Abstract
Bladder cancer is a malignancy characterized by significant heterogeneity. RNA methylation has received an increasing amount of attention in recent years. RNA data were collected from the GEO database, and cell subsets were classified according to specific cell markers. Epithelial, immunological, and fibroblast cells were clustered individually to explore the tumor heterogeneity. To distinguish between malignant and benign cells, the InferCNV R package was employed. The monocle2 R package was used for pseudotime analysis. The Decouple R package was used for transcription factor analysis of each cell subgroup, and PROGENy was used to predict the activity of pathways related to tumors. The target lncRNA was screened for model construction. In addition, the qPCR experiment was used to detect the transcription level of lncRNA. Epithelial cells, fibroblasts, and T cells significantly differ in tumor and normal tissues. The lncRNAs related to m6A/m5C/m1A were intersected to construct the model. Finally, six model lncRNAs (PSMB8–AS1, THUMPD3–AS1, U47924.27, XXbac–B135H6.15, MIR99AHG, and C14orf132) were screened. High-risk individuals were shown to have a better prognosis. qPCR experiments showed that the model lncRNA was differentially expressed between normal and tumor cells. Immunotherapy will be more effective in treating individuals with lower risk than those with higher risk using 4 candidate drugs. The prognostic m6A/m5C/m1A-related lncRNA model was constructed for evaluating the clinical outcomes of bladder cancer patients and guiding clinical medication.
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Thanks are due to Dr. Chen for his technical support.
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Ma-Baoluo, Ye-Fangdie, and Sun-Zhou were involved in the final development of the project and manuscript preparation. LianMing Fan, Jie Wang, Zhiya Zhang, and Zili Zuo wrote the manuscript draft and analyzed the data. Yunfei Liu participated in the completion of the work.
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Fan, L., Wang, J., Zhang, Z. et al. Identification of RNA methylation-related lncRNAs for prognostic assessment and immunotherapy in bladder cancer—based on single cell/Bulk RNA sequencing data. Funct Integr Genomics 24, 56 (2024). https://doi.org/10.1007/s10142-024-01283-5
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DOI: https://doi.org/10.1007/s10142-024-01283-5