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Clinically advanced and metastatic pure mucinous carcinoma of the breast: a comprehensive genomic profiling study.
Breast Cancer Res Treat 2016; 155(2):405-13BC

Abstract

PURPOSE

Pure mucinous breast carcinoma (pmucBC) is a distinctive variant of breast cancer (BC) featuring an excellent overall prognosis. However, on rare occasions, pmucBC pursues an aggressive clinical course. We queried whether comprehensive genomic profiling (CGP) would uncover clinically relevant genomic alterations (CRGA) that could lead to targeted therapy treatment for patients with an advanced and metastatic form of pmucBC.

METHODS

From a series of 51,238 total cancer samples, which included 5605 cases of clinically advanced BC and 22 cases of stage IV pmucBC, DNA was extracted from 40 microns of FFPE sections. Comprehensive genomic profiling was performed using a hybrid-capture, adaptor ligation-based next generation sequencing assay to a mean coverage depth of 564X. The results were analyzed for all classes of genomic alterations (GA) including base substitutions, insertions and deletions, select rearrangements, and copy number changes. Clinically relevant genomic alterations were defined as those indicating possible treatment with anti-cancer drugs on the market or in registered clinical trials.

RESULTS

Samples were obtained from breast (11), lymph nodes (3), chest wall (2), liver (2), soft tissue (2), bone (1), and pleura (1). The median age of the 22 pmucBC patients was 57 years (range 32-79 years). Three pmucBCs were grade 1, 17 were grade 2, and 2 were grade 3. Twenty-one (95 %) pmucBC were ER+, 18 (82 %) were PR+, and 3 (14 %) were HER2+ by IHC and/or FISH. A total of 132 GA were identified (6.0 GA per tumor), including 53 CRGA, for a mean of 2.4 GA per tumor. Amplification of FGFR1 or ZNF703, located within the same amplicon, was found in 8 of 22 cases (36 %). This enrichment of FGFR1 amplification in 36 % of pmucBC versus 11 % of non-mucinous ER+ BC (601 cases) was significant (p < 0.005). Other frequently altered genes of interest in pmucBC were CCND1 and the FGF3/FGF4/FGF19 amplicon (27 %), often co-amplified together. ERBB2/HER2 alterations were identified in 5 pmucBC (23 %): ERBB2 amplification was found in 3 of 3 cases (100 %) that were HER2+ by IHC and/or FISH; 1 pmucBC was negative for HER2 overexpression by IHC, but positive for amplification by CGP; and 2 pmucBC harbored the ERBB2 substitutions D769Y and V777L (one sample also featured ERBB2 amplification). The enrichment of ERBB2 GA in metastatic pmucBC versus non-metastatic primary pmucBC was significant (p = 0.03). CRGA were also found in 20 additional genes including PIK3CA (5), BRCA1 (1), TSC2 (1), STK11 (1), AKT3 (1), and ESR1 (1).

CONCLUSIONS

Metastatic pmucBC is a distinct form of breast cancer that features a relatively high frequency of CRGA, including a significant enrichment of FGFR1 alterations and a high frequency of ERBB2 alterations when compared with non-metastatic pmucBC. These findings suggest that CGP can identify a variety of known and emerging therapy targets that have the potential to improve outcomes for patients with clinically advanced and metastatic forms of this disease.

Authors+Show Affiliations

Department of Pathology, Mail Code 81, Albany Medical College, 47 New Scotland Avenue, Albany, NY, 12208, USA. rossj@mail.amc.edu. Foundation Medicine, Inc., Cambridge, MA, USA. rossj@mail.amc.edu.Foundation Medicine, Inc., Cambridge, MA, USA.Department of Pathology, Mail Code 81, Albany Medical College, 47 New Scotland Avenue, Albany, NY, 12208, USA.Foundation Medicine, Inc., Cambridge, MA, USA.Foundation Medicine, Inc., Cambridge, MA, USA.Department of Pathology, Mail Code 81, Albany Medical College, 47 New Scotland Avenue, Albany, NY, 12208, USA.Foundation Medicine, Inc., Cambridge, MA, USA.Foundation Medicine, Inc., Cambridge, MA, USA.Foundation Medicine, Inc., Cambridge, MA, USA.Foundation Medicine, Inc., Cambridge, MA, USA.Foundation Medicine, Inc., Cambridge, MA, USA.Foundation Medicine, Inc., Cambridge, MA, USA.Foundation Medicine, Inc., Cambridge, MA, USA.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26762307

