Abstract
Cell differentiation, the process by which stem cells acquire specialized functions, underpins embryonic development, tissue homeostasis, and regeneration. This process is governed by evolutionarily conserved signaling pathways, including Wnt, Notch, Hedgehog, TGF-β, and Hippo, which integrate extracellular cues with intrinsic genetic programs to determine cell fate. Here, we provide a comprehensive overview of the molecular architecture of these pathways, spanning ligand-receptor interactions to downstream transcriptional regulation. We further highlight multilayered regulatory mechanisms such as epigenetic modifications, non-coding RNAs, feedback loops, and pathway crosstalk that fine-tune signaling outputs to ensure spatiotemporal precision in fate decisions. We also discuss how tissue-specific contexts and interactions among these pathways generate distinct differentiation outcomes in different organs and disease settings. Dysregulation of these networks contributes to diverse pathological states, driving uncontrolled proliferation in cancer, maladaptive remodeling in cardiovascular disease, neuronal loss in neurodegeneration, metabolic imbalance, digestive dysfunction, chronic inflammation in respiratory and autoimmune diseases, and skeletal disorders. Reflecting their clinical importance, we also summarize recent therapeutic advances, including small-molecule inhibitors, monoclonal antibodies, gene-based strategies, and pathway-modulating compounds, which target these pathways to restore normal cellular function. Particular attention is given to distinguishing preclinical findings from clinical applications and to the translational challenges of pathway-targeted therapies. Collectively, this review underscores the central role of differentiation-related signaling in health and disease and highlights emerging opportunities for therapeutic intervention.