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Xia Y, He X, Renshaw L, Martinez-Perez C, Kay C, Gray M, Meehan J, Parker JS, Perou CM, Carey LA, Dixon JM, Turnbull A. Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer. Clin Cancer Res 2022; 28:3618-3629. [PMID: 35653148 PMCID: PMC7613305 DOI: 10.1158/1078-0432.ccr-21-3189] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/04/2022] [Accepted: 05/31/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Endocrine therapy resistance (ETR) remains the greatest challenge in treating patients with hormone receptor-positive breast cancer. We set out to identify molecular mechanisms underlying ETR through in-depth genomic analysis of breast tumors. EXPERIMENTAL DESIGN We collected pre-treatment and sequential on-treatment tumor samples from 35 patients with estrogen receptor-positive breast cancer treated with neoadjuvant then adjuvant endocrine therapy; 3 had intrinsic resistance, 19 acquired resistance, and 13 remained sensitive. Response was determined by changes in tumor volume neoadjuvantly and by monitoring for adjuvant recurrence. Twelve patients received two or more lines of endocrine therapy, with subsequent treatment lines being initiated at the time of development of resistance to the previous endocrine therapy. DNA whole-exome sequencing and RNA sequencing were performed on all samples, totalling 169 unique specimens. DNA mutations, copy-number alterations, and gene expression data were analyzed through unsupervised and supervised analyses to identify molecular features related to ETR. RESULTS Mutations enriched in ETR included ESR1 and GATA3. The known ESR1 D538G variant conferring ETR was identified, as was a rarer E380Q variant that confers endocrine hypersensitivity. Resistant tumors which acquired resistance had distinct gene expression profiles compared with paired sensitive tumors, showing elevated pathways including ER, HER2, GATA3, AKT, RAS, and p63 signaling. Integrated analysis in individual patients highlighted the diversity of ETR mechanisms. CONCLUSIONS The mechanisms underlying ETR are multiple and characterized by diverse changes in both somatic genetic and transcriptomic profiles; to overcome resistance will require an individualized approach utilizing genomic and genetic biomarkers and drugs tailored to each patient.
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Affiliation(s)
- Youli Xia
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Xiaping He
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lorna Renshaw
- Edinburgh Breast Unit Western General Hospital, Edinburgh, United Kingdom
| | - Carlos Martinez-Perez
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Charlene Kay
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark Gray
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - James Meehan
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Joel S. Parker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Charles M. Perou
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lisa A. Carey
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Division of Hematology-Oncology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - J. Michael Dixon
- Edinburgh Breast Unit Western General Hospital, Edinburgh, United Kingdom.,Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Arran Turnbull
- Edinburgh Cancer Research Center, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom.,Corresponding Author: Arran Turnbull, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, 2XU Crewe Road South, Edinburgh, United Kingdom. Phone: 4413-1651-8694; E-mail:
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LCCC 1025: a phase II study of everolimus, trastuzumab, and vinorelbine to treat progressive HER2-positive breast cancer brain metastases. Breast Cancer Res Treat 2018; 171:637-648. [PMID: 29938395 DOI: 10.1007/s10549-018-4852-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/07/2018] [Indexed: 01/09/2023]
Abstract
PURPOSE HER2 + breast cancer (BC) is an aggressive subtype with high rates of brain metastases (BCBM). Two-thirds of HER2 + BCBM demonstrate activation of the PI3K/mTOR pathway driving resistance to anti-HER2 therapy. This phase II study evaluated everolimus (E), a brain-permeable mTOR inhibitor, trastuzumab (T), and vinorelbine (V) in patients with HER2 + BCBM. PATIENTS AND METHODS Eligible patients had progressive HER2 + BCBM. The primary endpoint was intracranial response rate (RR); secondary objectives were CNS clinical benefit rate (CBR), extracranial RR, time to progression (TTP), overall survival (OS), and targeted sequencing of tumors from enrolled patients. A two-stage design distinguished intracranial RR of 5% versus 20%. RESULTS 32 patients were evaluable for toxicity, 26 for efficacy. Intracranial RR was 4% (1 PR). CNS CBR at 6 mos was 27%; at 3 mos 65%. Median intracranial TTP was 3.9 mos (95% CI 2.2-5). OS was 12.2 mos (95% CI 0.6-20.2). Grade 3-4 toxicities included neutropenia (41%), anemia (16%), and stomatitis (16%). Mutations in TP53 and PIK3CA were common in BCBM. Mutations in the PI3K/mTOR pathway were not associated with response. ERBB2 amplification was higher in BCBM compared to primary BC; ERBB2 amplification in the primary BC trended toward worse OS. CONCLUSION While intracranial RR to ETV was low in HER2 + BCBM patients, one-third achieved CNS CBR; TTP/OS was similar to historical control. No new toxicity signals were observed. Further analysis of the genomic underpinnings of BCBM to identify tractable prognostic and/or predictive biomarkers is warranted. CLINICAL TRIAL (NCT01305941).
