1471-2164-13-279 1471-2164 Research article <p>Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus</p> TchitchekNicolasnicolas.tchitchek@ihes.fr JacquelinBéatricebeatrice.jacquelin@pasteur.fr WinckerPatrickhuettel@mpipz.mpg.de DossatCarolecdossat@genoscope.cns.fr SilvaDaCorinnedasilva@genoscope.cns.fr WeissenbachJeanjean.weissenbach@genoscope.cns.fr BlancherAntoineblancher.a@chu-toulouse.fr Müller-TrutwinMichaelammuller@pasteur.fr BeneckeArndtarndt@ihes.fr

Institut des Hautes Études Scientifiques - Centre National de la Recherche Scientifique, Bures-sur-Yvette, France

Institut Pasteur, Unité de Régulation des Infections Rétrovirales, Paris, France

CEA, Institut de Génomique, Genoscope, Evry, France

Laboratoire d’Immunologie, CHU Rangueil, Toulouse, France

Vaccine Research Institute, Institut Mondor de Recherche Biomédicale, INSERM U955, Créteil, France

BMC Genomics
<p>Human and rodent genomics</p>
1471-2164 2012 13 1 279 http://www.biomedcentral.com/1471-2164/13/279 10.1186/1471-2164-13-27922726727
24201211620122262012 2012Tchitchek et al.; licensee BioMed Central Ltd.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background

African Green Monkeys (AGM) are amongst the most frequently used nonhuman primate models in clinical and biomedical research, nevertheless only few genomic resources exist for this species. Such information would be essential for the development of dedicated new generation technologies in fundamental and pre-clinical research using this model, and would deliver new insights into primate evolution.

Results

We have exhaustively sequenced an Expression Sequence Tag (EST) library made from a pool of Peripheral Blood Mononuclear Cells from sixteen Chlorocebus sabaeus monkeys. Twelve of them were infected with the Simian Immunodeficiency Virus. The mononuclear cells were or not stimulated in vitro with Concanavalin A, with lipopolysacharrides, or through mixed lymphocyte reaction in order to generate a representative and broad library of expressed sequences in immune cells. We report here 37,787 sequences, which were assembled into 14,410 contigs representing an estimated 12% of the C. sabaeus transcriptome. Using data from primate genome databases, 9,029 assembled sequences from C. sabaeus could be annotated. Sequences have been systematically aligned with ten cDNA references of primate species including Homo sapiens, Pan troglodytes, and Macaca mulatta to identify ortholog transcripts. For 506 transcripts, sequences were quasi-complete. In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.

Conclusions

The EST library we provide here will prove useful in gene annotation efforts for future sequencing of the African Green Monkey genomes. Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

Background

Nonhuman primates (NHP) are used in many areas of biomedical research because of their close relationship to humans. Indeed, for some human diseases, such as for HCV and HIV infections, they still represent the only available animal model. Moreover, optimal drug safety assessment and vaccine development are in many instances dependent on NHPs. Nowadays, the knowledge of their genome and transcriptome becomes critical for an efficient and parsimonious use of these models. The genome of the Chimpanzee (Pan troglodytes) 1 , Indian rhesus macaque (Indian Macaca mulatta) 2 , Orangutan (Pongo abelii 3 , Chinese rhesus macaque (Chinese Macaca mulatta 4 and Cynomolgus macaque (Macaca fascicularis 4 5 have been sequenced, and sequencing of several other NHP genomes is ongoing 6 7 . The African Green Monkey (AGM) is a widely used species in biomedical research for studies in the field of immunology, neuroscience (such as Parkinson’s disease 8 9 , cardiovascular disease 10 , cell biology 11 12 13 , pharmacology 14 and infectious diseases 15 16 17 18 19 . AGMs are one of the 40 natural hosts of the Simian Immunodeficiency Virus (SIV). They are particularly interesting models for studying of AIDS as this species is protected against the disease. Despite chronic infection by SIV, they generally do not develop any clinical symptoms 19 20 and hence are used to identify correlates of protection 19 20 21 . AGMs are divided into four species, named vervet (Chlorocebus pygerythrus), grivet (Chlorocebus aethiops), sabaeus (Chlorocebus sabaeus) and tantalus ( Chlorocebus tantalus). Among them, the vervet and sabaeus species have been most extensively studied 22 23 24 25 26 27 . Three hundred years ago, AGMs that belonged to the C. sabaeus species were transferred during slave trade from West/Central Africa to the Caribbean islands 28 . The only large breeding centers for AGMs are now located in these Islands, and the C. sabaeus species is now becoming the most studied AGM model for SIV and in biomedical research in general. In the context of viral infections such as with SIV, one of the main issues for the development of treatments and vaccines against human diseases, is to better understand the host transcriptomic responses of immune cells as the host immune response is mainly responsible for the outcome of the infection. Moreover, due to the important amount of genes expressed in case of activation, immune cells are relevant for revealing significant parts of the host transcriptome. So far, research involving AGMs, especially using gene expression profiling, were limited by the lack of sufficient gene sequence information and most studies were dependent on tools developed for human and more recently macaque species 7 29 30 . This limitation is a major problem since sequenced genes from AGMs revealed significant nucleotide differences from the human and even the macaque genomes 31 32 33 , and more information on AGM gene sequences are therefore urgently needed. It should be noted however, that the difference between NHP and humans is higher at the level of which gene is expressed, rather than at the nucleotide diversity level 34 . In addition, it has been shown that NHP cells express additional genes that are not expressed in humans 35 , and we have shown in a previous study that C. sabaeus express up to 16,000 genes in peripheral CD4+ cells, with 990 being specific of the species 36 . Annotating such sequences is challenging given that limited information is available and only few hundreds sequences of C. sabaeus are currently present in the GeneBank 37 database (Additional file 1: Figure S1). In this study, we constructed, sequenced and annotated a C. sabaeus EST (Expression Sequence Tag) library obtained from Peripheral Blood Mononuclear Cells (PBMC), as a tool for annotating AGM reference genomes, in order to allow the generation of technologies dedicated to analyze the immune responses in this species, as well as providing immediate valuable information to better understand the molecular and cellular mechanisms involved in AIDS resistance.

<p>Additional file 1</p>

Figure S1. Number of AGM sequences published over the last years. Progression of AGM sequences published during the last two decades: this graph shows the number of AGM nucleotide sequences entered over each 5 year period in the NCBI nucleotide database with the number of sequences to be published in our EST library.

Click here for file

Results

Composition and assembly of the Chlorocebus sabaeus PBMC EST library

Our aim was to obtain the sequence information for the genes expressed in C. sabaeus immune cells. In order to be representative, we collected fresh PBMC from twelve SIV-infected and four non infected animals. In order to identify as many distinct transcripts as possible, we in vitro stimulated these cells or not with Concanavalin A (ConA), lipopolysaccharides (LPS) and by mixed lymphocyte reactions (MLR), as these stimuli upregulate mRNA expression of many genes. The different stimuli were chosen to activate distinct cellular receptors (T cell receptor, Toll-like receptors) and stimulate distinct immune cells (lymphocytes and antigen-presenting cells). Total RNA preparations from the stimulated and unstimulated cells were pooled and a cDNA library constructed. Sequences were obtained and sequence quality filtering showed that 37,787 ESTs were present in the library. They had a mean length of 563 nucleotides per EST with a standard deviation of 167 nucleotides (Figure 1A). The 37,787 ESTs have been assembled into 3,853 contigs (overlapping or embedded ESTs) and 10,557 singletons (not assembled ESTs). The median number of ESTs per contig was 3 with some outlier contigs being composed of up to 941 ESTs (Figure 1B). The mean length of the 14,410 assembled and singletons ESTs averages at 943 nucleotides (Figure 1C). The total length represented by our AGM EST library is about 21.106 nucleotides and the total length of the assembled distinct transcripts 9.106 nucleotides. Since the total length of the known M. mulatta distinct transcripts corresponds to 72.106 nucleotides in the Ensembl database 38 , our AGM sequences represent 12% of the M. mulatta transcriptome and potentialy a similar fraction of the AGM transcriptome.

<p>Figure 1</p>

Composition and alignment distribution of the EST library and the assembled distinct transcripts

Composition and alignment distribution of the EST library and the assembled distinct transcripts. (A) Distribution of the length of the 37,787 original ESTs. The median EST length is equal to 618 nucleotides, the mean EST length is 563 nucleotides, and the standard deviation of the distribution is 167 nucleotides. (B) Distribution of the number of ESTs per contig in the ESTs assembly. The median number of ESTs per contig is equal to 3 ESTs, the mean number of ESTs per contig is 7 ESTs, and the standard deviation of the distribution is 27 ESTs. (C) Distribution of the length of the 14,410 distinct transcripts. The median sequence length is equal to 847 nucleotides, the mean sequence length is 943 nucleotides, and the standard deviation of the distribution is 388 nucleotides. The contribution of the assembled ESTs is shown in red while the contribution of singleton ESTs is shown in blue. (D) Distribution of the number of matched cDNA reference-mapped for both the 37,787 original ESTs (shown in yellow) and the 14,410 distinct transcripts (shown in green).

