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Bagheri M, Mohamed GA, Mohamed Saleem MA, Ognjenovic NB, Lu H, Kolling FW, Wilkins OM, Das S, LaCroix IS, Nagaraj SH, Muller KE, Gerber SA, Miller TW, Pattabiraman DR. Pharmacological induction of chromatin remodeling drives chemosensitization in triple-negative breast cancer. Cell Rep Med 2024; 5:101504. [PMID: 38593809 PMCID: PMC11031425 DOI: 10.1016/j.xcrm.2024.101504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/11/2023] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Targeted therapies have improved outcomes for certain cancer subtypes, but cytotoxic chemotherapy remains a mainstay for triple-negative breast cancer (TNBC). The epithelial-to-mesenchymal transition (EMT) is a developmental program co-opted by cancer cells that promotes metastasis and chemoresistance. There are no therapeutic strategies specifically targeting mesenchymal-like cancer cells. We report that the US Food and Drug Administration (FDA)-approved chemotherapeutic eribulin induces ZEB1-SWI/SNF-directed chromatin remodeling to reverse EMT that curtails the metastatic propensity of TNBC preclinical models. Eribulin induces mesenchymal-to-epithelial transition (MET) in primary TNBC in patients, but conventional chemotherapy does not. In the treatment-naive setting, but not after acquired resistance to other agents, eribulin sensitizes TNBC cells to subsequent treatment with other chemotherapeutics. These findings provide an epigenetic mechanism of action of eribulin, supporting its use early in the disease process for MET induction to prevent metastatic progression and chemoresistance. These findings warrant prospective clinical evaluation of the chemosensitizing effects of eribulin in the treatment-naive setting.
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Affiliation(s)
- Meisam Bagheri
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Gadisti Aisha Mohamed
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | | | - Nevena B Ognjenovic
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Hanxu Lu
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Fred W Kolling
- Center for Quantitative Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Owen M Wilkins
- Center for Quantitative Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | | | - Ian S LaCroix
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia; Translational Research Institute, Brisbane, QLD 4102, Australia
| | - Kristen E Muller
- Department of Pathology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Scott A Gerber
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Todd W Miller
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA; Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA; Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA.
| | - Diwakar R Pattabiraman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.
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Preiss NK, Kamal Y, Wilkins OM, Li C, Kolling FW, Trask HW, Usherwood YK, Cheng C, Frost HR, Usherwood EJ. Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20. Life Sci Alliance 2023; 6:e202201683. [PMID: 37414528 PMCID: PMC10326419 DOI: 10.26508/lsa.202201683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
Members of the BTB-ZF transcription factor family regulate the immune system. Our laboratory identified that family member Zbtb20 contributes to the differentiation, recall responses, and metabolism of CD8 T cells. Here, we report a characterization of the transcriptional and epigenetic signatures controlled by Zbtb20 at single-cell resolution during the effector and memory phases of the CD8 T cell response. Without Zbtb20, transcriptional programs associated with memory CD8 T cell formation were up-regulated throughout the CD8 T response. A signature of open chromatin was associated with genes controlling T cell activation, consistent with the known impact on differentiation. In addition, memory CD8 T cells lacking Zbtb20 were characterized by open chromatin regions with overrepresentation of AP-1 transcription factor motifs and elevated RNA- and protein-level expressions of the corresponding AP-1 components. Finally, we describe motifs and genomic annotations from the DNA targets of Zbtb20 in CD8 T cells identified by cleavage under targets and release under nuclease (CUT&RUN). Together, these data establish the transcriptional and epigenetic networks contributing to the control of CD8 T cell responses by Zbtb20.
