Analysis of macaque BTN3A genes and transcripts in the extended MHC: conserved orthologs of human γδ T cell modulators
Butyrophilins (BTN), specifically BTN3A, play a central role in the modulation of γδ T cells, which are mainly present in gut and mucosal tissues. BTN3A1 is known, for example, to activate Vγ9Vδ2 T cells by means of a phosphoantigen interaction. In the extended HLA region, three genes are located, designated BTN3A1, BTN3A2 and BTN3A3, which were also defined in rhesus macaques. In contrast to humans, rhesus monkeys have an additional gene, BTN3A3Like, which has the features of a pseudogene. cDNA analysis of 32 Indian rhesus and 16 cynomolgus macaques originating from multiple-generation families revealed that all three genes are oligomorphic, and the deduced amino acids display limited variation. The macaque BTN3A alleles segregated together with MHC alleles, proving their location in the extended (Major Histocompatibility Complex) MHC. BTN3A nearly full-length transcripts of macaques and humans cluster tightly together in the phylogenetic tree, suggesting that the genes represent true orthologs of each other. Despite the limited level of polymorphism, 15 Mamu- and 14 Mafa-BTN3A haplotypes were defined, and, as in humans, all three BTN3A genes are transcribed in PBMCs and colon tissues. In addition to regular full-length transcripts, a high number of various alternative splicing (AS) products were observed for all BTN3A alleles, which may result in different isoforms. The comparable function of certain subsets of γδ T cells in human and non-human primates in concert with high levels of sequence conservation observed for the BTN3A transcripts presents the opportunity to study these not yet well understood molecules in macaques as a model species.
KeywordsBTN3A MHC Macaques Gamma-delta T cells Alternative splicing
T cells are an essential component of the adaptive immune system and use cell surface bound receptors (TCRs) to recognize ligands that may signal the presence of intracellular infections or cellular stress. In addition to T cells that express a T cell receptor composed of a heterodimer of an α and a β chain, another T cell lineage expresses a different set of receptors consisting of a γ and a δ chain instead. Although much less abundant than αβ T cells in peripheral blood, these γδ T cells are highly plentiful in tissues such as skin, the intestines and the reproductive tract (Adams et al. 2015). Moreover, they represent an important effector subset of innate-like T lymphocytes (Rhodes et al. 2016). In contrast to TCRs of the αβ lineage, however, which recognize antigenic peptides in the context of classical or non-classical MHC class I (MHC-I) molecules, some γδ-T cells recognize lipid molecules presented by MHC-like molecules such as CD1d and CD1c. Additionally, there are others, which can directly detect antigens, sometimes even without presentation via a canonical, antigen-presenting MHC or MHC-like molecule (Bai et al. 2012; Luoma et al. 2014; Roy et al. 2014). The most thoroughly investigated subset represents the Vγ9Vδ2 T cells, which are the dominant population of γδ-T cells in human peripheral blood, with potent activity regarding certain microbial infections and cancers (Gober et al. 2003; Morita et al. 2007). Vγ9Vδ2 T cells respond specifically to pyrophosphates derived from microbial sources or malignant cells. These phosphoantigens (pAg) are recognized in a TCR-dependent manner, but in contrast to αβ-T cells, they apparently do not require MHC molecules for pAg-dependent activation. Recently, molecules belonging to the butyrophilin (BTN) protein family, specifically butyrophilin-3A (BTN3A), were identified as an essential component in the pAg activation pathway of Vγ9Vδ2 T cells (Abeler-Dorner et al. 2012; Afrache et al. 2012; Karunakaran and Herrmann 2014; Rhodes et al. 2016; Vavassori et al. 2013). BTN3A proteins are cell-surface receptors expressed on a broad variety of cell types, including immune cells and some malignant cells such as ovarian cancer (Arnett and Viney 2014). They belong to the Ig-like superfamily and are evolutionarily and structurally related to the cluster of B7 costimulatory molecules