Comparative transcriptome analysis between rhesus macaques(Macaca mulatta) and crab-eating macaques(M. fascicularis)

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

BARN:Behavior-Aware Relation Network for multi-label behavior detection in socially housed macaques

Quantification of behaviors in macaques provides crucial support for various scientific disciplines,including pharmacology,neuroscience,and ethology.Despite recent advancements in the analysis of macaque behavior,research on multi-label behavior detection in socially housed macaques,including consideration of interactions among them,remains scarce.Given the lack of relevant approaches and datasets,we developed the Behavior-Aware Relation Network(BARN)for multi-label behavior detection of socially housed macaques.Our approach models the relationship of behavioral similarity between macaques,guided by a behavior-aware module and novel behavior classifier,which is suitable for multi-label classification.We also constructed a behavior dataset of rhesus macaques using ordinary RGB cameras mounted outside their cages.The dataset included 65?913 labels for19 behaviors and 60?367 proposals,including identities and locations of the macaques.Experimental results showed that BARN significantly improved the baseline SlowFast network and outperformed existing relation networks.In conclusion,we successfully achieved multilabel behavior detection of socially housed macaques with both economic efficiency and high accuracy.

Superior intestinal integrity and limited microbial translocation are associated with lower immune activation in SIVmac239-infected northern pig-tailed macaques(Macaca leonina)

Microbial translocation is a cause of systemic immune activation in HIV/SIV infection. In the present study, we found a lower CD8+ T cell activation level in Macaca leonina (northern pig-tailed macaques, NPMs) than in Macaca mulatta (Chinese rhesus macaques, ChRMs) during SIVmac239 infection. Furthermore, the levels of plasma LPS-binding protein and soluble CD14 in NPMs were lower than those in ChRMs. Compared with ChRMs, SIV-infected NPMs had lower Chiu scores, representing relatively normal intestinal mucosa. In addition, no obvious damage to the ileum or colon epithelial barrier was observed in either infected or uninfected NPMs, which differed to that found in ChRMs. Furthermore, no significant microbial translocation (Escherichia coli) was detected in the colon or ileum of infected or uninfected NPMs, which again differed to that observed in ChRMs. In conclusion, NPMs retained superior intestinal integrity and limited microbial translocation during SIV infection, which may contribute to their lower immune activation compared with ChRMs.

Age-related rhesus macaque models of COVID-19

Background:Since December 2019,an outbreak of the Corona Virus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus(SARS-CoV-2)in Wuhan,China,has become a public health emergency of international concern.The high fatality of aged cases caused by SARS-CoV-2 was a need to explore the possible age-related phenomena with non-human primate models.Methods:Three 3-5 years old and two 15 years old rhesus macaques were intratracheally infected with SARS-CoV-2,and then analyzed by clinical signs,viral replication,chest X-ray,histopathological changes and immune response.Results:Viral replication of nasopharyngeal swabs,anal swabs and lung in old monkeys was more active than that in young monkeys for 14 days after SARS-CoV-2 challenge.Monkeys developed typical interstitial pneumonia characterized by thickened alveolar septum accompanied with inflammation and edema,notably,old monkeys exhibited diffuse severe interstitial pneumonia.Viral antigens were detected mainly in alveolar epithelial cells and macrophages.Conclusion:SARS-CoV-2 caused more severe interstitial pneumonia in old monkeys than that in young monkeys.Rhesus macaque models infected with SARS-CoV-2 provided insight into the pathogenic mechanism and facilitated the development of vaccines and therapeutics against SARS-CoV-2 infection.

Interchange between grooming and infant handling in female Tibetan macaques(Macaca thibetana)

In some non-human primates, infants function as a social tool that can bridge relationships among group members. Infants are a desired commodity for group members, and mothers control access to them. The biological market theory suggests that grooming is widespread and represents a commodity that can be exchanged for infant handling. As a limited resource, however, the extent to which infants are interchanged between mothers(females with an infant) and non-mothers(potential handlers,females without an infant) remains unclear. In this study, we collected behavioral data to investigate the relationship between grooming and infant handling in free-ranging Tibetan macaques(Macaca thibetana)at Mt. Huangshan, China. Our results showed that females with infants received more grooming than females without infants. After her infant was handled,mother females received more grooming than they did during daily grooming interactions. However, with the increasing number of infants within the social group, both the grooming that mothers received and the grooming that non-mothers invested for handling infants decreased. We also found that non-mothers invested more time in grooming to gain access to younger infants than older infants. Our results provide evidence that infants are social commodities for both mother and non-mother females. Mothers use infants for obtain grooming and non-mothers use grooming to gain access to infants. The current study implies a bidirectional and complex interchange pattern between grooming and infant handling to compensate for the dyadic grooming disparity in non-human primates.

