The proteomic and immunopeptidomic landscape of non-small cell lung cancer

Introduction: Non-small cell lung carcinoma (NSCLC) is the most common type of lung cancer, with adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC) being the most prevailing histological subtypes with distinct biological signatures. Correct classification and accurate molecular profiling are essential for effective therapeutic guidance. In this research, we performed an in-depth mass spectrometry (MS)-based proteomic study of a large patient cohort representing the two aforementioned subtypes of NSCLC. This MS-based profiling of LUAD and LUSC revealed proteomic alterations that might determine their clinical behavior. High-coverage proteome analysis opens the possibility to unravel the mechanisms of immune evasion in NSCLC. Moreover, additional immunopeptidomics study should elucidate distinct tumor-associated antigens, that are pivotal for the development of epitope-specific cancer immunotherapies.

Methods: In our work, the patient-derived samples were processed with an optimized, semi-automated single-pot, solid-phase enhanced sample preparation (SP3-beads) workflow utilizing a Bravo pipetting platform. Thereby, extracted proteins were digested and the resulting peptides were analyzed via liquid-chromatography tandem-mass spectrometry (LC-MS/MS).

For the immunopeptidome study, we established and optimized a workflow to enrich HLA-I and HLA-II-bound antigens. This workflow involves automated affinity purification with crosslinked monoclonal antibodies, performed on a AssayMAP Bravo platform. This adaptable method enables processing of fresh frozen tissue from biopsies, among a variety of sample types.

Results: The MS-analysis of the patient cohort (consisting of LUAD (n = 83), LUSC (n = 70), and tumor-adjacent (n = 138)) resulted in high proteome coverage of a total of over 10000 unique proteins. Initial statistical analysis shows significant differences between LUAD and LUSC and suggests a possible distinction based on patient's gender.

In our pilot study of the immunopeptidome, we successfully identified > 4000 peptides after HLA class I enrichment and > 7500 peptides after HLA class II enrichment. As for the patient cohort, the initial analysis of HLA-I enriched samples revealed a total of 40k unique peptides acquired in data independet acquisition. This coverage enables a robust analysis of the immunopeptidome, providing valuable insights into antigen presentation. Furthermore, a de novo sequencing analysis of the HLA-I peptides was performed.

Outlook: Deep proteomic coverage of a large patient cohort enables us to gain deeper insight into the fundamental molecular biology of LUAD and LUSC. The further immunopeptidomic investigation gives a promising outlook to reveal a subset of tumor-associated antigens unique to each NSCLC subtype, offering precise targets for epitope-specific cancer immunotherapies. This study should facilitate the development of personalized immunotherapies tailored to each patient's tumor profile.