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Affiliation(s)
- Nicholas K Preiss
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Yasmin Kamal
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Owen M Wilkins
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Chenyang Li
- Genomic Medicine Department, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX, USA
| | - Fred W Kolling
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Heidi W Trask
- Genomics and Molecular Biology Shared Resource, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Young-Kwang Usherwood
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Hildreth R Frost
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Edward J Usherwood
- Microbiology and Immunology Department, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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Bagheri M, Aisha Mohamed G, Mohamed Saleem MA, Ognjenovic NB, Lu H, Kolling FW, Wilkins OM, Das S, La Croix IS, Nagaraj SH, Muller KE, Gerber SA, Miller TW, Pattabiraman DR. Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression. bioRxiv 2023:2023.04.19.537586. [PMID: 37131809 PMCID: PMC10153261 DOI: 10.1101/2023.04.19.537586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The epithelial-mesenchymal transition (EMT) is a developmental program co-opted by tumor cells that aids the initiation of the metastatic cascade. Tumor cells that undergo EMT are relatively chemoresistant, and there are currently no therapeutic avenues specifically targeting cells that have acquired mesenchymal traits. We show that treatment of mesenchymal-like triple-negative breast cancer (TNBC) cells with the microtubule-destabilizing chemotherapeutic eribulin, which is FDA-approved for the treatment of advanced breast cancer, leads to a mesenchymal-epithelial transition (MET). This MET is accompanied by loss of metastatic propensity and sensitization to subsequent treatment with other FDA-approved chemotherapeutics. We uncover a novel epigenetic mechanism of action that supports eribulin pretreatment as a path to MET induction that curtails metastatic progression and the evolution of therapy resistance.
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Affiliation(s)
- Meisam Bagheri
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
| | - Gadisti Aisha Mohamed
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
| | | | - Nevena B. Ognjenovic
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
| | - Hanxu Lu
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
| | - Fred W. Kolling
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
| | - Owen M. Wilkins
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover NH 03755 USA
| | | | - Ian S. La Croix
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
| | - Shivashankar H. Nagaraj
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane QLD 4102, Australia
| | - Kristen E. Muller
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
| | - Scott A. Gerber
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
| | - Todd W. Miller
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
| | - Diwakar R. Pattabiraman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover NH 03755, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
- Lead contact
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Mohamed GA, Mahmood S, Ognjenovic NB, Lee MK, Wilkins OM, Christensen BC, Muller KE, Pattabiraman DR. Lineage plasticity enables low-ER luminal tumors to evolve and gain basal-like traits. Breast Cancer Res 2023; 25:23. [PMID: 36859337 PMCID: PMC9979432 DOI: 10.1186/s13058-023-01621-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
Stratifying breast cancer into specific molecular or histologic subtypes aids in therapeutic decision-making and predicting outcomes; however, these subtypes may not be as distinct as previously thought. Patients with luminal-like, estrogen receptor (ER)-expressing tumors have better prognosis than patients with more aggressive, triple-negative or basal-like tumors. There is, however, a subset of luminal-like tumors that express lower levels of ER, which exhibit more basal-like features. We have found that breast tumors expressing lower levels of ER, traditionally considered to be luminal-like, represent a distinct subset of breast cancer characterized by the emergence of basal-like features. Lineage tracing of low-ER tumors in the MMTV-PyMT mouse mammary tumor model revealed that basal marker-expressing cells arose from normal luminal epithelial cells, suggesting that luminal-to-basal plasticity is responsible for the evolution and emergence of basal-like characteristics. This plasticity allows tumor cells to gain a new lumino-basal phenotype, thus leading to intratumoral lumino-basal heterogeneity. Single-cell RNA sequencing revealed SOX10 as a potential driver for this plasticity, which is known among breast tumors to be almost exclusively expressed in triple-negative breast cancer (TNBC) and was also found to be highly expressed in low-ER tumors. These findings suggest that basal-like tumors may result from the evolutionary progression of luminal tumors with low ER expression.
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Affiliation(s)
- Gadisti Aisha Mohamed
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Sundis Mahmood
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Nevena B Ognjenovic
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
| | - Owen M Wilkins
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Brock C Christensen
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Kristen E Muller
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
| | - Diwakar R Pattabiraman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, 03755, USA.