Parasites may exit immunocompromised northern pig-tailed macaques (Macaca leonina)infected with SIVmac239

Parasites can increase infection rates and pathogenicity in immunocompromised human immunodeficiency virus(HIV) patients. However, in vitro studies and epidemiological investigations also suggest that parasites might escape immunocompromised hosts during HIV infection.Due to the lack of direct evidence from animal experiments, the effects of parasitic infections on immunocompromised hosts remain unclear. Here,we detected 14 different parasites in six northern pig-tailed macaques(NPMs) before or at the 50 th week of simian immunodeficiency virus(SIV) infection by ELISA. The NPMs all carried parasites before viral injection. At the 50 th week after viral injection, the individuals with negative results in parasitic detection(i.e., 08247 and 08287) were characterized as the Parasites Exit(PE) group, with the other individuals(i.e., 09203, 09211, 10205, and 10225) characterized as the Parasites Remain(PR) group. Compared with the PR group, the NPMs in the PE group showed higher viral loads, lower CD4^+T cells counts, and lower CD4/CD8 rates. Additionally, the PE group had higher immune activation and immune exhaustion of both CD4^+and CD8^+T cells. Pathological observation showed greater injury to the liver, cecum, colon,spleen, and mesenteric lymph nodes in the PE group.This study showed more seriously compromised immunity in the PE group, strongly indicating that parasites might exit an immunocompromised host.

Metagenomic comparison of the rectal microbiota between rhesus macaques(Macaca mulatta) and cynomolgus macaques(Macaca fascicularis)

Rhesus macaques(Macaca mulatta) and cynomolgus macaques(Macaca fascicularis) are frequently used in establishing animal models for human diseases. To determine the differences in gut microbiota between these species, rectal swabs from 20 rhesus macaques and 21 cynomolgus macaques were collected, and the microbial composition was examined by deep sequencing of the 16 S rR NA gene. We found that the rectal microbiota of cynomolgus macaques exhibited significantly higher alpha diversity than that of rhesus macaques, although the observed number of operational taxonomic units(OTUs) was almost the same. The dominant taxa at both the phylum and genus levels were similar between the two species, although the relative abundances of these dominant taxa were significantly different between them. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States(PICRUSt) showed significant differences in the functional components between the microbiota of the two species, in particular the lipopolysaccharide(LPS) synthesis proteins. The above data indicated significant differences in microbial composition and function between these two closely related macaque species, which should be taken into consideration in the future selection of these animals for disease models.

Co-transplantation of macaque autologous Schwann cells and human embryonic nerve stem cells in treatment of macaque Parkinson's disease

Objective:To investigate the therapeutic effects of co-transplantation with Schwann cells（SCs） and human embryonic nerve stem cells（NSCs） on macaque Parkinson’s disease（PD）.Methods: Macaque autologous SCs and human embryonic NSCs were adopled for the treatment of macaque PD.Results:Six months after transplantation,positron emission computerized tomography showed that 18F-FP-β-CIT was significantly concentrated in the injured striatum in the cotransplanted group.Immunohistoehemieal staining of transplanted area tissue showed migration of tyrosine hydroxylase positive cells from the transplant area to the surrounding area was significantly increased in the co-transplanted group.Conclusions:Co-transplantation of SCs and NSCs could effectively cure PD in macaques.SCs harvested from the autologous peripheral nerves can avoid rejection and the ethics problems,so it is expected to be applied clinically.

