Delineating the non-conventional MHC class I and class II peptidome of influenza

描述流感的非传统 MHC I 类和 II 类肽组

• 批准号: 10171775
• 负责人: Laurence Crane Eisenlohr
• 金额: $ 21万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-01 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10171775
• 关键词: Antigen-Presenting Cells; Antigens; Autoantigens; Autoimmune Diseases; Biological Assay; CD4 Positive T Lymphocytes; CD8-Positive T-Lymphocytes; CD8B1 gene; Cell physiology; Cells; Cellular biology; Codon Nucleotides; Collaborations; Communicable Diseases; Complex; Coupled; Data; Databases; Development; Endoplasmic Reticulum Degradation Pathway; Epitope Mapping; Epitopes; Extracellular Space; Flow Cytometry; Frequencies; Future; Gene Expression; Genetic Transcription; Genome; Goals; Histocompatibility Antigens Class II; Host Defense; Immune; Immune system; Immunity; In Vitro; Infection; Infectious Agent; Influenza; Investigation; Light; Liquid Chromatography; MHC Class I Genes; Mainstreaming; Major Histocompatibility Complex; Malignant Neoplasms; Mass Spectrum Analysis; Mediating; Methods; Modeling; Modification; Mus; Nature; Oligonucleotides; Outcome; Peptides; Peripheral; Phosphorylation; Post-Translational Protein Processing; Prevalence; Production; Proteins; Proteome; Publications; Publishing; RNA; RNA Processing; RNA Splicing; Reading Frames; Research; Ribosomal Frameshifting; Site-Directed Mutagenesis; Surface Antigens; System; T cell response; T-Cell Activation; T-Lymphocyte; Techniques; Terminator Codon; Testing; Therapeutic; Tissues; Translating; Translation Initiation; Translations; Tumor Antigens; Work; adaptive immune response; antigen processing; cytokine; flu; glycosylation; immunogenicity; interest; mouse model; multicatalytic endopeptidase complex; pathogen; polypeptide; prophylactic; response; synthetic peptide; tandem mass spectrometry; virtual

PROJECT SUMMARY A cornerstone of adaptive immune responses to infectious agents, cancers and self-tissues is the activation of CD4+ and CD8+ T cells by antigen-derived peptides (epitopes) complexed with Major Histocompatibility Complex class II and class I molecules (MHC-II and -I), respectively. Accordingly, identification of T cell-activating peptides is frequently a critical step in the development of rational prophylactic and therapeutic strategies. Most methods for identification are guided by the prevailing view that peptides are excerpted from the products of conventional transcription, RNA processing and translation. However, we and other labs have demonstrated that MHC-I- and -II-bound peptides can be derived from a wide array of non-canonical mechanisms, including initiation of translation in an alternative reading frame, initiation at a non-AUG codon, co-translational frameshifting, and proteasome-mediated post-translational peptide splicing. Currently, non-conventional epitopes are of peripheral interest, perhaps because many fundamental questions concerning their significance remain unanswered. We do not understand: 1) the fraction of all presented peptides that are non-conventional, 2) whether all the mechanisms underlying non-canonical peptide production have been described, 3) the relative frequencies with which different mechanisms produce non-conventional epitopes, 4) the extent to which non-conventional epitopes drive T cell responses to infectious agents, cancers and self-antigens, and, 5) the prevalence of MHC- II-presented non-canonical peptides, most examples thus far being MHC-I-restricted. With respect to question 4, a recent publication and our preliminary data indicate that non-canonical peptides can drive strong, immunodominant T cell responses. With respect to question 5, the Eisenlohr lab has developed a model of MHC- II-restricted peptide production that is far more complex than generally envisioned. Thus, many of the mechanisms that produce MHC-I-restricted non-conventional epitopes should apply to MHC-II. Through a highly complementary collaboration between the Eisenlohr and Ternette labs, via cutting-edge mass spectrometry, well-developed immune recognition assays, and an array of methods to identify mechanisms underlying non- conventional epitope expression, we will test the hypothesis that both MHC-I and MHC-II non-canonical epitopes, produced by a variety of mechanisms, drive a substantial portion of the TCD8+ and TCD4+ responses to influenza. In addition to potentially uncovering new fundamental cell biology, outcomes could substantially alter the view of host defenses against a high priority infectious disease, pointing to new prophylactic and therapeutic strategies. In addition, we envision the work launching several lines of future investigation, including: 1) assessing the protective capacities of non-conventional epitope-specific T cells, 2) elucidating the antigen processing machinery that produces non-conventional epitopes, 3) identifying the determinants of immunodominance and functionality with respect to conventional vs non-conventional epitopes, and 4) carrying out similar analyses with other infectious agents, cancers and autoimmune diseases.

