Spatially Resolved, Multiregion Proteomics for Prediction of Immunotherapy Outcome in Deficient Mismatch Repair Metastatic Colorectal Cancer
Bahar Saberzadeh-Ardestani, Zhenglong Liu, Mariam I. Stein, Will A. Sherman, Christy E. Trussoni, Charles W. Abbott, Dongyao Yan, Skyler Smith, Kandavel Shanmugam, Rondell P. Graham, Alos Diallo, Joshua Levy, Tamás Ördög, Frank A. Sinicrope
Abstract
PURPOSE: Digital proteomic profiling was performed to identify spatial context in relationship to patient response and survival after anti-PD-1 therapy in metastatic colorectal cancer. EXPERIMENTAL DESIGN: Primary colorectal cancers with deficient mismatch repair from patients treated with anti-PD-1 antibodies were analyzed (N = 30) using digital spatial profiling (GeoMx nCounter). At the invasive margin, 71 proteins were profiled in 10 regions of interest/slide that were segmented into 3 compartments labeled with pan-cytokeratin (epithelia), CD45 (stromal cells), and SYTO13 (nuclei). In an independent cohort (n = 13), digital spatial profiling data and single-cell transcriptomic data were analyzed. Differential protein abundance, after Benjamini-Hochberg correction, was examined by clinical response and progression-free survival (PFS) using multivariable Cox regression. RESULTS: Protein abundance varied significantly between epithelial and stromal compartments. Nonresponders to anti-PD-1 showed higher fibronectin and smooth muscle actin abundance in the epithelial compartment that was associated with significantly shorter PFS (adjusted HR: 6.49 and 4.52, respectively; P < 0.05). In CD45+ stroma, increased expression of proteins related to T cells (CD3 and CD4), NK cells (CD56), antigen presentation (CD40), immune activation (CD27, ICOS), and apoptosis (GZMA) were found in responders (vs nonresponders) to anti-PD-1; each marker was significantly associated with longer patient PFS (0.02 < adjusted HR < 0.17; P < 0.05). In a separate cohort, consistent results by compartment were found for fibronectin and CD56. Gene expression data revealed that fibronectin and smooth muscle actin were primarily derived from cancer-associated fibroblasts. CONCLUSIONS: Spatially resolved protein profiles within microenvironments of deficient mismatch repair colorectal cancers can influence patient response and survival after anti-PD-1, highlighting their potential clinical significance.