Identification and Functional Validation of the Novel Antimalarial Resistance Locus <em>PF10_0355</em> in <em>Plasmodium falciparum</em>

The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (∼1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.恶性疟原虫（Plasmodium falciparum）对包括人体免疫系统、抗疟药物在内的环境压力具备适应能力，这使得疟疾始终是公共卫生领域的持续负担。阐明此类适应性演化的遗传基础，对于成功开展疟疾防控干预至关重要。为此，我们研发了一款可检测超过17000个单核苷酸多态性（single nucleotide polymorphisms，约1个SNP/千碱基）的高密度基因分型阵列，并将其应用于来自三大洲的57株经体外培养适应的疟原虫。我们对种群内部及种群间的全基因组遗传多样性进行了系统表征，并鉴定出多个携带自然选择信号的基因座，提示这些位点在近期适应性演化中发挥了关键作用。此外，我们开展了全基因组关联研究（genome-wide association study，GWAS），搜寻与13种抗疟药物耐药性相关的基因座；最终检测到了已知及全新的耐药基因座，其中包括一个新的卤泛群（halofantrine）耐药基因座PF10_0355。通过功能验证实验，我们证实PF10_0355基因过表达会降低疟原虫对卤泛群、甲氟喹（mefloquine）与苯芴醇（lumefantrine）的敏感性，但对结构无关的抗疟药物敏感性无显著影响；同时证实基因拷贝数增加可介导耐药性。本研究的全基因组关联分析及后续功能验证结果证实，全基因组研究方法具备阐明疟原虫基因组中功能关键基因座的潜力。