Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer

Liebler, D.C.; Holzer, Timothy R.; Haragan, Alexander; Morrison, Ryan D.; Reising, Leslie O'Neill; Ackermann, Bradley L.; Fill, Jeff A.; Schade, Andrew E.; Gruver, Aaron M.

doi:10.1038/s41598-020-66902-0

Cited by 19 publications

(13 citation statements)

References 48 publications

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“…In addition to phenotypic stratification, we leveraged upon the high multiplexing capabilities of CODEX to include functional markers, particularly immunoregulatory proteins that are essential for the study of cancer immunology and immunotherapy. Specifically, we focused on eight functional immune molecules that are the targets of approved or in trial immunotherapies: ICOS, IDO-1, LAG-3, OX40, PD-1, PD-L1, TIM-3, and VISTA (Figure 4A) (2,(33)(34)(35)(36)(37). Representative examples of the staining pattern of these markers on T cells, macrophages, and tumor cells are shown (Figure 4A).…”

Section: Resultsmentioning

confidence: 99%

“…Multiplexed imaging studies utilizing 20-60 markers are generally required to achieve novel biomarker discovery studies (16,19,23,26,48). The 56-marker panel described here enables rigorous immunophenotyping and incorporates eight high value immunomodulatory proteins-ICOS, IDO-1, LAG-3, OX40, PD-1, PD-L1, TIM-3, and VISTA-that will empower further work into a better mechanistic understanding of immunotherapeutic responses (2,(33)(34)(35)(36)(37). This study also identified major differences in immunoregulatory protein expression between cell-types in CTCL, consistent with that previously observed with other tumor types (40).…”

Section: Discussionmentioning

confidence: 99%

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Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging

et al. 2021

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Immunotherapies are revolutionizing cancer treatment by boosting the natural ability of the immune system. In addition to antibodies against traditional checkpoint molecules or their ligands (i.e., CTLA-4, PD-1, and PD-L1), therapies targeting molecules such as ICOS, IDO-1, LAG-3, OX40, TIM-3, and VISTA are currently in clinical trials. To better inform clinical care and the design of therapeutic combination strategies, the co-expression of immunoregulatory proteins on individual immune cells within the tumor microenvironment must be robustly characterized. Highly multiplexed tissue imaging platforms, such as CO-Detection by indEXing (CODEX), are primed to meet this need by enabling >50 markers to be simultaneously analyzed in single-cells on formalin-fixed paraffin-embedded (FFPE) tissue sections. Assembly and validation of antibody panels is particularly challenging, with respect to the specificity of antigen detection and robustness of signal over background. Herein, we report the design, development, optimization, and application of a 56-marker CODEX antibody panel to eight cutaneous T cell lymphoma (CTCL) patient samples. This panel is comprised of structural, tumor, and immune cell markers, including eight immunoregulatory proteins that are approved or currently undergoing clinical trials as immunotherapy targets. Here we provide a resource to enable extensive high-dimensional, spatially resolved characterization of the tissue microenvironment across tumor types and imaging modalities. This framework provides researchers with a readily applicable blueprint to study tumor immunology, tissue architecture, and enable mechanistic insights into immunotherapeutic targets.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging

et al. 2021

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“…In our study, the risk alleles of PDCD1LG2 rs2381282, rs12237624, and rs78096119 were negatively associated with PD-L2 expression in non-tumor tissue, but not in tumor tissue. The expression and prognostic value of PD-L2 expression in lung cancer have been previously reported (52)(53)(54). The interaction between PD-L2 and PD-1 inhibits strong B7-CD28 signals at low antigen concentrations.…”

Section: Discussionmentioning

confidence: 92%

Programmed Death Ligand 2 Gene Polymorphisms Are Associated With Lung Adenocarcinoma Risk in Female Never-Smokers

