Corless, Christopher L.

Abstract The goal of this study was to develop a high-plex assay to simultaneously quantitate 27 established and novel breast cancer (BC)-related, immune protein and phosphoprotein biomarkers using the GeoMx® Digital Spatial Profiler (DSP). The custom assay performance was compared to standard clinical BC biomarker assays (e.g.ER, PR, HER2, Ki67) across the spectrum of BC subtypes and in multiple laboratories. Commercially available antibodies to 27 BC-related protein biomarkers, including ER, PR, HER2, Ki-67, AR, immune-related (e.g. PD-L1) and several cell cycle/proliferation markers were oligonucleotide-tagged, and verified by immunohistochemistry for performance against untagged antibodies. The tagged antibodies were combined with 3 isotype controls and 2 housekeeping proteins into a custom BC high-plex assay for DSP. Confirmation of target specificity was done on a custom tissue microarray (TMA) (Run control) composed of (un)treated cancer cell lines and normal tissues. For clinical BC samples, each biopsy had 4x600 µm regions of interest segmented into pan-Cytokeratin+ tumoral epithelium and pan-Cytokeratin- adjacent stroma segments. With targeted UV light, oligonucleotides were collected from each segment sequentially and quantitated with nCounter. Raw counts were geomean normalized for analysis. Intra-site and inter-site assay reproducibility was assessed with the TMA and serial FFPE sections from BC biopsies. Quantitation of proteins showed high reproducibility within sites (e.g. Run 1 v. Run 2, p>0.05 for all protein targets) and the high-plex custom assay showed good concordance between 3 participating laboratories. GeoMx DSP-derived protein data correlated well with orthogonal methodologies performed on a sample subset including immunohistochemistry, reverse phase protein array, DNA and RNA-sequencing. For example, DSP protein counts for p53 protein were higher in tumors with TP53 point mutation than those with truncating TP53 alterations. Expanded sample testing is underway with 120 well-characterized breast cancer biopsies of various histologies, immune subtypes (e.g. TIL scores) and clinical biomarker phenotypes (e.g. ER+/HER2-/Ki-67 high BC; ER+/HER2-/Ki-67 low BC; HER2+ BC; ER-/PR-/HER2- BC).Our preliminary data demonstrate that this custom high-plex BC assay can quantitate protein biomarkers across a wide dynamic range with high intra-lab and inter-lab reproducibility. The assay requirement of a single 5-µm tissue section facilitates complex biomarker profiling in biopsies with limited material. The custom assay alone or in combination with other targeted DSP protein modules can simultaneously interrogate the biomarker profile, immune-based and other drug target profile, and immune microenvironment of BC specimens, providing a novel approach for actionable tumor subtyping. For research use only. Not for use in diagnostic procedures. Citation Format: Christopher Corless, Amber Bridgeman, Jinho Lee, Gary Geiss, Sarah Warren, Sarah Church, Joseph M. Beechem, E Aubrey Thompson, Jodi Carter. Development of a custom high-plex GeoMx digital spatial profiler breast cancer protein biomarker assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3484.

Abstract Context. —Establishing adequate interobserver agreement is crucial not only for standardization of patient care but also to ensure validity of findings in multi-institutional trials. Objective. —To evaluate interobserver agreement in assessing chronic hepatitis C (HCV) and acute cellular rejection (ACR) among 17 hepatopathologists involved in the “Hepatitis C 3” trial. Design. —The trial is a randomized multicenter (17 institutions) study involving 312 patients undergoing transplantation for HCV. Patients are randomized to 3 treatment arms. For final data analysis, all biopsy specimens are reviewed by a central pathologist (G.J.N.). Recurrence of HCV is evaluated according to the Batts and Ludwig schema. The 1997 Banff schema is used to evaluate ACR. To assess interobserver agreement, hematoxylin-eosin–stained sections from 11 liver biopsy specimens (6 HCV and 5 ACR) were sent by the central pathologist to 16 local pathologists from 13 institutions. Statistical analysis was performed on raw ACR/HCV data as well as data grouped according to clinically significant primary endpoint cutoffs. Results. —Statistically significant agreement was found among all participating pathologists ( P < .001). On κ analysis, the degree of agreement was rated “moderate” for HCV grade and stage and ACR global grading (κ = 0.30, 0.33, and 0.37, respectively). Interobserver agreement was weaker for rejection activity index scoring of ACR (κ = 0.15). A stronger degree of agreement was found when scores were grouped based on endpoint cutoffs (κ = 0.76 “almost perfect” for HCV and 0.62 “substantial” for ACR). Conclusions. —An overall statistically significant interobserver agreement was found among 17 pathologists using the 1997 Banff schema and the Batts and Ludwig schema.

