicity. Given the continued and renewed interest in Platyrrhines as biomedical models, it is a necessary to have a better and more complete understanding of their immune system and its implications for research. Immunoglobulins (Ig) are the main proteins that mediate humoral immunity. These proteins have evolved as part of an adaptive immune response system derived from ancient vertebrates. There are at least four Ig classes in Prosimians, whereas five have been reported in Catarrhines. Information on the structure and evolution of the loci containing immunoglobulin heavy chain constant genes (Igh) in Platyrrhines, however, is limited. Here, Igh loci were characterized in 10 Platyrrhines using the available whole genome sequences. Human and Macaca Igh loci were also assessed to compare them with their Platyrrhines counterparts. Differences in Igh locus structure were observed between Platyrrhines and Catarrhines. Noteworthy changes occur in the γ gene, which encodes a key Ig involved in organism defense that would favor protection after vaccination. The remarkable differences between the immunoglobulin proteins of Platyrrhines and Catarrhines warrant a cautionary message to biomedical researchers.

Recently integrated Alu insertions in the squirrel monkey (Saimiri) lineage and application for population analyses

BACKGROUND

The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey (Saimiri), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups.

RESULTS

PCR analyses were performed on a DNA panel of 32 squirrel monkey individuals for 382 Alu insertion events ≤2% diverged from 46 different Alu subfamily consensus sequences, 25 Saimiri specific and 21 NWM specific Alu subfamilies. Of the 382 loci, 110 were polymorphic for presence / absence among squirrel monkey individuals, 35 elements from 14 different Saimiri specific Alu subfamilies and 75 elements from 19 different NWM specific Alu subfamilies (13 of 46 subfamilies analyzed did not contain polymorphic insertions). Of the 110 Alu insertion polymorphisms, 51 had species informative allele frequency distributions between Saimiri sciureus and Saimiri boliviensis groups.

CONCLUSIONS

This study confirms the evolution of Alu subfamilies in Saimiri and provides evidence for an ongoing and prolific expansion of these elements in Saimiri with many active subfamilies concurrently propagating. The subset of polymorphic Alu insertions with species informative allele frequency distribution between Saimiri sciureus and Saimiri boliviensis will be instructive for specimen identification and conservation biology.

Differential modulatory effects of cocaine on marmoset monkey recognition memory

Acute and repeated exposure to cocaine alters the cognitive performance of humans and animals. How each administration schedule affects the same memory task has yet to be properly established in nonhuman primates. Therefore, we assessed the performance of marmoset monkeys in a spontaneous object-location (SOL) recognition memory task after acute and repeated exposure to cocaine (COC; 5mg/kg, ip). Two identical neutral stimuli were explored on the 10-min sample trial, after which preferential exploration of the displaced vs the stationary object was analyzed on the 10-min test trial. For the acute treatment, cocaine was given immediately after the sample presentation, and spatial recognition was then tested after a 24-h interval. For the repeated exposure schedule, daily cocaine injections were given on 7 consecutive days. After a 7-day drug-free period, the SOL task was carried out with a 10-min intertrial interval. When given acutely postsample, COC improved the marmosets' recognition memory, whereas it had a detrimental effect after the repeated exposure. Thus, depending on the administration schedule, COC exerted opposing effects on the marmosets' ability to recognize spatial changes. This agrees with recent studies in rodents and the recognition impairment seen in human addicts. Further studies related to the effects of cocaine's acute×prior drug history on the same cognitive domain are warranted.

Scopolamine Induces Deficits in Spontaneous Object-Location Recognition and Fear-Learning in Marmoset Monkeys

The non-selective muscarinic receptor antagonist scopolamine (SCP) induces memory deficits in both animals and humans. However, few studies have assessed the effects of amnesic agents on memory functions of marmosets – a small-bodied neotropical primate that is becoming increasingly used as a translational model for several neuropathologies. Here we assessed the effects of an acute SCP administration (0.03 mg/kg, sc) on the behavior of adult marmoset monkeys in two tasks. In the spontaneous object-location (SOL) recognition task, two identical neutral stimuli were explored on the sample trial, after which preferential exploration of the displaced versus the stationary object was analyzed on the test trial. In the fear-motivated behavior (FMB) procedure, the same subjects were submitted to an initial baseline trial, followed by an exposure period to a snake model and lastly a post-exposure trial. All trials and inter-trial intervals lasted 10 min for both tests. Results showed that on the SOL test trial, the saline group explored the displaced object significantly longer than its identical stationary counterpart, whereas SCP-treated marmosets explored both objects equivalently. In the FMB test, the saline group – but not the SCP-treated animals – spent significantly less time where the stimulus had been specifically encountered and more time being vigilant of their surroundings, compared to pre-exposure levels. Drug-related effects on general activity, overall exploration (SOL task) and behavioral response to the aversive stimulus (FMB task) were not observed. SCP thus impaired the marmosets’ short-term ability to detect changes associated with the spatial location of ethologically irrelevant (SOL task) and relevant stimuli (FMB task). Similar results have been reported in other animal species. Marmosets may thus help reduce the translational gap between pre-clinical studies and memory-associated human pathologies.