Single-nucleus transcriptomic profiling of multiple organs in a rhesus macaque model of SARS-CoV-2 infection

Infection with severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) causes diverse clinical manifestations and tissue injuries in multiple organs.However, cellular and molecular understanding of SARS-CoV-2 infection-associated pathology and immune defense features in different organs remains incomplete. Here, we profiled approximately 77 000single-nucleus transcriptomes of the lung, liver,kidney, and cerebral cortex in rhesus macaques(Macaca mulatta) infected with SARS-CoV-2 and healthy controls. Integrated analysis of the multiorgan dataset suggested that the liver harbored the strongest global transcriptional alterations. We observed prominent impairment in lung epithelial cells, especially in AT2 and ciliated cells, and evident signs of fibrosis in fibroblasts. These lung injury characteristics are similar to those reported in patients with coronavirus disease 2019(COVID-19).Furthermore, we found suppressed MHC class I/II molecular activity in the lung, inflammatory response in the liver, and activation of the kynurenine pathway,which induced the development of an immunosuppressive microenvironment. Analysis of the kidney dataset highlighted tropism of tubule cells to SARS-CoV-2, and we found membranous nephropathy(an autoimmune disease) caused by podocyte dysregulation. In addition, we identified the pathological states of astrocytes and oligodendrocytes in the cerebral cortex, providing molecular insights into COVID-19-related neurological implications. Overall, our multi-organ single-nucleus transcriptomic survey of SARS-CoV-2-infected rhesus macaques broadens our understanding of disease features and antiviral immune defects caused by SARS-CoV-2 infection,which may facilitate the development of therapeutic interventions for COVID-19.

Dysbiosis of gut microbiome affecting small intestine morphology and immune balance:a rhesus macaque model

There is a growing appreciation for the specific health benefits conferred by commensal microbiota on their hosts.Clinical microbiota analysis and animal studies in germ-free or antibiotic-treated mice have been crucial for improving our understanding of the role of the microbiome on the host mucosal surface;however,studies on the mechanisms involved in microbiome-host interactions remain limited to small animal models.Here,we demonstrated that rhesus monkeys under short-term broad-spectrum antibiotic treatment could be used as a model to study the gut mucosal host-microbiome niche and immune balance with steady health status.Results showed that the diversity and community structure of the gut commensal bacteria in rhesus monkeys were both disrupted after antibiotic treatment.Furthermore,the 16S rDNA amplicon sequencing results indicated that Escherichia-Shigella were predominant in stool samples 9 d of treatment,and the abundances of bacterial functional genes and predicted KEGG pathways were significantly changed.In addition to inducing aberrant morphology of small intestinal villi,the depletion of gut commensal bacteria led to increased proportions of CD3+T,CD4+T,and CD16+NK cells in peripheral blood mononuclear cells(PBMCs),but decreased numbers of Treg and CD20+B cells.The transcriptome of PBMCs from antibiotic-treated monkeys showed that the immune balance was affected by modulation of the expression of many functional genes,including IL-13,VCAM1,and LGR4.

Multilocus phylogeny suggests a distinct species status for the Nepal population of Assam macaques(Macaca assamensis):implications for evolution and conservation

Phylogenetic relationships within the sinica-group of macaques based on morphological,behavioral,and molecular characteristics have remained controversial.The Nepal population of Assam macaques(Macaca assamensis)(NPAM),the westernmost population of the species,is morphologically distinct but has never been used in phylogenetic analyses.Here,the phylogenetic relationship of NPAM with other congeners was tested using multiple mitochondrial and Ychromosomal loci.The divergence times and evolutionary genetic distances among macaques were also estimated.Results revealed two major mitochondrial DNA clades of macaques under the sinica-group:the first clade included M.thibetana,M.sinica,and eastern subspecies of Assam macaque(M.assamensis assamensis);the second clade included M.radiata together with species from the eastern and central Himalaya,namely,M.leucogenys,M.munzala,and NPAM.Among the second-clade species,NPAM was the first to diverge from the other members of the clade around 1.9 million years ago.Our results revealed that NPAM is phylogenetically distinct from the eastern Assam macaques and closer to other species and hence may represent a separate species.Because of its phylogenetic distinctiveness,isolated distribution,and small population size,the Nepal population of sinica-group macaques warrants detailed taxonomic revision and high conservation priority.

