Language

週五, 14 六月 2024 15:01

Enhanced Proteomic Coverage in Tissue Microenvironment by Immune Cell Subtype Library-assisted DIA-MS

林國儀
Molecular & Cellular Proteomics
June 14, 2024

Immune cells that infiltrate the tumor microenvironment (TME) play crucial roles in shaping cancer development and influencing clinical outcomes and therapeutic responses. However, obtaining a comprehensive proteomic snapshot of tumor-infiltrating immunity in clinical specimens is often hindered by small sample amounts and a low proportion of immune infiltrating cells in the TME. To enable in-depth and highly sensitive profiling of microscale tissues, we established an immune cell-enriched library-assisted strategy for data-independent acquisition mass spectrometry (DIA-MS). Firstly, 6 immune cell subtype-specific spectral libraries were established from sorted CD8+, CD4+ T lymphocytes, B lymphocytes, natural killer cells, dendritic cells, and macrophages in murine mesenteric lymph nodes (MLNs), covering 7,815 protein groups with surface markers and immune cell-enriched proteins. The feasibility of microscale immune proteomic profiling was demonstrated on 1 μg tissue protein from the tumor of murine colorectal cancer (CRC) models using single-shot DIA; the immune cell-enriched library increased coverage to quantify 7,419 proteins compared to directDIA analysis (6,978 proteins). The enhancement enabled the mapping of 841 immune function-related proteins and exclusive identification of many low-abundant immune proteins, such as CD1D1, and CD244, demonstrating high sensitivity for immune landscape profiling. This approach was employed to characterize the MLNs in CRC models, aiming to elucidate the mechanism underlying their involvement in cancer development within the TME. Even with a low percentage of immune cell infiltration (0.25-3%) in the tumor, our results illuminate down-regulation in the adaptive immune signaling pathways (C-type lectin receptor signaling, chemokine signaling, etc.), T cell receptor signaling, and Th1/Th2/Th17 cell differentiation, suggesting an immunosuppressive status in MLNs of CRC models. The DIA approach using the immune cell-enriched libraries showcased deep coverage and high sensitivity that can facilitate illumination of the immune proteomic landscape for microscale samples.

Full content

 

論文集