Inter- and intra- species comparisons

We then compared the ESTs to available transcriptomes of other primate species for annotation purposes and for quantification of transcript homologs. In order to get a general as well as a specific view, we used both the total 37,787 ESTs of the original library and the assembled distinct transcript library. They were aligned to available cDNA datasets of the following ten primate species: Callithrix jacchus (Ouistiti), Gorilla gorilla (Gorilla), Homo sapiens (Human), M. mulatta, Microcebus murinus (Mouse lemur), Nomascus leucogeny (Gibbon), Otolemur garnettii (Bushbaby), P. troglodytes, P. abelii, and Tarsuis syrichta (Tarsier) (Table 1). We applied stringent criteria for alignments. Thus, high-quality alignments have been filtered to only keep for each EST the best alignment for each species which maps at least 80% of the ESTs. 31,211 of the 37,787 total ESTs and 9,029 of the 14,410 assembled sequences could be aligned on cDNAs of at least one species. 29,191 of the total ESTs and 7,985 of the assembled ESTs have been aligned on at least two cDNA references. 1,628 of the total ESTs and 135 of the assembled ESTs have been aligned on all the 10 species, while 6,576 of the total ESTs and 5,384 of the assembled ESTs could not be mapped to any cDNA reference sets and are then potentially specific to the C. sabaeus transcriptome or highly diverse orthologs (Figure 1D). ESTs of the total and assembled AGM libraries have also been aligned to the draft assembly of the M. fascicularis genome 5 and a sequencing read library of the C. sabaeus genome 39 . Alignment results have been filtered to only keep for each EST the 5 best mapped reads when possible of the C. sabaeus draft scaffold genome, and the best mapped genomic position on the M. fascicularis draft assembly genome. Table 2 provides a summary of the results of the alignments with the 10 cDNA references and the 2 draft genomes. The highest number of aligned ESTs for both

<p>Table 1</p>

Species name

Release version

Number of transcripts

Number of genes

For each species, the release version of the cDNA reference used and the number of transcripts and genes that composed the cDNA reference are indicated. All the cDNA references have been retrieved from the Ensembl 38 database.

C. jacchus

Cjacchus3.2.1.63

55,137

32,339

G. gorilla

gorGor3.63

35,727

29,216

H. sapiens

GRCh37.63

174,598

53,894

M. mulatta

MMUL_1.63

44,725

30,247

M. murinus

micMur1.63

25,035

25,036

N. leucogeny

Nleu1.0.63

31,550

26,526

O. garnettii

BUSHBABY1.63

22,804

22,800

P. troglodytes

CHIMP2.1.63

41,488

27,116

P. abelii

PPYG2.63

31,566

28,088

T. syrichta

tarSyr1.63

20,261

20,215

Composition details of the cDNA references

<p>Table 2</p>

Species name

Target type

Original ESTs

Assembled and singleton ESTs

a.e.

m.t.

m.g.

a.e.

m.t.

m.g.

For both the 37,787 originals ESTs and the 14,410 distinct transcripts, the number of aligned ESTs (a.e.) on the cDNA references (cDNA ref.), draft scaffold genome (d. scaf.), and draft assembly genome (d. assem.) are indicated. The number of mapped transcripts (m.t.) and mapped genes (m.g.) are also indicated for the cDNA references.

C. jacchus

cDNA ref.

24,461 (64.73%)

5,951

5,051

5,954 (41.31%)

4,928

4,504

G. gorilla

cDNA ref.

23,633 (62.54%)

5,162

4,948

6,008 (41.69%)

4,622

4,527

H. sapiens

cDNA ref.

30,117 (79.70%)

9,208

6,529

8,708 (60.43%)

7,316

6,128

M. mulatta

cDNA ref.

24,213 (64.07%)

5,439

4,763

5,657 (39,25%)

4,585

4,273

M. murinus

cDNA ref.

8,618 (22.80%)

1,770

1,770

1,240 (08.60%)

1,138

1,138

N. leucogeny

cDNA ref.

22,600 (59.80%)

4,949

4,749

5,672 (39.36%)

4,389

4,296

O. garnettii

cDNA ref.

7,564 (20.01%)

1,431

1,431

930 (06.45%)

861

861

P. troglodytes

cDNA ref.

25,196 (66.67%)

5,699

5,156

6,332 (43.94%)

5,012

4,756

P. abelii

cDNA ref.

18,904 (50.02%)

4,149

3,989

4,274 (29.65%)

3,415

3,340

T. syrichta

cDNA ref.

5,327 (14.09%)

1,348

1,346

908 (06.30%)

854

854

C. sabaeus

d. scaf.

37,409 (98.99%)

14,139 (98,11%)

M. fascicularis

d. assem.

35,686 (94,44%)

13,392 (92.93%)

Alignment results of ESTs on the different cDNA references and genomes

the original and the assembled ESTs was found for the H. sapiens (∼80% of the original ESTs and ∼60% of the distinct transcripts) probably due to the relatively higher degree of investigation of this genome. The higher frequence as to compared to the ones of NHP is thus due to the broader sequence information from human genomes and does not reflect the biological distances between the species. The C. jacchus, G. gorilla, M. mulatta, N. leucogeny, P. troglodytes species had relatively high-proportions of aligned ESTs (∼63% of the original ESTs and ∼41% of the distinct transcripts), and the M. murinus, O. garnettii, T. syrichta species had equally low-proportions of aligned ESTs (∼18% of the original library and ∼7% of the distinct transcripts). The P. abelii species had an intermediate proportion of aligned ESTs (∼50% of the library and ∼30% of the distinct transcripts). We then performed Venn Diagrams between AGM and cDNA of the NHP species showing the highest proportions of aligned ESTs (M. mulatta, N. leucogeny, P. troglodytes, and H. sapiens), 31,005 of the 37,787 original ESTs and 8,909 of the 14,410 distinct transcrips could been aligned on at least one of the cDNA references (Figures 2A and 2B). 23,450 of the original ESTs (62.05%) were shared between the H. sapiens and M. mulatta species. AGM shared 25,196 sequences (66.67%) with those of M. mulatta, and 17,743 (46.95%) with the four species. The number of mapped ESTs on the C. sabaeus and M. fascicularis draft genomes is highly significant for both the original ESTs and the assembled and singletons ESTs, and almost the totality of the ESTs are commonly mapped ESTs between the two genomes (Figures 2A and 2B). Note that the alignment to the draft genomes was performed using low-specificity alignment parameters and thus is not directly comparable to the alignments of the EST libraries. Overall, while giving different specific alignment information, the number of mapped transcripts and mapped genes for both the 37,787 originals ESTs and the 14,410 distinct transcripts are convergent in the number of mapped genes and proportional with the genomic distances that exist among these species.

<p>Figure 2</p>

Inter- and intra- species alignment comparisons

Inter- and intra- species alignment comparisons. (A) 4-set Venn diagram showing the intersections among the 4 sets of original ESTs aligned on the H. sapiens, M. mulatta, P. troglodytes, and P. abelii species, and 2-set Venn diagram showing the intersections between the 2 sets of original ESTs aligned over the C. sabaeus and M. fascicularis species. (B) Idem as A for the distinct transcripts.

Specific comparison with the Macaca mulatta transcriptome

The M. mulatta species is the closest primate species to the C. sabaeus for which significant genomic information is available. In order to gain additional information about the transcript fragments that we provide, we annotated them with the particular section positions of the messenger RNAs available for the M. mulatta species. We specified for each EST of the assembled library the positions of the 5’-untranslated region (5’UTR), coding DNA sequence (CDS), and 3’-untranslated region (3’UTR) based on the M. mulatta cDNA reference annotations. Among the 14,410 assembled ESTs, 11,211 could be annotated: 6,244 ESTs with the 5’UTR, 9,657 ESTs with the CDS, and 5,313 ESTs with the 3’UTR. We report 506 M. mulatta transcripts that have been mapped to more than 90% by an EST (Additional file 2: Table S1). CXCL10 (Figure 3) and S100A4 (Additional file 3: Figure S2) are part of these transcripts and given as examples.

<p>Additional file 2</p>

Table S1. List of the highly covered Macaca mulatta ortholog transcripts. List of the 506 M. mulatta ortholog transcripts that have been highly covered an assembled EST. For each M. mulatta transcript, the Ensembl transcript Id, the gene symbol, and the assembled EST that mapped the transcript at least at 90% are given.

Click here for file

<p>Additional file 3</p>

Figure S2. Alignment details for the S100A4 gene. Alignment details for the S100 calcium binding protein A4 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000015358). Assembled ESTs have been aligned at different positions of the gene: (1) Contig3147. Same legend and nomenclature as in Figure 3.

Click here for file

<p>Figure 3</p>

Alignment details for the CXCL10 gene

Alignment details for the CXCL10 gene. Alignment details for the C-X-C motif chemokine 10 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000029391). Assembled ESTs have been aligned at different positions of the gene: (1) Contig2229.

