1
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Nuechterlein N, Shelbourn A, Szulzewsky F, Arora S, Casad M, Pattwell S, Merino-Galan L, Sulman E, Arowa S, Alvinez N, Jung M, Brown D, Tang K, Jackson S, Stoica S, Chittaboina P, Banasavadi-Siddegowda YK, Wirsching HG, Stella N, Shapiro L, Paddison P, Patel AP, Gilbert MR, Abdullaev Z, Aldape K, Pratt D, Holland EC, Cimino PJ. Haploinsufficiency of phosphodiesterase 10A activates PI3K/AKT signaling independent of PTEN to induce an aggressive glioma phenotype. Genes Dev 2024; 38:273-288. [PMID: 38589034 PMCID: PMC11065166 DOI: 10.1101/gad.351350.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/27/2024] [Indexed: 04/10/2024]
Abstract
Glioblastoma is universally fatal and characterized by frequent chromosomal copy number alterations harboring oncogenes and tumor suppressors. In this study, we analyzed exome-wide human glioblastoma copy number data and found that cytoband 6q27 is an independent poor prognostic marker in multiple data sets. We then combined CRISPR-Cas9 data, human spatial transcriptomic data, and human and mouse RNA sequencing data to nominate PDE10A as a potential haploinsufficient tumor suppressor in the 6q27 region. Mouse glioblastoma modeling using the RCAS/tv-a system confirmed that Pde10a suppression induced an aggressive glioma phenotype in vivo and resistance to temozolomide and radiation therapy in vitro. Cell culture analysis showed that decreased Pde10a expression led to increased PI3K/AKT signaling in a Pten-independent manner, a response blocked by selective PI3K inhibitors. Single-nucleus RNA sequencing from our mouse gliomas in vivo, in combination with cell culture validation, further showed that Pde10a suppression was associated with a proneural-to-mesenchymal transition that exhibited increased cell adhesion and decreased cell migration. Our results indicate that glioblastoma patients harboring PDE10A loss have worse outcomes and potentially increased sensitivity to PI3K inhibition.
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Affiliation(s)
- Nicholas Nuechterlein
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Allison Shelbourn
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Michelle Casad
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Siobhan Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Leyre Merino-Galan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Erik Sulman
- Department of Radiation Oncology, New York University Grossman School of Medicine, New York, New York 11220, USA
| | - Sumaita Arowa
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Neriah Alvinez
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Miyeon Jung
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Desmond Brown
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kayen Tang
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Sadhana Jackson
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Stefan Stoica
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Prashant Chittaboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Yeshavanth K Banasavadi-Siddegowda
- Molecular and Therapeutics Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital, University of Zurich, Zurich 8091, Switzerland
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Linda Shapiro
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Patrick Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anoop P Patel
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina 27710, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Patrick J Cimino
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA;
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2
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Rao A, Zhang X, Cillo AR, Sussman JH, Sandlesh P, Tarbay AC, Mallela AN, Cardello C, Krueger K, Xu J, Li A, Xu J, Patterson J, Akca E, Angione A, Jaman E, Kim WJ, Allen J, Venketeswaran A, Zinn PO, Parise R, Beumer J, Duensing A, Holland EC, Ferris R, Bagley SJ, Bruno TC, Vignali DAA, Agnihotri S, Amankulor NM. All-trans retinoic acid induces durable tumor immunity in IDH-mutant gliomas by rescuing transcriptional repression of the CRBP1-retinoic acid axis. bioRxiv 2024:2024.04.09.588752. [PMID: 38645178 PMCID: PMC11030316 DOI: 10.1101/2024.04.09.588752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Diffuse gliomas are epigenetically dysregulated, immunologically cold, and fatal tumors characterized by mutations in isocitrate dehydrogenase (IDH). Although IDH mutations yield a uniquely immunosuppressive tumor microenvironment, the regulatory mechanisms that drive the immune landscape of IDH mutant (IDHm) gliomas remain unknown. Here, we reveal that transcriptional repression of retinoic acid (RA) pathway signaling impairs both innate and adaptive immune surveillance in IDHm glioma through epigenetic silencing of retinol binding protein 1 (RBP1) and induces a profound anti-inflammatory landscape marked by loss of inflammatory cell states and infiltration of suppressive myeloid phenotypes. Restorative retinoic acid therapy in murine glioma models promotes clonal CD4 + T cell expansion and induces tumor regression in IDHm, but not IDH wildtype (IDHwt), gliomas. Our findings provide a mechanistic rationale for RA immunotherapy in IDHm glioma and is the basis for an ongoing investigator-initiated, single-center clinical trial investigating all-trans retinoic acid (ATRA) in recurrent IDHm human subjects.
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3
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Schmid S, Russell ZR, Yamashita AS, West ME, Parrish AG, Walker J, Rudoy D, Yan JZ, Quist DC, Gessesse BN, Alvinez N, Cimino PJ, Kumasaka DK, Parchment RE, Holland EC, Szulzewsky F. ERK signaling promotes resistance to TRK kinase inhibition in NTRK fusion-driven glioma mouse models. bioRxiv 2024:2024.03.13.584849. [PMID: 38558981 PMCID: PMC10979979 DOI: 10.1101/2024.03.13.584849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pediatric-type high-grade gliomas frequently harbor gene fusions involving receptor tyrosine kinase genes, including neurotrophic tyrosine kinase receptor (NTRK) fusions. Clinically, these tumors show high initial response rates to tyrosine kinase inhibition but ultimately recur due to the accumulation of additional resistance-conferring mutations. Here, we developed a series of genetically engineered mouse models of treatment-naïve and -experienced NTRK1/2/3 fusion-driven gliomas. Both the TRK kinase domain and the N-terminal fusion partners influenced tumor histology and aggressiveness. Treatment with TRK kinase inhibitors significantly extended survival of NTRK fusion-driven glioma mice in a fusion- and inhibitor-dependent manner, but tumors ultimately recurred due to the presence of treatment-resistant persister cells. Finally, we show that ERK activation promotes resistance to TRK kinase inhibition and identify MEK inhibition as a potential combination therapy. These models will be invaluable tools for preclinical testing of novel inhibitors and to study the cellular responses of NTRK fusion-driven gliomas to therapy.
