Abstract 5418: Comprehensive genomic profiling of HER2low breast carcinomas unveils unique genomic features and actionable genetic alterations
Authors: Berrino Enrico , Annaratone Laura , Sarotto Ivana , Zecchillo Maria Cecilia , Casorzo Laura , Ponzone Riccardo , Montemurro Filippo , Sapino Anna , Marchio Caterina 
Published: June 2022

Abstract
Introduction & Purpose: “HER2low breast cancer” is an operational term identifying breast carcinomas (BCs) displaying a HER2 score 1+ or score 2+ in immunohistochemistry (IHC) and lacking HER2 amplification. This paradigm shift in HER2 assessment in BC stems from substantial antitumor activity of potent antibody-drug conjugates (ADCs) targeting the HER2 receptor on the tumor cell membrane. Whether these tumors constitute a distinct pathological entity is a matter of debate.
Experimental procedures: To dissect the biology of HER2low BCs we performed a high throughput mutational analysis coupled with gene expression profiling on 98 HER2low BCs [34 cases score 1+ (1), 15 cases score 2+ HER2 not amplified (2N), 49 cases score 2+ with HER2 copy numbers in the equivocal range (2E)], of which 89 were estrogen receptor (ER)-positive, and 9 ER-negative. DNA and RNA were extracted and subjected to targeted DNA sequencing (Illumina TSO500 panel) and targeted gene expression analysis (NanoString BC360 panel). Mutation rates were compared with in silico data from 1317 samples of the MSK Breast Cancer cohort (PMID: 30205045).
Results: The most frequently mutated genes were PIK3CA (33/98, 33%), GATA3 (18/98, 18%), TP53 (17/98, 17%), HER2 (8/98, 8%, private to 2E cases). Tumor mutational burden mean values were significantly higher in score 1+ compared to score 2+ cases (p= 0.04), with a single score 1+ tumor harboring microsatellite instability (MSI). Mutational signatures 1, 5 and 13 (APOBEC) were the most prevalent, with signature 30 being private to HER2 score 1+ cases. Comparative statistics revealed mutational drift of HER2low BCs from both HER2 negative (19 differentially mutated genes) and HER2 positive BCs (11 differentially mutated genes). Potentially actionable genetic alterations (OncoKB classes) accounted for 43 SNVs (predominantly HER2 and PIK3CA mutations) and 17 CNVs (e.g. MET amplification and PTEN homozygous deletions), including a MSI tumor, distributed over 47 independent patients.Subgroup stratifications based on gene expression were observed when considering genes involved in angiogenesis, stromal marker and cytokines signalling. HER2 mRNA levels were significantly higher in 2E versus 2N and in 2E versus 1. Differential gene expression Kegg pathway analysis identified RTK activation restricted to 2E cases.
Conclusions: HER2low BCs harbour a different mutational landscape from ER- and grade- matched HER2 positive and HER2 negative BCs. Differences across IHC score classes within HER2low carcinomas were demonstrated, with the 2E category showing distinct features (private HER2 mutations, HER2 mRNA levels significantly higher compared to the other groups, RTK pathway activation). Of note, besides the option of ADCs we demonstrate that up to 48% of cases may be targeted with different approaches exploiting actionable alterations.
Citation Format: Enrico Berrino, Laura Annaratone, Ivana Sarotto, Maria Cecilia Zecchillo, Laura Casorzo, Riccardo Ponzone, Filippo Montemurro, Anna Sapino, Caterina Marchio. Comprehensive genomic profiling of HER2low breast carcinomas unveils unique genomic features and actionable genetic alterations [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 5418.