CD80 and CD86 (Abeler-Dorner et al. 2012; Afrache et al. 2012; Rhodes et al. 2016). They exhibit two extracellular domains, IgV and IgC (Williams and Barclay 1988), and a transmembrane part. In contrast to the B7 molecule, however, most BTN molecules also contain a cytosolic B30.2 (PRYSPRY) domain, which is separated from the transmembrane domain by several very short exons, which are called heptads (Rhodes et al. 2001). BTN3A genes belong to a multigene family, which maps in humans to the extended MHC class I region and comprises three genes: BTN3A1, BTN3A2 and BTN3A3 (Horton et al. 2004; Rhodes et al. 2001, 2016). BTN3A1 and BTN3A3 contain the intracellular B30.2 domain, which is absent in BTN3A2. Although the prominent role of BTN3A1 in pAg-induced Vγ9Vδ2 T cell activation is well documented, the working mechanism is not yet fully understood, and the extracellular ligand for BTN3A1 molecules is still unknown. There is strong support for the intracellular sensing of pAg through the B30.2 domain of BTN3A1-mediating Vγ9Vδ2 T cell activation (Harly et al. 2012; Palakodeti et al. 2012; Peigne et al. 2017; Rhodes et al. 2015; Sandstrom et al. 2014). Additionally, crystallographic studies illustrated that BTN3A1 molecules may exist in two potential dimer conformations, and pAg-induced conformational changes of the intracellular domain of BTN3A1 might also involve dimer conversion (Gu et al. 2017, 2018; Palakodeti et al. 2012). While BTN3A1 is necessary for pAg-induced Vγ9Vδ2 T cell activation, this molecule alone may not be sufficient to conduct the activation process. Two cytoskeletal mediators have been identified, and named Periplakin and RhoB GTPase, which interact directly with BTN3A1, and may as such be involved in the activation process (Rhodes et al. 2015; Sebestyen et al. 2016). Additionally, recent work postulates that ABC transporters play a role in BTN3A-dependent γδ T cell activation by way of cytokine secretion (Rhodes et al. 2018). Furthermore, a co-expression and multimerization of BTN3A1 with its sister molecules BTN3A2 and BTN3A3 may be necessary for their function, comparable to a concerted action as documented for other BTN molecules (Di Marco Barros et al. 2016; Gu et al. 2018; Rhodes et al. 2015).
BTN3A proteins indeed play a role in T cell proliferation and cytokine production, which was manifested through the use of BTN3A-specific antibodies. One of the antibodies, 20.1, triggers Vγ9Vδ2 T cell activation, whereas a different antibody, 103.2, works as an antagonist and blocks pAg-induced T cell activation (Arnett and Viney 2014; Harly et al. 2012). The functional importance of BTN3A molecules was illustrated in a xenotransplantation model by the agonist antibody 20.1, which was able to enhance the Vγ9Vδ2 T cell-mediated killing of leukaemia cells (Benyamine et al. 2016). Moreover, the influence of BTN3A1 in stimulating anti-tumour effector Vγ9Vδ2 T cells in zolodronate-treated colorectal cancer cells was documented as well (Zocchi et al. 2017).
Mutations in BTN genes may influence disease outcome, since polymorphisms in BTN3A2 are associated with an increased susceptibility to developing type I diabetes (Viken et al. 2009). BTN3A genes are highly conserved in evolution and have been defined not only in higher primates but also in some other placental mammals such as the alpaca (Karunakaran et al. 2014). The three human BTN3A genes are the result of two successful rounds of duplications during the radiation of primates (Afrache et al. 2017). All three BTN3A genes seem to be present in hominoids (humans and great apes) and Old World monkeys (OWM). The concerted evolution of these genes resulted in a strong homogenization of the IgV domain in hominoids, where the sequences of BTN3A1 and BTN3A3 are replaced by BTN3A2. This homogenization of the IgV domain appears to be absent in OWM (Afrache et al. 2017).
Despite the increasing interest in BTN3A as immune modulators of Vγ9Vδ2 T cells, nothing is known so far about the possible levels of polymorphism and their distribution in OWM species such as macaques. Therefore, large families of rhesus and cynomolgus macaques were analysed for their BTN3A genes by cloning and Sanger sequencing.