Advantages of nonhuman primates as preclinical models for evaluating stem cell-based therapies for Parkinson's disease

The derivation of dopaminergic neurons from induced pluripotent stem cells brings new hope for a patient-specific, stem cell-based replacement therapy to treat Parkinson's disease (PD) and related neurodegenerative diseases; and this novel cell-based approach has already proven effective in animal models. However, there are several aspects of this procedure that have yet to be optimized to the extent required for translation to an optimal cell-based transplantation protocol in humans. These challenges include pinpointing the optimal graft location, appropriately scaling up the graft volume, and minimizing the risk of chronic immune rejection, among others. To advance this procedure to the clinic, it is imperative that a model that accurately and fully recapitulates characteristics most pertinent to a cell-based transplantation to the human brain is used to optimize key technical aspects of the procedure. Nonhuman primates mimic humans in multiple ways including similarities in genomics, neuroanatomy, neurophysiology, immunogenetics, and age-related changes in immune function. These characteristics are critical to the establishment of a relevant model in which to conduct preclinical studies to optimize the efficacy and safety of cell-based therapeutic approaches to the treatment of PD. Here we review previous studies in rodent models, and emphasize additional advantages afforded by nonhuman primate models in general, and the baboon model in particular, for preclinical optimization of cell-based therapeutic approaches to the treatment of PD and other neurodegenerative diseases. We outline current unresolved challenges to the successful application of stem cell therapies in humans and propose that the baboon model in particular affords a number of traits that render it most useful for preclinical studies designed to overcome these challenges.

X-ray pelvimetry in common marmoset (Callithrix jacchus - LINNAEUS, 1758)

ABSTRACT The common marmoset is an important Neotropical primate for biomedical research. With the intention of providing pelvimetric values that allow the selection of animals with better characteristics for reproduction, we studied the X-ray of the pelvis, in ventro-dorsal projection of 12 adult animals, six males and six females, belonging to the National Center of Primates - CENP. The measurements were made to right diagonal diameters (RDD), left diagonal diameter (LDD), bi-iliac middle diameter (BIMD), bi-iliac upper diameter (BIUD), bi-iliac lower diameter (BILD), sacrum-pubic diameter (SPD), and the input area of the pelvis (IAP), which were compared in relation to sex and bodily correlated with the biometrics. The results of the means and standard deviations regarding pelvimetry (cm) were: for the RDD in males of 1.91±0.14 and in the females of 2.05±0.08; LDD in males of 1.85±0.16 and in females of 2.03± 0.08; BIMD in males of 1.46±0.12 and in the females of 1.5±0; BIUD showed in males 1.3±0.1 and in females of 1.3±0.06; BILD in males of 1.35±0.15 and in females of 1.25±0.08; SPD in males of 1.68±0.09 and in females of 1.93±0.13; IAP in males of 1.9±0.26 and in the females of 2.23±0.13. It was concluded that the pelvis of Callithrix jacchus could be classified as dolicopelvic type, there is sexual dimorphism in relation to the pelvis of adult animals and that the bodily measurements have low positive correlation with pelvic measurements.

The Effect of Anesthesia on Blood Pressure Measured Noninvasively by Using the Tail-Cuff Method in Marmosets (Callithrix jacchus)

In this study, we evaluated the validity of measuring blood pressure (BP) noninvasively in marmosets by using the tail-cuff method. The number of measurements needed for a valid reading was calculated by plotting the average SD of 5 consecutive readings in 10 naïve marmosets; the SD for both systolic and diastolic BP readings plateaued after 4 readings. To evaluate how anesthesia (alphaxalone, 15 mg/kg IM) affected BP in marmosets, we measured 4 animals every minute for 60 min after injection. The average length of anesthesia was 47.3 ± 13.2 min. The variability in the systolic and diastolic BP was the smallest at 10 to 30 min after injection (systolic SD, 6.29 mm Hg; diastolic SD, 5.27 mm Hg) and almost doubled at 30 to 60 min after injection (systolic SD, 13.5 mm Hg; diastolic SD, 12.3 mm Hg). The within- and between-session repeatability and reproducibility were calculated by measuring 12 marmosets twice at the same time of day (±1 h) 1 wk apart. The coefficients of repeatability and reproducibility were 1.98% and 14.5% for systolic BP and 3.37% and 16.2% for diastolic BP, respectively. Our results indicate that using the volumetric tail-cuff method to measure BP noninvasively in anesthetized marmosets is safe and feasible. The measures are least variable within 10 to 30 min after the injection of anesthetic, and variability increases slightly between sessions.

