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Brockman QR, Scherer A, McGivney GR, Gutierrez WR, Rytlewski J, Sheehan A, Warrier A, Laverty EA, Roughton G, Carnevale NC, Knepper-Adrian V, Dodd RD. Discrepancies in indel software resolution with somatic CRISPR/Cas9 tumorigenesis models. Sci Rep 2023; 13:14798. [PMID: 37684258 PMCID: PMC10491828 DOI: 10.1038/s41598-023-41109-1] [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: 11/30/2022] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
CRISPR/Cas9 gene editing has evolved from a simple laboratory tool to a powerful method of in vivo genomic engineering. As the applications of CRISPR/Cas9 technology have grown, the need to characterize the breadth and depth of indels generated by editing has expanded. Traditionally, investigators use one of several publicly-available platforms to determine CRISPR/Cas9-induced indels in an edited sample. However, to our knowledge, there has not been a cross-platform comparison of available indel analysis software in samples generated from somatic in vivo mouse models. Our group has pioneered using CRISPR/Cas9 to generate somatic primary mouse models of malignant peripheral nerve sheath tumors (MPNSTs) through genetic editing of Nf1. Here, we used sequencing data from the in vivo editing of the Nf1 gene in our CRISPR/Cas9 tumorigenesis model to directly compare results across four different software platforms. By analyzing the same genetic target across a wide panel of cell lines with the same sequence file, we are able to draw systematic conclusions about the differences in these software programs for analysis of in vivo-generated indels. Surprisingly, we report high variability in the reported number, size, and frequency of indels across each software platform. These data highlight the importance of selecting indel analysis platforms specific to the context that the gene editing approach is being applied. Taken together, this analysis shows that different software platforms can report widely divergent indel data from the same sample, particularly if larger indels are present, which are common in somatic, in vivo CRISPR/Cas9 tumor models.
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Affiliation(s)
- Qierra R Brockman
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Amanda Scherer
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Gavin R McGivney
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
- Cancer Biology Training Program, University of Iowa, Iowa City, IA, USA
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Wade R Gutierrez
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Cancer Biology Training Program, University of Iowa, Iowa City, IA, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Jeffrey Rytlewski
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Alexa Sheehan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Akshaya Warrier
- Cancer Biology Training Program, University of Iowa, Iowa City, IA, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Emily A Laverty
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Grace Roughton
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Nina C Carnevale
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Vickie Knepper-Adrian
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA
| | - Rebecca D Dodd
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, 375 Newton Rd, 5206 MERF, Iowa City, IA, 52246, USA.
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA.
- Cancer Biology Training Program, University of Iowa, Iowa City, IA, USA.
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2
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Kohlmeyer JL, Lingo JJ, Kaemmer CA, Scherer A, Warrier A, Voigt E, Garay JAR, McGivney GR, Brockman QR, Tang A, Calizo A, Pollard K, Zhang X, Hirbe AC, Pratilas CA, Leidinger M, Breheny P, Chimenti MS, Sieren JC, Monga V, Tanas MR, Meyerholz DK, Darbro BW, Dodd RD, Quelle DE. CDK4/6-MEK Inhibition in MPNSTs Causes Plasma Cell Infiltration, Sensitization to PD-L1 Blockade, and Tumor Regression. Clin Cancer Res 2023; 29:3484-3497. [PMID: 37410426 PMCID: PMC10528807 DOI: 10.1158/1078-0432.ccr-23-0749] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 07/03/2023] [Indexed: 07/07/2023]
Abstract