Quantification of expressed sequences and functional pathway analysis of the EST library

In order to have a quantitative view of the expressed sequences of the C. sabaeus PBMC, we identified the most expressed transcripts in our EST library based on the M. mulatta homolog transcripts. Based on the 44,725 transcripts of the M. mulatta cDNA reference and the 14,410 ESTs of the original ESTs library, we calculated for each transcript the number of sequences mapped and obtained a list of the 50 most expressed M. mulatta ortholog transcripts in our EST library (Table 3). Among these most expressed transcripts, the hemoglobin beta (HBB) and alpha (HBA) genes were present, which might reflect a red blood cells contaminations of the PBMC, as well as more specific immune-related genes, such as CD74 and Granzyme B (GZMB). Some EST which correspond to genes which play an important role in immune responses against pathogens have been aligned: IRF7 (Figure 4), CD4 (Additional file 4: Figure S3), IFNG (Additional file 5: Figure S4), IFNGR1 (Additional file 6: Figure S5), IFNGR2 (Additional file 7: Figure S6). For all these transcripts, EST alignment positions as well as protein domains are given. Furthermore, in order to identify the over-represented pathways in our AGM EST library, we performed a functional canonical pathway analysis based on the list of the 9,208 H. sapiens transcripts uniquely mapped by the 37,787 original ESTs. Most of the canonical pathways found as statistically significantly over-represented are related to B and T cell signaling, and immune response pathways (Table 4). For instance, the “CD28 signaling in T Helper Cells”, “iCOS-iCOSL signaling in T Helper Cells”, “B Cell receptor Signaling” (Additional file 8: Figure S7A), and “T Cell receptor signaling” (Additional file 8: Figure S7B) pathways belong to the list of pathways found as significantly over-represented in our AGM library, as well as the “Glucocorticoid receptor signaling”, “Role of NFAT in regulation of the immune response” (Additional file 9: Figure S8A), “Antigen presentation pathway” (Additional file 9: Figure S8B), “JAK/STAT signaling”, and many different “Interleukin signaling” pathways. As a result of the in vitro stimulation of SIV-infected PBMC, the “NF-κB Activation by viruses” (Additional file 10: Figure S9A) and “Induction of apoptosis by HIV-1” (Additional file 10: Figure S9B) pathways are also significantly over-represented. Consistent with the stimulation by LPS, the “Interferon Signaling” (Figure 5A) and “Toll-like Receptor Signaling” (Figure 5B) pathways are also found significantly over-represented. Finally, ConA is capable of triggering positive selection in mature T cells by cross-linking the TCR with high avidity 40 41 and we found 8 pathways corresponding to these functions being induced (Table 4). The over-representation of gene transcripts belonging to these pathways of the immune system further indicates that this library is a valuable resource for profiling global gene expression in AGM immune cells. Overall, these gene and pathway information are consistent with what we could expect from an EST PBMC library.

<p>Additional file 4</p>

Figure S3. Alignment details for the CD4 gene. Alignment details for the CD4 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000018518). Assembled ESTs have been aligned at different positions of the gene: (1) PP0ADA62YL02FM1. Same legend and nomenclature as in Figure 3.

Click here for file

<p>Additional file 5</p>

Figure S4. Alignment details for the IFNG gene. Alignment details for the Interferon-gamma gene of the M. mulatta species (Ensembl ID: ENSMMUT00000027007). Assembled ESTs have been aligned at different positions of the gene: (1) Contig3283 (2) PP0ADA26YB24FM1. Same legend and nomenclature as in Figure 3.

Click here for file

<p>Additional file 6</p>

Figure S5. Alignment details for the IFNGR1 gene. Alignment details for the Interferon Gamma Receptor 1 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000016941). Assembled ESTs have been aligned at different positions of the gene: (1) Contig705 (2) PP0ADA55YK24FM1. Same legend and nomenclature as in Figure 3.

Click here for file

<p>Additional file 7</p>

Figure S6. Alignment details for the IFNGR2 gene. Alignment details for the Interferon Gamma Receptor 2 gene of the M. mulatta species (Ensembl ID: ENSMMUG00000005508). Assembled ESTs have been aligned at different positions of the gene: (1) PP0ADA19YK11FM1. Same legend and nomenclature as in Figure 3.

Click here for file

<p>Additional file 8</p>

Figure S7. Representation of the “B cell receptor signaling” and “T cell receptor signaling” pathways. (A) Representation of the “B cell receptor signaling” pathway. (B) Representation of the “T cell receptor signaling” pathway. Same legend and nomenclature as in Figure 5.

Click here for file

<p>Additional file 9</p>

Figure S8. Representation of the “Role of NFAT in regulation of the immune response” and “Antigen presentation” pathways. (A) Representation of the “Role of NFAT in regulation of the immune response” pathway. (B) Representation of the “Antigen presentation” pathway. Same legend and nomenclature as in Figure 5.

Click here for file

<p>Additional file 10</p>

Figure S9. Representation of the “NF-κB activation by viruses” and “Induction of apoptosis by HIV-1” pathways. (A) Representation of the “NF-κB activation by viruses” pathway. (B) Representation of the “Induction of apoptosis by HIV-1” pathway. Same legend and nomenclature as in Figure 5.

Click here for file

<p>Table 3</p>

Transcript ID

Gene symbol

Gene description

Count

For each of the 44,725 transcripts of the M. mulatta cDNA reference, we calculated the number of original ESTs mapped, and obtained a list of the 50 most expressed M. mulatta ortholog transcripts in our EST library. For each of the most expressed M. mulatta ortholog transcript, the Ensembl transcript ID, the gene symbol, the gene description, and the number of mapped ESTs is given.

ENSMMUT00000006876

HBB_MACMU

Hemoglobin subunit beta

941

ENSMMUT00000045385

LOC712934

699

ENSMMUT00000012750

CD74

526

ENSMMUT00000015401

Q3YAP9_MACMU

eukaryotic translation elongation factor 1 alpha 1

519

ENSMMUT00000000859

HBA_MACMU

Hemoglobin subunit alpha

296

ENSMMUT00000017004

LOC712553

257

ENSMMUT00000038286

MTRNR2-like (LOC100499503)

232

ENSMMUT00000005322

B2MG_MACMU

Beta-2-microglobulin

212

ENSMMUT00000005104

LOC708526

208

ENSMMUT00000043999

RPL3

ribosomal protein L3

208

ENSMMUT00000038271

COX2_MACMU

Cytochrome c oxidase subunit 2

194

ENSMMUT00000027050

DRA_MACMU

Mamu class II histocompatibility antigen, DR alpha chain

191

ENSMMUT00000038268

Q6IYH3_MACMU

ATP synthase F0 subunit 6

185

ENSMMUT00000029930

Q3YAP9_MACMU

eukaryotic translation elongation factor 1 alpha 1

173

ENSMMUT00000045510

Q9GMG8_MACMU

acidic ribosomal phosphoprotein PO

173

ENSMMUT00000023666

LOC710590

155

ENSMMUT00000039116

LOC714576

144

ENSMMUT00000027943

B0Z9V5_MACMU

major histocompatibility complex, class I, E

143

ENSMMUT00000038267

Q6IYH2_MACMU

cytochrome c oxidase subunit III

135

ENSMMUT00000010560

B5MBT6_MACMU

ribosomal protein L13a

133

ENSMMUT00000032800

UBB

polyubiquitin-B

133

ENSMMUT00000010558

Q3YAQ2_MACMU

ribosomal protein S11

131

ENSMMUT00000011109

ribosomal protein S2 (RPS2)

131

ENSMMUT00000015005

LOC711043

129

ENSMMUT00000020179

GZMB

126

ENSMMUT00000033466

Q6IEB8_MACMU

interferon alpha-inducible protein 27

123

ENSMMUT00000038664

LOC719242

123

ENSMMUT00000008204

Q6IUG4_MACMU

glyceraldehyde-3-phosphate dehydrogenase

122

ENSMMUT00000029999

RPS20

116

ENSMMUT00000032342

TPT1

116

ENSMMUT00000012806

Q9GMG8_MACMU

acidic ribosomal phosphoprotein PO

115

ENSMMUT00000005819

SRGN

107

ENSMMUT00000040341

Q9MXS5_MACMU

MHC class I antigen

106

ENSMMUT00000014609

LOC711421

105

ENSMMUT00000004034

LOC710901

104

ENSMMUT00000009232

EEF1G

eukaryotic translation elongation factor 1 gamma

103

ENSMMUT00000027208

A2TJ58_MACMU

major histocompatibility complex, class II, DP alpha

94

ENSMMUT00000013155

Q6RHR8_MACMU

actin, cytoplasmic 1

93

ENSMMUT00000041082

E0WHM2_MACMU

MHC class I antigen

92

ENSMMUT00000043841

RPS3

89

ENSMMUT00000022628

A8QWZ5_MACMU

MHC class I antigen

86

ENSMMUT00000000617

RPL12

60S ribosomal protein L12

85

ENSMMUT00000018897

RPS6

84

ENSMMUT00000025324

ARHGDIB

79

ENSMMUT00000011502

A3F8W8_MACMU

MHC class II antigen

77

ENSMMUT00000040916

A3F8W8_MACMU

MHC class II antigen

76

ENSMMUT00000005540

LOC718964

75

ENSMMUT00000018430

75

ENSMMUT00000041189

A9XN15_MACMU

major histocompatibility complex, class I, A

73

ENSMMUT00000015586

Q6UIS1_MACMU

Actin beta subunit

72

List of the 50 most expressed M. mulatta ortholog transcripts in present EST library

<p>Figure 4</p>

Alignment details for the the IRF7 gene

Alignment details for the the IRF7 gene. Alignment details for the Interferon regulatory factor 7 gene of the M. mulatta species (Ensembl ID: ENSMMUT00000009923). Assembled ESTs have been aligned at different positions of the gene: (1) Contig3553, (2) Contig866, (3) Contig1898. Same legend and nomenclature as in Figure 3.

