DNA helicases BLM, RECQL4 and PIF1 as therapeutic targets in cancer

DNA helicases are essential for genome maintenance as they play critical roles in DNA replication, transcription, recombination, and DNA damage repair. In cancer, DNA helicases have dual roles since both inactivating mutations and overexpression can lead to tumor development. The clinical success of inhibiting proteins involved in DNA damage repair for cancer treatment encourages exploration of the potential use of DNA helicase inhibitors as therapeutic agents. However, the role of BLM, RECQL4 and PIF1 DNA helicases in cancer progression remains poorly investigated and the existing inhibitors of these helicases are far from clinical use. This study aims to analyze the impact of BLM, RECQL4 and PIF1 on cancer patient prognosis and to validate newly generated inhibitors of these helicases in cancer cells. To achieve this purpose, we analyzed genomic and transcriptomic alterations of BLM, RECQL4 and PIF1 in large pan-cancer publicly available datasets and their association with patient survival and other clinical parameters. We observed that RECQL4 high amplifications and BLM and RECQL4 mutations are common in cancer patients, while genomic alterations in PIF1 are rare. Additionally, we found that the absence of BLM mutations and the presence of RECQL4 high amplifications are generally associated with poor overall survival, increased metastasis rate, and reduced microsatellite instability and tumor mutational burden. Furthermore, gene set enrichment analysis indicated that immune signaling was downregulated in samples with high RECQL4 amplification. Further analysis of cohorts of melanoma patients treated with immune checkpoint inhibitors showed that high RECQL4 levels were linked to decreased recruitment of intra-tumoral immune cells, resulting in a poorer response to anti-PD-1 treatment. To investigate the interplay between RECQL4 and immune signaling, we generated RECQL4 overexpressing melanoma cell lines. Proteomics and secretomics analyses of these cells revealed RECQL4-driven downregulation of MHC-II molecules and cytokines involved in immune cell recruitment and activity. Regarding transcriptional changes, we found that BLM, RECQL4 and PIF1 expression is upregulated in tumor tissues compared to healthy adjacent tissues. This increased expression is correlated with worse overall survival and serves as a reliable independent prognostic factor for cancer patient survival. Finally, in collaboration with our industrial partners, we tested newly generated compounds targeting BLM and PIF1. We analyzed the effects of various inhibitors on cell survival, proliferation, migration, and cell cycle in melanoma cells. Our results showed that LDC088619 and ED770968 are the most potent BLM and PIF1 inhibitors, respectively, significantly altering cellular functions. However, further analyses are still required to validate their potential as therapeutic agents. In conclusion, this thesis paves the way for the use of BLM, RECQL4 and PIF1 as prognostic factors for poor survival in cancer. In addition, we propose their suitability as therapeutic targets for cancer treatment and identified promising compounds for targeting BLM and PIF1. Notably, this study reveals the potential role of RECQL4 in immune evasion and proposes that targeting RECQL4 might improve the response to immunotherapy.