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癌症抗原数据库和分析资源:为癌症免疫学共同体建立新的生物信息学资源的蓝图。

The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community.

机构信息

Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States.

Department of Medicine, University of California San Diego, La Jolla, CA, United States.

出版信息

Front Immunol. 2021 Aug 24;12:735609. doi: 10.3389/fimmu.2021.735609. eCollection 2021.

Abstract

Recent years have witnessed a dramatic rise in interest towards cancer epitopes in general and particularly neoepitopes, antigens that are encoded by somatic mutations that arise as a consequence of tumorigenesis. There is also an interest in the specific T cell and B cell receptors recognizing these epitopes, as they have therapeutic applications. They can also aid in basic studies to infer the specificity of T cells or B cells characterized in bulk and single-cell sequencing data. The resurgence of interest in T cell and B cell epitopes emphasizes the need to catalog all cancer epitope-related data linked to the biological, immunological, and clinical contexts, and most importantly, making this information freely available to the scientific community in a user-friendly format. In parallel, there is also a need to develop resources for epitope prediction and analysis tools that provide researchers access to predictive strategies and provide objective evaluations of their performance. For example, such tools should enable researchers to identify epitopes that can be effectively used for immunotherapy or in defining biomarkers to predict the outcome of checkpoint blockade therapies. We present here a detailed vision, blueprint, and work plan for the development of a new resource, the ancer pitope atabase and nalysis esource (CEDAR). CEDAR will provide a freely accessible, comprehensive collection of cancer epitope and receptor data curated from the literature and provide easily accessible epitope and T cell/B cell target prediction and analysis tools. The curated cancer epitope data will provide a transparent benchmark dataset that can be used to assess how well prediction tools perform and to develop new prediction tools relevant to the cancer research community.

摘要

近年来,人们对癌症表位(特别是新表位)的兴趣大增,这些抗原是由肿瘤发生过程中产生的体细胞突变所编码的。人们还对识别这些表位的特定 T 细胞和 B 细胞受体感兴趣,因为它们具有治疗应用价值。它们还可以帮助在基础研究中推断大量和单细胞测序数据中所描述的 T 细胞或 B 细胞的特异性。对 T 细胞和 B 细胞表位的兴趣再次兴起,强调了需要编目所有与生物学、免疫学和临床背景相关的癌症表位相关数据,最重要的是,以用户友好的格式将这些信息免费提供给科学界。与此同时,还需要开发表位预测和分析工具资源,为研究人员提供预测策略,并对其性能进行客观评估。例如,此类工具应使研究人员能够识别可有效用于免疫疗法或定义生物标志物以预测检查点阻断疗法结果的表位。我们在这里提出了一个详细的愿景、蓝图和工作计划,用于开发一个新的资源,即癌症表位数据库和分析资源 (CEDAR)。CEDAR 将提供一个免费访问的、全面的癌症表位和受体数据集合,这些数据是从文献中整理出来的,并提供易于访问的表位和 T 细胞/B 细胞靶标预测和分析工具。经过整理的癌症表位数据将提供一个透明的基准数据集,可用于评估预测工具的性能,并开发与癌症研究界相关的新预测工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/570d/8421848/6109ca50cf8d/fimmu-12-735609-g001.jpg

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