Understanding the genesis of the spliced immunopeptidome

主要组织相容性复合体（MHC）分子对抗原的呈递是生物体生命中的重要过程。成千上万的这种抗原存在于我们身体几乎所有细胞的表面。这些抗原是在细胞内蛋白质降解后产生的蛋白质片段（或肽）。总的来说，这种肽的海洋被称为免疫肽组，可以使用先进的技术进行表征。到目前为止，质谱（MS）技术是分析免疫肽组的首选方法。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，证明人类细胞中相当大比例的免疫肽组是由基因组中不编码的肽组成的。它们可能是一种非常不了解的机制的结果，称为肽剪接。剪接肽的存在对免疫系统生物学的所有方面的潜在影响是非常重要的，因为它们的存在显著地拓宽了呈递给免疫系统的抗原肽的库。然而，破译剪接的免疫肽组的组成是非常具有挑战性的。事实上，剪接肽是完全不可预测的基因组信息和MS技术代表了迄今为止唯一的方法来确定他们在全球范围内。迄今为止，全世界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组。在我们的小组中，我们最近发现，在作为模型的小鼠中分析的免疫肽组的显著比例是由这样的剪接肽组成的。这些发现提出了重要的一点，即剪接肽的产生和呈递是整个进化过程中保守的生物学过程。剪接肽是随机产生的吗？事实上，人们对它们的起源知之甚少。我们的研究计划的目的是测试的假设，即剪接的免疫肽组的起源是系统地精心策划的明确定义的催化过程中，在细胞内的多个水平进行调节。首先，我们将在蛋白质组范围内研究肽剪接和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组的全球组成的贡献。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计划的长期目标是深入了解MHC分子如何产生和呈递剪接肽。这将使我们能够预测它们，并最终使新生物系统的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.