<p>Table 4</p>

Canonical pathway

−log (q-value)

gen a / gen b

List of the top 50 canonical pathways found as statistically significantly over-represented in the functional pathway analysis of the EST library. For each canonical pathway, the associated multiple testing corrected p-value (shown as −log(q-value)) is indicated as well as the ratio between the number ge n a of genes of the pathway mapped by the EST library and the total number ge n b of genes defining the pathway.

Protein Ubiquitination Pathway

16.80

148/274 (54%)

Glucocorticoid Receptor Signaling

16.80

148/295 (50%)

Oxidative Phosphorylation

15.00

92/159 (58%)

Mitochondrial Dysfunction

14.00

86/175 (49%)

CD28 Signaling in T Helper Cells

13.70

77/132 (58%)

Regulation of eIF4 and p70S6K Signaling

11.90

69/132 (52%)

Role of NFAT in Regulation of the Immune Response

10.70

97/200 (49%)

EIF2 Signaling

10.60

57/101 (56%)

PI3K/AKT Signaling

10.50

73/140 (52%)

iCOS-iCOSL Signaling in T Helper Cells

10.50

67/122 (55%)

B Cell Receptor Signaling

10.10

83/156 (53%)

Regulation of IL-2 Expression in Lymphocytes

9.70

53/89 (60%)

Integrin Signaling

9.48

104/209 (50%)

PKCθ Signaling in T Lymphocytes

8.93

68/142 (48%)

Hypoxia Signaling in the Cardiovascular System

8.93

46/68 (68%)

CTLA4 Signaling in Cytotoxic T Lymphocytes

8.52

57/98 (58%)

mTOR Signaling

8.51

79/162 (49%)

T Cell Receptor Signaling

8.43

59/109 (54%)

Type I Diabetes Mellitus Signaling

8.32

64/121 (53%)

Production of Nitric Oxide and ROS in Macrophages

8.32

83/187 (44%)

Ubiquinone Biosynthesis

8.05

45/112 (40%)

Molecular Mechanisms of Cancer

7.64

152/377 (40%)

Estrogen Receptor Signaling

7.54

70/136 (51%)

Antigen Presentation Pathway

7.20

30/43 (70%)

Apoptosis Signaling

7.19

53/96 (55%)

G2/M DNA Damage Checkpoint Regulation

7.19

32/49 (65%)

Prostate Cancer Signaling

6.96

49/97 (51%)

Phospholipase C Signaling

6.79

109/260 (42%)

Huntington’s Disease Signaling

6.78

104/238 (44%)

Chronic Myeloid Leukemia Signaling

6.65

54/105 (51%)

Pancreatic Adenocarcinoma Signaling

6.61

59/119 (50%)

IL-8 Signaling

6.60

86/193 (45%)

PI3K Signaling in B Lymphocytes

6.50

69/143 (48%)

Breast Cancer Regulation by Stathmin1

6.49

93/208 (45%)

IL-2 Signaling

6.31

35/58 (60%)

NF-κB Activation by Viruses

6.26

44/82 (54%)

IL-15 Signaling

6.23

39/68 (57%)

T Helper Cell Differentiation

6.15

42/72 (58%)

TREM1 Signaling

6.05

35/66 (53%)

Fcγ Receptor-mediated Phagocytosis in Macrophages

5.98

52/102 (51%)

Pyrimidine Metabolism

5.85

70/213 (33%)

GM-CSF Signaling

5.69

38/67 (57%)

Induction of Apoptosis by HIV1

5.64

37/66 (56%)

Dendritic Cell Maturation

5.64

78/188 (41%)

NRF2-mediated Oxidative Stress Response

5.63

86/193 (45%)

Purine Metabolism

5.56

117/391 (30%)

fMLP Signaling in Neutrophils

5.50

57/128 (45%)

JAK/Stat Signaling

5.42

37/64 (58%)

HMGB1 Signaling

5.40

51/100 (51%)

IL-4 Signaling

5.40

40/73 (55%)

Top 50 canonical pathways found as significantly over-represented in present EST library

<p>Figure 5</p>

Representation of the “Interferon Signaling” and “Toll-like Receptor Signaling” pathways

Representation of the “Interferon Signaling” and “Toll-like Receptor Signaling” pathways. (A) Representation of the “Interferon Signaling” pathway. (B) Representation of the “Toll-like Receptor Signaling” pathway. Genes present in the EST library are shown in gray.

Analysis of the inter-species genomic relationships

Analysis of genomic relationships among species is an important way for studying evolution of genomic features. The relationships of the C. sabaeus EST with the 10 above described primate species for which the cDNA references were available have been quantified. For each one of the 1,628 ESTs aligned on all the cDNA references, multiple sequence alignment scores have been computed. Based on these pairwise alignment scores, an average genomic distance matrix has been computed (Table 5) and a phylogenetic tree constructed (Figure 6A). As it would be expected, the H. sapiens and P. troglodytes are clustered together, as it is also the case for the C. sabaeus and M. mulatta. The G. gorilla, P. abelii, and N. leucogeny were located between these two clusters, and the C. jacchus, M. murinus, O. garnettii, and T. syrichta are segregated from other species. By comparing only to the more related species, phylogenetic trees have also been computed with a higher number of AGM ESTs with all the 14,410 assembled transcripts (Figure 6B). Finally, trees have been constructed for specific sections of the transcripts: 5’UTR regions (Figure 6C), CDS sections (Figure 6D), and 3’UTR regions (Figure 6E). Both the phylogenetic trees restricted on the CDS and 3’UTR sections show a clusterisation of the C. sabaeus with the M. mulatta and a strong segregation with other species. Interestingly, the phylogenetic tree restricted on the 5’UTR sections revealed a different shape. C. sabaeus and the N. leucogeny species clustered together, suggesting distinct selective pressures in the 5’UTR as compared to other regions.

<p>Table 5</p>

C. sabaeus

G. gorilla

H. sapiens

M. mulatta

M. murinus

N. leucogeny

O. garnettii

P. troglodytes

P. abelii

T. syrichta

Pairwise genomic distance matrix computed using the ESTs of the original library and the cDNA references of the 10 primates species for which the cDNA references were available. For pairs of species, the average multiple alignment score calculated over the 1,628 commonly aligned sequences is given. Scores have been rescaled by multiplication by 104.

C. jacchus

474

445

430

474

804

445

906

442

442

862

C. sabaeus

272

260

140

751

284

856

272

289

832

G. gorilla

103

263

741

191

858

117

200

830

H. sapiens

248

712

173

835

78

176

808

M. mulatta

754

266

873

259

290

842

M. murinus

753

770

734

743

897

N. leucogeny

876

185

224

842

O. garnettii

850

880

1006

P. troglodytes

191

824

P. abelii

859

Pairwise genomic distance matrix of the 11 primate species

<p>Figure 6</p>

Evolutionary relationships among primates species

Evolutionary relationships among primates species. (A) phylogenetic tree of the 11 primate species for which the cDNA references were available calculated based on the 1,628 common original ESTs. (B) phylogenetic tree of the old world monkeys and human species calculated based on the 8,788 common assembled ESTs. (C) phylogenetic tree of the old world monkeys and human restricted to the 5’UTR of the transcripts calculated based on the 1,016 common assembled ESTs. (D) phylogenetic tree of the old world monkeys and human restricted to the coding sequence of the transcripts calculated based on the 8,024 common assembled ESTs. (E) phylogenetic tree of the old world monkeys and human restricted to the 3’UTR of the transcripts calculated based on the 2,209 common assembled ESTs.

