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Patrón LA, Yeoman H, Wilson S, Tang N, Berens ME, Gokhale V, Suzuki TC. Novel Brain-Penetrant, Small-Molecule Tubulin Destabilizers for the Treatment of Glioblastoma. Biomedicines 2024; 12:406. [PMID: 38398008 PMCID: PMC10887108 DOI: 10.3390/biomedicines12020406] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Glioblastoma (GB) is the most lethal brain cancer in adults, with a 5-year survival rate of 5%. The standard of care for GB includes maximally safe surgical resection, radiation, and temozolomide (TMZ) therapy, but tumor recurrence is inevitable in most GB patients. Here, we describe the development of a blood-brain barrier (BBB)-penetrant tubulin destabilizer, RGN3067, for the treatment of GB. RGN3067 shows good oral bioavailability and achieves high concentrations in rodent brains after oral dosing (Cmax of 7807 ng/mL (20 μM), Tmax at 2 h). RGN3067 binds the colchicine binding site of tubulin and inhibits tubulin polymerization. The compound also suppresses the proliferation of the GB cell lines U87 and LN-18, with IC50s of 117 and 560 nM, respectively. In four patient-derived GB cell lines, the IC50 values for RGN3067 range from 148 to 616 nM. Finally, in a patient-derived xenograft (PDX) mouse model, RGN3067 reduces the rate of tumor growth compared to the control. Collectively, we show that RGN3067 is a BBB-penetrant small molecule that shows in vitro and in vivo efficacy and that its design addresses many of the physicochemical properties that prevent the use of microtubule destabilizers as treatments for GB and other brain cancers.
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Affiliation(s)
| | | | | | - Nanyun Tang
- Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - Michael E Berens
- Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
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2
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Noll A, Myers C, Biery MC, Meechan M, Tahiri S, Rajendran A, Berens ME, Paine D, Byron S, Zhang J, Winter C, Pakiam F, Leary SES, Cole BL, Jackson ER, Dun MD, Foster JB, Evans MK, Pattwell SS, Olson JM, Vitanza NA. Therapeutic HDAC inhibition in hypermutant diffuse intrinsic pontine glioma. Neoplasia 2023; 43:100921. [PMID: 37603953 PMCID: PMC10465940 DOI: 10.1016/j.neo.2023.100921] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023]
Abstract
Constitutional mismatch repair deficiency (CMMRD) is a cancer predisposition syndrome associated with the development of hypermutant pediatric high-grade glioma, and confers a poor prognosis. While therapeutic histone deacetylase (HDAC) inhibition of diffuse intrinsic pontine glioma (DIPG) has been reported; here, we use a clinically relevant biopsy-derived hypermutant DIPG model (PBT-24FH) and a CRISPR-Cas9 induced genetic model to evaluate the efficacy of HDAC inhibition against hypermutant DIPG. We screened PBT-24FH cells for sensitivity to a panel of HDAC inhibitors (HDACis) in vitro, identifying two HDACis associated with low nanomolar IC50s, quisinostat (27 nM) and romidepsin (2 nM). In vivo, quisinostat proved more efficacious, inducing near-complete tumor regression in a PBT-24FH flank model. RNA sequencing revealed significant quisinostat-driven changes in gene expression, including upregulation of neural and pro-inflammatory genes. To validate the observed potency of quisinostat in vivo against additional hypermutant DIPG models, we tested quisinostat in genetically-induced mismatch repair (MMR)-deficient DIPG flank tumors, demonstrating that loss of MMR function increases sensitivity to quisinostat in vivo. Here, we establish the preclinical efficacy of quisinostat against hypermutant DIPG, supporting further investigation of epigenetic targeting of hypermutant pediatric cancers with the potential for clinical translation. These findings support further investigation of HDAC inhibitors against pontine high-grade gliomas, beyond only those with histone mutations, as well as against other hypermutant central nervous system tumors.
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Affiliation(s)
- Alyssa Noll
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Molecular and Cellular Biology Graduate Program and Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Carrie Myers
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Matthew C Biery
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael Meechan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sophie Tahiri
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Molecular Mechanisms of Disease Graduate Program, University of Washington, Seattle, WA, USA
| | - Asmitha Rajendran
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Biomedical Informatics and Medical Education Graduate Program, University of Washington, Seattle, WA, USA
| | - Michael E Berens
- Cancer & Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Danyelle Paine
- Cancer & Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Sara Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Jiaming Zhang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Conrad Winter
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Fiona Pakiam
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sarah E S Leary
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Bonnie L Cole
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Evangeline R Jackson
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Matthew D Dun
- Cancer Signalling Research Group, School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia; Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia; Paediatric Program, Mark Hughes Foundation Centre for Brain Cancer Research, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
| | - Jessica B Foster
- Division of Oncology, The Children's Hospital of Philadelphia, Philidelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Myron K Evans
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Siobhan S Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - James M Olson
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA.
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3
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DeLuca V, Digumarti P, Berens ME. Abstract 4794: Deciphering tumor recurrence post-therapy: Interactions between the tumor microenvironment and therapy-induced senescent glioblastoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4794] [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: 04/07/2023]
Abstract
Abstract
Glioblastoma (GBM) remains one of the most lethal forms of cancer due, in part, to the capacity of tumor cells to persist during therapy and then recover. Understanding how these residual tumor cells survive is therefore imperative to developing more effective treatment strategies. We have demonstrated that GBM cells, including those from patient-derived xenografts, undergo a state of therapy-induced senescence (TIS) rather than cell death following temozolomide (TMZ) and radiation (IR). Both TMZ and IR treatment at physiologically relevant doses result in elevated senescence-associated-β-galactosidase, altered morphology, p21 induction, and increased expression of the senescence-associated-heterochromatic-foci marker H3K9Me3. Further, despite TIS-induction in a majority of the residual cells post-treatment, GBM viable cell number increases after a prolonged stasis, indicating that populations are capable of reentering a proliferative state. However, our current understanding of how the tumor microenvironment influences this growth arrest and subsequent proliferative recovery is underdeveloped. We aim to bridge that gap by investigating the paracrine communications between astrocytes and GBM cells undergoing IR-induced senescence in order to identify how these interactions foster disease progression. Current studies are focused on evaluating the effect of astrocytes on the induction and durability of TIS in GBM cells. Proteomic studies will be pursued to characterize the secretome of astrocyte-GBM co-cultures and identify factors that drive GBM senescent response to IR. Finally, based on preliminary data demonstrating that normal astrocytes are also damaged by IR, we will undertake mechanistic studies to understand how cell-intrinsic events within the astrocyte population drive extrinsic-influence on GBM cells. We anticipate that these identified signaling events may serve as potential therapeutic targets.
Citation Format: Valerie DeLuca, Priya Digumarti, Michael E. Berens. Deciphering tumor recurrence post-therapy: Interactions between the tumor microenvironment and therapy-induced senescent glioblastoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4794.
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Affiliation(s)
- Valerie DeLuca
- 1TGen (The Translational Genomics Research Institute), Phoenix, AZ
| | - Priya Digumarti
- 1TGen (The Translational Genomics Research Institute), Phoenix, AZ
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4
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Budhraja KK, McDonald BR, Stephens MD, Contente-Cuomo T, Markus H, Farooq M, Favaro PF, Connor S, Byron SA, Egan JB, Ernst B, McDaniel TK, Sekulic A, Tran NL, Prados MD, Borad MJ, Berens ME, Pockaj BA, LoRusso PM, Bryce A, Trent JM, Murtaza M. Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer. Sci Transl Med 2023; 15:eabm6863. [PMID: 36630480 PMCID: PMC10080578 DOI: 10.1126/scitranslmed.abm6863] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 10/04/2021] [Accepted: 12/16/2022] [Indexed: 01/13/2023]
Abstract
Genome-wide fragmentation patterns in cell-free DNA (cfDNA) in plasma are strongly influenced by cellular origin due to variation in chromatin accessibility across cell types. Such differences between healthy and cancer cells provide the opportunity for development of novel cancer diagnostics. Here, we investigated whether analysis of cfDNA fragment end positions and their surrounding DNA sequences reveals the presence of tumor-derived DNA in blood. We performed genome-wide analysis of cfDNA from 521 samples and analyzed sequencing data from an additional 2147 samples, including healthy individuals and patients with 11 different cancer types. We developed a metric based on genome-wide differences in fragment positioning, weighted by fragment length and GC content [information-weighted fraction of aberrant fragments (iwFAF)]. We observed that iwFAF strongly correlated with tumor fraction, was higher for DNA fragments carrying somatic mutations, and was higher within genomic regions affected by copy number amplifications. We also calculated sample-level means of nucleotide frequencies observed at genomic positions spanning fragment ends. Using a combination of iwFAF and nine nucleotide frequencies from three positions surrounding fragment ends, we developed a machine learning model to differentiate healthy individuals from patients with cancer. We observed an area under the receiver operative characteristic curve (AUC) of 0.91 for detection of cancer at any stage and an AUC of 0.87 for detection of stage I cancer. Our findings remained robust with as few as 1 million fragments analyzed per sample, demonstrating that analysis of fragment ends can become a cost-effective and accessible approach for cancer detection and monitoring.
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Affiliation(s)
- Karan K. Budhraja
- Department of Surgery and Center for Human Genomics and Precision Medicine, University of Wisconsin–Madison; Madison, WI 53705, USA
| | - Bradon R. McDonald
- Department of Surgery and Center for Human Genomics and Precision Medicine, University of Wisconsin–Madison; Madison, WI 53705, USA
| | - Michelle D. Stephens
- Department of Surgery and Center for Human Genomics and Precision Medicine, University of Wisconsin–Madison; Madison, WI 53705, USA
| | | | - Havell Markus
- Pennsylvania State University, Hershey, PA 17033, USA
| | - Maria Farooq
- Department of Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Patricia F. Favaro
- Department of Surgery and Center for Human Genomics and Precision Medicine, University of Wisconsin–Madison; Madison, WI 53705, USA
| | - Sydney Connor
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Sara A. Byron
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | | | | | | | | | | | - Michael D. Prados
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | | | | | | | - Jeffrey M. Trent
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Muhammed Murtaza
- Department of Surgery and Center for Human Genomics and Precision Medicine, University of Wisconsin–Madison; Madison, WI 53705, USA
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5
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Vitanza NA, Wilson AL, Huang W, Seidel K, Brown C, Gustafson JA, Yokoyama JK, Johnson AJ, Baxter BA, Koning RW, Reid AN, Meechan M, Biery MC, Myers C, Rawlings-Rhea SD, Albert CM, Browd SR, Hauptman JS, Lee A, Ojemann JG, Berens ME, Dun MD, Foster JB, Crotty EE, Leary SE, Cole BL, Perez FA, Wright JN, Orentas RJ, Chour T, Newell EW, Whiteaker JR, Zhao L, Paulovich AG, Pinto N, Gust J, Gardner RA, Jensen MC, Park JR. Intraventricular B7-H3 CAR T Cells for Diffuse Intrinsic Pontine Glioma: Preliminary First-in-Human Bioactivity and Safety. Cancer Discov 2023; 13:114-131. [PMID: 36259971 PMCID: PMC9827115 DOI: 10.1158/2159-8290.cd-22-0750] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [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: 07/13/2022] [Revised: 09/13/2022] [Accepted: 10/13/2022] [Indexed: 01/16/2023]
Abstract
Diffuse intrinsic pontine glioma (DIPG) remains a fatal brainstem tumor demanding innovative therapies. As B7-H3 (CD276) is expressed on central nervous system (CNS) tumors, we designed B7-H3-specific chimeric antigen receptor (CAR) T cells, confirmed their preclinical efficacy, and opened BrainChild-03 (NCT04185038), a first-in-human phase I trial administering repeated locoregional B7-H3 CAR T cells to children with recurrent/refractory CNS tumors and DIPG. Here, we report the results of the first three evaluable patients with DIPG (including two who enrolled after progression), who received 40 infusions with no dose-limiting toxicities. One patient had sustained clinical and radiographic improvement through 12 months on study. Patients exhibited correlative evidence of local immune activation and persistent cerebrospinal fluid (CSF) B7-H3 CAR T cells. Targeted mass spectrometry of CSF biospecimens revealed modulation of B7-H3 and critical immune analytes (CD14, CD163, CSF-1, CXCL13, and VCAM-1). Our data suggest the feasibility of repeated intracranial B7-H3 CAR T-cell dosing and that intracranial delivery may induce local immune activation. SIGNIFICANCE This is the first report of repeatedly dosed intracranial B7-H3 CAR T cells for patients with DIPG and includes preliminary tolerability, the detection of CAR T cells in the CSF, CSF cytokine elevations supporting locoregional immune activation, and the feasibility of serial mass spectrometry from both serum and CSF. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Nicholas A. Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Corresponding Author: Nicholas A. Vitanza, Seattle Children's Research Institute, M/S JMB-8, 1900 9th Avenue, Seattle, WA 98101. Phone: 206-884-4084; E-mail:
| | | | - Wenjun Huang
- Seattle Children's Therapeutics, Seattle, Washington
| | - Kristy Seidel
- Seattle Children's Therapeutics, Seattle, Washington
| | - Christopher Brown
- Seattle Children's Therapeutics, Seattle, Washington.,Therapeutic Cell Production Core, Seattle Children's Research Institute, Seattle, Washington
| | | | | | | | | | | | | | - Michael Meechan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Matthew C. Biery
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Carrie Myers
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | | | - Catherine M. Albert
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Samuel R. Browd
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Jason S. Hauptman
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Amy Lee
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Jeffrey G. Ojemann
- Division of Neurosurgery, Seattle Children's Hospital and Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Michael E. Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Matthew D. Dun
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, Callaghan, Australia.,Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, Australia
| | - Jessica B. Foster
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Erin E. Crotty
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Sarah E.S. Leary
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Bonnie L. Cole
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington
| | - Francisco A. Perez
- Department of Radiology, Seattle Children's Hospital, Seattle, Washington
| | - Jason N. Wright
- Department of Radiology, Seattle Children's Hospital, Seattle, Washington
| | - Rimas J. Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Tony Chour
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Evan W. Newell
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Navin Pinto
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington
| | - Juliane Gust
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington.,Division of Pediatric Neurology, Department of Neurology, University of Washington, Seattle, Washington
| | - Rebecca A. Gardner
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Seattle Children's Therapeutics, Seattle, Washington
| | | | - Julie R. Park
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington.,Seattle Children's Therapeutics, Seattle, Washington
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6
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Ferdosi SR, Taylor B, Lee M, Tang N, Peng S, Bybee R, Reid G, Hartman L, Garcia-Mansfield K, Sharma R, Pirrotte P, Ma J, Parisian AD, Furnari F, Dhruv HD, Berens ME. PTEN loss drives resistance to the neddylation inhibitor MLN4924 in glioblastoma and can be overcome with TOP2A inhibitors. Neuro Oncol 2022; 24:1857-1868. [PMID: 35305088 PMCID: PMC9629460 DOI: 10.1093/neuonc/noac067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Neddylation inhibition, affecting posttranslational protein function and turnover, is a promising therapeutic approach to cancer. We report vulnerability to MLN4924 or pevonedistat (a neddylation inhibitor) in a subset of glioblastoma (GBM) preclinical models and identify biomarkers, mechanisms, and signatures of differential response. METHODS GBM sequencing data were queried for genes associated with MLN4924 response status; candidates were validated by molecular techniques. Time-course transcriptomics and proteomics revealed processes implicated in MLN4924 response. RESULTS Vulnerability to MLN4924 is associated with elevated S-phase populations, re-replication, and DNA damage. Transcriptomics and shotgun proteomics depict PTEN signaling, DNA replication, and chromatin instability pathways as significant differentiators between sensitive and resistant models. Loss of PTEN and its nuclear functions is associated with resistance to MLN4924. Time-course proteomics identified elevated TOP2A in resistant models through treatment. TOP2A inhibitors combined with MLN4924 prove synergistic. CONCLUSIONS We show that PTEN status serves as both a novel biomarker for MLN4924 response in GBM and reveals a vulnerability to TOP2A inhibitors in combination with MLN4924.
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Affiliation(s)
- Shayesteh R Ferdosi
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Brett Taylor
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Matthew Lee
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Nanyun Tang
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Sen Peng
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Rita Bybee
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - George Reid
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Lauren Hartman
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Krystine Garcia-Mansfield
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Ritin Sharma
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Jianhui Ma
- Ludwig Cancer Research, San Diego Branch, La Jolla, CA 92093, USA
| | | | - Frank Furnari
- Ludwig Cancer Research, San Diego Branch, La Jolla, CA 92093, USA
- Department of Pathology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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7
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Kelly RJ, Whitsett TG, Snipes GJ, Dobin SM, Finholt J, Settele N, Priest EL, Youens K, Wallace LB, Schwartz G, Wong L, Henderson SM, Gowan AC, Fonkem E, Juarez MI, Murray CE, Wu J, Van Keuren-Jensen K, Pirrotte P, Highlander S, Contente T, Baker A, Victorino J, Berens ME. The Texas Immuno-Oncology Biorepository, a statewide biospecimen collection and clinical informatics system to enable longitudinal tumor and immune profiling. Proc (Bayl Univ Med Cent) 2022; 36:1-7. [PMID: 36578607 PMCID: PMC9762845 DOI: 10.1080/08998280.2022.2114129] [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] [Indexed: 12/31/2022] Open
Abstract
A detailed understanding of the molecular and immunological changes that occur longitudinally across tumors exposed to immune checkpoint inhibitors is a significant knowledge gap in oncology. To address this unmet need, we created a statewide biospecimen collection and clinical informatics system to enable longitudinal tumor and immune profiling and to enhance translational research. The Texas Immuno-Oncology Biorepository (TIOB) consents patients to collect, process, store, and analyze serial biospecimens of tissue, blood, urine, and stool from a diverse population of over 100,000 cancer patients treated each year across the Baylor Scott & White Health system. Here we sought to demonstrate that these samples were fit for purpose with regard to downstream multi-omic assays. Plasma, urine, peripheral blood mononuclear cells, and stool samples from 11 enrolled patients were collected from various cancer types. RNA isolated from extracellular vesicles derived from plasma and urine was sufficient for transcriptomics. Peripheral blood mononuclear cells demonstrated excellent yield and viability. Ten of 11 stool samples produced RNA quality to enable microbiome characterization. Sample acquisition and processing methods are known to impact sample quality and performance. We demonstrate that consistent acquisition methodology, sample preparation, and sample storage employed by the TIOB can produce high-quality specimens, suited for employment in a wide array of multi-omic platforms, enabling comprehensive immune and molecular profiling.