et al. 2021

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ObjectivesLung cancer in never-smokers is a distinct disease associated with a different genomic landscape, pathogenesis, risk factors, and immune checkpoint inhibitor responses compared to those observed in smokers. This study aimed to identify novel single nucleotide polymorphisms (SNPs) of programmed death-1 (encoded by PDCD1) and its ligands, programmed death ligand 1 (CD274) and 2 (PDCD1LG2), associated with lung cancer risk in never-smoking women.Materials and MethodsDuring September 2002 and July 2012, we enrolled never-smoking female patients with lung adenocarcinoma (LUAD) (n=1153) and healthy women (n=1022) from six tertiary hospitals in Taiwan. SNP data were obtained and analyzed from the genome-wide association study dataset and through an imputation method. The expression quantitative trait loci (eQTL) analysis was performed in both tumor and non-tumor tissues for the correlation between genetic expression and identified SNPs.ResultsA total of 12 PDCD1LG2 SNPs related to LUAD risk were identified in never-smoking women, including rs2381282, rs4742103, rs4237162, rs4742104, rs12237624, rs78096119, rs6476988, rs7857315, rs10975178, rs7854413, rs56001683, and rs7858319. Among them, six tagged PDCD1LG2 SNPs rs2381282, rs4742103, rs4237162, rs4742104, rs78096119, and rs56001683 were significantly associated with LUAD risk. Specifically, two PDCD1LG2 SNPs, rs12237624 and rs78096119, were associated with previous pulmonary tuberculosis infection in relation to LUAD susceptibility. Through an eQTL assay, we found that rs2381282 (p < 0.001), rs12237624 (p = 0.019), and rs78096119 (p = 0.019) were associated with the expression levels of programed death ligand 2.ConclusionsNovel SNPs of programed death ligand 2 associated with lung adenocarcinoma risk were identified. Among them, two SNPs were associated with pulmonary tuberculosis infection in relation to lung adenocarcinoma susceptibility. These SNPs may help to stratify high-risk populations of never-smokers during lung cancer screening.

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“…A recent study exploring PD-L1 expression in lung cancers using parallel reaction monitoring-based mass spectrometry (MS) showed a wide dynamic range of PD-L1 expression across samples. 12 However, concordance in PD-L1 expression between continuous MS data and qualitative IHC-based measurements was weak and the broad dynamic range was only partially captured by the IHC platform. 12 For a therapeutic perspective, quantitative human epidermal growth factor receptor 2 (HER2) measurements in breast cancer specimens have shown superior performance in predicting response to targeted therapies compared with IHC-based, semi-quantitative measurements.…”

Section: Introductionmentioning

confidence: 99%

“…12 However, concordance in PD-L1 expression between continuous MS data and qualitative IHC-based measurements was weak and the broad dynamic range was only partially captured by the IHC platform. 12 For a therapeutic perspective, quantitative human epidermal growth factor receptor 2 (HER2) measurements in breast cancer specimens have shown superior performance in predicting response to targeted therapies compared with IHC-based, semi-quantitative measurements. [13][14][15][16] The wider dynamic range captured by these quantitative platforms has been addressed as a key element for increasing precision and for accurately distinguishing responders from non-responders, especially from IHC-negative specimens.…”

Section: Introductionmentioning

confidence: 99%

PD-L1 quantification across tumor types using the reverse phase protein microarray: implications for precision medicine

Baldelli

Hodge

Bellezza

et al. 2021

J Immunother Cancer

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BackgroundAnti-programmed cell death protein 1 and programmed cell death ligand 1 (PD-L1) agents are broadly used in first-line and second-line treatment across different tumor types. While immunohistochemistry-based assays are routinely used to assess PD-L1 expression, their clinical utility remains controversial due to the partial predictive value and lack of standardized cut-offs across antibody clones. Using a high throughput immunoassay, the reverse phase protein microarray (RPPA), coupled with a fluorescence-based detection system, this study compared the performance of six anti-PD-L1 antibody clones on 666 tumor samples.MethodsPD-L1 expression was measured using five antibody clones (22C3, 28–8, CAL10, E1L3N and SP142) and the therapeutic antibody atezolizumab on 222 lung, 71 ovarian, 52 prostate and 267 breast cancers, and 54 metastatic lesions. To capture clinically relevant variables, our cohort included frozen and formalin-fixed paraffin-embedded samples, surgical specimens and core needle biopsies. Pure tumor epithelia were isolated using laser capture microdissection from 602 samples. Correlation coefficients were calculated to assess concordance between antibody clones. For two independent cohorts of patients with lung cancer treated with nivolumab, RPPA-based PD-L1 measurements were examined along with response to treatment.ResultsMedian-center PD-L1 dynamic ranged from 0.01 to 39.37 across antibody clones. Correlation coefficients between the six antibody clones were heterogeneous (range: −0.48 to 0.95) and below 0.50 in 61% of the comparisons. In nivolumab-treated patients, RPPA-based measurement identified a subgroup of tumors, where low PD-L1 expression equated to lack of response.ConclusionsContinuous RPPA-based measurements capture a broad dynamic range of PD-L1 expression in human specimens and heterogeneous concordance levels between antibody clones. This high throughput immunoassay can potentially identify subgroups of tumors in which low expression of PD-L1 equates to lack of response to treatment.

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Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer

Cited by 19 publications

References 48 publications

Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging

Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging

Programmed Death Ligand 2 Gene Polymorphisms Are Associated With Lung Adenocarcinoma Risk in Female Never-Smokers

PD-L1 quantification across tumor types using the reverse phase protein microarray: implications for precision medicine

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