PURPOSE Malignant peripheral nerve sheath tumors (MPNST) are lethal, Ras-driven sarcomas that lack effective therapies. We investigated effects of targeting cyclin-dependent kinases 4 and 6 (CDK4/6), MEK, and/or programmed death-ligand 1 (PD-L1) in preclinical MPNST models. EXPERIMENTAL DESIGN Patient-matched MPNSTs and precursor lesions were examined by FISH, RNA sequencing, IHC, and Connectivity-Map analyses. Antitumor activity of CDK4/6 and MEK inhibitors was measured in MPNST cell lines, patient-derived xenografts (PDX), and de novo mouse MPNSTs, with the latter used to determine anti-PD-L1 response. RESULTS Patient tumor analyses identified CDK4/6 and MEK as actionable targets for MPNST therapy. Low-dose combinations of CDK4/6 and MEK inhibitors synergistically reactivated the retinoblastoma (RB1) tumor suppressor, induced cell death, and decreased clonogenic survival of MPNST cells. In immune-deficient mice, dual CDK4/6-MEK inhibition slowed tumor growth in 4 of 5 MPNST PDXs. In immunocompetent mice, combination therapy of de novo MPNSTs caused tumor regression, delayed resistant tumor outgrowth, and improved survival relative to monotherapies. Drug-sensitive tumors that regressed contained plasma cells and increased cytotoxic T cells, whereas drug-resistant tumors adopted an immunosuppressive microenvironment with elevated MHC II-low macrophages and increased tumor cell PD-L1 expression. Excitingly, CDK4/6-MEK inhibition sensitized MPNSTs to anti-PD-L1 immune checkpoint blockade (ICB) with some mice showing complete tumor regression. CONCLUSIONS CDK4/6-MEK inhibition induces a novel plasma cell-associated immune response and extended antitumor activity in MPNSTs, which dramatically enhances anti-PD-L1 therapy. These preclinical findings provide strong rationale for clinical translation of CDK4/6-MEK-ICB targeted therapies in MPNST as they may yield sustained antitumor responses and improved patient outcomes.
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Affiliation(s)
- Jordan L Kohlmeyer
- Molecular Medicine Graduate Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Joshua J Lingo
- Cancer Biology Graduate Program, University of Iowa, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
| | - Courtney A Kaemmer
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Amanda Scherer
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Akshaya Warrier
- Cancer Biology Graduate Program, University of Iowa, Iowa City, Iowa
- Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Ellen Voigt
- Cancer Biology Graduate Program, University of Iowa, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | | | - Gavin R McGivney
- Cancer Biology Graduate Program, University of Iowa, Iowa City, Iowa
| | - Qierra R Brockman
- Molecular Medicine Graduate Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Amy Tang
- Department of Microbiology and Molecular Cell Biology, Leroy T. Canoles Jr. Cancer Center, Eastern Virginia Medical School, Norfolk, Virginia
| | - Ana Calizo
- Department of Oncology, Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Kai Pollard
- Department of Oncology, Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Xiaochun Zhang
- Division of Medical Oncology, Washington University, St. Louis, Missouri
| | - Angela C Hirbe
- Division of Medical Oncology, Washington University, St. Louis, Missouri
| | - Christine A Pratilas
- Department of Oncology, Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Mariah Leidinger
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Patrick Breheny
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, Iowa
| | - Michael S Chimenti
- Iowa Institute of Human Genetics, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Jessica C. Sieren
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Department of Radiation, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Varun Monga
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Munir R Tanas
- Molecular Medicine Graduate Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
- Cancer Biology Graduate Program, University of Iowa, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - David K Meyerholz
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Benjamin W Darbro
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Rebecca D Dodd
- Molecular Medicine Graduate Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
- Cancer Biology Graduate Program, University of Iowa, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
- Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Dawn E Quelle
- Molecular Medicine Graduate Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
- Cancer Biology Graduate Program, University of Iowa, Iowa City, Iowa
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa
- Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, Iowa
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
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3
