Myrto Moutafi1, Sandra Martinez-Morilla1, Prajan Divakar2, Ioannis Vathiotis1, Niki Gavrielatou1, Thazin Nwe Aung1, Vesal Yaghoobi1, Aileen I Fernandez1, Jon Zugazagoitia3, Roy S Herbst4, Kurt A Schalper5, David L Rimm6. 1. Department of Pathology, Yale School of Medicine, New Haven, Connecticut. 2. NanoString Technologies, Seattle, Washington. 3. Section of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain. 4. Section of Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut. 5. Department of Pathology, Yale School of Medicine, New Haven, Connecticut; Section of Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut. 6. Department of Pathology, Yale School of Medicine, New Haven, Connecticut; Section of Oncology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut. Electronic address: david.rimm@yale.edu.
Abstract
INTRODUCTION: Despite the clinical efficacy of immune checkpoint inhibitors (ICIs) in NSCLC, only approximately 20% of patients remain disease-free at 5 years. Here, we use digital spatial profiling to find candidate biomarker proteins associated with ICI resistance. METHODS: Pretreatment samples from 56 patients with NSCLC treated with ICI were analyzed using the NanoString GeoMx digital spatial profiling method. A panel of 71 photocleavable oligonucleotide-labeled primary antibodies was used for protein detection in four molecular compartments (tumor, leukocytes, macrophages, and immune stroma). Promising candidates were orthogonally validated with quantitative immunofluorescence. Available pretreatment samples from 39 additional patients with NSCLC who received ICI and 236 non-ICI-treated patients with operable NSCLC were analyzed to provide independent cohort validation. RESULTS: Biomarker discovery using the protein-based molecular compartmentalization strategy allows 284 protein variables to be assessed for association with ICI resistance by univariate analysis using continuous log-scaled data. Of the 71 candidate protein biomarkers, CD66b in the CD45+CD68 molecular compartment (immune stroma) predicted significantly shorter overall survival (OS) (hazard ratio [HR] 1.31, p = 0.016) and was chosen for validation. Orthogonal validation by quantitative immunofluorescence illustrated that CD66b was associated with resistance to ICI therapy but not prognostic for poor outcomes in untreated NSCLC (discovery cohort [OS HR 2.49, p = 0.026], validation cohort [OS HR 2.05, p = 0.046], non-ICI-treated cohort [OS HR 1.67, p = 0.06]). CONCLUSIONS: Using the technique, we have discovered that CD66b expression is indicative of resistance to ICI therapy in NSCLC. Given that CD66b identifies neutrophils, further studies are warranted to characterize the role of neutrophils in ICI resistance.
INTRODUCTION: Despite the clinical efficacy of immune checkpoint inhibitors (ICIs) in NSCLC, only approximately 20% of patients remain disease-free at 5 years. Here, we use digital spatial profiling to find candidate biomarker proteins associated with ICI resistance. METHODS: Pretreatment samples from 56 patients with NSCLC treated with ICI were analyzed using the NanoString GeoMx digital spatial profiling method. A panel of 71 photocleavable oligonucleotide-labeled primary antibodies was used for protein detection in four molecular compartments (tumor, leukocytes, macrophages, and immune stroma). Promising candidates were orthogonally validated with quantitative immunofluorescence. Available pretreatment samples from 39 additional patients with NSCLC who received ICI and 236 non-ICI-treated patients with operable NSCLC were analyzed to provide independent cohort validation. RESULTS: Biomarker discovery using the protein-based molecular compartmentalization strategy allows 284 protein variables to be assessed for association with ICI resistance by univariate analysis using continuous log-scaled data. Of the 71 candidate protein biomarkers, CD66b in the CD45+CD68 molecular compartment (immune stroma) predicted significantly shorter overall survival (OS) (hazard ratio [HR] 1.31, p = 0.016) and was chosen for validation. Orthogonal validation by quantitative immunofluorescence illustrated that CD66b was associated with resistance to ICI therapy but not prognostic for poor outcomes in untreated NSCLC (discovery cohort [OS HR 2.49, p = 0.026], validation cohort [OS HR 2.05, p = 0.046], non-ICI-treated cohort [OS HR 1.67, p = 0.06]). CONCLUSIONS: Using the technique, we have discovered that CD66b expression is indicative of resistance to ICI therapy in NSCLC. Given that CD66b identifies neutrophils, further studies are warranted to characterize the role of neutrophils in ICI resistance.
Authors: Christopher R Merritt; Giang T Ong; Sarah E Church; Kristi Barker; Patrick Danaher; Gary Geiss; Margaret Hoang; Jaemyeong Jung; Yan Liang; Jill McKay-Fleisch; Karen Nguyen; Zach Norgaard; Kristina Sorg; Isaac Sprague; Charles Warren; Sarah Warren; Philippa J Webster; Zoey Zhou; Daniel R Zollinger; Dwayne L Dunaway; Gordon B Mills; Joseph M Beechem Journal: Nat Biotechnol Date: 2020-05-11 Impact factor: 54.908