Citation

Ross, Jeffrey S., et al. "Clinically Advanced and Metastatic Pure Mucinous Carcinoma of the Breast: a Comprehensive Genomic Profiling Study." Breast Cancer Research and Treatment, vol. 155, no. 2, 2016, pp. 405-13.
Ross JS, Gay LM, Nozad S, et al. Clinically advanced and metastatic pure mucinous carcinoma of the breast: a comprehensive genomic profiling study. Breast Cancer Res Treat. 2016;155(2):405-13.
Ross, J. S., Gay, L. M., Nozad, S., Wang, K., Ali, S. M., Boguniewicz, A., ... Stephens, P. J. (2016). Clinically advanced and metastatic pure mucinous carcinoma of the breast: a comprehensive genomic profiling study. Breast Cancer Research and Treatment, 155(2), pp. 405-13. doi:10.1007/s10549-016-3682-6.
Ross JS, et al. Clinically Advanced and Metastatic Pure Mucinous Carcinoma of the Breast: a Comprehensive Genomic Profiling Study. Breast Cancer Res Treat. 2016;155(2):405-13. PubMed PMID: 26762307.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Clinically advanced and metastatic pure mucinous carcinoma of the breast: a comprehensive genomic profiling study. AU - Ross,Jeffrey S, AU - Gay,Laurie M, AU - Nozad,Sahar, AU - Wang,Kai, AU - Ali,Siraj M, AU - Boguniewicz,Ann, AU - Khaira,Depinder, AU - Johnson,Adrienne, AU - Elvin,Julia A, AU - Vergilio,Jo-Anne, AU - Suh,James, AU - Miller,Vincent A, AU - Stephens,Philip J, Y1 - 2016/01/13/ PY - 2015/12/31/received PY - 2016/01/04/accepted PY - 2016/1/15/entrez PY - 2016/1/15/pubmed PY - 2016/10/16/medline KW - Comprehensive genomic profiling KW - DNA sequencing KW - ERBB2 KW - FGFR1 KW - Mucinous breast carcinoma SP - 405 EP - 13 JF - Breast cancer research and treatment JO - Breast Cancer Res. Treat. VL - 155 IS - 2 N2 - PURPOSE: Pure mucinous breast carcinoma (pmucBC) is a distinctive variant of breast cancer (BC) featuring an excellent overall prognosis. However, on rare occasions, pmucBC pursues an aggressive clinical course. We queried whether comprehensive genomic profiling (CGP) would uncover clinically relevant genomic alterations (CRGA) that could lead to targeted therapy treatment for patients with an advanced and metastatic form of pmucBC. METHODS: From a series of 51,238 total cancer samples, which included 5605 cases of clinically advanced BC and 22 cases of stage IV pmucBC, DNA was extracted from 40 microns of FFPE sections. Comprehensive genomic profiling was performed using a hybrid-capture, adaptor ligation-based next generation sequencing assay to a mean coverage depth of 564X. The results were analyzed for all classes of genomic alterations (GA) including base substitutions, insertions and deletions, select rearrangements, and copy number changes. Clinically relevant genomic alterations were defined as those indicating possible treatment with anti-cancer drugs on the market or in registered clinical trials. RESULTS: Samples were obtained from breast (11), lymph nodes (3), chest wall (2), liver (2), soft tissue (2), bone (1), and pleura (1). The median age of the 22 pmucBC patients was 57 years (range 32-79 years). Three pmucBCs were grade 1, 17 were grade 2, and 2 were grade 3. Twenty-one (95 %) pmucBC were ER+, 18 (82 %) were PR+, and 3 (14 %) were HER2+ by IHC and/or FISH. A total of 132 GA were identified (6.0 GA per tumor), including 53 CRGA, for a mean of 2.4 GA per tumor. Amplification of FGFR1 or ZNF703, located within the same amplicon, was found in 8 of 22 cases (36 %). This enrichment of FGFR1 amplification in 36 % of pmucBC versus 11 % of non-mucinous ER+ BC (601 cases) was significant (p < 0.005). Other frequently altered genes of interest in pmucBC were CCND1 and the FGF3/FGF4/FGF19 amplicon (27 %), often co-amplified together. ERBB2/HER2 alterations were identified in 5 pmucBC (23 %): ERBB2 amplification was found in 3 of 3 cases (100 %) that were HER2+ by IHC and/or FISH; 1 pmucBC was negative for HER2 overexpression by IHC, but positive for amplification by CGP; and 2 pmucBC harbored the ERBB2 substitutions D769Y and V777L (one sample also featured ERBB2 amplification). The enrichment of ERBB2 GA in metastatic pmucBC versus non-metastatic primary pmucBC was significant (p = 0.03). CRGA were also found in 20 additional genes including PIK3CA (5), BRCA1 (1), TSC2 (1), STK11 (1), AKT3 (1), and ESR1 (1). CONCLUSIONS: Metastatic pmucBC is a distinct form of breast cancer that features a relatively high frequency of CRGA, including a significant enrichment of FGFR1 alterations and a high frequency of ERBB2 alterations when compared with non-metastatic pmucBC. These findings suggest that CGP can identify a variety of known and emerging therapy targets that have the potential to improve outcomes for patients with clinically advanced and metastatic forms of this disease. SN - 1573-7217 UR - https://www.unboundmedicine.com/medline/citation/26762307/Clinically_advanced_and_metastatic_pure_mucinous_carcinoma_of_the_breast:_a_comprehensive_genomic_profiling_study_ L2 - https://doi.org/10.1007/s10549-016-3682-6 DB - PRIME DP - Unbound Medicine ER -