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Garcia NMG, Becerra JN, McKinney BJ, DiMarco AV, Wu F, Fitzgibbon M, Alvarez JV. APOBEC3 activity promotes the survival and evolution of drug-tolerant persister cells during acquired resistance to EGFR inhibitors in lung cancer. bioRxiv 2023:2023.07.02.547443. [PMID: 37461590 PMCID: PMC10350004 DOI: 10.1101/2023.07.02.547443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
APOBEC mutagenesis is one of the most common endogenous sources of mutations in human cancer and is a major source of genetic intratumor heterogeneity. High levels of APOBEC mutagenesis are associated with poor prognosis and aggressive disease across diverse cancers, but the mechanistic and functional impacts of APOBEC mutagenesis on tumor evolution and therapy resistance remain relatively unexplored. To address this, we investigated the contribution of APOBEC mutagenesis to acquired therapy resistance in a model of EGFR-mutant non-small cell lung cancer. We find that inhibition of EGFR in lung cancer cells leads to a rapid and pronounced induction of APOBEC3 expression and activity. Functionally, APOBEC expression promotes the survival of drug-tolerant persister cells (DTPs) following EGFR inhibition. Constitutive expression of APOBEC3B alters the evolutionary trajectory of acquired resistance to the EGFR inhibitor gefitinib, making it more likely that resistance arises through de novo acquisition of the T790M gatekeeper mutation and squamous transdifferentiation during the DTP state. APOBEC3B expression is associated with increased expression of the squamous cell transcription factor ΔNp63 and squamous cell transdifferentiation in gefitinib-resistant cells. Knockout of ΔNp63 in gefitinibresistant cells reduces the expression of the p63 target genes IL1a/b and sensitizes these cells to the thirdgeneration EGFR inhibitor osimertinib. These results suggest that APOBEC activity promotes acquired resistance by facilitating evolution and transdifferentiation in DTPs, and suggest that approaches to target ΔNp63 in gefitinib-resistant lung cancers may have therapeutic benefit.
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Affiliation(s)
- Nina Marie G Garcia
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine
| | - Jessica N Becerra
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Brock J McKinney
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center
| | - Ashley V DiMarco
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine
| | - Feinan Wu
- Genomics and Bioinformatics, Fred Hutchinson Cancer Center
| | | | - James V Alvarez
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center
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DiMarco AV, Qin X, McKinney BJ, Garcia NMG, Van Alsten SC, Mendes EA, Force J, Hanks BA, Troester MA, Owzar K, Xie J, Alvarez JV. APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses. Cancer Immunol Res 2021; 10:70-86. [PMID: 34795033 DOI: 10.1158/2326-6066.cir-21-0146] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/23/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022]
Abstract
The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are enriched in the HER2 subtype of breast cancer and are associated with immunotherapy response in diverse cancer types. However, the direct consequences of APOBEC mutagenesis on the tumor immune microenvironment have not been thoroughly investigated. To address this, we developed syngeneic murine mammary tumor models with inducible expression of APOBEC3B. We found that APOBEC activity induced antitumor adaptive immune responses and CD4+ T cell-mediated, antigen-specific tumor growth inhibition. Although polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected, suggesting that APOBEC-mediated genetic heterogeneity limits antitumor adaptive immune responses. Consistent with the observed immune infiltration in APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to anti-CTLA-4 checkpoint inhibition and led to a complete response to combination anti-CTLA-4 and anti-HER2 therapy. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures and clonality as biomarkers predicting immunotherapy response in HER2-positive (HER2+) breast cancers.
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Affiliation(s)
- Ashley V DiMarco
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Xiaodi Qin
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | - Brock J McKinney
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Nina Marie G Garcia
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Sarah C Van Alsten
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Elizabeth A Mendes
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Jeremy Force
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Durham, North Carolina
| | - Brent A Hanks
- Division of Medical Oncology, Department of Medicine, Duke Cancer Institute, Durham, North Carolina
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | - Jichun Xie
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina
| | - James V Alvarez
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina.
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Newcomb R, Dean E, McKinney BJ, Alvarez JV. Context-dependent effects of whole-genome duplication during mammary tumor recurrence. Sci Rep 2021; 11:14932. [PMID: 34294755 PMCID: PMC8298634 DOI: 10.1038/s41598-021-94332-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/06/2021] [Indexed: 12/24/2022] Open
Abstract
Whole-genome duplication (WGD) generates polyploid cells possessing more than two copies of the genome and is among the most common genetic abnormalities in cancer. The frequency of WGD increases in advanced and metastatic tumors, and WGD is associated with poor prognosis in diverse tumor types, suggesting a functional role for polyploidy in tumor progression. Experimental evidence suggests that polyploidy has both tumor-promoting and suppressing effects, but how polyploidy regulates tumor progression remains unclear. Using a genetically engineered mouse model of Her2-driven breast cancer, we explored the prevalence and consequences of whole-genome duplication during tumor growth and recurrence. While primary tumors in this model are invariably diploid, nearly 40% of recurrent tumors undergo WGD. WGD in recurrent tumors was associated with increased chromosomal instability, decreased proliferation and increased survival in stress conditions. The effects of WGD on tumor growth were dependent on tumor stage. Surprisingly, in recurrent tumor cells WGD slowed tumor formation, growth rate and opposed the process of recurrence, while WGD promoted the growth of primary tumors. These findings highlight the importance of identifying conditions that promote the growth of polyploid tumors, including the cooperating genetic mutations that allow cells to overcome the barriers to WGD tumor cell growth and proliferation.
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Affiliation(s)
- Rachel Newcomb
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, 27710, USA
| | - Emily Dean
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, 27710, USA
| | - Brock J McKinney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, 27710, USA
| | - James V Alvarez
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, 27710, USA.
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Fox DB, Garcia NMG, McKinney BJ, Lupo R, Noteware LC, Newcomb R, Liu J, Locasale JW, Hirschey MD, Alvarez JV. NRF2 activation promotes the recurrence of dormant tumour cells through regulation of redox and nucleotide metabolism. Nat Metab 2020; 2:318-334. [PMID: 32691018 PMCID: PMC7370851 DOI: 10.1038/s42255-020-0191-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/13/2020] [Indexed: 11/08/2022]
Abstract
The survival and recurrence of dormant tumour cells following therapy is a leading cause of death in cancer patients. The metabolic properties of these cells are likely distinct from those of rapidly growing tumours. Here we show that Her2 down-regulation in breast cancer cells promotes changes in cellular metabolism, culminating in oxidative stress and compensatory upregulation of the antioxidant transcription factor, NRF2. NRF2 is activated during dormancy and in recurrent tumours in animal models and breast cancer patients with poor prognosis. Constitutive activation of NRF2 accelerates recurrence, while suppression of NRF2 impairs it. In recurrent tumours, NRF2 signalling induces a transcriptional metabolic reprogramming to re-establish redox homeostasis and upregulate de novo nucleotide synthesis. The NRF2-driven metabolic state renders recurrent tumour cells sensitive to glutaminase inhibition, which prevents reactivation of dormant tumour cells in vitro, suggesting that NRF2-high dormant and recurrent tumours may be targeted. These data provide evidence that NRF2-driven metabolic reprogramming promotes the recurrence of dormant breast cancer.
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Affiliation(s)
- Douglas B Fox
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Nina Marie G Garcia
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Brock J McKinney
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Ryan Lupo
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Laura C Noteware
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Rachel Newcomb
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Juan Liu
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Matthew D Hirschey
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University Medical Center, Durham, NC, USA
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Durham, NC, USA
| | - James V Alvarez
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
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