Maria Koutra, Paschalis Evangelidis, Apostolia Papalexandri, Tasoula Touloumenidou, Emmanouel Hatzipantelis, Ioanna Sakellari, Eleni Gavriilaki, Athanasios Tragiannidis
Acute Lymphoblastic Leukemia (ALL) is a highly heterogeneous hematological malignancy characterized by diverse genetic alterations. Advances in genomic and transcriptomic profiling have enabled refined ALL classification, improving clinical management and patient outcomes. This review provides a comparative evaluation of RNA sequencing methodologies for studying gene expression in ALL. Specifically, bulk RNA sequencing enables transcriptome-wide profiling at the population level, while targeted RNA sequencing provides enhanced sensitivity for detecting clinically relevant alterations. Moreover, single-cell RNA sequencing offers cellular-resolution analysis of leukemic heterogeneity and clonal architecture, whereas spatial transcriptomic analyses further reveal leukemic cell types within their microenvironment. Together, these transcriptomic methodologies have transformed the understanding of leukemia biology and enabled improved disease classification, risk stratification, and personalized medicine. Furthermore, integrating multi-omics approaches has the potential to reshape the clinical management of ALL by shifting treatment from broad chemotherapy to precision medicine. The future of transcriptomic profiling in ALL depends on the strategic integration of existing methodologies to achieve a comprehensive and clinically actionable understanding of leukemic biology.