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Comprehensive DNA Methylation Analysis Using a Methyl-CpG-binding Domain Capture-based Method in Chronic Lymphocytic Leukemia Patients
Published on: June 16, 2017
DNA methylome and single-cell transcriptome analyses reveal CDA as a potential druggable target for ALK
Haejeong Heo1,2, Jong-Hwan Kim3, Hyun Jung Lim1,2
1Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
Abstract:
Acquired resistance to inhibitors of anaplastic lymphoma kinase (ALK) is a major clinical challenge for ALK fusion-positive non-small-cell lung cancer (NSCLC). In the absence of secondary ALK mutations, epigenetic reprogramming is one of the main mechanisms of drug resistance, as it leads to phenotype switching that occurs during the epithelial-to-mesenchymal transition (EMT). Although drug-induced epigenetic reprogramming is believed to alter the sensitivity of cancer cells to anticancer treatments, there is still much to learn about overcoming drug resistance. In this study, we used an in vitro model of ceritinib-resistant NSCLC and employed genome-wide DNA methylation analysis in combination with single-cell (sc) RNA-seq to identify cytidine deaminase (CDA), a pyrimidine salvage pathway enzyme, as a candidate drug target. CDA was hypomethylated and upregulated in ceritinib-resistant cells. CDA-overexpressing cells were rarely but definitively detected in the naïve cell population by scRNA-seq, and their abundance was increased in the acquired-resistance population. Knockdown of CDA had antiproliferative effects on resistant cells and reversed the EMT phenotype. Treatment with epigenome-related nucleosides such as 5-formyl-2'-deoxycytidine selectively ablated CDA-overexpressing resistant cells via accumulation of DNA damage. Collectively, our data suggest that targeting CDA metabolism using epigenome-related nucleosides represents a potential new therapeutic strategy for overcoming ALK inhibitor resistance in NSCLC.
Insights
Acquired resistance to anaplastic lymphoma kinase (ALK) inhibitors in non-small-cell lung cancer (NSCLC) can be overcome by targeting cytidine deaminase (CDA). Targeting CDA metabolism with epigenome-related nucleosides shows promise for treating resistant NSCLC.
Area of Science:
- Oncology
- Molecular Biology
- Pharmacology
Background:
- Acquired resistance to anaplastic lymphoma kinase (ALK) inhibitors presents a significant clinical hurdle in ALK-positive non-small-cell lung cancer (NSCLC).
- Epigenetic reprogramming, particularly epithelial-to-mesenchymal transition (EMT), is a key mechanism driving drug resistance in the absence of secondary ALK mutations.
- Understanding and overcoming drug-induced epigenetic alterations is crucial for improving therapeutic outcomes.
Purpose of the Study:
- To identify novel therapeutic targets for overcoming acquired resistance to ALK inhibitors in NSCLC.
- To investigate the role of epigenetic reprogramming and its associated molecular mechanisms in drug resistance.
- To evaluate the potential of targeting cytidine deaminase (CDA) as a strategy to re-sensitize resistant NSCLC cells to treatment.
Main Methods:
- Utilized an in vitro model of ceritinib-resistant NSCLC.
- Performed genome-wide DNA methylation analysis and single-cell RNA sequencing (scRNA-seq).
- Assessed the effects of CDA knockdown and treatment with epigenome-related nucleosides (e.g., 5-formyl-2'-deoxycytidine).
Main Results:
- Identified cytidine deaminase (CDA), a pyrimidine salvage enzyme, as a target; CDA was hypomethylated and upregulated in resistant cells.
- scRNA-seq revealed increased abundance of CDA-overexpressing cells in the acquired-resistance population.
- CDA knockdown inhibited proliferation and reversed EMT in resistant cells; nucleoside treatment selectively eliminated CDA-overexpressing cells via DNA damage.
Conclusions:
- Targeting CDA metabolism represents a promising therapeutic strategy for overcoming ALK inhibitor resistance in NSCLC.
- Epigenome-related nucleosides demonstrate potential for selectively eliminating resistant cancer cells.
- This study provides a foundation for developing novel treatments for drug-resistant NSCLC.
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