ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2025
High-Throughput Single-Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Emerging role of long non‑coding RNAs in the Rho/ROCK signaling pathway in tumor metastasis (Review).International journal of molecular medicine · 2025Review
- Spatial omics technology potentially promotes the progress of tumor immunotherapy.British journal of cancer · 2025Review
- High-Throughput Single-Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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13 authors.
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Abstract
Puncture biopsy, especially those preserved by formalin fixed paraffin embedding (FFPE) samples, play an important role in various research purposes. Diverse single-nucleus RNA sequencing (snRNA-seq) techniques have been developed for FFPE samples, however, how to perform high-throughput snRNA-seq on small FFPE puncture samples is still a challenge. Here, the previously developed snRNA-seq technique (snRandom-seq) is optimized by implementing a pre-indexing procedure for the minimal puncture FFPE samples. In analyzing 20 samples from various solid tumors, optimized snRandom-seq still detected ≈17 000 genes and 12 000 long non-coding RNAs (lncRNAs), achieving precise clustering based on tissue origin. A head-to-head comparison with 10× Genomics on fresh biopsy samples showed a similar gene detection rate, with significantly enhanced lncRNA detection, indicating that the optimized snRandom-seq technique maintains its established gene detection advantages even when applied to small samples. Utilizing 7 puncture FFPE samples of liver metastases from 3 colorectal cancer patients pre- and post-immunotherapy, the cellular developmental trajectories are reconstructed and revealed dynamic spatiotemporal heterogeneity during treatment, including insights into pseudoprogression of immunotherapy. Therefore, the optimized snRandom-seq offers a solution for high-throughput single-cell RNA and non-coding RNA analysis in minimal puncture FFPE sample.
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