Complex Analysis Group, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad-121001, India.
Mol Omics. 2021 Apr 1;17(2):296-306. doi: 10.1039/d0mo00138d. Epub 2021 Feb 17.
We analyze high throughput proteomics data reflecting the response of the Mφ-like THP1 cell line to Mycobacterium tuberculosis (M. tuberculosis) infection. M. tuberculosis's engagement with the host's metabolic pathways is a known strategy employed by the pathogen to shift the balance in its favour. Our study revisits this strategy through the integration of the temporal proteomics data in the genome-scale metabolic model (GSMM) giving context-specific GSMMs. THP1 cells were infected with H37Ra, H37Rv, BND433 and JAL2287 strains of M. tuberculosis and the host response was studied at 6, 18, 30 and 42 hours after infection. We have developed a modified flux balance analysis (FBA), which does not use an objective function, to find the fluxes of metabolic reactions in different strains and stages of infection and have revealed different functional modules. Hence, we have established a method of rewiring using GSMMs to explore potential strategies to change the flux state of virulent M. tuberculosis infected macrophages as against their avirulent counterparts. Our methodology gives a correlation between different flux states, the extent of which was interpreted as the extent of rewiring. The accuracy of the results from the proposed methodology was validated with gene knockout experimental data. We found that more than one reaction has to be rewired simultaneously to alter virulent to an avirulent response. The identified modules showed influence across the investigated strains and time points suggesting that these reactions could be therapeutically targeted. This novel methodology is now available for use in other systems.
我们分析了高通量蛋白质组学数据，这些数据反映了 Mφ 样 THP1 细胞系对结核分枝杆菌（M. tuberculosis）感染的反应。结核分枝杆菌与宿主代谢途径的相互作用是病原体用来改变其有利平衡的已知策略。我们通过整合基因组规模代谢模型（GSMM）中的时间蛋白质组学数据来重新审视这一策略，从而提供了特定于上下文的 GSMM。THP1 细胞被 H37Ra、H37Rv、BND433 和 JAL2287 株结核分枝杆菌感染，在感染后 6、18、30 和 42 小时研究宿主反应。我们开发了一种改进的通量平衡分析（FBA），该方法不使用目标函数，以找到不同菌株和感染阶段代谢反应的通量，并揭示了不同的功能模块。因此，我们使用 GSMM 建立了一种重新布线的方法，以探索改变毒力结核分枝杆菌感染的巨噬细胞通量状态的潜在策略，而不是它们的无毒对应物。我们的方法在不同通量状态之间建立了相关性，其程度可以解释为重新布线的程度。提出的方法的结果的准确性通过基因敲除实验数据进行了验证。我们发现，要改变毒力到无毒反应，必须同时重新布线多个反应。鉴定的模块显示出在整个研究的菌株和时间点上的影响，表明这些反应可以作为治疗靶点。这种新的方法现在可用于其他系统。
