Genomic profiling of breast cancer brain metastases reveals targetable alterations.

Authors

Sheheryar Kabraji

Sheheryar Kairas Kabraji

Dana Farber Cancer Institute, Boston, MA

Sheheryar Kairas Kabraji , Liam F. Spurr , Melissa E Hughes , Yvonne Y. Li , Jose Pablo Leone , Ana Christina Garrido-Castro , Romualdo Barroso-Sousa , Janet Files , Gregory Kirkner , Bruce E. Johnson , Eric P. Winer , Andrew D. Cherniack , Nancy U. Lin

Organizations

Dana Farber Cancer Institute, Boston, MA, Dana-Farber Cancer Institute, Boston, MA, Instituto do Cancer do Estado de São Paulo, São Paulo, Brazil, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, Broad Institute of MIT and Harvard, Cambridge, MA

Research Funding

U.S. National Institutes of Health
U.S. National Institutes of Health, Other Foundation, Other Government Agency, Pharmaceutical/Biotech Company, Fashion Footwear Association of New York

Background: Genomic characterization of breast cancer brain metastases (BCBMs) has thus far been limited. The objective of this study was to describe the landscape of genomic alterations in patients (pts) with BCBMs. Methods: Targeted next-generation DNA sequencing of > 300 cancer-related genes (OncoPanel) was prospectively performed on primary and metastatic (met) tumors in 321 pts with a diagnosis of BCBM between August 2016 and April 2019 at Dana-Farber Cancer Institute (table). Enrichment analysis of genomic alterations was performed using a two-sided Fisher exact test and differences in tumor mutation burden (TMB) between groups were assessed using two-sided Mann-Whitney U test. Multiple comparison correction was performed using the Benjamini-Hochberg procedure. Results: All subtypes were represented in BCBM (25 HR+/HER2-; 24 HR+/HER2+; 27 HR-/HER2+; 18 TNBC; 5 unknown; n = 99) and extracranial (EC) samples: (96 HR+/HER2-; 32 HR+/HER2+; 22 HR-/HER2+; 41 TNBC; 31 unknown; n = 222). BCBMs were found most commonly to have mutations or copy number alterations in TP53, ERBB2, PIK3CA, GATA3, PTEN, ESR1, CDH1, BRCA2, ARID1A, BRCA1 (>5% frequency, table). Two pts acquired ERBB2 amplification (amp) between the matched primary breast sample and brain met. In pair-wise comparisons of BCBMs to unmatched primaries or EC mets, only ERBB2 amp was significantly enriched (table, † = adjusted p < 0.05). There was no significant difference in TMB between BCBM and EC mets (median 9.12 vs 7.26, p = 0.15). In contrast, TMB was significantly higher in BCBMs compared to unmatched primaries (median 9.12 vs 7.26, p=0.005). Conclusions: BCBMs display similar mutations and copy number alterations compared to primary tumors and EC mets in pts with BCBM. These data suggest that BCBMs contain actionable genomic alterations that are most often also reflected in EC disease. Alterations in ERBB2, PIK3CA/PTEN, and BRCA1/2 represent potentially targetable alterations in pts with BCBM.

Genomic alteration by anatomic site % (n).

Genomic alterationMatched
Unmatched
BCBM (n=16)Primary (n=13), Met (n=3)BCBM (n=99)Primary (n=125)EC met (n=85)
ERBB2 amp62.5 (10)50 (8)53.5 (56) †24.8 (31)17.6 (15)
TP53 mut12.5 (2)31.25 (5)48.4 (48)45.6 (57)42.4 (36)
PIK3CA mut12.5 (2)18.75 (3)24.2 (24)22.4 (28)25.8 (22)
ARID1A mut0 (0)6.25 (1)7 (7)4 (5)5.8 (5)
ESR1 mut6.25 (1)6.25 (1)6 (6)1.6 (2)12.9 (11)
BRCA2 mut12.5 (2)6.25 (1)5 (5)5.6 (7)4.7 (4)
GATA3 mut0 (0)18.75 (3)5 (5)6.4 (8)10.5 (9)
CDH1 mut0 (0)0 (0)5 (5)10 (8)5.8 (5)
PTEN mut6.25 (1)6.25 (1)3 (3)4.8 (6)10.5 (9)
BRCA1 mut0 (0)6.25 (1)3 (3)0.8 (1)4.7 (4)

Disclaimer

This material on this page is ©2024 American Society of Clinical Oncology, all rights reserved. Licensing available upon request. For more information, please contact licensing@asco.org

Abstract Details

Meeting

2020 ASCO Virtual Scientific Program

Session Type

Poster Session

Session Title

Central Nervous System Tumors

Track

Central Nervous System Tumors

Sub Track

Brain Metastases

Citation

J Clin Oncol 38: 2020 (suppl; abstr 2525)

DOI

10.1200/JCO.2020.38.15_suppl.2525

Abstract #

2525

Poster Bd #

16

Abstract Disclosures

Similar Abstracts

Abstract

2024 ASCO Annual Meeting

Impact of HER2 low status on genomic signatures in triple negative breast cancer (TNBC).

First Author: Melissa Taylor

Abstract

2023 ASCO Annual Meeting

Genomic characterization of the GATA3 mutational landscape in breast cancer.

First Author: Jason A Mouabbi