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Updated: Jun 5, 2026
"Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome
Published on: March 24, 2023
Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential
Audrey Kishishita1,2, Sabine Cismoski1,2, Tianna Grant3,4,5
1Graduate Program in Chemistry and Chemical Biology, University of California-San Francisco, San Francisco, CA, USA.
Abstract:
The complement of tumor cell surface proteins, or "surfaceome", is a rich source of potential immunotherapy targets. To move beyond expression-based target discovery, we previously described "structural surfaceomics," combining crosslinking mass spectrometry (XL-MS) with surface protein biotinylation to identify conformation-selective targets. In our prior work, we applied this method to a single model of acute myeloid leukemia (AML), identifying active integrin beta-2 as a promising target. Here, we expand structural surfaceomics to identify additional immunotherapy targets and surface protein biology across additional models of AML, multiple myeloma, and prostate cancer, as well as donor peripheral blood mononuclear cells. Utilizing these models and different chemical crosslinkers, we compile an extensive database of 5,209 crosslinks. We characterize both shared and unique crosslink-based features, identifying 1,612 disease model-specific crosslinks, including 212 potentially defining tumor-specific conformations based on distance constraint violations relative to AlphaFold predictions. We further implement a suite of emerging modeling tools to predict tumor-specific protein structures. We probe crosslinking patterns suggesting multiple myeloma-specific CD48 and AML-specific integrin α1/β4 heterodimer conformations. This work establishes a resource for cancer structural biology by implementation of structural surfaceomics. Our findings also point toward more realistic protein design models, potentially enabling systematic detection of targetable cancer-specific epitopes for next-generation immunotherapies.
Insights
Structural surfaceomics identifies novel cancer immunotherapy targets by analyzing protein structures on tumor cells. This approach reveals unique protein conformations in leukemia, myeloma, and prostate cancer, paving the way for next-generation immunotherapies.
Area of Science:
- Cancer Biology
- Structural Biology
- Immunotherapy
Background:
- The tumor cell surfaceome is a key resource for immunotherapy targets.
- Traditional methods focus on protein expression, limiting target discovery.
- Structural surfaceomics offers a conformation-selective approach to identify novel targets.
Purpose of the Study:
- To expand structural surfaceomics to diverse cancer models (AML, multiple myeloma, prostate cancer).
- To identify novel immunotherapy targets and understand surface protein biology.
- To create a comprehensive database of crosslinks and disease-specific conformations.
Main Methods:
- Combined crosslinking mass spectrometry (XL-MS) with surface protein biotinylation.
- Applied structural surfaceomics across multiple cancer models and healthy donor cells.
- Utilized emerging modeling tools and AlphaFold predictions to analyze protein structures.
Main Results:
- Compiled an extensive database of 5,209 crosslinks.
- Identified 1,612 disease model-specific crosslinks, including 212 potentially defining tumor-specific conformations.
- Probed conformations suggesting multiple myeloma-specific CD48 and AML-specific integrin α1/β4 heterodimers.
Conclusions:
- Structural surfaceomics provides a valuable resource for cancer structural biology.
- Identified potential tumor-specific epitopes for next-generation immunotherapies.
- Highlights the potential of realistic protein design models for cancer research.
