snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses
Abstract Differences in prognostic outcomes are prevalent in patients with colorectal cancer liver metastases. Comparative analysis of tissue samples, particularly applying single-cell transcriptome sequencing technology, can provide a deeper understanding of potential impacting factors. However, lo...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-12-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-024-04323-8 |
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| author | Hongyu Chen Xiang Zhang Qing Cheng Xiner Shen Linghui Zeng Yongcheng Wang Longjiang Fan Weiqin Jiang |
| author_facet | Hongyu Chen Xiang Zhang Qing Cheng Xiner Shen Linghui Zeng Yongcheng Wang Longjiang Fan Weiqin Jiang |
| author_sort | Hongyu Chen |
| collection | DOAJ |
| description | Abstract Differences in prognostic outcomes are prevalent in patients with colorectal cancer liver metastases. Comparative analysis of tissue samples, particularly applying single-cell transcriptome sequencing technology, can provide a deeper understanding of potential impacting factors. However, long-term monitoring for prognosis determination necessitates extended preservation of tissue samples using formalin-fixed and paraffin-embedded (FFPE) treatments, which can cause substantial RNA degradation, presenting challenges to single-cell or single-nucleus sequencing. In this study, employing snRandom-seq, a single-nucleus RNA sequencing (snRNA-seq) technology specifically for FFPE samples, we tested multiple lesion samples from 18 distinctive colorectal cancer liver metastasis cases with diverse prognostic outcomes that have been preserved for at least three years (mostly over five years). The process yielded expression data from 82,285 cells. The high-quality snRNA-seq data demonstrate the feasibility of single-nucleus sequencing in long-term preserved FFPE samples, offering potential insights into the heterogeneity between different prognoses of colorectal cancer liver metastases, and the relationship between the heterogeneity within different lesions of the same patient and prognosis. |
| format | Article |
| id | doaj-art-1a10c8845cac45af8247968d6257acab |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-1a10c8845cac45af8247968d6257acab2024-12-29T12:10:12ZengNature PortfolioScientific Data2052-44632024-12-0111111010.1038/s41597-024-04323-8snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognosesHongyu Chen0Xiang Zhang1Qing Cheng2Xiner Shen3Linghui Zeng4Yongcheng Wang5Longjiang Fan6Weiqin Jiang7School of Medicine, Hangzhou City UniversityDepartment of Colorectal Surgery, the First Affiliated Hospital, Zhejiang University School of MedicineInstitute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang UniversityInstitute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang UniversitySchool of Medicine, Hangzhou City UniversityLiangzhu Laboratory, Zhejiang University Medical CenterInstitute of Bioinformatics and James D. Watson Institute of Genome Sciences, Zhejiang UniversityDepartment of Colorectal Surgery, the First Affiliated Hospital, Zhejiang University School of MedicineAbstract Differences in prognostic outcomes are prevalent in patients with colorectal cancer liver metastases. Comparative analysis of tissue samples, particularly applying single-cell transcriptome sequencing technology, can provide a deeper understanding of potential impacting factors. However, long-term monitoring for prognosis determination necessitates extended preservation of tissue samples using formalin-fixed and paraffin-embedded (FFPE) treatments, which can cause substantial RNA degradation, presenting challenges to single-cell or single-nucleus sequencing. In this study, employing snRandom-seq, a single-nucleus RNA sequencing (snRNA-seq) technology specifically for FFPE samples, we tested multiple lesion samples from 18 distinctive colorectal cancer liver metastasis cases with diverse prognostic outcomes that have been preserved for at least three years (mostly over five years). The process yielded expression data from 82,285 cells. The high-quality snRNA-seq data demonstrate the feasibility of single-nucleus sequencing in long-term preserved FFPE samples, offering potential insights into the heterogeneity between different prognoses of colorectal cancer liver metastases, and the relationship between the heterogeneity within different lesions of the same patient and prognosis.https://doi.org/10.1038/s41597-024-04323-8 |
| spellingShingle | Hongyu Chen Xiang Zhang Qing Cheng Xiner Shen Linghui Zeng Yongcheng Wang Longjiang Fan Weiqin Jiang snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses Scientific Data |
| title | snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses |
| title_full | snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses |
| title_fullStr | snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses |
| title_full_unstemmed | snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses |
| title_short | snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses |
| title_sort | snrna seq of long preserved ffpe samples from colorectal liver metastasis lesions with diverse prognoses |
| url | https://doi.org/10.1038/s41597-024-04323-8 |
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