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
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Hinds JW, Feris EJ, Wilkins OM, Deary LT, Wang X, Cole MD. S146L in MYC is a context-dependent activating substitution in cancer development. PLoS One 2022; 17:e0272771. [PMID: 36018850 PMCID: PMC9417018 DOI: 10.1371/journal.pone.0272771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/26/2022] [Indexed: 11/19/2022] Open
Abstract
MYC is one of the most dysregulated oncogenes and is thought to be fundamental to tumor formation and/or maintenance in many cancer types. This dominant pro-tumor activity makes MYC an attractive target for cancer therapy. However, MYC is a transcription factor lacking enzymatic activity, and the structure of one of its two domains is unknown e.g., its transactivation domain. Consequently, few direct MYC-targeting therapies have been developed, and none have been successful in the clinic. Nevertheless, significant effort has been devoted to understanding the mechanisms of oncogenic MYC activity with the objective of uncovering novel vulnerabilities of MYC-dependent cancers. These extensive investigations have revealed in detail how MYC translocation, amplification, and other upstream perturbations contribute to MYC activity in cancer. However, missense mutations of the MYC gene have remained relatively understudied for their potential role in MYC-mediated oncogenesis. While the function of several low-frequency mutations in MYC have been described, our understanding of other equally or more frequent mutations is incomplete. Herein, we define the function of a recurrent missense mutation in MYC resulting in the substitution S146L. This mutation enhances the interaction between MYC and its cofactor TRRAP and may enhance oncogenic MYC activity in certain cellular contexts.
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Affiliation(s)
- John W. Hinds
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Edmond J. Feris
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Owen M. Wilkins
- Center for Quantitative Biology (CQB), Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, Unites States of America
| | - Luke T. Deary
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Xiaofeng Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
| | - Michael D. Cole
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, Unites States of America
- Dartmouth Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, Unites States of America
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Brown MS, Abdollahi B, Wilkins OM, Lu H, Chakraborty P, Ognjenovic NB, Muller KE, Jolly MK, Christensen BC, Hassanpour S, Pattabiraman DR. Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer. Sci Adv 2022; 8:eabj8002. [PMID: 35921406 PMCID: PMC9348802 DOI: 10.1126/sciadv.abj8002] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/16/2022] [Indexed: 05/04/2023]
Abstract
The epithelial-to-mesenchymal transition (EMT) is frequently co-opted by cancer cells to enhance migratory and invasive cell traits. It is a key contributor to heterogeneity, chemoresistance, and metastasis in many carcinoma types, where the intermediate EMT state plays a critical tumor-initiating role. We isolate multiple distinct single-cell clones from the SUM149PT human breast cell line spanning the EMT spectrum having diverse migratory, tumor-initiating, and metastatic qualities, including three unique intermediates. Using a multiomics approach, we identify CBFβ as a key regulator of metastatic ability in the intermediate state. To quantify epithelial-mesenchymal heterogeneity within tumors, we develop an advanced multiplexed immunostaining approach using SUM149-derived orthotopic tumors and find that the EMT state and epithelial-mesenchymal heterogeneity are predictive of overall survival in a cohort of stage III breast cancer. Our model reveals previously unidentified insights into the complex EMT spectrum and its regulatory networks, as well as the contributions of epithelial-mesenchymal plasticity (EMP) in tumor heterogeneity in breast cancer.
