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Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer
Daniel C Liebler1, Timothy R Holzer2, Alexander Haragan3
1Protypia, Inc, Nashville, TN, USA. daniel.liebler@protypia.com.
Abstract:
New therapeutics targeting immune checkpoint proteins have significantly advanced treatment of non-small cell lung cancer (NSCLC), but protein level quantitation of drug targets presents a critical problem. We used multiplexed, targeted mass spectrometry (MS) to quantify immunotherapy target proteins PD-1, PD-L1, PD-L2, IDO1, LAG3, TIM3, ICOSLG, VISTA, GITR, and CD40 in formalin-fixed, paraffin-embedded (FFPE) NSCLC specimens. Immunohistochemistry (IHC) and MS measurements for PD-L1 were weakly correlated, but IHC did not distinguish protein abundance differences detected by MS. PD-L2 abundance exceeded PD-L1 in over half the specimens and the drug target proteins all displayed different abundance patterns. mRNA correlated with protein abundance only for PD-1, PD-L1, and IDO1 and tumor mutation burden did not predict abundance of any protein targets. Global proteome analyses identified distinct proteotypes associated with high PD-L1-expressing and high IDO1-expressing NSCLC. MS quantification of multiple drug targets and tissue proteotypes can improve clinical evaluation of immunotherapies for NSCLC.
Insights
Quantifying immunotherapy targets in non-small cell lung cancer (NSCLC) is challenging. Multiplexed mass spectrometry (MS) offers a more accurate method than immunohistochemistry (IHC) for measuring protein levels, improving immunotherapy evaluation.
Area of Science:
- Oncology
- Immunology
- Proteomics
Background:
- Immune checkpoint inhibitors have advanced non-small cell lung cancer (NSCLC) treatment.
- Accurate quantitation of drug target proteins in NSCLC tissue is crucial but problematic.
- Current methods like immunohistochemistry (IHC) have limitations in protein-level assessment.
Purpose of the Study:
- To quantify multiple immune checkpoint proteins in formalin-fixed, paraffin-embedded (FFPE) NSCLC specimens using multiplexed targeted mass spectrometry (MS).
- To compare MS quantification with IHC for PD-L1 and assess correlations with mRNA and tumor mutation burden.
- To identify proteotypes associated with specific protein expression patterns in NSCLC.
Main Methods:
- Utilized multiplexed, targeted mass spectrometry (MS) to quantify ten immune checkpoint proteins (PD-1, PD-L1, PD-L2, IDO1, LAG3, TIM3, ICOSLG, VISTA, GITR, CD40).
- Analyzed formalin-fixed, paraffin-embedded (FFPE) non-small cell lung cancer (NSCLC) specimens.
- Correlated MS protein quantitation with immunohistochemistry (IHC) for PD-L1, mRNA expression, and tumor mutation burden.
- Performed global proteome analysis to identify tissue proteotypes.
Main Results:
- MS provided more detailed protein abundance data than IHC for PD-L1, with weak correlation between the two methods.
- PD-L2 abundance exceeded PD-L1 in over half of the specimens analyzed.
- Protein abundance correlated with mRNA only for PD-1, PD-L1, and IDO1; tumor mutation burden did not predict target protein abundance.
- Distinct proteotypes were identified in NSCLC with high PD-L1 or high IDO1 expression.
Conclusions:
- Multiplexed targeted MS is a powerful tool for quantifying multiple immunotherapy targets in FFPE NSCLC specimens.
- MS offers a more comprehensive approach than IHC for assessing protein drug targets.
- Quantification of multiple drug targets and tissue proteotypes via MS can enhance the clinical evaluation of NSCLC immunotherapies.
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