1
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Wang C, Ma A, Li Y, McNutt ME, Zhang S, Zhu J, Hoyd R, Wheeler CE, Robinson LA, Chan CH, Zakharia Y, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Singer EA, Ikeguchi AP, McCarter MD, Denko N, Tinoco G, Husain M, Jin N, Osman AE, Eljilany I, Tan AC, Coleman SS, Denko L, Riedlinger G, Schneider BP, Spakowicz D, Ma Q. A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset. Cancer Res Commun 2024; 4:293-302. [PMID: 38259095 PMCID: PMC10840455 DOI: 10.1158/2767-9764.crc-23-0213] [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] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/26/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024]
Abstract
Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10%-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, microbial graph attention (MEGA), to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of nine cancer centers in the Oncology Research Information Exchange Network. This package has three unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2,704 tumor RNA sequencing samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors. SIGNIFICANCE Studying the tumor microbiome in high-throughput sequencing data is challenging because of the extremely sparse data matrices, heterogeneity, and high likelihood of contamination. We present a new deep learning tool, MEGA, to refine the organisms that interact with tumors.
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Affiliation(s)
- Cankun Wang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Yingjie Li
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Megan E. McNutt
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Shiqi Zhang
- Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, Ohio
| | - Jiangjiang Zhu
- Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, Ohio
| | - Rebecca Hoyd
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Caroline E. Wheeler
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Lary A. Robinson
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Carlos H.F. Chan
- University of Iowa, Holden Comprehensive Cancer Center, Iowa City, Iowa
| | - Yousef Zakharia
- Division of Oncology, Hematology and Blood & Marrow Transplantation, University of Iowa, Holden Comprehensive Cancer Center, Iowa City, Iowa
| | - Rebecca D. Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Cornelia M. Ulrich
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Sheetal Hardikar
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Ahmad A. Tarhini
- Departments of Cutaneous Oncology and Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Eric A. Singer
- Department of Urologic Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Alexandra P. Ikeguchi
- Department of Hematology/Oncology, Stephenson Cancer Center of University of Oklahoma, Oklahoma City, Oklahoma
| | - Martin D. McCarter
- Department of Surgery, University of Colorado School of Medicine, Aurora, Colorado
| | - Nicholas Denko
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Gabriel Tinoco
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Marium Husain
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Ning Jin
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Afaf E.G. Osman
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Islam Eljilany
- Clinical Science Lab – Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Aik Choon Tan
- Departments of Oncological Science and Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Samuel S. Coleman
- Departments of Oncological Science and Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Louis Denko
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Gregory Riedlinger
- Department of Precision Medicine, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Bryan P. Schneider
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, Indiana
| | - Daniel Spakowicz
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, Ohio
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
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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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3
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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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4
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Wheeler CE, Coleman SS, Hoyd R, Denko L, Chan CHF, Churchman ML, Denko N, Dodd RD, Eljilany I, Hardikar S, Husain M, Ikeguchi AP, Jin N, Ma Q, McCarter MD, Osman AEG, Robinson LA, Singer EA, Tinoco G, Ulrich CM, Zakharia Y, Spakowicz D, Tarhini AA, Tan AC. The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors. bioRxiv 2023:2023.05.24.542123. [PMID: 37292921 PMCID: PMC10245822 DOI: 10.1101/2023.05.24.542123] [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: 06/10/2023]
Abstract
Emerging evidence supports the important role of the tumor microbiome in oncogenesis, cancer immune phenotype, cancer progression, and treatment outcomes in many malignancies. In this study, we investigated the metastatic melanoma tumor microbiome and potential roles in association with clinical outcomes, such as survival, in patients with metastatic disease treated with immune checkpoint inhibitors (ICIs). Baseline tumor samples were collected from 71 patients with metastatic melanoma before treatment with ICIs. Bulk RNA-seq was conducted on the formalin-fixed paraffin-embedded (FFPE) tumor samples. Durable clinical benefit (primary clinical endpoint) following ICIs was defined as overall survival ≥24 months and no change to the primary drug regimen (responders). We processed RNA-seq reads to carefully identify exogenous sequences using the {exotic} tool. The 71 patients with metastatic melanoma ranged in age from 24 to 83 years, 59% were male, and 55% survived >24 months following the initiation of ICI treatment. Exogenous taxa were identified in the tumor RNA-seq, including bacteria, fungi, and viruses. We found differences in gene expression and microbe abundances in immunotherapy responsive versus non-responsive tumors. Responders showed significant enrichment of several microbes including Fusobacterium nucleatum, and non-responders showed enrichment of fungi, as well as several bacteria. These microbes correlated with immune-related gene expression signatures. Finally, we found that models for predicting prolonged survival with immunotherapy using both microbe abundances and gene expression outperformed models using either dataset alone. Our findings warrant further investigation and potentially support therapeutic strategies to modify the tumor microbiome in order to improve treatment outcomes with ICIs.
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Affiliation(s)
- Caroline E Wheeler
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Samuel S Coleman
- Departments of Oncological Science and Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Rebecca Hoyd
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Louis Denko
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Carlos H F Chan
- University of Iowa, Holden Comprehensive Cancer Center, Iowa City, IA, USA
| | | | - Nicholas Denko
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Rebecca D Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Islam Eljilany
- Clinical Science Lab -- Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Sheetal Hardikar
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Marium Husain
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Alexandra P Ikeguchi
- Department of Hematology/Oncology, Stephenson Cancer Center of University of Oklahoma, Oklahoma City, OK, USA
| | - Ning Jin
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Martin D McCarter
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Afaf E G Osman
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Lary A Robinson
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric A Singer
- Department of Urologic Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Gabriel Tinoco
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Cornelia M Ulrich
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Yousef Zakharia
- Division of Oncology, Hematology and Blood & Marrow Transplantation, University of Iowa, Holden Comprehensive Cancer Center, Iowa City, IA, USA
| | - Daniel Spakowicz
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Ahmad A Tarhini
- Departments of Cutaneous Oncology and Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Aik Choon Tan
- Departments of Oncological Science and Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
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5
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Wang C, Ma A, McNutt ME, Hoyd R, Wheeler CE, Robinson LA, Chan CH, Zakharia Y, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Singer EA, Ikeguchi AP, McCarter MD, Denko N, Tinoco G, Husain M, Jin N, Osman AE, Eljilany I, Tan AC, Coleman SS, Denko L, Riedlinger G, Schneider BP, Spakowicz D, Ma Q. A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset. bioRxiv 2023:2023.05.24.541982. [PMID: 37292990 PMCID: PMC10245834 DOI: 10.1101/2023.05.24.541982] [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: 06/10/2023]
Abstract
Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10-20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, MEGA, to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of 9 cancer centers in the Oncology Research Information Exchange Network (ORIEN). This package has 3 unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2704 tumor RNA-seq samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.
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Affiliation(s)
- Cankun Wang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Anjun Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus; OH, USA
| | - Megan E. McNutt
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Rebecca Hoyd
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Caroline E. Wheeler
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Lary A. Robinson
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Carlos H.F. Chan
- University of Iowa, Holden Comprehensive Cancer Center, Iowa City, IA, USA
| | - Yousef Zakharia
- Division of Oncology, Hematology and Blood & Marrow Transplantation, University of Iowa, Holden Comprehensive Cancer Center, Iowa City, IA, USA
| | - Rebecca D. Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Cornelia M. Ulrich
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Sheetal Hardikar
- Department of Population Health Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | - Ahmad A. Tarhini
- Departments of Cutaneous Oncology and Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Eric A. Singer
- Department of Urologic Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Alexandra P. Ikeguchi
- Department of Hematology/Oncology, Stephenson Cancer Center of University of Oklahoma, Oklahoma City, OK, USA
| | - Martin D. McCarter
- Department of Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nicholas Denko
- Department of Radiation Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Gabriel Tinoco
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Marium Husain
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Ning Jin
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Afaf E.G. Osman
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Islam Eljilany
- Clinical Science Lab -- Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Aik Choon Tan
- Departments of Oncological Science and Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Samuel S. Coleman
- Departments of Oncological Science and Biomedical Informatics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Louis Denko
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus; OH, USA
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Gregory Riedlinger
- Department of Precision Medicine, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Bryan P. Schneider
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
| | - Daniel Spakowicz
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus; OH, USA
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus; OH, USA
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6
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Bi J, Witt E, Voltarelli VA, Feig VR, Venkatachalam V, Boyce H, McGovern M, Gutierrez WR, Rytlewski JD, Bowman KR, Rhodes AC, Cook AN, Muller BN, Smith MG, Ramos AR, Panchal H, Dodd RD, Henry MD, Mailloux A, Traverso G, Otterbein LE, Byrne JD. Low-Cost, High-Pressure-Synthesized Oxygen-Entrapping Materials to Improve Treatment of Solid Tumors. Adv Sci (Weinh) 2023; 10:e2205995. [PMID: 36727291 PMCID: PMC10074083 DOI: 10.1002/advs.202205995] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/30/2022] [Indexed: 05/10/2023]
Abstract
Tumor hypoxia drives resistance to many cancer therapies, including radiotherapy and chemotherapy. Methods that increase tumor oxygen pressures, such as hyperbaric oxygen therapy and microbubble infusion, are utilized to improve the responses to current standard-of-care therapies. However, key obstacles remain, in particular delivery of oxygen at the appropriate dose and with optimal pharmacokinetics. Toward overcoming these hurdles, gas-entrapping materials (GeMs) that are capable of tunable oxygen release are formulated. It is shown that injection or implantation of these materials into tumors can mitigate tumor hypoxia by delivering oxygen locally and that these GeMs enhance responsiveness to radiation and chemotherapy in multiple tumor types. This paper also demonstrates, by comparing an oxygen (O2 )-GeM to a sham GeM, that the former generates an antitumorigenic and immunogenic tumor microenvironment in malignant peripheral nerve sheath tumors. Collectively the results indicate that the use of O2 -GeMs is promising as an adjunctive strategy for the treatment of solid tumors.
