Neha Bhongir

https://doi.org/10.64823/ijor.2601004

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technological advancement, overcoming the primary limitation of bulk-RNA sequencing–its inability to capture cellular heterogeneity. Consequently, scRNA-seq plays a pivotal role in characterising the complex cellular landscape of the tumor microenvironment. Composed of diverse populations, including immune and stromal cells, and characterised by intricate cell-to-cell interactions, the tumor microenvironment is a central driver of tumorigenesis. Examining these dynamic biological systems at the transcriptomic level enables detailed mapping of intercellular communications and facilitates the discovery of targeted therapeutic strategies. This review outlines the end-to-end scRNA-seq workflow, covering fundamental single-cell isolation methods, downstream computational analyses, and key analytical software, as well as their practical significance. Additionally, it highlights the integration of spatial transcriptomics, which provides crucial positional context to achieve a more comprehensive understanding of intra-tumoral heterogeneity. Special emphasis is placed on gynaecological malignancies, particularly cervical and endometrial cancers. Given the rising incidence of both malignancies in recent years, detailed characterisation of their specific microenvironments is critical for advancing diagnostic accuracy and therapeutic intervention. A comprehensive understanding of the progression of the cancer and drug resistance is critical to understand. Accordingly, key molecular alterations, potential gene targets, and emerging biomarkers are systematically reviewed. Finally, current technical constraints, recent technological advancements, and future perspectives for single-cell transcriptomics are evaluated.