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Affiliation(s)
- Sebastian Schmid
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Zachary R Russell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Alex Shimura Yamashita
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Madeline E West
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Abigail G Parrish
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julia Walker
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Dmytro Rudoy
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - James Z Yan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David C Quist
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Neriah Alvinez
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Patrick J Cimino
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debra K Kumasaka
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ralph E Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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4
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Szulzewsky F, Thirimanne HN, Holland EC. Meningioma: current updates on genetics, classification, and mouse modeling. Ups J Med Sci 2024; 129:10579. [PMID: 38571886 PMCID: PMC10989216 DOI: 10.48101/ujms.v129.10579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 04/05/2024] Open
Abstract
Meningiomas, the most common primary brain tumors in adults, are often benign and curable by surgical resection. However, a subset is of higher grade, shows aggressive growth behavior as well as brain invasion, and often recurs even after several rounds of surgery. Increasing evidence suggests that tumor classification and grading primarily based on histopathology do not always accurately predict tumor aggressiveness and recurrence behavior. The underlying biology of aggressive treatment-resistant meningiomas and the impact of specific genetic aberrations present in these high-grade tumors is still only insufficiently understood. Therefore, an in-depth research into the biology of this tumor type is warranted. More recent studies based on large-scale molecular data such as whole exome/genome sequencing, DNA methylation sequencing, and RNA sequencing have provided new insights into the biology of meningiomas and have revealed new risk factors and prognostic subtypes. The most common genetic aberration in meningiomas is functional loss of NF2 and occurs in both low- and high-grade meningiomas, whereas NF2-wildtype meningiomas are enriched for recurrent mutations in TRAF7, KLF4, AKT1, PI3KCA, and SMO and are more frequently benign. Most meningioma mouse models are based on patient-derived xenografts and only recently have new genetically engineered mouse models of meningioma been developed that will aid in the systematic evaluation of specific mutations found in meningioma and their impact on tumor behavior. In this article, we review recent advances in the understanding of meningioma biology and classification and highlight the most common genetic mutations, as well as discuss new genetically engineered mouse models of meningioma.
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Affiliation(s)
- Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, WA, USA
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5
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Henikoff S, Henikoff JG, Paranal RM, Greene JE, Zheng Y, Russell ZR, Szulzewsky F, Kugel S, Holland EC, Ahmad K. Direct measurement of RNA Polymerase II hypertranscription in cancer FFPE samples. bioRxiv 2024:2024.02.28.582647. [PMID: 38559075 PMCID: PMC10979862 DOI: 10.1101/2024.02.28.582647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Hypertranscription is widespread in aggressive human cancers. However detection relies on mRNAs, which are heavily processed and have variable half-lives, and on accurate cell number estimations. Previously we introduced FFPE-CUTAC, a genome-wide method for mapping RNA Polymerase II in formalin-fixed paraffin-embedded (FFPE) sections. Here we apply FFPE-CUTAC on slides and curls to demonstrate hypertranscription at regulatory elements and replication-coupled histone genes. We find that hypertranscription differs between transgene-driven mouse gliomas and scales with enhanced proliferation and reduced mitochondrial DNA. We also apply FFPE-CUTAC to identify tumor-specific patterns in assorted human tumor-normal pairs. We analyze the top-ranked 100 annotated regulatory elements that are hypertranscribed in most of the tumors and identify multiple loci around ERBB2 on Chromosome 17q12-21 in the breast and colon cancer samples, mapping likely HER2 amplifications punctuated by selective sweeps. Our results demonstrate that FFPE-CUTAC measurement of hypertranscription provides an affordable and sensitive genome-wide strategy for cancer diagnosis.
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Affiliation(s)
- Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jorja G. Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ronald M. Paranal
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jacob E. Greene
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Medicine and Mechanisms of Disease (M3D) PhD Program, University of Washington, Seattle, WA, USA
| | - Ye Zheng
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sita Kugel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kami Ahmad
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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6
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Chung CI, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X. Phase separation of YAP-MAML2 differentially regulates the transcriptome. Proc Natl Acad Sci U S A 2024; 121:e2310430121. [PMID: 38315854 PMCID: PMC10873646 DOI: 10.1073/pnas.2310430121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024] Open
Abstract
Phase separation (PS) drives the formation of biomolecular condensates that are emerging biological structures involved in diverse cellular processes. Recent studies have unveiled PS-induced formation of several transcriptional factor (TF) condensates that are transcriptionally active, but how strongly PS promotes gene activation remains unclear. Here, we show that the oncogenic TF fusion Yes-associated protein 1-Mastermind like transcriptional coactivator 2 (YAP-MAML2) undergoes PS and forms liquid-like condensates that bear the hallmarks of transcriptional activity. Furthermore, we examined the contribution of PS to YAP-MAML2-mediated gene expression by developing a chemogenetic tool that dissolves TF condensates, allowing us to compare phase-separated and non-phase-separated conditions at identical YAP-MAML2 protein levels. We found that a small fraction of YAP-MAML2-regulated genes is further affected by PS, which include the canonical YAP target genes CTGF and CYR61, and other oncogenes. On the other hand, majority of YAP-MAML2-regulated genes are not affected by PS, highlighting that transcription can be activated effectively by diffuse complexes of TFs with the transcriptional machinery. Our work opens new directions in understanding the role of PS in selective modulation of gene expression, suggesting differential roles of PS in biological processes.
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Affiliation(s)
- Chan-I. Chung
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Xiaoyu Yang
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Hongjiang Liu
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Zhimin Ma
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA98109
- Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Center, Seattle, WA98109
| | - Yin Shen
- Department of Neurology, Institute for Human Genetics, Weill Institute for Neurosciences, University of California, San Francisco, CA94158
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California–San Francisco, San Francisco, CA94158
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA94158
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7
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Wirsching HG, Felsberg J, Prummer M, Moisoiu V, Lourman R, Hertler C, Antonios M, Cimino PJ, Roth P, Gorlia T, Prins RM, Cloughesy T, Wen PY, Holland EC, Reifenberger G, Weller M. Spatial immune profiling of glioblastoma identifies an inflammatory, perivascular phenotype associated with longer survival. Acta Neuropathol 2023; 146:647-649. [PMID: 37573572 PMCID: PMC10499942 DOI: 10.1007/s00401-023-02617-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/15/2023]
Affiliation(s)
- Hans-Georg Wirsching
- Department of Neurology, University Hospital and University of Zurich, Frauenklinikstrasse 26, CH-8091, Zurich, Switzerland.