Discussion

AGMs have provided useful animal models in biomedical research for many years 17 42 43 44 45 46 47 48 49 50 . They are also becoming a more and more essential model to the study of human biology and disease, such as neurological disorders 51 52 and AIDS 19 53 . Several studies could not be conducted so far because of the insufficiency of genomic resources on this primate 7 . This is a major limitation in view of the information that new generation technologies can offer for the progress in development of strategies to prevent or treat human diseases. The growing interest for this model is shown through the increase of the number of sequences published in the NCBI nucleotide database for this species every year (Additional file 1: Figure S1) and the sequencing of its genome which is underway. Nevertheless, our recent survey (as of January 11, 2012) showed that while there were 11,413,043 and 225,854 nucleotide sequences available for H. sapiens and M. mulatta, respectively, there were still only 2,527 nucleotide sequences for AGM in the databases. The primary goal of this study was to enhance the development of an AGM genomic resource through the construction, sequencing and characterization of a PBMC cDNA library of AGM (C. sabaeus). The results could be used to expand genomic research activities on this species.

We focused here on the construction of a cDNA library on blood immune cells (PBMC) in order to get as much immune defense genes as possible which could help to the study of several disease mechanisms such as the understanding of AIDS resistance in AGM. Therefore, to increase the expression of such genes, the cells were challenged or not with immune-relevant stimuli (ConA, LPS, MLR). We also chose to work on both, SIV-infected and non-infected animals, in order to eventually reveal new genes that might have a unique role in AIDS resistance in this natural host. The sequencing of the cDNAs yielded 37,787 ESTs with 14,410 assembled and singletons ESTs which cover 12% of the transcriptome. For annotation purpose, we aligned the 14,410 cDNA sequences of our library to the known cDNA libraries of 10 other primate species including the human one. Of the 31,005 ESTs identified, as many as 6,576 ESTs did not match any gene reported in the database. This high number of novel sequences might be due to the fact that the genomes of the other NHP species are not sufficiently annotated yet. However, a few of them might be true new gene candidates. Indeed, the stimulation used might have revealed a number of silent genes only expressed under the condition of infection.

As one would expect, at the CDS level, the divergence between C. sabaeus and M. mulatta was lower than between C. sabaeus and the other primate species. The gene distance at the non-coding regions was higher than in the CDS and higher for 5’UTR than 3’UTR. Interestingly, the 5’UTR of C. sabaeus did not cluster any more with M. mulatta, at least not consistently. This is in line with the fact that on average, 5’ and 3’ UTRs are less conserved across species than protein-coding sequences, with the 5’UTR being the most divergent, but still more conserved than untranscribed sequences 54 55 . It has been shown that high differences in the 5’UTR of orthologous genes correlate with their expression levels 56 . Indeed, this region is rich in regulatory elements. Changes in the regulation of gene expression levels play an important role in phenotypic diversity among closely related organisms 57 58 . The high distances observed at the 5’UTR region between the different primate species studied here might reflect part of these changes (Additional file 11: Table S2). However, we can not exclude that on one hand, our analyses might have misestimated the gene distance of UTR or ESTs in general, between the C. sabaeus and other species, as the length of the ESTs of our library are shorter (943 nucleotides) than the average length of human and macaque cDNAs (1,500 nucleotides) in the databases. On the other hand we might have overestimated this distance as compared to the rest of the transcriptome because the genes included in this library are mostly immune-related, thus among the most known divergent genes 59 .

<p>Additional file 11</p>

Table S2. Genomic distance matrix between the Chlorocebus sabaeus species and the old world monkeys and humans species. Genomic distance matrix computed between the ESTs of the original library and the mapped sequences of 7 old world monkey and human cDNA references restricted or not to specific regions of the transcripts (5’UTR, coding sequence, 3’UTR). For each comparing, the average multiple alignment score calculated over the commonly aligned sequences (c.a.s.) is given. Scores have been rescaled by multiplication by 104.

Click here for file

To further analyze the library, we determined the biological pathways represented by the 14,410 annotated ESTs. Among more general pathways (protein ubiquitination pathway, mitochondrial pathway), many pathways were related to the immune system (T cell activation, B cell activation) indicating the immune-specificity of the starting cells. The immune pathways appear well conserved in AGM, with most of the key components found in our library under the stimulation condition used (Figure 5 and Additional file 8: Figures S7, Additional file 9: Figures S8 and Additional file 10: Figures S9). Ubiquitously expressed genes, such as ribosomal proteins, housekeeping genes and mitochondrial pathway, are also included in this library and could be useful when using cell lines derived from AGM such as COS-7 and Vero cells. We studied in more detail genes which are of major importance for host immune defenses, such as IFN-γ, IFNGR, CXCL10 and IRF7 60 61 62 . For the IFN-γreceptor (IFNGR), it has been shown in humans that any variation having a significant impact on IFNGR function is not tolerated 63 . Therefore, the deletion observed in the cytoplasmic tail of IFNGR1 in AGM as compared to macaque might either not have any functional consequence on this pathway or give to this species a yet unknown evolutionary advantage. Thus, it would be interesting to compare the sequence of AGM IFNGR1 with other SIV natural hosts in order to evaluate if this might play a role in AIDS resistance. CXCL10 (or IP-10) is a chemokine involved in the recruitment of cells of the immune system to sites of inflammation and is induced by IFN-α and IFN-γ 60 . Alteration of IP-10 expression has been associated with inflammatory diseases including infectious diseases, immune dysfunction and tumor development 64 65 . We did not find any difference at the amino acid level between the CXCL10 from C. sabaeus and the one from M. mulatta. This conservation suggests that any variation having an impact on CXCL10 function could be deleterious. IRF7 encodes a transcription factor which plays a role in the activation of virus-inducible cellular genes, including the type I interferon genes. The partial sequences from our library did not show the same mutations that were suggested to play a role in AIDS-resistance in another SIV-natural host, the sooty mangabey 66 . The mutations in IRF7 reported in one SM 66 , were however also either not confirmed when studied in a large number of SM animals or found to be non-fixed and with no effects on the phenotype even when present in homozygosity (Johnson Z, Silvestri G, and Bosinger SE, personal communication). However, as this is not the same species, the mutations could be at other sites, or the mechanisms of AIDS resistance might be different between AGM and sooty mangabey. As our library was constructed on a pool of cells from 16 different animals, the sequences obtained are not representative of the inter-individual variability and need to be verified on the individual level for further studies.

To our knowledge, this is the first time that abundant genetic information on AGM is given. In this study, a total of 37,787 ESTs were sequenced, from which 14,410 contigs and singletons were identified, covering 12% of the AGM transcriptome. Moreover, this cDNA library provides both a large collection of novel transcripts and a detailed annotation of immune genes. The high volume of apparently novel AGM sequences suggests that our data could be a useful resource for future genomic investigation.

Methods

Construction and sequencing of the EST library

Twelve SIV-infected and four non-infected C. sabaeus (from Caribbean islands) were used in this study. The Central Committee for Animals at Institut Pasteur, Paris, France, reviewed and approved the use and care of animals. The experiments were performed according to national and European guidelines. Whole blood was collected from monkeys under anesthesia in heparinized tubes. PBMC were isolated from whole blood by density gradient centrifugation using the Lymphocyte Separation Medium 1077 (PAA Laboratories GmbH) and activated or not with different stimuli in RPMI-1640 with 10% fetal calf serum. For ConA activation (from Canavalia ensiformis (Sigma-Aldrich, St. Louis, MO, USA)): 4.106 of isolated PBMC were plated with 10μg.m l −1 of ConA for 2, 6, 24, 36 or 72h. For LPS (E.Coli 0111:B4 Sigma (L2630)) activation: 4.106 of isolated PBMC were plated with 10μg.m l −1 of LPS for 2, 6, 24, 36 or 72 hours. The MLR were done by mixing 4.106 of isolated PBMC with 4.105 PBMC from another animal for 2, 6, 24, 36 or 72h. Unstimulated cells were also kept for further RNA extraction. Total RNA was extracted from harvested cells by using the RNeasy®; Mini Kit (Qiagen, Courtaboeuf, France) following the manufacturer’s instructions. Briefly, cells were lysed in 350μl of RLT buffer, run over a QiaShredder column (Qiagen) to ensure homogeneous lysis, and resuspended in 30μl of sterile water. We added a DNase-RNase free (Qiagen) treatment on the column to eliminate any potential DNA contamination of RNA preparations. The quality and concentration of RNA was assessed as before 36 . The libraries were plated, arrayed robotically and bacterial clones have their plasmid DNA amplified using phi29 polymerase. The plasmids were end-sequenced by the Genoscope using BigDye Termination kits on Applied Biosystems 3730xl DNA Analysers.

EST quality filtering

Poly-A and poly-T tails have been trimmed from the sequenced ESTs by using the trimest tool 67 (default parameters have been used) while starting and ending terminal N’s have been trimmed from the sequences using the trimseq tool 67 (a threshold cutoff parameter of 20% of Ns in a window of 30 nucleotides has been used).

Assembly of the EST library

Assembly of ESTs into contigs has been performed using the EGassembler 68 tool. EGassembler aligns and merges sequence fragments resulting from shotgun sequencing or gene transcripts fragments in order to reconstruct the original segment or gene (an overlap identity cutoff parameter of 80% has been used).

cDNA references and genomes used in this study

The C. jacchus, G. gorilla, H. sapiens, M. mulatta, M. murinus, N. leucogeny, O. garnettii, P. troglodytes, P. abelii, and T. syrichta cDNA references have been retrieved from the Ensembl 38 database. The sequencing of the C. sabaeus genome is currently in progress as part of an international collaborative effort at the Washington University Genome Center 39 and the draft scaffold genome release of this project has been used in this study. The draft assembly of the M. fascicularis genome used in this study is available through the ENA 69 database via accession numbers from FR874244 to FR874264 5 .