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7
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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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8
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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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9
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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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10
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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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11
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Meyerholz DK, Leidinger MR, Goeken JA, Businga TR, Akers A, Vizuett S, Kaemmer CA, Kohlmeyer JL, Dodd RD, Quelle DE. Utility of CD138/syndecan-1 immunohistochemistry for localization of plasmacytes is tissue-dependent in B6 mice. BMC Res Notes 2022; 15:219. [PMID: 35752869 PMCID: PMC9233769 DOI: 10.1186/s13104-022-06100-5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Objective Inflammation is present in many diseases and identification of immune cell infiltration is a common assessment. CD138 (syndecan-1) is a recommended immunohistochemical marker for human plasmacytes although it is also expressed in various epithelia and tumors. Similarly, CD138 is a marker for murine plasmacytes, but its tissue immunostaining is not well-defined. Endogenous CD138 expression is an important confounding factor when evaluating plasmacyte infiltration. We studied two plasmacyte markers (CD138 and Kappa light chains) for endogenous immunostaining in five organs and one tumor from B6 mice. Results Plasmacytes in Peyer’s patches were positive for CD138 and Kappa markers without endogenous immunostaining. Endogenous CD138 immunostaining was widespread in liver, kidney, lung and a malignant peripheral nerve sheath tumor (MPNST) versus regionalized immunostaining in skin and small intestine wall. Endogenous Kappa immunostaining was absent in all tissues except for plasmacytes. Tissues with widespread endogenous CD138 immunostaining were contrasted by absence of endogenous Kappa immunostaining. Here, plasmacytes would not be distinguished by CD138, but would be obvious by Kappa immunostaining. Our study suggests that utility of immunostaining for plasmacytes by CD138 is tissue dependent in mice. Additionally, Kappa immunostaining may be a useful alternative in mouse tissues with confounding endogenous CD138 immunostaining.
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Affiliation(s)
| | | | - J Adam Goeken
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | | | - Allison Akers
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | | | - Courtney A Kaemmer
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA, USA
| | | | - Rebecca D Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Dawn E Quelle
- Department of Pathology, University of Iowa, Iowa City, IA, USA.,Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA, USA
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12
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Spakowicz D, Hoyd R, Wheeler CE, Zakharia Y, Dodd RD, Ose J, Hardikar S, Tarhini AA, Robinson LA, Singer EA, Carpten JD, Chan CHF, Ikeguchi A, Ulrich CM, McCarter M. Pan-cancer analysis of exogenous (microbial) sequences in tumor transcriptome data from the ORIEN consortium and their association with cancer and tumor microenvironment. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3113] [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: 11/20/2022] Open
Abstract
3113 Background: The tumor microbiome holds great potential for its ability to characterize various aspects of cancer biology and as a target for rational manipulation. For many cancer types, little is known about the role of microbes and in what contexts they affect clinical outcomes. Non-human (i.e. exogenous) sequences can be observed in low abundance within high throughput sequencing data of tumors. Here, we describe a collaboration among members of The Oncology Research Information Exchange Network (ORIEN) to leverage tumor biopsy RNAseq data collected under a shared protocol and generated at a single site to better understand the tumor microbiome, its association with prognostic features of the tumor microenvironment (TME) such as hypoxia, and how it may be used to improve clinical outcomes. Methods: Tumor RNAseq samples from 10 primary source locations including the tissues colon, lung, pancreas, and skin from ORIEN and similar cancers from The Cancer Genome Atlas (TCGA) were processed through the exoTIC (exogenous sequencing in tumors and immune cells) pipeline to identify and count exogenous sequences, filter contaminants, and normalize across datasets. Gene expression signatures of the TME, such as hypoxia, were calculated using ‘tmesig’. Microbe relative abundances were modeled with primary tumor location and hypoxia score using a gamma-distributed generalized linear regression via the stats package in R. Results: We analyzed RNAseq data of 2892 and 2720 tumors from ORIEN and TCGA, respectively. Patients’ ages were significantly greater in the ORIEN than the TCGA dataset (62 vs 58 yo, t-test p<0.001). The ORIEN data contained more sarcoma samples than TCGA (n = 691 vs 259) with roughly equivalent numbers in other cancer types. Fewer microbes were significantly associated with the hypoxia score than with cancer type (n = 32 vs 210). This trend was observed in both the ORIEN and TCGA datasets. The largest effect sizes were observed between microbes and small cell lung cancer. Conclusions: We found microbial sequences in all ORIEN and TCGA tumor RNAseq samples tested. Cancer type showed more significant associations with microbes than a hypoxia signature. These observations merit further investigation into the interaction between microbes and the TME. [Table: see text]
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Affiliation(s)
- Daniel Spakowicz
- Division of Medical Oncology, Department of Internal Medicine & Department of Biomedical Informatics, Ohio State University, Columbus, OH
| | - Rebecca Hoyd
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH
| | - Caroline E. Wheeler
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH
| | | | | | - Jennifer Ose
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Sheetal Hardikar
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Ahmad A. Tarhini
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Lary A. Robinson
- Department of Thoracic Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Eric A. Singer
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | | | | | | | - Cornelia M Ulrich
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT
| | - Martin McCarter
- University of Colorado Comprehensive Cancer Center, Aurora, CO
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13
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Rytlewski J, Brockman QR, Dodd RD, Milhem M, Monga V. Epigenetic modulation in sensitizing metastatic sarcomas to therapies and overcoming resistance. Cancer Drug Resist 2022; 5:25-35. [PMID: 35582536 PMCID: PMC8992584 DOI: 10.20517/cdr.2021.88] [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] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/04/2021] [Accepted: 12/02/2021] [Indexed: 11/12/2022]
Abstract
Sarcomas are a class of rare malignancies of mesenchymal origin with a heterogeneous histological spectrum. They are classically associated with poor outcomes, especially once metastasized. A path to improving clinical outcomes may be made through modifying the epigenome, where a variety of sarcomas demonstrate changes that contribute to their oncogenic phenotypes. This Perspective article identifies and describes changes in the sarcoma genome, while discussing specific epigenetic changes and their effect on clinical outcomes. Clinical attempts at modulating epigenetics in sarcoma are reviewed, as well as potential implications of these studies. Epigenetic targets to reverse and delay chemotherapy resistance are discussed. Future directions with primary next steps are proposed to invigorate the current understanding of epigenetic biomarkers to enact targeted therapies to epigenetic phenotypes of sarcoma subtypes. Modifications to prior studies, as well as proposed clinical steps, are also addressed.
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Affiliation(s)
- Jeff Rytlewski
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Qierra R Brockman
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Rebecca D Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
| | - Mohammed Milhem
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
| | - Varun Monga
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242, USA
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14
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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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15
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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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16
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Kohlmeyer JL, Gordon DJ, Tanas MR, Dodd RD, Monga V, Darbro BW, Quelle DE. Combination therapies for MPNSTs targeting RABL6A-RB1 signaling. Oncotarget 2021; 12:10-14. [PMID: 33456709 PMCID: PMC7800773 DOI: 10.18632/oncotarget.27862] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 01/15/2023] Open
Abstract
Precision medicine relies on a detailed molecular understanding of disease pathogenesis. Here, we consider urgently needed therapeutic options for malignant peripheral nerve sheath tumors (MPNSTs) based on emerging insights into druggable pathway alterations found to drive this deadly cancer. Recent observations demonstrate an essential role for an oncogenic GTPase, RABL6A, in promoting MPNST progression through hyperactivation of cyclin-dependent kinases (CDKs) and inactivation of the retinoblastoma (RB1) tumor suppressor. Monotherapies with CDK4/6 inhibitors have shown limited efficacy and durability in pre-clinical studies of MPNSTs and in clinical studies of other tumors. Therefore, we discuss the rationale and clinical benefits of inhibiting multiple RABL6A effectors, particularly CDK4/6 and MEK kinases, in targeted combination therapies suitable for MPNSTs and other Ras-driven malignancies.