| | - Jörg Felsberg
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Michael Prummer
- NEXUS Personalized Health Technologies and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Vlad Moisoiu
- Department of Neurology, University Hospital and University of Zurich, Frauenklinikstrasse 26, CH-8091, Zurich, Switzerland
| | - Roxanne Lourman
- Department of Neurology, University Hospital and University of Zurich, Frauenklinikstrasse 26, CH-8091, Zurich, Switzerland
| | - Caroline Hertler
- Department of Radiation Oncology, Competence Center for Palliative Care, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michelle Antonios
- Department of Neurology, University Hospital and University of Zurich, Frauenklinikstrasse 26, CH-8091, Zurich, Switzerland
| | - Patrick J Cimino
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Patrick Roth
- Department of Neurology, University Hospital and University of Zurich, Frauenklinikstrasse 26, CH-8091, Zurich, Switzerland
| | - Thierry Gorlia
- European Organization for Research and Treatment of Cancer, Brussels, Belgium
| | - Robert M Prins
- Department of Neurosurgery, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Timothy Cloughesy
- Department of Neurosurgery, University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University and University Hospital Düsseldorf, Düsseldorf, Germany
- Partner Site Essen/Düsseldorf, German Cancer Consortium (DKTK), Düsseldorf, Germany
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Frauenklinikstrasse 26, CH-8091, Zurich, Switzerland
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8
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Henikoff S, Henikoff JG, Ahmad K, Paranal RM, Janssens DH, Russell ZR, Szulzewsky F, Kugel S, Holland EC. Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag. Nat Commun 2023; 14:5930. [PMID: 37739938 PMCID: PMC10516967 DOI: 10.1038/s41467-023-41666-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/14/2023] [Indexed: 09/24/2023] Open
Abstract
For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
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Affiliation(s)
- Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Jorja G Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kami Ahmad
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ronald M Paranal
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Derek H Janssens
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Zachary R Russell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sita Kugel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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9
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Miroshnikova YA, Mouw JK, Barnes JM, Pickup MW, Lakins JN, Kim Y, Lobo K, Persson AI, Reis GF, McKnight TR, Holland EC, Phillips JJ, Weaver VM. Author Correction: Tissue mechanics promote IDH1-dependent HIF1α-tenascin C feedback to regulate glioblastoma aggression. Nat Cell Biol 2023; 25:787-788. [PMID: 37016139 DOI: 10.1038/s41556-023-01126-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Affiliation(s)
- Yekaterina A Miroshnikova
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, California, 94143, USA
| | - Janna K Mouw
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, California, 94143, USA
| | - J Matthew Barnes
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, California, 94143, USA
| | - Michael W Pickup
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, California, 94143, USA
| | - Johnathan N Lakins
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, California, 94143, USA
| | - Youngmi Kim
- Division of Human Biology and Solid Tumor Translational Research, Fred Hutchinson Cancer Research Center, Department of Neurosurgery and Alvord Brain Tumor Center, University of Washington, Seattle, Washington, 98109, USA
| | - Khadjia Lobo
- Magnetic Resonance Science Center, Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, 94143, USA
| | - Anders I Persson
- Department of Neurology, University of California, San Francisco, California, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, 94158, USA
- Brain Tumor Research Center, Helen Diller Family Cancer Research Center, University of California San Francisco, San Francisco, California, 94143, USA
- UCSF Comprehensive Cancer Center, Helen Diller Family Cancer Research Center, University of California San Francisco, San Francisco, California, 94143, USA
| | - Gerald F Reis
- Department of Pathology, University of California, San Francisco, California, 94143, USA
| | - Tracy R McKnight
- Magnetic Resonance Science Center, Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, 94143, USA
| | - Eric C Holland
- Division of Human Biology and Solid Tumor Translational Research, Fred Hutchinson Cancer Research Center, Department of Neurosurgery and Alvord Brain Tumor Center, University of Washington, Seattle, Washington, 98109, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, 94158, USA
- Brain Tumor Research Center, Helen Diller Family Cancer Research Center, University of California San Francisco, San Francisco, California, 94143, USA
- UCSF Comprehensive Cancer Center, Helen Diller Family Cancer Research Center, University of California San Francisco, San Francisco, California, 94143, USA
- Department of Pathology, University of California, San Francisco, California, 94143, USA
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California San Francisco, San Francisco, California, 94143, USA.
- Department of Anatomy and Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, 94143, USA.
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, 94143, USA.
- UCSF Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, 94143, USA.
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10
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Arora S, Szulzewsky F, Jensen M, Nuechterlein N, Pattwell SS, Holland EC. Visualizing genomic characteristics across an RNA-Seq based reference landscape of normal and neoplastic brain. Sci Rep 2023; 13:4228. [PMID: 36918656 PMCID: PMC10014937 DOI: 10.1038/s41598-023-31180-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
In order to better understand the relationship between normal and neoplastic brain, we combined five publicly available large-scale datasets, correcting for batch effects and applying Uniform Manifold Approximation and Projection (UMAP) to RNA-Seq data. We assembled a reference Brain-UMAP including 702 adult gliomas, 802 pediatric tumors and 1409 healthy normal brain samples, which can be utilized to investigate the wealth of information obtained from combining several publicly available datasets to study a single organ site. Normal brain regions and tumor types create distinct clusters and because the landscape is generated by RNA-Seq, comparative gene expression profiles and gene ontology patterns are readily evident. To our knowledge, this is the first meta-analysis that allows for comparison of gene expression and pathways of interest across adult gliomas, pediatric brain tumors, and normal brain regions. We provide access to this resource via the open source, interactive online tool Oncoscape, where the scientific community can readily visualize clinical metadata, gene expression patterns, gene fusions, mutations, and copy number patterns for individual genes and pathway over this reference landscape.
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Affiliation(s)
- Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA
| | - Matt Jensen
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA
| | - Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, 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, University of Washington School of Medicine, Seattle, WA, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA.
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11
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Rajendran S, Hu Y, Canella A, Peterson C, Gross A, Cam M, Nazzaro M, Haffey A, Serin-Harmanci A, Distefano R, Nigita G, Wang W, Kreatsoulas D, Li Z, Sepeda JA, Sas A, Hester ME, Miller KE, Elemento O, Roberts RD, Holland EC, Rao G, Mardis ER, Rajappa P. Single-cell RNA sequencing reveals immunosuppressive myeloid cell diversity during malignant progression in a murine model of glioma. Cell Rep 2023; 42:112197. [PMID: 36871221 DOI: 10.1016/j.celrep.2023.112197] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 06/13/2022] [Revised: 11/22/2022] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
Recent studies have shown the importance of the dynamic tumor microenvironment (TME) in high-grade gliomas (HGGs). In particular, myeloid cells are known to mediate immunosuppression in glioma; however, it is still unclear if myeloid cells play a role in low-grade glioma (LGG) malignant progression. Here, we investigate the cellular heterogeneity of the TME using single-cell RNA sequencing in a murine glioma model that recapitulates the malignant progression of LGG to HGG. LGGs show increased infiltrating CD4+ and CD8+ T cells and natural killer (NK) cells in the TME, whereas HGGs abrogate this infiltration. Our study identifies distinct macrophage clusters in the TME that show an immune-activated phenotype in LGG but then evolve to an immunosuppressive state in HGG. We identify CD74 and macrophage migration inhibition factor (MIF) as potential targets for these distinct macrophage populations. Targeting these intra-tumoral macrophages in the LGG stage may attenuate their immunosuppressive properties and impair malignant progression.