Identification of Owl Monkey CD4 Receptors Broadly Compatible with Early-Stage HIV-1 Isolates

Most HIV-1 variants isolated from early-stage human infections do not use nonhuman primate versions of the CD4 receptor for cellular entry, or they do so poorly. We and others have previously shown that CD4 has experienced strong natural selection over the course of primate speciation, but it is unclear whether this selection has influenced the functional characteristics of CD4 as an HIV-1 receptor. Surprisingly, we find that selection on CD4 has been most intense in the New World monkeys, animals that have never been found to harbor lentiviruses related to HIV-1. Based on this, we sampled CD4 genetic diversity within populations of individuals from seven different species, including five species of New World monkeys. We found that some, but not all, CD4 alleles found in Spix's owl monkeys (Aotus vociferans) encode functional receptors for early-stage human HIV-1 isolates representing all of the major group M clades (A, B, C, and D). However, only some isolates of HIV-1 subtype C can use the CD4 receptor encoded by permissive Spix's owl monkey alleles. We characterized the prevalence of functional CD4 alleles in a colony of captive Spix's owl monkeys and found that 88% of surveyed individuals are homozygous for permissive CD4 alleles, which encode an asparagine at position 39 of the receptor. We found that the CD4 receptors encoded by two other species of owl monkeys (Aotus azarae and Aotus nancymaae) also serve as functional entry receptors for early-stage isolates of HIV-1.

IMPORTANCE

Nonhuman primates, particularly macaques, are used for preclinical evaluation of HIV-1 vaccine candidates. However, a significant limitation of the macaque model is the fact that most circulating HIV-1 variants cannot use the macaque CD4 receptor to enter cells and have to be adapted to these species. This is particularly true for viral variants from early stages of infection, which represent the most relevant vaccine targets. In this study, we found that some individuals from captive owl monkey populations harbor CD4 alleles that are compatible with a broad collection of HIV-1 isolates, including those isolated from early in infection in highly affected populations and representing diverse subtypes.

Alu elements and the phylogeny of capuchin (Cebus and Sapajus) monkeys

Three families of New World monkeys, the Pitheciidae, Atelidae, and Cebidae, are currently recognized. The monophyly of the Cebidae is supported unequivocally by the presence of ten unique Alu elements, which are absent from the other two families. In this paper, the five genomic regions containing these Alu elements were sequenced in specimens representing nine capuchin (Cebus, Sapajus) species in order to identify mutations that may help elucidate the taxonomy and phylogenetic relationships of the cebids. The results confirmed the presence of previously described Alu elements in the capuchins. An Alu insertion present in the Cebidae2 genomic region belonging to the AluSc subfamily was amplified and sequenced only in Sapajus. No amplified or unspecific product was obtained for all other species studied here. An AluSc insertion present in the CeSa1 region was found only in Cebus, Sapajus, and Saimiri. Cebidae4 was characterized by two insertions, an AluSz6 shared by all cebids, and a complete SINE (AluSx3) found only in the capuchins (Cebus and Sapajus). The genomic region Cebidae5 revealed two insertion events, one of the AluSx subfamily, which was shared by all cebids, and another (AluSc8), that was unique to Cebus, offering a straightforward criterion for the differentiation of the two genera, Cebus and Sapajus. The Cebidae6 region showed four distinct insertion events: a 52-bp simple repeat ((TATG) n), two very ancient repeats (MIRc) and a TcMar-Tigger shared by all New World monkeys studied so far, and an Alu insertion of the AluSx subfamily present exclusively in the cebids. The phylogenetic tree confirmed the division of the capuchins into two genera, Cebus and Sapajus, and suggested the southern species Sapajus nigritus robustus and S. cay as the earliest and second earliest offshoots in this genus, respectively. This supports a southern origin for the Sapajus radiation.

De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences

Background

Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque, the common marmoset (Callithrix jacchus), a New World primate, offers important advantages in comparison to other primates, such as an accelerated lifespan. To conduct Next Generation expression studies or to study primate evolution, a high quality annotation of the marmoset genome is required. The availability of marmoset transcriptome data from five tissues, including both raw sequences and assembled transcripts, will aid in the annotation of the newly released marmoset assembly.