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Affiliation(s)
- Meredith S. Brown
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Behnaz Abdollahi
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Owen M. Wilkins
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, NH 03756, USA
| | - Hanxu Lu
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Priyanka Chakraborty
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Nevena B. Ognjenovic
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Kristen E. Muller
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Brock C. Christensen
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, NH 03756, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Saeed Hassanpour
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, NH 03756, USA
| | - Diwakar R. Pattabiraman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
- Norris Cotton Cancer Center, Geisel School of Medicine, Lebanon, NH 03756, USA
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Lee MK, Brown MS, Wilkins OM, Pattabiraman DR, Christensen BC. Distinct cytosine modification profiles define epithelial-to-mesenchymal cell-state transitions. Epigenomics 2022; 14:519-535. [PMID: 35382559 PMCID: PMC9118069 DOI: 10.2217/epi-2022-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Epithelial-to-mesenchymal transition (EMT) is an early step in the invasion-metastasis cascade, involving progression through intermediate cell states. Due to challenges with isolating intermediate cell states, genome-wide cytosine modifications that define transition are not completely understood. Methods: The authors measured multiple DNA cytosine modification marks and chromatin accessibility across clonal populations residing in specific EMT states. Results: Clones exhibiting more intermediate EMT phenotypes demonstrated increased 5-hydroxymethylcytosine and decreased 5-methylcytosine. Open chromatin regions containing increased 5-hydroxymethylcytosine CpG loci were enriched in EMT transcription factor motifs and were associated with Rho GTPases. Conclusion: The results indicate the importance of both distinct and shared epigenetic profiles associated with EMT processes that may be targeted to prevent EMT progression.
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Affiliation(s)
- Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Meredith S Brown
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Owen M Wilkins
- Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, NH 03756, USA
| | - Diwakar R Pattabiraman
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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Lee MK, Brown MS, Wilkins OM, Pattabiraman DR, Christensen BC. Abstract 2115: Multicomponent epigenetic profiling of intermediate epithelial-to-mesenchymal states in triple negative breast cancer identifies distinct regulatory signatures. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epithelial-to-mesenchymal transition (EMT) is an early step in the invasion-metastasis cascade, involving cellular progression through a number of intermediate states through the transition. Due to difficulty in isolating cells with intermediate EMT phenotypes, it has been challenging to investigate their molecular characteristics. Here, we describe multicomponent epigenetic profiles of phenotypes across the EMT spectrum. Six single cell clones on different points of the EMT spectrum were isolated from SUM149 cells, a heterogeneous ER/PR negative inflammatory breast cancer line. Methylation (mC) and hydroxymethylation (hmC) of >860,000 CpGs sites were measured with tandem oxidative bisulfite treatment and Illumina EPIC arrays, global chromatin accessibility was determined using Assay for Transposase Accessible Chromatin (ATAC) seq, and gene expression was measured using RNA-seq. We observed distinct mC and hmC profiles of the EMT intermediate clones compared to clones at either the epithelial or mesenchymal extremes. Intermediate clones demonstrated 17,862 CpGs with significantly higher hmC and 7,903 CpGs with significant hypomethylation, compared to the distal clones (FDR < 0.01). CpGs with higher hmC were enriched in regulatory regions such as promoters (OR = 2.87, p < 0.001), while hypomethylated CpGs were enriched in regions within the gene bodies. High hmC included CpGs located in promoters of key epithelial genes CDH1 and OCLN. In addition, 1,653 differentially accessible chromatin regions from ATAC-seq also were identified in intermediate clones (FDR < 0.1). Differentially accessible regions in the intermediate clones were associated with extracellular matrix organization (q-val = 0.04) in Reactome Pathway analysis. Although a large proportion of differentially accessible regions where differential hmC and mC CpGs were enriched tracked to distal intergenic regions (30.8%) and introns (28.1%), we did not observe significant enrichment of differential cytosine modifications overlapping with the differentially accessible chromatin regions which indicates the importance of multicomponent measures of epigenetic states. In genes with differentially accessible regions and hydroxymethylated CpGs, intermediate clones showed higher gene expression than distal clones. In particular, RUNX3 was observed to harbor all differential chromatin accessibility, hmC and mC CpGs, in intermediate clones. There was a stronger correlation between hmC and gene expression for differentially hydroxymethylated CpGs within accessible regions (R = 0.54, p < 0.01) than within non-accessible regions (R = 0.45, p = 0.02). Our results indicate both shared and distinct epigenetic profiles on the EMT spectrum at the cytosine and chromatin level regulate EMT processes and may be targeted to prevent the progression of EMT.
