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Conroy JM , Pabla S , Nesline MK , Glenn ST , Papanicolau-Sengos A , Burgher B , Andreas J , Giamo V , Wang Y , Lenzo FL , Bshara W , Khalil M , Dy GK , Madden KG , Shirai K , Dragnev K , Tafe LJ , Zhu J , Labriola M , Marin D , McCall SJ , Clarke J , George DJ , Zhang T , Zibelman M , Ghatalia P , Araujo-Fernandez I , de la Cruz-Merino L , Singavi A , George B , MacKinnon AC , Thompson J , Singh R , Jacob R , Kasuganti D , Shah N , Day R , Galluzzi L , Gardner M , Morrison C
Next generation sequencing of PD-L1 for predicting response to immune checkpoint inhibitors
J Immunother Cancer. 2019 Jan 24;7(1) :18
PMID: 30678715    PMCID: PMC6346512    URL: https://www.ncbi.nlm.nih.gov/pubmed/30678715
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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.
2051-1426 Conroy, Jeffrey M Pabla, Sarabjot Nesline, Mary K Glenn, Sean T Papanicolau-Sengos, Antonios Burgher, Blake Andreas, Jonathan Giamo, Vincent Wang, Yirong Lenzo, Felicia L Bshara, Wiam Khalil, Maya Dy, Grace K Madden, Katherine G Shirai, Keisuke Dragnev, Konstantin Tafe, Laura J Zhu, Jason Labriola, Matthew Marin, Daniele McCall, Shannon J Clarke, Jeffrey George, Daniel J Zhang, Tian Zibelman, Matthew Ghatalia, Pooja Araujo-Fernandez, Isabel de la Cruz-Merino, Luis Singavi, Arun George, Ben MacKinnon, Alexander C Thompson, Jonathan Singh, Rajbir Jacob, Robin Kasuganti, Deepa Shah, Neel Day, Roger Galluzzi, Lorenzo Gardner, Mark Morrison, Carl ORCID: http://orcid.org/0000-0002-3441-8363 Journal Article England J Immunother Cancer. 2019 Jan 24;7(1):18. doi: 10.1186/s40425-018-0489-5.