Multiomic Profiling of Tyrosine Kinase Inhibitor-Resistant K562 Cells Suggests Metabolic Reprogramming To Promote Cell Survival

Resistance to chemotherapy can occur
through a wide variety of
mechanisms. Resistance to tyrosine kinase inhibitors (TKIs) often
arises from kinase mutationshowever, “off-target”
resistance occurs but is poorly understood. Previously, we established
cell line resistance models for three TKIs used in chronic myeloid
leukemia treatment, and found that resistance was not attributed entirely
to failure of kinase inhibition. Here, we performed global, integrated
proteomic and transcriptomic profiling of these cell lines to describe
mechanisms of resistance at the protein and gene expression level.
We used whole transcriptome sequencing and SWATH-based data-independent
acquisition mass spectrometry (DIA-MS), which does not require isotopic
labels and provides quantitative measurements of proteins in a comprehensive,
unbiased fashion. The proteomic and transcriptional data were correlated
to generate an integrated understanding of the gene expression and
protein alterations associated with TKI resistance. We defined mechanisms
of resistance and two novel markers, CA1 and alpha-synuclein, that
were common to all TKIs tested. Resistance to all of the TKIs was
associated with oxidative stress responses, hypoxia signatures, and
apparent metabolic reprogramming of the cells. Metabolite profiling
and glucose-dependence experiments showed that resistant cells had
routed their metabolism through glycolysis (particularly through the
pentose phosphate pathway) and exhibited disruptions in mitochondrial
metabolism. These experiments are the first to report a global, integrated
proteomic, transcriptomic, and metabolic analysis of TKI resistance.
These data suggest that although the mechanisms are complex, targeting
metabolic pathways along with TKI treatment may overcome pan-TKI resistance.

化疗耐药可通过多种机制产生。酪氨酸激酶抑制剂（tyrosine kinase inhibitors, TKIs）耐药通常由激酶突变引发，但“脱靶”耐药虽有发生，其机制却尚未阐明。此前，我们构建了三种用于慢性髓系白血病治疗的酪氨酸激酶抑制剂（TKIs）细胞耐药模型，发现耐药并非完全由激酶抑制失效导致。本研究对上述细胞系开展了全景式整合蛋白质组与转录组分析，旨在从蛋白质与基因表达层面解析耐药机制。我们采用全转录组测序技术，以及基于SWATH的数据非依赖性采集质谱（data-independent acquisition mass spectrometry, DIA-MS）——该技术无需同位素标记，可实现全面且无偏倚的蛋白质定量检测。将蛋白质组与转录组数据进行关联分析，以整合解析与酪氨酸激酶抑制剂（TKIs）耐药相关的基因表达与蛋白质组改变。我们明确了耐药机制，并鉴定出两种新型耐药标志物——碳酸酐酶1（CA1）与α-突触核蛋白（alpha-synuclein），其在所有受试酪氨酸激酶抑制剂（TKIs）的耐药细胞中均存在异常表达。所有受试酪氨酸激酶抑制剂（TKIs）的耐药机制均与氧化应激应答、缺氧特征及细胞代谢重编程显著相关。代谢组分析与葡萄糖依赖性实验结果显示，耐药细胞的代谢通路转向糖酵解（尤以磷酸戊糖途径为甚），并出现线粒体代谢紊乱。本研究首次报道了针对酪氨酸激酶抑制剂（TKIs）耐药的全景式整合蛋白质组、转录组及代谢组分析。研究结果表明，尽管耐药机制复杂，但联合靶向代谢通路与酪氨酸激酶抑制剂（TKIs）治疗，或可克服泛酪氨酸激酶抑制剂耐药。