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Gutierrez WR, Rytlewski JD, Scherer A, Roughton GA, Carnevale NC, Vyas KY, McGivney GR, Brockman QR, Knepper-Adrian V, Dodd RD. Loss of Nf1 and Ink4a/Arf Are Associated with Sex-Dependent Growth Differences in a Mouse Model of Embryonal Rhabdomyosarcoma. Curr Issues Mol Biol 2023; 45:1218-1232. [PMID: 36826025 PMCID: PMC9955904 DOI: 10.3390/cimb45020080] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is an aggressive form of cancer that accounts for half of all pediatric soft tissue sarcomas. Little progress has been made in improving survival outcomes over the past three decades. Mouse models of rhabdomyosarcoma are a critical component of translational research aimed at understanding tumor biology and developing new, improved therapies. Though several models exist, many common mutations found in human rhabdomyosarcoma tumors remain unmodeled and understudied. This study describes a new model of embryonal rhabdomyosarcoma driven by the loss of Nf1 and Ink4a/Arf, two mutations commonly found in patient tumors. We find that this new model is histologically similar to other previously-published rhabdomyosarcoma models, although it substantially differs in the time required for tumor onset and in tumor growth kinetics. We also observe unique sex-dependent phenotypes in both primary and newly-developed orthotopic syngeneic allograft tumors that are not present in previous models. Using in vitro and in vivo studies, we examined the response to vincristine, a component of the standard-of-care chemotherapy for RMS. The findings from this study provide valuable insight into a new mouse model of rhabdomyosarcoma that addresses an ongoing need for patient-relevant animal models to further translational research.
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Affiliation(s)
- Wade R. Gutierrez
- Cancer Biology Graduate Program, University of Iowa, Iowa City, IA 52242, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | | | - Amanda Scherer
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Grace A. Roughton
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Nina C. Carnevale
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Krisha Y. Vyas
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Gavin R. McGivney
- Cancer Biology Graduate Program, University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA 52242, USA
| | - Qierra R. Brockman
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, IA 52242, USA
| | | | - Rebecca D. Dodd
- Cancer Biology Graduate Program, University of Iowa, Iowa City, IA 52242, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, IA 52242, USA
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4
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Brockman QR, Scherer A, McGivney GR, Gutierrez WR, Voigt A, Isaacson A, Laverty EA, Roughton G, Knepper-Adrian V, Darbro B, Tanas MR, Stipp C, Dodd RD. Abstract A024: PRC2 loss drives MPNST metastasis and matrix remodeling. Cancer Res 2022. [DOI: 10.1158/1538-7445.cancepi22-a024] [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: 12/03/2022]
Abstract
Abstract
Epigenetic reprogramming alters gene transcription in response to different cellular cues and can occur at both the DNA level as well as histone post-translational modifications. Polycomb repressive complex 2 (PRC2) is a common epigenetic modifier that is responsible for adding methyl groups to the twenty-seventh lysine of histone 3. This modification is associated with decreased gene transcription and recruits complexes that further compact chromatin. PRC2 mutations have been implicated in the tumorigenesis of many cancer types; however, the role that PRC2 plays in tumorigenesis is complex and not well understood. PRC2 loss-of-function mutations have been identified in malignant peripheral nerve sheath tumors (MPNST), an aggressive sarcoma. PRC2 mutations are found in the EED and SUZ12 subunits in 70-92% of tumors. There are currently no effective therapies for MPNSTs resulting in a poor prognosis for individuals with inoperable tumors. Using a CRISPR/Cas9 system to delete EED or SUZ12, we developed in vitro and in vivo models to further study the biology of PRC2 loss in MPNSTs. Our data suggests that loss of PRC2 subunits increases the expression of extra-cellular matrix (ECM) remodeling genes, promotes cell migration in vitro, and increases pulmonary metastasis in vivo. We also observed that loss of either EED or SUZ12 increases collagen handling and a clustering metastatic phenotype. Additionally, loss of H3K27me3 was correlated with increased ECM and ECM remodeling genes as well as metastasis and overall survival in patient RNA-seq and tumor microarray data, respectively. Further characterization of the underlying mechanisms of PRC2-dependent metastasis will allow us to better understand the role of PRC2 in MPNST biology and test novel therapies for these patients.
