Multi-omics analysis unveils the predictive value of IGF2BP3/SPHK1 signaling in cancer stem cells for prognosis and immunotherapeutic response in muscle-invasive bladder cancer

• Published in: Journal of translational medicine 2024-10, Vol.22 (1), p.900-21, Article 900
• Main Authors: Wang, Yaobang, Song, Wuyue, Feng, Chao, Wu, Shulin, Qin, Zezu, Liu, Tao, Ye, Yu, Huang, Rong, Xie, Yuanliang, Tang, Zhong, Wang, Qiuyan, Li, Tianyu
• Format: Article
• Language: English
• Subjects: Aged; Binding proteins; Bladder cancer; Cancer stem cells; Cell Line, Tumor; Cell Proliferation; Development and progression; Drug therapy; Female; Gene Expression Regulation, Neoplastic; Genetic aspects; Health aspects; Humans; IGF2BP3; Immunotherapy; Male; Middle Aged; Multiomics; Muscle invasive bladder cancer; Muscles - metabolism; Muscles - pathology; Neoplasm Invasiveness; Neoplastic Stem Cells - metabolism; Neoplastic Stem Cells - pathology; Phosphotransferases; Physiological aspects; Prognosis; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; Signal Transduction; SPHK1; Tumor Microenvironment; Urinary Bladder Neoplasms - genetics; Urinary Bladder Neoplasms - immunology; Urinary Bladder Neoplasms - metabolism; Urinary Bladder Neoplasms - pathology
• ISSN: 1479-5876; 1479-5876
• DOI: 10.1186/s12967-024-05685-8

Muscle invasive bladder cancer (MIBC) is a life-threatening malignant tumor characterized by high metastasis rates, poor prognosis, and limited treatment options. Immune checkpoint inhibitors (ICIs) targeting PD-1 and PD-L1 represent an emerging treatment for MIBC immunotherapy. However, the characteristics of patients likely to benefit from immunotherapy remain unclear. We performed single-cell mass cytometry (CyTOF) analysis of 179,483 single cells to characterize potential immunotherapy-related cancer stem cells (CSCs)-like populations in the tumor microenvironment of 38 MIBC tissues. The upregulated expression of IGF2BP3 in CD274 + ALDH + CSC-like cells, which was associated with poor clinical prognosis, was analyzed by bulk RNA-sequencing data from an in-house cohort. The functional role of IGF2BP3 was determined through cell proliferation, colony formation, cell apoptosis and sphere formation assays. The regulation of SPHK1 expression by IGF2BP3 was  investigated using methylated RNA immunoprecipitation sequencing (MeRIP-seq) and bulk RNA-sequencing (bulk RNA-seq). We further utilized single-nucleus RNA sequencing (snRNA-seq) data from 67,988 cells of 25 MIBC tissues and single-cell RNA sequencing (scRNA-seq) data from MIBC patient-derived organoids to characterize the molecular features of bladder cancer cells co-expressing IGF2BP3 and SPHK1. Spatial transcriptomics (ST) and co-detection by indexing (CODEX) analysis were used to describe the spatial distribution and interactions of IGF2BP3 + SPHK1 + bladder cancer cells and immune cells. A subset of CD274 + ALDH + CSC-like cells was identified, associating with immunosuppression and low survival rates in MIBC patients. IGF2BP3, an m6A reader gene, was found to be upregulated in the CD274 + ALDH + CSC-like cell population and linked to poor clinical prognosis in MIBC. Knockout of IGF2BP3 dramatically promoted cell apoptosis and reduced cell proliferation in T24 cells. By integrating MeRIP-seq and bulk RNA-seq analyses, we identified SPHK1 served as a substrate for IGF2BP3 in an m6A-dependent manner. Further snRNA-seq, scRNA-seq, ST, and CODEX analysis revealed a closer topographical distance between IGF2BP3 + SPHK1 + bladder cancer cells and exhausted CD8 + T cells, providing one explanation for the superior response to immunotherapy in IGF2BP3 + SPHK1 + bladder cancer cells-enriched patients. Finally, an ICI-associated signature was developed based on the enriched genes of IGF2BP3 + SPHK1 + bladder