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Affiliation(s)
- Jordan L Kohlmeyer
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, Iowa, USA.,Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, Iowa, USA
| | - David J Gordon
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Munir R Tanas
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, Iowa, USA.,Department of Pathology, University of Iowa, Iowa City, Iowa, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Rebecca D Dodd
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, Iowa, USA.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Varun Monga
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Benjamin W Darbro
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Dawn E Quelle
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, Iowa, USA.,Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, Iowa, USA.,Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
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17
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Yong C, Moose DL, Bannick N, Gutierrez WR, Vanneste M, Svensson R, Breheny P, Brown JA, Dodd RD, Cohen MB, Henry MD. Locally invasive, castrate-resistant prostate cancer in a Pten/Trp53 double knockout mouse model of prostate cancer monitored with non-invasive bioluminescent imaging. PLoS One 2020; 15:e0232807. [PMID: 32986721 PMCID: PMC7521703 DOI: 10.1371/journal.pone.0232807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/10/2020] [Indexed: 11/18/2022] Open
Abstract
Here we have improved an existing mouse model of prostate cancer based on prostate-specific deletion of Pten and Trp53 by incorporating a Cre-activatable luciferase reporter. By coupling the deletion of those genes to the activation of a luciferase reporter, we were able to monitor tumor burden non-invasively over time. We show that, consistent with previous reports, deletion of both Pten and Trp53 on a C57BL/6 background accelerates tumor growth and results in both the loss of androgen receptor expression and castrate resistant tumors as compared with loss of Pten alone. Loss of Trp53 results in the development of sarcomatoid histology and the expression of markers of epithelial-to-mesenchymal transition Zeb1 and vimentin, with kinetics and penetrance dependent on whether one or both alleles of Trp53 were deleted. Homozygous deletion of Trp53 and Pten resulted in uniformly lethal disease by 25 weeks. While we were able to detect locally invasive disease in the peritoneal cavity in aggressive tumors from the double knockout mice, we were unable to detect lymphatic or hematogenous metastatic disease in lymph nodes or at distant sites.
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Affiliation(s)
- Courtney Yong
- Department of Urology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Devon L Moose
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Nadine Bannick
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Wade R Gutierrez
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America.,Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Marion Vanneste
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Robert Svensson
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Patrick Breheny
- Department of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, United States of America
| | - James A Brown
- Department of Urology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
| | - Rebecca D Dodd
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States of America
| | - Michael B Cohen
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Michael D Henry
- Department of Urology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America.,Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, United States of America.,Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America.,Department of Radiation Oncology, Carver College of Medicine, University of Iowa, Iowa City, IA, United States of America
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18
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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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19
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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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20
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Kohlmeyer JL, Kaemmer CA, Pulliam C, Maharjan CK, Samayoa AM, Major HJ, Cornick KE, Knepper-Adrian V, Khanna R, Sieren JC, Leidinger MR, Meyerholz DK, Zamba KD, Weimer JM, Dodd RD, Darbro BW, Tanas MR, Quelle DE. RABL6A Is an Essential Driver of MPNSTs that Negatively Regulates the RB1 Pathway and Sensitizes Tumor Cells to CDK4/6 Inhibitors. Clin Cancer Res 2020; 26:2997-3011. [PMID: 32086342 DOI: 10.1158/1078-0432.ccr-19-2706] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/20/2019] [Accepted: 02/18/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Malignant peripheral nerve sheath tumors (MPNST) are deadly sarcomas that lack effective therapies. In most MPNSTs, the retinoblastoma (RB1) tumor suppressor is disabled by hyperactivation of cyclin-dependent kinases (CDK), commonly through loss of CDK-inhibitory proteins such as p27(Kip1). RABL6A is an inhibitor of RB1 whose role in MPNSTs is unknown. To gain insight into MPNST development and establish new treatment options, we investigated RABL6A-RB1 signaling and CDK inhibitor-based therapy in MPNSTs. EXPERIMENTAL DESIGN We examined patient-matched MPNSTs and precursor lesions by RNA sequencing (RNA-Seq) and IHC. Molecular and biological effects of silencing RABL6A and/or p27 in MPNST lines and normal human Schwann cells were determined. Tumor-suppressive effects of CDK inhibitors were measured in MPNST cells and orthotopic tumors. RESULTS RABL6A was dramatically upregulated in human MPNSTs compared with precursor lesions, which correlated inversely with p27 levels. Silencing RABL6A caused MPNST cell death and G1 arrest that coincided with p27 upregulation, CDK downregulation, and RB1 activation. The growth-suppressive effects of RABL6A loss, and its regulation of RB1, were largely rescued by p27 depletion. Importantly, reactivation of RB1 using a CDK4/6 inhibitor (palbociclib) killed MPNST cells in vitro in an RABL6A-dependent manner and suppressed MPNST growth in vivo. Low-dose combination of drugs targeting multiple RB1 kinases (CDK4/6, CDK2) had enhanced antitumorigenic activity associated with potential MPNST cell redifferentiation. CONCLUSIONS RABL6A is a new driver of MPNST pathogenesis that acts in part through p27-RB1 inactivation. Our results suggest RB1 targeted therapy with multiple pathway drugs may effectively treat MPNSTs.
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Affiliation(s)
- Jordan L Kohlmeyer
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, Iowa.,The Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, Iowa
| | - Courtney A Kaemmer
- The Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, Iowa
| | - Casey Pulliam
- Human Toxicology Graduate Program, University of Iowa, Iowa City, Iowa
| | - Chandra K Maharjan
- The Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, Iowa
| | | | - Heather J Major
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
| | | | | | - Rajesh Khanna
- Department of Pharmacology, University of Arizona, Tucson, Arizona
| | | | | | | | - K D Zamba
- Department of Biostatistics, University of Iowa, Iowa City, Iowa
| | - Jill M Weimer
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, South Dakota
| | - Rebecca D Dodd
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, Iowa.,Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | | | - Munir R Tanas
- Department of Pathology, University of Iowa, Iowa City, Iowa
| | - Dawn E Quelle
- Molecular Medicine Graduate Program, University of Iowa, Iowa City, Iowa. .,The Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, Iowa.,Department of Pathology, University of Iowa, Iowa City, Iowa
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21
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White KA, Swier VJ, Cain JT, Kohlmeyer JL, Meyerholz DK, Tanas MR, Uthoff J, Hammond E, Li H, Rohret FA, Goeken A, Chan CH, Leidinger MR, Umesalma S, Wallace MR, Dodd RD, Panzer K, Tang AH, Darbro BW, Moutal A, Cai S, Li W, Bellampalli SS, Khanna R, Rogers CS, Sieren JC, Quelle DE, Weimer JM. A porcine model of neurofibromatosis type 1 that mimics the human disease. JCI Insight 2018; 3:120402. [PMID: 29925695 DOI: 10.1172/jci.insight.120402] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 02/08/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022] Open
Abstract
Loss of the NF1 tumor suppressor gene causes the autosomal dominant condition, neurofibromatosis type 1 (NF1). Children and adults with NF1 suffer from pathologies including benign and malignant tumors to cognitive deficits, seizures, growth abnormalities, and peripheral neuropathies. NF1 encodes neurofibromin, a Ras-GTPase activating protein, and NF1 mutations result in hyperactivated Ras signaling in patients. Existing NF1 mutant mice mimic individual aspects of NF1, but none comprehensively models the disease. We describe a potentially novel Yucatan miniswine model bearing a heterozygotic mutation in NF1 (exon 42 deletion) orthologous to a mutation found in NF1 patients. NF1+/ex42del miniswine phenocopy the wide range of manifestations seen in NF1 patients, including café au lait spots, neurofibromas, axillary freckling, and neurological defects in learning and memory. Molecular analyses verified reduced neurofibromin expression in swine NF1+/ex42del fibroblasts, as well as hyperactivation of Ras, as measured by increased expression of its downstream effectors, phosphorylated ERK1/2, SIAH, and the checkpoint regulators p53 and p21. Consistent with altered pain signaling in NF1, dysregulation of calcium and sodium channels was observed in dorsal root ganglia expressing mutant NF1. Thus, these NF1+/ex42del miniswine recapitulate the disease and provide a unique, much-needed tool to advance the study and treatment of NF1.