ESTs alignment procedures

Alignment of the ESTs on the cDNA references and on the M. fascicularis draft assembly genome has been done using the BLAST tool 70 (an Expect value cutoff parameter of 10 has been used). Alignment results have been filtered to only keep for each EST the best alignment for each species that has at least a support of 80% with the EST sequence. Alignment of the ESTs on the C. sabaeus draft scaffold genome has been performed using the CBRC-LAST 71 based online tool available on the website of the Washington University Genome Center 72 .

Functional pathway analysis

The functional pathway analysis of the EST library has been performed using Ingenuity Pathways Analysis (IPA, Ingenuity®; Systems). IPA examines expressed genes in the context of known biological functions and pathways, mapping each gene identifier in a dataset to its corresponding molecule in the Ingenuity Pathways Knowledge Base (IPKB). P-values attributed to each pathway representing the statistical over-representation significance have been calculated by using the right-tailed Fisher’s exact test and have been adjusted using the Benjamini-Hochberg Multiple Testing correction 73 . Over the 9,208 H. sapiens transcripts uniquely mapped by the 37,787 original ESTs, 8,579 have been identified by the IPKB and then used in the functional analysis.

Quantification of the evolutionary relationships and construction of the phylogenetic trees

Quantification of the evolutionary relationships among ESTs and EST mapped sequences has been performed using the Needleman-Wunsch multiple alignment algorithm 74 . Distance among sequences has been calculated using the Jukes-Cantor method 75 (maximum likelihood estimate) based on the NUC44 scoring matrix. Phylogenetic trees have been constructed by using the Unweighted Pair Group Method Average linking method (UPGMA, group average 76 .

Data accessibility

The 37,787 ESTs are available on the dbEST 77 database via the library entry named “C. sabaeus PBMC EST Library” (accession: LIBEST_027323) and via Accession Numbers from JK088433 to JK126219. Each EST entry has been annotated with its associated contig (for assembled ESTs), its best high-quality mapped transcript with the corresponding gene for each cDNA reference, its 5 best mapped reads (when available) on the C. sabaeus draft scaffold genome, and the genomic position of its best alignment on the M. fascicularis draft assembly genome.

Competing interests

The authors declare no competing interests.

Authors’ contributions

NT – bioinformatics and analysis of the library, writing of ms; BJ – cell isolation and library preparation, writing of ms; PW, CD, CDS, JW – library construction and sequencing; ABl – candidate gene analysis; MMT, ABe – project design, supervision, funding, writing of ms. All authors read and approved the final manuscript.

Acknowledgements

The authors are grateful to Brendan Bell for his critical comments on the manuscript. This work has been partially funded through the Agence Nationale de Recherches sur le SIDA et les hépatites virales (ANRS) and the Genopole Evry. The sequencing of the EST library has been funded through a Genoscope grant 2006/73.