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Affiliation(s)
- Ronan J. Kelly
- Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas,Corresponding author: Ronan J. Kelly, MD, MBA, Charles A. Sammons Cancer Center, Baylor University Medical Center, 3420 Worth Street, Suite 550, Dallas, TX75246 (e-mail: ); Michael E. Berens, PhD, Cancer & Cell Biology Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ85004 (e-mail: )
| | - Timothy G. Whitsett
- Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - G. Jackson Snipes
- Department of Pathology, Baylor University Medical Center, Dallas, Texas
| | - Sheila M. Dobin
- Department of Pathology, Baylor Scott & White Medical Center – Temple, Temple, Texas
| | | | | | | | - Kenneth Youens
- Department of Pathology, Baylor University Medical Center, Dallas, Texas
| | - Lucy B. Wallace
- Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas,Texas A&M Health Science Center, Dallas, Texas
| | - Gary Schwartz
- Department of Thoracic Surgery, Baylor University Medical Center, Dallas, Texas
| | - Lucas Wong
- Texas A&M Health Science Center, Dallas, Texas,Department of Hematology and Medical Oncology, Baylor Scott & White Medical Center – Temple, Temple, Texas
| | | | - Alan C. Gowan
- Baylor Scott & White Vasicek Cancer Treatment Center – Temple, Temple, Texas
| | - Ekokobe Fonkem
- Texas A&M Health Science Center, Dallas, Texas,Department of Neurosurgery, Baylor Scott & White Medical Center – Temple, Temple, Texas
| | - Maria I. Juarez
- Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Christal E. Murray
- Department of Hematology and Medical Oncology, Baylor Scott & White Medical Center – Temple, Temple, Texas,Baylor Scott & White Cancer Center – Round Rock, Round Rock, Texas
| | - Jeffrey Wu
- Department of Cardiac and Thoracic Surgery, Baylor Scott & White All Saints Medical Center, Fort Worth, Texas
| | | | - Patrick Pirrotte
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Sarah Highlander
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Tania Contente
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Angela Baker
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jose Victorino
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Michael E. Berens
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona,Corresponding author: Ronan J. Kelly, MD, MBA, Charles A. Sammons Cancer Center, Baylor University Medical Center, 3420 Worth Street, Suite 550, Dallas, TX75246 (e-mail: ); Michael E. Berens, PhD, Cancer & Cell Biology Division, Translational Genomics Research Institute, 445 N. Fifth Street, Phoenix, AZ85004 (e-mail: )
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8
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Shelton AK, Smithberger E, Butler M, Stamper A, Bash RE, Angus SP, East MP, Johnson GL, Berens ME, Furnari FB, Miller R. Abstract 3248: Acquired resistance to targeted inhibitors in EGFR-driven glioblastoma: Identification of dual kinase targets. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3248] [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
Glioblastoma (GBM) is a devastating primary brain tumor with <5% 5-year survival. CDKN2A deletion (~60%) and EGFR amplification (~55%) mutations frequently co-occur in these tumors. EGFR is an attractive therapeutic target due to its mutational frequency and availability of brain-penetrant tyrosine kinase inhibitors (TKI). Several EGFR TKI have failed clinically, due in part to acquired resistance. To mechanistically examine this type of resistance, we used a panel of ten genetically engineered mouse astrocyte lines harboring Cdkn2a deletion and EGFRvIII, a common (~30%) activating mutation. Resistant cells were generated via long-term exposure to gefitinib or erlotinib, either in vitro or in vivo. Both transcriptomic (RNAseq) and proteomic (multiplexed inhibitor beads with mass spectrometry, MIB-MS) experiments showed that cell lines clustered primarily by resistance phenotype and secondarily by method of resistance development when analyzed using principal component analysis and unsupervised hierarchical clustering. Kinases involved in proliferation and differentiation signaling pathways (ex: Pdgfrb, Pdk2, Tnik, Mapk3, Fgfr2) were upregulated in both RNAseq and MIB-MS datasets and thus represent putative druggable targets for dual kinase inhibition. Analysis of commonly upregulated kinases and their commercially available inhibitors revealed dovitinib and dasatinib, two brain-penetrant drugs approved for other cancer indications, as candidates for dual inhibition with an EGFR TKI. Resistant cell lines were all more sensitive to dovitinib than their drug-naïve parents; however, sensitivity to dasatinib varied. BLISS analysis of dual treatment with EGFR TKI neratinib and dasatinib or dovitinib revealed synergistic drug interactions in most lines. Additionally, drug-naïve cells displayed a robust, acute proteomic response to EGFR TKI afatinib over 48h, while the response of resistant lines was significantly blunted. This model system can also be used to examine acute vs. long-term kinome response to EGFR TKI. Acute response was examined by treating drug-naïve cells with afatinib over 48h, and long-term kinome rewiring was observed by comparing untreated cells to gefitinib- and erlotinib-resistant cell lines. Combing both RNAseq datasets for kinases upregulated in both drug-naïve cells over a 48h EGFR TKI treatment course and in resistant cell lines compared to their sensitive parents reveals 21 and 13 common kinases, respectively, at p<0.001. Eight of these kinases (Cdk19, Ddr1, Kalrn, Khk, Mapk3, Pink1, Tnik, Ulk2) appear in both the in vitro and in vivo datasets, indicating a conserved kinome response regardless of method of resistance generation. Overall, integrated kinome profiling in GBM models with defined mutational profiles provides a powerful framework to identify novel therapeutic targets that could significantly alter current treatment paradigms.
Citation Format: Abigail K. Shelton, Erin Smithberger, Madison Butler, Allie Stamper, Ryan E. Bash, Steve P. Angus, Michael P. East, Gary L. Johnson, Michael E. Berens, Frank B. Furnari, Ryan Miller. Acquired resistance to targeted inhibitors in EGFR-driven glioblastoma: Identification of dual kinase targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3248.
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Affiliation(s)
| | | | - Madison Butler
- 1University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Ryan E. Bash
- 2University of Alabama Birmingham, Birmingham, AL
| | | | - Michael P. East
- 1University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Gary L. Johnson
- 1University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Ryan Miller
- 2University of Alabama Birmingham, Birmingham, AL
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9
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Smithberger E, Shelton AK, Bash RE, Butler MK, Flores AR, Stamper A, Angus SP, East MP, Johnson GL, Berens ME, Furnari FB, Miller R. Abstract 1857: Glioblastoma growth is suppressed dual inhibition of EGFR and CDK6 kinases. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1857] [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
Glioblastoma (GBM) is a malignant brain tumor that has proven difficult to treat, despite expressing promising targets such as EGFRvIII. EGFRvIII, a mutant version of the epidermal growth factor receptor (EGFR), is constitutively active and not present in normal brain cells. The tumor specificity of EGFRvIII and the frequent EGFR amplification seen in GBM make EGFR a potentially attractive therapeutic target; however, clinical studies have shown little to no efficacy for EGFR tyrosine kinase inhibitors (TKI). One reason for this lack of efficacy may be adaptive resistance. We used RNA sequencing and multiplexed inhibitor beads with mass spectrometry (MIB-MS) to study the transcriptomes and kinomes of genetically engineered mouse astrocytes to investigate this resistance and identify potential targets for dual inhibition. Out of 329 kinases detected by MIB-MS, 76 were differentially expressed between cells with Cdkn2a deletion (“C”) and cells that also overexpressed EGFRvIII (“CEv3”). Thirty-four of these kinases were overexpressed in the CEv3 cells relative to the parental C cells (log2 fold change of 5.6, p<1x105). One of these kinases, Cdk6, is also significantly overexpressed in CEv3 cells versus cells that have a further loss of function mutation of Pten (“CEv3P”) (log2 fold change of 5.6, p<1x105). Despite this significant differential expression at the protein level, RNA expression of Cdk6 was similar between cell lines. When these cells were treated with the CDK6 inhibitor abemaciclib, CEv3 cells were found to be significantly more sensitive to inhibition than C and CEv3P cells (IC50 of 0.10 μM vs. 0.18 μM and 0.23 μM, respectively). Similarly, when cells were treated with abemaciclib in combination with the EGFR inhibitor neratinib, there was significantly higher synergy in CEv3 cells than C or CEv3P cells. Genotypically-matched patient-derived xenograft (PDX) cells were assayed for EGFR-CDK6 inhibitor synergy and showed a similar pattern of greater synergy in cells with EGFRvIII overexpression and functional PTEN than cells with EGFRvIII overexpression and PTEN loss. CEv3 and CEv3P cells were orthotopically implanted into mice and treated with neratinib, abemaciclib, or a combination. In CEv3-injected mice, combination treatment led to significantly longer survival than either single agent or control treatment. However, in CEv3P-injected mice, no survival difference was seen between any of the treatment arms. Taken together, these data provide strong evidence that CDK6 is a promising target for combination treatment with EGFR inhibitors in glioblastoma.
Citation Format: Erin Smithberger, Abigail K. Shelton, Ryan E. Bash, Madison K. Butler, Alex R. Flores, Allie Stamper, Steven P. Angus, Michael P. East, Gary L. Johnson, Michael E. Berens, Frank B. Furnari, Ryan Miller. Glioblastoma growth is suppressed dual inhibition of EGFR and CDK6 kinases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1857.
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Affiliation(s)
| | | | - Ryan E. Bash
- 2University of Alabama at Birmingham, Birmingham, AL
| | | | | | - Allie Stamper
- 2University of Alabama at Birmingham, Birmingham, AL
| | | | - Michael P. East
- 1University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Gary L. Johnson
- 1University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Ryan Miller
- 2University of Alabama at Birmingham, Birmingham, AL
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10
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Wang GM, Cioffi G, Patil N, Waite KA, Lanese R, Ostrom Q, Kruchko C, Berens ME, Connor JR, Lathia JD, Rubin JB, Barnholtz-Sloan JS. Importance of the intersection of age and sex to understand variation in incidence and survival for primary malignant gliomas. Neuro Oncol 2021; 24:302-310. [PMID: 34387331 PMCID: PMC8804884 DOI: 10.1093/neuonc/noab199] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Gliomas are the most common type of malignant brain and other CNS tumors, accounting for 80.8% of malignant primary brain and CNS tumors. They cause significant morbidity and mortality. This study investigates the intersection between age and sex to better understand variation of incidence and survival for glioma in the United States. Methods Incidence data from 2000 to 2017 were obtained from CBTRUS, which obtains data from the NPCR and SEER, and survival data from the CDC’s NPCR. Age-adjusted incidence rate ratios (IRR) per 100 000 were generated to compare male-to-female incidence by age group. Cox proportional hazard models were performed by age group, generating hazard ratios to assess male-to-female survival differences. Results Overall, glioma incidence was higher in males. Male-to-female incidence was lowest in ages 0-9 years (IRR: 1.04, 95% CI: 1.01-1.07, P = .003), increasing with age, peaking at 50-59 years (IRR: 1.56, 95% CI: 1.53-1.59, P < .001). Females had worse survival for ages 0-9 (HR: 0.93, 95% CI: 0.87-0.99), though male survival was worse for all other age groups, with the difference highest in those 20-29 years (HR: 1.36, 95% CI: 1.28-1.44). Incidence and survival differences by age and sex also varied by histological subtype of glioma. Conclusions To better understand the variation in glioma incidence and survival, investigating the intersection of age and sex is key. The current work shows that the combined impact of these variables is dependent on glioma subtype. These results contribute to the growing understanding of sex and age differences that impact cancer incidence and survival.
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Affiliation(s)
- Gi-Ming Wang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH.,Case Western Reserve University School of Medicine, Cleveland, OH
| | - Gino Cioffi
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH.,Cleveland Center for Health Outcomes Research (CCHOR), Cleveland, OH.,Case Western Reserve University School of Medicine, Cleveland, OH.,Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, IL
| | - Nirav Patil
- Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, IL.,Research and Education Institute, University Hospitals Health System (UHHS), Cleveland, OH
| | - Kristin A Waite
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH.,Cleveland Center for Health Outcomes Research (CCHOR), Cleveland, OH.,Case Western Reserve University School of Medicine, Cleveland, OH.,Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, IL
| | - Robert Lanese
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH.,Case Western Reserve University School of Medicine, Cleveland, OH
| | - Quinn Ostrom
- Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, IL.,Department of Neurosurgery, Duke University, Durham, NC
| | - Carol Kruchko
- Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, IL
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute (Tgen), Phoenix, AZ
| | - James R Connor
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA
| | - Justin D Lathia
- Deparment of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Joshua B Rubin
- Departments of Pediatrics and Neuroscience, Washington University School of Medicine, St. Louis, MO
| | - Jill S Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH.,Cleveland Center for Health Outcomes Research (CCHOR), Cleveland, OH.,Case Western Reserve University School of Medicine, Cleveland, OH.,Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, IL.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH.,Cleveland Institute for Computational Biology, Cleveland, OH.,Research Health Analytics and Informatics, University Hospitals Health System (UHHS), Cleveland, OH
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11
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Lee ME, Tang N, Ahluwalia M, Fonkem E, Fink K, Dhurv H, Dhurv H, Berens ME, Peng S. Abstract 180: Identifying signatures of vulnerability through machine learning in an umbrella trial for glioblastoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-180] [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
Glioblastoma is characterized by intra- and inter-tumoral heterogeneity. An umbrella trial tests multiple investigational treatment arms depending on corresponding biomarker signatures. A contingency of an efficient umbrella trial is a suite of preferably orthogonal molecular biomarkers to classify patients into the likely-most-beneficial arm. Assigning thresholds of molecular signatures to classify a patient as a “most-likely responder” for one specific treatment arm is a crucial task. Gene Set Variation Analysis (GSVA) of specimens from a GBM clinical trial of methoxyamine associated differential enrichment in DNA repair pathways activities with patient response. However, the large number of DNA-repair related pathways confound confident “high” enrichment of responder, as well as obscuring to what degree each feature contributes to the likelihood of a patient's response. Here, we utilized semi-supervised machine learning, Entropy-Regularized Logistic Regression (ERLR) to predict vulnerability classification. By first training all available data using semi-supervised algorithms we transformed unclassified TCGA GBM samples with highest certainty of predicted response into a self-labeled dataset. In this case, we developed a predictive model which has a larger sample size and potential better performance. Our umbrella trial design currently includes three treatment arms for GBM patients: arsenic trioxide, methoxyamine, and pevonedistat. Each treatment arm manifests its own signature developed by the above (or similar) machine learning pipeline based on selected gene mutation status and whole transcriptome data. In order to increase the robustness and scalability (with future more treatment arms), we also developed a multi-label classification ensemble model that's capable of predicting a probability of “fitness” of each novel therapeutic agent for each patient. By expansion to three, independent treatment arms within a single umbrella trial, a “mock” stratification of TCGA GBM patients labeled 56% of all cases into at least one “high likelihood of response” arm. Predicted vulnerability using genomic data from preclinical PDX models placed 4 out of 6 models into a “high likelihood of response” regimen. Our utilization of multiple vulnerability signatures in an umbrella trial demonstrates how a precision medicine model can support an efficient clinical trial for heterogeneous diseases such as GBM.
Citation Format: Matthew Eric Lee, Nanyun Tang, Manmeet Ahluwalia, Ekokobe Fonkem, Karen Fink, Harshil Dhurv, Harshil Dhurv, Michael E. Berens, Sen Peng. Identifying signatures of vulnerability through machine learning in an umbrella trial for glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 180.
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Affiliation(s)
| | - Nanyun Tang
- 1The Translational Genomics Research Institute, Phoenix, AZ
| | | | | | - Karen Fink
- 4Baylor Scott & White Health, Dallas, TX
| | - Harshil Dhurv
- 1The Translational Genomics Research Institute, Phoenix, AZ
| | - Harshil Dhurv
- 1The Translational Genomics Research Institute, Phoenix, AZ
| | | | - Sen Peng
- 1The Translational Genomics Research Institute, Phoenix, AZ
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12
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Iyer J, Akkad A, Tang N, Berens ME, Zenhausern F, Gu J. Abstract 2984: Building an in vitro blood brain barrier model to test the influence of tight junction gene alleles on disruption by focused ultrasound to treat brain tumors. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2984] [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
Treating primary or metastatic tumors in the brain (glioblastomas, melanoma, lung cancer, breast cancer) proves challenging by virtue of the protective function of the blood brain barrier (BBB). Recently, it has been shown that low intensity focused ultrasonic (LIFU) waves stably cavitate infused microbubbles which then mechanically disrupt the tight junctions of the BBB. This leads to temporary, recoverable opening of the BBB, and passage of otherwise disqualified cancer-therapeutic drugs at precise locations targeted by the focused ultrasound. To date, potential genetic influences on the durability and vulnerability of tight junctions to LIFU have not been elucidated, nor have the determinants of tight junction repair post LIFU been thoroughly investigated. We report the development of an ultrasound transparent organ-on-chip model to test LIFU with microbubble infusion treatment on a cell-engineered BBB. The BBB is developed using brain-specific endothelial cells derived from genomically characterized immortalized pluripotent stem cells (iPSC). Furthermore, to test genetic variation effects we propose that alleles coding for the proteins involved in tight junction assembly contribute to LIFU disruption variability. Developing preclinical models of the BBB to accommodate cell sources with tight junction genes of different allele makeup will shed light on how individuals will respond to different ultrasound frequencies. The in vitro BBB device is composed of two orthogonally stacked fluidic channels formed by top and bottom polydimethylsiloxane (PDMS) membranes and a middle polyester membrane with 3 µm pores. An ultrasound system is constructed with a waveform generator, amplifier, and 1MHz ultrasound transducer. A 0.5 MHz receiving transducer and a digital storage oscilloscope are used for stable cavitation monitoring. Nanobubbles (FUS Instruments) transduce the LIFU into a mechanical vibration force to disrupt the BBB. To deliver the ultrasonic waves, the device is submerged in degassed DI water in a custom tank. Fluid flow was achieved, and subharmonic ultrasound signal is observed using the digital oscilloscope with Fast Fourier Transform (FFT). Preliminary results convey stable cavitation with LIFU and the formation of tight junctions in a brain microvascular endothelial cell monolayer in the device, eventually leading to a versatile platform to evaluate genetic-based vulnerability of the BBB.
Citation Format: Jayashree Iyer, Adam Akkad, Nanyun Tang, Michael E. Berens, Frederic Zenhausern, Jian Gu. Building an in vitro blood brain barrier model to test the influence of tight junction gene alleles on disruption by focused ultrasound to treat brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2984.
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Affiliation(s)
| | - Adam Akkad
- 2The University of Arizona College of Medicine, Phoenix, AZ
| | - Nanyun Tang
- 1Translational Genomics Research Institute, Phoenix, AZ
| | | | | | - Jian Gu
- 2The University of Arizona College of Medicine, Phoenix, AZ
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13
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Tang N, Leskoske K, Garcia-Mansfield K, Sharma R, Tolson H, Pirrotte P, Berens ME. Abstract 318: Multi-omics to edge into precision medicine for DIPG. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-318] [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
Effective targeted cancer therapies are limited due to lack of our understanding of disease pathogenesis at the molecular level. Diffuse intrinsic pontine glioma (DIPG) is an incurable pediatric brain tumor with 80% of DIPGs harboring H3F3A (H3.3) mutation that lead to a substitution of methionine for lysine at position 27 (K27M). The tumors bearing H3.3K27M mutation arise throughout the midline structures with global depletion of H3.3K27 me3 (trimethylation). These histone mutations modify the epigenome and alter oncogenic transcription, causing oncogenic insults to progenitor cells in early neurodevelopment (PMID: 30453529). To determine the reprogramming pathways in the cell context of H3.3K27M tumors, we conducted liquid chromatography-mass spectrometry-based proteomic and phosphoproteomic analysis on seven patient-derived DIPG cell lines that can be stably passaged in serum-free neural stem cell media and displayed distinct morphologies, growth rates and chromosome abnormalities (PMID: 21368213). Three normal neuronal stem cell lines were included as non-tumor brain cells for comparison. Pathway analysis identified 29 pathways that are significantly altered in DIPG compared to normal brain cells at both the protein abundance and phosphosite level. Notably, AKT and MAPK associated PI3K signaling, VEGF signaling, mTOR signaling, and HIF1a signaling were differentially active in H3.3K27M tumors compared to healthy control cell lines. We saw significantly higher activity of multiple kinases involved in axon guidance and cytoskeletal remodeling in DIPG, such as PTK2B, DYRK2, TTBK2 and MARK2. This is the first time to report an increased abundance and kinase activity of Pyk2 protein (coded by PTK2B), a close homologue of FAK and its associated signaling in DIPG. Overexpression and autophosphorylation of Pyk2 are required to stimulate glioma cell migration (PMIDs: 15967096, 18648907). Pyk2 has also been proposed to act in concert with Src to link Gi- or Gq-coupled receptors with the mitogen-activated protein (MAP) kinase signaling pathway (PMID:12960403). Because of the shared signaling across kinase pathways, targeting activated Pyk2 in DIPG may complement inhibitors of other dysregulated signaling networks in DIPG such as MAPK2, VEGFR, PI3K and Src. Our data also found that IL13RA2 was upregulated in DIPG; others have shown that increased expression of IL13RA2 is associated with poor prognosis in GBM (PMIDs: 32913543, 30366424). We conclude that for H3 K27M DIPG tumors, campaigns to target Pyk2, MAPK2, VEGFR, PI3K, Src and IL13Ra2 using small molecules that traverse the blood brain barrier loom as promising opportunities for drug development.