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Affiliation(s)
- Katherine A White
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Vicki J Swier
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Jacob T Cain
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, South Dakota, USA
| | | | | | | | - Johanna Uthoff
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,Department of Biomedical Engineering at the University of Iowa, Iowa City, Iowa, USA
| | - Emily Hammond
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,Department of Biomedical Engineering at the University of Iowa, Iowa City, Iowa, USA
| | - Hua Li
- Department of Molecular Genetics and Microbiology and.,University of Florida Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | | | | | - Chun-Hung Chan
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, South Dakota, USA
| | | | | | - Margaret R Wallace
- Department of Molecular Genetics and Microbiology and.,University of Florida Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | - Rebecca D Dodd
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Karin Panzer
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Amy H Tang
- Department of Microbiology and Molecular Cell Biology, Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia
| | - Benjamin W Darbro
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA.,Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Aubin Moutal
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA
| | - Song Cai
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA
| | - Wennan Li
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA
| | | | - Rajesh Khanna
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA
| | | | - Jessica C Sieren
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA.,Department of Biomedical Engineering at the University of Iowa, Iowa City, Iowa, USA.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Dawn E Quelle
- Molecular Medicine Program.,Department of Pathology, and.,Department of Pharmacology and.,Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, USA
| | - Jill M Weimer
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, South Dakota, USA.,Department of Pediatrics, Sanford School of Medicine at the University of South Dakota, Sioux Falls, South Dakota, USA
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22
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Peacock JD, Pridgeon MG, Tovar EA, Essenburg CJ, Bowman M, Madaj Z, Koeman J, Boguslawski EA, Grit J, Dodd RD, Khachaturov V, Cardona DM, Chen M, Kirsch DG, Maina F, Dono R, Winn ME, Graveel CR, Steensma MR. Genomic Status of MET Potentiates Sensitivity to MET and MEK Inhibition in NF1-Related Malignant Peripheral Nerve Sheath Tumors. Cancer Res 2018; 78:3672-3687. [PMID: 29720369 DOI: 10.1158/0008-5472.can-17-3167] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/08/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023]
Abstract
Malignant peripheral nerve sheath tumors (MPNST) are highly resistant sarcomas that occur in up to 13% of individuals with neurofibromatosis type I (NF1). Genomic analysis of longitudinally collected tumor samples in a case of MPNST disease progression revealed early hemizygous microdeletions in NF1 and TP53, with progressive amplifications of MET, HGF, and EGFR To examine the role of MET in MPNST progression, we developed mice with enhanced MET expression and Nf1 ablation (Nf1fl/ko;lox-stop-loxMETtg/+;Plp-creERTtg/+ ; referred to as NF1-MET). NF1-MET mice express a robust MPNST phenotype in the absence of additional mutations. A comparison of NF1-MET MPNSTs with MPNSTs derived from Nf1ko/+;p53R172H;Plp-creERTtg/+ (NF1-P53) and Nf1ko/+;Plp-creERTtg/+ (NF1) mice revealed unique Met, Ras, and PI3K signaling patterns. NF1-MET MPNSTs were uniformly sensitive to the highly selective MET inhibitor, capmatinib, whereas a heterogeneous response to MET inhibition was observed in NF1-P53 and NF1 MPNSTs. Combination therapy of capmatinib and the MEK inhibitor trametinib resulted in reduced response variability, enhanced suppression of tumor growth, and suppressed RAS/ERK and PI3K/AKT signaling. These results highlight the influence of concurrent genomic alterations on RAS effector signaling and therapy response to tyrosine kinase inhibitors. Moreover, these findings expand our current understanding of the role of MET signaling in MPNST progression and identify a potential therapeutic niche for NF1-related MPNSTs.Significance: Longitudinal genomic analysis reveals a positive selection for MET and HGF copy number gain early in malignant peripheral nerve sheath tumor progression. Cancer Res; 78(13); 3672-87. ©2018 AACR.
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Affiliation(s)
- Jacqueline D Peacock
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan.,College of Health Professions, Ferris State University, Big Rapids, Michigan
| | - Matthew G Pridgeon
- Spectrum Health System, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Elizabeth A Tovar
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Curt J Essenburg
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Megan Bowman
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan
| | - Julie Koeman
- Genomics Core, Van Andel Research Institute, Grand Rapids, Michigan
| | - Elissa A Boguslawski
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Jamie Grit
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Rebecca D Dodd
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Vadim Khachaturov
- Spectrum Health System, Helen DeVos Children's Hospital, Grand Rapids, Michigan
| | - Diana M Cardona
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Mark Chen
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina.,Department Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
| | - Flavio Maina
- Aix-Marseille Univ, CNRS, IBDM, Marseille, France
| | - Rosanna Dono
- Aix-Marseille Univ, CNRS, IBDM, Marseille, France
| | - Mary E Winn
- Bioinformatics and Biostatistics Core, Van Andel Research Institute, Grand Rapids, Michigan
| | - Carrie R Graveel
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan
| | - Matthew R Steensma
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan. .,Spectrum Health System, Helen DeVos Children's Hospital, Grand Rapids, Michigan.,Michigan State University College of Human Medicine, Grand Rapids, Michigan
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23
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Huang J, Chen M, Whitley MJ, Kuo HC, Xu ES, Walens A, Mowery YM, Mater DV, Eward WC, Cardona DM, Luo L, Ma Y, Lopez OM, Nelson CE, Robinson-Hamm JN, Reddy A, Dave SS, Gersbach CA, Dodd RD, Kirsch DG. Abstract A17: Generation and comparison of CRISPR/Cas9 and Cre-mediated genetically engineered mouse models of sarcoma. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.sarcomas17-a17] [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
Genetically engineered mouse models (GEMMs) that employ site-specific recombinase (SSR) technology are important tools for cancer research, and recently the CRISPR/Cas9 system has been increasingly utilized to model cancer in mice. Here, we used CRISPR/Cas9 to generate two primary mouse models of sarcoma, undifferentiated pleomorphic sarcoma (UPS) in a GEMM, and malignant peripheral nerve sheath tumor (MPNST) in wild-type mice, to demonstrate the versatility of the system to generate multiple soft-tissue sarcoma subtypes. Because CRISPR technology is becoming more prevalent in cancer modeling, it is critical to thoroughly evaluate if these models are indeed comparable as tools to study cancer biology compared to conventional GEMMs initiated by recombinase technology. We used two Kras-driven sarcoma models of UPS generated with either Cre recombinase technology or CRISPR/Cas9 technology and compared the mutational profiles, histology, and growth kinetics of these models. KrasLSL-G12D/+; Rosa26LSL-Cas9-EGFP/+ (KC) mice received intramuscular delivery of an adenovirus expressing Cre recombinase and a single guide RNA (sgRNA) targeting Trp53. Cre-mediated expression of oncogenic Kras and Cas9, in combination with CRISPR/Cas9-mediated knockout of Trp53, was sufficient to generate primary soft-tissue sarcomas. Compared to the Cre/loxP model, we determined that sarcomas generated with CRISPR/Cas9 had similar growth kinetics, histology, copy number variation, and mutational load as assessed by whole-exome sequencing. We also demonstrated that off-target mutations in the sarcomas initiated by the Cas9 endonuclease were rare in tumors. Finally, we analyzed the Cas9-mediated indels present in tumors as genetic barcodes, which will enable future studies of tumor heterogeneity and clonality. These results show that sarcomas generated with CRISPR/Cas9 technology are similar to sarcomas generated with conventional modeling techniques. Ultimately this work corroborates CRISPR/Cas9-generated mouse models with traditional GEMMs phenotypically and genotypically, and expands the range of sarcoma mouse models available for research.
Citation Format: Jianguo Huang, Mark Chen, Melodi Javid Whitley, Hsuan-Cheng Kuo, Eric S. Xu, Andrea Walens, Yvonne M. Mowery, David Van Mater, William C. Eward, Diana M. Cardona, Lixia Luo, Yan Ma, Omar M. Lopez, Christopher E. Nelson, Jacqueline N. Robinson-Hamm, Anupama Reddy, Sandeep S. Dave, Charles A. Gersbach, Rebecca D. Dodd, David G. Kirsch. Generation and comparison of CRISPR/Cas9 and Cre-mediated genetically engineered mouse models of sarcoma [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr A17.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Yan Ma
- 1Duke University, Durham, NC,
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24
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Dodd RD, Lee CL, Overton T, Huang W, Eward WC, Luo L, Ma Y, Ingram DR, Torres KE, Cardona DM, Lazar AJ, Kirsch DG. NF1 +/- Hematopoietic Cells Accelerate Malignant Peripheral Nerve Sheath Tumor Development without Altering Chemotherapy Response. Cancer Res 2017; 77:4486-4497. [PMID: 28646022 PMCID: PMC5839126 DOI: 10.1158/0008-5472.can-16-2643] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/09/2017] [Accepted: 06/12/2017] [Indexed: 12/11/2022]
Abstract
Haploinsufficiency in the tumor suppressor NF1 contributes to the pathobiology of neurofibromatosis type 1, but a related role has not been established in malignant peripheral nerve sheath tumors (MPNST) where NF1 mutations also occur. Patients with NF1-associated MPNST appear to have worse outcomes than patients with sporadic MPNST, but the mechanism underlying this correlation is not understood. To define the impact of stromal genetics on the biology of this malignancy, we developed unique mouse models that reflect the genetics of patient-associated MPNST. Specifically, we used adenovirus-Cre injections to generate MPNST in Nf1Flox/Flox; Ink4a/ArfFlox/Flox and Nf1Flox/-; Ink4a/ArfFlox/Flox paired littermate mice to model tumors from NF1-wild-type and NF1-associated patients, respectively. In these models, Nf1 haploinsufficiency in hematopoietic cells accelerated tumor onset and increased levels of tumor-infiltrating immune cells comprised of CD11b+ cells, monocytes, and mast cells. We observed that mast cells were also enriched in human NF1-associated MPNST. In a coclinical trial to examine how the tumor microenvironment influences the response to multiagent chemotherapy, we found that stromal Nf1 status had no effect. Taken together, our results clarify the role of the NF1-haploinsufficient tumor microenvironment in MPNST. Cancer Res; 77(16); 4486-97. ©2017 AACR.