Citation Format: Qierra R. Brockman, Amanda Scherer, Gavin R. McGivney, Wade R. Gutierrez, Andrew Voigt, Alexandra Isaacson, Emily A. Laverty, Grace Roughton, Vickie Knepper-Adrian, Benjamin Darbro, Munir R. Tanas, Christopher Stipp, Rebecca D. Dodd. PRC2 loss drives MPNST metastasis and matrix remodeling. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A024.
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5
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Gutierrez WR, Scherer A, Rytlewski JD, Laverty EA, Sheehan AP, McGivney GR, Brockman QR, Knepper-Adrian V, Roughton GA, Quelle DE, Gordon DJ, Monga V, Dodd RD. Augmenting chemotherapy with low-dose decitabine through an immune-independent mechanism. JCI Insight 2022; 7:159419. [PMID: 36227698 PMCID: PMC9746804 DOI: 10.1172/jci.insight.159419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/16/2022] [Accepted: 10/11/2022] [Indexed: 12/15/2022] Open
Abstract
The DNA methyltransferase inhibitor decitabine has classically been used to reactivate silenced genes and as a pretreatment for anticancer therapies. In a variation of this idea, this study explores the concept of adding low-dose decitabine (DAC) following administration of chemotherapy to bolster therapeutic efficacy. We find that addition of DAC following treatment with the chemotherapy agent gemcitabine improves survival and slows tumor growth in a mouse model of high-grade sarcoma. Unlike prior studies in epithelial tumor models, DAC did not induce a robust antitumor T cell response in sarcoma. Furthermore, DAC synergizes with gemcitabine independently of the immune system. Mechanistic analyses demonstrate that the combination therapy induces biphasic cell cycle arrest and apoptosis. Therapeutic efficacy was sequence dependent, with gemcitabine priming cells for treatment with DAC through inhibition of ribonucleotide reductase. This study identifies an apparently unique application of DAC to augment the cytotoxic effects of conventional chemotherapy in an immune-independent manner. The concepts explored in this study represent a promising paradigm for cancer treatment by augmenting chemotherapy through addition of DAC to increase tolerability and improve patient response. These findings have widespread implications for the treatment of sarcomas and other aggressive malignancies.
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Affiliation(s)
- Wade R Gutierrez
- Cancer Biology Graduate Program.,Medical Scientist Training Program.,Holden Comprehensive Cancer Center.,Department of Internal Medicine
| | - Amanda Scherer
- Holden Comprehensive Cancer Center.,Department of Internal Medicine
| | | | | | - Alexa P Sheehan
- Holden Comprehensive Cancer Center.,Department of Internal Medicine.,Molecular Medicine Graduate Program
| | - Gavin R McGivney
- Cancer Biology Graduate Program.,Holden Comprehensive Cancer Center.,Department of Internal Medicine.,Department of Molecular Physiology and Biophysics
| | - Qierra R Brockman
- Holden Comprehensive Cancer Center.,Department of Internal Medicine.,Molecular Medicine Graduate Program
| | | | | | - Dawn E Quelle
- Cancer Biology Graduate Program.,Medical Scientist Training Program.,Holden Comprehensive Cancer Center.,Molecular Medicine Graduate Program.,Department of Neuroscience and Pharmacology.,Department of Pathology, and
| | - David J Gordon
- Holden Comprehensive Cancer Center.,Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
| | - Varun Monga
- Holden Comprehensive Cancer Center.,Department of Internal Medicine
| | - Rebecca D Dodd
- Cancer Biology Graduate Program.,Medical Scientist Training Program.,Holden Comprehensive Cancer Center.,Department of Internal Medicine.,Molecular Medicine Graduate Program
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6
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Brockman QR, Scherer A, McGivney GR, Gutierrez WR, Voigt AP, Isaacson AL, Laverty EA, Roughton G, Knepper-Adrian V, Darbro B, Tanas MR, Stipp CS, Dodd RD. PRC2 loss drives MPNST metastasis and matrix remodeling. JCI Insight 2022; 7:157502. [PMID: 36066973 DOI: 10.1172/jci.insight.157502] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The histone methyltransferase PRC2 plays a complex role in cancer. Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas with frequent loss-of-function mutations in PRC2 that are associated with poor outcome. Here, we identify a critical role for PRC2 loss in driving MPNST metastasis. PRC2-dependent metastatic phenotypes include increased collagen-dependent invasion, upregulation of matrix remodeling enzymes, and elevated lung metastasis in orthotopic mouse models. Furthermore, clinical sample analysis determines that PRC2 loss correlates with metastatic disease, increased fibrosis, and decreased survival in MPNST patients. These results may have broad implications for PRC2 function across multiple cancers and provide a strong rationale for investigating potential therapies targeting ECM remodeling enzymes and tumor fibrosis to improve outcomes in MPNST patients.