Already in the beginning of the century, alternative splicing (AS) was observed in addition to constitutive splicing by Sanger sequencing specifically for human BTN3A transcripts, indicating that AS occurs far more frequently in these genes than in others (Rhodes et al. 2001). With more recent NGS techniques, AS has been documented in various genes of the immune system as well, and the different splicing mechanisms have been extensively described (Bruijnestijn et al. 2018; Keren et al. 2010; Voorter et al. 2016). In the present study, various isoforms of macaque BTN3A transcripts that were generated by AS have been documented, and the most frequent splice events have been characterized in detail.
Material and methods
We analysed DNA samples of 32 rhesus macaques of Indian origin belonging to two families of four generations and 16 cynomolgus macaques of various origins including different Indonesian islands as well as the Indonesian continent, belonging to two families of two generations, respectively. These animals belong to outbred breeding colonies that are housed at the BPRC, the Netherlands, and had been extensively characterized beforehand for their MHC class I and II haplotypes (Doxiadis et al. 2013; de Groot et al. 2014).
Genomic DNA (gDNA) of exon 2 of one rhesus macaque family (family sire C68; no. 19) was analysed, followed by a cDNA analysis of all animals for exon 2 to exon 9 of the BTN3A1 and BTN3A3 genes, exon 2 to exon 7 of the BTN3A2 gene and exon 2 of the pseudogene BTN3ALlike.
Genomic DNA isolation and BTN3A exon 2 gDNA sequencing
gDNA of the selected animals was extracted from EDTA blood samples or from immortalized B cell lines using a standard salting out procedure. Exon 2 amplification was performed as described using adapted primers originally published by Rhodes and co-workers (Rhodes et al. 2001) (Suppl. Table 1). Amplicons were sequenced and analysed as described below.
RNA isolation, cDNA preparation, cloning and sequencing
RNA was isolated from immortalized B cell lines or freshly prepared PBMCs (RNeasy kit, Qiagen) and was used for the synthesis of cDNA with the RevertAid First Strand cDNA synthesis Kit (Thermo scientific). BTN3A1, BTN3A2 and BTN3A3 sequences (exon 1 [partly] to exon 9) were gained by PCR on cDNA using newly designed primer sets for the specific amplification of all three BTN3As. The amplification of BTN3A3Like alleles was only successful by using a specific exon 2 5′primer and an exon 4 3′primer (Suppl. Table 1). Primers were synthesized by Invitrogen. PCR was performed in a 50-μl reaction containing 0.02 U/μl of Phusion High-Fidelity DNA polymerase enzyme with 0.3 μM of each primer, 250 μM dNTPs, 1× Phusion buffer HF, 3%DMSO (Invitrogen, Life Technologies) and 200 ng cDNA. The cycling parameters were a 2-min 98 °C initial denaturation step, followed by 30 cycles (35 cycles for BTN3A1) of a 30-s 98 °C denaturation step, a 30-s annealing step (54 °C for BTN3A1, 59 °C for BTN3A2 and 55 °C for BTN3A3) and a 90-s 72 °C extension step. A final extension step was performed at 72 °C for 7 min. PCR products were purified using a geneJet Gel Extraction Kit (Thermo Scientific™), and the purified amplicons were cloned into the pJET vector using the CloneJET PCR cloning kit, both according to the manufacturer’s guidelines (Thermo Scientific™). The cloned amplicons were then transformed in Escherichia coli-XL1-blue cells with the TransformAid Bacterial Transformation Kit (Thermo Scientific™). Per animal, a minimum of 32 clones was selected, and plasmid DNA was isolated using a standard mini-preparation procedure. The purified plasmid DNA was sequenced on an ABI 3500 genetic analyser (Applied Biosystems, Foster City, USA). The sequencing reaction was performed by 2 μM pJET primer, 1 μl BigDye terminator and 2 μl of 5× sequencing buffer in a total volume of 10 μl (Thermo Scientific™). The resulting sequences were analysed using the Sequence Navigator program (Applied Biosystems, Foster City, USA). BTN sequences were revised manually by applying the Lasergene 12 SeqMan Pro Sequence Alignment Editor. Allele definitions are based on at least two clones with identical sequences from different monkeys or on independent PCRs from one monkey. The sequences were named in accordance with the general nomenclature rules of the ImmunoPolymorphismDatabase (IPD-MHC database of nonhuman primates [NHP]) (de Groot et al. 2012) and sent to the NCBI database (Accession numbers: BTN3A1: LT992538-LT992545 and LT992494-LT992501; BTN3A2: LT992546-LT992555; BTN3A3: LT993304-LT993321 and BTN3A1L: LT993431-LT993437). The BTN3A3 pseudogene sequence of the olive baboon was extracted from the NCBI database (Accession no. XM_009198763).
