Open Access

Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus

  • Nicolas Tchitchek1,
  • Béatrice Jacquelin2,
  • Patrick Wincker3,
  • Carole Dossat3,
  • Corinne Da Silva3,
  • Jean Weissenbach3,
  • Antoine Blancher4,
  • Michaela Müller-Trutwin2Email author and
  • Arndt Benecke1, 5Email author
Contributed equally
BMC Genomics201213:279

DOI: 10.1186/1471-2164-13-279

Received: 2 April 2012

Accepted: 11 June 2012

Published: 22 June 2012

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 [1113], pharmacology [14] and infectious diseases [1519]. 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 [1921]. 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 [2227]. 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 [3133], 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.

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.
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-279/MediaObjects/12864_2012_Article_4552_Fig1_HTML.jpg
Figure 1

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
Table 1

Composition details of the cDNA references

Species name

Release version

Number of transcripts

Number of genes

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

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.

Table 2

Alignment results of ESTs on the different cDNA references and genomes

Species name

Target type

Original ESTs

Assembled and singleton ESTs

  

a.e.

m.t.

m.g.

a.e.

m.t.

m.g.

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%)

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.

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.
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-279/MediaObjects/12864_2012_Article_4552_Fig2_HTML.jpg
Figure 2

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.
https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-279/MediaObjects/12864_2012_Article_4552_Fig3_HTML.jpg
Figure 3

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.
Table 3

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

Transcript ID

Gene symbol

Gene description

Count

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

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.

https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-279/MediaObjects/12864_2012_Article_4552_Fig4_HTML.jpg
Figure 4

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.

Table 4

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

Canonical pathway

−log(q-value)

gen a /gen b

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-κ B 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%)

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.

https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-279/MediaObjects/12864_2012_Article_4552_Fig5_HTML.jpg
Figure 5

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.
Table 5

Pairwise genomic distance matrix of the 11 primate species

 

C. sabaeus

G. gorilla

H. sapiens

M. mulatta

M. murinus

N. leucogeny

O. garnettii

P. troglodytes

P. abelii

T. syrichta

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 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.

https://static-content.springer.com/image/art%3A10.1186%2F1471-2164-13-279/MediaObjects/12864_2012_Article_4552_Fig6_HTML.jpg
Figure 6

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, 4250]. 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].

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 [6062]. For the IFN-γ receptor (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.

Notes

Declarations

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.

Authors’ Affiliations

(1)
Institut des Hautes Études Scientifiques - Centre National de la Recherche Scientifique
(2)
Institut Pasteur, Unité de Régulation des Infections Rétrovirales
(3)
CEA, Institut de Génomique
(4)
Laboratoire d’Immunologie, CHU Rangueil
(5)
Vaccine Research Institute, Institut Mondor de Recherche Biomédicale

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