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Siegel MB, He X, Hoadley KA, Hoyle A, Pearce JB, Garrett AL, Kumar S, Moylan VJ, Brady CM, Van Swearingen AE, Marron D, Gupta GP, Thorne LB, Kieran N, Livasy C, Mardis ER, Parker JS, Chen M, Anders CK, Carey LA, Perou CM. Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer. J Clin Invest 2018; 128:1371-1383. [PMID: 29480819 PMCID: PMC5873890 DOI: 10.1172/jci96153] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/21/2017] [Indexed: 12/22/2022] Open
Abstract
Breast cancer metastasis remains a clinical challenge, even within a single patient across multiple sites of the disease. Genome-wide comparisons of both the DNA and gene expression of primary tumors and metastases in multiple patients could help elucidate the underlying mechanisms that cause breast cancer metastasis. To address this issue, we performed DNA exome and RNA sequencing of matched primary tumors and multiple metastases from 16 patients, totaling 83 distinct specimens. We identified tumor-specific drivers by integrating known protein-protein network information with RNA expression and somatic DNA alterations and found that genetic drivers were predominantly established in the primary tumor and maintained through metastatic spreading. In addition, our analyses revealed that most genetic drivers were DNA copy number changes, the TP53 mutation was a recurrent founding mutation regardless of subtype, and that multiclonal seeding of metastases was frequent and occurred in multiple subtypes. Genetic drivers unique to metastasis were identified as somatic mutations in the estrogen and androgen receptor genes. These results highlight the complexity of metastatic spreading, be it monoclonal or multiclonal, and suggest that most metastatic drivers are established in the primary tumor, despite the substantial heterogeneity seen in the metastases.
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Affiliation(s)
- Marni B. Siegel
- Department of Genetics
- Lineberger Comprehensive Cancer Center
| | | | | | | | - Julia B. Pearce
- Division of Hematology-Oncology, Department of Medicine, School
of Medicine
| | - Amy L. Garrett
- Division of Hematology-Oncology, Department of Medicine, School
of Medicine
| | | | | | | | | | | | - Gaorav P. Gupta
- Lineberger Comprehensive Cancer Center
- Department of Radiation Oncology, School of Medicine, University
of North Carolina (UNC) at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Niamh Kieran
- Division of Hematology-Oncology, Department of Medicine, School
of Medicine
| | - Chad Livasy
- Department of Pathology and Laboratory Medicine, and
- Department of Pathology, Levine Cancer Institute, Carolinas
Medical Center, Carolinas HealthCare System, Charlotte, North Carolina, USA
| | - Elaine R. Mardis
- The Research Institute at Nationwide Children’s Hospital, The
Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Joel S. Parker
- Department of Genetics
- Lineberger Comprehensive Cancer Center
| | - Mengjie Chen
- Department of Biostatistics, UNC at Chapel Hill, Chapel Hill,
North Carolina, USA
| | - Carey K. Anders
- Lineberger Comprehensive Cancer Center
- Division of Hematology-Oncology, Department of Medicine, School
of Medicine
| | - Lisa A. Carey
- Lineberger Comprehensive Cancer Center
- Division of Hematology-Oncology, Department of Medicine, School
of Medicine
| | - Charles M. Perou
- Department of Genetics
- Lineberger Comprehensive Cancer Center
- Department of Pathology and Laboratory Medicine, and
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