Citation Format: Nanyun Tang, Kristin Leskoske, Krystine Garcia-Mansfield, Ritin Sharma, Hannah Tolson, Patrick Pirrotte, Michael E. Berens. Multi-omics to edge into precision medicine for DIPG [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 318.
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Affiliation(s)
- Nanyun Tang
- Translational Genomics Research Institute (TGen), Phoenix, AZ
| | | | | | - Ritin Sharma
- Translational Genomics Research Institute (TGen), Phoenix, AZ
| | - Hannah Tolson
- Translational Genomics Research Institute (TGen), Phoenix, AZ
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14
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Yang W, Lathia JD, Connor JR, Berens ME, Barnholtz-Sloan JS, Rubin JB. OMIC-10. TRANSCRIPTOMIC ANALYSIS REVEALS SEX DIFFERENCES IN PEDIATRIC BRAIN MECHANISMS. Neuro Oncol 2021. [PMCID: PMC8168252 DOI: 10.1093/neuonc/noab090.157] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A significant male overrepresentation exists in cancer incidence and in cancer-related deaths. This is true in all regions of the world and across the lifespan. We published an analysis of adult glioblastoma transcriptomes in which we identified sex-biased molecular features that distinguished the longest surviving male and female patients. Male GBM was characterized by decreased expression of positive regulators of the cell, while female GBM was characterized by decreased expression of intermediates in integrin signaling. To determine whether similar sex differences exist in pediatric brain tumors (pBTs), we accessed 860 pBT transcriptomes, representing all diagnostic categories and ages through the Children’s Brain Tumor Network. Unsupervised Bayesian nearest neighbor analysis of gene expression revealed distinct male and female expression patterns indicating fundamental differences exist in pBTs as a function of sex. Similar to our adult GBM analysis, male pBTs were distinguished from female pBTs by the involvement of cell cycle regulatory pathways. In contrast to adult GBM, female pBTs were characterized by involvement of metabolism and inflammatory/ immunity pathways. Interestingly, these sex differences were also evident in a parallel analysis of 209 of neuroblastoma cases. Focused analysis of the most common malignant pBTs (high-grade glioma, medulloblastoma, and ependymoma) revealed that each disease type exhibited significant sex differences in molecular profile, involving distinct pathways in each tumor type. Together, these data indicate that sex-based differences in molecular mechanisms exist in pBTs, and imply that sex-specific approaches to pBT treatment might yield improved outcomes for all patients.
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Affiliation(s)
- Wei Yang
- Department of Genetics, Washington University School of Medicine University School of Medicine, St Louis, MO, USA
| | - Justin D Lathia
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, OH, USA
| | - James R Connor
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
| | | | - Jill S Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine & University Hospitals, Cleveland, OH, USA
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO, USA
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15
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Rusert JM, Juarez EF, Brabetz S, Jensen J, Garancher A, Chau LQ, Tacheva-Grigorova SK, Wahab S, Udaka YT, Finlay D, Seker-Cin H, Reardon B, Gröbner S, Serrano J, Ecker J, Qi L, Kogiso M, Du Y, Baxter PA, Henderson JJ, Berens ME, Vuori K, Milde T, Cho YJ, Li XN, Olson JM, Reyes I, Snuderl M, Wong TC, Dimmock DP, Nahas SA, Malicki D, Crawford JR, Levy ML, Van Allen EM, Pfister SM, Tamayo P, Kool M, Mesirov JP, Wechsler-Reya RJ. Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Cancer Res 2020; 80:5393-5407. [PMID: 33046443 DOI: 10.1158/0008-5472.can-20-1655] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 05/22/2020] [Revised: 09/04/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Medulloblastoma is among the most common malignant brain tumors in children. Recent studies have identified at least four subgroups of the disease that differ in terms of molecular characteristics and patient outcomes. Despite this heterogeneity, most patients with medulloblastoma receive similar therapies, including surgery, radiation, and intensive chemotherapy. Although these treatments prolong survival, many patients still die from the disease and survivors suffer severe long-term side effects from therapy. We hypothesize that each patient with medulloblastoma is sensitive to different therapies and that tailoring therapy based on the molecular and cellular characteristics of patients' tumors will improve outcomes. To test this, we assembled a panel of orthotopic patient-derived xenografts (PDX) and subjected them to DNA sequencing, gene expression profiling, and high-throughput drug screening. Analysis of DNA sequencing revealed that most medulloblastomas do not have actionable mutations that point to effective therapies. In contrast, gene expression and drug response data provided valuable information about potential therapies for every tumor. For example, drug screening demonstrated that actinomycin D, which is used for treatment of sarcoma but rarely for medulloblastoma, was active against PDXs representing Group 3 medulloblastoma, the most aggressive form of the disease. Functional analysis of tumor cells was successfully used in a clinical setting to identify more treatment options than sequencing alone. These studies suggest that it should be possible to move away from a one-size-fits-all approach and begin to treat each patient with therapies that are effective against their specific tumor. SIGNIFICANCE: These findings show that high-throughput drug screening identifies therapies for medulloblastoma that cannot be predicted by genomic or transcriptomic analysis.
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Affiliation(s)
- Jessica M Rusert
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Edwin F Juarez
- Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Sebastian Brabetz
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - James Jensen
- Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Alexandra Garancher
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Lianne Q Chau
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Silvia K Tacheva-Grigorova
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Sameerah Wahab
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Yoko T Udaka
- Rady Children's Hospital San Diego, San Diego, California
| | - Darren Finlay
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Huriye Seker-Cin
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Brendan Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Susanne Gröbner
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | - Jonas Ecker
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Lin Qi
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Mari Kogiso
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Yuchen Du
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, Illinois
| | - Patricia A Baxter
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, Illinois
| | - Jacob J Henderson
- Papé Family Pediatric Research Institute, Department of Pediatrics, and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Kristiina Vuori
- Tumor Microenvironment and Cancer Immunology Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yoon-Jae Cho
- Papé Family Pediatric Research Institute, Department of Pediatrics, and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Xiao-Nan Li
- Brain Tumor Program, Texas Children's Cancer Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children's Hospital of Chicago, Department of Pediatrics, Northwestern University, Chicago, Illinois
| | - James M Olson
- Fred Hutchinson Cancer Research Center and Seattle Children's Hospital, Seattle, Washington
| | - Iris Reyes
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - Matija Snuderl
- Department of Pathology, NYU Langone Health, New York, New York
| | - Terence C Wong
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - Shareef A Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, California
| | - Denise Malicki
- Rady Children's Hospital, San Diego, California
- Department of Pathology, University of California San Diego, La Jolla, California
- Department of Pediatrics, University of California San Diego, La Jolla, California
| | - John R Crawford
- Rady Children's Hospital, San Diego, California
- Department of Pediatrics, University of California San Diego, La Jolla, California
- Department of Neurosciences, University of California San Diego, La Jolla, California
| | - Michael L Levy
- Rady Children's Hospital, San Diego, California
- Department of Surgery, University of California San Diego, La Jolla, California
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology and Hematology, University Hospital Heidelberg, Heidelberg, Germany
| | - Pablo Tamayo
- Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego, La Jolla, California
- Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.
- Rady Children's Institute for Genomic Medicine, San Diego, California
- Department of Pediatrics, University of California San Diego, La Jolla, California
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16
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Tang N, Reid G, Miller CR, Berens ME. Abstract 3681: Selective vulnerability of GBM PDX to a panel of EGFR tyrosine kinase inhibitors. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3681] [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
Glioblastoma (GBM), a particularly aggressive form of primary brain tumor, has poor survival due to a lack of effective treatments and high recurrence. Epidermal growth factor receptor (EGFR) (mapped to 7p 11.2), is frequently amplified and mutated (>50%) in GBM, and is suggested as a potential therapeutic target. To correlate chemo-vulnerability with genomic aberrations and further determine biomarkers for targeted therapies, a panel of seven EGFR tyrosine kinase inhibitors were tested in a selected nine human GBM patient-derived xenograft (PDX) panel; these preclinical models harbor different mutation combinations of CDKN2A deletion (C), PTEN deletion (P), wild-type EGFR (E) and/or EGFRvIII (Ev3) overexpression. A single agent drug dose response assay (DDR) was performed on GBM PDX neurospheres using drug concentrations ranging from 100uM to 0.5nM with a 12-point serial 3-fold dilution scheme. The cytotoxic efficacy of EGFR inhibition was dependent on both the PDX line and the EFGR inhibitor applied. GBM59 and GBM76 – both triple CEv3P mutants – were the most responsive to EGFR inhibition relative to the other GBM models tested. For GBM59, the IC50 values of afatinib, canertinib and neratinib, were sub-micromolar, and low micromolar (<3uM) for erlotinib, gefitinib and lapatinib. GBM76 had IC50 values of 1-8uM with all seven EGFR inhibitors including AZD3759. However, GBM155 and GBM126 with CEv3 but wildtype PTEN only responded to afatinib, canertinib and neratinib at low micromolar IC50 values (<3uM) but not to erlotinib, gefitinib and lapatinib. A deletion in PTEN may sensitize GBM cells with CEv3 mutations to erlotinib, gefitinib and lapatinib in vitro. The other group of GBM PDX lines (C only) represented by GBM122, GBM150 and GBM182 responded well to afatinib, canertinib and neratinib with IC50 values of 2- 9uM. GBM156 with CE had a similar profile to the group of C only or CEv3. GBM56 with CP showed the most resistance with mild responses to afatinib, canertinib and neratinib, as observed in its high micromolar IC50 values (6-9uM). Overall, neratinib is the most effective compound among the tested EGFR inhibitors based on IC50 values. Canertinib, the triple tyrosine kinase inhibitor against EGFR/HER2/ErbB-4, is the second most effective agent. Afatinib has similar drug efficacy to canertinib. All three compounds moderately inhibit all GBM PDX lines. The drug response mechanism and its correlation with the mutation status of CDKN2A, EGFR, and PTEN will be further investigated cross a broad array of GBM PDX models. Supported by NIH NCI R01 CA204136
Citation Format: Nanyun Tang, George Reid, C Ryan Miller, Michael E. Berens. Selective vulnerability of GBM PDX to a panel of EGFR tyrosine kinase inhibitors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3681.
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Affiliation(s)
- Nanyun Tang
- 1Translational Genomics Research Institute, Phoenix, AZ
| | - George Reid
- 1Translational Genomics Research Institute, Phoenix, AZ
| | - C Ryan Miller
- 2O'Neal Comprehensive Cancer Center, and Comprehensive Neuroscience Center, University of Alabama at Birmingham, Birmingham, AL
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17
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Iyer JS, Tang N, Ferdosi SR, Gokhale V, Hurley LH, Dhruv HD, Berens ME. Abstract 5822: Targeting an immortalization mutation to control glioblastoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5822] [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
Glioblastoma multiforme (GBM), the most aggressive primary brain cancer, is a heterogeneous disease. Standard treatment of temozolomide and radiation therapy has remained unchanged for the past thirty years. However, over 80% of GBM tumors have a telomerase reverse transcriptase (TERT) promoter mutation, or TPM. Telomerase is an enzyme containing the catalytic subunit, telomerase reverse transcriptase (TERT), that mediates telomere elongation in the nucleus. In the absence of any effective molecular targeting therapy for GBM, the elucidation of oncogenic signaling of TERT could open new avenues in GBM treatment. Canonically, mutations of TERT, which result in TERT upregulation, maintain telomere length in the nucleus and promote indefinite proliferation of cancer cells. However, a non-canonical function of TERT in the mitochondria has recently been suggested. We screened GBM cell models against a novel small molecule inhibitor (RG1534, Reglagene Inc.) that interferes with the functionality of a mutated TERT promoter. RG1534 selectively suppresses glioma cell viability without affecting non-transformed normal human astrocytes. A dose dependent response was observed in glioma cell lines, resulting in a decrease in TERT mRNA expression. To validate this, TERT protein levels in glioma cells treated with RG1534 were measured and results showed a reduction in expression post treatment. More interestingly, RG1534 treatment leads to rapid induction of apoptosis in glioma cell line which does not correlate with the time course of the telomere shortening effect. Based on prior findings that mitochondrial TERT is involved in DNA damage, we conducted the fractionation of various glioma cell lines to measure the protein expression of TERT in subcellular compartments. We observed a higher expression of TERT in the mitochondria compared to the nucleus. This suggests that TERT may have non-canonical functions outside of telomeric elongation. In summary, our results demonstrate that non-canonical functions of TERT may play a critical role in glioma pathobiology and warrants further study.
Citation Format: Jayashree S. Iyer, Nanyun Tang, Shayesteh R. Ferdosi, Vijay Gokhale, Laurence H. Hurley, Harshil D. Dhruv, Michael E. Berens. Targeting an immortalization mutation to control glioblastoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5822.
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Affiliation(s)
| | - Nanyun Tang
- 1Translational Genomics Institute, Phoenix, AZ
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18
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Blomquist MR, Ensign SF, D'Angelo F, Phillips JJ, Ceccarelli M, Peng S, Halperin RF, Caruso FP, Garofano L, Byron SA, Liang WS, Craig DW, Carpten JD, Prados MD, Trent JM, Berens ME, Iavarone A, Dhruv H, Tran NL. Temporospatial genomic profiling in glioblastoma identifies commonly altered core pathways underlying tumor progression. Neurooncol Adv 2020; 2:vdaa078. [PMID: 32743548 PMCID: PMC7388612 DOI: 10.1093/noajnl/vdaa078] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Tumor heterogeneity underlies resistance and disease progression in glioblastoma (GBM), and tumors most commonly recur adjacent to the surgical resection margins in contrast non-enhancing (NE) regions. To date, no targeted therapies have meaningfully altered overall patient survival in the up-front setting. The aim of this study was to characterize intratumoral heterogeneity in recurrent GBM using bulk samples from primary resection and recurrent samples taken from contrast-enhancing (EN) and contrast NE regions. Methods Whole exome and RNA sequencing were performed on matched bulk primary and multiple recurrent EN and NE tumor samples from 16 GBM patients who received standard of care treatment alone or in combination with investigational clinical trial regimens. Results Private mutations emerge across multi-region sampling in recurrent tumors. Genomic clonal analysis revealed increased enrichment in gene alterations regulating the G2M checkpoint, Kras signaling, Wnt signaling, and DNA repair in recurrent disease. Subsequent functional studies identified augmented PI3K/AKT transcriptional and protein activity throughout progression, validated by phospho-protein levels. Moreover, a mesenchymal transcriptional signature was observed in recurrent EN regions, which differed from the proneural signature in recurrent NE regions. Conclusions Subclonal populations observed within bulk resected primary GBMs transcriptionally evolve across tumor recurrence (EN and NE regions) and exhibit aberrant gene expression of common signaling pathways that persist despite standard or targeted therapy. Our findings provide evidence that there are both adaptive and clonally mediated dependencies of GBM on key pathways, such as the PI3K/AKT axis, for survival across recurrences.
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Affiliation(s)
- Mylan R Blomquist
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, Arizona, USA.,Department of Neurosurgery, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | | | - Fulvio D'Angelo
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, USA
| | - Joanna J Phillips
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | | | - Sen Peng
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Rebecca F Halperin
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Francesca P Caruso
- Department of Science and Technology, Università degli Studi del Sannio, Benevento, Italy
| | - Luciano Garofano
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, USA.,Department of Science and Technology, Università degli Studi del Sannio, Benevento, Italy
| | - Sara A Byron
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Winnie S Liang
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - David W Craig
- Department of Translational Genomics, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - John D Carpten
- Department of Translational Genomics, University of Southern California Keck School of Medicine, Los Angeles, California, USA
| | - Michael D Prados
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Jeffrey M Trent
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, New York, USA
| | - Harshil Dhruv
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Nhan L Tran
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, Arizona, USA.,Department of Neurosurgery, Mayo Clinic Arizona, Scottsdale, Arizona, USA
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19
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Dong M, Cioffi G, Wang J, Waite KA, Ostrom QT, Kruchko C, Lathia JD, Rubin JB, Berens ME, Connor J, Barnholtz-Sloan JS. Sex Differences in Cancer Incidence and Survival: A Pan-Cancer Analysis. Cancer Epidemiol Biomarkers Prev 2020; 29:1389-1397. [PMID: 32349967 DOI: 10.1158/1055-9965.epi-20-0036] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/01/2020] [Accepted: 04/24/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Sex plays an important role in the incidence, prognosis, and mortality of cancers, but often is not considered in disease treatment. METHODS We quantified sex differences in cancer incidence using the United States Cancer Statistics (USCS) public use database and sex differences in cancer survival using Surveillance, Epidemiology, and End Results (SEER) public use data from 2001 to 2016. Age-adjusted male-to-female incidence rate ratios (IRR) with 95% confidence intervals (CI) were generated by primary cancer site, race, and age groups. In addition, age-adjusted hazard ratios with 95% CI by sex within site were generated. RESULTS In general, cancer incidence and overall survival were lower in males than females, with Kaposi sarcoma (IRR: 9.751; 95% CI, 9.287-10.242; P < 0.001) having highest male-to-female incidence, and thyroid cancers (HR, 1.774; 95% CI, 1.707-1.845) having largest male-to-female survival difference. Asian or Pacific Islanders had particularly high male-to-female incidence in larynx cancers (IRR: 8.199; 95% CI, 7.203-9.363; P < 0.001), relative to other races. Among primary brain tumors, germ cell tumors had the largest male-to-female incidence (IRR: 3.03; 95% CI, 2.798-3.284, P < 0.001). CONCLUSIONS Overall, incidence and survival of cancer vary significantly by sex, with males generally having lower incidence and survival compared with females. Male-to-female incidence differences were also noted across race and age groups. These results provide strong evidence that the fundamental biology of sex differences affects cancers of all types. IMPACT This study represents the most recent and comprehensive reporting of sex differences in cancer incidence and survival in the United States. Identifying disadvantaged groups is critical as it can provide useful information to improve cancer survival, as well as to better understand the etiology and pathogenesis of specific cancers.
