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Shi DD, Savani MR, Abdullah KG, McBrayer SK. Emerging roles of nucleotide metabolism in cancer. Trends Cancer 2023; 9:624-635. [PMID: 37173188 PMCID: PMC10967252 DOI: 10.1016/j.trecan.2023.04.008] [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: 02/24/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023]
Abstract
Nucleotides are substrates for multiple anabolic pathways, most notably DNA and RNA synthesis. Since nucleotide synthesis inhibitors began to be used for cancer therapy in the 1950s, our understanding of how nucleotides function in tumor cells has evolved, prompting a resurgence of interest in targeting nucleotide metabolism for cancer therapy. In this review, we discuss recent advances that challenge the idea that nucleotides are mere building blocks for the genome and transcriptome and highlight ways that these metabolites support oncogenic signaling, stress resistance, and energy homeostasis in tumor cells. These findings point to a rich network of processes sustained by aberrant nucleotide metabolism in cancer and reveal new therapeutic opportunities.
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Affiliation(s)
- Diana D Shi
- Department of Radiation Oncology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Milan R Savani
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harrold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.
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2
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El Shami M, Savani MR, Gattie LC, Smith B, Hicks WH, Rich JN, Richardson TE, McBrayer SK, Abdullah KG. Human plasma-like medium facilitates metabolic tracing and enables upregulation of immune signaling pathways in glioblastoma explants. bioRxiv 2023:2023.05.29.542774. [PMID: 37398280 PMCID: PMC10312566 DOI: 10.1101/2023.05.29.542774] [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: 07/04/2023]
Abstract
Purpose Metabolism within the tumor microenvironment (TME) represents an increasing area of interest to understand glioma initiation and progression. Stable isotope tracing is a technique critical to the study of tumor metabolism. Cell culture models of this disease are not routinely cultured under physiologically relevant nutrient conditions and do not retain cellular heterogeneity present in the parental TME. Moreover, in vivo, stable isotope tracing in intracranial glioma xenografts, the gold standard for metabolic investigation, is time consuming and technically challenging. To provide insights into glioma metabolism in the presence of an intact TME, we performed stable isotope tracing analysis of patient-derived, heterocellular Surgically eXplanted Organoid (SXO) glioma models in human plasma-like medium (HPLM). Methods Glioma SXOs were established and cultured in conventional media or transitioned to HPLM. We evaluated SXO cytoarchitecture and histology, then performed spatial transcriptomic profiling to identify cellular populations and differential gene expression patterns. We performed stable isotope tracing with 15N2-glutamine to evaluate intracellular metabolite labeling patterns. Results Glioma SXOs cultured in HPLM retain cytoarchitecture and cellular constituents. Immune cells in HPLM-cultured SXOs demonstrated increased transcription of immune-related signatures, including innate immune, adaptive immune, and cytokine signaling programs. 15N isotope enrichment from glutamine was observed in metabolites from diverse pathways, and labeling patterns were stable over time. Conclusion To enable ex vivo, tractable investigations of whole tumor metabolism, we developed an approach to conduct stable isotope tracing in glioma SXOs cultured under physiologically relevant nutrient conditions. Under these conditions, SXOs maintained viability, composition, and metabolic activity while exhibiting increased immune-related transcriptional programs.
