Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.
Population genomic scan for candidate signatures of balancing selection to guide antigen characterization in malaria parasites.
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DOI：
10.1371/journal.pgen.1002992
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Conway DJ
中科院分区：
文献类型：
--
作者：
Amambua-Ngwa A;Tetteh KK;Manske M;Gomez-Escobar N;Stewart LB;Deerhake ME;Cheeseman IH;Newbold CI;Holder AA;Knuepfer E;Janha O;Jallow M;Campino S;Macinnis B;Kwiatkowski DP;Conway DJ
脊椎动物的获得性免疫在地方病病原体中保持多态性，导致平衡选择的可识别特征。为了全面调查人类疟疾寄生虫恶性疟原虫中这种选择下的基因，我们在冈比亚流行人群的临床分离株中产生了寄生虫的配对末端短读段序列，将其映射到3D 7菌株参考基因组，以获得65个分离株的高质量全基因组编码序列数据。少数基因没有可靠地定位，包括高变var、rifin和stevor家族，但是对于至少50个分离株，5，056个基因（基因组中所有基因的90.9%）具有>70%的序列覆盖度，最小读取深度为5，其中2，853个基因包含3个或更多个单核苷酸多态性（SNP），用于多态性位点频谱分析。在负偏频率的总体背景下，正如从历史种群扩张结合纯化选择所预期的那样，确定了具有指示异常中间频率的特征的基因的边远少数。比较具有不同阶段特异性的基因，这些特征在那些在侵入红细胞的裂殖子阶段具有峰值表达的基因中最常见。clag、PfMC-2 TM、surfin和msp 3样基因家族的成员具有高度代表性，最强的签名是在msp 3样基因PF10_0355中。在45个临床和11个实验室适应的分离株生长到含裂殖子的裂殖体阶段的msp 3样转录物的分析揭示了PF10_0355的令人惊讶的低表达。在不同的克隆寄生虫系中，蛋白产物在少数成熟寄生虫中表达（在大多数系中<1%，在克隆HB 3中<10%），并且分别培养的HB 3的8个亚克隆具有中间的阳性频率谱（0.9至7.5%），表明该多态性抗原的时相可变表达。这一点和其他确定的目标平衡选择，现在优先功能研究。获得性免疫应答的记忆成分选择编码病原体的重要靶抗原的基因中的多态性的独特模式。这些可以通过调查平衡选择的证据来检测，如先前在对编码疟疾寄生虫抗原的基因的分析中所示，所述疟疾寄生虫抗原是天然获得性免疫的候选靶标。为了进行全面筛选，以发现主要的人类疟疾寄生虫恶性疟原虫的免疫靶点，对西非的一个流行人群进行了采样，并从65个临床分离株中获得了基因组序列数据，从而可以分析几乎所有蛋白质编码基因的多态性。先前通过毛细管重测序在独立人群样本中研究的抗原基因在全基因组分析中具有高度一致的指数，并且这已经确定了具有更强的平衡选择证据的其他基因，现在优先用于功能研究和潜在的疫苗候选。与这种选择一致的统计特征在侵入红细胞的阶段具有峰值表达的基因中特别常见，并且代表了几个基因家族的成员。最强的签名是在msp 3样基因PF10_0355中，因此我们研究了寄生虫中的转录本和蛋白质产物，揭示了一种意想不到的相变量表达模式。平衡选择下多态性抗原表达的变化可能比以前认为的更常见，需要进一步研究以评估疫苗候选人。
Acquired immunity in vertebrates maintains polymorphisms in endemic pathogens, leading to identifiable signatures of balancing selection. To comprehensively survey for genes under such selection in the human malaria parasite Plasmodium falciparum, we generated paired-end short-read sequences of parasites in clinical isolates from an endemic Gambian population, which were mapped to the 3D7 strain reference genome to yield high-quality genome-wide coding sequence data for 65 isolates. A minority of genes did not map reliably, including the hypervariable var, rifin, and stevor families, but 5,056 genes (90.9% of all in the genome) had >70% sequence coverage with minimum read depth of 5 for at least 50 isolates, of which 2,853 genes contained 3 or more single nucleotide polymorphisms (SNPs) for analysis of polymorphic site frequency spectra. Against an overall background of negatively skewed frequencies, as expected from historical population expansion combined with purifying selection, the outlying minority of genes with signatures indicating exceptionally intermediate frequencies were identified. Comparing genes with different stage-specificity, such signatures were most common in those with peak expression at the merozoite stage that invades erythrocytes. Members of clag, PfMC-2TM, surfin, and msp3-like gene families were highly represented, the strongest signature being in the msp3-like gene PF10_0355. Analysis of msp3-like transcripts in 45 clinical and 11 laboratory adapted isolates grown to merozoite-containing schizont stages revealed surprisingly low expression of PF10_0355. In diverse clonal parasite lines the protein product was expressed in a minority of mature schizonts (<1% in most lines and ∼10% in clone HB3), and eight sub-clones of HB3 cultured separately had an intermediate spectrum of positive frequencies (0.9 to 7.5%), indicating phase variable expression of this polymorphic antigen. This and other identified targets of balancing selection are now prioritized for functional study. The memory component of acquired immune responses selects for distinctive patterns of polymorphism in genes encoding important target antigens of pathogens. These are detectable by surveying for evidence of balancing selection, as previously illustrated in analyses of genes encoding malaria parasite antigens that are candidate targets of naturally acquired immunity. For a comprehensive screen to discover targets of immunity in the major human malaria parasite Plasmodium falciparum, an endemic population in West Africa was sampled and genome sequence data obtained from 65 clinical isolates, allowing analysis of polymorphism in almost all protein-coding genes. Antigen genes previously studied by capillary re-sequencing in independent population samples had highly concordant indices in the genome-wide analysis here, and this has identified other genes with stronger evidence of balancing selection, now prioritized for functional study and potential vaccine candidacy. The statistical signatures consistent with such selection were particularly common in genes with peak expression at the stage that invades erythrocytes, and members of several gene families were represented. The strongest signature was in the msp3-like gene PF10_0355, so we studied the transcript and protein product in parasites, revealing an unexpected pattern of phase variable expression. Variation in expression of polymorphic antigens under balancing selection may be more common than previously thought, requiring further study to assess vaccine candidacy.
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