Cancer Stem Cell Biology: DNA Repair Mechanisms, Therapeutic Resistance, and Emerging Treatment Strategies

Abstract

: DNA is continuously challenged by endogenous and exogenous insults, generating lesions that threaten genomic stability. Normal stem cells preserve genome integrity through highly coordinated DNA damage response (DDR) networks involving efficient base excision repair (BER), homologous recombination (HR), cell-cycle checkpoints, and TP53-mediated quality control. Cancer stem cells (CSCs), a rare tumor subpopulation responsible for tumor initiation, metastasis, relapse, and therapeutic resistance, exploit these protective mechanisms while acquiring distinct DNA repair adaptations. This review examines how stemness-associated signaling pathways, including Hedgehog, Notch, and Wnt/ β -catenin, interact with DDR programs to promote CSC survival under genotoxic stress. CSCs frequently exhibit enhanced HR activity driven by RAD51 and BRCA1/2, increased tolerance to replication stress, and sustained DNA repair capacity, contributing to resistance against chemotherapy and radiotherapy. Simultaneously, many CSC populations retain selective deficiencies in non-homologous end joining (NHEJ), nucleotide excision repair (NER), or BER, creating therapeutically exploitable vulnerabilities. We further discuss emerging DDR regulators, including HMCES-mediated protection of abasic sites and polymerase theta (Pol θ )-dependent alternative end joining, as well as the influence of tumor microenvironmental factors such as hypoxia, extracellular vesicles, and cancer-associated fibroblasts on CSC repair capacity and plasticity. We summarize current and emerging therapeutic strategies targeting CSC-specific DDR dependencies, including PARP, ATR, CHK1, and Pol θ inhibitors, replication stress-inducing agents, developmental pathway inhibitors, antibody-drug conjugates carrying topoisomerase I inhibitor payloads, and immunotherapeutic approaches. Particular emphasis is placed on synthetic-lethal strategies and biomarker-guided patient stratification using homologous recombination deficiency signatures, RAD51 foci, and SLFN11 expression. Understanding the unique DDR landscape of CSCs may facilitate the development of rational combination therapies capable of overcoming therapeutic resistance and improving long-term cancer control.