Phylogenetic analysis of exon 2 and of exons 2–6 of BTN3A alleles
The evolutionary history of the BTNA3 alleles was inferred using the neighbour-joining method and the optimal tree. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. The analyses involved 37 (gDNA exon 2) and 56 (cDNA exon 2 to exon 6) sequences, respectively. Codon positions included were 1st + 2nd + 3rd + noncoding. All ambiguous positions were removed for each sequence pair. There was a total of 348 (exon 2) and 879 (exon 2 to exon 6) positions, respectively, in the final dataset. Evolutionary analyses were conducted in MEGA7.
Alternative splice products observed for all BTN3A transcripts were categorized according to their frequency and splice mechanism (Suppl. Table 2). All observed splice events were substantiated by the prediction and scoring of the alternative and actual splice sites using three different in silico prediction tools. The selected tools were the Maximum Entropy Modeling Scan (MaxEntScan; MES) (Yeo and Burge 2004), the Position Weight Matrix (PWM) via SpliceView (Rogozin and Milanesi 1997) and the Human Splice Finder (HSF) (Desmet et al. 2009). These tools use different output value ranges, but the higher score always implies a better-predicted splice site. It should be noted that whether or not a splice event occurs, the scores do not provide a threshold, and the scores should only be used to compare related splice sites.
Exon 2 analyses of Mamu-BTN3A genes
Mamu- and Mafa-BTN3A allele discovery
Furthermore, the positions of the variable, macaque-specific amino acids of all three BTN3A gene products are scattered over the coding sequence and not concentrated on certain positions (Fig. 3a–c), as contrasts the situation for the peptide binding site of the polymorphic MHC molecules (Hughes and Nei 1988). Exon 2 of BTN3A1, however, which encodes the IgV domain, forms an exception; the same four variable, macaque-specific amino acid positions are encoded within this exon, resulting in two different amino acids (Fig. 3a).
Mamu- and Mafa-BTN3A haplotype definition
The co-segregation of the alleles of all three BTN3A genes and those of the BTN3A3Like pseudogene within the macaque families confirm duplication of the BTN3A genes and their localization in close proximity to each other on the chromosome. We were able to define 15 and 14 BTN3A haplotypes in the two rhesus and cynomolgus macaque families, respectively. Figure 2 and Suppl. Fig. 1 show the pedigrees of the two rhesus macaque families with their deduced BTN3A haplotypes, whereas in Fig. 4, the pedigrees of both cynomolgus macaque families and deduced BTN3A haplotypes are illustrated. Whereas the two rhesus macaque families share about half of their haplotypes, the two cynomolgus macaque families have no BTN3A haplotypes in common.
Additionally, mapping of the BTN3A genes within the extended MHC complex of the rhesus macaque is confirmed by the co-segregation of most of the BTN3A haplotypes with the MHC haplotypes defined beforehand. The co-segregation of MHC haplotypes and BTN3A alleles is also observed in the two cynomolgus macaque families (data not shown). As expected in accordance with the long distance between both regions (> 3 Mb), crossing over events between BTN3A and MHC haplotypes can be postulated as well as point mutations, leading to new allele/haplotype definitions. The deduced MHC-BTN3A haplotypes of the rhesus macaque family 2 are given as examples (Suppl. Fig. 1).