Social rank and cortisol among female rhesus macaques(Macaca mulatta)

In animal societies,some stressful events can lead to higher levels of physiological stress.Such stressors,like social rank,also predict an increased vulnerability to an array of diseases.However,the physiological relationship between social rank and stress varies between different species,as well as within groups of a single species.For example,dominant individuals are more socially stressed at times,while at other times it is the subordinate ones who experience this stress.Together,these variations make it difficult to assess disease vulnerability as connected to social interactions.In order to learn more about how physiological rank relationships vary between groups of a single species,cortisol measurements from hair samples were used to evaluate the effects of dominance rank on long-term stress levels in despotic and less stringent female rhesus macaque hierarchal groups.In despotic groups,cortisol levels were found not to be correlated with social rank,but a negative correlation was found between social rank and cortisol levels in less stringent hierarchies.Low ranking monkeys in less stringent groups secreted elevated levels of cortisol compared to higher ranking animals.These data suggest that variations in the strictness of the dominance hierarchy are determining factors in rank related stress physiology.The further consideration of nonhuman primate social system diversity and the linear degree of their hierarchies may allow for the development of valid rank-related stress models that will help increase our understanding and guide the development of new therapeutics for diseases related to human socioeconomic status.

Chromosome-level genome assembly of Tibetan macaque(Macaca thibetana) and species-specific structural variations

DEAR EDITOR,The Tibetan macaque(Macaca thibetana)is an endemic species in China belonging to the sinica group in the genus Macaca.Within the genus,it is the largest in body size and has a wide geographic distribution,with a population size second only to rhesus macaques(M.mulatta).Here,using PacBio long-read sequencing and Hi-C technology,we assembled the first chromosome-level genome of the Tibetan macaque,with a size of 2.82 Gb,contig N50 of 48.75 Mb,and scaffold N50 of 150.62 Mb,anchored to 22 chromosomes.

Experimental studies of autologous macaque vein endothelial cell transplantation onto blood vessel prostheses

Objective: To lay a theoretical foundation for the clinical application of autologous endothelial cell transplantation. Methods: Macaques endothelial cells from the superficial veins were cultivated in vitro for 13. 89±1. 36d. The multiplied macrophages were lined in vitro onto the luminal surface of expanded polytetrafluoroethylene(ePTFE) grafts precoated with fibrin glue and fibronectin, then cultivated again for 9 d. Fifteen macaque monkeyswere divided randomly into two groups. The common iliac arteries of the experimental animals (n-10) were replaced with endothelialized grafts, those of control (n=5) with untreated ones. Results: The number of endothelialcells increased 147. 93±88. 68 times. All the cells were diploid cells with a purity of 99%. The content of both 6keto-PGFla and vWF in the media showed no significant difference between the primary and subculture passages.Two hours and 9 days after cell seeding, the luminal surface of grafts was covered completely by a spindle-like endothelial monolayer and an even fibrin glue matrix could be seen underneath. Nine days after seeding, the densecondensation of cytoskeleton on the luminal and hasal side of the cells was apparently increased. Four weeks aftergrafts implantation 8/9 of the experimental grafts, with an intima thickness of 80±12 μm, were patent, while the5 control grafts were all occluded. Conclusion: Endothelial cell transplantation could effectively increase the patency rate of synthetic blood vessel prosthesis.

Macaques Contribute to New Breakthroughs in Autism Research

A China-U.S. joint research team has made new breakthroughs in developing nonhuman primate models for autism research. This does much to pave the way for possible drug discovery and gene therapy of the disorder. The research was conducted by scientists from the Shenzhen Institutes of Advanced Technology (SIAT) under the Chinese Academy of Sciences, Massachusetts Institute of Technology (MIT), Sun Yat-Sen University, and South China Agricultural University.

Endangered Wildlife Conservation Enhances Regional Economic Development: A Case Study of Tibetan Macaque (<i>Macaca thibetana</i>) and Fuxi Village in Mount Huangshan, China

The economic development of key biodiversity conservation areas and their conservation measures are underpinned by a mutually complementary and synergistic development model. Regional economic development depends on conservation awareness in biodiversity conservation areas. Moreover, the effectiveness of biodiversity conservation can be indicated by endangered wildlife conservation. This study investigated the current conservation of Huangshan Tibetan macaque (Macaca thibetana)—an endemic endangered species in the Mount Huangshan Scenic Area located in a biodiversity conservation hotspot in China, the conservation awareness of residents and visitors, and changes in local economic income through field survey. It provides inspiration and a characteristic demonstration to build a synergistic model of endangered wildlife conservation, biodiversity maintenance, and sustainable regional economic development.

