ALDH1A1 and HLTF modulate the activity of lysosomal autophagy inhibitors in cancer cells

Lysosomal autophagy inhibitors (LAI) such as hydroxychloroquine (HCQ) have significant activity in a subset of cancer cell lines. LAIs are being evaluated in cancer clinical trials, but genetic determinants of sensitivity to LAIs are unknown, making it difficult to predict which tumors would be most susceptible. Here we characterize differentially expressed genes in HCQ-sensitive (-S) and -resistant (-R) cancer cells. Notably, expression of canonical macroautophagy/autophagy genes was not associated with sensitivity to HCQ. Expression patterns of ALDH1A1 (aldehyde dehydrogenase 1 family member A1) and HLTF (helicase like transcription factor) identified HCQ-S (ALDH1A1_high HLTF_low; ALDH1A1_low HLTF_low) and HCQ-R (ALDH1A1_low HLTF_high) cells. ALDH1A1 overexpression was found to enhance LAI cell entry and cytotoxicity without directly affecting lysosome function or autophagic flux. Expression of HLTF allows repair of DNA damage caused by LAI-induced reactive oxygen species, leading to HCQ resistance. Sensitivity to HCQ is increased in cells where <i>HLTF</i> is silenced by promoter methylation. HLTF overexpression blunted the antitumor efficacy of chloroquine derivatives in vitro and in vivo. Analysis of tumor RNA sequencing data from &gt;700 patients in the Cancer Genome Atlas identified cancers including colon cancer, renal cell carcinoma, and gastric cancers, that were enriched for the HCQ-S or HCQ-R signature. These results provide mechanistic insights into LAI efficacy, and guidance for LAI clinical development.

溶酶体自噬抑制剂（lysosomal autophagy inhibitors，LAI）如羟氯喹（hydroxychloroquine，HCQ）在部分癌细胞系中展现出显著抗肿瘤活性。目前LAIs正处于癌症临床试验阶段，但LAIs敏感性的遗传决定因素仍未明确，这使得难以预测哪些肿瘤对其最为易感。本研究对羟氯喹敏感（HCQ-S）与耐药（HCQ-R）癌细胞中的差异表达基因进行了系统表征。值得注意的是，经典巨自噬/自噬相关基因的表达与HCQ敏感性并无关联。醛脱氢酶1家族成员A1（aldehyde dehydrogenase 1 family member A1，ALDH1A1）与解旋酶样转录因子（helicase like transcription factor，HLTF）的表达模式可区分HCQ-S细胞（ALDH1A1_high HLTF_low；ALDH1A1_low HLTF_low）与HCQ-R细胞（ALDH1A1_low HLTF_high）。研究发现，ALDH1A1过表达可增强LAI的细胞摄取效率与细胞毒性，且不会直接影响溶酶体功能或自噬流。HLTF的表达可修复LAI诱导活性氧介导的DNA损伤，进而导致HCQ耐药。当<i>HLTF</i>因启动子甲基化而沉默时，细胞对HCQ的敏感性显著升高。HLTF过表达会在体内外削弱氯喹衍生物的抗肿瘤功效。对癌症基因组图谱（Cancer Genome Atlas）中700余例患者的肿瘤RNA测序数据进行分析后发现，结直肠癌、肾细胞癌及胃癌等多种癌症均富集了HCQ-S或HCQ-R特征谱。本研究结果为阐明LAI的抗肿瘤作用机制提供了全新见解，并为LAI的临床研发提供了重要指导。