In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies.,Molecular Immunology

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In-depth mining of the immunopeptidome of an acute myeloid leukemia cell line using complementary ligand enrichment and data acquisition strategies.
Molecular Immunology ( IF 3.2 ) Pub Date : 2020-05-05 , DOI: 10.1016/j.molimm.2020.04.008
Kirti Pandey ₁ , Nicole A Mifsud ₁ , Terry C C Lim Kam Sian ₁ , Rochelle Ayala ₁ , Nicola Ternette ₂ , Sri H Ramarathinam ₁ , Anthony W Purcell ₁

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The identification of T cell epitopes derived from tumour specific antigens remains a significant challenge for the development of peptide-based vaccines and immunotherapies. The use of mass spectrometry-based approaches (immunopeptidomics) can provide powerful new avenues for the identification of such epitopes. In this study we report the use of complementary peptide antigen enrichment methods and a comprehensive mass spectrometric acquisition strategy to provide in-depth immunopeptidome data for the THP-1 cell line, a cell line used widely as a model of human leukaemia. To accomplish this, we combined robust experimental workflows that incorporated ultrafiltration or off-line reversed phase chromatography to enrich peptide ligand as well as a multifaceted data acquisition strategy using an Orbitrap Fusion LC-MS instrument. Using the combined datasets from the two ligand enrichment methods we gained significant depth in immunopeptidome coverage by identifying a total of 41,816 HLA class I peptides from THP-1 cells, including a significant number of peptides derived from different oncogenes or over expressed proteins associated with cancer. The physicochemical properties of the HLA-bound peptides dictated their recovery using the two ligand enrichment approaches and their distribution across the different precursor charge states considered in the data acquisition strategy. The data highlight the complementarity of the two enrichment procedures, and in cases where sample is not limiting, suggest that the combination of both approaches will yield the most comprehensive immunopeptidome information.

中文翻译：

使用互补配体富集和数据采集策略，对急性髓样白血病细胞系的免疫肽组进行深入挖掘。

源自肿瘤特异性抗原的T细胞表位的鉴定仍然是开发基于肽的疫苗和免疫疗法的重大挑战。基于质谱的方法（免疫肽组学）的使用可以为鉴定这些表位提供强大的新途径。在这项研究中，我们报告了使用互补肽抗原富集方法和全面的质谱采集策略来为THP-1细胞系（一种广泛用作人类白血病模型的细胞系）提供深入的免疫肽组数据。为了实现这一目标，我们结合了强大的实验工作流程，这些工作流程结合了超滤或离线反相色谱法来丰富肽配体，并使用Orbitrap Fusion LC-MS仪器进行了多方面的数据采集。使用两种配体富集方法的组合数据集，我们从THP-1细胞中鉴定出总共41,816种HLA I类肽，包括相当数量的衍生自不同癌基因或与癌症相关的过表达蛋白的肽，从而在免疫肽组覆盖方面取得了重要进展。HLA结合肽的物理化学性质决定了它们使用两种配体富集方法的回收率以及它们在数据采集策略中考虑的不同前体电荷状态的分布。数据突出了这两种富集程序的互补性，并且在样品不受限制的情况下，表明两种方法的组合将产生最全面的免疫肽组信息。

更新日期：2020-05-05

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