Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice

The outcome of an encounter with Mycobacterium tuberculosis (Mtb) depends on the pathogen's ability to adapt to the heterogeneous immune response of the host. Understanding this interplay has proven difficult, largely because experimentally tractable small animal models do not recapitulate the heterogenous disease observed in natural infections. We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to associate bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection and represent reproducible models of qualitatively distinct immune states. Global analysis of Mtb mutant fitness across the CC panel revealed that a large fraction of the pathogen's genome is necessary for adaptation to specific host microenvironments. Both immunological and bacterial traits were associated with genetic variants distributed across the mouse genome, elucidating the complex genetic landscape that underlies host-pathogen interactions in a diverse population. Overall design: Subject mice (48 Collaborative Cross strains, 8 Collaborative Cross parents, 4 k/o strains) were infected via tail vein injection with a saturated M. tuberculosis himar1 transposon library. Animals were sacrificed after 4 weeks, or earlier if moribund, and Tn-Seq was performed after library recovery from harvested spleens. In the majority of cases, two replicates were obtained per mouse strain, 6 replicates in the case of in vitro-grown libraries.

宿主与结核分枝杆菌（Mycobacterium tuberculosis, Mtb）接触后的转归，取决于病原体适应宿主异质性免疫应答的能力。阐明这一相互作用始终颇具挑战，核心原因在于现有实验可及的小型动物模型无法复现自然感染中观察到的异质性疾病表型。本研究借助遗传多样性丰富的协作杂交（Collaborative Cross, CC）小鼠面板，结合结核分枝杆菌突变体文库，将细菌的遗传需求与宿主遗传学及免疫状态相关联。研究结果表明，不同CC品系对感染的易感性差异显著，可作为具有明确免疫状态的可重复研究模型。对CC面板中结核分枝杆菌突变体适应度的全局分析显示，病原体基因组的绝大部分区段均需参与特定宿主微环境的适应过程。免疫相关与细菌相关的性状均与分布于小鼠基因组的遗传变异存在显著关联，由此阐明了多样化种群中宿主-病原体相互作用背后的复杂遗传调控图谱。
实验整体设计：受试小鼠（包含48种CC品系、8种CC亲本品系以及4种基因敲除（knockout, KO）菌株）经尾静脉注射接种饱和浓度的结核分枝杆菌himar1转座子突变体文库。实验动物于感染4周后实施安乐死，若出现濒死状态则提前处死；从收获的脾脏中回收突变体文库后，开展转座子测序（Transposon Sequencing, Tn-Seq）。多数情况下，每株小鼠设置2次生物学重复；体外培养的文库则设置6次生物学重复。