Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
Massachusetts General Hospital, Boston, MA, 02114, USA.
Nat Commun. 2023 Apr 3;14(1):1851. doi: 10.1038/s41467-023-37547-0.
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each 'ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.
对蛋白质组、磷酸化蛋白质组和乙酰化蛋白质组的连续多组学分析，提供了对疾病病理和治疗中涉及的蛋白质表达、细胞信号转导、串扰和表观遗传途径变化的深入了解。然而，用于理解蛋白质降解和抗原呈递的泛素组和 HLA 肽组数据收集尚未被序列化，而是需要使用不同的协议对单独的样本进行平行处理。在这里，我们提出了 MONTE，这是一种高度敏感的多组学天然组织富集工作流程，可从同一组织样本中连续、深度分析 HLA-I 和 HLA-II 免疫肽组、泛素组、蛋白质组、磷酸化蛋白质组和乙酰化蛋白质组。我们证明，序列化不会影响每个“ome”的覆盖深度和定量精度，并且 HLA 免疫肽组学的添加能够鉴定来自癌症/睾丸抗原和患者特异性新抗原的肽。我们使用一小部分患者肺腺癌肿瘤评估了 MONTE 工作流程的技术可行性。