<p>Initial sequence of the chimpanzee genome and comparison with the human genome</p>SequencingTCConsortiumANature20054377055698710.1038/nature0407216136131<p>Evolutionary and biomedical insights from the rhesus macaque genome</p>GibbsRARogersJKatzeMGBumgarnerRWeinstockGMMardisERRemingtonKAStrausbergRLVenterJCWilsonRKBatzerMABustamanteCDEichlerEEHahnMWHardisonRCMakovaKDMillerWMilosavljevicAPalermoRESiepelASikelaJMAttawayTBellSBernardKEBuhayCJChandraboseMNDaoMDavisCDelehauntyKDDingYDinhHHDugan-RochaSFultonLAGabisiRAGarnerTTGodfreyJHawesACHernandezJHinesSHolderMHumeJJhangianiSNJoshiVKhanZMKirknessEFCreeAFowlerRGLeeSLewisLRLiZLiuYSMooreSMMuznyDNazarethLVNgoDNOkwuonuGOPaiGParkerDPaulHAPfannkochCPohlCSRogersYHRuizSJSaboASantibanezJSchneiderBWSmithSMSodergrenESvatekAFUtterbackTRVattathilSWarrenWWhiteCSChinwallaATFengYHalpernALHillierLWHuangXMinxPNelsonJOPepinKHQinXSuttonGGVenterEWalenzBPWallisJWWorleyKCYangSPJonesSMMarraMARocchiMScheinJEBaertschRClarkeLCsürösMGlasscockJHarrisRAHavlakPJacksonARJiangHLiuYMessinaDNShenYSongHXZWylieTZhangLBirneyEHanKKonkelMKLeeJSmitAFAUllmerBWangHXingJBurhansRChengZKarroJEMaJRaneyBSheXCoxMJDemuthJPDumasLJHanSGHopkinsJKarimpour-FardAKimYHPollackJRVinarTAddo-QuayeCDegenhardtJDenbyAHubiszMJIndapAKosiolCLahnBTLawsonHAMarkleinANielsenRVallenderEJClarkAGFergusonBHernandezRDHiraniKKehrer-SawatzkiHKolbJPatilSPuLLRenYSmithDGWheelerDASchenckIBallEVChenRCooperDNGiardineBHsuFKentWJLeskANelsonDLO’brienWEPrüferKStensonPDWallaceJCKeHLiuXMWangPXiangAPYangFBarberGPHausslerDKarolchikDKernADKuhnRMSmithKEZwiegASScience2007316582222223417431167<p>Comparative and demographic analysis of orang-utan genomes</p>LockeDPHillierLWWarrenWCWorleyKCNazarethLVMuznyDMYangSPWangZChinwallaATMinxPMitrevaMCookLDelehauntyKDFronickCSchmidtHFultonLAFultonRSNelsonJOMagriniVPohlCGravesTAMarkovicCCreeADinhHHHumeJKovarCLFowlerGRLunterGMeaderSHegerAPontingCPMarques-BonetTAlkanCChenLChengZKiddJMEichlerEEWhiteSSearleSVilellaAJChenYFlicekPMaJRaneyBSuhBBurhansRHerreroJHausslerDFariaRFernandoODarréFFarréDGazaveEOlivaMNavarroARobertoRCapozziOArchidiaconoNValleGDPurgatoSRocchiMKonkelMKWalkerJAUllmerBBatzerMASmitAFAHubleyRCasolaCSchriderDRHahnMWQuesadaVPuenteXSOrdoñezGRLópez-OtínCVinarTBrejovaBRatanAHarrisRSMillerWKosiolCLawsonHATaliwalVMartinsALSiepelARoyChoudhuryAMaXDegenhardtJBustamanteCDGutenkunstRNMailundTDutheilJYHobolthASchierupMHRyderOAYoshinagaYDe JongPJWeinstockGMRogersJMardisERGibbsRAWilsonRKNature2011469733152953310.1038/nature09687306077821270892<p>Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques</p>YanGZhangGFangXZhangYLiCLingFCooperDNLiQLiYVan GoolAJDuHChenJChenRZhangPHuangZThompsonJRMengYBaiYWangJZhuoMWangTHuangYWeiLLiJWangZHuHYangPLeLStensonPDLiBLiuXBallEVAnNHuangQZhangYFanWZhangXLiYWangWKatzeMGSuBNielsenRYangHWangJWangXWangJNat Biotechnol2011291118621221076<p>Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment</p>EbelingMKüngESeeABrogerCSteinerGBerreraMHeckelTIniguezLAlbertTSchmuckiRGenome Research201121101746175610.1101/gr.123117.111320229121862625<p>Primate genomes for biomedicine</p>BosingerSEJohnsonZPSilvestriGNat Biotechnol2011291198398410.1038/nbt.203222068533<p>Systems biology of natural simian immunodeficiency virus infections</p>BosingerSJacquelinBBeneckeASilvestriGMüller-TrutwinMCurrent Opinion in HIV and AIDS201271717810.1097/COH.0b013e32834dde0122134342<p>Enduring cognitive deficits and cortical dopamine dysfunction in monkeys after long-term administration of phencyclidine</p>JentschJDRedmondDEElsworthJDTaylorJRYoungrenKDRothRHScience1997277532895395510.1126/science.277.5328.9539252326<p>Severe long-term 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced parkinsonism in the vervet monkey (Cercopithecus aethiops sabaeus)</p>TaylorJRElsworthJDRothRHSladekJRRedmondDENeuroscience199781374575510.1016/S0306-4522(97)00214-59316026<p>An Antibody Against the Exosite of the Cloned Thrombin Receptor Inhibits Experimental Arterial Thrombosis in the African Green Monkey</p>CookJJSitkoGRBednarBCondraCMellottMJFengDMNuttRFShaferJAGouldRJConnollyTMCirculation199591122961297110.1161/01.CIR.91.12.29617796507<p>A novel Vero cell line for use as a mammalian host-vector system in serum-free medium</p>OhnoTWangXKurashimaJSaijo-KuritaKHironoMCytotechnology19917316517210.1007/BF003659271368119<p>Qualification of working cell banks for the Vero cell line to produce licensed human vaccines</p>Vincent-FalquetJCPeyronLSouvrasMMoulinJCTektoffJPatetJDevelopments in Biological Standardization1989701531562759347<p>Authentication of African green monkey cell lines using human short tandem repeat markers</p>AlmeidaJHillCColeKBMC Biotechnology20111110210.1186/1472-6750-11-102322162822059503<p>Exploration of the African green monkey as a preclinical pharmacokinetic model: intravenous pharmacokinetic parameters</p>WardKWCoonDJMagieraDBhadresaSNisbettELawrenceMSDrug metabolism and disposition the biological fate of chemicals200836471572010.1124/dmd.107.01931518227143<p>A neutralizing human monoclonal antibody protects african green monkeys from hendra virus challenge</p>BossartKNGeisbertTWFeldmannHZhuZFeldmannFGeisbertJBYanLFengYRBriningDScottDWangYDimitrovASCallisonJChanYPHickeyACDimitrovDSBroderCCRockxBScience translational medicine20113105105ra10310.1126/scitranslmed.3002901331362522013123<p>Inhalation efficacy of RFI-641 in an African green monkey model of RSV infection</p>WeissWJMurphyTLynchMEFryeJBuklanAGrayBLenoyEMitelmanSO’ConnellJQuartuccioSJournal of Medical Primatology2003322828810.1034/j.1600-0684.2003.00014.x12823630SwearengenJBiodefense: research methodology and animal modelsBoca Raton, (FL): CRC Press2006<p>Isolation of simian immunodeficiency virus from African green monkeys and seroepidemiologic survey of the virus in various non-human primates</p>OhtaYMasudaTTsujimotoHIshikawaKKodamaTMorikawaSNakaiMHonjoSHayamiMInternational journal of cancer Journal international du cancer1988411151222447023<p>African non human primates infected by SIV - why don’t they get sick? Lessons from studies on the early phase of non-pathogenic SIV infection</p>LiovatASJacquelinBPloquinMJBarré-SinoussiFMüller-TrutwinMCCurrent HIV Research20097395010.2174/15701620978704854619149553<p>Toward an AIDS vaccine: lessons from natural simian immunodeficiency virus infections of African nonhuman primate hosts</p>SodoraDLAllanJSApetreiCBrenchleyJMDouekDCElseJGEstesJDHahnrHHirschVMKaurAKirchhoffFMuller-TrutwinMPandreaISchmitzJESilvestriGNat Med200915886186510.1038/nm.2013278270719661993<p>Natural SIV Infection: Immunological Aspects</p>JacquelinBZahnRCBarré-SinoussiFSchmitzJEKaurAMüller-TrutwinMCModels of Protection Against HIV/SIV: How some Humans and Many Monkeys have Learned to deal Successfully with HIV & SIVNew York: Academic Press (Elsevier)Pancino G, Silvestri G, Fowke K4780<p>High Levels of Viral Replication during Primary Simian Immunodeficiency Virus SIVagm Infection Are Rapidly and Strongly Controlled in African Green Monkeys</p>DiopOMGueyeADias-TavaresMKornfeldCFayeAAvePHuerreMCorbetSBarre-SinoussiFMüller-TrutwinMCJournal of Virology200074167538754710.1128/JVI.74.16.7538-7547.200011227410906207<p>Wide range of viral load in healthy african green monkeys naturally infected with simian immunodeficiency virus</p>GoldsteinSOurmanovIBrownCRBeerBEElkinsWRPlishkaRBuckler-WhiteAHirschVMJournal of Virology20007424117441175310.1128/JVI.74.24.11744-11753.200011245711090174<p>Viral load in tissues during the early and chronic phase of non-pathogenic SIVagm infection</p>GueyeADiopOMPloquinMJYKornfeldCFayeACumontMCHurtrelBBarré-SinoussiFMüller-TrutwinMCJournal of Medical Primatology2004332839710.1111/j.1600-0684.2004.00057.x15061721<p>Antiinflammatory profiles during primary SIV infection in African green monkeys are associated with protection against AIDS</p>KornfeldCPloquinMJYPandreaIFayeAOnangaRApetreiCPoaty-MavoungouVRouquetPEstaquierJMortaraLJournal of Clinical Investigation2005115410821091106289515761496<p>Impact of viral factors on very early in vivo replication profiles in simian immunodeficiency virus SIVagm-infected African green monkeys</p>PandreaIKornfeldCPloquinMJYApetreiCFayeARouquetPRoquesPSimonFBarré-SinoussiFMüller-TrutwinMCDiopOMJournal of Virology200579106249625910.1128/JVI.79.10.6249-6259.2005109172915858009<p>Inhibition of Adaptive Immune Responses Leads to a Fatal Clinical Outcome in SIV-Infected Pigtailed Macaques but Not Vervet African Green Monkeys</p>SchmitzJEZahnRCBrownCRRettMDLiMTangHPryputniewiczSByrumRAKaurAMontefioriDCAllanJSGoldsteinSHirschVMPLoS Pathogens200951214<p>Simian Immunodeficiency Virus SIVagm.sab Infection of Carribean African Green Monkeys: a New Model for the Study of SIV Pathogenesis in Natural Hosts</p>PandreaIApetreiCDufourJDillonNBarbercheckJMetzgerMJacquelinBBohmRMarxPABarre-SinoussiFHirschVMMüller-TrutwinMCLacknerAAVeazeyRSJournal of Virology200680104858486710.1128/JVI.80.10.4858-4867.2006147206816641277<p>Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response</p>JacquelinBMayauVTargatBLiovatASKunkelDPetitjeanGDilliesMARoquesPButorCSilvestriGGiavedoniLDLebonPBarré-SinoussiFBeneckeAMüller-TrutwinMCJournal of Clinical Investigation20091191235443555278680519959873<p>Transcriptional Profiling in Pathogenic and Non-Pathogenic SIV Infections Reveals Significant Distinctions in Kinetics and Tissue Compartmentalization</p>LedererSFavreDWaltersKAProllSKanwarBKasakowZBaskinCRPalermoRMcCuneJMKatzeMGPLoS Pathogens20095215<p>Relation between phylogeny of African green monkey CD4 genes and their respective simian immunodeficiency virus genes</p>FomsgaardAMüller-TrutwinMCDiopOHansenJMathiotCCorbetSBarré-SinoussiFAllanJSJournal of Medical Primatology199726312012810.1111/j.1600-0684.1997.tb00043.x9379478<p>Frequent