Abstract P3-08-03: <i>HOXB13</i> is coamplified with <i>HER2</i> in a subset of breast cancers
Authors: Dennis Sgroi, Maristela Onozato, Irene Mitsiades, Ryan McMullin, Daniel Hicks, Angela Volorio, Esther Rheinbay
Journal: Cancer Research (2022)

Abstract Background: The Breast Cancer Index (BCI) is an algorithmic gene expression-based signature comprised of two functional biomarker panels, the Molecular Grade Index (MGI) and the two-gene ratio, HOXB13/IL17BR. The HOXB13/IL17BR ratio has been shown to predict endocrine response across several different treatment scenarios, and the homeobox factor, HOXB13, is the primary determinant of endocrine benefit and response. Previously, we found that HOXB13 gene expression was positively correlated with HER2 in estrogen receptor-positive (ER+) but not ER-negative (ER-) tumors. To validate these findings, we examined HOXB13 gene expression in The Cancer Genome Atlas (TCGA) breast cancer cohort. In addition, considering that the HOXB13 gene locus resides 9 megabases from the HER2 locus at chromosome 17q21-22, we examined whether HOXB13 was coamplified with HER2 in HER2-positive breast cancers. Methods: Messenger RNA (mRNA) sequencing (mRNAseq) data from the TCGA breast cancer dataset were used to correlate HOXB13 gene expression with immunohistochemical (IHC)-based HER2 expression in ER+ (ER+PR+, ER+PR-) and ER- (ER-PR+ and ER-PR-) breast cancers. Thresholded copy number data from GISTIC output and mRNAseq data from the TCGA datasets were used to correlate HER2 and HOXB13 gene amplification (at least 4 inferred copies) with HOXB13 gene expression in IHC-based ER+ (n= 562) and ER- (n=163) breast cancer subsets. Formalin-fixed paraffin embedded (FFPE) samples from 80 consecutive HER2-amplified invasive breast carcinomas (64 ER+, 16 ER-) diagnosed between 2010 and 2013 were retrospectively collected from the MGH clinical archives and processed for fluorescence in situ hybridization (FISH) for HER2 (spectrum orange) HOXB13 (spectrum green) and CEP17 (spectrum blue). A ratio of &amp;gt; 2.0 HER2 and HOXB13 to CEP17 signals in at least 60 interphase tumor cell nuclei was considered as amplification of HER2 and HOXB13.Results: In the TCGA breast tumors, HOXB13 gene expression was significantly higher in HER2 positive (by IHC status) tumors in both ER+ (p= 3.7 x10-5) and ER- (p= 4.7 x10-4) tumors compared to HER2-negative samples. In HER2+ TCGA breast tumors, genomic analysis revealed co-amplification of HOXB13 with HER2 in 27% of all tumors, and 25.3% and 31.7% in the ER+ and ER- subsets, respectively. Amplification of the HOXB13 locus alone was observed in 2.4% of HER2-non amplified ER+ and ER- TCGA tumors. In the TCGA cohort, median HOXB13 gene expression was not significantly different when comparing HER2-amplified and HER2/HOXB13 coamplified ER+ (p= 0.33) and ER- (p=0.052) tumors, HER2-amplified and HER2-nonamplified ER+ (p=0.42) and ER- (p=0.67) tumors, and HER2/HOXB13 coamplified and HER2-nonamplified ER+ (p=0.50) and ER- (p=0.11) tumors. Lastly, in the consecutive case series of 80 HER2-amplified breast cancers from MGH, HOXB13 was coamplified in 23% of all tumors, and 23.4% and 18.75% in the ER+ and ER- subsets, respectively. Conclusion: HOXB13 was coamplified with HER2 in a substantial subset of TCGA and MGH primary breast cancers irrespective of ER status. Citation Format: Dennis Sgroi, Maristela Onozato, Irene Mitsiades, Ryan McMullin, Daniel Hicks, Angela Volorio, Esther Rheinbay. HOXB13 is coamplified with HER2 in a subset of breast cancers [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-08-03.