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Affiliation(s)
- Qierra R Brockman
- Department of Internal Medicine, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Amanda Scherer
- Department of Internal Medicine, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Gavin R McGivney
- Cancer Biology Graduate Program, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Wade R Gutierrez
- The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Andrew P Voigt
- Department of Ophthalmology and Visual Science, University of Iowa, Iowa City, United States of America
| | - Alexandra L Isaacson
- Department of Pathology, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Emily A Laverty
- Department of Internal Medicine, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Grace Roughton
- Department of Internal Medicine, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Vickie Knepper-Adrian
- Department of Internal Medicine, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Benjamin Darbro
- Department of Pediatrics, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Munir R Tanas
- Department of Pathology, The University of Iowa Carver College of Medicine, Iowa City, United States of America
| | - Christopher S Stipp
- Department of Biology, University of Iowa, Iowa City, United States of America
| | - Rebecca D Dodd
- Department of Internal Medicine, The University of Iowa Carver College of Medicine, Iowa City, United States of America
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7
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Kohlmeyer JL, Kaemmer CA, Lingo JJ, Voigt E, Leidinger MR, McGivney GR, Scherer A, Koppenhafer SL, Gordon DJ, Breheny P, Meyerholz DK, Tanas MR, Dodd RD, Quelle DE. Oncogenic RABL6A promotes NF1-associated MPNST progression in vivo. Neurooncol Adv 2022; 4:vdac047. [PMID: 35571990 PMCID: PMC9092646 DOI: 10.1093/noajnl/vdac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas with complex molecular and genetic alterations. Powerful tumor suppressors CDKN2A and TP53 are commonly disrupted along with NF1, a gene that encodes a negative regulator of Ras. Many additional factors have been implicated in MPNST pathogenesis. A greater understanding of critical drivers of MPNSTs is needed to guide more informed targeted therapies for patients. RABL6A is a newly identified driver of MPNST cell survival and proliferation whose in vivo role in the disease is unknown. Methods Using CRISPR-Cas9 targeting of Nf1 + Cdkn2a or Nf1 + Tp53 in the mouse sciatic nerve to form de novo MPNSTs, we investigated the biological significance of RABL6A in MPNST development. Terminal tumors were evaluated by western blot, qRT-PCR, and immunohistochemistry. Results Mice lacking Rabl6 displayed slower tumor progression and extended survival relative to wildtype animals in both genetic contexts. YAP oncogenic activity was selectively downregulated in Rabl6-null, Nf1 + Cdkn2a lesions whereas loss of RABL6A caused upregulation of the CDK inhibitor, p27, in all tumors. Paradoxically, both models displayed elevated Myc protein and Ki67 staining in terminal tumors lacking RABL6A. In Nf1 + p53 tumors, cellular atypia and polyploidy were evident and increased by RABL6A loss. Conclusions These findings demonstrate that RABL6A is required for optimal progression of NF1 mutant MPNSTs in vivo in both Cdkn2a and p53 inactivated settings. However, sustained RABL6A loss may provide selective pressure for unwanted alterations, including increased Myc, cellular atypia, and polyploidy, that ultimately promote a hyper-proliferative tumor phenotype akin to drug-resistant lesions.