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Affiliation(s)
| | - Gino Cioffi
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Cleveland Center for Health Outcomes Research (CCHOR), Cleveland, Ohio.,Case Western Reserve University School of Medicine, Cleveland, Ohio.,Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, Illinois
| | - Jacqueline Wang
- Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Kristin A Waite
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Cleveland Center for Health Outcomes Research (CCHOR), Cleveland, Ohio.,Case Western Reserve University School of Medicine, Cleveland, Ohio.,Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, Illinois
| | - Quinn T Ostrom
- Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, Illinois.,Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, Texas
| | - Carol Kruchko
- Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, Illinois
| | - Justin D Lathia
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Joshua B Rubin
- Departments of Pediatrics and Neuroscience, Washington University School of Medicine, St. Louis, Missouri
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute (Tgen), Phoenix, Arizona
| | - James Connor
- Department of Neurosurgery, Penn State College of Medicine, Hershey, Pennsylvania
| | - Jill S Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio. .,Cleveland Center for Health Outcomes Research (CCHOR), Cleveland, Ohio.,Case Western Reserve University School of Medicine, Cleveland, Ohio.,Central Brain Tumor Registry of the United States (CBTRUS), Hinsdale, Illinois.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Cleveland Institute for Computational Biology, Cleveland, Ohio.,Research Health Analytics and Informatics, University Hospitals Health System (UHHS), Cleveland, Ohio
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20
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Vaubel RA, Tian S, Remonde D, Schroeder MA, Mladek AC, Kitange GJ, Caron A, Kollmeyer TM, Grove R, Peng S, Carlson BL, Ma DJ, Sarkar G, Evers L, Decker PA, Yan H, Dhruv HD, Berens ME, Wang Q, Marin BM, Klee EW, Califano A, LaChance DH, Eckel-Passow JE, Verhaak RG, Sulman EP, Burns TC, Meyer FB, O'Neill BP, Tran NL, Giannini C, Jenkins RB, Parney IF, Sarkaria JN. Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma. Clin Cancer Res 2020; 26:1094-1104. [PMID: 31852831 PMCID: PMC7056576 DOI: 10.1158/1078-0432.ccr-19-0909] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [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: 03/21/2019] [Revised: 05/25/2019] [Accepted: 12/12/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Glioblastoma is the most frequent and lethal primary brain tumor. Development of novel therapies relies on the availability of relevant preclinical models. We have established a panel of 96 glioblastoma patient-derived xenografts (PDX) and undertaken its genomic and phenotypic characterization. EXPERIMENTAL DESIGN PDXs were established from glioblastoma, IDH-wildtype (n = 93), glioblastoma, IDH-mutant (n = 2), diffuse midline glioma, H3 K27M-mutant (n = 1), and both primary (n = 60) and recurrent (n = 34) tumors. Tumor growth rates, histopathology, and treatment response were characterized. Integrated molecular profiling was performed by whole-exome sequencing (WES, n = 83), RNA-sequencing (n = 68), and genome-wide methylation profiling (n = 76). WES data from 24 patient tumors was compared with derivative models. RESULTS PDXs recapitulate many key phenotypic and molecular features of patient tumors. Orthotopic PDXs show characteristic tumor morphology and invasion patterns, but largely lack microvascular proliferation and necrosis. PDXs capture common and rare molecular drivers, including alterations of TERT, EGFR, PTEN, TP53, BRAF, and IDH1, most at frequencies comparable with human glioblastoma. However, PDGFRA amplification was absent. RNA-sequencing and genome-wide methylation profiling demonstrated broad representation of glioblastoma molecular subtypes. MGMT promoter methylation correlated with increased survival in response to temozolomide. WES of 24 matched patient tumors showed preservation of most genetic driver alterations, including EGFR amplification. However, in four patient-PDX pairs, driver alterations were gained or lost on engraftment, consistent with clonal selection. CONCLUSIONS Our PDX panel captures the molecular heterogeneity of glioblastoma and recapitulates many salient genetic and phenotypic features. All models and genomic data are openly available to investigators.
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Affiliation(s)
| | | | - Dioval Remonde
- Brody School of Medicine at East Carolina University, Greenville, North Carolina
| | | | | | | | | | | | | | - Sen Peng
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | | | | | - Lisa Evers
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | | | | | | | | | | | | | | | | | | | - Roel G Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Erik P Sulman
- New York University Langone Health, New York, New York
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21
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Yang W, Warrington NM, Taylor SJ, Whitmire P, Carrasco E, Singleton KW, Wu N, Lathia JD, Berens ME, Kim AH, Barnholtz-Sloan JS, Swanson KR, Luo J, Rubin JB. Sex differences in GBM revealed by analysis of patient imaging, transcriptome, and survival data. Sci Transl Med 2020; 11:11/473/eaao5253. [PMID: 30602536 DOI: 10.1126/scitranslmed.aao5253] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 08/20/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022]
Abstract
Sex differences in the incidence and outcome of human disease are broadly recognized but, in most cases, not sufficiently understood to enable sex-specific approaches to treatment. Glioblastoma (GBM), the most common malignant brain tumor, provides a case in point. Despite well-established differences in incidence and emerging indications of differences in outcome, there are few insights that distinguish male and female GBM at the molecular level or allow specific targeting of these biological differences. Here, using a quantitative imaging-based measure of response, we found that standard therapy is more effective in female compared with male patients with GBM. We then applied a computational algorithm to linked GBM transcriptome and outcome data and identified sex-specific molecular subtypes of GBM in which cell cycle and integrin signaling are the critical determinants of survival for male and female patients, respectively. The clinical relevance of cell cycle and integrin signaling pathway signatures was further established through correlations between gene expression and in vitro chemotherapy sensitivity in a panel of male and female patient-derived GBM cell lines. Together, these results suggest that greater precision in GBM molecular subtyping can be achieved through sex-specific analyses and that improved outcomes for all patients might be accomplished by tailoring treatment to sex differences in molecular mechanisms.
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Affiliation(s)
- Wei Yang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole M Warrington
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sara J Taylor
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paula Whitmire
- Precision Neurotherapeutics Innovation Program, Mathematical NeuroOncology Lab, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Eduardo Carrasco
- Precision Neurotherapeutics Innovation Program, Mathematical NeuroOncology Lab, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Kyle W Singleton
- Precision Neurotherapeutics Innovation Program, Mathematical NeuroOncology Lab, Mayo Clinic, Phoenix, AZ 85054, USA
| | - Ningying Wu
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO 63110, USA.,School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland OH, 44195, USA
| | | | - Albert H Kim
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kristin R Swanson
- Precision Neurotherapeutics Innovation Program, Mathematical NeuroOncology Lab, Mayo Clinic, Phoenix, AZ 85054, USA.,School of Mathematical and Statistical Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jingqin Luo
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St Louis, MO 63110, USA. .,Siteman Cancer Center Biostatistics Core, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA. .,Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
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22
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Nesterova DS, Midya V, Zacharia BE, Proctor EA, Lee SY, Stetson LC, Lathia JD, Rubin JB, Waite KA, Berens ME, Barnholtz-Sloan JS, Connor JR. Sexually dimorphic impact of the iron-regulating gene, HFE, on survival in glioblastoma. Neurooncol Adv 2020; 2:vdaa001. [PMID: 32642673 PMCID: PMC7212901 DOI: 10.1093/noajnl/vdaa001] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background The median survival for patients with glioblastoma (GBM), the most common primary malignant brain tumor in adults, has remained approximately 1 year for more than 2 decades. Recent advances in the field have identified GBM as a sexually dimorphic disease. It is less prevalent in females and they have better survival compared to males. The molecular mechanism of this difference has not yet been established. Iron is essential for many biological processes supporting tumor growth and its regulation is impacted by sex. Therefore, we interrogated the expression of a key component of cellular iron regulation, the HFE (homeostatic iron regulatory) gene, on sexually dimorphic survival in GBM. Methods We analyzed TCGA microarray gene expression and clinical data of all primary GBM patients (IDH-wild type) to compare tumor mRNA expression of HFE with overall survival, stratified by sex. Results In low HFE expressing tumors (below median expression, n = 220), survival is modulated by both sex and MGMT status, with the combination of female sex and MGMT methylation resulting in over a 10-month survival advantage (P < .0001) over the other groups. Alternatively, expression of HFE above the median (high HFE, n = 240) is associated with significantly worse overall survival in GBM, regardless of MGMT methylation status or patient sex. Gene expression analysis uncovered a correlation between high HFE expression and expression of genes associated with immune function. Conclusions The level of HFE expression in GBM has a sexually dimorphic impact on survival. Whereas HFE expression below the median imparts a survival benefit to females, high HFE expression is associated with significantly worse overall survival regardless of established prognostic factors such as sex or MGMT methylation.
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Affiliation(s)
- Darya S Nesterova
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Vishal Midya
- Division of Biostatistics & Bioinformatics, Pennsylvania State University, Hershey, Pennsylvania, USA
| | - Brad E Zacharia
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Elizabeth A Proctor
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA.,Department of Pharmacology, Pennsylvania State University, Hershey, Pennsylvania, USA.,Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sang Y Lee
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Lindsay C Stetson
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Justin D Lathia
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, USA.,Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kristin A Waite
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Department of Population Health and Quantitative Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Department of Population Health and Quantitative Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - James R Connor
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
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23
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Johansen ML, Stetson LC, Vadmal V, Waite K, Berens ME, Connor JR, Lathia J, Rubin JB, Barnholtz-Sloan JS. Gliomas display distinct sex-based differential methylation patterns based on molecular subtype. Neurooncol Adv 2020; 2:vdaa002. [PMID: 32642674 PMCID: PMC7212920 DOI: 10.1093/noajnl/vdaa002] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Gliomas are the most common type of primary brain tumor and one of many cancers where males are diagnosed with greater frequency than females. However, little is known about the sex-based molecular differences in glioblastomas (GBMs) or lower grade glioma (non-GBM) subtypes. DNA methylation is an epigenetic mechanism involved in regulating gene transcription. In glioma and other cancers, hypermethylation of specific gene promoters downregulates transcription and may have a profound effect on patient outcome. The purpose of this study was to determine if sex-based methylation differences exist in different glioma subtypes. Methods Molecular and clinical data from glioma patients were obtained from The Cancer Genome Atlas and grouped according to tumor grade and molecular subtype (IDH1/2 mutation and 1p/19q chromosomal deletion). Sex-specific differentially methylated probes (DMPs) were identified in each subtype and further analyzed to determine if they were part of differentially methylated regions (DMRs) or associated with differentially methylated DNA transcription regulatory binding motifs. Results Analysis of methylation data in 4 glioma subtypes revealed unique sets of both sex-specific DMPs and DMRs in each subtype. Motif analysis based on DMP position also identified distinct sex-based sets of DNA-binding motifs that varied according to glioma subtype. Downstream targets of 2 of the GBM-specific transcription binding sites, NFAT5 and KLF6, showed differential gene expression consistent with increased methylation mediating downregulation. Conclusion DNA methylation differences between males and females in 4 glioma molecular subtypes suggest an important, sex-specific role for DNA methylation in epigenetic regulation of gliomagenesis.
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Affiliation(s)
- Mette L Johansen
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - L C Stetson
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Vachan Vadmal
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kristin Waite
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Cleveland Center for Health Outcomes Research, Cleveland, Ohio, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - James R Connor
- Department of Neurosurgery, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Justin Lathia
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Joshua B Rubin
- Departments of Pediatrics and Neuroscience, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Cleveland Center for Health Outcomes Research, Cleveland, Ohio, USA
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24
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Stetson LC, Ostrom QT, Schlatzer D, Liao P, Devine K, Waite K, Couce ME, Harris PLR, Kerstetter-Fogle A, Berens ME, Sloan AE, Islam MM, Rajaratnam V, Mirza SP, Chance MR, Barnholtz-Sloan JS. Proteins inform survival-based differences in patients with glioblastoma. Neurooncol Adv 2020; 2:vdaa039. [PMID: 32642694 PMCID: PMC7212893 DOI: 10.1093/noajnl/vdaa039] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Improving the care of patients with glioblastoma (GB) requires accurate and reliable predictors of patient prognosis. Unfortunately, while protein markers are an effective readout of cellular function, proteomics has been underutilized in GB prognostic marker discovery. METHODS For this study, GB patients were prospectively recruited and proteomics discovery using liquid chromatography-mass spectrometry analysis (LC-MS/MS) was performed for 27 patients including 13 short-term survivors (STS) (≤10 months) and 14 long-term survivors (LTS) (≥18 months). RESULTS Proteomics discovery identified 11 941 peptides in 2495 unique proteins, with 469 proteins exhibiting significant dysregulation when comparing STS to LTS. We verified the differential abundance of 67 out of these 469 proteins in a small previously published independent dataset. Proteins involved in axon guidance were upregulated in STS compared to LTS, while those involved in p53 signaling were upregulated in LTS. We also assessed the correlation between LS MS/MS data with RNAseq data from the same discovery patients and found a low correlation between protein abundance and mRNA expression. Finally, using LC-MS/MS on a set of 18 samples from 6 patients, we quantified the intratumoral heterogeneity of more than 2256 proteins in the multisample dataset. CONCLUSIONS These proteomic datasets and noted protein variations present a beneficial resource for better predicting patient outcome and investigating potential therapeutic targets.
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Affiliation(s)
- L C Stetson
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Quinn T Ostrom
- Department of Medicine and Division of Hematology-Oncology, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Daniela Schlatzer
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Peter Liao
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Karen Devine
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kristin Waite
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences and Cleveland Center for Health Outcomes Research (CCHOR), Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Marta E Couce
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Peggy L R Harris
- Brain Tumor and Neuro-Oncology Center & Center of Excellence, Translational Neuro-Oncology, Department of Neurosurgery, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Amber Kerstetter-Fogle
- Brain Tumor and Neuro-Oncology Center & Center of Excellence, Translational Neuro-Oncology, Department of Neurosurgery, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Michael E Berens
- Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Brain Tumor and Neuro-Oncology Center & Center of Excellence, Translational Neuro-Oncology, Department of Neurosurgery, Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Mohammad M Islam
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Vilashini Rajaratnam
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Shama P Mirza
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Mark R Chance
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Center for Proteomics and Bioinformatics and Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Population and Quantitative Health Sciences and Cleveland Center for Health Outcomes Research (CCHOR), Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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25
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Berens ME, Sood A, Barnholtz-Sloan JS, Graf JF, Cho S, Kim S, Kiefer J, Byron SA, Halperin RF, Nasser S, Adkins J, Cuyugan L, Devine K, Ostrom Q, Couce M, Wolansky L, McDonough E, Schyberg S, Dinn S, Sloan AE, Prados M, Phillips JJ, Nelson SJ, Liang WS, Al-Kofahi Y, Rusu M, Zavodszky MI, Ginty F. Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas. PLoS One 2019; 14:e0219724. [PMID: 31881020 PMCID: PMC6934292 DOI: 10.1371/journal.pone.0219724] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 06/27/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
Glioma is recognized to be a highly heterogeneous CNS malignancy, whose diverse cellular composition and cellular interactions have not been well characterized. To gain new clinical- and biological-insights into the genetically-bifurcated IDH1 mutant (mt) vs wildtype (wt) forms of glioma, we integrated data from protein, genomic and MR imaging from 20 treatment-naïve glioma cases and 16 recurrent GBM cases. Multiplexed immunofluorescence (MxIF) was used to generate single cell data for 43 protein markers representing all cancer hallmarks, Genomic sequencing (exome and RNA (normal and tumor) and magnetic resonance imaging (MRI) quantitative features (protocols were T1-post, FLAIR and ADC) from whole tumor, peritumoral edema and enhancing core vs equivalent normal region were also collected from patients. Based on MxIF analysis, 85,767 cells (glioma cases) and 56,304 cells (GBM cases) were used to generate cell-level data for 24 biomarkers. K-means clustering was used to generate 7 distinct groups of cells with divergent biomarker profiles and deconvolution was used to assign RNA data into three classes. Spatial and molecular heterogeneity metrics were generated for the cell data. All features were compared between IDH mt and IDHwt patients and were finally combined to provide a holistic/integrated comparison. Protein expression by hallmark was generally lower in the IDHmt vs wt patients. Molecular and spatial heterogeneity scores for angiogenesis and cell invasion also differed between IDHmt and wt gliomas irrespective of prior treatment and tumor grade; these differences also persisted in the MR imaging features of peritumoral edema and contrast enhancement volumes. A coherent picture of enhanced angiogenesis in IDHwt tumors was derived from multiple platforms (genomic, proteomic and imaging) and scales from individual proteins to cell clusters and heterogeneity, as well as bulk tumor RNA and imaging features. Longer overall survival for IDH1mt glioma patients may reflect mutation-driven alterations in cellular, molecular, and spatial heterogeneity which manifest in discernable radiological manifestations.
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Affiliation(s)
- Michael E. Berens
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
- * E-mail: (MEB); (AS); (FG)
| | - Anup Sood
- GE Research Center, Niskayuna, NY, United States of America
- * E-mail: (MEB); (AS); (FG)
| | - Jill S. Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - John F. Graf
- GE Research Center, Niskayuna, NY, United States of America
| | - Sanghee Cho
- GE Research Center, Niskayuna, NY, United States of America
| | - Seungchan Kim
- Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, TX, United States of America
| | - Jeffrey Kiefer
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Sara A. Byron
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Rebecca F. Halperin
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Sara Nasser
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Jonathan Adkins
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Lori Cuyugan
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Karen Devine
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Quinn Ostrom
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Marta Couce
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Leo Wolansky
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | | | | | - Sean Dinn
- GE Research Center, Niskayuna, NY, United States of America
| | - Andrew E. Sloan
- Department of Neurosurgery, University Hospitals-Seidman Cancer Center, Cleveland, OH, United States of America
| | - Michael Prados
- Department of Neurological Surgery, Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
| | - Joanna J. Phillips
- Department of Neurological Surgery, Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
| | - Sarah J. Nelson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, United States of America
| | - Winnie S. Liang
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | | | - Mirabela Rusu
- GE Research Center, Niskayuna, NY, United States of America
| | | | - Fiona Ginty
- GE Research Center, Niskayuna, NY, United States of America
- * E-mail: (MEB); (AS); (FG)
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26
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Vaske OM, Bjork I, Salama SR, Beale H, Tayi Shah A, Sanders L, Pfeil J, Lam DL, Learned K, Durbin A, Kephart ET, Currie R, Newton Y, Swatloski T, McColl D, Vivian J, Zhu J, Lee AG, Leung SG, Spillinger A, Liu HY, Liang WS, Byron SA, Berens ME, Resnick AC, Lacayo N, Spunt SL, Rangaswami A, Huynh V, Torno L, Plant A, Kirov I, Zabokrtsky KB, Rassekh SR, Deyell RJ, Laskin J, Marra MA, Sender LS, Mueller S, Sweet-Cordero EA, Goldstein TC, Haussler D. Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer. JAMA Netw Open 2019; 2:e1913968. [PMID: 31651965 PMCID: PMC6822083 DOI: 10.1001/jamanetworkopen.2019.13968] [Citation(s) in RCA: 27] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
IMPORTANCE Pediatric cancers are epigenetic diseases; therefore, considering tumor gene expression information is necessary for a complete understanding of the tumorigenic processes. OBJECTIVE To evaluate the feasibility and utility of incorporating comparative gene expression information into the precision medicine framework for difficult-to-treat pediatric and young adult patients with cancer. DESIGN, SETTING, AND PARTICIPANTS This cohort study was conducted as a consortium between the University of California, Santa Cruz (UCSC) Treehouse Childhood Cancer Initiative and clinical genomic trials. RNA sequencing (RNA-Seq) data were obtained from the following 4 clinical sites and analyzed at UCSC: British Columbia Children's Hospital (n = 31), Lucile Packard Children's Hospital at Stanford University (n = 80), CHOC Children's Hospital and Hyundai Cancer Institute (n = 46), and the Pacific Pediatric Neuro-Oncology Consortium (n = 24). The study dates were January 1, 2016, to March 22, 2017. EXPOSURES Participants underwent tumor RNA-Seq profiling as part of 4 separate clinical trials at partner hospitals. The UCSC either downloaded RNA-Seq data from a partner institution for analysis in the cloud or provided a Docker pipeline that performed the same analysis at a partner institution. The UCSC then compared each participant's tumor RNA-Seq profile with more than 11 000 uniformly analyzed tumor profiles from pediatric and young adult patients with cancer, downloaded from public data repositories. These comparisons were used to identify genes and pathways that are significantly overexpressed in each patient's tumor. Results of the UCSC analysis were presented to clinical partners. MAIN OUTCOMES AND MEASURES Feasibility of a third-party institution (UCSC Treehouse Childhood Cancer Initiative) to obtain tumor RNA-Seq data from patients, conduct comparative analysis, and present analysis results to clinicians; and proportion of patients for whom comparative tumor gene expression analysis provided useful clinical and biological information. RESULTS Among 144 samples from children and young adults (median age at diagnosis, 9 years; range, 0-26 years; 72 of 118 [61.0%] male [26 patients sex unknown]) with a relapsed, refractory, or rare cancer treated on precision medicine protocols, RNA-Seq-derived gene expression was potentially useful for 99 of 144 samples (68.8%) compared with DNA mutation information that was potentially useful for only 34 of 74 samples (45.9%). CONCLUSIONS AND RELEVANCE This study's findings suggest that tumor RNA-Seq comparisons may be feasible and highlight the potential clinical utility of incorporating such comparisons into the clinical genomic interpretation framework for difficult-to-treat pediatric and young adult patients with cancer. The study also highlights for the first time to date the potential clinical utility of harmonized publicly available genomic data sets.
