Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers
Abstract Long non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) in tumor-immune. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here, a multiple-step pipeline was developed t...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02550-z |
| _version_ | 1797453928036564992 |
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| author | Yue Gao Xinyue Wang Longlong Dong Changfan Qu Qianyi Lu Peng Wang Mengyu Xin Wen Zheng Chenyu Liu Shangwei Ning |
| author_facet | Yue Gao Xinyue Wang Longlong Dong Changfan Qu Qianyi Lu Peng Wang Mengyu Xin Wen Zheng Chenyu Liu Shangwei Ning |
| author_sort | Yue Gao |
| collection | DOAJ |
| description | Abstract Long non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) in tumor-immune. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here, a multiple-step pipeline was developed to identify cancer- and immune-context ICP and lncRNA cooperative regulation pairs (ICPaLncCRPs) across cancers. Immune-related ICPs and lncRNAs were extracted follow immune cell lines and immunologic constant of rejection groups. ICPaLncCRP networks were constructed, which likely to modulate tumor-immune by specific patterns. Common and specific hub ICPaLncs such as MIR155HG, TRG-AS1 and PCED1B-AS1 maybe play central roles in prognosis and circulating. Moreover, these hub ICPaLncs were significantly correlated with immune cell infiltration based on bulk and single-cell RNA sequencing data. Some ICPaLncCRPs such as IDO1-MIR155HG could predict three- and five-year prognosis of melanoma in two independent datasets. We also validated that some ICPaLncCRPs could effectively predict ICI-response follow six independent datasets. Collectively, this study will enhance our understanding of lncRNA functions and accelerate discovery of lncRNA-based biomarkers in ICI treatment. |
| first_indexed | 2024-03-09T15:29:56Z |
| format | Article |
| id | doaj.art-22b90e0cfecc46f5abb1f106849e3722 |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-03-09T15:29:56Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
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| spelling | doaj.art-22b90e0cfecc46f5abb1f106849e37222023-11-26T12:17:58ZengNature PortfolioScientific Data2052-44632023-09-0110111510.1038/s41597-023-02550-zIdentifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancersYue Gao0Xinyue Wang1Longlong Dong2Changfan Qu3Qianyi Lu4Peng Wang5Mengyu Xin6Wen Zheng7Chenyu Liu8Shangwei Ning9College of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityCollege of Bioinformatics Science and Technology, Harbin Medical UniversityAbstract Long non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) in tumor-immune. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here, a multiple-step pipeline was developed to identify cancer- and immune-context ICP and lncRNA cooperative regulation pairs (ICPaLncCRPs) across cancers. Immune-related ICPs and lncRNAs were extracted follow immune cell lines and immunologic constant of rejection groups. ICPaLncCRP networks were constructed, which likely to modulate tumor-immune by specific patterns. Common and specific hub ICPaLncs such as MIR155HG, TRG-AS1 and PCED1B-AS1 maybe play central roles in prognosis and circulating. Moreover, these hub ICPaLncs were significantly correlated with immune cell infiltration based on bulk and single-cell RNA sequencing data. Some ICPaLncCRPs such as IDO1-MIR155HG could predict three- and five-year prognosis of melanoma in two independent datasets. We also validated that some ICPaLncCRPs could effectively predict ICI-response follow six independent datasets. Collectively, this study will enhance our understanding of lncRNA functions and accelerate discovery of lncRNA-based biomarkers in ICI treatment.https://doi.org/10.1038/s41597-023-02550-z |
| spellingShingle | Yue Gao Xinyue Wang Longlong Dong Changfan Qu Qianyi Lu Peng Wang Mengyu Xin Wen Zheng Chenyu Liu Shangwei Ning Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers Scientific Data |
| title | Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers |
| title_full | Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers |
| title_fullStr | Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers |
| title_full_unstemmed | Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers |
| title_short | Identifying immune checkpoint-related lncRNA biomarkers for immunotherapy response and prognosis in cancers |
| title_sort | identifying immune checkpoint related lncrna biomarkers for immunotherapy response and prognosis in cancers |
| url | https://doi.org/10.1038/s41597-023-02550-z |
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