Citation Format: Min Kyung Lee, Meredith S. Brown, Owen M. Wilkins, Diwakar R. Pattabiraman, Brock C. Christensen. Multicomponent epigenetic profiling of intermediate epithelial-to-mesenchymal states in triple negative breast cancer identifies distinct regulatory signatures [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2115.
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Rojas IY, Moyer BJ, Ringelberg CS, Wilkins OM, Pooler DB, Ness DB, Coker S, Tosteson TD, Lewis LD, Chamberlin MD, Tomlinson CR. Kynurenine-Induced Aryl Hydrocarbon Receptor Signaling in Mice Causes Body Mass Gain, Liver Steatosis, and Hyperglycemia. Obesity (Silver Spring) 2021; 29:337-349. [PMID: 33491319 PMCID: PMC10782555 DOI: 10.1002/oby.23065] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/30/2022]
Abstract
OBJECTIVE The aryl hydrocarbon receptor (AHR) plays a key role in obesity. In vitro studies revealed that the tryptophan metabolite kynurenine (Kyn) activates AHR signaling in cultured hepatocytes. The objective of this study was to determine whether Kyn activated the AHR in mice to induce obesity. METHODS Mice were fed a low-fat diet and the same diet supplemented with Kyn. Body mass, liver status, and the expression of identified relevant genes were determined. RESULTS Kyn caused mice to gain significant body mass, develop fatty liver and hyperglycemia, and increase expression levels of cytochrome P450 1B1 and stearoyl-CoA desaturase 1. The hyperglycemia was accompanied with decreased insulin levels, which may have been due to the repression of genes involved in insulin secretion. Kyn plasma concentrations and BMI were measured in female patients, and a significant association was observed between Kyn and age in patients with obesity but not in patients who were lean. CONCLUSIONS Results show that (1) Kyn or a metabolite thereof is a ligand responsible for inducing AHR-based obesity, fatty liver, and hyperglycemia in mice; (2) plasma Kyn levels increase with age in women with obesity but not in lean women; and (3) an activated AHR is necessary but not sufficient to attain obesity, a status that also requires fat in the diet.
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Affiliation(s)
- Itzel Y. Rojas
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Benjamin J. Moyer
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Carol S. Ringelberg
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Owen M. Wilkins
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Darcy B. Pooler
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Dylan B. Ness
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Shodeinde Coker
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Tor D. Tosteson
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Biomedical Data Science, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Lionel D. Lewis
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Mary D. Chamberlin
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Medicine, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Craig R. Tomlinson
- Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Molecular & Systems Biology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
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10
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Muse ME, Titus AJ, Salas LA, Wilkins OM, Mullen C, Gregory KJ, Schneider SS, Crisi GM, Jawale RM, Otis CN, Christensen BC, Arcaro KF. Enrichment of CpG island shore region hypermethylation in epigenetic breast field cancerization. Epigenetics 2020; 15:1093-1106. [PMID: 32255732 PMCID: PMC7518670 DOI: 10.1080/15592294.2020.1747748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/14/2020] [Accepted: 03/05/2020] [Indexed: 12/31/2022] Open
Abstract
While changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumour DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumour. Matched tumour, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select epithelial cells from normal tissue, and neoplastic cells from tumour for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array. We identified substantially more CpG loci that were differentially methylated between contralateral-normal and tumour (63,271 CpG loci q < 0.01), than between ipsilateral-normal and tumour (38,346 CpG loci q < 0.01). We identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p < 0.01). In this comparison, hypomethylated loci were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3 and hypermethylated loci were significantly enriched for CpG island shore regions. In addition, progression of shore hypermethylation was observed in tumours compared to matched ipsilateral normal tissue, and these alterations tracked to several well-established tumour suppressor genes. Our results indicate an epigenetic field effect in surrounding histologically normal tissue. This work offers an opportunity to focus investigations of early DNA methylation alterations in breast carcinogenesis and potentially develop epigenetic biomarkers of disease risk. ABBREVIATIONS DCIS: ductal carcinoma in situ; GO: gene ontology; OR: odds ratio; CI: confidence interval; TFBS: transcription factor binding site; LOLA: Locus Overlap Analysis.
