SPTEdU-seq enables parallel optics-free newborn cell tracking and spatial total transcriptional dynamics in intact...

Area of Science:

• Molecular Biology
• Genomics
• Developmental Biology

Background:

• Understanding biological processes requires mapping gene expression and cell proliferation over time and space.
• Existing spatial transcriptomics methods are limited, capturing only protein-coding transcripts and static snapshots, thus missing non-coding RNAs and dynamic cellular events.

Purpose of the Study:

• To develop a novel method, SPTEdU-seq, that integrates spatial total transcriptomics with 5-ethynyl-2'-deoxyuridine (EdU) tracking.
• To enable simultaneous profiling of gene expression, including non-coding RNAs and splicing isoforms, and cell proliferation dynamics within intact biological tissues.
• To overcome limitations of current methods by providing ultrahigh sensitivity and eliminating the need for optical imaging through single-molecule probe design.

Main Methods:

• SPTEdU-seq combines spatial transcriptomics with EdU labeling for proliferation tracking.
• Utilizes single-molecule probe design for high sensitivity detection of coding and non-coding transcripts, including splicing isoforms.
• Applies the method to developing and adult mouse brains, murine ischemic stroke models, and human renal tumors.

Main Results:

• Revealed spatial long non-coding RNA (lncRNA) patterns and reconstructed developmental trajectories in mouse brains.
• Enabled spatiotemporal lineage tracing and mapped regeneration dynamics post-ischemic stroke, identifying a specific astrocyte subtype in a pro-repair niche.
• Uncovered tumor-associated splicing alterations and detected 3p loss in renal tumors, revealing previously inaccessible cell interaction networks in microenvironments.

Conclusions:

• SPTEdU-seq provides a powerful framework for investigating cell fate dynamics in development, regeneration, and cancer.
• The method enhances the understanding of non-coding RNA roles and cellular interactions in complex biological systems.
• SPTEdU-seq offers unprecedented insights into dynamic biological processes at a spatial and temporal resolution.