Neural Integration of Audiovisual Sensory Inputs in Macaque Amygdala and Adjacent Regions

Integrating multisensory inputs to generate accurate perception and guide behavior is among the most critical functions of the brain.Subcortical regions such as the amygdala are involved in sensory processing including vision and audition,yet their roles in multisensory integration remain unclear.In this study,we systematically investigated the function of neurons in the amygdala and adjacent regions in integrating audiovisual sensory inputs using a semi-chronic multi-electrode array and multiple combinations of audiovisual stimuli.From a sample of 332 neurons,we showed the diverse response patterns to audiovisual stimuli and the neural characteristics of bimodal over unimodal modulation,which could be classified into four types with differentiated regional origins.Using the hierarchical clustering method,neurons were further clustered into five groups and associated with different integrating functions and sub-regions.Finally,regions distinguishing congruent and incongruent bimodal sensory inputs were identified.Overall,visual processing dominates audiovisual integration in the amygdala and adjacent regions.Our findings shed new light on the neural mechanisms of multisensory integration in the primate brain.

Genetic structure and recent population demographic history of Taihangshan macaque(Macaca mulatta tcheliensis),North China

Massive actions have been and are being taken into protecting the world’s primates from extinction,while the study of the properties of genetic diversity,demographic history,and ecological relationships will benefit the understand-ing of the long-term survival of a species.The Taihangshan macaque(Macaca mulatta tcheliensis),a subspecies of rhesus macaque(Macaca mulatta),is endemic to China and currently restricted to southern Mt.Taihangshan area.Herein,we evaluated the genetic diversity,population structure,and demographic history of this subspecies using mitochondrial(Cytb and high variable region I:HVR I)and nuclear markers(microsatellite loci)of 131 in-dividuals collected from 9 localities covering the distribution range of this subspecies.Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades,THS-east and THS-west.Low genetic diversity(π:0.00266±0.00016)but high haplotype diversity(Hd:0.80352±0.015)were detected in the Taihangshan macaques,particularly in THS-east.Analyses of demographic history suggested that the Taihangshan macaques experiencedfirst a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years.We suggest that bridging the neighbor populations(i.e.setting corridors)would facilitate the male-mediated geneflow and subsequently increase the genetic diversity of the Taihangshan macaque populations.

Differential Transcriptomic Landscapes of SARS-CoV-2 Variants in Multiple Organs from Infected Rhesus Macaques

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)caused the persistent coronavirus disease 2019(COVID-19)pandemic,which has resulted in millions of deaths worldwide and brought an enormous public health and global economic burden.The recurring global wave of infections has been exacerbated by growing variants of SARS-CoV-2.In this study,the virological characteristics of the original SARS-CoV-2 strain and its variants of concern(VOCs;including Alpha,Beta,and Delta)in vitro,as well as differential transcriptomic landscapes in multiple organs(lung,right ventricle,blood,cerebral cortex,and cerebellum)from the infected rhesus macaques,were elucidated.The original strain of SARS-CoV-2 caused a stronger innate immune response in host cells,and its VOCs markedly increased the levels of subgenomic RNAs,such as N,Orf9b,Orf6,and Orf7ab,which are known as the innate immune antagonists and the inhibitors of antiviral factors.Intriguingly,the original SARS-CoV-2 strain and Alpha variant induced larger alteration of RNA abundance in tissues of rhesus monkeys than Beta and Delta variants did.Moreover,a hyperinflammatory state and active immune response were shown in the right ventricles of rhesus monkeys by the up-regulation of inflammation-and immune-related RNAs.Furthermore,peripheral blood may mediate signaling transmission among tissues to coordinate the molecular changes in the infected individuals.Collectively,these data provide insights into the pathogenesis of COVID-19 at the early stage of infection by the original SARS-CoV-2 strain and its VOCs.

Allomaternal care and‘adoption'in an edge-of-range population of Taihangshan macaques in Northern China

Among mammals,mothers provide maternal care and protection starting from gestation and they ensure nutritional supply via lactation after birth(Clutton-Brock 1991).However,in social mammals,infants may also be cared for by a variety of other group members,such as fathers,siblings,a host of more distant relatives,and even unrelated individuals.Care by individuals other than the mother is known as allomaternal care(nonmaternal care)(Ishizuka 2020).Moreover,adoption of an orphaned infant is a special case of allomaternal care(Chaves et al.2020).