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Affiliation(s)
- Meghan E. Muse
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Alexander J. Titus
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Lucas A. Salas
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Owen M. Wilkins
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Chelsey Mullen
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Kelly J. Gregory
- Pioneer Valley Life Sciences Institute, Baystate Medical Center, Springfield, MA, USA
| | - Sallie S. Schneider
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
- Pioneer Valley Life Sciences Institute, Baystate Medical Center, Springfield, MA, USA
| | - Giovanna M. Crisi
- Department of Pathology, University of Massachusetts Medical School-Baystate Health, Springfield, MA, USA
| | - Rahul M. Jawale
- Department of Pathology, University of Massachusetts Medical School-Baystate Health, Springfield, MA, USA
| | - Christopher N. Otis
- Department of Pathology, University of Massachusetts Medical School-Baystate Health, Springfield, MA, USA
| | - Brock C. Christensen
- Department of Epidemiology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
- Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Hanover, NH, USA
- Department of Community & Family Medicine, Dartmouth Geisel School of Medicine, Hanover, NH, USA
| | - Kathleen F. Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
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11
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Wilkins OM, Johnson KC, Houseman EA, King JE, Marsit CJ, Christensen BC. Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 2019; 15:398-418. [PMID: 31842685 PMCID: PMC7153548 DOI: 10.1080/15592294.2019.1695332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Despite recent evidence that 5-hydroxymethylcytosine (5hmC) possesses roles in gene regulation distinct from 5-methylcytosine (5mC), relatively little is known regarding the functions of 5hmC in mammalian tissues. To address this issue, we utilized an approach combining both paired bisulfite (BS) and oxidative bisulfite (oxBS) DNA treatment, to resolve genome-wide patterns of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC was differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity, such as heterochromatin and repressed Polycomb regions, were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. Furthermore, genes containing abundant 5hmC were enriched among those actively transcribed in normal breast tissue. Finally, in independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Primarily, our findings identify genomic loci containing abundant 5hmC in breast tissues and provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue. Additionally, these data suggest 5hmC may participate in gene regulatory programs that are dysregulated during breast-related carcinogenesis.
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Affiliation(s)
- Owen M Wilkins
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - E Andres Houseman
- Department of Biostatistics, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Jessica E King
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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12
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Wilkins OM, Titus AJ, Salas LA, Gui J, Eliot M, Butler RA, Sturgis EM, Li G, Kelsey KT, Christensen BC. MicroRNA-Related Genetic Variants Associated with Survival of Head and Neck Squamous Cell Carcinoma. Cancer Epidemiol Biomarkers Prev 2018; 28:127-136. [PMID: 29880533 DOI: 10.1158/1055-9965.epi-18-0002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/23/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is commonly diagnosed at an advanced stage, and prognosis for such patients is poor. There remains a gap in our understanding of genetic variants related with HNSCC prognosis. miRNA-related single nucleotide polymorphisms (miR-SNPs) are a class of genetic variants with gene-regulatory potential. METHODS We used a genome-scale approach and independent patient populations in a two-stage approach to test 40,286 common miR-SNPs for association with HNSCC survival in the discovery population (n = 847), and selected the strongest associations for replication in validation phase cases (n = 1,236). Furthermore, we leveraged miRNA interaction databases and miRNA expression data from The Cancer Genome Atlas, to provide functional insight for the identified and replicated associations. RESULTS Joint population analyses identified novel miR-SNPs associated with overall survival in oral and laryngeal cancers. rs1816158, located within long noncoding RNA MIR100HG, was associated with overall survival in oral cavity cancer (HR, 1.56; 95% confidence interval (CI), 1.21-2.00). In addition, expression of MIR100HG-embedded miRNA, miR-100, was significantly associated with overall survival in an independent cohort of HNSCC cases (HR, 1.25; 95% CI, 1.06-1.49). A SNP in the 3'UTR of SH3BP4 (rs56161233) that overlaps predicted miRNA-binding sites and is predicted to disrupt several miRNA-mRNA interactions was associated with overall survival of laryngeal cancer (HR, 2.57; 95% CI, 1.71-3.86). CONCLUSIONS This work reveals novel miR-SNPs associated with HNSCC survival, and utilizes miRNA-mRNA interaction and expression data to provide functional support for these associations. IMPACT These findings extend our understanding of how genetic variation contributes to HNSCC survival, and may contribute to future prognostic models for improved risk stratification.
