Genetic control of cross-resistances in P. falciparum

描述（由申请方提供）：对多种抗疟药物具有耐药性的恶性疟原虫寄生虫的出现和传播是疟疾研究面临的一个关键挑战。目前的耐药性研究强调单基因耐药性决定因素的作用，并导致鉴定突变作为耐药性的标志。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性提供了生理基础;因此，鉴定对不同药物的反应所涉及的共同基因机制将为寄生虫分离株对新化合物产生耐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中的高分辨率连锁图和精确的药物反应测量，数量性状基因座（QTL）定位可以精确定位控制这些性状的基因组区域，以靶向位置候选基因搜索，并指导单核苷酸多态性（SNP）和局部基因转录的分析。该提议的假设是，相关的药物反应是共享的遗传机制的结果，该遗传机制可以通过比较QTL作图定位到特定的基因座，从而有效地使用基因组工具来确定交叉抗性的基因。将使用两个特定目的来发现这些基因：1）测量HB 3 xDd 2遗传杂交的后代中的药物应答并绘制控制这些表型的基因座。对抗疟化合物的反应将单独和组合进行评分，QTL作图将确定控制这些性状的基因座的数量、相对效应和位置。将对遗传图谱进行统计学叠加，以确定不同药物应答的共同基因座。2)整合这些基因座与主要和比较序列和转录谱，以确定候选基因。序列标记位点将遗传基因座与DNA重叠群连接起来，并有助于搜索位置候选基因，从这些基因中可以在单核苷酸多态性（SNP）中检测到结构变体，并用于世界各地寄生虫分离株的关联作图。将使用定量PCR和长寡核苷酸微阵列评价基因座特异性转录，以鉴定与药物反应一致的遗传表达多态性。

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.