N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer
Objectives: Identification of m6A- related lncRNAs associated with BC diagnosis and prognosis. Methods: From the TCGA database, we obtained transcriptome data and corresponding clinical information (including histopathological and CT imaging data) for 408 patients. And bioinformatics, computational...
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Translational Oncology |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1936523322002406 |
| _version_ | 1811178117352390656 |
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| author | Ziye Huang Guang Wang Yuyun Wu Tongxin Yang Lishi Shao Bowei Yang Pei Li Jiongming Li |
| author_facet | Ziye Huang Guang Wang Yuyun Wu Tongxin Yang Lishi Shao Bowei Yang Pei Li Jiongming Li |
| author_sort | Ziye Huang |
| collection | DOAJ |
| description | Objectives: Identification of m6A- related lncRNAs associated with BC diagnosis and prognosis. Methods: From the TCGA database, we obtained transcriptome data and corresponding clinical information (including histopathological and CT imaging data) for 408 patients. And bioinformatics, computational histopathology, and radiomics were used to identify and analyze diagnostic and prognostic biomarkers of m6A-related lncRNAs in BC. Results: 3 significantly high-expressed m6A-related lncRNAs were significantly associated with the prognosis of BC. The BC samples were divided into two subgroups based on the expression of the 3 lncRNAs. The overall survival of patients in cluster 2 was significantly lower than that in cluster 1. The immune landscape results showed that the expression of PD-L1, T cells follicular helper, NK cells resting, and mast cells activated in cluster 2 were significantly higher, and naive B cells, plasma cells, T cells regulatory (Tregs), and mast cells resting were significantly lower. Computational histopathology results showed a significantly higher percentage of tumor-infiltrating lymphocytes (TILs) in cluster 2. The radiomics results show that the 3 eigenvalues of diagnostics image-original minimum, diagnostics image-original maximum, and original GLCM inverse variance are significantly higher in cluster 2. High expression of 2 bridge genes in the PPI network of 30 key immune genes predicts poorer disease-free survival, while immunohistochemistry showed that their expression levels were significantly higher in high-grade BC than in low-grade BC and normal tissue. Conclusion: Based on the results of immune landscape, computational histopathology, and radiomics, these 3 m6A-related lncRNAs may be diagnostic and prognostic biomarkers for BC. |
| first_indexed | 2024-04-11T06:13:52Z |
| format | Article |
| id | doaj.art-4329976be2d74f91bf8a9da06a288871 |
| institution | Directory Open Access Journal |
| issn | 1936-5233 |
| language | English |
| last_indexed | 2024-04-11T06:13:52Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Translational Oncology |
| spelling | doaj.art-4329976be2d74f91bf8a9da06a2888712022-12-22T04:41:08ZengElsevierTranslational Oncology1936-52332023-01-0127101581N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancerZiye Huang0Guang Wang1Yuyun Wu2Tongxin Yang3Lishi Shao4Bowei Yang5Pei Li6Jiongming Li7The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan, 650101, P.R. ChinaThe Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan, 650101, P.R. ChinaThe Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan, 650101, P.R. ChinaThe Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan, 650101, P.R. ChinaThe Department of Imageology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan, 650101, P.R. ChinaThe Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan, 650101, P.R. ChinaThe Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan, 650101, P.R. China; Corresponding author.The Department of Urology, The Second Affiliated Hospital of Kunming Medical University, No. 374 Dian-Mian Avenue, Kunming, Yunnan, 650101, P.R. China; Corresponding author.Objectives: Identification of m6A- related lncRNAs associated with BC diagnosis and prognosis. Methods: From the TCGA database, we obtained transcriptome data and corresponding clinical information (including histopathological and CT imaging data) for 408 patients. And bioinformatics, computational histopathology, and radiomics were used to identify and analyze diagnostic and prognostic biomarkers of m6A-related lncRNAs in BC. Results: 3 significantly high-expressed m6A-related lncRNAs were significantly associated with the prognosis of BC. The BC samples were divided into two subgroups based on the expression of the 3 lncRNAs. The overall survival of patients in cluster 2 was significantly lower than that in cluster 1. The immune landscape results showed that the expression of PD-L1, T cells follicular helper, NK cells resting, and mast cells activated in cluster 2 were significantly higher, and naive B cells, plasma cells, T cells regulatory (Tregs), and mast cells resting were significantly lower. Computational histopathology results showed a significantly higher percentage of tumor-infiltrating lymphocytes (TILs) in cluster 2. The radiomics results show that the 3 eigenvalues of diagnostics image-original minimum, diagnostics image-original maximum, and original GLCM inverse variance are significantly higher in cluster 2. High expression of 2 bridge genes in the PPI network of 30 key immune genes predicts poorer disease-free survival, while immunohistochemistry showed that their expression levels were significantly higher in high-grade BC than in low-grade BC and normal tissue. Conclusion: Based on the results of immune landscape, computational histopathology, and radiomics, these 3 m6A-related lncRNAs may be diagnostic and prognostic biomarkers for BC.http://www.sciencedirect.com/science/article/pii/S1936523322002406BiomarkerDiagnosisRadiomicsUrinary bladder neoplasmsPrognosis |
| spellingShingle | Ziye Huang Guang Wang Yuyun Wu Tongxin Yang Lishi Shao Bowei Yang Pei Li Jiongming Li N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer Translational Oncology Biomarker Diagnosis Radiomics Urinary bladder neoplasms Prognosis |
| title | N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer |
| title_full | N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer |
| title_fullStr | N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer |
| title_full_unstemmed | N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer |
| title_short | N6-methyladenosine-related lncRNAs in combination with computational histopathology and radiomics predict the prognosis of bladder cancer |
| title_sort | n6 methyladenosine related lncrnas in combination with computational histopathology and radiomics predict the prognosis of bladder cancer |
| topic | Biomarker Diagnosis Radiomics Urinary bladder neoplasms Prognosis |
| url | http://www.sciencedirect.com/science/article/pii/S1936523322002406 |
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