Sir Run Run Shaw Hospital

Understanding biological processes requires spatiotemporal mapping of proliferative and transcriptional dynamics. Current spatial transcriptomics methods capture only protein-coding transcripts and static snapshots, obscuring non-coding RNAs (ncRNAs) and dynamic events. We developed SPTEdU-seq, integrating spatial total transcriptomics with 5-ethynyl-2'-deoxyuridine tracking to co-profile gene expression and proliferation dynamics. SPTEdU-seq demonstrates ultrahigh sensitivity for coding and non-coding transcripts and for splicing isoforms, with single-molecule probe design eliminating optical imaging. Applied to developing and adult mouse brains, it revealed spatial lncRNA patterns, reconstructed developmental trajectories, and enabled spatiotemporal lineage tracing. In murine ischemic stroke, it mapped regeneration dynamics and identified an Igfbp5+ astrocyte subtype within a pro-repair niche. In mouse and human renal tumors, it uncovered tumor-associated splicing and detected diagnostic 3p loss. By profiling newborn and resident cells in intact microenvironments, it unveiled previously inaccessible interaction networks. SPTEdU-seq thus establishes a powerful framework for investigating cell fate dynamics in regeneration, development, and cancer.

The neurovascular unit (NVU) is a multicellular system functioning to maintain healthy brain homeostasis and regulate the exchange of essential elements between the blood and the brain. Recent studies have shown that, in response to ischemic stroke (IS), the NVU undergoes dynamic structural remodeling and metabolic dysfunction, revealing new features of IS pathogenesis. Recent breakthroughs in single-cell multiomics provide emerging evidence regarding the spatiotemporal heterogeneity of NVU responses to IS. To date, clinical treatments for IS-induced brain injury remain very limited. These new studies have advanced our knowledge of the dynamic cellular and molecular changes of the NVU after IS, paving the way for new therapeutic strategies.