Abstract 2564: Integrated transcriptomic, proteomic, and metabolomic analyses of human and mouse T cell leukemia
Authors: Chu Ching-Yu , Chen Szu-Yuan , Chueh Fu-Yu , Cheng Mei-Ling , Yu Chao-Lan 
Published: September 2020

Abstract
Nuclear and mitochondrial crosstalk plays an important role in regulating diverse cellular functions. It is contributed partly by non-canonical signaling in these two key subcellular compartments. Disruption of this signaling network has been shown to associate with oncogenic transformation. Our lab has long-term interests in studying the molecular mechanisms of cellular transformation by the oncogenic lymphocyte-specific protein tyrosine kinase (Lck). Previous reports from our lab show novel roles of Lck in both nucleus and mitochondrion of human and mouse T leukemic cell lines that exhibit metabolic reprogramming. However, it remains largely unclear how dysregulated nuclear and mitochondrial crosstalk leads to altered cellular metabolism in Lck-transformed leukemic cells.
The purpose of our study is to combine transcriptomic, proteomic, and metabolomic approaches to establish a link between altered nuclear gene expression, mitochondrial activity, and metabolic shift in Lck-transformed leukemic cells. For human T cell leukemia, we compared Jurkat T cells with its Lck-deficient derivative Jcam cell line. For mouse T cell leukemia, we compared EL4 cells that express normal levels of Lck and LSTRA cells that overexpress active Lck kinase. For additional verification, Jcam cells were reconstituted with wild-type Lck and EL4 cells were transfected with constitutively-active Lck mutant kinase. Total RNAs were subjected to transcriptomic analysis to identify genes significantly upregulated or downregulated in Lck-transformed cells. Tyrosine-phosphorylated proteins were enriched from Lck-transformed cells and identified by LC-MS/MS. Hydrophilic metabolites were extracted from whole cells and subjected to targeted metabolomic analysis using LC-MS/MS.
Pathway analysis of our transcriptomic data revealed significant changes of gene expression involved in several pathways, including cell adhesion and glycolysis pathways. We verified several glycolytic genes downregulated in Lck-transformed cells. These targets were further confirmed by reduced levels of corresponding metabolites. Proteomic analysis identified a set of novel target proteins potentially phosphorylated by Lck. Cyclin-dependent kinase 1 (CDK1) is of particular interest because its phosphorylation status correlates with its activity in regulating electron transport chain functions within mitochondrion. Our data suggest a link between tyrosine-phosphorylated CDK1 and reduced mitochondrial respiration.
In conclusion, integrated transcriptomic, proteomic, and metabolomic analyses enabled us to identify novel target genes regulated, proteins phosphorylated, and metabolites altered in Lck-transformed leukemic cells. Collectively, our data demonstrate a unique pattern of metabolic reprogramming both similar and distinct from the well-known Warburg effect in cancer cells.
Citation Format: Ching-Yu Chu, Szu-Yuan Chen, Fu-Yu Chueh, Mei-Ling Cheng, Chao-Lan Yu. Integrated transcriptomic, proteomic, and metabolomic analyses of human and mouse T cell leukemia [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2564.