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Affiliation(s)
- Mohamad El Shami
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Milan R Savani
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75235, USA
| | - Lauren C Gattie
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Bailey Smith
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75235, USA
| | - William H Hicks
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Jeremy N Rich
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Timothy E Richardson
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Samuel K McBrayer
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX, 75235, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
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3
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Pal S, Kaplan JP, Nguyen H, Stopka SA, Savani MR, Regan MS, Nguyen QD, Jones KL, Moreau LA, Peng J, Dipiazza MG, Perciaccante AJ, Zhu X, Hunsel BR, Liu KX, Alexandrescu S, Drissi R, Filbin MG, McBrayer SK, Agar NYR, Chowdhury D, Haas-Kogan DA. A druggable addiction to de novo pyrimidine biosynthesis in diffuse midline glioma. Cancer Cell 2022; 40:957-972.e10. [PMID: 35985342 PMCID: PMC9575661 DOI: 10.1016/j.ccell.2022.07.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 12/18/2022]
Abstract
Diffuse midline glioma (DMG) is a uniformly fatal pediatric cancer driven by oncohistones that do not readily lend themselves to drug development. To identify druggable targets for DMG, we conducted a genome-wide CRISPR screen that reveals a DMG selective dependency on the de novo pathway for pyrimidine biosynthesis. This metabolic vulnerability reflects an elevated rate of uridine/uracil degradation that depletes DMG cells of substrates for the alternate salvage pyrimidine biosynthesis pathway. A clinical stage inhibitor of DHODH (rate-limiting enzyme in the de novo pathway) diminishes uridine-5'-phosphate (UMP) pools, generates DNA damage, and induces apoptosis through suppression of replication forks-an "on-target" effect, as shown by uridine rescue. Matrix-assisted laser desorption/ionization (MALDI) mass spectroscopy imaging demonstrates that this DHODH inhibitor (BAY2402234) accumulates in the brain at therapeutically relevant concentrations, suppresses de novo pyrimidine biosynthesis in vivo, and prolongs survival of mice bearing intracranial DMG xenografts, highlighting BAY2402234 as a promising therapy against DMGs.
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Affiliation(s)
- Sharmistha Pal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jakub P Kaplan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Huy Nguyen
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Milan R Savani
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Kristen L Jones
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Lisa A Moreau
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jingyu Peng
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marina G Dipiazza
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Andrew J Perciaccante
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Xiaoting Zhu
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Bradley R Hunsel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kevin X Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Sanda Alexandrescu
- Department of Pathology, Harvard Medical School Boston, Boston Children's Hospital, 300 Longwood Avenue, Bader 104, Boston, MA 02115, USA
| | - Rachid Drissi
- Center for Childhood Cancer and Blood Diseases, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dipanjan Chowdhury
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daphne A Haas-Kogan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Radiation Oncology, Brigham and Women's Hospital, Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA.
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4
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Shi DD, Savani MR, Levitt MM, Wang AC, Endress JE, Bird CE, Buehler J, Stopka SA, Regan MS, Lin YF, Puliyappadamba VT, Gao W, Khanal J, Evans L, Lee JH, Guo L, Xiao Y, Xu M, Huang B, Jennings RB, Bonal DM, Martin-Sandoval MS, Dang T, Gattie LC, Cameron AB, Lee S, Asara JM, Kornblum HI, Mak TW, Looper RE, Nguyen QD, Signoretti S, Gradl S, Sutter A, Jeffers M, Janzer A, Lehrman MA, Zacharias LG, Mathews TP, Losman JA, Richardson TE, Cahill DP, DeBerardinis RJ, Ligon KL, Xu L, Ly P, Agar NYR, Abdullah KG, Harris IS, Kaelin WG, McBrayer SK. De novo pyrimidine synthesis is a targetable vulnerability in IDH mutant glioma. Cancer Cell 2022; 40:939-956.e16. [PMID: 35985343 PMCID: PMC9515386 DOI: 10.1016/j.ccell.2022.07.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/09/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022]
Abstract
Mutations affecting isocitrate dehydrogenase (IDH) enzymes are prevalent in glioma, leukemia, and other cancers. Although mutant IDH inhibitors are effective against leukemia, they seem to be less active in aggressive glioma, underscoring the need for alternative treatment strategies. Through a chemical synthetic lethality screen, we discovered that IDH1-mutant glioma cells are hypersensitive to drugs targeting enzymes in the de novo pyrimidine nucleotide synthesis pathway, including dihydroorotate dehydrogenase (DHODH). We developed a genetically engineered mouse model of mutant IDH1-driven astrocytoma and used it and multiple patient-derived models to show that the brain-penetrant DHODH inhibitor BAY 2402234 displays monotherapy efficacy against IDH-mutant gliomas. Mechanistically, this reflects an obligate dependence of glioma cells on the de novo pyrimidine synthesis pathway and mutant IDH's ability to sensitize to DNA damage upon nucleotide pool imbalance. Our work outlines a tumor-selective, biomarker-guided therapeutic strategy that is poised for clinical translation.