Findings

RNA was extracted from five tissues: skeletal muscle, bladder and hippocampus from a male common marmoset, and cerebral cortex and cerebellum from a female common marmoset. All five RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the NCBI Sequence Read Archive. Transcripts were assembled, annotated and deposited in the NCBI Transcriptome Shotgun Assembly database.

Conclusions

We have provided a high quality annotation of 51,163 transcripts with full-length coding sequence. This set represented a total of 10,833 unique genes. In addition to providing empirical support for the existence of these 10,833 genes, we also provide sequence information for 2,422 genes that were not previously identified in the Ensembl annotation of the marmoset genome.

Parallel evolution of a self-signal: humans and new world monkeys independently lost the cell surface sugar Neu5Gc

Human sialic acid biology is unusual and thought to be unique among mammals. Humans lack a functional cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) protein and cannot synthesize the sugar Neu5Gc, an innate mammalian signal of self. Losing this sugar changed how humans interact with some of our deadliest pathogens: malaria, influenza, and streptococcus among others. We show that the New World monkeys, comprising the third of all primate species, have human-like sialic acid biology. They have lost Neu5Gc because of an independent CMAH inactivation ~30 million years ago (mya) (compared to ~3 mya in hominids). This parallel loss of Neu5Gc opens sialic acid biology to comparative phylogenetic analysis and reveals an unexpected conservation priority. New World monkeys risk infection by human pathogens that can recognize cells in the absence of Neu5Gc. This striking molecular convergence provides a mechanism that could explain the long-standing observation that New World monkeys are susceptible to some human diseases that cannot be transmitted to other primates.

In transition: primate genomics at a time of rapid change

The field of nonhuman primate genomics is undergoing rapid change and making impressive progress. Exploiting new technologies for DNA sequencing, researchers have generated new whole-genome sequence assemblies for multiple primate species over the past 6 years. In addition, investigations of within-species genetic variation, gene expression and RNA sequences, conservation of non-protein-coding regions of the genome, and other aspects of comparative genomics are moving at an accelerating speed. This progress is opening a wide array of new research opportunities in the analysis of comparative primate genome content and evolution. It also creates new possibilities for the use of nonhuman primates as model organisms in biomedical research. This transition, based on both new technology and the new information being generated in regard to human genetics, provides an important justification for reevaluating the research goals, strategies, and study designs used in primate genetics and genomics.

Characterising a microsatellite for DRB typing in Aotus vociferans and Aotus nancymaae (Platyrrhini)

Non-human primates belonging to the Aotus genus have been shown to be excellent experimental models for evaluating drugs and vaccine candidates against malaria and other human diseases. The immune system of this animal model must be characterised to assess whether the results obtained here can be extrapolated to humans. Class I and II major histocompatibility complex (MHC) proteins are amongst the most important molecules involved in response to pathogens; in spite of this, the techniques available for genotyping these molecules are usually expensive and/or time-consuming. Previous studies have reported MHC-DRB class II gene typing by microsatellite in Old World primates and humans, showing that such technique provides a fast, reliable and effective alternative to the commonly used ones. Based on this information, a microsatellite present in MHC-DRB intron 2 and its evolutionary patterns were identified in two Aotus species (A. vociferans and A. nancymaae), as well as its potential for genotyping class II MHC-DRB in these primates.

The repertoire of MHC class I genes in the common marmoset: evidence for functional plasticity

In humans, the classical antigen presentation function of major histocompatibility complex (MHC) class I molecules is controlled by the human leukocyte antigen HLA -A, HLA-B and HLA-C loci. A similar observation has been made for great apes and Old World monkey species. In contrast, a New World monkey species such as the cotton-top tamarin (Saguinus oedipus) appears to employ the G locus for its classical antigen presentation function. At present, little is known about the classical MHC class I repertoire of the common marmoset (Callithrix jacchus), another New World monkey that is widely used in biomedical research. In the present population study, no evidence has been found for abundant transcription of classical I class genes. However, in each common marmoset, four to seven different G-like alleles were detected, suggesting that the ancestral locus has been subject to expansion. Segregation studies provided evidence for at least two G-like genes present per haplotype, which are transcribed by a variety of cell types. The alleles of these Caja-G genes cluster in separate lineages, suggesting that the loci diversified considerably after duplication. Phylogenetic analyses of the introns confirm that the Caja-G loci cluster in the vicinity of HLA-G, indicating that both genes shared an ancestor. In contrast to HLA-G, Caja-G shows considerable polymorphism at the peptide-binding sites. This observation, together with the lack of detectable transcripts of A and B-like genes, indicates that Caja-G genes have taken over the function of classical class I genes. These data highlight the extreme plasticity of the MHC class I gene system.

Sequencing and comparative analysis of the gorilla MHC genomic sequence

Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.