Genetic control of cross-resistances in P. falciparum

描述(由申请人提供)：对多种抗疟疾药物产生抗药性的恶性疟原虫的出现和传播是疟疾研究面临的一项重大挑战。耐药研究目前强调单基因耐药决定因素的作用，并已将突变确定为耐药的标志。然而，这种对单个耐药基因的关注忽略了耐药基因发挥作用的基因组背景，即药物选择所选择的多基因途径和细胞过程。这些基因网络中的调节性和补偿性背景突变为相关的药物反应和交叉耐药提供了生理学基础；因此，识别与不同药物反应有关的共同基因机制将为寄生虫分离株对新化合物产生抗药性的能力提供标记。恶性疟原虫基因组序列和相关工具提供了将基因序列与复杂表型联系起来的机会。通过利用遗传杂交后代的高分辨率连锁图谱和精确的药物反应测量，数量性状基因座(QTL)定位可以精确地定位控制这些性状的基因组区域以定位候选基因，并指导单核苷酸多态(SNP)分析和局部基因转录。这一建议的假设是，相关的药物反应是共同遗传机制的结果，这些遗传机制可以通过比较QTL定位到特定的基因座，从而有效地利用基因组工具来定位交叉耐药的基因。有两个特定的目的将被用来寻找这些基因：1)测量HB3xDd2遗传杂交后代的药物反应，并定位控制这些表型的基因座。对抗疟药物的反应将单独和组合进行评分，QTL作图将识别控制这些特性的基因座的数量、相对效应和位置。基因图谱将在统计上叠加，以识别不同药物反应的共同基因座。2)将这些基因座与原始序列、比较序列和转录图谱进行整合，以确定候选基因。序列标记位点将把遗传位点与DNA重叠群联系起来，便于搜索位置候选基因，从中可以检测到单核苷酸多态(SNP)中的结构变异，并用于世界各地寄生虫分离株的关联图谱。将使用定量聚合酶链式反应和长寡核苷酸微阵列来评估位点特异性转录，以确定与药物反应一致的可遗传表达多态。

DESCRIPTION (provided by the applicant): The emergence and spread of Plasmodium falciparum parasites resistant to a wide array of antimalarial drugs is a critical challenge facing malaria research. Drug resistance studies currently emphasize the role of single-gene determinants of resistance, and have led to identification of mutations as markers of drug resistances. However, this focus on individual resistance genes ignores the genomic context in which resistance genes function, that is, the multigene pathways and cellular processes that have been co-opted by drug selection. Modulatory and compensatory "background" mutations in these gene networks provide a physiological basis for correlated drug responses and cross resistances; consequently, identification of common gene mechanisms involved in responses to different drugs will provide markers for the capacity of a parasite isolate to develop resistance to new compounds. The P. falciparum genome sequence and associated tools provide an opportunity to connect gene sequences to complex phenotypes. By exploiting a high-resolution linkage map and precise drug response measurements in the progeny of a genetic cross, quantitative trait loci (QTL) mapping can pinpoint regions of the genome controlling these traits to target positional candidate gene searches, and to guide analysis of single nucleotide polymorphisms (SNP) and local gene transcription. The hypothesis of this proposal is that correlated drug responses are the result of shared genetic mechanisms that can be mapped to specific loci by comparative QTL mapping, leading to efficient use of genomic tools to pinpoint genes that underlie cross resistances. Two Specific Aims will be used to find these genes: 1) To measure drug responses in progeny of the HB3 xDd2 genetic cross and to map the loci controlling these phenotypes. Responses to antimalarial compounds will be scored individually and in combinations, and QTL mapping will identify the number, relative effects, and positions of loci controlling these traits. Genetic profiles will be statistically superimposed to identify loci common to different drug responses. 2) To integrate these loci with primary and comparative sequences and transcription profiles to identify candidate genes. Sequence tagged sites will link genetic loci to DNA contigs and facilitate the search for positional candidate genes from which structural variants can be detected in single nucleotide polymorphisms (SNP) and used for association mapping in parasite isolates from around the world. Locus-specific transcription will be evaluated using quantitative PCR and long oligonucleotide micro-arrays to identify heritable expression polymorphisms that coincide with drug responses.