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Affiliation(s)
- Diana D Shi
- Department of Radiation Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA 02215, USA; Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Milan R Savani
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael M Levitt
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adam C Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Jennifer E Endress
- Ludwig Cancer Center, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Cylaina E Bird
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Joseph Buehler
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sylwia A Stopka
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael S Regan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yu-Fen Lin
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Vinesh T Puliyappadamba
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenhua Gao
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Januka Khanal
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Laura Evans
- Bayer HealthCare Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Joyce H Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Lei Guo
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yi Xiao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Min Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bofu Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Rebecca B Jennings
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis M Bonal
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Misty S Martin-Sandoval
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tammie Dang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren C Gattie
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Amy B Cameron
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Sungwoo Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea
| | - John M Asara
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Harley I Kornblum
- Department of Molecular and Medical Pharmacology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Psychiatry and Behavioral Sciences, and Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90024, USA
| | - Tak W Mak
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2M9, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ryan E Looper
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Quang-De Nguyen
- Lurie Family Imaging Center, Center for Biomedical Imaging in Oncology, Dana-Farber Cancer Institute, Boston, MA 02210, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Gradl
- Bayer AG, Muellerstrasse 178, 13353 Berlin, Germany
| | | | - Michael Jeffers
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, NJ 07981, USA
| | | | - Mark A Lehrman
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren G Zacharias
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Julie-Aurore Losman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Timothy E Richardson
- Department of Pathology, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Keith L Ligon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Children's Hospital Boston, Boston, MA 02115, USA
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population & Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nathalie Y R Agar
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Isaac S Harris
- Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.
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5
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Buehler JD, Bird CE, Savani MR, Gattie LC, Hicks WH, Levitt MM, El Shami M, Hatanpaa KJ, Richardson TE, McBrayer SK, Abdullah KG. Semi-Automated Computational Assessment of Cancer Organoid Viability Using Rapid Live-Cell Microscopy. Cancer Inform 2022; 21:11769351221100754. [PMID: 35652106 PMCID: PMC9150230 DOI: 10.1177/11769351221100754] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/27/2022] [Indexed: 11/26/2022] Open
Abstract
The creation of patient-derived cancer organoids represents a key advance in preclinical modeling and has recently been applied to a variety of human solid tumor types. However, conventional methods used to assess in vivo tumor tissue treatment response are poorly suited for the evaluation of cancer organoids because they are time-intensive and involve tissue destruction. To address this issue, we established a suite of 3-dimensional patient-derived glioma organoids, treated them with chemoradiotherapy, stained organoids with non-toxic cell dyes, and imaged them using a rapid laser scanning confocal microscopy method termed "Apex Imaging." We then developed and tested a fragmentation algorithm to quantify heterogeneity in the topography of the organoids as a potential surrogate marker of viability. This algorithm, SSDquant, provides a 3-dimensional visual representation of the organoid surface and a numerical measurement of the sum-squared distance (SSD) from the derived mass center of the organoid. We tested whether SSD scores correlate with traditional immunohistochemistry-derived cell viability markers (cellularity and cleaved caspase 3 expression) and observed statistically significant associations between them using linear regression analysis. Our work describes a quantitative, non-invasive approach for the serial measurement of patient-derived cancer organoid viability, thus opening new avenues for the application of these models to studies of cancer biology and therapy.
