Abstract PS18-27: Integrated immuno-genomic analyses in early breast cancer: Results from the Scandinavian breast group 2004-1 (SBG-2004-1) randomized phase II trial
Authors: Zerdes Ioannis , Simonetti Michele , Matikas Alexios , Harbers Luuk , Zhang Ning , Salgkamis Dimitrios , Agartz Susanne , Zacharouli Markella , Moreno-Ruiz Pablo , Hartman Johan , Mezheyeuski Artur , Bergh Jonas , Crosetto Nicola , Foukakis Theodoros 
Published: February 2021

Abstract
Background: Given the emerging role of immune-related biomarkers in breast cancer (BC), little is known about specific immune cell composition patterns and genomic alterations and how these could interact in early BC setting. The aim of this proof-of-principle study is to describe immuno-genomic correlates within the tumor microenvironment using newly developed techniques for multiplexed fluorescent immunohistochemistry (mfIHC, Mezheyeuski et al., J Pathol. 2018) and high-throughput low-input genome sequencing (CUTseq, Zhang et al., Nat Commun 2019). Methods: The randomized SBG-2004-1 phase II trial evaluated the feasibility of tailored and dose-dense epirubicin and cyclophosphamide followed by docetaxel (EC→T) as adjuvant chemotherapy for early BC, enrolling a total of 124 patients. CUTseq was applied to gDNA extracted from archival low-input formalin-fixed paraffin-embedded (FFPE) tissue as well as peripheral blood samples of BC patients. mfIHC was performed on FFPE tissue microarrays, allowing simultaneous detection of six immune markers (CD4, CD8, PD-L1, PD-1, FoxP3, CD68) and quantification in an automated and tissue-compartment manner (Vectra® Polaris™ automated quantitative pathology imaging system and inForm® software, Akoya Biosciences). Patient characteristics and 10-year follow-up data were also available. Associations of different immune cell patterns and DNA copy number alterations (CNAs) with clinicopathological parameters and survival outcomes were evaluated using standard statistical methods.Results: 69/124 (55.6%) and 82/124 (66.1%) FFPE samples were available for CNA profiling (blood gDNA for normalization, n=33) and mfIHC, respectively. MYC gene was the most commonly amplified cancer-associated gene (n=44, 63.8%), and other frequent alterations included ERBB2 (n=31, 44.9%) and PIK3CA (n=14, 20.3%) amplification as well as TP53 (n=29, 42%) and PTEN (n=16, 23.2%) deletion. CNA burden (i.e., the percentage of the genome either amplified or deleted) was significantly correlated with higher tumor grade (p=0.013) but was not prognostic for relapse-free survival. CD4+ T-cells were the most abundant immune cell subpopulation, followed by CD68+ macrophages. The immune checkpoint markers PD-L1 and PD-1 were mostly expressed in CD4+ T-cells in both tumor and stroma compartments, while stromal PD-1+CD8+ and PD-1+CD68+ cell subsets were also among the ones with the higher cell density. CD4+ T-cell density was significantly correlated with tumor size, whereas the different immune cell infiltration patterns were not found to be prognostic. Combined immuno-genomic analyses revealed that high CNA burden was inversely associated with intra-tumoral CD4+ (Spearman’s r=-0.33, p=0.01) and CD8+ infiltration (Spearman’s r=-0.37, p=0.004). Conclusions: The present study indicates the feasibility of CNA profiling by CUTseq and immuno-profiling by mfIHC in FFPE samples obtained from BC patients. Moreover, our data provide a link between genomic alterations and the immune landscape in early BC and set the basis for further application of CUTseq and mfIHC in larger patient cohorts.
Citation Format: Ioannis Zerdes, Michele Simonetti, Alexios Matikas, Luuk Harbers, Ning Zhang, Dimitrios Salgkamis, Susanne Agartz, Markella Zacharouli, Pablo Moreno-Ruiz, Johan Hartman, Artur Mezheyeuski, Jonas Bergh, Nicola Crosetto, Theodoros Foukakis. Integrated immuno-genomic analyses in early breast cancer: Results from the Scandinavian breast group 2004-1 (SBG-2004-1) randomized phase II trial [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-27.