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Affiliation(s)
- Olena M. Vaske
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Isabel Bjork
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Sofie R. Salama
- University of California, Santa Cruz Genomics Institute, Santa Cruz
- Howard Hughes Medical Institute, University of California, Santa Cruz
| | - Holly Beale
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Avanthi Tayi Shah
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco
| | - Lauren Sanders
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Jacob Pfeil
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Du L. Lam
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Katrina Learned
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Ann Durbin
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Ellen T. Kephart
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Rob Currie
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Yulia Newton
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Teresa Swatloski
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Duncan McColl
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - John Vivian
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Jingchun Zhu
- University of California, Santa Cruz Genomics Institute, Santa Cruz
| | - Alex G. Lee
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco
| | - Stanley G. Leung
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco
| | - Aviv Spillinger
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco
| | - Heng-Yi Liu
- Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco
| | - Winnie S. Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | - Sara A. Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona
| | | | - Adam C. Resnick
- Center for Data Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Norman Lacayo
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Sheri L. Spunt
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Arun Rangaswami
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Van Huynh
- CHOC Children’s Hospital, Hyundai Cancer Institute, Orange, California
| | - Lilibeth Torno
- CHOC Children’s Hospital, Hyundai Cancer Institute, Orange, California
| | - Ashley Plant
- CHOC Children’s Hospital, Hyundai Cancer Institute, Orange, California
| | - Ivan Kirov
- CHOC Children’s Hospital, Hyundai Cancer Institute, Orange, California
| | | | - S. Rod Rassekh
- British Columbia Children’s Hospital Research Institute, British Columbia Children’s Hospital, Vancouver, British Columbia, Canada
| | - Rebecca J. Deyell
- British Columbia Children’s Hospital Research Institute, British Columbia Children’s Hospital, Vancouver, British Columbia, Canada
| | | | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard S. Sender
- CHOC Children’s Hospital, Hyundai Cancer Institute, Orange, California
| | - Sabine Mueller
- Department of Neurology, University of California, San Francisco
- Department of Neurosurgery, University of California, San Francisco
- Department of Pediatrics, University of California, San Francisco
| | | | - Theodore C. Goldstein
- University of California, Santa Cruz Genomics Institute, Santa Cruz
- Now with Anthem, Inc, Palo Alto, California
| | - David Haussler
- University of California, Santa Cruz Genomics Institute, Santa Cruz
- Howard Hughes Medical Institute, University of California, Santa Cruz
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27
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Fons NR, Sundaram RK, Breuer GA, Peng S, McLean RL, Kalathil AN, Schmidt MS, Carvalho DM, Mackay A, Jones C, Carcaboso ÁM, Nazarian J, Berens ME, Brenner C, Bindra RS. PPM1D mutations silence NAPRT gene expression and confer NAMPT inhibitor sensitivity in glioma. Nat Commun 2019; 10:3790. [PMID: 31439867 PMCID: PMC6706443 DOI: 10.1038/s41467-019-11732-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 11/06/2018] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Pediatric high-grade gliomas are among the deadliest of childhood cancers due to limited knowledge of early driving events in their gliomagenesis and the lack of effective therapies available. In this study, we investigate the oncogenic role of PPM1D, a protein phosphatase often found truncated in pediatric gliomas such as DIPG, and uncover a synthetic lethal interaction between PPM1D mutations and nicotinamide phosphoribosyltransferase (NAMPT) inhibition. Specifically, we show that mutant PPM1D drives hypermethylation of CpG islands throughout the genome and promotes epigenetic silencing of nicotinic acid phosphoribosyltransferase (NAPRT), a key gene involved in NAD biosynthesis. Notably, PPM1D mutant cells are shown to be sensitive to NAMPT inhibitors in vitro and in vivo, within both engineered isogenic astrocytes and primary patient-derived model systems, suggesting the possible application of NAMPT inhibitors for the treatment of pediatric gliomas. Overall, our results reveal a promising approach for the targeting of PPM1D mutant tumors, and define a critical link between oncogenic driver mutations and NAD metabolism, which can be exploited for tumor-specific cell killing.
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Affiliation(s)
- Nathan R Fons
- Department of Pathology, Yale University, New Haven, CT, 06520, USA.,Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Ranjini K Sundaram
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Gregory A Breuer
- Department of Pathology, Yale University, New Haven, CT, 06520, USA.,Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Sen Peng
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, 85004, USA
| | - Ryan L McLean
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Aravind N Kalathil
- Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA
| | - Mark S Schmidt
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Diana M Carvalho
- Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Alan Mackay
- Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Chris Jones
- Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, UK
| | | | - Javad Nazarian
- Children's National Health System, Washington, DC, 20010, USA
| | - Michael E Berens
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, 85004, USA.
| | - Charles Brenner
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA.
| | - Ranjit S Bindra
- Department of Pathology, Yale University, New Haven, CT, 06520, USA. .,Department of Therapeutic Radiology, Yale University, New Haven, CT, 06520, USA.
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Smithberger E, Shelton AK, Butler MK, Flores AR, Bash RE, Angus SP, Sciaky N, Dhruv HD, Johnson GL, Berens ME, Furnari FB, Miller CR. Abstract 3019: Dynamic kinome profiling of EGFRvIII-driven murine astrocyte models of glioblastoma reveals targets for dual kinase inhibitor therapy. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3019] [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
Glioblastoma (GBM) is an aggressive brain tumor with few effective treatments. Epidermal growth factor receptor (EGFR) is frequently amplified and mutated in GBM, leading to trials of several EGFR tyrosine kinase inhibitors, but none have proven successful. One potential reason for failure is acquired resistance, particularly acute, adaptive responses in the kinome. To study this adaptive resistance mechanism, we used RNA-seq and multiplex inhibitor bead/mass spectrometry (MIB-MS) to analyze transcriptomes and kinomes of genetically-engineered murine astrocytes with genotypes commonly seen in human GBM. We previously showed that 38% (86 of 228) of the expressed kinome varied among a panel of genetically diverse murine astrocytes harboring Cdkn2a deletion (C) plus Pten deletion (CP), wild-type human EGFR (CE) or EGFRvIII (CEv3) overexpression, or both overexpressed EGFRvIII and Pten deletion (CEv3P). Pairwise genotype comparisons revealed multiple differentially activated kinases, including Pdgfrb, Fgfr2, Lyn, Ddr1, and several Ephrin family members. We further investigated these potential targets for dual therapy with EGFR TKI by examining the transcriptional response of cultured astrocytes at 4, 24, and 48 hours after 3 μM afatinib. Afatinib induced no kinome changes in C and only 3 kinases (Fn3k, Prkg2, and Syk) were altered in CP astrocytes. Despite similar baseline gene expression profiles, CE astrocytes overexpressing wild-type EGFR responded significantly differently than C astrocytes without. Five kinases (Dclk1, Epha3, Epha7, Fgfr3, and Prkg1) were induced, while 14 were repressed. Six were similarly repressed in CEv3 (Bub1, Nek2, Pask, Plk4, Prkcb, and Vrk1). Whereas the kinase transcriptome response was blunted in C, CP, and CE astrocytes, afatinib induced altered expression of significantly more kinases in CEv3 (82) and CEv3P cells (49). One particularly attractive target in CEv3 astrocytes was Epha4, which afatinib induced >40-fold. Dual inhibition of EGFRvIII and Epha4 kinases may thus provide an opportunity for more effective targeted therapy.
Citation Format: Erin Smithberger, Abigail K. Shelton, Madison K. Butler, Alex R. Flores, Ryan E. Bash, Steven P. Angus, Noah Sciaky, Harshil D. Dhruv, Gary L. Johnson, Michael E. Berens, Frank B. Furnari, C. Ryan Miller. Dynamic kinome profiling of EGFRvIII-driven murine astrocyte models of glioblastoma reveals targets for dual kinase inhibitor therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3019.
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Affiliation(s)
| | | | | | | | | | | | - Noah Sciaky
- 1University of North Carolina, Chapel Hill, NC
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Shelton A, Smithberger E, Butler M, Flores A, Bash R, Angus S, Sciaky N, Dhruv H, Johnson GL, Berens ME, Furnari F, Miller CR. Abstract 331: Dynamic kinome targeting reveals kinases involved in acquired resistance to tyrosine kinase inhibitors in EGFR-driven glioblastomas. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-331] [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
Glioblastoma (GBM) is a devastating primary brain tumor with limited treatment options. Extensive molecular characterization has revealed two particularly frequent mutations: CDKN2A deletion (50-60%) and EGFR (40-50%). EGFRvIII (~35%) is a constitutively active truncation mutant with exons 2-7 deleted. EGFR is a particularly attractive therapeutic target due to frequent activating mutations, such as EGFRvIII, and ready availability of multiple targeted inhibitors. Several EGFR tyrosine kinase inhibitors (TKI) have failed clinically, due in part to acquired resistance. To mechanistically examine this type of resistance, we used genetically-engineered mouse astrocytes harboring homozygous deletions of Cdkn2a, as well as EGFRvIII (CEv3). CEv3 astrocytes were made intrinsically resistant to the EGFR TKI gefitinib or erlotinib via long-term exposure, both in vitro and in vivo. We found that long-term gefitinib or erlotinib exposure conferred variable levels of cross resistance to a panel of second- and third-generation EGFR TKI (ΔIC50 1.12-36.1-fold), relative to non-resistant parent lines. We have previously shown that dynamic kinome reprogramming may be responsible for TKI resistance in glioblastoma. Therefore, we used a chemical proteomics method, multiplexed inhibitor beads and mass spectrometry (MIB-MS), to examine changes in the expressed and functional kinome, in both the presence or absence of one of several EGFR TKI known to penetrate the blood-brain barrier. Additionally, we performed RNA sequencing (RNA-seq) to inspect transcriptomic alterations in response to these drugs. RNA-seq showed that resistant CEv3 mouse astrocytes clustered separately from their non-resistant in vitro and in vivo counterparts. Acquired resistance also induced transcriptome alterations governing cellular metabolism, including upregulation of metabolic pathways and downregulation of RNA processing genes. Importantly, the kinase transcriptome was rewired, as 67 kinases were differentially expressed across parental and resistant cell lines (Q<0.001). Probing the dynamic kinome response to afatinib, an EGFR TKI, using RNA-seq identified two potential kinases involved in acute, adaptive resistance to afatinib, Bmx and Ntrk3. Integrated kinome profiling using RNA-seq and MIB-MS in murine models of GBM with defined mutational profiles provides a powerful framework to define novel therapeutic targets that could significantly alter current treatment paradigms.
Citation Format: Abby Shelton, Erin Smithberger, Madison Butler, Alex Flores, Ryan Bash, Steve Angus, Noah Sciaky, Harshil Dhruv, Gary L. Johnson, Michael E. Berens, Frank Furnari, C. Ryan Miller. Dynamic kinome targeting reveals kinases involved in acquired resistance to tyrosine kinase inhibitors in EGFR-driven glioblastomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 331.
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Gittleman H, Ostrom QT, Stetson LC, Waite K, Hodges TR, Wright CH, Wright J, Rubin JB, Berens ME, Lathia J, Connor JR, Kruchko C, Sloan AE, Barnholtz-Sloan JS. Sex is an important prognostic factor for glioblastoma but not for nonglioblastoma. Neurooncol Pract 2019; 6:451-462. [PMID: 31832215 DOI: 10.1093/nop/npz019] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Glioblastoma (GBM) is the most common and most malignant glioma. Nonglioblastoma (non-GBM) gliomas (WHO Grades II and III) are invasive and also often fatal. The goal of this study is to determine whether sex differences exist in glioma survival. Methods Data were obtained from the National Cancer Database (NCDB) for years 2010 to 2014. GBM (WHO Grade IV; N = 2073) and non-GBM (WHO Grades II and III; N = 2963) were defined using the histology grouping of the Central Brain Tumor Registry of the United States. Non-GBM was divided into oligodendrogliomas/mixed gliomas and astrocytomas. Sex differences in survival were analyzed using Kaplan-Meier and multivariable Cox proportional hazards models adjusted for known prognostic variables. Results There was a female survival advantage in patients with GBM both in the unadjusted (P = .048) and adjusted (P = .003) models. Unadjusted, median survival was 20.1 months (95% CI: 18.7-21.3 months) for women and 17.8 months (95% CI: 16.9-18.7 months) for men. Adjusted, median survival was 20.4 months (95% CI: 18.9-21.6 months) for women and 17.5 months (95% CI: 16.7-18.3 months) for men. When stratifying by age group (18-55 vs 56+ years at diagnosis), this female survival advantage appeared only in the older group, adjusting for covariates (P = .017). Women (44.1%) had a higher proportion of methylated MGMT (O6-methylguanine-DNA methyltransferase) than men (38.4%). No sex differences were found for non-GBM. Conclusions Using the NCDB data, there was a statistically significant female survival advantage in GBM, but not in non-GBM.
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Affiliation(s)
- Haley Gittleman
- Central Brain Tumor Registry of the United States, Hinsdale, IL.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH.,Department of Population Health and Quantitative Sciences, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Quinn T Ostrom
- Central Brain Tumor Registry of the United States, Hinsdale, IL.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - L C Stetson
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Kristin Waite
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH.,Department of Population Health and Quantitative Sciences, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Tiffany R Hodges
- Department of Neurological Surgery, University Hospitals of Cleveland and Case Western University School of Medicine, OH.,Seidman Cancer Center, University Hospitals of Cleveland, OH
| | - Christina H Wright
- Department of Neurological Surgery, University Hospitals of Cleveland and Case Western University School of Medicine, OH
| | - James Wright
- Department of Neurological Surgery, University Hospitals of Cleveland and Case Western University School of Medicine, OH
| | | | | | - Justin Lathia
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH.,Cleveland Clinic, Lerner Research Institute, OH
| | - James R Connor
- Department of Neurosurgery, Penn State Cancer Institute, Penn State, State College
| | - Carol Kruchko
- Central Brain Tumor Registry of the United States, Hinsdale, IL
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH.,Department of Neurological Surgery, University Hospitals of Cleveland and Case Western University School of Medicine, OH.,Seidman Cancer Center, University Hospitals of Cleveland, OH
| | - Jill S Barnholtz-Sloan
- Central Brain Tumor Registry of the United States, Hinsdale, IL.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH.,Department of Population Health and Quantitative Sciences, Case Western Reserve University School of Medicine, Cleveland, OH
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Mueller S, Jain P, Liang WS, Kilburn L, Kline C, Gupta N, Panditharatna E, Magge SN, Zhang B, Zhu Y, Crawford JR, Banerjee A, Nazemi K, Packer RJ, Petritsch CK, Truffaux N, Roos A, Nasser S, Phillips JJ, Solomon D, Molinaro A, Waanders AJ, Byron SA, Berens ME, Kuhn J, Nazarian J, Prados M, Resnick AC. A pilot precision medicine trial for children with diffuse intrinsic pontine glioma-PNOC003: A report from the Pacific Pediatric Neuro-Oncology Consortium. Int J Cancer 2019; 145:1889-1901. [PMID: 30861105 DOI: 10.1002/ijc.32258] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/21/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
This clinical trial evaluated whether whole exome sequencing (WES) and RNA sequencing (RNAseq) of paired normal and tumor tissues could be incorporated into a personalized treatment plan for newly diagnosed patients (<25 years of age) with diffuse intrinsic pontine glioma (DIPG). Additionally, whole genome sequencing (WGS) was compared to WES to determine if WGS would further inform treatment decisions, and whether circulating tumor DNA (ctDNA) could detect the H3K27M mutation to allow assessment of therapy response. Patients were selected across three Pacific Pediatric Neuro-Oncology Consortium member institutions between September 2014 and January 2016. WES and RNAseq were performed at diagnosis and recurrence when possible in a CLIA-certified laboratory. Patient-derived cell line development was attempted for each subject. Collection of blood for ctDNA was done prior to treatment and with each MRI. A specialized tumor board generated a treatment recommendation including up to four FDA-approved agents based upon the genomic alterations detected. A treatment plan was successfully issued within 21 business days from tissue collection for all 15 subjects, with 14 of the 15 subjects fulfilling the feasibility criteria. WGS results did not significantly deviate from WES-based therapy recommendations; however, WGS data provided further insight into tumor evolution and fidelity of patient-derived cell models. Detection of the H3F3A or HIST1H3B K27M (H3K27M) mutation using ctDNA was successful in 92% of H3K27M mutant cases. A personalized treatment recommendation for DIPG can be rendered within a multicenter setting using comprehensive next-generation sequencing technology in a clinically relevant timeframe.
