Understanding the genesis of the spliced immunopeptidome

主要组织相容性复合体（MHC）分子呈递抗原是生物体生命的一个重要过程。我们体内几乎所有细胞的表面都有成千上万的抗原。这些抗原是细胞内蛋白质降解后产生的蛋白质片段（或多肽）。总的来说，这个多肽的海洋被称为免疫肽穹窿，可以使用先进的技术来表征。到目前为止，质谱（MS）技术是免疫肽球分析的首选方法。目前抗原呈递的教条是免疫T细胞可以识别由基因组编码的肽。出乎意料的是，两项具有里程碑意义的研究提供了证据，证明人类细胞中免疫肽丘的很大一部分是由基因组中未编码的肽组成的。它们可能是一种被称为肽剪接的鲜为人知的机制的结果。剪接肽的存在对免疫系统生物学的各个方面的潜在影响是非常重要的，因为它们的存在极大地扩大了呈现给免疫系统的抗原肽库。然而，破译剪接的免疫肽球的组成是非常具有挑战性的。事实上，从基因组信息来看，剪接肽是完全不可预测的，而质谱技术是迄今为止在全球范围内识别它们的唯一方法。迄今为止，世界上只有少数研究人员开发了适当的资源和专业知识来分析剪接的免疫肽球。在我们小组中，我们最近发现，在小鼠模型中分析的免疫肽丘中有很大一部分是由这种剪接的肽组成的。这些发现提出了一个重要的观点，即剪接肽的产生和呈现是一个保守的生物进化过程。剪接肽是随机产生的吗？事实上，我们对它们的起源知之甚少。我们的研究计划的目的是验证这样一个假设，即剪接免疫肽球的发生是由细胞内多个水平调节的明确的催化过程系统地安排的。首先，我们将在蛋白质组范围内研究肽剪接与蛋白质构象变化之间的全局关系。其次，我们将评估蛋白酶体催化亚基对剪接免疫肽球的整体组成的贡献。第三，我们将评估自噬和其他蛋白酶在催化肽剪接中的作用。我们NSERC项目的长期目标是深入了解拼接肽是如何产生的，并由MHC分子呈现。这将使我们能够预测它们，并最终使新的生物系统工程能够控制它们的产生和免疫功能。

Presentation of antigens by major histocompatibility complex (MHC) molecules is a vital process in the life of an organism. Thousands of such antigens are presented on the surface of virtually all cells in our body. Those antigens are protein fragments (or peptides) that are generated following degradation of proteins inside the cell. Collectively, this ocean of peptides is referred to as the immunopeptidome and can be characterized using advanced technologies. Until now, mass spectrometry (MS) technology is the method of choice for the analysis of the immunopeptidome. The current dogma in antigen presentation is that immune T cells can recognize peptides that are encoded by the genome. Unexpectedly, two landmark studies provided evidences that a significant proportion of the immunopeptidome, in human cells, is composed of peptides that are not encoded in the genome. They may be the result of a very poorly understood mechanism referred to as peptide splicing. The potential implications of the presence of spliced peptides for all facets of the immune system biology is very significant, because their presence dramatically widens the repertoire of antigenic peptides presented to the immune system. However, deciphering the composition of the spliced immunopeptidome is very challenging. In fact, spliced peptides are completely unpredictable from genomic information and MS technologies represent so far the only approach to identify them on a global scale. To date, only a handful of researchers worldwide have developed the appropriate resources and expertise to analyse the spliced immunopeptidome. In our group, we recently found that a significant proportion of the immunopeptidome, analyzed in the mouse as model, is composed of such spliced peptides. These discoveries raise the important point that generation and presentation of spliced peptides is a conserved biological process across evolution. Are spliced peptides randomly generated? In fact, very little is known about their genesis. The objective of our research program is to test the hypothesis that genesis of the spliced immunopeptidome is systematically orchestrated by well-defined catalytic processes regulated at multiple levels inside the cell. First, we will investigate the global relationship between peptide splicing and protein conformational changes on a proteome-wide scale. Second, we will assess the contribution of the proteasome catalytic subunits to the global composition of the spliced immunopeptidome. Third, we will evaluate the role of autophagy and other proteases in catalyzing peptide splicing. The long-term objective of our NSERC program is to gain in-depth understanding of how spliced peptides are generated and presented by MHC molecules. This will allow us to predict them, and will ultimately enable the engineering of new biological systems to control their generation and function in immunity.