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Affiliation(s)
- Joseph D Buehler
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cylaina E Bird
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Milan R Savani
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lauren C Gattie
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - William H Hicks
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael M Levitt
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mohamad El Shami
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kimmo J Hatanpaa
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pathology, Division of Neuropathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Timothy E Richardson
- Department of Pathology and Laboratory Medicine and Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Disease Research, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Samuel K McBrayer
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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6
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Wei S, Yin D, Yu S, Lin X, Savani MR, Du K, Ku Y, Wu D, Li S, Liu H, Tian M, Chen Y, Bowie M, Hariharan S, Waitkus M, Keir ST, Sugarman ET, Deek RA, Labrie M, Khasraw M, Lu Y, Mills GB, Herlyn M, Wu K, Liu L, Wei Z, Flaherty KT, Abdullah K, Zhang G, Ashley DM. Antitumor Activity of a Mitochondrial-Targeted HSP90 Inhibitor in Gliomas. Clin Cancer Res 2022; 28:2180-2195. [PMID: 35247901 DOI: 10.1158/1078-0432.ccr-21-0833] [Citation(s) in RCA: 8] [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: 03/04/2021] [Revised: 08/31/2021] [Accepted: 03/01/2022] [Indexed: 02/05/2023]
Abstract
PURPOSE To investigate the antitumor activity of a mitochondrial-localized HSP90 inhibitor, Gamitrinib, in multiple glioma models, and to elucidate the antitumor mechanisms of Gamitrinib in gliomas. EXPERIMENTAL DESIGN A broad panel of primary and temozolomide (TMZ)-resistant human glioma cell lines were screened by cell viability assays, flow cytometry, and crystal violet assays to investigate the therapeutic efficacy of Gamitrinib. Seahorse assays were used to measure the mitochondrial respiration of glioma cells. Integrated analyses of RNA sequencing (RNAseq) and reverse phase protein array (RPPA) data were performed to reveal the potential antitumor mechanisms of Gamitrinib. Neurospheres, patient-derived organoids (PDO), cell line-derived xenografts (CDX), and patient-derived xenografts (PDX) models were generated to further evaluate the therapeutic efficacy of Gamitrinib. RESULTS Gamitrinib inhibited cell proliferation and induced cell apoptosis and death in 17 primary glioma cell lines, 6 TMZ-resistant glioma cell lines, 4 neurospheres, and 3 PDOs. Importantly, Gamitrinib significantly delayed the tumor growth and improved survival of mice in both CDX and PDX models in which tumors were either subcutaneously or intracranially implanted. Integrated computational analyses of RNAseq and RPPA data revealed that Gamitrinib exhibited its antitumor activity via (i) suppressing mitochondrial biogenesis, OXPHOS, and cell-cycle progression and (ii) activating the energy-sensing AMP-activated kinase, DNA damage, and stress response. CONCLUSIONS These preclinical findings established the therapeutic role of Gamitrinib in gliomas and revealed the inhibition of mitochondrial biogenesis and tumor bioenergetics as the primary antitumor mechanisms in gliomas.