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Affiliation(s)
- Jordan L Kohlmeyer
- Molecular Medicine Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- The Department of Neuroscience and Pharmacology, The University of Iowa, Iowa City, Iowa, USA
| | - Courtney A Kaemmer
- The Department of Neuroscience and Pharmacology, The University of Iowa, Iowa City, Iowa, USA
| | - Joshua J Lingo
- Cancer Biology Graduate Program, The University of Iowa, Iowa City, Iowa, USA
| | - Ellen Voigt
- Cancer Biology Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- Medical Scientist Training Program, The University of Iowa, Iowa City, Iowa, USA
| | - Mariah R Leidinger
- The Department of Pathology, The University of Iowa, Iowa City, Iowa, USA
| | - Gavin R McGivney
- Cancer Biology Graduate Program, The University of Iowa, Iowa City, Iowa, USA
| | - Amanda Scherer
- The Department of Internal Medicine, The University of Iowa, Iowa City, Iowa, USA
| | | | - David J Gordon
- Molecular Medicine Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- Cancer Biology Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- Medical Scientist Training Program, The University of Iowa, Iowa City, Iowa, USA
- The Department of Pediatrics, The University of Iowa, Iowa City, Iowa, USA
- The Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, Iowa, USA
| | - Patrick Breheny
- Department of Biostatistics, The University of Iowa, Iowa City, Iowa, USA
- The Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, Iowa, USA
| | - David K Meyerholz
- The Department of Pathology, The University of Iowa, Iowa City, Iowa, USA
| | - Munir R Tanas
- Molecular Medicine Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- Cancer Biology Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- The Department of Pathology, The University of Iowa, Iowa City, Iowa, USA
- The Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, Iowa, USA
| | - Rebecca D Dodd
- Molecular Medicine Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- Cancer Biology Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- Medical Scientist Training Program, The University of Iowa, Iowa City, Iowa, USA
- The Department of Internal Medicine, The University of Iowa, Iowa City, Iowa, USA
- The Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, Iowa, USA
| | - Dawn E Quelle
- Molecular Medicine Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- Cancer Biology Graduate Program, The University of Iowa, Iowa City, Iowa, USA
- Medical Scientist Training Program, The University of Iowa, Iowa City, Iowa, USA
- The Department of Neuroscience and Pharmacology, The University of Iowa, Iowa City, Iowa, USA
- The Department of Pathology, The University of Iowa, Iowa City, Iowa, USA
- The Holden Comprehensive Cancer Center, The University of Iowa, Iowa City, Iowa, USA
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Gutierrez WR, Scherer A, McGivney GR, Brockman QR, Knepper-Adrian V, Laverty EA, Roughton GA, Dodd RD. Divergent immune landscapes of primary and syngeneic Kras-driven mouse tumor models. Sci Rep 2021; 11:1098. [PMID: 33441747 PMCID: PMC7806664 DOI: 10.1038/s41598-020-80216-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/06/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022] Open
Abstract
Immune cells play critical functions in cancer, and mice with intact immune systems are vital to understanding tumor immunology. Both genetically engineered mouse models (GEMMs) and syngeneic cell transplant approaches use immunocompetent mice to define immune-dependent events in tumor development and progression. Due to their rapid and reproducible nature, there is expanded interest in developing new syngeneic tools from established primary tumor models. However, few studies have examined the extent that syngeneic tumors reflect the immune profile of their originating primary models. Here, we describe comprehensive immunophenotyping of two well-established GEMMs and four new syngeneic models derived from these parental primary tumors. To our knowledge, this is the first systematic analysis comparing immune landscapes between primary and orthotopic syngeneic tumors. These models all use the same well-defined human-relevant driver mutations, arise at identical orthotopic locations, and are generated in mice of the same background strain. This allows for a direct and focused comparison of tumor immune landscapes in carefully controlled mouse models. We identify key differences between the immune infiltrate of GEMM models and their corresponding syngeneic tumors. Most notable is the divergence of T cell populations, with different proportions of CD8+ T cells and regulatory T cells across several models. We also observe immune variation across syngeneic tumors derived from the same primary model. These findings highlight the importance of immune variance across mouse modeling approaches, which has strong implications for the design of rigorous and reproducible translational studies.