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Affiliation(s)
- Sakthi Rajendran
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Yang Hu
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alessandro Canella
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Clayton Peterson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Gross
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Maren Cam
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Matthew Nazzaro
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Abigail Haffey
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Rosario Distefano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Wesley Wang
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Daniel Kreatsoulas
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Zihai Li
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jesse A Sepeda
- Department of Neurology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Neuroscience Research Institute, The Ohio State University, Columbus, OH, USA
| | - Andrew Sas
- Department of Neurology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Neuroscience Research Institute, The Ohio State University, Columbus, OH, USA
| | - Mark E Hester
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Neurology, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ryan D Roberts
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Eric C Holland
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ganesh Rao
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Prajwal Rajappa
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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12
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Mitchell K, Sprowls SA, Arora S, Shakya S, Silver DJ, Goins CM, Wallace L, Roversi G, Schafer RE, Kay K, Miller TE, Lauko A, Bassett J, Kashyap A, D'Amato Kass J, Mulkearns-Hubert EE, Johnson S, Alvarado J, Rich JN, Holland EC, Paddison PJ, Patel AP, Stauffer SR, Hubert CG, Lathia JD. WDR5 represents a therapeutically exploitable target for cancer stem cells in glioblastoma. Genes Dev 2023; 37:86-102. [PMID: 36732025 PMCID: PMC10069451 DOI: 10.1101/gad.349803.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023]
Abstract
Glioblastomas (GBMs) are heterogeneous, treatment-resistant tumors driven by populations of cancer stem cells (CSCs). However, few molecular mechanisms critical for CSC population maintenance have been exploited for therapeutic development. We developed a spatially resolved loss-of-function screen in GBM patient-derived organoids to identify essential epigenetic regulators in the SOX2-enriched, therapy-resistant niche and identified WDR5 as indispensable for this population. WDR5 is a component of the WRAD complex, which promotes SET1 family-mediated Lys4 methylation of histone H3 (H3K4me), associated with positive regulation of transcription. In GBM CSCs, WDR5 inhibitors blocked WRAD complex assembly and reduced H3K4 trimethylation and expression of genes involved in CSC-relevant oncogenic pathways. H3K4me3 peaks lost with WDR5 inhibitor treatment occurred disproportionally on POU transcription factor motifs, including the POU5F1(OCT4)::SOX2 motif. Use of a SOX2/OCT4 reporter demonstrated that WDR5 inhibitor treatment diminished cells with high reporter activity. Furthermore, WDR5 inhibitor treatment and WDR5 knockdown altered the stem cell state, disrupting CSC in vitro growth and self-renewal, as well as in vivo tumor growth. These findings highlight the role of WDR5 and the WRAD complex in maintaining the CSC state and provide a rationale for therapeutic development of WDR5 inhibitors for GBM and other advanced cancers.
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Affiliation(s)
- Kelly Mitchell
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
| | - Samuel A Sprowls
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sajina Shakya
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Daniel J Silver
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Christopher M Goins
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA;
| | - Lisa Wallace
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Gustavo Roversi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Rachel E Schafer
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Kristen Kay
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Adam Lauko
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Medical Scientist Training Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - John Bassett
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anjali Kashyap
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Jonathan D'Amato Kass
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Erin E Mulkearns-Hubert
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Sadie Johnson
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Joseph Alvarado
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Jeremy N Rich
- University of Pittsburgh Medical Center Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anoop P Patel
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, Washington 98195, USA
| | - Shaun R Stauffer
- Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
| | - Christopher G Hubert
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Justin D Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44106, USA;
- Case Comprehensive Cancer Center, Cleveland, Ohio 44106, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44106, USA
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio 44106, USA
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13
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Arora S, Szulzewsky F, Jensen M, Nuechterlein N, Pattwell SS, Holland EC. An RNA seq-based reference landscape of human normal and neoplastic brain. Res Sq 2023:rs.3.rs-2448083. [PMID: 36711972 PMCID: PMC9882693 DOI: 10.21203/rs.3.rs-2448083/v1] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In order to better understand the relationship between normal and neoplastic brain, we combined five publicly available large-scale datasets, correcting for batch effects and applying Uniform Manifold Approximation and Projection (UMAP) to RNA-seq data. We assembled a reference Brain-UMAP including 702 adult gliomas, 802 pediatric tumors and 1409 healthy normal brain samples, which can be utilized to investigate the wealth of information obtained from combining several publicly available datasets to study a single organ site. Normal brain regions and tumor types create distinct clusters and because the landscape is generated by RNA seq, comparative gene expression profiles and gene ontology patterns are readily evident. To our knowledge, this is the first meta-analysis that allows for comparison of gene expression and pathways of interest across adult gliomas, pediatric brain tumors, and normal brain regions. We provide access to this resource via the open source, interactive online tool Oncoscape, where the scientific community can readily visualize clinical metadata, gene expression patterns, gene fusions, mutations, and copy number patterns for individual genes and pathway over this reference landscape.
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Affiliation(s)
| | | | | | | | - Siobhan S Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute
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14
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Hoellerbauer P, Biery MC, Arora S, Rao Y, Girard EJ, Mitchell K, Dighe P, Kufeld M, Kuppers DA, Herman JA, Holland EC, Soroceanu L, Vitanza NA, Olson JM, Pritchard JR, Paddison PJ. Functional genomic analysis of adult and pediatric brain tumor isolates. bioRxiv 2023:2023.01.05.522885. [PMID: 36711964 PMCID: PMC9881972 DOI: 10.1101/2023.01.05.522885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Adult and pediatric tumors display stark differences in their mutation spectra and chromosome alterations. Here, we attempted to identify common and unique gene dependencies and their associated biomarkers among adult and pediatric tumor isolates using functional genetic lethal screens and computational modeling. Methods We performed CRISRP-Cas9 lethality screens in two adult glioblastoma (GBM) tumor isolates and five pediatric brain tumor isolates representing atypical teratoid rhabdoid tumors (ATRT), diffuse intrinsic pontine glioma, GBM, and medulloblastoma. We then integrated the screen results with machine learning-based gene-dependency models generated from data from >900 cancer cell lines. Results We found that >50% of candidate dependencies of 280 identified were shared between adult GBM tumors and individual pediatric tumor isolates. 68% of screen hits were found as nodes in our network models, along with shared and tumor-specific predictors of gene dependencies. We investigated network predictors associated with ADAR, EFR3A, FGFR1 (pediatric-specific), and SMARCC2 (ATRT-specific) gene dependency among our tumor isolates. Conclusions The results suggest that, despite harboring disparate genomic signatures, adult and pediatric tumor isolates share a preponderance of genetic dependences. Further, combining data from primary brain tumor lethality screens with large cancer cell line datasets produced valuable insights into biomarkers of gene dependency, even for rare cancers. Importance of the Study Our results demonstrate that large cancer cell lines data sets can be computationally mined to identify known and novel gene dependency relationships in adult and pediatric human brain tumor isolates. Gene dependency networks and lethality screen results represent a key resource for neuro-oncology and cancer research communities. We also highlight some of the challenges and limitations of this approach.
