High‐Throughput Single‐Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer
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 sn...
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Wiley
2025-01-01
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| Series: | Advanced Science |
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| Online Access: | https://doi.org/10.1002/advs.202410713 |
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| author | Weiqin Jiang Xiang Zhang Ziye Xu Qing Cheng Xiaohan Li Yuyi Zhu Fangru Lu Ling Dong Linghui Zeng Weixiang Zhong Yongcheng Wang Longjiang Fan Hongyu Chen |
| author_facet | Weiqin Jiang Xiang Zhang Ziye Xu Qing Cheng Xiaohan Li Yuyi Zhu Fangru Lu Ling Dong Linghui Zeng Weixiang Zhong Yongcheng Wang Longjiang Fan Hongyu Chen |
| author_sort | Weiqin Jiang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-f6e1688093244592ae7e8c3129a8d595 |
| institution | Kabale University |
| issn | 2198-3844 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj-art-f6e1688093244592ae7e8c3129a8d5952025-01-29T09:50:19ZengWileyAdvanced Science2198-38442025-01-01124n/an/a10.1002/advs.202410713High‐Throughput Single‐Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of CancerWeiqin Jiang0Xiang Zhang1Ziye Xu2Qing Cheng3Xiaohan Li4Yuyi Zhu5Fangru Lu6Ling Dong7Linghui Zeng8Weixiang Zhong9Yongcheng Wang10Longjiang Fan11Hongyu Chen12Department of Colorectal Surgery the First Affiliated Hospital Zhejiang University School of Medicine Hangzhou 310003 ChinaDepartment of Colorectal Surgery the First Affiliated Hospital Zhejiang University School of Medicine Hangzhou 310003 ChinaLiangzhu Laboratory Zhejiang University Medical Center Hangzhou 311121 ChinaInstitute of Bioinformatics and James D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 310058 ChinaInstitute of Bioinformatics and James D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 310058 ChinaLiangzhu Laboratory Zhejiang University Medical Center Hangzhou 311121 ChinaLiangzhu Laboratory Zhejiang University Medical Center Hangzhou 311121 ChinaM20 Genomics Hangzhou 310030 ChinaSchool of Medicine Hangzhou City University Hangzhou 316021 ChinaDepartment of Pathology First Affiliated Hospital College of Medicine Zhejiang University Hangzhou 310003 ChinaLiangzhu Laboratory Zhejiang University Medical Center Hangzhou 311121 ChinaInstitute of Bioinformatics and James D. Watson Institute of Genome Sciences Zhejiang University Hangzhou 310058 ChinaSchool of Medicine Hangzhou City University Hangzhou 316021 ChinaAbstract 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.https://doi.org/10.1002/advs.202410713FFPE samplenoncoding RNApuncture biopsypseudoprogressionspatiotemporal heterogeneity |
| spellingShingle | Weiqin Jiang Xiang Zhang Ziye Xu Qing Cheng Xiaohan Li Yuyi Zhu Fangru Lu Ling Dong Linghui Zeng Weixiang Zhong Yongcheng Wang Longjiang Fan Hongyu Chen High‐Throughput Single‐Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer Advanced Science FFPE sample noncoding RNA puncture biopsy pseudoprogression spatiotemporal heterogeneity |
| title | High‐Throughput Single‐Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer |
| title_full | High‐Throughput Single‐Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer |
| title_fullStr | High‐Throughput Single‐Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer |
| title_full_unstemmed | High‐Throughput Single‐Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer |
| title_short | High‐Throughput Single‐Nucleus RNA Profiling of Minimal Puncture FFPE Samples Reveals Spatiotemporal Heterogeneity of Cancer |
| title_sort | high throughput single nucleus rna profiling of minimal puncture ffpe samples reveals spatiotemporal heterogeneity of cancer |
| topic | FFPE sample noncoding RNA puncture biopsy pseudoprogression spatiotemporal heterogeneity |
| url | https://doi.org/10.1002/advs.202410713 |
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