AS of BTN3A in macaque species
Nearly as often, splice events mediated by alternative 3′ SS (#6, #4, #10) were detected, whereas splice events mediated by alternative 5′ SS (#5) were far less frequently observed (Fig. 7b). Additionally, alternative splice sites resulted in the partial retention of introns, often in combination with exon skipping, but always introducing a stop codon so that no intact gene product would be formed. One of these splice events resulted in a deletion of 112 bp, and was mediated by alternative 3′ and 5′ splice sites in exon 2. This AS was frequently observed in all three BTN3A transcripts and the BTN3ALike pseudogene (Fig. 7c), although no bona fide gene product could be expected. All three in silico models predicted identical scores for the alternative splice sites that mediate the event in the transcripts of BTN3A (pseudo)genes. The PWM model did not detect the alternative 3′ SS at all. Compared to the actual splice site scores, the alternative splice site scores were lower for all models, suggesting that constitutive splicing is dominant over this alternative splicing event (Suppl. Table 2).
The distribution analysis of BTN3A genes in rhesus and cynomolgus macaque families confirmed the presence of the three genes BTN3A1, BTN3A2 and BTN3A3 in all animals tested (Afrache et al. 2017). In addition, the discovery of a pseudogene, named BTN3A3Like, was facilitated by exon 2 analysis. This pseudogene appears, however, to be absent in hominoids, who instead have a BTN2A pseudogene (Rhodes et al. 2016). This observation confirms the flexibility of the region not only in humans but also in OWM such as macaques.
Allelic variation of all BTN3A genes was documented for rhesus as well as cynomolgus macaques, although the degree of polymorphism is quite low, with the lowest variation observed for BTN3A2 followed by BTN3A3 and BTN3A1. The latter gene has, however, a remarkably conserved exon 2 (IgV region), and no non-synonymous mutations in exon 4 (TM) and exons 6–8 (heptads) were observed. BTN3A3 shows no non-synonymous variations in exons 5–8 (heptads) and only one in exon 4 (TM region) and exon 9 (intracellular B30.2 part), respectively. As may be expected for a pseudogene, which experiences no purifying selection, the allelic variation observed in exon 2 of BTN3A3Like is higher than in those of the BTN3A genes (Fig. 2). In concordance with the level of polymorphism observed in macaque MHC genes (Doxiadis et al. 2013), BTN3A alleles and haplotypes are more variable in cynomolgus monkeys than in rhesus macaques of Indian origin as represented in our cohort.
Furthermore, phylogenetic analysis of exon 2 showed that HOM exon 2 sequences of the three BTN3A genes fall apart from the gene clusters of OWM and that they do not branch in a gene-specific manner as do the alleles of OWM (Fig. 1). The homogenization, replacing IgV-encoding sequences of BTN3A1, BTN3A2 and BTN3A3 in HOM, has recently been described (Afrache et al. 2017). This phenomenon appears to be the result of an ancient recombination between the 5′ region of a BTN3A1Like gene and the 3′ region of a BTN3A2-like gene, resulting in a chimeric BTN3A3 gene. Our data suggest that this ancient recombination process took place after the divergence of OWM and HOM ~ 25 myr ago, since the homogenization is not observed in OWM.
In addition to the exon 2 sequences of BTN3A3Like genes of diverse macaque species (Fig. 1), a database search revealed the presence of a BTN3A3Like sequence in the olive baboon. In contrast to the macaque pseudogene sequences, however, which all have the stop codon at amino acid 94 in exon 2, the olive baboon sequence already has a stop codon at amino acid 32. In the latter, a sequence of 258 bp is integrated after exon 1, which seems to originate from the 3′ untranslated region of the BTN3A2 gene. The existence of such a chimeric pseudogene seems to provide additional evidence that intragenic recombination processes are a common feature within the BTN region.
