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The human ATP binding cassette (ABC) family of transporter proteins plays an important role in the maintenance of homeostasis in vivo. The aim of this study is to evaluate the potential diagnostic, prognostic, and therapeutic value of the ABCA10 gene in BRCA. We found that ABCA10 expression was downregulated in different subgroups of breast cancer and strongly correlated with pathological stage in BRCA patients. Low expression of ABCA10 was associated with BRCA patients showing shorter overall survival (OS). ABCA10 expression may be regulated by promoter methylation, copy number variation (CNV) and kinase, and is associated with immune infiltration. Our study also demonstrated the potential role of ABCA10 modifications in tumor microenvironment (TME) cellular infiltration. Nevertheless, the regulatory mechanism remains unknown and immunotherapy is marginal in BRCA. We demonstrate the expression of different ABCA10 modulators in breast cancer associated with genetic variants, deletions, tumor mutation burden (TMB) and TME. Mutations in ABCA10 are positively associated with different immune cells in six different immune databases and play an important role in immune cell infiltration in breast cancer. Overall, this study provides evidence that ABCA10 could become the potential targets for precision treatment and new biomarkers in the prognosis of breast cancer.

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Mutations in the isocitrate dehydrogenase gene (IDH1) are involved in the progression of tumors. Although IDH1 has a role in various tumors, its clinical relevance and its expression in response to the immune response have not been investigated in prostate adenocarcinoma (PRAD). In the present study, we investigated the utility of IDH1 as a prognostic biomarker for PRAD by analyzing IDH1 mRNA expression and its association with patient survival and immune cell infiltration. IDH1 mRNA expression was significantly higher in PRAD tissue than in normal tissue, and Kaplan–Meier survival analysis showed that IDH1 expression was significantly associated with poor prognosis in PRAD patients. To elucidate the mechanisms involved, the correlation between IDH1 expression and the level of immune cell infiltration, in particular of immunosuppressive cells such as CD8+ T-cells, CD4+ T-cells, and macrophages, was further analyzed by single-cell RNA sequencing. We also screened a pharmacogenetic database for IDH1-specific drugs that inhibited high expression in PRAD. In the present study, we used a combination of databases to identify a significant correlation between IDH1 expression and cellular infiltration and to explain the mechanism by which IDH1 confers poor prognosis in PRAD, thus demonstrating the relevance of IDH1 expression as a prognostic biomarker with clinical utility in PRAD patients.

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.