Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancer
Abstract We aimed to create a NK cell marker genes-based signature to predict immunotherapy response and prognosis in colorectal cancer. We integrated scRNA-seq data from four Gene Expression Omnibus (GEO) samples and performed Weighted gene correlation network analysis (WGCNA) based on 587 the Canc...
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| Format: | Article |
| Language: | English |
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Springer
2025-02-01
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| Series: | Discover Oncology |
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| Online Access: | https://doi.org/10.1007/s12672-025-01842-7 |
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| _version_ | 1823861793345241088 |
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| author | Xiaoyu Qin Wenjuan Xu Jinxiu Wu Ming Li |
| author_facet | Xiaoyu Qin Wenjuan Xu Jinxiu Wu Ming Li |
| author_sort | Xiaoyu Qin |
| collection | DOAJ |
| description | Abstract We aimed to create a NK cell marker genes-based signature to predict immunotherapy response and prognosis in colorectal cancer. We integrated scRNA-seq data from four Gene Expression Omnibus (GEO) samples and performed Weighted gene correlation network analysis (WGCNA) based on 587 the Cancer Genome Atlas (TCGA) colorectal cancer samples to uncover NK cell-related genes. We identified 1080 NK cell-related core genes and 276 NK cell-related feature genes based on WGCNA and clustering and annotation of scRNA-seq data, respectively. Six key NK cell-related prognostic signature genes were obtained by univariate and LASSO regression analyses, including ADAM8, CTSD, CCL4, IL2RB, TTC38, and PLEK. Two validation cohorts from the GEO dataset, comprising 124 and 201 samples respectively, were used. The signature was significantly associated with overall survival and correlated with immune cell infiltration, immune and stromal scores, and immune checkpoint genes. Furthermore, the signature was associated with the homologous recombination deficiency (HRD) and T-cell receptor (TCR) scores. In conclusion, our study proposes a new prognostic signature based on NK cell marker genes, which may serve as a potential tool to predict overall survival and immunotherapy response for CRC patients. |
| format | Article |
| id | doaj-art-3d6f73f24804497eace2618ed4a03a8a |
| institution | Kabale University |
| issn | 2730-6011 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Springer |
| record_format | Article |
| series | Discover Oncology |
| spelling | doaj-art-3d6f73f24804497eace2618ed4a03a8a2025-02-09T12:43:28ZengSpringerDiscover Oncology2730-60112025-02-0116111610.1007/s12672-025-01842-7Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancerXiaoyu Qin0Wenjuan Xu1Jinxiu Wu2Ming Li3Department of Gastroenterology, Shanghai Pudong New Area Gongli HospitalDepartment of General Surgery, Shanghai Punan HospitalDepartment of General Surgery, Shanghai Punan HospitalDepartment of General Surgery, Shanghai Punan HospitalAbstract We aimed to create a NK cell marker genes-based signature to predict immunotherapy response and prognosis in colorectal cancer. We integrated scRNA-seq data from four Gene Expression Omnibus (GEO) samples and performed Weighted gene correlation network analysis (WGCNA) based on 587 the Cancer Genome Atlas (TCGA) colorectal cancer samples to uncover NK cell-related genes. We identified 1080 NK cell-related core genes and 276 NK cell-related feature genes based on WGCNA and clustering and annotation of scRNA-seq data, respectively. Six key NK cell-related prognostic signature genes were obtained by univariate and LASSO regression analyses, including ADAM8, CTSD, CCL4, IL2RB, TTC38, and PLEK. Two validation cohorts from the GEO dataset, comprising 124 and 201 samples respectively, were used. The signature was significantly associated with overall survival and correlated with immune cell infiltration, immune and stromal scores, and immune checkpoint genes. Furthermore, the signature was associated with the homologous recombination deficiency (HRD) and T-cell receptor (TCR) scores. In conclusion, our study proposes a new prognostic signature based on NK cell marker genes, which may serve as a potential tool to predict overall survival and immunotherapy response for CRC patients.https://doi.org/10.1007/s12672-025-01842-7Colorectal cancerNatural killer cellsScRNA-seqImmunotherapy responsePrognosis |
| spellingShingle | Xiaoyu Qin Wenjuan Xu Jinxiu Wu Ming Li Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancer Discover Oncology Colorectal cancer Natural killer cells ScRNA-seq Immunotherapy response Prognosis |
| title | Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancer |
| title_full | Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancer |
| title_fullStr | Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancer |
| title_full_unstemmed | Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancer |
| title_short | Integration of single-cell and bulk RNA-sequencing data to construct and validate a signature based on NK cell marker genes to predict immunotherapy response and prognosis in colorectal cancer |
| title_sort | integration of single cell and bulk rna sequencing data to construct and validate a signature based on nk cell marker genes to predict immunotherapy response and prognosis in colorectal cancer |
| topic | Colorectal cancer Natural killer cells ScRNA-seq Immunotherapy response Prognosis |
| url | https://doi.org/10.1007/s12672-025-01842-7 |
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