项目摘要 对感染因子、癌症和自身组织的适应性免疫应答的基石是激活免疫应答。 通过与主要组织相容性复合物复合的抗原衍生肽（表位）的CD 4+和CD 8 + T细胞 II类和I类分子（MHC-II和-I）。因此，T细胞活化肽的鉴定 通常是制定合理预防和治疗策略的关键步骤。大多数方法 用于鉴定的肽是从常规的生物制品中提取的， 转录、RNA加工和翻译。然而，我们和其他实验室已经证明，MHC-I和 - II-结合肽可以来源于广泛的非典型机制，包括启动 在替代阅读框中翻译，在非AUG密码子处起始，共翻译移码，和 蛋白酶体介导的翻译后肽剪接。目前，非常规表位是外周的， 这可能是因为关于其重要性的许多基本问题仍然没有答案。我们 我不明白：1）所有呈现的肽的分数是非常规的，2）是否所有的 已经描述了非典型肽产生的潜在机制，3）与 不同的机制产生非常规表位，4）非常规表位的程度 表位驱动T细胞对感染因子、癌症和自身抗原的应答，以及，5）MHC-1的流行， II呈递的非规范肽，迄今为止大多数实例是MHC-I限制性的。关于问题 4，最近的出版物和我们的初步数据表明，非经典肽可以驱动强大， 免疫显性T细胞应答。关于问题5，艾森洛尔实验室已经开发了一个MHC模型- II-限制性肽生产比通常设想的复杂得多。因此许多 产生MHC-I限制性非常规表位的机制应适用于MHC-II。通过一个高度 Eisenlohr和Ternette实验室之间的互补合作，通过尖端的质谱， 完善的免疫识别试验，以及一系列方法来识别非免疫系统的潜在机制。 常规表位表达，我们将检验MHC-I和MHC-II非典型表位， 由多种机制产生，驱动了大部分TCD 8+和TCD 4+对流感的反应。 除了可能揭示新的基础细胞生物学之外，结果可能会大大改变对细胞生物学的看法。 宿主对高优先级传染病的防御，指向新的预防和治疗策略。 此外，我们设想这项工作将在未来开展几项调查，包括：1）评估 非常规表位特异性T细胞的保护能力，2）阐明抗原加工 产生非常规表位的机制，3）鉴定免疫显性的决定因素， 关于常规表位与非常规表位的功能性，和4）进行类似的分析， 其他传染性病原体、癌症和自身免疫性疾病。

项目成果

MARS an improved de novo peptide candidate selection method for non-canonical antigen target discovery in cancer.

• DOI: 10.1038/s41467-023-44460-z
• 发表时间: 2024-01-22
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Liao, Hanqing;Barra, Carolina;Zhou, Zhicheng;Peng, Xu;Woodhouse, Isaac;Tailor, Arun;Parker, Robert;Carre, Alexia;Borrow, Persephone;Hogan, Michael J.;Paes, Wayne;Eisenlohr, Laurence C.;Mallone, Roberto;Nielsen, Morten;Ternette, Nicola
• 通讯作者: Ternette, Nicola