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基于体外机器学习的 CAR T 免疫突触质量测量与患者临床结果相关。

In vitro machine learning-based CAR T immunological synapse quality measurements correlate with patient clinical outcomes.

机构信息

Department of Pathology, Immunology and Laboratory Medicine, Rutgers University-New Jersey Medical School, Newark, New Jersey, United States of America.

Center for Immunity and Inflammation, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey, United States of America.

出版信息

PLoS Comput Biol. 2022 Mar 18;18(3):e1009883. doi: 10.1371/journal.pcbi.1009883. eCollection 2022 Mar.


DOI:10.1371/journal.pcbi.1009883
PMID:35303007
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8955962/
Abstract

The human immune system consists of a highly intelligent network of billions of independent, self-organized cells that interact with each other. Machine learning (ML) is an artificial intelligence (AI) tool that automatically processes huge amounts of image data. Immunotherapies have revolutionized the treatment of blood cancer. Specifically, one such therapy involves engineering immune cells to express chimeric antigen receptors (CAR), which combine tumor antigen specificity with immune cell activation in a single receptor. To improve their efficacy and expand their applicability to solid tumors, scientists optimize different CARs with different modifications. However, predicting and ranking the efficacy of different "off-the-shelf" immune products (e.g., CAR or Bispecific T-cell Engager [BiTE]) and selection of clinical responders are challenging in clinical practice. Meanwhile, identifying the optimal CAR construct for a researcher to further develop a potential clinical application is limited by the current, time-consuming, costly, and labor-intensive conventional tools used to evaluate efficacy. Particularly, more than 30 years of immunological synapse (IS) research data demonstrate that T cell efficacy is not only controlled by the specificity and avidity of the tumor antigen and T cell interaction, but also it depends on a collective process, involving multiple adhesion and regulatory molecules, as well as tumor microenvironment, spatially and temporally organized at the IS formed by cytotoxic T lymphocytes (CTL) and natural killer (NK) cells. The optimal function of cytotoxic lymphocytes (including CTL and NK) depends on IS quality. Recognizing the inadequacy of conventional tools and the importance of IS in immune cell functions, we investigate a new strategy for assessing CAR-T efficacy by quantifying CAR IS quality using the glass-support planar lipid bilayer system combined with ML-based data analysis. Previous studies in our group show that CAR-T IS quality correlates with antitumor activities in vitro and in vivo. However, current manually quantified IS quality data analysis is time-consuming and labor-intensive with low accuracy, reproducibility, and repeatability. In this study, we develop a novel ML-based method to quantify thousands of CAR cell IS images with enhanced accuracy and speed. Specifically, we used artificial neural networks (ANN) to incorporate object detection into segmentation. The proposed ANN model extracts the most useful information to differentiate different IS datasets. The network output is flexible and produces bounding boxes, instance segmentation, contour outlines (borders), intensities of the borders, and segmentations without borders. Based on requirements, one or a combination of this information is used in statistical analysis. The ML-based automated algorithm quantified CAR-T IS data correlates with the clinical responder and non-responder treated with Kappa-CAR-T cells directly from patients. The results suggest that CAR cell IS quality can be used as a potential composite biomarker and correlates with antitumor activities in patients, which is sufficiently discriminative to further test the CAR IS quality as a clinical biomarker to predict response to CAR immunotherapy in cancer. For translational research, the method developed here can also provide guidelines for designing and optimizing numerous CAR constructs for potential clinical development. Trial Registration: ClinicalTrials.gov NCT00881920.

摘要

人体免疫系统由数十亿个独立的、自我组织的细胞组成,这些细胞相互作用。机器学习 (ML) 是一种人工智能 (AI) 工具,可自动处理大量的图像数据。免疫疗法彻底改变了血液癌症的治疗方法。具体来说,其中一种疗法涉及对免疫细胞进行工程改造,使其表达嵌合抗原受体 (CAR),该受体将肿瘤抗原特异性与单个受体中的免疫细胞激活相结合。为了提高其疗效并将其适用性扩展到实体瘤,科学家们用不同的修饰优化不同的 CAR。然而,预测和对不同的“现成”免疫产品(例如,CAR 或双特异性 T 细胞衔接器 [BiTE])的疗效进行排名,并选择临床应答者,在临床实践中是具有挑战性的。同时,为了进一步开发潜在的临床应用,确定研究人员的最佳 CAR 结构受到当前耗时,昂贵且劳动强度大的常规工具评估疗效的限制。特别是,30 多年的免疫突触(IS)研究数据表明,T 细胞的功效不仅受到肿瘤抗原和 T 细胞相互作用的特异性和亲和力的控制,还取决于一个集体过程,涉及多种粘附和调节分子,以及肿瘤微环境,在细胞毒性 T 淋巴细胞(CTL)和自然杀伤(NK)细胞形成的免疫突触中具有时空组织。细胞毒性淋巴细胞(包括 CTL 和 NK)的最佳功能取决于 IS 质量。认识到传统工具的不足以及 IS 在免疫细胞功能中的重要性,我们通过使用基于 ML 的数据分析来量化 CAR-T 的免疫突触质量,研究了评估 CAR-T 疗效的新策略。我们小组的先前研究表明,CAR-T 的免疫突触质量与体外和体内的抗肿瘤活性相关。然而,当前手动量化的免疫突触质量数据分析既耗时又费力,并且准确性,可重复性和可重复性低。在这项研究中,我们开发了一种新的基于 ML 的方法,可以快速准确地量化数千个 CAR 细胞免疫突触图像。具体来说,我们使用人工神经网络(ANN)将对象检测纳入分割。所提出的 ANN 模型提取了最有用的信息来区分不同的免疫突触数据集。网络输出灵活,可生成边界框,实例分割,轮廓线(边界),边界强度和无边界分割。根据要求,可在统计分析中使用此信息的一种或组合。基于患者的 Kappa-CAR-T 细胞,直接从患者中治疗的临床应答者和非应答者的 CAR-T 免疫突触数据的 ML 自动化算法定量分析表明,CAR 细胞免疫突触质量可用作潜在的复合生物标志物,与患者的抗肿瘤活性相关,该方法具有足够的鉴别力,可以进一步测试 CAR 免疫突触质量作为癌症 CAR 免疫治疗反应的临床生物标志物。对于转化研究,这里开发的方法还可以为设计和优化用于潜在临床开发的众多 CAR 构建体提供指导。试验注册:ClinicalTrials.gov NCT00881920。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/a017416c8dfb/pcbi.1009883.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/6617397795da/pcbi.1009883.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/013f250de1e2/pcbi.1009883.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/91c75111b1f1/pcbi.1009883.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/9009ff413392/pcbi.1009883.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/5a1aea63cf6e/pcbi.1009883.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/8a0b614a08bc/pcbi.1009883.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/6bc400d9dae1/pcbi.1009883.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/a017416c8dfb/pcbi.1009883.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/6617397795da/pcbi.1009883.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/013f250de1e2/pcbi.1009883.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/91c75111b1f1/pcbi.1009883.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/9009ff413392/pcbi.1009883.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/5a1aea63cf6e/pcbi.1009883.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/8a0b614a08bc/pcbi.1009883.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/6bc400d9dae1/pcbi.1009883.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/e331/8955962/a017416c8dfb/pcbi.1009883.g008.jpg

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