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Grants
- P30 CA086862 NCI NIH HHS
- T32 GM007337 NIGMS NIH HHS
- T32 GM067795 NIGMS NIH HHS
- Pharmacology Training Grant, University of Iowa, United States
- Medical Scientist Training Program, University of Iowa, United States
- Holden Comprehensive Cancer Center, University of Iowa, United States
- Sarcoma Multidisciplinary Oncology Group, University of Iowa, United States
- NCI Core Grant, Holden Comprehensive Cancer Center, University of Iowa, United States
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Affiliation(s)
- Wade R Gutierrez
- Cancer Biology Graduate Program, Carver College of Medicine, University of Iowa, 285 Newton Rd, 3269C CBRB, Iowa City, IA, 52246, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Amanda Scherer
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Gavin R McGivney
- Cancer Biology Graduate Program, Carver College of Medicine, University of Iowa, 285 Newton Rd, 3269C CBRB, Iowa City, IA, 52246, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
| | - Qierra R Brockman
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, IA, USA
| | | | - Emily A Laverty
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Grace A Roughton
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Rebecca D Dodd
- Cancer Biology Graduate Program, Carver College of Medicine, University of Iowa, 285 Newton Rd, 3269C CBRB, Iowa City, IA, 52246, USA.
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA.
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA.
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, IA, USA.
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.
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Dodd RD, Scherer A, Huang W, McGivney GR, Gutierrez WR, Laverty EA, Ashcraft KA, Stephens VR, Yousefpour P, Saha S, Knepper-Adrian V, Floyd W, Chen M, Ma Y, Mastria EM, Cardona DM, Eward WC, Chilkoti A, Kirsch DG. Tumor Subtype Determines Therapeutic Response to Chimeric Polypeptide Nanoparticle-based Chemotherapy in Pten-deleted Mouse Models of Sarcoma. Clin Cancer Res 2020; 26:5036-5047. [PMID: 32718998 PMCID: PMC7641033 DOI: 10.1158/1078-0432.ccr-19-2597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/07/2019] [Revised: 04/07/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Nanoparticle-encapsulated drug formulations can improve responses to conventional chemotherapy by increasing drug retention within the tumor and by promoting a more effective antitumor immune response than free drug. New drug delivery modalities are needed in sarcomas because they are often chemoresistant cancers, but the rarity of sarcomas and the complexity of diverse subtypes makes it challenging to investigate novel drug formulations. EXPERIMENTAL DESIGN New drug formulations can be tested in animal models of sarcomas where the therapeutic response of different formulations can be compared using mice with identical tumor-initiating mutations. Here, using Cre/loxP and CRISPR/Cas9 techniques, we generated two distinct mouse models of Pten-deleted soft-tissue sarcoma: malignant peripheral nerve sheath tumor (MPNST) and undifferentiated pleomorphic sarcoma (UPS). We used these models to test the efficacy of chimeric polypeptide doxorubicin (CP-Dox), a nanoscale micelle formulation, in comparison with free doxorubicin. RESULTS The CP-Dox formulation was superior to free doxorubicin in MPNST models. However, in UPS tumors, CP-Dox did not improve survival in comparison with free doxorubicin. While CP-Dox treatment resulted in elevated intratumoral doxorubicin concentrations in MPNSTs, this increase was absent in UPS tumors. In addition, elevation of CD8+ T cells was observed exclusively in CP-Dox-treated MPNSTs, although these cells were not required for full efficacy of the CP nanoparticle-based chemotherapy. CONCLUSIONS These results have important implications for treating sarcomas with nanoparticle-encapsulated chemotherapy by highlighting the tumor subtype-dependent nature of therapeutic response.