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Affiliation(s)
- Owen M Wilkins
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Alexander J Titus
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Melissa Eliot
- Department of Epidemiology, Brown University, Providence, Rhode Island
| | - Rondi A Butler
- Department of Epidemiology, Brown University, Providence, Rhode Island
| | - Erich M Sturgis
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
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13
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Wilkins OM, Titus AJ, Gui J, Eliot M, Butler RA, Sturgis EM, Li G, Kelsey KT, Christensen BC. Genome-scale identification of microRNA-related SNPs associated with risk of head and neck squamous cell carcinoma. Carcinogenesis 2017; 38:986-993. [PMID: 28582492 PMCID: PMC5862295 DOI: 10.1093/carcin/bgx056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Polymorphisms in microRNAs and their target sites can disrupt microRNA-dependent gene regulation, and have been associated with cancer susceptibility. However, genome-scale analyses of microRNA-related genetic variation in cancer are lacking. We tested the associations of ~40 000 common [minor allele frequency (MAF) ≥5%], microRNA-related single nucleotide polymorphisms (miR-SNPs), with risk of head and neck squamous cell carcinoma (HNSCC) in a discovery population, and validated selected loci in an independent population among a total of 2198 cases and 2180 controls. Joint analyses across the discovery and validation populations revealed six novel miR-SNP associations with risk of HNSCC. An upstream variant of MIR548H4 (rs7834169), replicated its association with overall HNSCC risk as well as risk of oral cavity cancer. Four other variants were specifically associated with oral cavity cancer risk (rs16914640, rs1134367, rs7306991 and rs1373756). 3'UTR variant of HADH, rs221347 and rs4975616, located within known cancer risk locus 5p15.33, were specific to risk of laryngeal cancer. High confidence predicted microRNA binding sites were identified for CLEC2D, LOC37443, KDM8 and HADH overlapping rs16914640, rs7306991, rs1134367 and rs221347, respectively. Furthermore, we identified several microRNA interactions with KDM8 and HADH predicted to be disrupted by genetic variation at rs1134367 and rs221347. These results suggest microRNA-related genetic variation may contribute to the genetic susceptibility of HNSCC, and that more powerful evaluation of this class of genetic variation and their relationship with cancer risk is warranted.
