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Development and Performance of a CD8 Gene Signature for Characterizing Inflammation in the Tumor Microenvironment across Multiple Tumor Types

Péter M. Szabó, Saumya Pant, Scott Ely, Keyur Desai, Esperanza Anguiano, Lisu Wang, Robin Edwards, George Green, Nancy R. Zhang

2021Journal of Molecular Diagnostics20 citationsDOIOpen Access PDF

Abstract

Across multiple tumor types, immune checkpoint inhibitors (ICIs) have demonstrated clinical benefit to patients with cancer, yet there is a need to identify predictive biomarkers of response to these therapies. A multiparameter gene expression profiling–based tumor inflammation assay may offer robust characterization of the tumor microenvironment, thereby extending the utility of single-gene analysis or immunohistochemistry (IHC) in predicting response to ICIs. The authors interrogated 1778 commercially procured, formalin-fixed, paraffin-embedded samples using gene expression profiling and pathology-assisted digital CD8 IHC. A machine-learning approach was used to develop gene expression signatures that predicted CD8+ immune cell abundance as surrogates for tumor inflammation in melanoma and squamous cell carcinoma of the head and neck samples. An assay for a 16-gene CD8 signature was developed and analytically validated across 12 tumor types. CD8 signature scores correlated with CD8 IHC in a platform-independent manner, and inflammation prevalence was similar between assay methods for all tumor types except prostate cancer and small cell lung cancer. In retrospective analyses, CD8 signature scores were associated with progression-free survival and overall survival with nivolumab in patients with urothelial carcinoma from CheckMate 275. This study demonstrated that the CD8 signature assay can be used to accurately quantify CD8+ immune cell abundance in the tumor microenvironment and has potential clinical utility for determining patients with cancer likely to respond to ICIs. Across multiple tumor types, immune checkpoint inhibitors (ICIs) have demonstrated clinical benefit to patients with cancer, yet there is a need to identify predictive biomarkers of response to these therapies. A multiparameter gene expression profiling–based tumor inflammation assay may offer robust characterization of the tumor microenvironment, thereby extending the utility of single-gene analysis or immunohistochemistry (IHC) in predicting response to ICIs. The authors interrogated 1778 commercially procured, formalin-fixed, paraffin-embedded samples using gene expression profiling and pathology-assisted digital CD8 IHC. A machine-learning approach was used to develop gene expression signatures that predicted CD8+ immune cell abundance as surrogates for tumor inflammation in melanoma and squamous cell carcinoma of the head and neck samples. An assay for a 16-gene CD8 signature was developed and analytically validated across 12 tumor types. CD8 signature scores correlated with CD8 IHC in a platform-independent manner, and inflammation prevalence was similar between assay methods for all tumor types except prostate cancer and small cell lung cancer. In retrospective analyses, CD8 signature scores were associated with progression-free survival and overall survival with nivolumab in patients with urothelial carcinoma from CheckMate 275. This study demonstrated that the CD8 signature assay can be used to accurately quantify CD8+ immune cell abundance in the tumor microenvironment and has potential clinical utility for determining patients with cancer likely to respond to ICIs. Immune checkpoint inhibitors (ICIs) targeting the programmed death-1/programmed death ligand 1 (PD-1/PD-L1) axis have demonstrated significant clinical benefit across a range of tumor types.1Büttner R. Longshore J.W. Lopez-Rios F. Merkelbach-Bruse S. Normanno N. Rouleau E. Penault-Llorca F. Implementing TMB measurement in clinical practice: considerations on assay requirements.ESMO Open. 2019; 4: e000442Abstract Full Text Full Text PDF PubMed Scopus (131) Google Scholar There is, however, a critical need to identify subsets of patients who are likely to respond to ICIs or alternative therapies.2Chan T.A. Yarchoan M. Jaffee E. Swanton C. Quezada S.A. Stenzinger A. Peters S. Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic.Ann Oncol. 2019; 30: 44-56Abstract Full Text Full Text PDF PubMed Scopus (692) Google Scholar Precision medicine is an emerging approach for guiding treatment for patients with cancer, considering the molecular and genomic variability between tumors.3Malone M. profiling for cancer PubMed Scopus Google Scholar and methods have developed to the tumor microenvironment to identify biomarkers for patients who are likely to respond to a biomarkers are and in to tumor that to of tumor and can to an to and R. R. M. A. E. M. C. A. N. A. A. genomic biomarkers for checkpoint PubMed Scopus Google M. M. E. A. A. S.A. A. clinical response to PubMed Scopus Google M. S. S. M. M. C. E. M. immunohistochemistry study in clinical of Oncol. Full Text Full Text PDF PubMed Scopus Google F. F. N. F. C. A. S. M. A. A. M. for treatment of PubMed Scopus Google A. A. M. F. N. N. S. in with PubMed Scopus Google N. A. S. R. S. R. F. N. T.A. and microenvironment immunotherapy with Full Text Full Text PDF PubMed Scopus Google A. N. F. C. R. C. T.A. to in cell lung PubMed Scopus Google C. The Full Text Full Text PDF PubMed Scopus Google Scholar A in the has associated with clinical in patients with E. Immune checkpoint and potential PubMed Scopus Google M. M. C. E. C. C. A. immune PubMed Scopus Google S. of and in the melanoma tumor microenvironment is Scopus Google Scholar and inflammation biomarkers are and in for with the clinical of ICIs across multiple tumor M. M. E. F. N. S. R. Peters S. E. nivolumab in or lung PubMed Scopus Google M. M. M. A. R. M. and of in patients with and clinical Oncol. 