HLTF gene silencing: a novel determinant of sensitivity to autophagy inhibition

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DESCRIPTION (provided by applicant): Autophagy is a lysosome-dependent degradative process that protects cancer cells from metabolic and therapeutic stress. Autophagy is up regulated in most advanced cancers and has identified as a new target for cancer therapy. Autophagy inhibition with chloroquine (CQ) derivatives augments the efficacy of many anticancer therapies. Numerous clinical trials are testing the combination of variety of anticancer agents with hydroxychloroquine (HCQ), but there currently is no biomarker that can focus the development of HCQ combinations or regimens involving novel emerging autophagy inhibitors into patient subsets that will most likely benefit from this strategy. To identify a candidate biomarker of sensitivity to autophagy inhibition, a microarray analysis of differentially expressed genes in HCQ-sensitive and HCQ-resistant human cancer cell lines was conducted. The most down regulated gene in HCQ-sensitive cells was helicase- like transcription factor (HLTF), an understudied tumor suppressor gene involved in multiple aspects of maintaining genomic integrity during replication stress. HLTF expression is silenced by promoter methylation in 20-40% of lung, colon, and gastric carcinomas. In a large panel of cell lines HLTF gene silencing was found almost exclusively in cell lines that were sensitive to HCQ. Forced expression of HLTF in HLTF silenced cells conferred resistance to HCQ. The link between autophagy inhibition and HLTF may be through oxidative DNA damage that was observed soon after HCQ treatment. A methylation-specific PCR assay was able to detect HLTF methylation status of tumors in the serum samples of patients with melanoma and breast cancer indicating that HLTF gene silencing is common across multiple malignancies and a serum assay may be able to classify patients as HLTF gene silenced or expressed. This proposal will test the hypotheses that a) HLTF gene silencing confers sensitivity to autophagy inhibitors by allowing oxidative DNA damage to go unrepaired~ b) A clinical grade assay for HLTF promoter methylation in the serum or tumors of patients can be a sensitive and specific assay for HLTF gene silencing c) HLTF gene silencing is common in a number of malignancies and predicts of clinical response in patients treated with HCQ. Knowledge gained from completion of these specific aims will establish a new mechanistic framework that links autophagy inhibition to the DNA damage response. This work will shed light on the functions of commonly silenced tumor suppressor gene HLTF and will determine which malignancies should be a target for the development of autophagy inhibitors. Finally, as novel autophagy inhibitors are currently being developed for clinical trials in cancer patients, completion of these aims will provide the supporting data necessary for future development of a CLIA approved predictive assay that could be used to enroll the patients most likely to benefit from autophagy inhibitors.