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Affiliation(s)
- Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
| | - Matt C Biery
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Yiyun Rao
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Kelly Mitchell
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Pratiksha Dighe
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Megan Kufeld
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Daniel A Kuppers
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
| | - Liliana Soroceanu
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Nicholas A Vitanza
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Justin R Pritchard
- Huck Institute for the Life Sciences, Pennsylvania State University, State College, PA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA USA
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15
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Arora S, Szulzewsky F, Jensen M, Nuechterlein N, Pattwell SS, Holland EC. An RNA seq-based reference landscape of human normal and neoplastic brain. bioRxiv 2023:2023.01.03.522658. [PMID: 36711910 PMCID: PMC9881953 DOI: 10.1101/2023.01.03.522658] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In order to better understand the relationship between normal and neoplastic brain, we combined five publicly available large-scale datasets, correcting for batch effects and applying Uniform Manifold Approximation and Projection (UMAP) to RNA-seq data. We assembled a reference Brain-UMAP including 702 adult gliomas, 802 pediatric tumors and 1409 healthy normal brain samples, which can be utilized to investigate the wealth of information obtained from combining several publicly available datasets to study a single organ site. Normal brain regions and tumor types create distinct clusters and because the landscape is generated by RNA seq, comparative gene expression profiles and gene ontology patterns are readily evident. To our knowledge, this is the first meta-analysis that allows for comparison of gene expression and pathways of interest across adult gliomas, pediatric brain tumors, and normal brain regions. We provide access to this resource via the open source, interactive online tool Oncoscape, where the scientific community can readily visualize clinical metadata, gene expression patterns, gene fusions, mutations, and copy number patterns for individual genes and pathway over this reference landscape.
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Affiliation(s)
- Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109
| | - Matt Jensen
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109
| | - Nicholas Nuechterlein
- Paul Allen School of Computer Science & Engineering, University of Washington, Seattle, WA
| | - Siobhan S Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109
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16
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Becker H, Castaneda-Vega S, Patzwaldt K, Przystal JM, Walter B, Michelotti FC, Canjuga D, Tatagiba M, Pichler B, Beck SC, Holland EC, la Fougère C, Tabatabai G. Multiparametric Longitudinal Profiling of RCAS-tva-Induced PDGFB-Driven Experimental Glioma. Brain Sci 2022; 12:1426. [PMID: 36358353 PMCID: PMC9688186 DOI: 10.3390/brainsci12111426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 12/31/2023] Open
Abstract
Glioblastomas are incurable primary brain tumors harboring a heterogeneous landscape of genetic and metabolic alterations. Longitudinal imaging by MRI and [18F]FET-PET measurements enable us to visualize the features of evolving tumors in a dynamic manner. Yet, close-meshed longitudinal imaging time points for characterizing temporal and spatial metabolic alterations during tumor evolution in patients is not feasible because patients usually present with already established tumors. The replication-competent avian sarcoma-leukosis virus (RCAS)/tumor virus receptor-A (tva) system is a powerful preclinical glioma model offering a high grade of spatial and temporal control of somatic gene delivery in vivo. Consequently, here, we aimed at using MRI and [18F]FET-PET to identify typical neuroimaging characteristics of the platelet-derived growth factor B (PDGFB)-driven glioma model using the RCAS-tva system. Our study showed that this preclinical glioma model displays MRI and [18F]FET-PET features that highly resemble the corresponding established human disease, emphasizing the high translational relevance of this experimental model. Furthermore, our investigations unravel exponential growth dynamics and a model-specific tumor microenvironment, as assessed by histology and immunochemistry. Taken together, our study provides further insights into this preclinical model and advocates for the imaging-stratified design of preclinical therapeutic interventions.
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Affiliation(s)
- Hannes Becker
- Department of Neurology & Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Center for Neuro-Oncology, Comprehensive Cancer Center, University Hospital Tübingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
- Department of Neurosurgery, University Hospital Tubingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
| | - Salvador Castaneda-Vega
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tuebingen, 72072 Tubingen, Germany
- Department of Nuclear Medicine and Clinical Molecular Imaging, Eberhard Karls University Tuebingen, 72072 Tubingen, Germany
| | - Kristin Patzwaldt
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tuebingen, 72072 Tubingen, Germany
| | - Justyna M. Przystal
- Department of Neurology & Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Center for Neuro-Oncology, Comprehensive Cancer Center, University Hospital Tübingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
- German Translational Cancer Consortium (DKTK), DKFZ Partner Site, 72072 Tubingen, Germany
| | - Bianca Walter
- Department of Neurology & Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Center for Neuro-Oncology, Comprehensive Cancer Center, University Hospital Tübingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
| | - Filippo C. Michelotti
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tuebingen, 72072 Tubingen, Germany
| | - Denis Canjuga
- Department of Neurology & Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Center for Neuro-Oncology, Comprehensive Cancer Center, University Hospital Tübingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
| | - Marcos Tatagiba
- Department of Neurology & Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Center for Neuro-Oncology, Comprehensive Cancer Center, University Hospital Tübingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
- Department of Neurosurgery, University Hospital Tubingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
| | - Bernd Pichler
- Department of Nuclear Medicine and Clinical Molecular Imaging, Eberhard Karls University Tuebingen, 72072 Tubingen, Germany
- German Translational Cancer Consortium (DKTK), DKFZ Partner Site, 72072 Tubingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University, 72072 Tubingen, Germany
| | - Susanne C. Beck
- Department of Neurology & Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Center for Neuro-Oncology, Comprehensive Cancer Center, University Hospital Tübingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, DC 98109, USA
| | - Christian la Fougère
- Department of Nuclear Medicine and Clinical Molecular Imaging, Eberhard Karls University Tuebingen, 72072 Tubingen, Germany
- German Translational Cancer Consortium (DKTK), DKFZ Partner Site, 72072 Tubingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University, 72072 Tubingen, Germany
| | - Ghazaleh Tabatabai
- Department of Neurology & Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Center for Neuro-Oncology, Comprehensive Cancer Center, University Hospital Tübingen, Eberhard Karls University Tubingen, 72072 Tubingen, Germany
- German Translational Cancer Consortium (DKTK), DKFZ Partner Site, 72072 Tubingen, Germany
- Cluster of Excellence iFIT (EXC 2180) “Image Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University, 72072 Tubingen, Germany
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17
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Pattwell SS, Arora S, Nuechterlein N, Zager M, Loeb KR, Cimino PJ, Holland NC, Reche-Ley N, Bolouri H, Almiron Bonnin DA, Szulzewsky F, Phadnis VV, Ozawa T, Wagner MJ, Haffner MC, Cao J, Shendure J, Holland EC. Oncogenic role of a developmentally regulated NTRK2 splice variant. Sci Adv 2022; 8:eabo6789. [PMID: 36206341 PMCID: PMC9544329 DOI: 10.1126/sciadv.abo6789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Temporally regulated alternative splicing choices are vital for proper development, yet the wrong splice choice may be detrimental. Here, we highlight a previously unidentified role for the neurotrophin receptor splice variant TrkB.T1 in neurodevelopment, embryogenesis, transformation, and oncogenesis across multiple tumor types in humans and mice. TrkB.T1 is the predominant NTRK2 isoform across embryonic organogenesis, and forced overexpression of this embryonic pattern causes multiple solid and nonsolid tumors in mice in the context of tumor suppressor loss. TrkB.T1 also emerges as the predominant NTRK isoform expressed in a wide range of adult and pediatric tumors, including those harboring tropomyosin receptor kinase fusions. Affinity purification-mass spectrometry proteomic analysis reveals distinct interactors with known developmental and oncogenic signaling pathways such as Wnt, transforming growth factor-β, Sonic Hedgehog, and Ras. From alterations in splicing factors to changes in gene expression, the discovery of isoform specific oncogenes with embryonic ancestry has the potential to shape the way we think about developmental systems and oncology.