4: PubMed Scopus Google S. A. R. R. A. S. and in PubMed Scopus Google R. N. M. Longshore J.W. Lopez-Rios F. Penault-Llorca F. 1 immunohistochemistry a of and clinical in lung Oncol. PubMed Scopus Google Scholar CD8+ immune using immunohistochemistry can be used as a for inflammation that is associated with in a range of tumor of in the of the immune in PubMed Scopus Google T.A. E. or the of immune in PubMed Scopus Google C. CD8+ as a in lung a of lung PubMed Scopus Google Scholar on tumor immune or may be of a and clinical of ICIs in patients with has to the of a of IHC and for tumor J.W. of IHC and assay and across multiple PubMed Scopus Google Scholar In to biomarkers of tumor that with are as surrogates for potential immune using using and tumor burden have associated with clinical of ICIs across a of tumor A. A. M. F. N. N. S. in with PubMed Scopus Google N. A. S. R. S. R. F. 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A. clinical response to PubMed Scopus Google M. gene expression profiling from small and and clinical formalin-fixed, paraffin-embedded using the 2019; Full Text Full Text PDF PubMed Scopus Google Scholar gene are for profiling tumor for multiple genomic in and R. Longshore J.W. Lopez-Rios F. Merkelbach-Bruse S. Normanno N. Rouleau E. Penault-Llorca F. Implementing TMB measurement in clinical practice: considerations on assay requirements.ESMO Open. 2019; 4: e000442Abstract Full Text Full Text PDF PubMed Scopus (131) Google A. M. M. R. A. S. S.A. F. of burden with in patients with with analysis of the Oncol. Full Text Full Text PDF PubMed Scopus Google A. M. burden for TMB in clinical samples to immunotherapy treatment 2019; PubMed Scopus Google Scholar expression profiling have used to the of multiple tumor types and gene expression signatures of tumor R. R. M. A. E. M. C. A. N. A. A. genomic biomarkers for checkpoint PubMed Scopus Google M. M. E. A. A. S.A. 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Implementing TMB measurement in clinical practice: considerations on assay requirements.ESMO Open. 2019; 4: e000442Abstract Full Text Full Text PDF PubMed Scopus (131) Google A. M. burden for TMB in clinical samples to immunotherapy treatment 2019; PubMed Scopus Google Scholar of in for clinical on and as as to and R. Longshore J.W. Lopez-Rios F. Merkelbach-Bruse S. Normanno N. Rouleau E. Penault-Llorca F. Implementing TMB measurement in clinical practice: considerations on assay requirements.ESMO Open. 2019; 4: e000442Abstract Full Text Full Text PDF PubMed Scopus (131) Google A. M. burden for TMB in clinical samples to immunotherapy treatment 2019; PubMed Scopus Google C. Peters S. N. and for clinical 2019; Full Text Full Text PDF PubMed Scopus Google and for of an in with a Scholar a for analysis of M. Quezada S.A. Swanton C. of tumor PubMed Scopus Google C. F. M. of the of in PubMed Scopus Google Scholar the of gene expression to with and to significant to M. 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A. genomic biomarkers for checkpoint PubMed Scopus Google Scholar that gene expression signatures may methods of and may to medicine for patients with R. R. M. A. E. M. C. A. N. A. A. genomic biomarkers for checkpoint PubMed Scopus Google A. M. A. A. A. C. N. and gene expression and to in urothelial PubMed Scopus Google M. C. biomarkers for immune checkpoint and for 2019; PubMed Scopus Google S. C. of for predicting response to checkpoint a and Oncol. 2019; PubMed Scopus Google Scholar This study demonstrated that an analytically validated gene expression assay for the 16-gene CD8 signature can identify an in the and may identify patients that are from potential to CD8 signature on In of patients with the CD8 signature was associated with the clinical of is to the predictive of the CD8 signature in patients likely to respond to ICIs and to the clinical utility of gene expression signatures to medicine in patients with cancer.

Topics & Concepts

Tumor microenvironmentGene signatureNivolumabCD8Immune systemLung cancerGene expression profilingImmunohistochemistryCancer researchTumor-infiltrating lymphocytesBiologyImmunotherapyMedicineImmunologyOncologyGene expressionGeneGeneticsCancer Immunotherapy and BiomarkersFerroptosis and cancer prognosisImmunotherapy and Immune Responses
Development and Performance of a CD8 Gene Signature for Characterizing Inflammation in the Tumor Microenvironment across Multiple Tumor Types | Litcius