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同源重组相关特征预测转移性尿路上皮癌的预后和免疫治疗反应

Homologous Recombination Related Signatures Predict Prognosis and Immunotherapy Response in Metastatic Urothelial Carcinoma.

作者信息

Li Pan, Chen Chaohu, Li Jianpeng, Yang Li, Wang Yuhan, Dong Zhilong, Mi Jun, Zhang Yunxin, Wang Juan, Wang Hanzhang, Rodriguez Ronald, Tian Junqiang, Wang Zhiping

机构信息

Department of Urology, Lanzhou University Second Hospital, Lanzhou, China.

Key Laboratory of Gansu Province for Urological Diseases, Lanzhou, China.

出版信息

Front Genet. 2022 Apr 26;13:875128. doi: 10.3389/fgene.2022.875128. eCollection 2022.


DOI:10.3389/fgene.2022.875128
PMID:35559013
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9086193/
Abstract

This study used homologous recombination (HR) related signatures to develop a clinical prediction model for screening immune checkpoint inhibitors (ICIs) advantaged populations and identify hub genes in advanced metastatic urothelial carcinoma. The single-sample gene enrichment analysis and weighted gene co-expression network analysis were applied to identify modules associated with immune response and HR in IMvigor210 cohort samples. The principal component analysis was utilized to determine the differences in HR-related module gene signature scores across different tissue subtypes and clinical variables. Risk prediction models and nomograms were developed using differential gene expression analysis associated with HR scores, least absolute shrinkage and selection operator, and multivariate proportional hazards model regression. Additionally, hub genes were identified by analyzing the contribution of HR-related genes to principal components and overall survival analysis. Finally, clinical features from GSE133624, GSE13507, the TCGA, and other data sets were analyzed to validate the relationship between hub genes and tumor growth and mutation. The HR score was significantly higher in the complete/partial response group than in the stable/progressive disease group. The majority of genes associated with HR were discovered to be involved in the cell cycle and others. Genomically unstable, high tumor level, and high immune level samples all exhibited significantly higher HR score than other sample categories, and higher HR scores were related to improved survival following ICIs treatment. The risk scores for , , , , , and were identified, and the training and verification groups had markedly different survival times. The risk score, tumor neoantigen burden, mismatch repair, and cell cycle regulation were discovered to be independent predictors of survival time following immunotherapy. Patients with a high level of expression of hub genes such as , , and had a greater chance of surviving following immunotherapy. These genes are expressed at significantly higher levels in tumors, high-grade cancer, and invasive cancer than other categories, and are associated with TP53 and RB1 mutations. HR-related genes are upregulated in genomically unstable samples, the survival time of mUC patients after treatment with ICIs can be predicted using a normogram model based on HR signature.

摘要

本研究使用同源重组(HR)相关特征来开发一种临床预测模型,用于筛选免疫检查点抑制剂(ICI)优势人群,并识别晚期转移性尿路上皮癌中的枢纽基因。应用单样本基因富集分析和加权基因共表达网络分析来识别IMvigor210队列样本中与免疫反应和HR相关的模块。利用主成分分析来确定不同组织亚型和临床变量之间HR相关模块基因特征评分的差异。使用与HR评分相关的差异基因表达分析、最小绝对收缩和选择算子以及多变量比例风险模型回归来开发风险预测模型和列线图。此外,通过分析HR相关基因对主成分的贡献和总体生存分析来识别枢纽基因。最后,分析来自GSE133624、GSE13507、TCGA和其他数据集的临床特征,以验证枢纽基因与肿瘤生长和突变之间的关系。完全/部分缓解组的HR评分显著高于稳定/疾病进展组。发现大多数与HR相关的基因参与细胞周期等过程。基因组不稳定、肿瘤水平高和免疫水平高的样本的HR评分均显著高于其他样本类别,且较高的HR评分与ICI治疗后生存率提高相关。确定了 、 、 、 、 和 的风险评分,训练组和验证组的生存时间明显不同。发现风险评分、肿瘤新抗原负担、错配修复和细胞周期调节是免疫治疗后生存时间的独立预测因素。 、 和 等枢纽基因高表达的患者免疫治疗后存活机会更大。这些基因在肿瘤、高级别癌症和浸润性癌症中的表达水平明显高于其他类别,且与TP53和RB1突变相关。基因组不稳定样本中HR相关基因上调,基于HR特征的列线图模型可预测mUC患者ICI治疗后的生存时间。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/204990a1116f/fgene-13-875128-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/543fe0a1c559/fgene-13-875128-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/720198d33dec/fgene-13-875128-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/dfecab804524/fgene-13-875128-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/2cb796b030ca/fgene-13-875128-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/63c2019f9c5e/fgene-13-875128-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/95d11b3a9df7/fgene-13-875128-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/3211812db566/fgene-13-875128-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/fe267fc04956/fgene-13-875128-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/9385191a4eb8/fgene-13-875128-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/204990a1116f/fgene-13-875128-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/543fe0a1c559/fgene-13-875128-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/720198d33dec/fgene-13-875128-g002.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/63c2019f9c5e/fgene-13-875128-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/95d11b3a9df7/fgene-13-875128-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/3211812db566/fgene-13-875128-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/fe267fc04956/fgene-13-875128-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/9385191a4eb8/fgene-13-875128-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/784a/9086193/204990a1116f/fgene-13-875128-g010.jpg

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[1]
Homologous Recombination Related Signatures Predict Prognosis and Immunotherapy Response in Metastatic Urothelial Carcinoma.

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[5]
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引用本文的文献

[1]
FAM72A promotes UNG2 degradation and mutagenesis in human cancer cells.

Sci Rep. 2025-7-2

[2]
RAD54L promotes progression of hepatocellular carcinoma via the homologous recombination repair pathway.

Funct Integr Genomics. 2023-4-18

[3]
Clinically relevant fusion oncogenes: detection and practical implications.

Ther Adv Med Oncol. 2022-12-26

本文引用的文献

[1]
European experts consensus: BRCA/homologous recombination deficiency testing in first-line ovarian cancer.

Ann Oncol. 2022-3

[2]
Genomic Instability and Cancer Risk Associated with Erroneous DNA Repair.

Int J Mol Sci. 2021-11-12

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Biochim Biophys Acta Rev Cancer. 2022-1

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Eur Urol. 2022-1

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Alterations of DNA damage response pathway: Biomarker and therapeutic strategy for cancer immunotherapy.

Acta Pharm Sin B. 2021-10

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CD8 T effector and immune checkpoint signatures predict prognosis and responsiveness to immunotherapy in bladder cancer.

Oncogene. 2021-10

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Trends Cell Biol. 2022-1

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Front Immunol. 2021

[10]
RAD51AP1 Loss Attenuates Colorectal Cancer Stem Cell Renewal and Sensitizes to Chemotherapy.

Mol Cancer Res. 2021-9

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