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Affiliation(s)
- Sabine Mueller
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.,Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Payal Jain
- Center for Data-Driven Discovery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Winnie S Liang
- Translational Genomic Research Institute (TGEN), Phoenix, AZ, USA
| | - Lindsay Kilburn
- Center for Cancer and Blood Disorders, Children's National Health System, Washington, DC, USA.,Brain Tumor Institute, Children's National Health System, Washington, DC, USA
| | - Cassie Kline
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Eshini Panditharatna
- Brain Tumor Institute, Children's National Health System, Washington, DC, USA.,Research Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Suresh N Magge
- Division of Neurosurgery, Children's National Health System, Washington, DC, USA
| | - Bo Zhang
- Center for Data-Driven Discovery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Anu Banerjee
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Kellie Nazemi
- Doernbecher Children's Hospital, Oregon Health & Science University, Portland, OR, USA
| | - Roger J Packer
- Brain Tumor Institute, Children's National Health System, Washington, DC, USA
| | - Claudia K Petritsch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nathalene Truffaux
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Alison Roos
- Translational Genomic Research Institute (TGEN), Phoenix, AZ, USA
| | - Sara Nasser
- Translational Genomic Research Institute (TGEN), Phoenix, AZ, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.,Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - David Solomon
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Annette Molinaro
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Angela J Waanders
- Center for Data-Driven Discovery, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Children's Brain Tumor Tissue Consortium, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sara A Byron
- Translational Genomic Research Institute (TGEN), Phoenix, AZ, USA
| | - Michael E Berens
- Translational Genomic Research Institute (TGEN), Phoenix, AZ, USA
| | - John Kuhn
- College of Pharmacy, University of Texas Health Science Center, San Antonio, TX, USA
| | - Javad Nazarian
- Center for Data-Driven Discovery, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Cancer and Blood Disorders, Children's National Health System, Washington, DC, USA.,Brain Tumor Institute, Children's National Health System, Washington, DC, USA.,Research Center for Genetic Medicine, Children's National Health System, Washington, DC, USA
| | - Michael Prados
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Adam C Resnick
- Center for Data-Driven Discovery, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Children's Brain Tumor Tissue Consortium, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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Halperin RF, Liang WS, Kulkarni S, Tassone EE, Adkins J, Enriquez D, Tran NL, Hank NC, Newell J, Kodira C, Korn R, Berens ME, Kim S, Byron SA. Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples. Front Oncol 2019; 9:119. [PMID: 30949446 PMCID: PMC6435595 DOI: 10.3389/fonc.2019.00119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 07/16/2018] [Accepted: 02/11/2019] [Indexed: 12/28/2022] Open
Abstract
Archival tumor samples represent a rich resource of annotated specimens for translational genomics research. However, standard variant calling approaches require a matched normal sample from the same individual, which is often not available in the retrospective setting, making it difficult to distinguish between true somatic variants and individual-specific germline variants. Archival sections often contain adjacent normal tissue, but this tissue can include infiltrating tumor cells. As existing comparative somatic variant callers are designed to exclude variants present in the normal sample, a novel approach is required to leverage adjacent normal tissue with infiltrating tumor cells for somatic variant calling. Here we present lumosVar 2.0, a software package designed to jointly analyze multiple samples from the same patient, built upon our previous single sample tumor only variant caller lumosVar 1.0. The approach assumes that the allelic fraction of somatic variants and germline variants follow different patterns as tumor content and copy number state change. lumosVar 2.0 estimates allele specific copy number and tumor sample fractions from the data, and uses a to model to determine expected allelic fractions for somatic and germline variants and to classify variants accordingly. To evaluate the utility of lumosVar 2.0 to jointly call somatic variants with tumor and adjacent normal samples, we used a glioblastoma dataset with matched high and low tumor content and germline whole exome sequencing data (for true somatic variants) available for each patient. Both sensitivity and positive predictive value were improved when analyzing the high tumor and low tumor samples jointly compared to analyzing the samples individually or in-silico pooling of the two samples. Finally, we applied this approach to a set of breast and prostate archival tumor samples for which tumor blocks containing adjacent normal tissue were available for sequencing. Joint analysis using lumosVar 2.0 detected several variants, including known cancer hotspot mutations that were not detected by standard somatic variant calling tools using the adjacent tissue as presumed normal reference. Together, these results demonstrate the utility of leveraging paired tissue samples to improve somatic variant calling when a constitutional sample is not available.
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Affiliation(s)
- Rebecca F Halperin
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Winnie S Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Sidharth Kulkarni
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Erica E Tassone
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Jonathan Adkins
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Daniel Enriquez
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | | | | | - James Newell
- HonorHealth Scottsdale Shea Medical Center, Scottsdale, AZ, United States
| | - Chinnappa Kodira
- GE Global Research Center, Niskayuna, NY, United States.,PureTech Health, Boston, MA, United States
| | - Ronald Korn
- Imaging Endpoints, Scottsdale, AZ, United States.,HonorHealth Scottsdale Shea Medical Center, Scottsdale, AZ, United States
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Seungchan Kim
- Prairie View A&M University, Prairie View, TX, United States
| | - Sara A Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, United States
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Affiliation(s)
- Quinn T Ostrom
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Joshua B Rubin
- Department of Pediatrics and Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri
| | - Justin D Lathia
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
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Ostrom QT, Coleman W, Huang W, Rubin JB, Lathia JD, Berens ME, Speyer G, Liao P, Wrensch MR, Eckel-Passow JE, Armstrong G, Rice T, Wiencke JK, McCoy LS, Hansen HM, Amos CI, Bernstein JL, Claus EB, Houlston RS, Il’yasova D, Jenkins RB, Johansen C, Lachance DH, Lai RK, Merrell RT, Olson SH, Sadetzki S, Schildkraut JM, Shete S, Andersson U, Rajaraman P, Chanock SJ, Linet MS, Wang Z, Yeager M, Melin B, Bondy ML, Barnholtz-Sloan JS. Sex-specific gene and pathway modeling of inherited glioma risk. Neuro Oncol 2019; 21:71-82. [PMID: 30124908 PMCID: PMC6303471 DOI: 10.1093/neuonc/noy135] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 12/12/2022] Open
Abstract
Background To date, genome-wide association studies (GWAS) have identified 25 risk variants for glioma, explaining 30% of heritable risk. Most histologies occur with significantly higher incidence in males, and this difference is not explained by currently known risk factors. A previous GWAS identified sex-specific glioma risk variants, and this analysis aims to further elucidate risk variation by sex using gene- and pathway-based approaches. Methods Results from the Glioma International Case-Control Study were used as a testing set, and results from 3 GWAS were combined via meta-analysis and used as a validation set. Using summary statistics for nominally significant autosomal SNPs (P < 0.01 in a previous meta-analysis) and nominally significant X-chromosome SNPs (P < 0.01), 3 algorithms (Pascal, BimBam, and GATES) were used to generate gene scores, and Pascal was used to generate pathway scores. Results were considered statistically significant in the discovery set when P < 3.3 × 10-6 and in the validation set when P < 0.001 in 2 of 3 algorithms. Results Twenty-five genes within 5 regions and 19 genes within 6 regions reached statistical significance in at least 2 of 3 algorithms in males and females, respectively. EGFR was significantly associated with all glioma and glioblastoma in males only and a female-specific association in TERT, all of which remained nominally significant after conditioning on known risk loci. There were nominal associations with the BioCarta telomeres pathway in both males and females. Conclusions These results provide additional evidence that there may be differences by sex in genetic risk for glioma. Additional analyses may further elucidate the biological processes through which this risk is conferred.
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Affiliation(s)
- Quinn T Ostrom
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | - William Huang
- Case Western Reserve University, Cleveland, Ohio, USA
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA; Department of Neuroscience, Washington University School of Medicine, St Louis, Missouri, USA
| | - Justin D Lathia
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Gil Speyer
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Peter Liao
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Margaret R Wrensch
- Department of Neurological Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Georgina Armstrong
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Terri Rice
- Department of Neurological Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - John K Wiencke
- Department of Neurological Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Lucie S McCoy
- Department of Neurological Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Helen M Hansen
- Department of Neurological Surgery, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Elizabeth B Claus
- School of Public Health, Yale University, New Haven, Connecticut, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Dora Il’yasova
- Department of Epidemiology and Biostatistics, School of Public Health, Georgia State University, Atlanta, Georgia, USA
- Cancer Control and Prevention Program, Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, USA
| | - Christoffer Johansen
- Oncology Clinic, Finsen Center, Rigshospitalet and Survivorship Research Unit, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Daniel H Lachance
- Department of Neurology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, USA
| | - Rose K Lai
- Departments of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Ryan T Merrell
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Siegal Sadetzki
- Cancer and Radiation Epidemiology Unit, Gertner Institute, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | | | - Ulrika Andersson
- Department of Radiation Sciences, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, USA
| | - Martha S Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Panditharatna E, Kilburn LB, Aboian MS, Kambhampati M, Gordish-Dressman H, Magge SN, Gupta N, Myseros JS, Hwang EI, Kline C, Crawford JR, Warren KE, Cha S, Liang WS, Berens ME, Packer RJ, Resnick AC, Prados M, Mueller S, Nazarian J. Clinically Relevant and Minimally Invasive Tumor Surveillance of Pediatric Diffuse Midline Gliomas Using Patient-Derived Liquid Biopsy. Clin Cancer Res 2018; 24:5850-5859. [PMID: 30322880 DOI: 10.1158/1078-0432.ccr-18-1345] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/27/2018] [Accepted: 08/30/2018] [Indexed: 01/07/2023]
Abstract
PURPOSE Pediatric diffuse midline glioma (DMG) are highly malignant tumors with poor clinical outcomes. Over 70% of patients with DMG harbor the histone 3 p.K27M (H3K27M) mutation, which correlates with a poorer clinical outcome, and is also used as a criterion for enrollment in clinical trials. Because complete surgical resection of DMG is not an option, biopsy at presentation is feasible, but rebiopsy at time of progression is rare. While imaging and clinical-based disease monitoring is the standard of care, molecular-based longitudinal characterization of these tumors is almost nonexistent. To overcome these hurdles, we examined whether liquid biopsy allows measurement of disease response to precision therapy. EXPERIMENTAL DESIGN We established a sensitive and specific methodology that detects major driver mutations associated with pediatric DMGs using droplet digital PCR (n = 48 subjects, n = 110 specimens). Quantification of circulating tumor DNA (ctDNA) for H3K27M was used for longitudinal assessment of disease response compared with centrally reviewed MRI data. RESULTS H3K27M was identified in cerebrospinal fluid (CSF) and plasma in 88% of patients with DMG, with CSF being the most enriched for ctDNA. We demonstrated the feasibility of multiplexing for detection of H3K27M, and additional driver mutations in patient's tumor and matched CSF, maximizing the utility of a single source of liquid biome. A significant decrease in H3K27M plasma ctDNA agreed with MRI assessment of tumor response to radiotherapy in 83% (10/12) of patients. CONCLUSIONS Our liquid biopsy approach provides a molecularly based tool for tumor characterization, and is the first to indicate clinical utility of ctDNA for longitudinal surveillance of DMGs.
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Affiliation(s)
- Eshini Panditharatna
- Rese arch Center for Genetic Medicine, Children's National Health System, Washington, D.C.,Institute for Biomedical Sciences, George Washington University School of Medicine and Health Sciences, Washington, D.C
| | - Lindsay B Kilburn
- Center for Cancer and Blood Disorders, Children's National Health System, Washington D.C.,Brain Tumor Institute, Children's National Health System, Washington, D.C
| | - Mariam S Aboian
- Departments of Neurology, Pediatrics and Neurosurgery, University of California, San Francisco School of Medicine, San Francisco, California
| | - Madhuri Kambhampati
- Rese arch Center for Genetic Medicine, Children's National Health System, Washington, D.C
| | | | - Suresh N Magge
- Division of Neurosurgery, Children's National Health System, Washington, D.C
| | - Nalin Gupta
- Department of Neurological Surgery and Pediatrics, University of California San Francisco, San Francisco, California
| | - John S Myseros
- Division of Neurosurgery, Children's National Health System, Washington, D.C
| | - Eugene I Hwang
- Center for Cancer and Blood Disorders, Children's National Health System, Washington D.C.,Brain Tumor Institute, Children's National Health System, Washington, D.C
| | - Cassie Kline
- Pediatric Hematology-Oncology and Neurology, UCSF Benioff Children's Hospital, San Francisco, California
| | - John R Crawford
- Department of Neurosciences, UC San Diego School of Medicine, La Jolla, California
| | | | - Soonmee Cha
- Department of Radiology, University of California, San Francisco School of Medicine, San Francisco, California
| | - Winnie S Liang
- Translational Genomics Research Institute, Phoenix, Arizona
| | | | - Roger J Packer
- Brain Tumor Institute, Children's National Health System, Washington, D.C
| | - Adam C Resnick
- Center for Data-Driven Discovery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael Prados
- Departments of Neurology, Pediatrics and Neurosurgery, University of California, San Francisco School of Medicine, San Francisco, California
| | - Sabine Mueller
- Departments of Neurology, Pediatrics and Neurosurgery, University of California, San Francisco School of Medicine, San Francisco, California
| | - Javad Nazarian
- Rese arch Center for Genetic Medicine, Children's National Health System, Washington, D.C. .,Center for Cancer and Blood Disorders, Children's National Health System, Washington D.C.,Brain Tumor Institute, Children's National Health System, Washington, D.C.,Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, D.C
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Vitucci M, Irvin DM, McNeill RS, Schmid RS, Simon JM, Dhruv HD, Siegel MB, Werneke AM, Bash RE, Kim S, Berens ME, Miller CR. Genomic profiles of low-grade murine gliomas evolve during progression to glioblastoma. Neuro Oncol 2018; 19:1237-1247. [PMID: 28398584 DOI: 10.1093/neuonc/nox050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background Gliomas are diverse neoplasms with multiple molecular subtypes. How tumor-initiating mutations relate to molecular subtypes as these tumors evolve during malignant progression remains unclear. Methods We used genetically engineered mouse models, histopathology, genetic lineage tracing, expression profiling, and copy number analyses to examine how genomic tumor diversity evolves during the course of malignant progression from low- to high-grade disease. Results Knockout of all 3 retinoblastoma (Rb) family proteins was required to initiate low-grade tumors in adult mouse astrocytes. Mutations activating mitogen-activated protein kinase signaling, specifically KrasG12D, potentiated Rb-mediated tumorigenesis. Low-grade tumors showed mutant Kras-specific transcriptome profiles but lacked copy number mutations. These tumors stochastically progressed to high-grade, in part through acquisition of copy number mutations. High-grade tumor transcriptomes were heterogeneous and consisted of 3 subtypes that mimicked human mesenchymal, proneural, and neural glioblastomas. Subtypes were confirmed in validation sets of high-grade mouse tumors initiated by different driver mutations as well as human patient-derived xenograft models and glioblastoma tumors. Conclusion These results suggest that oncogenic driver mutations influence the genomic profiles of low-grade tumors and that these, as well as progression-acquired mutations, contribute strongly to the genomic heterogeneity across high-grade tumors.
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Affiliation(s)
- Mark Vitucci
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - David M Irvin
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Robert S McNeill
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Ralf S Schmid
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Jeremy M Simon
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Harshil D Dhruv
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Marni B Siegel
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Andrea M Werneke
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Ryan E Bash
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Seungchan Kim
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - Michael E Berens
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
| | - C Ryan Miller
- Curriculum in Genetics and Molecular Biology, Pathobiology and Translational Science Graduate Program, Division of Neuropathology, Department of Pathology and Laboratory Medicine, Carolina Institute for Developmental Disabilities and Department of Genetics, Lineberger Comprehensive Cancer Center, Neurosciences Center, and Department of Neurology, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina;Cancer & Cell Biology Division, Translational Genomics Institute (TGen), Phoenix, Arizona
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Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD. An anatomic transcriptional atlas of human glioblastoma. Science 2018; 360:660-663. [PMID: 29748285 DOI: 10.1126/science.aaf2666] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/30/2018] [Indexed: 12/20/2022]
Abstract
Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment.
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Affiliation(s)
- Ralph B Puchalski
- Allen Institute for Brain Science, Seattle, WA 98109, USA. .,Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Nameeta Shah
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA. .,Mazumdar Shaw Center for Translational Research, Bangalore 560099, India
| | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Steve R Nomura
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jae-Guen Yoon
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Michael Lankerovich
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Andrew F Boe
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Mike Chapin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Suvro Datta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xu Feng
- Radia Inc., Lynnwood, WA 98036, USA
| | - Michael Fisher
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Garrett Gee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Guangyu Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - John Hohmann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Parvinder Hothi
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kevin Joines
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ali Kriedberg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chris Lau
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hwahyung Lee
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Fuhui Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Naveed Mastan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Erika Mott
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chantal Murthy
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Eric Olson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zack Riley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Rosen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Andrew Sodt
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Don Marsh
- White Marsh Forests, Seattle, WA 98119, USA
| | - Robert C Rostomily
- Department of Neurosurgery, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.,Department of Neurological Surgery, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Allan Jones
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Haley R Gittleman
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Patrick J Cimino
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | - Megha S Uppin
- Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, India
| | - C Dirk Keene
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | | | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael E Berens
- TGen, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Neurology, Columbia University, New York, NY 10032, USA.,Department of Pathology, Columbia University, New York, NY 10032, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Charles Cobbs
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Greg D Foltz
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
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Berens ME, Barnholtz-Sloan JS, Rusu M, Graf J, Sood A, Cho S, Zavodszky M, Byron S, Halperin R, Fritz Y, Kim S, Ginty F. Abstract 3039: Role of IDH mutation status on molecular and spatial heterogeneity in glial tumors across progression and recurrence. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3039] [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
We developed and deployed a workflow for generating multi-scale, multiparametric imaging data, feature extraction and/or converting to higher scales which equips multiple analysis approaches to differentiate clinically variable phenotypes of glial tumors. The workflow quantifies spatial heterogeneity (concordance of adjoining cells) and molecular heterogeneity (varied cell states determined by protein abundance) of glial tumors at the genomic, tissue, and medical imaging scales including IDH mutation status and progression/recurrence status. A panel of 24 multiplexed immunofluorescence (MxIF) markers (addressing 9 hallmarks of cancer) was used to profile single cells (in the thousands) in tissue sections from each of 31 glial tumors (ranging from primary grade II to IV, and recurrent grade IV). Pre-resection multi-parameter MR images were feature extracted from discreet habitats (necrosis, enhancing, and edema); whole exome and transcriptome sequencing from bulk viable tumor were analyzed. By MxIF, the various states of individual cells from treatment-naive patient specimens resolved unsupervised into 7 clusters, for which Cluster 2 (including cells from 9 patients) and Cluster 6 (including cells from 8 patients) contained the two larger bundles of patient cases. When separated into IDHmt and IDHwt cases, cells from IDHmt cases frequently contained cell populations dominated by a single cluster (low molecular heterogeneity); cells from cases with IDHwt represented multiple different clusters (high molecular heterogeneity). In grade III astrocytomas, and grade IV recurrent glioblastomas, spatial heterogeneity of the hallmark “inducing angiogenesis” was elevated in the IDHmt tumors compared to IDHwt, while between the same groups, molecular heterogeneity was lower in the IDHmt cases than wild type. Edema from T1w post contrast MR imaging was found to be elevated in IDHwt gliomas relative to IDHmt, while enhancement was reduced in IDHwt compared to IDHmt tumors. The findings demonstrate that IDHmt gliomas, irrespective of grade, show less edema, greater enhancement, and greater spatial heterogeneity of the “inducing angiogenesis” hallmark but lower molecular heterogeneity than IDHwt tumors. Molecular heterogeneity of “cancer invasion” also differed between IDHmt and IDHwt cases. Longer survival duration following diagnosis for patients with IDHmt gliomas may reflect generalized altered molecular and spatial heterogeneity, which is a phenotype evident on medical imaging. [Clinically-annotated specimens originated from the Ohio Brain Tumor Study and the Ivy GBM Clinical Trials Consortium]
Citation Format: Michael E. Berens, Jill S. Barnholtz-Sloan, Miribella Rusu, John Graf, Anup Sood, Sanghee Cho, Maria Zavodszky, Sara Byron, Rebecca Halperin, Yi Fritz, Seungchan Kim, Fiona Ginty. Role of IDH mutation status on molecular and spatial heterogeneity in glial tumors across progression and recurrence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3039.