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Affiliation(s)
- Siobhan S. Pattwell
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Division of Pediatrics, Department Hematology/Oncology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
| | - Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Michael Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Keith R. Loeb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 325 9th Avenue, Box 359791, Seattle, WA 98104, USA
| | - Patrick J. Cimino
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 325 9th Avenue, Box 359791, Seattle, WA 98104, USA
| | - Nikolas C. Holland
- Center for Neural Science, New York University, 4 Washington Place, #809, New York, NY 10003, USA
- Department of Psychiatry, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | | | - Hamid Bolouri
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA 98101, USA
| | - Damian A. Almiron Bonnin
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
| | | | - Tatsuya Ozawa
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Michael J. Wagner
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
- Division of Medical Oncology, University of Washington, 825 Eastlake Ave E., Seattle, WA 98109, USA
| | - Michael C. Haffner
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, 325 9th Avenue, Box 359791, Seattle, WA 98104, USA
| | - Junyue Cao
- Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA 98109, USA
- Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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18
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Szulzewsky F, Arora S, Arakaki AKS, Sievers P, Almiron Bonnin DA, Paddison PJ, Sahm F, Cimino PJ, Gujral TS, Holland EC. Both YAP1-MAML2 and constitutively active YAP1 drive the formation of tumors that resemble NF2 mutant meningiomas in mice. Genes Dev 2022; 36:gad.349876.122. [PMID: 36008139 PMCID: PMC9480855 DOI: 10.1101/gad.349876.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022]
Abstract
YAP1 is a transcriptional coactivator regulated by the Hippo signaling pathway, including NF2. Meningiomas are the most common primary brain tumors; a large percentage exhibit heterozygous loss of chromosome 22 (harboring the NF2 gene) and functional inactivation of the remaining NF2 copy, implicating oncogenic YAP activity in these tumors. Recently, fusions between YAP1 and MAML2 have been identified in a subset of pediatric NF2 wild-type meningiomas. Here, we show that human YAP1-MAML2-positive meningiomas resemble NF2 mutant meningiomas by global and YAP-related gene expression signatures. We then show that expression of YAP1-MAML2 in mice induces tumors that resemble human YAP1 fusion-positive and NF2 mutant meningiomas by gene expression. We demonstrate that YAP1-MAML2 primarily functions by exerting TEAD-dependent YAP activity that is resistant to Hippo signaling. Treatment with YAP-TEAD inhibitors is sufficient to inhibit the viability of YAP1-MAML2-driven mouse tumors ex vivo. Finally, we show that expression of constitutively active YAP1 (S127/397A-YAP1) is sufficient to induce similar tumors, suggesting that the YAP component of the gene fusion is the critical driver of these tumors. In summary, our results implicate YAP1-MAML2 as a causal oncogenic driver and highlight TEAD-dependent YAP activity as an oncogenic driver in YAP1-MAML2 fusion meningioma as well as NF2 mutant meningioma in general.
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Affiliation(s)
- Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Aleena K S Arakaki
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Philipp Sievers
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | | | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Felix Sahm
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
| | - Patrick J Cimino
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Taranjit S Gujral
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
- Seattle Translational Tumor Research Center, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
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19
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Chan M, Holland EC, Gujral TS. Olverembatinib inhibits SARS-CoV-2-Omicron variant-mediated cytokine release in human peripheral blood mononuclear cells. EMBO Mol Med 2022; 14:e15919. [PMID: 35579119 PMCID: PMC9174875 DOI: 10.15252/emmm.202215919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 01/13/2023] Open
Affiliation(s)
- Marina Chan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Taranjit S Gujral
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.,Department of Pharmacology, University of Washington, Seattle, WA, USA
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20
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Yang H, Yuan L, Ibaragi S, Li S, Shapiro R, Vanli N, Goncalves KA, Yu W, Kishikawa H, Jiang Y, Hu AJ, Jay D, Cochran B, Holland EC, Hu GF. Angiogenin and plexin-B2 axis promotes glioblastoma progression by enhancing invasion, vascular association, proliferation and survival. Br J Cancer 2022; 127:422-435. [PMID: 35418212 PMCID: PMC9345892 DOI: 10.1038/s41416-022-01814-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Angiogenin is a multifunctional secreted ribonuclease that is upregulated in human cancers and downregulated or mutationally inactivated in neurodegenerative diseases. A role for angiogenin in glioblastoma was inferred from the inverse correlation of angiogenin expression with patient survival but had not been experimentally investigated. METHODS Angiogenin knockout mice were generated and the effect of angiogenin deficiency on glioblastoma progression was examined. Angiogenin and plexin-B2 genes were knocked down in glioblastoma cells and the changes in cell proliferation, invasion and vascular association were examined. Monoclonal antibodies of angiogenin and small molecules were used to assess the therapeutic activity of the angiogenin-plexin-B2 pathway in both genetic and xenograft animal models. RESULTS Deletion of Ang1 gene prolonged survival of PDGF-induced glioblastoma in mice in the Ink4a/Arf-/-:Pten-/- background, accompanied by decreased invasion, vascular association and proliferation. Angiogenin upregulated MMP9 and CD24 leading to enhanced invasion and vascular association. Inhibition of angiogenin or plexin-B2, either by shRNA, monoclonal antibody or small molecule inhibitor, decreases sphere formation of patient-derived glioma stem cells, reduces glioblastoma proliferation and invasion and inhibits glioblastoma growth in both genetic and xenograft animal models. CONCLUSIONS Angiogenin and its receptor, plexin-B2, are a pair of novel regulators that mediate invasion, vascular association and proliferation of glioblastoma cells. Inhibitors of the angiogenin-plexin-B2 axis have therapeutic potential against glioblastoma.