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Affiliation(s)
| | | | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Melissa Eliot
- Department of Epidemiology, Brown University, Providence, RI 02912, USA
| | - Rondi A Butler
- Department of Epidemiology, Brown University, Providence, RI 02912, USA
| | - Erich M Sturgis
- Department of Head and Neck Surgery
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, TX 77030, USA
| | - Guojun Li
- Department of Head and Neck Surgery
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, TX 77030, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Brock C Christensen
- Department of Epidemiology
- Department of Molecular and Systems Biology and
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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14
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Weyburne ES, Wilkins OM, Sha Z, Williams DA, Pletnev AA, de Bruin G, Overkleeft HS, Goldberg AL, Cole MD, Kisselev AF. Inhibition of the Proteasome β2 Site Sensitizes Triple-Negative Breast Cancer Cells to β5 Inhibitors and Suppresses Nrf1 Activation. Cell Chem Biol 2017; 24:218-230. [PMID: 28132893 DOI: 10.1016/j.chembiol.2016.12.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/27/2016] [Accepted: 12/28/2016] [Indexed: 11/26/2022]
Abstract
The proteasome inhibitors carfilzomib (Cfz) and bortezomib (Btz) are used successfully to treat multiple myeloma, but have not shown clinical efficacy in solid tumors. Here we show that clinically achievable inhibition of the β5 site of the proteasome by Cfz and Btz does not result in loss of viability of triple-negative breast cancer cell lines. We use site-specific inhibitors and CRISPR-mediated genetic inactivation of β1 and β2 to demonstrate that inhibiting a second site of the proteasome, particularly the β2 site, sensitizes cell lines to Btz and Cfz in vitro and in vivo. Inhibiting both β5 and β2 suppresses production of the soluble, active form of the transcription factor Nrf1 and prevents the recovery of proteasome activity through induction of new proteasomes. These findings provide a strong rationale for the development of dual β5 and β2 inhibitors for the treatment of solid tumors.
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Affiliation(s)
- Emily S Weyburne
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Owen M Wilkins
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Zhe Sha
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David A Williams
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | | | - Gerjan de Bruin
- Gorlaeus Laboratories, Leiden Institute of Chemistry, 2333 CC Leiden, the Netherlands
| | - Hermann S Overkleeft
- Gorlaeus Laboratories, Leiden Institute of Chemistry, 2333 CC Leiden, the Netherlands
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael D Cole
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Department of Genetics, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Alexei F Kisselev
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.
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15
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Canfield K, Li J, Wilkins OM, Morrison MM, Ung M, Wells W, Williams CR, Liby KT, Vullhorst D, Buonanno A, Hu H, Schiff R, Cook RS, Kurokawa M. Receptor tyrosine kinase ERBB4 mediates acquired resistance to ERBB2 inhibitors in breast cancer cells. Cell Cycle 2015; 14:648-55. [PMID: 25590338 DOI: 10.4161/15384101.2014.994966] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Approximately 25% of breast cancers overexpress and depend on the receptor tyrosine kinase ERBB2, one of 4 ERBB family members. Targeted therapies directed against ERBB2 have been developed and used clinically, but many patients continue to develop resistance to such therapies. Although much effort has been focused on elucidating the mechanisms of acquired resistance to ERBB2-targeted therapies, the involvement of ERBB4 remains elusive and controversial. We demonstrate that genetic ablation of ERBB4, but not ERBB1-3, led to apoptosis in lapatinib-resistant cells, suggesting that the efficacy of pan-ERBB inhibitors was, at least in part, mediated by the inhibition of ERBB4. Moreover, ERBB4 was upregulated at the protein level in ERBB2+ breast cancer cell lines selected for acquired lapatinib resistance in vitro and in MMTV-Neu mice following prolonged lapatinib treatment. Knockdown of ERBB4 caused a decrease in AKT phosphorylation in resistant cells but not in sensitive cells, suggesting that ERBB4 activated the PI3K/AKT pathway in lapatinib-resistant cells. Importantly, ERBB4 knockdown triggered apoptosis not only in lapatinib-resistant cells but also in trastuzumab-resistant cells. Our results suggest that although ERBB4 is dispensable for naïve ERBB2+ breast cancer cells, it may play a key role in the survival of ERBB2+ cancer cells after they develop resistance to ERBB2 inhibitors, lapatinib and trastuzumab.
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Key Words
- EGFR
- EGFR, epidermal growth factor receptor
- ERK, extracellular regulated kinase
- FGFR, fibroblast growth factor receptor
- HER, human epidermal growth factor receptor
- HER2
- HER3
- HER4
- Herceptin
- MTS, 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium
- PI3K, phosphatidylinositol-4,5-bisphosphate 3-kinase
- Q-VD-OPh, quinolyl-valyl-O-methylaspartyl-[2,6-difluoro-phenoxy]-methyl ketone
- RTK, receptor tyrosine kinase
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