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Affiliation(s)
- Rebecca D Dodd
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Chang-Lung Lee
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Tess Overton
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Wesley Huang
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - William C Eward
- Department of Orthopaedic Surgery, Duke University, Durham, North Carolina
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Davis R Ingram
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keila E Torres
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Diana M Cardona
- Department of Pathology, Duke University, Durham, North Carolina
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina.
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
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25
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Huang J, Chen M, Whitley MJ, Kuo HC, Xu ES, Walens A, Mowery YM, Van Mater D, Eward WC, Cardona DM, Luo L, Ma Y, Lopez OM, Nelson CE, Robinson-Hamm JN, Reddy A, Dave SS, Gersbach CA, Dodd RD, Kirsch DG. Generation and comparison of CRISPR-Cas9 and Cre-mediated genetically engineered mouse models of sarcoma. Nat Commun 2017; 8:15999. [PMID: 28691711 PMCID: PMC5508130 DOI: 10.1038/ncomms15999] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 02/08/2017] [Accepted: 05/17/2017] [Indexed: 01/03/2023] Open
Abstract
Genetically engineered mouse models that employ site-specific recombinase technology are important tools for cancer research but can be costly and time-consuming. The CRISPR-Cas9 system has been adapted to generate autochthonous tumours in mice, but how these tumours compare to tumours generated by conventional recombinase technology remains to be fully explored. Here we use CRISPR-Cas9 to generate multiple subtypes of primary sarcomas efficiently in wild type and genetically engineered mice. These data demonstrate that CRISPR-Cas9 can be used to generate multiple subtypes of soft tissue sarcomas in mice. Primary sarcomas generated with CRISPR-Cas9 and Cre recombinase technology had similar histology, growth kinetics, copy number variation and mutational load as assessed by whole exome sequencing. These results show that sarcomas generated with CRISPR-Cas9 technology are similar to sarcomas generated with conventional modelling techniques and suggest that CRISPR-Cas9 can be used to more rapidly generate genotypically and phenotypically similar cancers.
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Affiliation(s)
- Jianguo Huang
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Mark Chen
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
- Medical Scientist Training Program, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Melodi Javid Whitley
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
- Medical Scientist Training Program, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Hsuan-Cheng Kuo
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Eric S. Xu
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Andrea Walens
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Yvonne M. Mowery
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David Van Mater
- Division of Hematology-Oncology, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - William C. Eward
- Department of Orthopedic Surgery, Duke University, Durham, North Carolina 27710, USA
| | - Diana M. Cardona
- Department of Pathology, Duke University, Durham, North Carolina 27710, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Omar M. Lopez
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Christopher E. Nelson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Jacqueline N. Robinson-Hamm
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Anupama Reddy
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Sandeep S. Dave
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
- Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Charles A. Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Rebecca D. Dodd
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
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26
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Huang J, Chen M, Whitley MJ, Kuo HC, Walens A, Mowery YM, Mater DV, Eward W, Cardona DM, Luo L, Ma Y, Nelson CE, Robinson-Hamm JN, Gersbach CA, Dodd RD, Kirsch DG. Abstract 2810: Using CRISPR/Cas9 to generate primary soft tissue sarcoma in genetically engineered and wild-type mice. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2810] [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
Genetically engineered mouse models (GEMMs) that employ site-specific recombinase (SSR) technology are important tools for pre-clinical studies, but this approach is costly and time-consuming. Here, we show that the CRISPR/Cas9 system can be used to efficiently complement existing GEMMs of sarcoma and generate primary sarcomas in wild type mice. Mice with the genotype KrasLSL-G12D/+; Rosa26LSL-Cas9-EGFP/+ received intramuscular delivery of an adenovirus expressing Cre recombinase and a single guide RNA (sgRNA) targeting Trp53. Cre-mediated expression of oncogenic Kras and Cas9, in combination with CRISPR/Cas9-mediated knockout of Trp53, was sufficient to generate primary soft tissue sarcomas. These tumors arose with kinetics similar to those generated using the Cre-loxP system to activate oncogenic Kras and delete Trp53 alleles. Additionally, we injected an adenovirus containing Cas9 and sgRNAs targeting Nf1 and Trp53 into the sciatic nerve of wild type mice. These mice formed malignant peripheral nerve sheath tumors (MPNSTs) in the same timeframe as MPNSTs generated using the Cre-loxP system to delete Nf1 and Ink4a/Arf alleles in GEMMs. These data demonstrate that CRISPR/Cas9 can be used to generate soft tissue sarcomas in wild type mice. Moreover, these results suggest that this technology can complement existing GEMMs for rapid assessment of tumor-modifying genes. These tools should decrease the time and expense associated with employing autochthonous mouse models of sarcoma for preclinical research.
Citation Format: Jianguo Huang, Mark Chen, Melodi J. Whitley, Hsuan-Cheng Kuo, Andrea Walens, Yvonne M. Mowery, David V. Mater, William Eward, Diana M. Cardona, Lixia Luo, Yan Ma, Christopher E. Nelson, Jacqueline N. Robinson-Hamm, Charles A. Gersbach, Rebecca D. Dodd, David G. Kirsch. Using CRISPR/Cas9 to generate primary soft tissue sarcoma in genetically engineered and wild-type mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2810. doi:10.1158/1538-7445.AM2017-2810
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Affiliation(s)
| | - Mark Chen
- 1Duke University Medical Center, Durham, NC
| | | | | | | | | | | | | | | | - Lixia Luo
- 1Duke University Medical Center, Durham, NC
| | - Yan Ma
- 1Duke University Medical Center, Durham, NC
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27
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Oldham M, Yoon P, Fathi Z, Beyer WF, Adamson J, Liu L, Alcorta D, Xia W, Osada T, Liu C, Yang XY, Dodd RD, Herndon JE, Meng B, Kirsch DG, Lyerly HK, Dewhirst MW, Fecci P, Walder H, Spector NL. X-Ray Psoralen Activated Cancer Therapy (X-PACT). PLoS One 2016; 11:e0162078. [PMID: 27583569 PMCID: PMC5008763 DOI: 10.1371/journal.pone.0162078] [Citation(s) in RCA: 17] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 08/17/2016] [Indexed: 11/18/2022] Open
Abstract
This work investigates X-PACT (X-ray Psoralen Activated Cancer Therapy): a new approach for the treatment of solid cancer. X-PACT utilizes psoralen, a potent anti-cancer therapeutic with current application to proliferative disease and extracorporeal photopheresis (ECP) of cutaneous T Cell Lymphoma. An immunogenic role for light-activated psoralen has been reported, contributing to long-term clinical responses. Psoralen therapies have to-date been limited to superficial or extracorporeal scenarios due to the requirement for psoralen activation by UVA light, which has limited penetration in tissue. X-PACT solves this challenge by activating psoralen with UV light emitted from novel non-tethered phosphors (co-incubated with psoralen) that absorb x-rays and re-radiate (phosphoresce) at UV wavelengths. The efficacy of X-PACT was evaluated in both in-vitro and in-vivo settings. In-vitro studies utilized breast (4T1), glioma (CT2A) and sarcoma (KP-B) cell lines. Cells were exposed to X-PACT treatments where the concentrations of drug (psoralen and phosphor) and radiation parameters (energy, dose, and dose rate) were varied. Efficacy was evaluated primarily using flow cell cytometry in combination with complimentary assays, and the in-vivo mouse study. In an in-vitro study, we show that X-PACT induces significant tumor cell apoptosis and cytotoxicity, unlike psoralen or phosphor alone (p<0.0001). We also show that apoptosis increases as doses of phosphor, psoralen, or radiation increase. Finally, in an in-vivo pilot study of BALBc mice with syngeneic 4T1 tumors, we show that the rate of tumor growth is slower with X-PACT than with saline or AMT + X-ray (p<0.0001). Overall these studies demonstrate a potential therapeutic effect for X-PACT, and provide a foundation and rationale for future studies. In summary, X-PACT represents a novel treatment approach in which well-tolerated low doses of x-ray radiation are delivered to a specific tumor site to generate UVA light which in-turn unleashes both short- and potentially long-term antitumor activity of photo-active therapeutics like psoralen.
