Journal Article

Next generation sequencing of PD-L1 for predicting response to immune checkpoint inhibitors

Zibelman, Matthew, Galluzzi, Lorenzo, Wang, Yirong, George, Ben, Dragnev, Konstantin, Clarke, Jeffrey, Zhang, Tian, Thompson, Jonathan, Nesline, Mary K., Andreas, Jonathan, Zhu, Jason, McCall, Shannon J., Madden, Katherine G., Araujo-Fernandez, Isabel, Singh, Rajbir, Jacob, Robin, Kasuganti, Deepa, Burgher, Blake, Shirai, Keisuke, Papanicolau-Sengos, Antonios, Labriola, Matthew, Glenn, Sean T., Dy, Grace K., Khalil, Maya, Singavi, Arun, Day, Roger, Marin, Daniele, George, Daniel J., Conroy, Jeffrey M., Lenzo, Felicia L., Morrison, Carl, MacKinnon, Alexander C., Pabla, Sarabjot, Ghatalia, Pooja, Shah, Neel, Bshara, Wiam, de la Cruz-Merino, Luis, Giamo, Vincent, Tafe, Laura J., Gardner, Mark

2019

Overview

Background PD-L1 immunohistochemistry (IHC) has been traditionally used for predicting clinical responses to immune checkpoint inhibitors (ICIs). However, there are at least 4 different assays and antibodies used for PD-L1 IHC, each developed with a different ICI. We set to test if next generation RNA sequencing (RNA-seq) is a robust method to determine PD-L1 mRNA expression levels and furthermore, efficacy of predicting response to ICIs as compared to routinely used, standardized IHC procedures. Methods A total of 209 cancer patients treated on-label by FDA-approved ICIs, with evaluable responses were assessed for PD-L1 expression by RNA-seq and IHC, based on tumor proportion score (TPS) and immune cell staining (ICS). A subset of serially diluted cases was evaluated for RNA-seq assay performance across a broad range of PD-L1 expression levels. Results Assessment of PD-L1 mRNA levels by RNA-seq demonstrated robust linearity across high and low expression ranges. PD-L1 mRNA levels assessed by RNA-seq and IHC (TPS and ICS) were highly correlated ( p  < 2e-16). Sub-analyses showed sustained correlation when IHC results were classified as high or low by clinically accepted cut-offs ( p  < 0.01), and results did not differ by tumor type or anti-PD-L1 antibody used. Overall, a combined positive PD-L1 result (≥1% IHC TPS and high PD-L1 expression by RNA-Seq) was associated with a 2-to-5-fold higher overall response rate (ORR) compared to a double negative result. Standard assessments of sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) showed that a PD-L1 positive assessment for melanoma samples by RNA-seq had the lowest sensitivity (25%) but the highest PPV (72.7%). Among the three tumor types analyzed in this study, the only non-overlapping confidence interval for predicting response was for “RNA-seq low vs high” in melanoma. Conclusions Measurement of PD-L1 mRNA expression by RNA-seq is comparable to PD-L1 expression by IHC both analytically and clinically in predicting ICI response. RNA-seq has the added advantages of being amenable to standardization and avoidance of interpretation bias. PD-L1 by RNA-seq needs to be validated in future prospective ICI clinical studies across multiple histologies.

• Publisher: BioMed Central,BioMed Central Ltd,BMJ Publishing Group LTD,BMJ Publishing Group
• Subject: Antibodies / Antineoplastic Agents, Immunological - therapeutic use / Atezolizumab / Avelumab / B7-H1 Antigen - antagonists & inhibitors / B7-H1 Antigen - genetics / B7-H1 Antigen - metabolism / Cancer / cancer immunotherapy / Cancer patients / Clinical trials / Cloning / Comparative analysis / Drug approval / Durvalumab / FDA approval / Gene expression / Humans / Immune checkpoint inhibitors / Immune response / Immunohistochemistry / Immunology / Immunotherapy / Immunotherapy Biomarkers / Medical research / Medicine / Medicine & Public Health / Melanoma / Messenger RNA / Metastasis / Monoclonal antibodies / Neoplasms - drug therapy / Neoplasms - genetics / Neoplasms - metabolism / Nivolumab / Oncology / Patients / Pembrolizumab / Research Article / RNA / RNA sequencing / RNA, Messenger - genetics / RNA-Seq / Targeted cancer therapy / Tumors