substitution polymorphisms in African green monkey CCR5 cluster at critical sites for infections by simian immunodeficiency virus SIVagm, implying ancient virus-host coevolution</p>KuhmannSEMadaniNDiopOMPlattEJMorvanJMüller-TrutwinMCBarré-SinoussiFKabatDJournal of Virology200175188449846010.1128/JVI.75.18.8449-8460.200111509011507190<p>Mutations in CCR5-coding sequences are not associated with SIV carrier status in African nonhuman primates</p>Müller-TrutwinMCCorbetSHansenJGeorges-CourbotMCDiopORigouletJBarré-SinoussiFFomsgaardAAIDS Research and Human Retroviruses1999151093193910.1089/08892229931064710408730<p>Genes Expressed in Specific Areas of the Human Fetal Cerebral Cortex Display Distinct Patterns of Evolution</p>Hassan B(Ed)PLoS ONE20116313<p>Cyclophilin A retrotransposition into TRIM5 explains owl monkey resistance to HIV-1</p>SayahDMSokolskajaEBerthouxLLubanJNature2004430699956957310.1038/nature0277715243629<p>Long oligonucleotide microarrays for African green monkey gene expression profile analysis</p>JacquelinBMayauVBrysbaertGRegnaultRDiopOMArenzana-SeisdedosFRoggeLCoppeeJYBarre-SinoussiFBeneckeAMüller-TrutwinMCFaseb Journal20072112326210.1096/fj.07-8271com17507667<p>GenBank: update</p>BensonDAKarsch-MizrachiILipmanDJOstellJWheelerDLNucleic Acids Res200432Database issueD23D2630877914681350<p>The Ensembl genome database project</p>HubbardTBarkerDBirneyECameronGChenYClarkLCoxTCuffJCurwenVDownTDurbinREyrasEGilbertJHammondMHuminieckiLKasprzykALehvaslaihoHLijnzaadPMelsoppCMonginEPettettRPocockMPotterSRustASchmidtESearleSSlaterGSmithJSpoonerWStabenauAStalkerJStupkaEUreta-VidalAVastrikIClampMNucleic Acids Res200230384110.1093/nar/30.1.389916111752248<p>Integrated Vervet/AGM Research & Resources</p>[http://www.genomequebec.mcgill.ca/compgen/vervet_research/genomics_genetics/]<p>Different doses of agonistic ligand drive the maturation of functional CD4 and CD8 T cells from immature precursors</p>LovattMYangTHStaussHJFisherAGMerkenschlagerMEuropean Journal of Immunology200030237138110.1002/1521-4141(200002)30:2<371::AID-IMMU371>3.0.CO;2-T10671192<p>Induction of cytokines by heat shock proteins and concanavalin A in murine splenocytes</p>WangYGaoBTsanMFCytokine2005323-414915410.1016/j.cyto.2005.09.00316289961<p>Enduring cognitive deficits and cortical dopamine dysfunction in monkeys after long-term administration of phencyclidine</p>JentschJDRedmondDEElsworthJDTaylorJRYoungrenKDRothRHScience1997277532895395510.1126/science.277.5328.9539252326<p>Severe long-term 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced parkinsonism in the vervet monkey (Cercopithecus aethiops sabaeus)</p>TaylorJRElsworthJDRothRHSladekJRRedmondDENeuroscience199781374575510.1016/S0306-4522(97)00214-59316026<p>A novel Vero cell line for use as a mammalian host-vector system in serum-free medium</p>OhnoTWangXKurashimaJSaijo-KuritaKHironoMCytotechnology19917316517210.1007/BF003659271368119<p>An Antibody Against the Exosite of the Cloned Thrombin Receptor Inhibits Experimental Arterial Thrombosis in the African Green Monkey</p>CookJJSitkoGRBednarBCondraCMellottMJFengDMNuttRFShaferJAGouldTMRobertJConnollyCirculation199591122961297110.1161/01.CIR.91.12.29617796507<p>Qualification of working cell banks for the Vero cell line to produce licensed human vaccines</p>Vincent-FalquetJCPeyronLSouvrasMMoulinJCTektoffJPatetJDevelopments in Biological Standardization1989701531562759347<p>Authentication of African green monkey cell lines using human short tandem repeat markers</p>AlmeidaJLHillCRColeKDBMC Biotechnology20111110210.1186/1472-6750-11-102322162822059503<p>Exploration of the African green monkey as a preclinical pharmacokinetic model: intravenous pharmacokinetic parameters</p>WardKWCoonDJMagieraDBhadresaSNisbettELawrenceMSDrug metabolism and disposition the biological fate of chemicals200836471572010.1124/dmd.107.01931518227143<p>A neutralizing human monoclonal antibody protects african green monkeys from hendra virus challenge</p>BossartKNGeisbertTWFeldmannHZhuZFeldmannFGeisbertJBYanLFengYRBriningDScottDScience translational medicine20113105105ra10310.1126/scitranslmed.3002901331362522013123<p>Inhalation efficacy of RFI-641 in an African green monkey model of RSV infection</p>WeissWJMurphyTLynchMEFryeJBuklanAGrayBLenoyEMitelmanSO’ConnellJQuartuccioSJournal of Medical Primatology2003322828810.1034/j.1600-0684.2003.00014.x12823630<p>From the Cover: Behavioral improvement in a primate Parkinson’s model is associated with multiple homeostatic effects of human neural stem cells</p>RedmondDEBjugstadKBTengYDOurednikVOurednikJWakemanDRParsonsXHGonzalezRBlanchardBCKimSUProceedings of the National Academy of Sciences200710429121751218010.1073/pnas.0704091104<p>Alzheimer’s disease abeta vaccine reduces central nervous system abeta levels in a non-human primate, the Caribrefn vervet</p>LemereCABeierschmittAIglesiasMSpoonerETBloomJKLeveroneJFZhengJBSeabrookTJLouardDLiDThe American journal of pathology200416528329710.1016/S0002-9440(10)63296-8161854215215183<p>Toward an AIDS vaccine: lessons from natural simian immunodeficiency virus infections of African nonhuman primate hosts</p>SodoraDLAllanJSApetreiCBrenchleyJMDouekDCElseJGEstesJDHahnrHHirschVMKaurANat Med200915886186510.1038/nm.2013278270719661993<p>Structural and functional features of eukaryotic mRNA untranslated regions</p>PesoleGMignoneFGissiCGrilloGLicciulliFLiuniSGene20012761-2738110.1016/S0378-1119(01)00674-611591473<p>Selection on Human Genes as Revealed by Comparisons to Chimpanzee cDNA</p>HellmannIZollnerSEnardWEbersbergerINickelBPaaboSGenome Research200313583183710.1101/gr.94490343091612727903<p>Substitution Rate and Structural Divergence of 5’UTR Evolution: Comparative Analysis Between Human and Cynomolgus Monkey cDNAs</p>OsadaNHirataMTanumaRKusudaJHidaMSuzukiYSuganoSGojoboriTShenCKJWuCIHashimotoKMolecular Biology and EvolutionOctober 2005221019761982<p>Molecular basis of evolutionary adaptation at the lactate dehydrogenase-B locus in the fish Fundulus heteroclitus</p>CrawfordDLPowersDAProceedings of the National Academy of Sciences of the United States of America198986239365936910.1073/pnas.86.23.93652984962594773<p>Expression profiling in primates reveals a rapid evolution of human transcription factors</p>GiladYOshlackASmythGKSpeedTPWhiteKPNature2006440708124224510.1038/nature0455916525476<p>Functional Comparison of Innate Immune Signaling Pathways in Primates</p>BarreiroLBMarioniJCBlekhmanRStephensMGiladYPLoS Genetics201061213<p>CXCL10/IP-10 in infectious diseases pathogenesis and potential therapeutic implications</p>LiuMGuoSHibbertJMJainVSinghNWilsonNOStilesJKCytokine growth factor reviews2011223121130320369121802343<p>The host type I interferon response to viral and bacterial infections</p>PerryAKChenGZhengDTangHChengGCell Research20051564072210.1038/sj.cr.729030915987599<p>Cross-regulation of signaling pathways by interferon-gamma: implications for immune responses and autoimmune diseases</p>HuXIvashkivLBImmunity200931453955010.1016/j.immuni.2009.09.002277422619833085<p>Evolutionary genetics evidence of an essential, nonredundant role of the IFN-? pathway in protective immunity</p>ManryJLavalGPatinEFornarinoSTichitMBouchierCBarreiroLBQuintana-MurciLHuman Mutation201132663364210.1002/humu.2148421448974<p>Evidence for an antagonist form of the chemokine CXCL10 in patients chronically infected with HCV</p>CasrougeADecalfJAhloulayMLababidiCMansourHVallet-PichardAMalletVMottezEMapesJFontanetAJournal of Clinical Investigation201112130831710.1172/JCI40594300713121183794<p>Finding their niche: chemokines directing cell migration in the thymus</p>BuntingMDComerfordIMcCollSRImmunology and Cell Biology201189218519610.1038/icb.2010.14221135866<p>Divergent TLR7 and TLR9 signaling and type I interferon production distinguish pathogenic and nonpathogenic AIDS virus infections</p>MandlJNBarryAPVanderfordTHKozyrNChavanRKluckingSBarratFJCoffmanRLStapransSIFeinbergMBNat Med200814101077108710.1038/nm.187118806803<p>EMBOSS: The European Molecular Biology Open Software Suite</p>RicePTrends in Genetics200016627627710.1016/S0168-9525(00)02024-210827456<p>EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments</p>Masoudi-NejadATonomuraKKawashimaSMoriyaYSuzukiMItohMKanehisaMEndoTGotoSNucleic Acids Res200634Web Server issueW459W462153877516845049<p>The European Nucleotide Archive</p>LeinonenRAkhtarRBirneyEBowerLCerdeno-TárragaAChengYClelandIFaruqueNGoodgameNGibsonRHoadGJangMPaksereshtNPlaisterSRadhakrishnanRReddyKSobhanySTen HoopenPVaughanRZaluninVCochraneGNucleic Acids Res201139Database issueD2831301380120972220<p>Basic local alignment search tool</p>AltschulSFGishWMillerWMyersEWLipmanDJJ Mol Biol199021534034102231712<p>Adaptive seeds tame genomic sequence comparison</p>KiełbasaSMWanRSatoKHortonPFrithMCGenome Research201121348749310.1101/gr.113985.110304486221209072<p>Integrated Vervet/AGM Research & Resources</p>[http://www.genomequebec.mcgill.ca/compgen/vervet_research/cgi-bin/vervet_seq_db.pl]<p>Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing</p>BenjaminiYHochbergYJournal of the Royal Statistical Society. Series B (Methodological)199557289300<p>A general method applicable to the search for similarities in the amino acid sequence of two proteins</p>NeedlemanSBWunschCDJ Mol Biol197048344345310.1016/0022-2836(70)90057-45420325JukesTHCantorCREvolution of Protein MoleculesNew York: Academy Press1969<p>A statistical method for evaluating systematic relationships</p>SokalRRMichenerCDUniversity of Kansas Scientific Bulletin1958282214091438<p>dbEST–database for “expressed sequence tags”</p>BoguskiMSLoweTMTolstoshevCMNat Genet19934433233310.1038/ng0893-3328401577