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Affiliation(s)
- Mark Oldham
- Dept. of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
| | - Paul Yoon
- Dept. of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Zak Fathi
- Immunolight LLC, Detroit, Michigan, United States of America
| | - Wayne F. Beyer
- QNS Group, LLC, Bahama, North Carolina, United States of America
| | - Justus Adamson
- Dept. of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Leihua Liu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David Alcorta
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Wenle Xia
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Takuya Osada
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Congxiao Liu
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Xiao Y. Yang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Rebecca D. Dodd
- Dept. of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - James E. Herndon
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Boyu Meng
- Dept. of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David G. Kirsch
- Dept. of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - H. Kim Lyerly
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Mark W. Dewhirst
- Dept. of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Peter Fecci
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Harold Walder
- Dept. of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Neil L. Spector
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
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28
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Sachdeva M, Mito JK, Lee CL, Zhang M, Li Z, Dodd RD, Cason D, Luo L, Ma Y, Van Mater D, Gladdy R, Lev DC, Cardona DM, Kirsch DG. MicroRNA-182 drives metastasis of primary sarcomas by targeting multiple genes. J Clin Invest 2016; 126:1606. [PMID: 27035817 DOI: 10.1172/jci86573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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29
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Dodd RD. Emerging targets in sarcoma: Rising to the challenge of RAS signaling in undifferentiated pleomorphic sarcoma. Cancer 2015; 122:17-9. [PMID: 26479175 DOI: 10.1002/cncr.29730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 01/29/2023]
Affiliation(s)
- Rebecca D Dodd
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
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30
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Sachdeva M, Dodd RD, Huang Z, Grenier C, Ma Y, Lev DC, Cardona DM, Murphy SK, Kirsch DG. Epigenetic silencing of Kruppel like factor-3 increases expression of pro-metastatic miR-182. Cancer Lett 2015; 369:202-11. [PMID: 26314219 DOI: 10.1016/j.canlet.2015.08.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 05/22/2015] [Revised: 08/19/2015] [Accepted: 08/19/2015] [Indexed: 10/23/2022]
Abstract
Accumulating evidence indicates that microRNAs (miRs) regulate cancer metastasis. We have shown that miR-182 drives sarcoma metastasis in vivo by coordinated regulation of multiple genes. Recently, we also demonstrated that in a subset of primary sarcomas that metastasize to the lung, miR-182 expression is elevated through binding of MyoD1 to the miR-182 promoter. However, it is not known if there are also transcription factors that inhibit miR-182 expression. Defining negative regulators of miR-182 expression may help explain why some sarcomas do not metastasize and may also identify pathways that can modulate miR-182 for therapeutic benefit. Here, we use an in silico screen, chromatin-immunoprecipitation, and luciferase reporter assays to discover that Kruppel like factor-3 (Klf-3) is a novel transcriptional repressor of miR-182. Knockdown of Klf-3 increases miR-182 expression, and stable overexpression of Klf-3, but not a DNA-binding mutant Klf-3, decreases miR-182 levels. Klf-3 expression is downregulated in both primary mouse and human metastatic sarcomas, and Klf-3 levels negatively correlate with miR-182 expression. Interestingly, Klf-3 also negatively regulates MyoD1, suggesting an alternative mechanism for Klf-3 to repress miR-182 expression in addition to direct binding of the miR-182 promoter. Using Methylation Specific PCR (MSP) and pyrosequencing assays, we found that Klf-3 is epigenetically silenced by DNA hypermethylation both in mouse and human sarcoma cells. Finally, we show the DNA methylation inhibitor 5'Azacytidine (Aza) restores Klf-3 expression while reducing miR-182 levels. Thus, our findings suggest that demethylating agents could potentially be used to modulate miR-182 levels as a therapeutic strategy.
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Affiliation(s)
- Mohit Sachdeva
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
| | - Rebecca D Dodd
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
| | - Dina C Lev
- Department of Cancer Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Diana M Cardona
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA; Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA; Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.
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Dodd RD, Sachdeva M, Mito JK, Eward WC, Brigman BE, Ma Y, Dodd L, Kim Y, Lev D, Kirsch DG. Myogenic transcription factors regulate pro-metastatic miR-182. Oncogene 2015; 35:1868-75. [PMID: 26234681 PMCID: PMC4523886 DOI: 10.1038/onc.2015.252] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/29/2015] [Accepted: 05/18/2015] [Indexed: 02/05/2023]
Abstract
Approximately thirty percent of patients with soft-tissue sarcoma die from pulmonary metastases. The mechanisms that drive sarcoma metastasis are not well understood. Recently, we identified miR-182 as a driver of sarcoma metastasis in a primary mouse model of soft-tissue sarcoma. We also observed elevated miR-182 in a subset of primary human sarcomas that metastasized to the lungs. Here, we show that myogenic differentiation factors regulate miR-182 levels to contribute to metastasis in mouse models. We find that MyoD directly binds the miR-182 promoter to increase miR-182 expression. Furthermore, mechanistic studies revealed that Pax7 can promote sarcoma metastasis in vivo through MyoD-dependent regulation of pro-metastatic miR-182. Taken together, these results suggest that sarcoma metastasis can be partially controlled through Pax7/MyoD-dependent activation of miR-182 and provide insight into the role that myogenic transcription factors play in sarcoma progression.
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Affiliation(s)
- R D Dodd
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - M Sachdeva
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - J K Mito
- Department Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - W C Eward
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, USA
| | - B E Brigman
- Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, USA
| | - Y Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - L Dodd
- Department of Pathology, University of North Carolina, Chapel Hill, NC, USA
| | - Y Kim
- Department of Clinical Pathology, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - D Lev
- The Sarcoma Research Center at The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - D G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA.,Department Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
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Abstract
We discuss the generation of primary soft tissue sarcomas in mice using the Cre-loxP system to activate conditional mutations in oncogenic Kras and the tumor suppressor p53 (LSL-Kras(G12D/+); p53(flox/flox)). Sarcomas can be generated either by adenoviral delivery of Cre recombinase, activation of transgenic Cre recombinase with tamoxifen, or through transplantation of isolated satellite cells with Cre activation in vitro. Various applications of these models are discussed, including anticancer therapies, metastasis, in vivo imaging, and genetic requirements for tumorigenesis.
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Affiliation(s)
- Rebecca D Dodd
- Duke University Medical Center, Box 91006, Durham, NC, 27708, USA
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Sachdeva M, Mito JK, Lee CL, Zhang M, Li Z, Dodd RD, Cason D, Luo L, Ma Y, Van Mater D, Gladdy R, Lev DC, Cardona DM, Kirsch DG. MicroRNA-182 drives metastasis of primary sarcomas by targeting multiple genes. J Clin Invest 2014; 124:4305-19. [PMID: 25180607 DOI: 10.1172/jci77116] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/25/2014] [Indexed: 12/22/2022] Open
Abstract
Metastasis causes most cancer deaths, but is incompletely understood. MicroRNAs can regulate metastasis, but it is not known whether a single miRNA can regulate metastasis in primary cancer models in vivo. We compared the expression of miRNAs in metastatic and nonmetastatic primary mouse sarcomas and found that microRNA-182 (miR-182) was markedly overexpressed in some tumors that metastasized to the lungs. By utilizing genetically engineered mice with either deletion of or overexpression of miR-182 in primary sarcomas, we discovered that deletion of miR-182 substantially decreased, while overexpression of miR-182 considerably increased, the rate of lung metastasis after amputation of the tumor-bearing limb. Additionally, deletion of miR-182 decreased circulating tumor cells (CTCs), while overexpression of miR-182 increased CTCs, suggesting that miR-182 regulates intravasation of cancer cells into the circulation. We identified 4 miR-182 targets that inhibit either the migration of tumor cells or the degradation of the extracellular matrix. Notably, restoration of any of these targets in isolation did not alter the metastatic potential of sarcoma cells injected orthotopically, but the simultaneous restoration of all 4 targets together substantially decreased the number of metastases. These results demonstrate that a single miRNA can regulate metastasis of primary tumors in vivo by coordinated regulation of multiple genes.
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Dodd RD, Mito JK, Eward WC, Chitalia R, Sachdeva M, Ma Y, Barretina J, Dodd L, Kirsch DG. NF1 deletion generates multiple subtypes of soft-tissue sarcoma that respond to MEK inhibition. Mol Cancer Ther 2013; 12:1906-17. [PMID: 23858101 PMCID: PMC3825462 DOI: 10.1158/1535-7163.mct-13-0189] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [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] [Indexed: 11/16/2022]
Abstract
Soft-tissue sarcomas are a heterogeneous group of tumors arising from connective tissue. Recently, mutations in the neurofibromin 1 (NF1) tumor suppressor gene were identified in multiple subtypes of human soft-tissue sarcomas. To study the effect of NF1 inactivation in the initiation and progression of distinct sarcoma subtypes, we have developed a novel mouse model of temporally and spatially restricted NF1-deleted sarcoma. To generate primary sarcomas, we inject adenovirus containing Cre recombinase into NF1(flox/flox); Ink4a/Arf(flox/flox) mice at two distinct orthotopic sites: intramuscularly or in the sciatic nerve. The mice develop either high-grade myogenic sarcomas or malignant peripheral nerve sheath tumor (MPNST)-like tumors, respectively. These tumors reflect the histologic properties and spectrum of sarcomas found in patients. To explore the use of this model for preclinical studies, we conducted a study of mitogen-activated protein kinase (MAPK) pathway inhibition with the MEK inhibitor PD325901. Treatment with PD325901 delays tumor growth through decreased cyclin D1 mRNA and cell proliferation. We also examined the effects of MEK inhibition on the native tumor stroma and find that PD325901 decreases VEGFα expression in tumor cells with a corresponding decrease in microvessel density. Taken together, our results use a primary tumor model to show that sarcomas can be generated by loss of NF1 and Ink4a/Arf, and that these tumors are sensitive to MEK inhibition by direct effects on tumor cells and the surrounding microenvironment. These studies suggest that MEK inhibitors should be further explored as potential sarcoma therapies in patients with tumors containing NF1 deletion.
