Background <p>Cancer stem cells (CSCs) are the small subpopulations of propagating tumor cells that cause resistance, relapse, and metastasis. Their maintenance is controlled by the specific signaling pathways, transcriptional and epigenetic regulators, and interactions with the tumor microenvironment (TME). Advances in high-resolution technologies are reshaping our understanding of CSC biology and its clinical relevance.</p> Area covered <p>This review outlines the genomic and epigenetic landscapes of CSCs, focusing on their regulation by key signaling pathways, transcription factors, and TME components. We summarize current therapeutic approaches, including pathway specific inhibitors, nanoparticle-based systems, immunotherapies, and epigenetic modulators, emphasizing their potential to disrupt CSC survival and niche supporting CSCs maintenance. Special attentions are given to advanced single-cell and spatial technologies like scRNA-seq, scATAC-seq, and spatial transcriptomics that enable the precise mapping of the CSC heterogeneity, stemness gene signature, chromatin assembly, and CSC-TME interactions.</p> Expert opinion <p>The increasing convergence of CSC biology, TME research, and technological advances in omics is opening up new horizons for precision oncology. Long term clinical benefits require combination of CSCs targeted approaches with strategies that reprogram the TME and overcome resistance. Emerging single-cell and spatial platforms provides high-resolution insights into CSC-TME dynamics and shows potential for translating basic understanding into clinical advances. Future work should focus on incorporating these tools into translational research pipelines. Integrating these datasets with the bioinformatics platforms and public databases will accelerate the biomarker discovery, newer therapy development, and patient stratification for precision oncology.</p>