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Affiliation(s)
- Shiyou Wei
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - Delong Yin
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina.,Department of Orthopedics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shengnan Yu
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina.,Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiang Lin
- Department of Computer Science, Ying Wu College of Computing, New Jersey Institute of Technology, Newark, New Jersey
| | - Milan R Savani
- Department of Neurosurgery, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kuang Du
- Department of Computer Science, Ying Wu College of Computing, New Jersey Institute of Technology, Newark, New Jersey
| | - Yin Ku
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Di Wu
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shasha Li
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hao Liu
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Meng Tian
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Neurosurgery Research Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yaohui Chen
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Michelle Bowie
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - Seethalakshmi Hariharan
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - Matthew Waitkus
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - Stephen T Keir
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - Eric T Sugarman
- Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania
| | - Rebecca A Deek
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health Sciences University, Portland, Oregon
| | - Mustafa Khasraw
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - Yiling Lu
- Division of Cancer Medicine, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health Sciences University, Portland, Oregon
| | | | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lunxu Liu
- Department of Thoracic Surgery, Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhi Wei
- Department of Computer Science, Ying Wu College of Computing, New Jersey Institute of Technology, Newark, New Jersey
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Kalil Abdullah
- Department of Neurosurgery, Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Gao Zhang
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina.,Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - David M Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina.,Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
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7
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Abdullah KG, Bird CE, Buehler JD, Gattie LC, Savani MR, Sternisha AC, Xiao Y, Levitt MM, Hicks WH, Li W, Ramirez DMO, Patel T, Garzon-Muvdi T, Barnett S, Zhang G, Ashley DM, Hatanpaa KJ, Richardson TE, McBrayer SK. Establishment of patient-derived organoid models of lower-grade glioma. Neuro Oncol 2022; 24:612-623. [PMID: 34850183 PMCID: PMC8972292 DOI: 10.1093/neuonc/noab273] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Historically, creating patient-derived models of lower-grade glioma (LGG) has been challenging, contributing to few experimental platforms that support laboratory-based investigations of this disease. Although organoid modeling approaches have recently been employed to create in vitro models of high-grade glioma (HGG), it is unknown whether this approach can be successfully applied to LGG. METHODS In this study, we developed an optimized protocol for the establishment of organoids from LGG primary tissue samples by utilizing physiologic (5%) oxygenation conditions and employed it to produce the first known suite of these models. To assess their fidelity, we surveyed key biological features of patient-derived organoids using metabolic, genomic, histologic, and lineage marker gene expression assays. RESULTS Organoid models were created with a success rate of 91% (n = 20/22) from primary tumor samples across glioma histological subtypes and tumor grades (WHO Grades 1-4), and a success rate of 87% (13/15) for WHO Grade 1-3 tumors. Patient-derived organoids recapitulated stemness, proliferative, and tumor-stromal composition profiles of their respective parental tumor specimens. Cytoarchitectural, mutational, and metabolic traits of parental tumors were also conserved. Importantly, LGG organoids were maintained in vitro for weeks to months and reanimated after biobanking without loss of integrity. CONCLUSIONS We report an efficient method for producing faithful in vitro models of LGG. New experimental platforms generated through this approach are well positioned to support preclinical studies of this disease, particularly those related to tumor immunology, tumor-stroma interactions, identification of novel drug targets, and personalized assessments of treatment response profiles.
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Affiliation(s)
- Kalil G Abdullah
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Cylaina E Bird
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joseph D Buehler
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lauren C Gattie
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Milan R Savani
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Alex C Sternisha
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Yi Xiao
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Michael M Levitt
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - William H Hicks
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Wenhao Li
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Denise M O Ramirez
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Toral Patel
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Tomas Garzon-Muvdi
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Samuel Barnett
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- O’Donnell Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Gao Zhang
- Duke University School of Medicine, Duke University, Durham, North Carolina,USA
| | - David M Ashley
- Duke University School of Medicine, Duke University, Durham, North Carolina,USA
| | - Kimmo J Hatanpaa
- Department of Pathology, Division of Neuropathology, University of Texas Southwestern Medical Center, Dallas, Texas,USA
| | - Timothy E Richardson
- Department of Pathology and Laboratory Medicine and The Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, San Antonio, Texas,USA
| | - Samuel K McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas,USA
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas,USA
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8
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Abstract
A recent study (Sulkowski et al., 2020) reveals that oncometabolites, which are produced by metabolic gene mutations in many cancers, sensitize cells to PARP inhibition by antagonizing histone demethylation and obscuring epigenetic marks that are necessary for efficient DNA repair.