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Affiliation(s)
| | | | | | | | | | | | | | - Sara Byron
- 1TGen (The Translational Genomics Research Institute), Phoenix, AZ
| | - Rebecca Halperin
- 1TGen (The Translational Genomics Research Institute), Phoenix, AZ
| | - Yi Fritz
- 2Case Western Reserve University Comprehensive Cancer Center, Cleveland, OH
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Smithberger E, Flores AR, Butler MK, Dhruv HD, Johnson GL, Berens ME, Furnari FB, Miller CR. Abstract 2372: Kinome profiling of non-germline, genetically engineered mouse models of glioblastoma driven by Cdkn2a, Egfr, and/or Pten mutations reveals genotype-dependent kinase targets. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2372] [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
The most attractive target for personalized medicine of glioblastoma (GBM) remains epidermal growth factor receptor (EGFR), due to its frequency in and specificity for the disease and the number of drugs that target its tyrosine kinase domain. Yet several EGFR tyrosine kinase inhibitors (TKI) have failed clinically, in part due to multiple molecular mechanisms of resistance. The most common oncogenic mutation in GBM is EGFRvIII, while the most common tumor suppressors lost are CDKN2A and PTEN. Mutations in these 3 genes frequently co-occur. To identify potentially attractive kinase targets for use in combination regiments with an EGFR TKI, we used multiplex inhibitor bead/mass spectrometry (MIB-MS) and RNA-seq to examine the baseline kinomes and transcriptomes of non-germline genetically engineered mouse (nGEM) models of GBM, specifically cultured Cdkn2a-null murine astrocytes (C) engineered to harbor human EGFRvIII (CEv3), Pten deletion (CP), or both (CEv3P). Among these 4 lines, 5.2-9.7% of the transcriptome was differentially expressed using DESeq2 at Q<0.001. Gene set analysis showed progressive loss of astrocyte and gain of stemness signatures in more heavily mutated cells (CEv3P>CEv3> CP>C), suggesting that EGFRvIII and Pten deletions cooperate to induce astrocyte de-differentiation into glioma stem cells (GSC). Principal components analysis showed a significant influence of both EGFRvIII (component 1, 44-48% variance) and Pten (component 2, ~33% variance) status on the transcriptome and kinome. Of the 228 expressed kinases detected using MIB-MS, 86 (38%) were differentially expressed in 1 or more genotypes. Integrated transcriptome and kinome analysis showed that Egfr was significantly over-expressed and hyperactive in EGFRvIII-mutated cells. Akt1 showed a non-expression driven increase in kinase activity in Pten-deleted cells, consistent with known effects of Pten on PI3K signaling. Pairwise genotype comparisons revealed 5-20 additional kinases that were differentially activated. Some, including Pdgfrb, Fgfr2, Lyn, Ddr1, and several members of the Ephrin family, represent potential targets for dual therapy with EGFR TKI. Clinically-curated human GBM patient-derived xenograft (PDX) models matched to CEv3P, CEv3, CP, and C nGEM models will afford comparisons in a patient-based preclinical setting for translational support. Functional kinome analysis using targeted EGFR TKI and MIB-MS in nGEM and PDX will help define the kinase networks required for EGFRvIII-driven GBM pathogenesis and may aid in the identification of novel treatment combinations.
Citation Format: Erin Smithberger, Alex R. Flores, Madison K. Butler, Harshil D. Dhruv, Gary L. Johnson, Michael E. Berens, Frank B. Furnari, C. Ryan Miller. Kinome profiling of non-germline, genetically engineered mouse models of glioblastoma driven by Cdkn2a, Egfr, and/or Pten mutations reveals genotype-dependent kinase targets [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2372.
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Affiliation(s)
| | - Alex R. Flores
- 1Univ. of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | | | - Frank B. Furnari
- 3Ludwig Institute for Cancer Research and University of California San Diego, San Diego, CA
| | - C. Ryan Miller
- 1Univ. of North Carolina at Chapel Hill, Chapel Hill, NC
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Chaudhuri L, Bybee RL, Hartman LK, Peng S, Finlay D, Vuori K, Berens ME, Dhruv HD. Abstract 881: Identifying the context of vulnerability to MLN4924 in glioblastoma (GBM). Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-881] [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
Neddylation is a post-translational mechanism that marks proteins for degradation through activity of NEDD8 Activating Enzyme (NAE). NAE activates cullin-RING ligases (CRL), which ubiquitylate selected substrates and mark them for proteosomal degradation. MLN4924, or Pevonedistat, targets NAE and inhibits Neddylation and induces apoptosis in sensitive cells. To assess the preferential sensitivity of cell lines to MLN4924, we performed a 10-point drug dose response (DDR) assay on long-term established GBM cell lines. Efficacy of MLN4924 in glioma cell lines was evaluated by measuring cell viability (CellTiterGlo®) and cell cycle progression (flow cytometry with propidium iodide staining). To identify mechanism of differential response to MLN4924 treatment, cell cycle regulatory pathway and DNA damage were also examined by Western blotting. GB1 (IC50 = 0.28 μM) & LN18 (IC50 = 0.19 μM) were established as sensitive and M059K (IC50 = 5.5 μM) & SNU1105 (IC50 = 20.9 μM) as non-sensitive cell lines based on the IC50 values. Flow cytometry analysis of DNA content revealed significant arrest of cells in G2/M even at low doses of 100 nM of MLN4924 preferentially in GB1 and LN18. This was consistent with an increase in CRL substrates p21, p27 and WEE1 in GB1 and LN18 possibly contributing to the G2/M arrest. While CDT1 accumulation was observed starting at 2h post MLN4924 treatment in sensitive cell lines, it took upto 8h for CDT1 accumulation in the non-sensitive cell lines. Increases in CDT1 induced re-replication causing massive arrest in G2/M phase lead to increased DNA damage, validated by higher expression of γH2AX in the sensitive cell lines. Additionally, we also investigated the efficacy of MLN4924 against orthotopic glioma PDX models in vitro and in vivo to validate our findings. In a cohort of glioblastoma PDX models we discovered that GBM PDX models with lower Neddylation gene set enrichment score (GBM116, GBM59, SF7300) were markedly more vulnerable to MLN4924 than GBM PDX models with higher Neddylation gene set enrichment score (GBM91 and GBM102) in vitro and in vivo. Orthotopic PDX models of selected GBM revealed survival prolongation of GBM116, but minimal survival benefit to GBM102 tumors. Validation of the predictive markers of vulnerability to MLN4924 in additional PDX models will set the stage for prospective clinical trials of MLN4924 in glioblastoma patients.
Citation Format: Leena Chaudhuri, Rita L. Bybee, Lauren K. Hartman, Sen Peng, Darren Finlay, Kristiina Vuori, Michael E. Berens, Harshil D. Dhruv. Identifying the context of vulnerability to MLN4924 in glioblastoma (GBM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 881.
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Affiliation(s)
| | - Rita L. Bybee
- 1Translational Genomics Research Institute, Phoenix, AZ
| | | | - Sen Peng
- 1Translational Genomics Research Institute, Phoenix, AZ
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41
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McNeill RS, Canoutas DA, Stuhlmiller TJ, Dhruv HD, Irvin DM, Bash RE, Angus SP, Herring LE, Simon JM, Skinner KR, Limas JC, Chen X, Schmid RS, Siegel MB, Van Swearingen AED, Hadler MJ, Sulman EP, Sarkaria JN, Anders CK, Graves LM, Berens ME, Johnson GL, Miller CR. Combination therapy with potent PI3K and MAPK inhibitors overcomes adaptive kinome resistance to single agents in preclinical models of glioblastoma. Neuro Oncol 2018; 19:1469-1480. [PMID: 28379424 DOI: 10.1093/neuonc/nox044] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Glioblastoma (GBM) is the most common and aggressive primary brain tumor. Prognosis remains poor despite multimodal therapy. Developing alternative treatments is essential. Drugs targeting kinases within the phosphoinositide 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) effectors of receptor tyrosine kinase (RTK) signaling represent promising candidates. Methods We previously developed a non-germline genetically engineered mouse model of GBM in which PI3K and MAPK are activated via Pten deletion and KrasG12D in immortalized astrocytes. Using this model, we examined the influence of drug potency on target inhibition, alternate pathway activation, efficacy, and synergism of single agent and combination therapy with inhibitors of these 2 pathways. Efficacy was then examined in GBM patient-derived xenografts (PDX) in vitro and in vivo. Results PI3K and mitogen-activated protein kinase kinase (MEK) inhibitor potency was directly associated with target inhibition, alternate RTK effector activation, and efficacy in mutant murine astrocytes in vitro. The kinomes of GBM PDX and tumor samples were heterogeneous, with a subset of the latter harboring MAPK hyperactivation. Dual PI3K/MEK inhibitor treatment overcame alternate effector activation, was synergistic in vitro, and was more effective than single agent therapy in subcutaneous murine allografts. However, efficacy in orthotopic allografts was minimal. This was likely due to dose-limiting toxicity and incomplete target inhibition. Conclusion Drug potency influences PI3K/MEK inhibitor-induced target inhibition, adaptive kinome reprogramming, efficacy, and synergy. Our findings suggest that combination therapies with highly potent, brain-penetrant kinase inhibitors will be required to improve patient outcomes.
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Affiliation(s)
- Robert S McNeill
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Demitra A Canoutas
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Timothy J Stuhlmiller
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Harshil D Dhruv
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - David M Irvin
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Ryan E Bash
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Steven P Angus
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Laura E Herring
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Jeremy M Simon
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Kasey R Skinner
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Juanita C Limas
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Xin Chen
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Ralf S Schmid
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Marni B Siegel
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Amanda E D Van Swearingen
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Michael J Hadler
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Erik P Sulman
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Jann N Sarkaria
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Carey K Anders
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Lee M Graves
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Michael E Berens
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Gary L Johnson
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - C Ryan Miller
- Pathobiology and Translational Science Graduate Program, Departments of Pathology and Laboratory Medicine, Biology, Pharmacology, Genetics, Medicine, and Neurology, Divisions of Neuropathology and Hematology/Oncology, Curriculum in Genetics and Molecular Biology, Lineberger Comprehensive Cancer Center, Proteomics Core Facility, Neurosciences Center, Carolina Institute for Developmental Disabilities, and Biological and Biomedical Sciences Program, University of North Carolina (UNC) School of Medicine, Chapel Hill, North Carolina; Cancer & Cell Biology Division, TGen, Phoenix, Arizona; Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota; Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas
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Sanai N, Li J, Boerner J, Stark K, Wu J, Kim S, Derogatis A, Mehta S, Dhruv HD, Heilbrun LK, Berens ME, LoRusso PM. Phase 0 Trial of AZD1775 in First-Recurrence Glioblastoma Patients. Clin Cancer Res 2018; 24:3820-3828. [PMID: 29798906 DOI: 10.1158/1078-0432.ccr-17-3348] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/12/2018] [Accepted: 03/02/2018] [Indexed: 11/16/2022]
Abstract
Purpose: AZD1775 is a first-in-class Wee1 inhibitor with dual function as a DNA damage sensitizer and cytotoxic agent. A phase I study of AZD1775 for solid tumors suggested activity against brain tumors, but a preclinical study indicated minimal blood-brain barrier penetration in mice. To resolve this controversy, we examined the pharmacokinetics and pharmacodynamics of AZD1775 in patients with first-recurrence, glioblastoma.Patients and Methods: Twenty adult patients received a single dose of AZD1775 prior to tumor resection and enrolled in either a dose-escalation arm or a time-escalation arm. Sparse pharmacokinetic blood samples were collected, and contrast-enhancing tumor samples were collected intraoperatively. AZD1775 total and unbound concentrations were determined by a validated LC/MS-MS method. Population pharmacokinetic analysis was performed to characterize AZD1775 plasma pharmacokinetic profiles. Pharmacodynamic endpoints were compared to matched archival tissue.Results: The AZD1775 plasma concentration-time profile following a single oral dose in patients with glioblastoma was well-described by a one-compartment model. Glomerular filtration rate was identified as a significant covariate on AZD1775 apparent clearance. AZD1775 showed good brain tumor penetration, with a median unbound tumor-to-plasma concentration ratio of 3.2, and achieved potential pharmacologically active tumor concentrations. Wee1 pathway suppression was inferred by abrogation of G2 arrest, intensified double-strand DNA breakage, and programmed cell death. No drug-related adverse events were associated with this study.Conclusions: In contrast to recent preclinical data, our phase 0 study of AZD 1775 in recurrent glioblastoma indicates good human brain tumor penetration, provides the first evidence of clinical biological activity in human glioblastoma, and confirms the utility of phase 0 trials as part of an accelerated paradigm for drug development in patients with glioma. Clin Cancer Res; 24(16); 3820-8. ©2018 AACRSee related commentary by Vogelbaum, p. 3790.
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Affiliation(s)
- Nader Sanai
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona.
| | - Jing Li
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Julie Boerner
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Karri Stark
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Jianmei Wu
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Seongho Kim
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Alanna Derogatis
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona
| | - Shwetal Mehta
- Ivy Brain Tumor Center, Barrow Neurological Institute, Phoenix, Arizona
| | - Harshil D Dhruv
- The Translational Genomics Research Institute, Phoenix, Arizona
| | - Lance K Heilbrun
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
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43
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Ostrom QT, Kinnersley B, Wrensch MR, Eckel-Passow JE, Armstrong G, Rice T, Chen Y, Wiencke JK, McCoy LS, Hansen HM, Amos CI, Bernstein JL, Claus EB, Il'yasova D, Johansen C, Lachance DH, Lai RK, Merrell RT, Olson SH, Sadetzki S, Schildkraut JM, Shete S, Rubin JB, Lathia JD, Berens ME, Andersson U, Rajaraman P, Chanock SJ, Linet MS, Wang Z, Yeager M, Houlston RS, Jenkins RB, Melin B, Bondy ML, Barnholtz-Sloan JS. Sex-specific glioma genome-wide association study identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21. Sci Rep 2018; 8:7352. [PMID: 29743610 PMCID: PMC5943590 DOI: 10.1038/s41598-018-24580-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 01/02/2018] [Accepted: 04/06/2018] [Indexed: 01/07/2023] Open
Abstract
Incidence of glioma is approximately 50% higher in males. Previous analyses have examined exposures related to sex hormones in women as potential protective factors for these tumors, with inconsistent results. Previous glioma genome-wide association studies (GWAS) have not stratified by sex. Potential sex-specific genetic effects were assessed in autosomal SNPs and sex chromosome variants for all glioma, GBM and non-GBM patients using data from four previous glioma GWAS. Datasets were analyzed using sex-stratified logistic regression models and combined using meta-analysis. There were 4,831 male cases, 5,216 male controls, 3,206 female cases and 5,470 female controls. A significant association was detected at rs11979158 (7p11.2) in males only. Association at rs55705857 (8q24.21) was stronger in females than in males. A large region on 3p21.31 was identified with significant association in females only. The identified differences in effect of risk variants do not fully explain the observed incidence difference in glioma by sex.
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Affiliation(s)
- Quinn T Ostrom
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Department of Population and Quantitative Heath Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Margaret R Wrensch
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Georgina Armstrong
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Terri Rice
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Yanwen Chen
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - John K Wiencke
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Lucie S McCoy
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Helen M Hansen
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Elizabeth B Claus
- School of Public Health, Yale University, New Haven, Connecticut, United States of America
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Dora Il'yasova
- Department of Epidemiology and Biostatistics, School of Public Health, Georgia State University, Atlanta, Georgia, United States of America
- Cancer Control and Prevention Program, Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christoffer Johansen
- Oncology clinic, Finsen Center, Rigshospitalet, Copenhagen, Denmark
- Survivorship Research Unit, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Daniel H Lachance
- Department of Neurology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rose K Lai
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Ryan T Merrell
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, United States of America
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Siegal Sadetzki
- Cancer and Radiation Epidemiology Unit, Gertner Institute, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Sanjay Shete
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Justin D Lathia
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ulrika Andersson
- Department of Radiation Sciences, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, United States of America
| | - Martha S Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, United States of America
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, United States of America
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Beatrice Melin
- Department of Radiation Sciences, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America.
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Peng S, Dhruv H, Armstrong B, Salhia B, Legendre C, Kiefer J, Parks J, Virk S, Sloan AE, Ostrom QT, Barnholtz-Sloan JS, Tran NL, Berens ME. Integrated genomic analysis of survival outliers in glioblastoma. Neuro Oncol 2018; 19:833-844. [PMID: 27932423 DOI: 10.1093/neuonc/now269] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background To elucidate molecular features associated with disproportionate survival of glioblastoma (GB) patients, we conducted deep genomic comparative analysis of a cohort of patients receiving standard therapy (surgery plus concurrent radiation and temozolomide); "GB outliers" were identified: long-term survivor of 33 months (LTS; n = 8) versus short-term survivor of 7 months (STS; n = 10). Methods We implemented exome, RNA, whole genome sequencing, and DNA methylation for collection of deep genomic data from STS and LTS GB patients. Results LTS GB showed frequent chromosomal gains in 4q12 (platelet derived growth factor receptor alpha and KIT) and 12q14.1 (cyclin-dependent kinase 4), and deletion in 19q13.33 (BAX, branched chain amino-acid transaminase 2, and cluster of differentiation 33). STS GB showed frequent deletion in 9p11.2 (forkhead box D4-like 2 and aquaporin 7 pseudogene 3) and 22q11.21 (Hypermethylated In Cancer 2). LTS GB showed 2-fold more frequent copy number deletions compared with STS GB. Gene expression differences showed the STS cohort with altered transcriptional regulators: activation of signal transducer and activator of transcription (STAT)5a/b, nuclear factor-kappaB (NF-κB), and interferon-gamma (IFNG), and inhibition of mitogen-activated protein kinase (MAPK1), extracellular signal-regulated kinase (ERK)1/2, and estrogen receptor (ESR)1. Expression-based biological concepts prominent in the STS cohort include metabolic processes, anaphase-promoting complex degradation, and immune processes associated with major histocompatibility complex class I antigen presentation; the LTS cohort features genes related to development, morphogenesis, and the mammalian target of rapamycin signaling pathway. Whole genome methylation analyses showed that a methylation signature of 89 probes distinctly separates LTS from STS GB tumors. Conclusion We posit that genomic instability is associated with longer survival of GB (possibly with vulnerability to standard therapy); conversely, genomic and epigenetic signatures may identify patients where up-front entry into alternative, targeted regimens would be a preferred, more efficacious management.
