Data_Sheet_1_Ubiquitin Modification Patterns of Clear Cell Renal Cell Carcinoma and the Ubiquitin Score to Aid Immunotherapy and Targeted Therapy.xls

Ubiquitin modification is the most common protein post-translational modification (PTM) process in organisms, and 1332 ubiquitin regulators have been identified in humans. Ubiquitin regulators, especially E3 ligases and deubiquitinases, are widely involved in immune processes. This study aims to explore the ubiquitin modification features of clear cell renal cell carcinoma (ccRCC) and to elucidate the role of such ubiquitin modifications in shaping anti-tumor immunity and individual benefits from immune checkpoint blockade (ICB). A comprehensive analysis was performed in the TCGA cohort (n = 530) and GEO cohort (n = 682). RNA sequencing data of 758 differentially expressed regulators, which was validated by the proteomics data, was used for k-means unsupervised consensus clustering and three ubiquitin patterns of ccRCC were identified. Then, we focused on the ubiquitin modification and tumor progression signatures, immune infiltration characteristics, and prognostic value. The three patterns with different ubiquitin modification signatures correspond to “immune desert phenotype,” “immune resistance phenotype,” and “immune-inflammatory phenotype,” respectively. To facilitate clinical application, we constructed a ubiquitin score to evaluate individual patients’ ubiquitination outcome, and it was demonstrated to be an independent risk factor for overall survival (OS) in multivariate Cox analysis. It was found that the high score group was correlated to higher immune cells infiltrating level and PD-1/PD-L1/CTLA-4 expression. More importantly, we found that the high score group was predicted to be sensitive to anti-PD-1 treatment, while the low-score group showed lower predicted IC50 values in treatment with Pazopanib and Axitinib. In summary, this study elucidated the potential link between ubiquitin modification and immune infiltration landscape of ccRCC for the first time and provided a new assessment protocol for the precise selection of treatment strategies for patients with advanced ccRCC.

泛素化修饰是生物体内最普遍的蛋白质翻译后修饰（PTM）过程，人类中已鉴定出1332种泛素调节因子。泛素调节因子，尤其是E3连接酶和去泛素化酶，在免疫过程中发挥着广泛的作用。本研究旨在探究透明细胞肾细胞癌（ccRCC）的泛素化修饰特征，并阐明此类泛素化修饰在塑造抗肿瘤免疫及个体从免疫检查点阻断（ICB）中获益中的角色。在TCGA队列（n=530）和GEO队列（n=682）中进行了全面分析。利用经蛋白质组学数据验证的758个差异表达调节因子的RNA测序数据，进行了k-means非监督一致性聚类，并确定了ccRCC的三个泛素化模式。随后，我们聚焦于泛素化修饰与肿瘤进展特征、免疫浸润特性和预后价值。具有不同泛素化修饰特征的三个模式分别对应“免疫荒漠表型”、“免疫耐药表型”和“免疫炎症表型”。为便于临床应用，我们构建了一个泛素评分，以评估个体患者的泛素化结果，并在多变量Cox分析中证实其为总生存期（OS）的独立风险因素。研究发现，高评分组与更高的免疫细胞浸润水平和PD-1/PD-L1/CTLA-4表达相关。更重要的是，我们发现高评分组对抗PD-1治疗敏感，而低评分组在帕唑帕尼和阿昔替尼治疗中表现出较低的预测IC50值。总之，本研究首次阐明了泛素化修饰与ccRCC免疫浸润景观之间的潜在联系，并为晚期ccRCC患者治疗策略的精准选择提供了新的评估方案。