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An alternatively spliced PD-L1 isoform PD-L1∆3, and PD-L2 expression in breast cancers: implications for eligibility
Didem Naz Dioken1, Ibrahim Ozgul1, Irem Yilmazbilek1
1Department of Biological Sciences, Middle East Technical University (METU), Dumlupinar Blv No:1 Universiteler Mah, Cankaya, 06800, Ankara, Türkiye.
Abstract:
Targeting PD-1/PD-L1 has shown substantial therapeutic response and unprecedented long-term durable responses in the clinic. However, several challenges persist, encompassing the prediction of treatment effectiveness and patient responses, the emergence of treatment resistance, and the necessity for additional biomarkers. Consequently, we comprehensively explored the often-overlooked isoforms of crucial immunotherapy players, leveraging transcriptomic analysis, structural modeling, and immunohistochemistry (IHC) data. Our investigation has led to the identification of an alternatively spliced isoform of PD-L1 that lacks exon 3 (PD-L1∆3) and the IgV domain required to interact with PD-1. PD-L1∆3 is expressed more than the canonical isoform in a subset of breast cancers and other TCGA tumors. Using the deep learning-based protein modeling tool AlphaFold2, we show the lack of a possible interaction between PD-L1∆3 and PD-1. In addition, we present data on the expression of an additional ligand for PD-1, PD-L2. PD-L2 expression is widespread and positively correlates with PD-L1 levels in breast and other tumors. We report enriched epithelial-mesenchymal transition (EMT) signature in high PD-L2 transcript expressing (PD-L2 > PD-L1) tumors in all breast cancer subtypes, highlighting potential crosstalk between EMT and immune evasion. Notably, the estrogen gene signature is downregulated in ER + breast tumors with high PD-L2. The data on PD-L2 IHC positivity but PD-L1 negativity in breast tumors, together with our results on PD-L1∆3, highlight the need to utilize PD-L2 and PD-L1 isoform-specific antibodies for staining patient tissue sections to offer a more precise prediction of the outcomes of PD-1/PD-L1 immunotherapy.
Insights
Researchers discovered a new PD-L1 isoform (PD-L1∆3) that cannot bind PD-1, and found PD-L2 expression linked to immune evasion in breast cancer. This highlights the need for isoform-specific antibodies in immunotherapy.
Area of Science:
- Immunology and Cancer Research
- Molecular Biology and Bioinformatics
Background:
- Targeting programmed cell death protein 1 (PD-1) and its ligand (PD-L1) has improved cancer immunotherapy outcomes.
- Challenges remain in predicting treatment response, managing resistance, and identifying reliable biomarkers for PD-1/PD-L1 therapy.
Purpose of the Study:
- To investigate the role of understudied isoforms of PD-1/PD-L1 pathway components in cancer.
- To identify novel biomarkers for predicting immunotherapy response.
Main Methods:
- Transcriptomic analysis, structural modeling using AlphaFold2, and immunohistochemistry (IHC) were employed.
- Expression levels of PD-L1 isoforms and PD-L2 were analyzed in various cancers, including breast cancer subtypes.
- Gene signatures, such as epithelial-mesenchymal transition (EMT) and estrogen receptor (ER) pathways, were assessed.
Main Results:
- An alternatively spliced PD-L1 isoform lacking exon 3 (PD-L1∆3), unable to interact with PD-1, was identified and found to be expressed in a subset of breast and other TCGA tumors.
- Programmed cell death ligand 2 (PD-L2) expression is widespread, correlates with PD-L1 levels, and is associated with an enriched epithelial-mesenchymal transition (EMT) signature in high PD-L2 expressing tumors.
- Estrogen gene signature is downregulated in ER-positive breast tumors with high PD-L2 expression, and PD-L2 positivity with PD-L1 negativity was observed in some breast tumors.
Conclusions:
- The identification of PD-L1∆3 and the association of PD-L2 with EMT and immune evasion suggest complex regulatory mechanisms in the PD-1/PD-L1 pathway.
- The findings underscore the critical need for isoform-specific antibodies to accurately assess PD-L1 and PD-L2 expression for predicting immunotherapy outcomes.
- Further research into PD-L2 and PD-L1 isoforms may reveal new therapeutic strategies and improve patient stratification for PD-1/PD-L1 blockade.
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