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Affiliation(s)
- Sen Peng
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA.,Department of Biomedical Informatics, Arizona State University, Scottsdale, Arizona, USA
| | - Harshil Dhruv
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Brock Armstrong
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Bodour Salhia
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Christophe Legendre
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Jeffrey Kiefer
- Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA
| | - Julianna Parks
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Selene Virk
- Case Comprehensive Cancer Center, Case Western University, Cleveland, Ohio, USA
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Case Western University, Cleveland, Ohio, USA
| | - Quinn T Ostrom
- Case Comprehensive Cancer Center, Case Western University, Cleveland, Ohio, USA
| | | | - Nhan L Tran
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA.,Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA.,Translational Genomic Research Institute, Phoenix, Arizona, USA
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Hangauer MJ, Viswanathan VS, Ryan MJ, Bole D, Eaton JK, Matov A, Galeas J, Dhruv HD, Berens ME, Schreiber SL, McCormick F, McManus MT. Abstract B098: GPX4 is a broadly shared gene vulnerability among residual tumors. Mol Cancer Ther 2018. [DOI: 10.1158/1535-7163.targ-17-b098] [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
The heterogeneity of tumor cells underlies acquired drug resistance to a variety of therapeutic approaches. The advent of next-generation sequencing has facilitated a wave of studies identifying genetic mutations, which may be preexisting or acquired during treatment, that drive drug resistance and tumor relapse. However, it has recently become clear that non-mutational mechanisms of drug resistance, such as cell state switching from an epithelial to mesenchymal state, can also play an important role in the process of acquired drug resistance. Non-mutational drug resistance is relatively poorly understood and represents fertile ground for the discovery of novel therapeutic targets. Drug-tolerant “persister” cells are an experimental model of non-mutational cancer drug resistance in which small fractions (<5%) of cells within cancer cell lines survive cytotoxic drug exposure despite lacking resistance-conferring mutations. These residual surviving persister cells occupy a reversible quiescent state with a unique chromatin landscape. Persister cells regrow and become resensitized to drug, reminiscent of clinical observations of secondary responses from retreatment after a drug holiday. Persister cells also eventually obtain genetic mutations and reenter the cell cycle after weeks or months of continuous drug exposure, modeling the process of acquisition of resistance-conferring genetic mutations in patients during treatment. Here, we report on our efforts to identify a widely shared gene vulnerability in persister cells that transcends tissue lineage, genetic mutation background, and drug treatment regimens. Through a functional genomics approach entailing RNA-seq, pathway analysis, and a focused chemical inhibitor screen, we have identified a gene, glutathione peroxidase 4 (GPX4), that is specifically essential to persister cells. When GPX4 is chemically inhibited or genetically ablated, persister cells across a wide range of tissue lineages undergo ferroptosis–a recently discovered mechanism of non-apoptotic caspase-independent cell death. Ferroptosis occurs when lipid peroxides accumulate in cells, and as the only human enzyme capable of scavenging lipid peroxides, GPX4 plays a key role in preventing ferroptosis. Compared to drug-naïve parental cells or nontransformed normal cells, persister cells are strongly differentially sensitive to GPX4 inhibition and ferroptosis. This sensitivity is the result of a disabled antioxidant program in persister cells marked by a global downregulation of antioxidant genes including Nrf2 targets, and decreased levels of reducing cofactors glutathione and NADPH. As a first step toward raising GPX4 as a promising preclinical drug target in vivo, we also show that targeting GPX4 in residual melanoma xenograft tumors prevents tumor relapse. Therefore, GPX4 is an extremely promising drug target that may be exploited to prevent tumor relapse across a wide spectrum of tumor types and drug treatments.
Citation Format: Matthew J. Hangauer, Vasanthi S. Viswanathan, Matthew J. Ryan, Dhruv Bole, John K. Eaton, Alexandre Matov, Jacqueline Galeas, Harshil D. Dhruv, Michael E. Berens, Stuart L. Schreiber, Frank McCormick, Michael T. McManus. GPX4 is a broadly shared gene vulnerability among residual tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B098.
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Affiliation(s)
| | | | | | - Dhruv Bole
- 1University of California, San Francisco, San Francisco, CA
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46
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Hangauer MJ, Viswanathan VS, Ryan MJ, Bole D, Eaton JK, Matov A, Galeas J, Dhruv HD, Berens ME, Schreiber SL, McCormick F, McManus MT. Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition. Nature 2017; 551:247-250. [PMID: 29088702 PMCID: PMC5933935 DOI: 10.1038/nature24297] [Citation(s) in RCA: 891] [Impact Index Per Article: 127.3] [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: 07/20/2016] [Accepted: 09/19/2017] [Indexed: 12/29/2022]
Abstract
Acquired drug resistance prevents cancer therapies from achieving stable and complete responses.1 Emerging evidence implicates a key role for nonmutational drug resistance mechanisms underlying the survival of residual cancer “persister” cells.2-4 The persister cell pool constitutes a reservoir from which drug-resistant tumours may emerge. Targeting persister cells therefore presents a therapeutic opportunity to impede tumour relapse.5 In an earlier report, we found that cancer cells in a high mesenchymal therapy-resistant cell state are dependent on the lipid hydroperoxidase GPX4 for survival.6 Here, we describe the discovery that a similar therapy-resistant cell state underlies the behavior of persister cells derived from a wide range of cancers and drug treatments. Consequently, we show that persister cells acquire a dependency on GPX4. We demonstrate that loss of GPX4 function results in selective persister cell ferroptotic death in vitro and prevents tumour relapse in vivo. These findings support targeting GPX4 as a therapeutic strategy to prevent acquired drug resistance.
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Affiliation(s)
- Matthew J Hangauer
- Department of Microbiology and Immunology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA.,UCSF Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94143, USA
| | | | - Matthew J Ryan
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Dhruv Bole
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94143, USA
| | - John K Eaton
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Alexandre Matov
- DataSet Analysis LLC, 155 Jackson Street, San Francisco, California 94111, USA
| | - Jacqueline Galeas
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94143, USA
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, 445 N 5th Street, Phoenix, Arizona 85004, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, 445 N 5th Street, Phoenix, Arizona 85004, USA
| | - Stuart L Schreiber
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94143, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA.,UCSF Diabetes Center, University of California San Francisco, 513 Parnassus Avenue, San Francisco, California 94143, USA
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47
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Byron SA, Tran NL, Halperin RF, Phillips JJ, Kuhn JG, de Groot JF, Colman H, Ligon KL, Wen PY, Cloughesy TF, Mellinghoff IK, Butowski NA, Taylor JW, Clarke JL, Chang SM, Berger MS, Molinaro AM, Maggiora GM, Peng S, Nasser S, Liang WS, Trent JM, Berens ME, Carpten JD, Craig DW, Prados MD. Prospective Feasibility Trial for Genomics-Informed Treatment in Recurrent and Progressive Glioblastoma. Clin Cancer Res 2017; 24:295-305. [PMID: 29074604 DOI: 10.1158/1078-0432.ccr-17-0963] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/15/2017] [Accepted: 10/03/2017] [Indexed: 01/16/2023]
Abstract
Purpose: Glioblastoma is an aggressive and molecularly heterogeneous cancer with few effective treatment options. We hypothesized that next-generation sequencing can be used to guide treatment recommendations within a clinically acceptable time frame following surgery for patients with recurrent glioblastoma.Experimental Design: We conducted a prospective genomics-informed feasibility trial in adults with recurrent and progressive glioblastoma. Following surgical resection, genome-wide tumor/normal exome sequencing and tumor RNA sequencing were performed to identify molecular targets for potential matched therapy. A multidisciplinary molecular tumor board issued treatment recommendations based on the genomic results, blood-brain barrier penetration of the indicated therapies, drug-drug interactions, and drug safety profiles. Feasibility of generating genomics-informed treatment recommendations within 35 days of surgery was assessed.Results: Of the 20 patients enrolled in the study, 16 patients had sufficient tumor tissue for analysis. Exome sequencing was completed for all patients, and RNA sequencing was completed for 14 patients. Treatment recommendations were provided within the study's feasibility time frame for 15 of 16 (94%) patients. Seven patients received treatment based on the tumor board recommendations. Two patients reached 12-month progression-free survival, both adhering to treatments based on the molecular profiling results. One patient remained on treatment and progression free 21 months after surgery, 3 times longer than the patient's previous time to progression. Analysis of matched nonenhancing tissue from 12 patients revealed overlapping as well as novel putatively actionable genomic alterations.Conclusions: Use of genome-wide molecular profiling is feasible and can be informative for guiding real-time, central nervous system-penetrant, genomics-informed treatment recommendations for patients with recurrent glioblastoma. Clin Cancer Res; 24(2); 295-305. ©2017 AACRSee related commentary by Wick and Kessler, p. 256.
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Affiliation(s)
- Sara A Byron
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Nhan L Tran
- Departments of Cancer Biology and Neurosurgery, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Rebecca F Halperin
- Quantitative Medicine & Systems Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California.,Department of Neuropathology, University of California, San Francisco, San Francisco, California
| | - John G Kuhn
- College of Pharmacy, University of Texas Health Science Center, San Antonio, Texas
| | - John F de Groot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Howard Colman
- Department of Neurosurgery, University of Utah Huntsman Cancer Institute, Salt Lake City, Utah
| | - Keith L Ligon
- Center for Neuro-Oncology, Dana-Farber Cancer Center, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts
| | - Timothy F Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.,Neuro-Oncology Program, The Ronald Reagan UCLA Medical Center, University of California, Los Angeles, Los Angeles, California
| | - Ingo K Mellinghoff
- Department of Neurology and Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas A Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Gerald M Maggiora
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Sen Peng
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Sara Nasser
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Winnie S Liang
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Jeffrey M Trent
- Genetic Basis of Human Disease Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Michael E Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - John D Carpten
- Department of Translational Genomics, University of Southern California, Los Angeles, California
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, California
| | - Michael D Prados
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California.
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Bell JB, Eckerdt F, Dhruv HD, Finlay D, Peng S, Kim S, Kroczynska B, Beauchamp EM, Alley K, Clymer J, Goldman S, Cheng SY, James CD, Nakano I, Horbinski C, Mazar AP, Vuori K, Kumthekar P, Raizer J, Berens ME, Platanias LC. Differential Response of Glioma Stem Cells to Arsenic Trioxide Therapy Is Regulated by MNK1 and mRNA Translation. Mol Cancer Res 2017; 16:32-46. [PMID: 29042487 DOI: 10.1158/1541-7786.mcr-17-0397] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/13/2017] [Accepted: 10/11/2017] [Indexed: 12/16/2022]
Abstract
Mesenchymal (MES) and proneural (PN) are two distinct glioma stem cell (GSC) populations that drive therapeutic resistance in glioblastoma (GBM). We screened a panel of 650 small molecules against patient-derived GBM cells to discover compounds targeting specific GBM subtypes. Arsenic trioxide (ATO), an FDA-approved drug that crosses the blood-brain barrier, was identified as a potent PN-specific compound in the initial screen and follow-up validation studies. Furthermore, MES and PN GSCs exhibited differential sensitivity to ATO. As ATO has been shown to activate the MAPK-interacting kinase 1 (MNK1)-eukaryotic translation initiation factor 4E (eIF4E) pathway and subsequent mRNA translation in a negative regulatory feedback manner, the mechanistic role of ATO resistance in MES GBM was explored. In GBM cells, ATO-activated translation initiation cellular events via the MNK1-eIF4E signaling axis. Furthermore, resistance to ATO in intracranial PDX tumors correlated with high eIF4E phosphorylation. Polysomal fractionation and microarray analysis of GBM cells were performed to identify ATO's effect on mRNA translation and enrichment of anti-apoptotic mRNAs in the ATO-induced translatome was found. Additionally, it was determined that MNK inhibition sensitized MES GSCs to ATO in neurosphere and apoptosis assays. Finally, examination of the effect of ATO on patients from a phase I/II clinical trial of ATO revealed that PN GBM patients responded better to ATO than other subtypes as demonstrated by longer overall and progression-free survival.Implications: These findings raise the possibility of a unique therapeutic approach for GBM, involving MNK1 targeting to sensitize MES GSCs to drugs like arsenic trioxide. Mol Cancer Res; 16(1); 32-46. ©2017 AACR.
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Affiliation(s)
- Jonathan B Bell
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Frank Eckerdt
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Darren Finlay
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Sen Peng
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Seungchan Kim
- Integrated Cancer Genomics Division, The Translational Genomics Research Institute, Phoenix, Arizona.,Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, Texas
| | - Barbara Kroczynska
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Elspeth M Beauchamp
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Medicine, Jesse Brown VA Medical Center, Chicago, Illinois
| | - Kristen Alley
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jessica Clymer
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Division of Hematology/Oncology/Stem Cell Transplantation, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Stewart Goldman
- Division of Hematology/Oncology/Stem Cell Transplantation, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Shi-Yuan Cheng
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - C David James
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ichiro Nakano
- Department of Neurosurgery and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Andrew P Mazar
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Developmental Therapeutics Core, Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois
| | - Kristiina Vuori
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Priya Kumthekar
- Division of Neuro-Oncology, Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jeffrey Raizer
- Division of Neuro-Oncology, Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois. .,Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois.,Department of Medicine, Jesse Brown VA Medical Center, Chicago, Illinois
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Roos A, Dhruv HD, Mathews IT, Inge LJ, Tuncali S, Hartman LK, Chow D, Millard N, Yin HH, Kloss J, Loftus JC, Winkles JA, Berens ME, Tran NL. Identification of aurintricarboxylic acid as a selective inhibitor of the TWEAK-Fn14 signaling pathway in glioblastoma cells. Oncotarget 2017; 8:12234-12246. [PMID: 28103571 PMCID: PMC5355340 DOI: 10.18632/oncotarget.14685] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 08/15/2016] [Accepted: 12/26/2016] [Indexed: 12/30/2022] Open
Abstract
The survival of patients diagnosed with glioblastoma (GBM), the most deadly form of brain cancer, is compromised by the proclivity for local invasion into the surrounding normal brain, which prevents complete surgical resection and contributes to therapeutic resistance. Tumor necrosis factor-like weak inducer of apoptosis (TWEAK), a member of the tumor necrosis factor (TNF) superfamily, can stimulate glioma cell invasion and survival via binding to fibroblast growth factor-inducible 14 (Fn14) and subsequent activation of the transcription factor NF-κB. To discover small molecule inhibitors that disrupt the TWEAK-Fn14 signaling axis, we utilized a cell-based drug-screening assay using HEK293 cells engineered to express both Fn14 and a NF-κB-driven firefly luciferase reporter protein. Focusing on the LOPAC1280 library of 1280 pharmacologically active compounds, we identified aurintricarboxylic acid (ATA) as an agent that suppressed TWEAK-Fn14-NF-κB dependent signaling, but not TNFα-TNFR-NF-κB driven signaling. We demonstrated that ATA repressed TWEAK-induced glioma cell chemotactic migration and invasion via inhibition of Rac1 activation but had no effect on cell viability or Fn14 expression. In addition, ATA treatment enhanced glioma cell sensitivity to both the chemotherapeutic agent temozolomide (TMZ) and radiation-induced cell death. In summary, this work reports a repurposed use of a small molecule inhibitor that targets the TWEAK-Fn14 signaling axis, which could potentially be developed as a new therapeutic agent for treatment of GBM patients.
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Affiliation(s)
- Alison Roos
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, Arizona 85259, USA
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Ian T Mathews
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Landon J Inge
- Norton Thoracic Institute, St Joseph's Hospital and Medical Center, Phoenix, AZ 85004, USA
| | - Serdar Tuncali
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, Arizona 85259, USA
| | - Lauren K Hartman
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Donald Chow
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Nghia Millard
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Holly H Yin
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Jean Kloss
- Department of Biochemistry and Molecular Biology, Mayo Clinic Arizona, Scottsdale, Arizona 85259, USA
| | - Joseph C Loftus
- Department of Biochemistry and Molecular Biology, Mayo Clinic Arizona, Scottsdale, Arizona 85259, USA
| | - Jeffrey A Winkles
- Department of Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Nhan L Tran
- Department of Cancer Biology, Mayo Clinic Arizona, Scottsdale, Arizona 85259, USA
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50
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Viswanathan VS, Ryan MJ, Dhruv HD, Gill S, Eichhoff OM, Seashore-Ludlow B, Kaffenberger SD, Eaton JK, Shimada K, Aguirre AJ, Viswanathan SR, Chattopadhyay S, Tamayo P, Yang WS, Rees MG, Chen S, Boskovic ZV, Javaid S, Huang C, Wu X, Tseng YY, Roider EM, Gao D, Cleary JM, Wolpin BM, Mesirov JP, Haber DA, Engelman JA, Boehm JS, Kotz JD, Hon CS, Chen Y, Hahn WC, Levesque MP, Doench JG, Berens ME, Shamji AF, Clemons PA, Stockwell BR, Schreiber SL. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature 2017; 547:453-457. [PMID: 28678785 DOI: 10.1038/nature23007] [Citation(s) in RCA: 1050] [Impact Index Per Article: 150.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 05/24/2017] [Indexed: 12/16/2022]
Abstract
Plasticity of the cell state has been proposed to drive resistance to multiple classes of cancer therapies, thereby limiting their effectiveness. A high-mesenchymal cell state observed in human tumours and cancer cell lines has been associated with resistance to multiple treatment modalities across diverse cancer lineages, but the mechanistic underpinning for this state has remained incompletely understood. Here we molecularly characterize this therapy-resistant high-mesenchymal cell state in human cancer cell lines and organoids and show that it depends on a druggable lipid-peroxidase pathway that protects against ferroptosis, a non-apoptotic form of cell death induced by the build-up of toxic lipid peroxides. We show that this cell state is characterized by activity of enzymes that promote the synthesis of polyunsaturated lipids. These lipids are the substrates for lipid peroxidation by lipoxygenase enzymes. This lipid metabolism creates a dependency on pathways converging on the phospholipid glutathione peroxidase (GPX4), a selenocysteine-containing enzyme that dissipates lipid peroxides and thereby prevents the iron-mediated reactions of peroxides that induce ferroptotic cell death. Dependency on GPX4 was found to exist across diverse therapy-resistant states characterized by high expression of ZEB1, including epithelial-mesenchymal transition in epithelial-derived carcinomas, TGFβ-mediated therapy-resistance in melanoma, treatment-induced neuroendocrine transdifferentiation in prostate cancer, and sarcomas, which are fixed in a mesenchymal state owing to their cells of origin. We identify vulnerability to ferroptic cell death induced by inhibition of a lipid peroxidase pathway as a feature of therapy-resistant cancer cells across diverse mesenchymal cell-state contexts.
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Affiliation(s)
| | - Matthew J Ryan
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Harshil D Dhruv
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, 445 N 5th Street, Phoenix, Arizona 85004, USA
| | - Shubhroz Gill
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Ossia M Eichhoff
- Department of Dermatology, University of Zurich, University Hospital of Zurich, Wagistrasse 14, CH-8952, Schlieren, Zürich, Switzerland
| | | | - Samuel D Kaffenberger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - John K Eaton
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Kenichi Shimada
- Laboratory of Systems Pharmacology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Andrew J Aguirre
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Srinivas R Viswanathan
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | | | - Pablo Tamayo
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA.,Moores Cancer Center &Department of Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Wan Seok Yang
- Department of Biological Sciences, St. John's University, 8000 Utopia Parkway, Queens, New York 11439, USA
| | - Matthew G Rees
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Sixun Chen
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Zarko V Boskovic
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Sarah Javaid
- Massachusetts General Hospital Cancer Center, 149 13th Street, Charlestown, Massachusetts 02129, USA
| | - Cherrie Huang
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Xiaoyun Wu
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yuen-Yi Tseng
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Elisabeth M Roider
- Department of Dermatology, University of Zurich, University Hospital of Zurich, Wagistrasse 14, CH-8952, Schlieren, Zürich, Switzerland
| | - Dong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - James M Cleary
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Jill P Mesirov
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA.,Moores Cancer Center &Department of Medicine, School of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, 149 13th Street, Charlestown, Massachusetts 02129, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Jeffrey A Engelman
- Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Jesse S Boehm
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Joanne D Kotz
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Cindy S Hon
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - William C Hahn
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University Hospital of Zurich, Wagistrasse 14, CH-8952, Schlieren, Zürich, Switzerland
| | - John G Doench
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, 445 N 5th Street, Phoenix, Arizona 85004, USA
| | - Alykhan F Shamji
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Paul A Clemons
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Department of Chemistry, Columbia University, 550 West 120th Street, New York, New York 10027, USA
| | - Stuart L Schreiber
- Broad Institute, 415 Main Street, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, USA
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