Abstract Lessons Learned Despite having significant rationale, S0502 failed to accrue for a number of reasons. Vetting a trial first, with scientific experts and funding agencies, does not guarantee success, especially when dealing with a rare tumor and/or one with an existing highly effective therapy. In the present case, adding an intravenous drug to an oral medication as part of a regimen expected to be continued for many years likely decreased patient (and physician) convenience and, thus, interest in the study. Background. Imatinib mesylate, a potent inhibitor of the KIT and PDGFR tyrosine kinases, is highly effective in the treatment of advanced gastrointestinal stromal tumors (GISTs). However, most imatinib-treated tumors eventually become resistant, accounting for a median progression-free survival of 19–23 months. Expression of vascular endothelial growth factor (VEGF) correlates with poor prognosis in GIST; bevacizumab, a monoclonal antibody against VEGF, is effective in a variety of solid tumors. We postulated combination therapy with imatinib plus bevacizumab would benefit patients with advanced GIST, particularly those reliant on VEGFA-dependent angiogenesis. Methods. Patients with metastatic or surgically unresectable GIST were eligible for this phase III open-label clinical trial, S0502. At registration, patients were randomly assigned to either imatinib 400 mg (standard) or 800 mg (patients with exon 9 KIT mutations), or imatinib plus bevacizumab, 7.5 mg/kg i.v. every 3 weeks. Patients were treated to progression, symptomatic deterioration, unacceptable toxicity, treatment delay greater than 4 weeks, or patient choice to withdraw from the study. The primary objective was to determine whether the addition of bevacizumab to imatinib would improve progression-free survival (PFS) in first-line treatment of incurable GIST. Results. S0502 opened on April 15, 2008. As of fall 2009, only 12 patients from at least 178 eligible SWOG centers plus those participating through Cancer Trials Support Unit had been entered in the study. Despite an aggressive promotion scheme involving the other cooperative groups and a major GIST patient advocacy group, accrual remained slow. The trial was closed on October 1, 2009, having accrued only 2% of the 572 patients planned. No scientific conclusions were forthcoming because of the small number of patients entered in the study. Two patients of the 6 in the combination arm reported grade 3 toxicities, 1 with proteinuria and 1 with fatigue, upper gastrointestinal hemorrhage, and anemia. Conclusion. No conclusions may be drawn from this trial and, thus, the combination of imatinib plus bevacizumab cannot be recommended for use.

Purpose The ACOSOG (American College of Surgeons Oncology Group) Z9001 (Alliance) study, a randomized, placebo-controlled trial, demonstrated that 1 year of adjuvant imatinib prolonged recurrence-free survival (RFS) after resection of primary GI stromal tumor (GIST). We sought to determine the pathologic and molecular factors associated with patient outcome. Patients and Methods There were 328 patients assigned to the placebo arm and 317 to the imatinib arm. Median patient follow-up was 74 months. There were 645 tumor specimens available for mitotic rate or mutation analysis. Results RFS remained superior in the imatinib arm (hazard ratio, 0.6; 95% CI, 0.43 to 0.75; Cox model–adjusted P < .001). On multivariable analysis of patients in the placebo arm, large tumor size, small bowel location, and high mitotic rate were associated with lower RFS, whereas tumor genotype was not significantly associated with RFS. Multivariable analysis of patients in the imatinib arm yielded similar findings. When comparing the two arms, imatinib therapy was associated with higher RFS in patients with a KIT exon 11 deletion of any type, but not a KIT exon 11 insertion or point mutation, KIT exon 9 mutation, PDGFRA mutation, or wild-type tumor, although some of these patient groups were small. Adjuvant imatinib did not seem to alter overall survival. Conclusion Our findings show that tumor size, location, and mitotic rate, but not tumor genotype, are associated with the natural history of GIST. Patients with KIT exon 11 deletions assigned to 1 year of adjuvant imatinib had a longer RFS.