Multidimensional Transcriptomics Unveils RNF34 as a Prognostic Biomarker and Potential Indicator of Chemotherapy Sensitivity in Wilms’ Tumour

• Published in: Molecular biotechnology 2024-05, Vol.66 (5), p.1132-1143
• Main Authors: Zheng, Jie, Liu, Fengling, Tuo, Jinwei, Chen, Siyu, Su, Jinxia, Ou, Xiuyi, Ding, Min, Chen, Haoran, Shi, Bo, Li, Yong, Chen, Xun, Wang, Congjun, Su, Cheng
• Format: Article
• Language: English
• Subjects: Antineoplastic Agents - pharmacology; Antineoplastic Agents - therapeutic use; Biochemistry; Biological Techniques; Biomarkers; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Biotechnology; Cancer; Cell Biology; Chemistry; Chemistry and Materials Science; Chemotherapy; Child, Preschool; Clinical decision making; Decision making; Drug Resistance, Neoplasm - genetics; Female; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene sequencing; Histology; Human Genetics; Humans; Immunosuppressive agents; Kidney Neoplasms - drug therapy; Kidney Neoplasms - genetics; Kidney Neoplasms - metabolism; Kidney Neoplasms - pathology; Male; Microenvironments; Original Paper; Patients; Pediatrics; Prognosis; Protein Science; Radiation therapy; snRNA; Survival; Transcriptome; Transcriptomes; Transcriptomics; Tumors; Ubiquitin-Protein Ligases - genetics; Ubiquitin-Protein Ligases - metabolism; Wilms Tumor - drug therapy; Wilms Tumor - genetics; Wilms Tumor - metabolism; Wilms Tumor - pathology
• ISSN: 1073-6085; 1559-0305
• DOI: 10.1007/s12033-023-01008-2

Nephroblastoma, colloquially known as Wilms’ tumour (WT), is the predominant malignant renal neoplasm arising in the paediatric population. Modern therapeutic approaches for WT incorporate a synergistic combination of surgical intervention, radiotherapy, and chemotherapy, which substantially ameliorate the overall patient survival rate. Despite this, the optimal sequence of chemotherapy and surgical intervention remains a matter of contention, with each strategy presenting its own strengths and weaknesses that could influence clinical decision-making. To make some headway on this clinical dilemma, we deployed a multidimensional transcriptomics integration approach by analysing bulk RNA sequencing data with 136 samples, as well as single-nucleus RNA sequencing (snRNA-seq) and paired spatial transcriptome sequencing (stRNA) data from 32 WT specimens. Our findings identified a distinct elevation of RNF34 expression within WT samples, which correlated with unfavourable prognostic outcomes. Leveraging the Genomics of Drug Sensitivity in Cancer (GDSC), we simultaneously revealed that patients with high expression of RNF34 have higher sensitivity to commonly used chemotherapy drugs for WT. Furthermore, our analysis of snRNA and stRNA data unveiled a reduced proportion of RNF34 expression in neoplastic cells after chemotherapy. Moreover, stRNA data delineated a significant association between a higher proportion of RNF34 expression in cancer cells and adverse features such as anaplastic histology and tumour recurrence. Intriguingly, we also observed a close association between elevated RNF34 expression and a characteristic exhausted tumour immune microenvironment. Collectively, our findings underscore the pivotal role of RNF34 in the prognostic prediction potential and treatment sensitivity of WT. This comprehensive analysis can potentially inform and refine clinical decision-making for WT patients and guide future studies towards the development of optimized, rational therapeutic strategies.