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Affiliation(s)
- Hailing Yang
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Liang Yuan
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Soichiro Ibaragi
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Shuping Li
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Robert Shapiro
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Nil Vanli
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Biochemistry, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Kevin A Goncalves
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Wenhao Yu
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Hiroko Kishikawa
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Yuxiang Jiang
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA
| | - Alexander J Hu
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Daniel Jay
- Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.,Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Brent Cochran
- Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.,Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Guo-Fu Hu
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA. .,Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA. .,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA. .,Department of Pathology, Harvard Medical School, Boston, MA, USA. .,Program in Biochemistry, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.
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21
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Dai J, Cimino PJ, Gouin KH, Grzelak CA, Barrett A, Lim AR, Long A, Weaver S, Saldin LT, Uzamere A, Schulte V, Clegg N, Pisarsky L, Lyden D, Bissell MJ, Knott S, Welm AL, Bielas JH, Hansen KC, Winkler F, Holland EC, Ghajar CM. Astrocytic laminin-211 drives disseminated breast tumor cell dormancy in brain. Nat Cancer 2022; 3:25-42. [PMID: 35121993 PMCID: PMC9469899 DOI: 10.1038/s43018-021-00297-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/27/2021] [Indexed: 02/08/2023]
Abstract
Although dormancy is thought to play a key role in the metastasis of breast tumor cells to the brain, our knowledge of the molecular mechanisms regulating disseminated tumor cell (DTC) dormancy in this organ is limited. Here using serial intravital imaging of dormant and metastatic triple-negative breast cancer lines, we identify escape from the single-cell or micrometastatic state as the rate-limiting step towards brain metastasis. We show that every DTC occupies a vascular niche, with quiescent DTCs residing on astrocyte endfeet. At these sites, astrocyte-deposited laminin-211 drives DTC quiescence by inducing the dystroglycan receptor to associate with yes-associated protein, thereby sequestering it from the nucleus and preventing its prometastatic functions. These findings identify a brain-specific mechanism of DTC dormancy and highlight the need for a more thorough understanding of tumor dormancy to develop therapeutic approaches that prevent brain metastasis.
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Affiliation(s)
- Jinxiang Dai
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Patrick J. Cimino
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA (USA)
| | - Kenneth H. Gouin
- Department of Biomedical Sciences; Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA (USA)
| | - Candice A. Grzelak
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - Alexander Barrett
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO (USA)
| | - Andrea R. Lim
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA),Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA (USA)
| | - Annalyssa Long
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - Stephanie Weaver
- Experimental Histopathology Core, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - Lindsey T. Saldin
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA (USA)
| | - Aiyedun Uzamere
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - Vera Schulte
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - Nigel Clegg
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - Laura Pisarsky
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - David Lyden
- Children’s Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children’s Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, (USA)
| | - Mina J. Bissell
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA (USA)
| | - Simon Knott
- Department of Biomedical Sciences; Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA (USA)
| | - Alana L. Welm
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT (USA)
| | - Jason H. Bielas
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA),Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA (USA),Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO (USA)
| | - Frank Winkler
- Neurology Clinic and National Center for Tumour Diseases, University Hospital Heidelberg, DKTK & Clinical Cooperation Unit Neurooncology, German Cancer Research Center, Heidelberg (Germany)
| | - Eric C. Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA (USA)
| | - Cyrus M. Ghajar
- Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA (USA),Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA (USA),To whom correspondence should be addressed: Cyrus M. Ghajar, PhD, Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., M5-A864, Seattle, WA 98109 (USA), , P. 206.667.7080, F. 206.667.2537, Jinxiang Dai, PhD, Public Health Sciences Division/Translational Research Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., M5-A864, Seattle, WA 98109 (USA), , P. 206.667.7082, F. 206.667.2537
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22
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Marshall JL, Peshkin BN, Yoshino T, Vowinckel J, Danielsen HE, Melino G, Tsamardinos I, Haudenschild C, Kerr DJ, Sampaio C, Rha SY, FitzGerald KT, Holland EC, Gallagher D, Garcia-Foncillas J, Juhl H. OUP accepted manuscript. Oncologist 2022; 27:272-284. [PMID: 35380712 PMCID: PMC8982374 DOI: 10.1093/oncolo/oyab048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- John L Marshall
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
- Corresponding author: John L. Marshall, MD, The Ruesch Center for the Cure of Gastrointestinal Cancers, Frederick P. Smith Endowed Chair, Chief, Hematology and Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, 3800 Reservoir Road, Washington, DC 20007, USA. Tel: +1 202 444 2223;
| | - Beth N Peshkin
- Georgetown University, Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | | | | | - Håvard E Danielsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Radiumhospitalet, Montebello, Oslo, Norway
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Ioannis Tsamardinos
- JADBio Gnosis DA, N. Plastira 100, Science and Technology Park of Crete and Institute of Applied and Computational Mathematics, Foundation for Research and Technology Hellas, Heraklion, GR, Greece
| | | | - David J Kerr
- Nuffield Division of Clinical and Laboratory Sciences, Level 4, Academic Block, John Radcliffe Infirmary, Headington, Oxford, UK
| | | | - Sun Young Rha
- Yonsei Cancer Center, Yonsei University College of Medicine, Seodaemun-Ku, Seoul, Korea
| | - Kevin T FitzGerald
- Department of Medical Humanities in the School of Medicine, Creighton University, Omaha, NE, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David Gallagher
- St. James’s Hospital/Trinity College Dublin, St. Raphael’s House, Dublin, Ireland
| | - Jesus Garcia-Foncillas
- Cancer Institute, Fundacion Jimenez Diaz University Hospital, Autonomous University, Madrid, Spain
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23
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Nuechterlein N, Shapiro LG, Holland EC, Cimino PJ. Machine learning modeling of genome-wide copy number alteration signatures reliably predicts IDH mutational status in adult diffuse glioma. Acta Neuropathol Commun 2021; 9:191. [PMID: 34863298 PMCID: PMC8645099 DOI: 10.1186/s40478-021-01295-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
Knowledge of 1p/19q-codeletion and IDH1/2 mutational status is necessary to interpret any investigational study of diffuse gliomas in the modern era. While DNA sequencing is the gold standard for determining IDH mutational status, genome-wide methylation arrays and gene expression profiling have been used for surrogate mutational determination. Previous studies by our group suggest that 1p/19q-codeletion and IDH mutational status can be predicted by genome-wide somatic copy number alteration (SCNA) data alone, however a rigorous model to accomplish this task has yet to be established. In this study, we used SCNA data from 786 adult diffuse gliomas in The Cancer Genome Atlas (TCGA) to develop a two-stage classification system that identifies 1p/19q-codeleted oligodendrogliomas and predicts the IDH mutational status of astrocytic tumors using a machine-learning model. Cross-validated results on TCGA SCNA data showed near perfect classification results. Furthermore, our astrocytic IDH mutation model validated well on four additional datasets (AUC = 0.97, AUC = 0.99, AUC = 0.95, AUC = 0.96) as did our 1p/19q-codeleted oligodendroglioma screen on the two datasets that contained oligodendrogliomas (MCC = 0.97, MCC = 0.97). We then retrained our system using data from these validation sets and applied our system to a cohort of REMBRANDT study subjects for whom SCNA data, but not IDH mutational status, is available. Overall, using genome-wide SCNAs, we successfully developed a system to robustly predict 1p/19q-codeletion and IDH mutational status in diffuse gliomas. This system can assign molecular subtype labels to tumor samples of retrospective diffuse glioma cohorts that lack 1p/19q-codeletion and IDH mutational status, such as the REMBRANDT study, recasting these datasets as validation cohorts for diffuse glioma research.