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Affiliation(s)
- Rebecca D Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa.
| | - Amanda Scherer
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Wesley Huang
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
| | - Gavin R McGivney
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Wade R Gutierrez
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
- Medical Scientist Training Program, University of Iowa, Iowa City, Iowa
| | - Emily A Laverty
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Kathleen A Ashcraft
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
| | | | - Parisa Yousefpour
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Soumen Saha
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | | | - Warren Floyd
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina
| | - Mark Chen
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina
| | - Yan Ma
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
| | - Eric M Mastria
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina
| | - Diana M Cardona
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - William C Eward
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, North Carolina
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - David G Kirsch
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina.
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina
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Scherer A, Stephens VR, McGivney GR, Gutierrez WR, Laverty EA, Knepper-Adrian V, Dodd RD. Distinct Tumor Microenvironments Are a Defining Feature of Strain-Specific CRISPR/Cas9-Induced MPNSTs. Genes (Basel) 2020; 11:genes11050583. [PMID: 32456131 PMCID: PMC7288323 DOI: 10.3390/genes11050583] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 05/05/2020] [Revised: 05/18/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022] Open
Abstract
The tumor microenvironment plays important roles in cancer biology, but genetic backgrounds of mouse models can complicate interpretation of tumor phenotypes. A deeper understanding of strain-dependent influences on the tumor microenvironment of genetically-identical tumors is critical to exploring genotype–phenotype relationships, but these interactions can be difficult to identify using traditional Cre/loxP approaches. Here, we use somatic CRISPR/Cas9 tumorigenesis approaches to determine the impact of mouse background on the biology of genetically-identical malignant peripheral nerve sheath tumors (MPNSTs) in four commonly-used inbred strains. To our knowledge, this is the first study to systematically evaluate the impact of host strain on CRISPR/Cas9-generated mouse models. Our data identify multiple strain-dependent phenotypes, including changes in tumor onset and the immune microenvironment. While BALB/c mice develop MPNSTs earlier than other strains, similar tumor onset is observed in C57BL/6, 129X1 and 129/SvJae mice. Indel pattern analysis demonstrates that indel frequency, type and size are similar across all genetic backgrounds. Gene expression and IHC analysis identify multiple strain-dependent differences in CD4+ T cell infiltration and myeloid cell populations, including M2 macrophages and mast cells. These data highlight important strain-specific phenotypes of genomically-matched MPNSTs that have implications for the design of future studies using similar in vivo gene editing approaches.
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Affiliation(s)
- Amanda Scherer
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.S.); (V.R.S.); (E.A.L.); (V.K.-A.)
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA; (G.R.M.); (W.R.G.)
| | - Victoria R. Stephens
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.S.); (V.R.S.); (E.A.L.); (V.K.-A.)
- PREP program, University of Iowa, Iowa City, IA 52242, USA
| | - Gavin R. McGivney
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA; (G.R.M.); (W.R.G.)
- Cancer Biology Graduate Program, University of Iowa, Iowa City, IA 52242, USA
| | - Wade R. Gutierrez
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA; (G.R.M.); (W.R.G.)
- Cancer Biology Graduate Program, University of Iowa, Iowa City, IA 52242, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA 52242, USA
| | - Emily A. Laverty
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.S.); (V.R.S.); (E.A.L.); (V.K.-A.)
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA; (G.R.M.); (W.R.G.)
| | - Vickie Knepper-Adrian
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.S.); (V.R.S.); (E.A.L.); (V.K.-A.)
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA; (G.R.M.); (W.R.G.)
| | - Rebecca D. Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.S.); (V.R.S.); (E.A.L.); (V.K.-A.)
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA; (G.R.M.); (W.R.G.)
- Correspondence: ; Tel.: +1-319-335-4962
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