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Affiliation(s)
- Rebecca D Dodd
- Corresponding Author: David G. Kirsch, Duke University Medical Center, Box 91006, Durham, NC 27708.
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35
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Epple LM, Dodd RD, Merz AL, Dechkovskaia AM, Herring M, Winston BA, Lencioni AM, Russell RL, Madsen H, Nega M, Dusto NL, White J, Bigner DD, Nicchitta CV, Serkova NJ, Graner MW. Induction of the unfolded protein response drives enhanced metabolism and chemoresistance in glioma cells. PLoS One 2013; 8:e73267. [PMID: 24039668 PMCID: PMC3748289 DOI: 10.1371/journal.pone.0073267] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [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: 07/26/2012] [Accepted: 07/22/2013] [Indexed: 02/07/2023] Open
Abstract
The unfolded protein response (UPR) is an endoplasmic reticulum (ER)-based cytoprotective mechanism acting to prevent pathologies accompanying protein aggregation. It is frequently active in tumors, but relatively unstudied in gliomas. We hypothesized that UPR stress effects on glioma cells might protect tumors from additional exogenous stress (ie, chemotherapeutics), postulating that protection was concurrent with altered tumor cell metabolism. Using human brain tumor cell lines, xenograft tumors, human samples and gene expression databases, we determined molecular features of glioma cell UPR induction/activation, and here report a detailed analysis of UPR transcriptional/translational/metabolic responses. Immunohistochemistry, Western and Northern blots identified elevated levels of UPR transcription factors and downstream ER chaperone targets in gliomas. Microarray profiling revealed distinct regulation of stress responses between xenograft tumors and parent cell lines, with gene ontology and network analyses linking gene expression to cell survival and metabolic processes. Human glioma samples were examined for levels of the ER chaperone GRP94 by immunohistochemistry and for other UPR components by Western blotting. Gene and protein expression data from patient gliomas correlated poor patient prognoses with increased expression of ER chaperones, UPR target genes, and metabolic enzymes (glycolysis and lipogenesis). NMR-based metabolomic studies revealed increased metabolic outputs in glucose uptake with elevated glycolytic activity as well as increased phospholipid turnover. Elevated levels of amino acids, antioxidants, and cholesterol were also evident upon UPR stress; in particular, recurrent tumors had overall higher lipid outputs and elevated specific UPR arms. Clonogenicity studies following temozolomide treatment of stressed or unstressed cells demonstrated UPR-induced chemoresistance. Our data characterize the UPR in glioma cells and human tumors, and link the UPR to chemoresistance possibly via enhanced metabolism. Given the role of the UPR in the balance between cell survival and apoptosis, targeting the UPR and/or controlling metabolic activity may prove beneficial for malignant glioma therapeutics.
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Affiliation(s)
- Laura M. Epple
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
- Cell and Molecular Biology Program, Cancer Biology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Rebecca D. Dodd
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Andrea L. Merz
- Cancer Center Metabolomics Core, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Anjelika M. Dechkovskaia
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthew Herring
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Benjamin A. Winston
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Alex M. Lencioni
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Rae L. Russell
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Helen Madsen
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Meheret Nega
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Nathaniel L. Dusto
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Jason White
- Department of Neurosurgery, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Darell D. Bigner
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, United States of America
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christopher V. Nicchitta
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Natalie J. Serkova
- Cancer Center Metabolomics Core, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
- Department of Anesthesiology, Anschutz Medical Center, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Michael W. Graner
- Cell and Molecular Biology Program, Cancer Biology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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Mito JK, Ferrer JM, Brigman BE, Lee CL, Dodd RD, Eward WC, Marshall LF, Cuneo KC, Carter JE, Ramasunder S, Kim Y, Lee WD, Griffith LG, Bawendi MG, Kirsch DG. Intraoperative detection and removal of microscopic residual sarcoma using wide-field imaging. Cancer 2012; 118:5320-30. [PMID: 22437667 PMCID: PMC3532657 DOI: 10.1002/cncr.27458] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 12/05/2011] [Accepted: 01/17/2012] [Indexed: 11/17/2022]
Abstract
BACKGROUND: The goal of limb-sparing surgery for a soft tissue sarcoma of the extremity is to remove all malignant cells while preserving limb function. After initial surgery, microscopic residual disease in the tumor bed will cause a local recurrence in approximately 33% of patients with sarcoma. To help identify these patients, the authors developed an in vivo imaging system to investigate the suitability of molecular imaging for intraoperative visualization. METHODS: A primary mouse model of soft tissue sarcoma and a wide field-of-view imaging device were used to investigate a series of exogenously administered, near-infrared (NIR) fluorescent probes activated by cathepsin proteases for real-time intraoperative imaging. RESULTS: The authors demonstrated that exogenously administered cathepsin-activated probes can be used for image-guided surgery to identify microscopic residual NIR fluorescence in the tumor beds of mice. The presence of residual NIR fluorescence was correlated with microscopic residual sarcoma and local recurrence. The removal of residual NIR fluorescence improved local control. CONCLUSIONS: The authors concluded that their technique has the potential to be used for intraoperative image-guided surgery to identify microscopic residual disease in patients with cancer. Cancer 2012. © 2012 American Cancer Society.
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Affiliation(s)
- Jeffrey K Mito
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27708, USA
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Abstract
Soft-tissue sarcomas (STSs) are rare mesenchymal tumors that arise from muscle, fat and connective tissue. Currently, over 75 subtypes of STS are recognized. The rarity and heterogeneity of patient samples complicate clinical investigations into sarcoma biology. Model organisms might provide traction to our understanding and treatment of the disease. Over the past 10 years, many successful animal models of STS have been developed, primarily genetically engineered mice and zebrafish. These models are useful for studying the relevant oncogenes, signaling pathways and other cell changes involved in generating STSs. Recently, these model systems have become preclinical platforms in which to evaluate new drugs and treatment regimens. Thus, animal models are useful surrogates for understanding STS disease susceptibility and pathogenesis as well as for testing potential therapeutic strategies.
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Mito JK, Ferrer JM, Brigman BE, Lee CL, Dodd RD, Eward WC, Marshall LF, Dankort D, McMahon M, Kim Y, Lee WD, Griffith LG, Bawendi MG, Kirsch DG. Abstract 4316: A novel wide field-of-view imaging device for real-time, intra-operative tumor bed assessment. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4316] [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
Limb-sparing surgery for extremity soft tissue sarcoma removes all cancer cells at the primary tumor site in the majority of patients. However, without radiation therapy, microscopic residual sarcoma cells left behind in the tumor bed will cause a tumor recurrence in approximately one-third of patients. Therefore, adjuvant radiation therapy is delivered to most patients, even when the tumor bed lacks residual cancer. Here, we present an imaging system for residual cancer assessment, consisting of a novel wide field-of-view imaging device and a protease-activated fluorescent probe. We demonstrate that this system directly images microscopic residual sarcoma cells in the tumor bed of mice when primary soft tissue sarcomas are resected. Moreover, this system can detect single tumor cells that have activated the fluorescent probe in vivo. This technology has the potential to be used as an intra-operative tool to identify microscopic residual disease for soft tissue sarcoma and other cancers with the goal of reducing rates of local recurrence, re-operation for positive margins, and adjuvant radiation therapy to tumor beds that lack residual cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4316.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Martin McMahon
- 4University of California San Francisco, San Francisco, CA
| | | | - W. David Lee
- 2Massachusetts Institute of Technology, Cambridge, MA
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Mito JK, Riedel RF, Dodd L, Lahat G, Lazar AJ, Dodd RD, Stangenberg L, Eward WC, Hornicek FJ, Yoon SS, Brigman BE, Jacks T, Lev D, Mukherjee S, Kirsch DG. Cross species genomic analysis identifies a mouse model as undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma. PLoS One 2009; 4:e8075. [PMID: 19956606 PMCID: PMC2779485 DOI: 10.1371/journal.pone.0008075] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 11/03/2009] [Indexed: 11/17/2022] Open
Abstract
Undifferentiated pleomorphic sarcoma/Malignant Fibrous Histiocytoma (MFH) is one of the most common subtypes of human soft tissue sarcoma. Using cross species genomic analysis, we define a geneset from the LSL-Kras(G12D); Trp53(Flox/Flox) mouse model of soft tissue sarcoma that is highly enriched in human MFH. With this mouse geneset as a filter, we identify expression of the RAS target FOXM1 in human MFH. Expression of Foxm1 is elevated in mouse sarcomas that metastasize to the lung and tissue microarray analysis of human MFH correlates overexpression of FOXM1 with metastasis. These results suggest that genomic alterations present in human MFH are conserved in the LSL-Kras(G12D); p53(Flox/Flox) mouse model of soft tissue sarcoma and demonstrate the utility of this pre-clinical model.