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Affiliation(s)
- Milan R Savani
- Medical Scientist Training Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kalil G Abdullah
- Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Samuel K McBrayer
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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9
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Green AM, Budagyan K, Hayer KE, Reed MA, Savani MR, Wertheim GB, Weitzman MD. Cytosine Deaminase APOBEC3A Sensitizes Leukemia Cells to Inhibition of the DNA Replication Checkpoint. Cancer Res 2017; 77:4579-4588. [PMID: 28655787 DOI: 10.1158/0008-5472.can-16-3394] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/18/2017] [Accepted: 06/22/2017] [Indexed: 12/27/2022]
Abstract
Mutational signatures in cancer genomes have implicated the APOBEC3 cytosine deaminases in oncogenesis, possibly offering a therapeutic vulnerability. Elevated APOBEC3B expression has been detected in solid tumors, but expression of APOBEC3A (A3A) in cancer has not been described to date. Here, we report that A3A is highly expressed in subsets of pediatric and adult acute myelogenous leukemia (AML). We modeled A3A expression in the THP1 AML cell line by introducing an inducible A3A gene. A3A expression caused ATR-dependent phosphorylation of Chk1 and cell-cycle arrest, consistent with replication checkpoint activation. Further, replication checkpoint blockade via small-molecule inhibition of ATR kinase in cells expressing A3A led to apoptosis and cell death. Although DNA damage checkpoints are broadly activated in response to A3A activity, synthetic lethality was specific to ATR signaling via Chk1 and did not occur with ATM inhibition. Our findings identify elevation of A3A expression in AML cells, enabling apoptotic sensitivity to inhibitors of the DNA replication checkpoint and suggesting it as a candidate biomarker for ATR inhibitor therapy. Cancer Res; 77(17); 4579-88. ©2017 AACR.
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Affiliation(s)
- Abby M Green
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Konstantin Budagyan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Katharina E Hayer
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Morgann A Reed
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Milan R Savani
- University of Pennsylvania College of Arts and Sciences, Philadelphia, Pennsylvania
| | - Gerald B Wertheim
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Matthew D Weitzman
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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10
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Simms-Waldrip TR, Sunkersett G, Coughlin LA, Savani MR, Arana C, Kim J, Kim M, Zhan X, Greenberg DE, Xie Y, Davies SM, Koh AY. Antibiotic-Induced Depletion of Anti-inflammatory Clostridia Is Associated with the Development of Graft-versus-Host Disease in Pediatric Stem Cell Transplantation Patients. Biol Blood Marrow Transplant 2017; 23:820-829. [PMID: 28192251 DOI: 10.1016/j.bbmt.2017.02.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [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: 11/23/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022]
Abstract
Adult stem cell transplantation (SCT) patients with graft-versus-host-disease (GVHD) exhibit significant disruptions in gut microbial communities. These changes are associated with higher overall mortality and appear to be driven by specific antibiotic therapies. It is unclear whether pediatric SCT patients who develop GVHD exhibit similar antibiotic-induced gut microbiota community changes. Here, we show that pediatric SCT patients (from Children's Medical Center Dallas, n = 8, and Cincinnati Children's Hospital, n = 7) who developed GVHD showed a significant decline, up to 10-log fold, in gut anti-inflammatory Clostridia (AIC) compared with those without GVHD. In fact, the development of GVHD is significantly associated with this AIC decline and with cumulative antibiotic exposure, particularly antibiotics effective against anaerobic bacteria (P = .003, Firth logistic regression analysis). Using metagenomic shotgun sequencing analysis, we were able to identify specific commensal bacterial species, including AIC, that were significantly depleted in GVHD patients. We then used a preclinical GVHD model to verify our clinical observations. Clindamycin depleted AIC and exacerbated GVHD in mice, whereas oral AIC supplementation increased gut AIC levels and mitigated GVHD in mice. Together, these data suggest that an antibiotic-induced AIC depletion in the gut microbiota is associated with the development of GVHD in pediatric SCT patients.
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Affiliation(s)
| | - Gauri Sunkersett
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Laura A Coughlin
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Milan R Savani
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jiwoong Kim
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas; Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Minsoo Kim
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas; Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xiaowei Zhan
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas; Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas; Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas
| | - David E Greenberg
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yang Xie
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas; Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas; Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Stella M Davies
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Andrew Y Koh
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas; Harold C. Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas.
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