Lifespan Health System, Providence, RI
Kristina Fanucci , Maryam B. Lustberg , Neal A. Fischbach , Maureen Pelletier , Abirami Sivapiragasam , Prashanth Ashok Kumar , Mansi Kallem , Natalie Danziger , Ethan Sokol , Smruthy Sivakumar , Dean C. Pavlick , Jeffrey S. Ross , Lajos Pusztai
Background: Pts with MBC whose tumors feature high TMB (≥ 10 mutations/Mb) are eligible for on label immune checkpoint inhibitor (ICI) treatment. This study evaluated the genomic landscape of MBC with “Ultra high” TMB, defined at > 20 mutations/Mb. Methods: 2049 MBC underwent hybrid capture-based CGP to evaluate all classes of genomic alterations (GA), TMB, microsatellite instability (MSI) and trinucleotide mutational signatures. HER2 IHC results were available in a subset of pts. PD-L1 expression on immunocytes was determined by IHC (Ventana SP142). Results: 45/2049 (2.2%) of MBC were UHTMB. 45 (100%) pts had metastatic disease. 38 (84%) had documented Stage IV disease and 7 documented axillary LN metastases at the time of sequencing. Local breast tumor was used for CGP in 19 (42.2%) MBC and metastatic site biopsy was used in 26 (57.8%). When compared with 2004 non-UHTMB pts with UHTMB were older (mean 64.6 yrs vs 58.2 yrs p < .0001), more often had lobular histology (40.0% vs 14.5% p < .0001) and ER+ disease (86.6% vs 70.0%). Of the 35 UHTMB cases with HER2 IHC data available, 11 (31.4%%) were HER2 IHC negative (0+), 21 (60.0%) were HER2-low status (9 1+ and 12 2+/ISH negative) and 3 (8.6%) were HER2 IHC positive (3+). 1/3 HER2 IHC2+ cases and 2/45 (4.4%) of all UHTMB cases were positive for HER2 copy number gain on CGP. UHTMB cases had more driver GA/tumor (mean 9.8 vs 5.7 p < .0001) and were less often TNBC (13.3% vs 27.0% p = .041) compared to non-UHTMB high cancers. Mutation signature analysis revealed APOBEC was predominant in UHTMB samples (82.5%); MMR signature was also observed in 10% of cases. MSI high status was significantly more frequent in UHTMB high cases (11.6% vs 0.4% p < .0001). GA more frequently identified in UHTMB cases included CDH1 (45.5% vs 14.3% p < .0001), PIK3CA (81.8% vs 37.9% p < .0001), CDKN2A (11.4% vs 3.2% p = .017), ARID1A (25.0% vs 5.0% p < .0001) and NF1 (20.5% vs 5.9% p = .0014). PD-L1 (CD274) gene amplification (2.3% vs 1.3%) or protein expression by the Ventana SP142 assay (57.14% vs 51.10%) were not significantly different among groups. Conclusions: UHTMB MBC is a rare, yet clinically important subset of clinically advanced breast cancer driven by APOBEC mutagenesis, with high incidence of ER+ lobular histology and frequent alterations in CDH1 and PIK3CA. In addition to potential benefit from ICI based treatment, UHTMB MBC present with a high frequency of HER2-low status which may impact therapy decisions for this rare disease.
Cases with 10-20 Mut/Mb (120) | Cases with TMB < 20 Mut/Mb (2004) | Cases with TMB >20 Mut/Mb (45) | P Value (TMB < 20 vs >20) | |
---|---|---|---|---|
Mean Age | 60.3 | 58.2 | 64.6 | 0.000 |
ER+ Status by IHC | 69.10% | 68.22% | 86.60% | 0.013 |
HER2+ Amplification by CGP | 14.17% | 8.87% | 6.81% | NS |
Frequency of ILC Status | 31.77% | 14.50% | 40.00% | < .0001 |
TNBC Status | 20.83% | 27.05% | 13.30% | 0.041 |
CDH1 | 27.10% | 14.32% | 45.50% | < .0001 |
PIK3CA | 55.10% | 37.86% | 81.80% | < .0001 |
MSI High Frequency | 1.81% | 0.40% | 11.60% | < .0001 |
Mean TMB | 12.500 | 3.5 | 32.4 | < .0001 |
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