In contrast to the phylogenetic analysis of exon 2, the phylogeny of the BTN3A transcripts of exons 2–6 of human and non-human primate sequences shows a gene-specific clustering (Fig. 5), confirming that macaque BTN3A genes are true orthologs of their human equivalents.
Based on the relationship of the animals and segregation profiles within the rhesus and cynomolgus macaque families, we were able to define several BTN3A haplotypes. In concordance with the higher polymorphism observed in cynomolgus monkeys, haplotypes are more variable in this species than they are in rhesus macaques, most probably due to their various origins from different parts of Indonesia. Physical mapping showed the localization of the different macaque BTN genes within the extended MHC class I region, which is comparable to the position of the human BTN region (Fig. 6). Frequent co-segregation of BTN3A alleles/haplotypes with the MHC haplotypes verifies their localization as has been described for humans (Horton et al. 2004).
Already at the beginning of the century, AS was observed by Sanger sequencing for human BTN3A transcripts, indicating that AS occurs far more frequently in these genes than in others (Rhodes et al. 2001). Recently, in BG genes, which represent family members of the BTN gene family in chicken, AS has also been defined by Sanger sequencing (Chen et al. 2018). A remarkable phenomenon is the high degree of AS that has been observed for alleles of all BTN3A genes and the pseudogene. In general—e.g. for MHC class I and II genes—AS is rarely revealed using the low-resolution Sanger sequencing technique and is only detected when NGS techniques have been used and even then in relatively low numbers. The fact that AS isoforms are detected by the Sanger method for macaque BTN3A genes suggests that these transcripts are generated at a fairly high frequency. One could imagine that isoforms of the BTN3A molecules that have been generated due to AS may play a specific role as Vγ9Vδ2 T cell modulators. Exon skipping comprised the most frequently observed AS events, especially those that included exon 4, which encodes for the transmembrane part section, as was observed for BTN3A1 and BTN3A2. Predicting the actual splice sites with three different in silico models did not answer the question as to why exon 4 skipping does not occur in BTN3A3. Intron 3, which is situated next to exon 4, does show a high degree of nucleotide variation between the different BTN3A genes. Moreover, intron 3 of BTN3A3 is longer than the equivalent structure of the other two BTN3A genes. All these differences may influence alternative splicing—for example, through the existence of additional silencer/enhancer motives and/or the formation of secondary structures, which may prevent the appearance of a certain exon within the transcript. It is therefore plausible to suggest that the intron sequences may be the reason that this AS event can be detected in the transcripts of only two of the three BTN3A genes.
Exon skipping that includes exon 4, which encodes the transmembrane section, may result in the generation of soluble molecules. Gu et al. (2018) have presented a model that postulates that BTN3A isoforms help BTN3A1, the pAg-sensing molecule expressed on the cell surface, to make a conformational change when activated. This change, including possible multimerization events, can then be recognized by Vγ9Vδ2 T cell receptors. Soluble molecules may be especially supportive in this process. In this case, the frequently observed AS isoforms may actually represent a regulation phenomenon that helps in activating BTN3A-positive cells. We mainly looked at transcripts of white blood cells, which are a proxy for what may happen elsewhere in the body. One wonders of course whether the AS profiles would be different in tissues in healthy or stressed conditions. Indeed, soluble BTN3A isoforms are detected in the supernatant of pancreatic cell lines and the plasma of pancreatic ductal adenocarcinoma patients. Soluble BTN3A and BTN3A1 were associated with a decreased overall survival rate of these patients (Benyamine et al. 2016; Blazquez et al. 2018). Consequently, soluble BTN3A molecules can serve as prognostic biomarkers, highlighting the value of macaques in clinical cancer research, in addition to their importance in future proof-of-concept studies for the protective features of Vγ9Vδ2 T cells—for instance, against M. tuberculosis or other infectious agents (Chen 2016).
The authors wish to thank F. van Hassel for preparing the figures and D. Devine for editing the manuscript.
This work was supported in part by NIAID contracts HHSN272201100013C and HHSN272201600007C.
Compliance with ethical standards
All applicable international, national and/or institutional guidelines for the care and use of animals were followed.
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