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Affiliation(s)
- Jeffrey K Mito
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
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40
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Yoon SS, Stangenberg L, Lee YJ, Rothrock C, Dreyfuss JM, Baek KH, Waterman PR, Nielsen GP, Weissleder R, Mahmood U, Park PJ, Jacks T, Dodd RD, Fisher CJ, Ryeom S, Kirsch DG. Efficacy of sunitinib and radiotherapy in genetically engineered mouse model of soft-tissue sarcoma. Int J Radiat Oncol Biol Phys 2009; 74:1207-16. [PMID: 19545786 DOI: 10.1016/j.ijrobp.2009.02.052] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [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: 11/25/2008] [Revised: 02/10/2009] [Accepted: 02/21/2009] [Indexed: 11/17/2022]
Abstract
PURPOSE Sunitinib (SU) is a multitargeted receptor tyrosine kinase inhibitor of the vascular endothelial growth factor and platelet-derived growth factor receptors. The present study examined SU and radiotherapy (RT) in a genetically engineered mouse model of soft tissue sarcoma (STS). METHODS AND MATERIALS Primary extremity STSs were generated in genetically engineered mice. The mice were randomized to treatment with SU, RT (10 Gy x 2), or both (SU+RT). Changes in the tumor vasculature before and after treatment were assessed in vivo using fluorescence-mediated tomography. The control and treated tumors were harvested and extensively analyzed. RESULTS The mean fluorescence in the tumors was not decreased by RT but decreased 38-44% in tumors treated with SU or SU+RT. The control tumors grew to a mean of 1378 mm(3) after 12 days. SU alone or RT alone delayed tumor growth by 56% and 41%, respectively, but maximal growth inhibition (71%) was observed with the combination therapy. SU target effects were confirmed by loss of target receptor phosphorylation and alterations in SU-related gene expression. Cancer cell proliferation was decreased and apoptosis increased in the SU and RT groups, with a synergistic effect on apoptosis observed in the SU+RT group. RT had a minimal effect on the tumor microvessel density and endothelial cell-specific apoptosis, but SU alone or SU+RT decreased the microvessel density by >66% and induced significant endothelial cell apoptosis. CONCLUSION SU inhibited STS growth by effects on both cancer cells and tumor vasculature. SU also augmented the efficacy of RT, suggesting that this combination strategy could improve local control of STS.
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Affiliation(s)
- Sam S Yoon
- Department of Surgery, Division of Surgical Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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Stephens SB, Dodd RD, Lerner RS, Pyhtila BM, Nicchitta CV. Analysis of mRNA partitioning between the cytosol and endoplasmic reticulum compartments of mammalian cells. Methods Mol Biol 2008; 419:197-214. [PMID: 18369985 DOI: 10.1007/978-1-59745-033-1_14] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
All eukaryotic cells display a dramatic partitioning of mRNAs between the cytosol and endoplasmic reticulum (ER) compartments-mRNAs encoding secretory and integral membrane proteins are highly enriched on ER-bound ribosomes and mRNAs encoding cytoplasmic/nucleoplasmic proteins are enriched on cytosolic ribosomes. In current views, this partitioning phenomenon occurs through positive selection-mRNAs encoding signal sequence-bearing proteins are directed into the signal recognition particle pathway early in translation and trafficked as mRNA/ribosome/nascent polypeptide chain complexes to the ER. In the absence of an encoded signal sequence, mRNAs undergo continued translation on cytosolic ribosomes. Recent genome-wide analyses of mRNA partitioning between the cytosol and the ER compartments have identified subsets of mRNAs that are non-canonically partitioned to the ER-although lacking an encoded signal sequence, they are translated on ER-bound ribosomes. These findings suggest that multiple, and as yet unidentified, pathways exist for directing mRNA partitioning in the cell. In this contribution, we briefly review the literature describing the subcellular partitioning patterns of mRNAs and present a detailed methodology for studying this fundamental, yet poorly understood process.
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Affiliation(s)
- Samuel B Stephens
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
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42
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Nicchitta CV, Lerner RS, Stephens SB, Dodd RD, Pyhtila B. Pathways for compartmentalizing protein synthesis in eukaryotic cells: the template-partitioning model. Biochem Cell Biol 2006; 83:687-95. [PMID: 16333319 DOI: 10.1139/o05-147] [Citation(s) in RCA: 40] [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] [Indexed: 11/22/2022] Open
Abstract
mRNAs encoding signal sequences are translated on endoplasmic reticulum (ER) -- bound ribosomes, whereas mRNAs encoding cytosolic proteins are translated on cytosolic ribosomes. The partitioning of mRNAs to the ER occurs by positive selection; cytosolic ribosomes engaged in the translation of signal-sequence-bearing proteins are engaged by the signal-recognition particle (SRP) pathway and subsequently trafficked to the ER. Studies have demonstrated that, in addition to the SRP pathway, mRNAs encoding cytosolic proteins can also be partitioned to the ER, suggesting that RNA partitioning in the eukaryotic cell is a complex process requiring the activity of multiple RNA-partitioning pathways. In this review, key findings on this topic are discussed, and the template-partitioning model, describing a hypothetical mechanism for RNA partitioning in the eukaryotic cell, is proposed.
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Stephens SB, Dodd RD, Brewer JW, Lager PJ, Keene JD, Nicchitta CV. Stable ribosome binding to the endoplasmic reticulum enables compartment-specific regulation of mRNA translation. Mol Biol Cell 2005; 16:5819-31. [PMID: 16221886 PMCID: PMC1289424 DOI: 10.1091/mbc.e05-07-0685] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [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] [Indexed: 11/11/2022] Open
Abstract
In eukaryotic cells, protein synthesis is compartmentalized; mRNAs encoding secretory/membrane proteins are translated on endoplasmic reticulum (ER)-bound ribosomes, whereas mRNAs encoding cytosolic proteins are translated on free ribosomes. mRNA partitioning between the two compartments occurs via positive selection: free ribosomes engaged in the translation of signal sequence-encoding mRNAs are trafficked from the cytosol to the ER. After translation termination, ER-bound ribosomes are thought to dissociate, thereby completing a cycle of mRNA partitioning. At present, the physiological basis for termination-coupled ribosome release is unknown. To gain insight into this process, we examined ribosome and mRNA partitioning during the unfolded protein response, key elements of which include suppression of the initiation stage of protein synthesis and polyribosome breakdown. We report that unfolded protein response (UPR)-elicited polyribosome breakdown resulted in the continued association, rather than release, of ER-bound ribosomes. Under these conditions, mRNA translation in the cytosol was suppressed, whereas mRNA translation on the ER was sustained. Furthermore, mRNAs encoding key soluble stress proteins (XBP-1 and ATF-4) were translated primarily on ER-bound ribosomes. These studies demonstrate that ribosome release from the ER is termination independent and identify new and unexpected roles for the ER compartment in the translational response to induction of the unfolded protein response.
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Affiliation(s)
- Samuel B Stephens
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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44
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Tyulina OV, Prokopieva VD, Dodd RD, Hawkins JR, Clay SW, Wilson DO, Boldyrev AA, Johnson P. In vitro effects of ethanol, acetaldehyde and fatty acid ethyl esters on human erythrocytes. Alcohol Alcohol 2002; 37:179-86. [PMID: 11912075 DOI: 10.1093/alcalc/37.2.179] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In vitro experiments were performed to determine if ethanol was metabolized by human erythrocytes and to investigate if ethanol or its metabolites, acetaldehyde and fatty acid ethyl esters, affected erythrocyte morphology and stability. No detectable metabolism of ethanol was found in erythrocytes, although ethanol itself caused an elevated rate of spontaneous haemolysis in erythrocyte preparations. Physiologically attainable levels of ethanol were found to stabilize erythrocytes against haemolysis induced by sodium hypochlorite, and the presence of ethanol caused a decrease in erythrocyte reactive oxygen species levels, although the mechanism for such a process is unknown. Both physiologically attainable and higher levels of acetaldehyde had no effects on erythrocyte morphology and stability even after a 16 h exposure. Fatty acid ethyl esters caused structural changes and instability in erythrocytes in vitro, but whether such changes occur in vivo has not been established. The results of these studies suggest that the deleterious effects of ethanol consumption on erythrocytes in vivo may be, at least in part, the result of direct effects of unmetabolized ethanol on erythrocyte components.
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Affiliation(s)
- O V Tyulina
- International Biotechnological Center and Center for Molecular Medicine of MV Lomonosov, Moscow State University, 119899 Moscow, Russia
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