{"title":"基于肿瘤免疫微环境建模,优化用于癌症治疗的患者特异性免疫检查点抑制剂疗法。","authors":"Yao Yao, Youhua Frank Chen, Qingpeng Zhang","doi":"10.1093/bib/bbae547","DOIUrl":null,"url":null,"abstract":"<p><p>Enhancing patient response to immune checkpoint inhibitors (ICIs) is crucial in cancer immunotherapy. We aim to create a data-driven mathematical model of the tumor immune microenvironment (TIME) and utilize deep reinforcement learning (DRL) to optimize patient-specific ICI therapy combined with chemotherapy (ICC). Using patients' genomic and transcriptomic data, we develop an ordinary differential equations (ODEs)-based TIME dynamic evolutionary model to characterize interactions among chemotherapy, ICIs, immune cells, and tumor cells. A DRL agent is trained to determine the personalized optimal ICC therapy. Numerical experiments with real-world data demonstrate that the proposed TIME model can predict ICI therapy response. The DRL-derived personalized ICC therapy outperforms predefined fixed schedules. For tumors with extremely low CD8 + T cell infiltration ('extremely cold tumors'), the DRL agent recommends high-dosage chemotherapy alone. For tumors with higher CD8 + T cell infiltration ('cold' and 'hot tumors'), an appropriate chemotherapy dosage induces CD8 + T cell proliferation, enhancing ICI therapy outcomes. Specifically, for 'hot tumors', chemotherapy and ICI are administered simultaneously, while for 'cold tumors', a mid-dosage of chemotherapy makes the TIME 'hotter' before ICI administration. However, in several 'cold tumors' with rapid resistant tumor cell growth, ICC eventually fails. This study highlights the potential of utilizing real-world clinical data and DRL algorithm to develop personalized optimal ICC by understanding the complex biological dynamics of a patient's TIME. Our ODE-based TIME dynamic evolutionary model offers a theoretical framework for determining the best use of ICI, and the proposed DRL agent may guide personalized ICC schedules.</p>","PeriodicalId":9209,"journal":{"name":"Briefings in bioinformatics","volume":"25 6","pages":""},"PeriodicalIF":6.8000,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503752/pdf/","citationCount":"0","resultStr":"{\"title\":\"Optimized patient-specific immune checkpoint inhibitor therapies for cancer treatment based on tumor immune microenvironment modeling.\",\"authors\":\"Yao Yao, Youhua Frank Chen, Qingpeng Zhang\",\"doi\":\"10.1093/bib/bbae547\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Enhancing patient response to immune checkpoint inhibitors (ICIs) is crucial in cancer immunotherapy. 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For tumors with higher CD8 + T cell infiltration ('cold' and 'hot tumors'), an appropriate chemotherapy dosage induces CD8 + T cell proliferation, enhancing ICI therapy outcomes. Specifically, for 'hot tumors', chemotherapy and ICI are administered simultaneously, while for 'cold tumors', a mid-dosage of chemotherapy makes the TIME 'hotter' before ICI administration. However, in several 'cold tumors' with rapid resistant tumor cell growth, ICC eventually fails. This study highlights the potential of utilizing real-world clinical data and DRL algorithm to develop personalized optimal ICC by understanding the complex biological dynamics of a patient's TIME. 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引用次数: 0
摘要
增强患者对免疫检查点抑制剂(ICIs)的反应在癌症免疫疗法中至关重要。我们的目标是创建一个数据驱动的肿瘤免疫微环境数学模型(TIME),并利用深度强化学习(DRL)来优化患者特异性 ICI 治疗联合化疗(ICC)。利用患者的基因组和转录组数据,我们开发了基于常微分方程(ODEs)的TIME动态进化模型,以描述化疗、ICIs、免疫细胞和肿瘤细胞之间的相互作用。对 DRL 代理进行训练,以确定个性化的最佳 ICC 疗法。利用真实世界数据进行的数值实验证明,所提出的 TIME 模型可以预测 ICI 治疗反应。DRL 衍生的个性化 ICC 疗法优于预定义的固定时间表。对于 CD8 + T 细胞浸润极低的肿瘤("极冷肿瘤"),DRL 代理建议单独使用大剂量化疗。对于 CD8 + T 细胞浸润较高的肿瘤("冷肿瘤 "和 "热肿瘤"),适当的化疗剂量可诱导 CD8 + T 细胞增殖,从而提高 ICI 治疗效果。具体来说,对于 "热肿瘤",化疗和 ICI 可同时进行;而对于 "冷肿瘤",化疗的中期剂量可使 TIME 在 ICI 给药前变得更 "热"。然而,在一些肿瘤细胞快速生长的 "冷肿瘤 "中,ICC最终失败。本研究强调了利用真实世界的临床数据和 DRL 算法,通过了解患者 TIME 的复杂生物动态,开发个性化最佳 ICC 的潜力。我们基于 ODE 的 TIME 动态进化模型为确定 ICI 的最佳使用提供了一个理论框架,而所提出的 DRL 代理可为个性化 ICC 计划提供指导。
Optimized patient-specific immune checkpoint inhibitor therapies for cancer treatment based on tumor immune microenvironment modeling.
Enhancing patient response to immune checkpoint inhibitors (ICIs) is crucial in cancer immunotherapy. We aim to create a data-driven mathematical model of the tumor immune microenvironment (TIME) and utilize deep reinforcement learning (DRL) to optimize patient-specific ICI therapy combined with chemotherapy (ICC). Using patients' genomic and transcriptomic data, we develop an ordinary differential equations (ODEs)-based TIME dynamic evolutionary model to characterize interactions among chemotherapy, ICIs, immune cells, and tumor cells. A DRL agent is trained to determine the personalized optimal ICC therapy. Numerical experiments with real-world data demonstrate that the proposed TIME model can predict ICI therapy response. The DRL-derived personalized ICC therapy outperforms predefined fixed schedules. For tumors with extremely low CD8 + T cell infiltration ('extremely cold tumors'), the DRL agent recommends high-dosage chemotherapy alone. For tumors with higher CD8 + T cell infiltration ('cold' and 'hot tumors'), an appropriate chemotherapy dosage induces CD8 + T cell proliferation, enhancing ICI therapy outcomes. Specifically, for 'hot tumors', chemotherapy and ICI are administered simultaneously, while for 'cold tumors', a mid-dosage of chemotherapy makes the TIME 'hotter' before ICI administration. However, in several 'cold tumors' with rapid resistant tumor cell growth, ICC eventually fails. This study highlights the potential of utilizing real-world clinical data and DRL algorithm to develop personalized optimal ICC by understanding the complex biological dynamics of a patient's TIME. Our ODE-based TIME dynamic evolutionary model offers a theoretical framework for determining the best use of ICI, and the proposed DRL agent may guide personalized ICC schedules.
期刊介绍:
Briefings in Bioinformatics is an international journal serving as a platform for researchers and educators in the life sciences. It also appeals to mathematicians, statisticians, and computer scientists applying their expertise to biological challenges. The journal focuses on reviews tailored for users of databases and analytical tools in contemporary genetics, molecular and systems biology. It stands out by offering practical assistance and guidance to non-specialists in computerized methodologies. Covering a wide range from introductory concepts to specific protocols and analyses, the papers address bacterial, plant, fungal, animal, and human data.
The journal's detailed subject areas include genetic studies of phenotypes and genotypes, mapping, DNA sequencing, expression profiling, gene expression studies, microarrays, alignment methods, protein profiles and HMMs, lipids, metabolic and signaling pathways, structure determination and function prediction, phylogenetic studies, and education and training.