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Affiliation(s)
- Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Linda G Shapiro
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Cimino
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, Division of Neuropathology, University of Washington, 325 9th Avenue, Box 359791, Seattle, WA, 98104, USA.
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24
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Arakaki AKS, Szulzewsky F, Gilbert MR, Gujral TS, Holland EC. Utilizing preclinical models to develop targeted therapies for rare central nervous system cancers. Neuro Oncol 2021; 23:S4-S15. [PMID: 34725698 PMCID: PMC8561121 DOI: 10.1093/neuonc/noab183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/21/2022] Open
Abstract
Patients with rare central nervous system (CNS) tumors typically have a poor prognosis and limited therapeutic options. Historically, these cancers have been difficult to study due to small number of patients. Recent technological advances have identified molecular drivers of some of these rare cancers which we can now use to generate representative preclinical models of these diseases. In this review, we outline the advantages and disadvantages of different models, emphasizing the utility of various in vitro and ex vivo models for target discovery and mechanistic inquiry and multiple in vivo models for therapeutic validation. We also highlight recent literature on preclinical model generation and screening approaches for ependymomas, histone mutated high-grade gliomas, and atypical teratoid rhabdoid tumors, all of which are rare CNS cancers that have recently established genetic or epigenetic drivers. These preclinical models are critical to advancing targeted therapeutics for these rare CNS cancers that currently rely on conventional treatments.
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Affiliation(s)
- Aleena K S Arakaki
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Taranjit S Gujral
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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25
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Chan M, Vijay S, McNevin J, McElrath MJ, Holland EC, Gujral TS. Machine learning identifies molecular regulators and therapeutics for targeting SARS-CoV2-induced cytokine release. Mol Syst Biol 2021; 17:e10426. [PMID: 34486798 PMCID: PMC8420181 DOI: 10.15252/msb.202110426] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 01/13/2023] Open
Abstract
Although 15-20% of COVID-19 patients experience hyper-inflammation induced by massive cytokine production, cellular triggers of this process and strategies to target them remain poorly understood. Here, we show that the N-terminal domain (NTD) of the SARS-CoV-2 spike protein substantially induces multiple inflammatory molecules in myeloid cells and human PBMCs. Using a combination of phenotypic screening with machine learning-based modeling, we identified and experimentally validated several protein kinases, including JAK1, EPHA7, IRAK1, MAPK12, and MAP3K8, as essential downstream mediators of NTD-induced cytokine production, implicating the role of multiple signaling pathways in cytokine release. Further, we found several FDA-approved drugs, including ponatinib, and cobimetinib as potent inhibitors of the NTD-mediated cytokine release. Treatment with ponatinib outperforms other drugs, including dexamethasone and baricitinib, inhibiting all cytokines in response to the NTD from SARS-CoV-2 and emerging variants. Finally, ponatinib treatment inhibits lipopolysaccharide-mediated cytokine release in myeloid cells in vitro and lung inflammation mouse model. Together, we propose that agents targeting multiple kinases required for SARS-CoV-2-mediated cytokine release, such as ponatinib, may represent an attractive therapeutic option for treating moderate to severe COVID-19.
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Affiliation(s)
- Marina Chan
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Siddharth Vijay
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - John McNevin
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - M Juliana McElrath
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Eric C Holland
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Taranjit S Gujral
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
- Department of PharmacologyUniversity of WashingtonSeattleWAUSA
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Ozawa T, Kaneko S, Szulzewsky F, Qiao Z, Takadera M, Narita Y, Kondo T, Holland EC, Hamamoto R, Ichimura K. Publisher Correction to: C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation. Acta Neuropathol Commun 2021; 9:100. [PMID: 34044883 PMCID: PMC8157639 DOI: 10.1186/s40478-021-01157-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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27
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Wagner MJ, Lyons YA, Siedel JH, Dood R, Nagaraja AS, Haemmerle M, Mangala LS, Chanana P, Lazar AJ, Wang WL, Ravi V, Holland EC, Sood AK. Combined VEGFR and MAPK pathway inhibition in angiosarcoma. Sci Rep 2021; 11:9362. [PMID: 33931674 PMCID: PMC8087824 DOI: 10.1038/s41598-021-88703-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
Angiosarcoma is an aggressive malignancy of endothelial cells that carries a high mortality rate. Cytotoxic chemotherapy can elicit clinical responses, but the duration of response is limited. Sequencing reveals multiple mutations in angiogenesis pathways in angiosarcomas, particularly in vascular endothelial growth factor (VEGFR) and mitogen-activated protein kinase (MAPK) signaling. We aimed to determine the biological relevance of these pathways in angiosarcoma. Tissue microarray consisting of clinical formalin-fixed paraffin embedded tissue archival samples were stained for phospho- extracellular signal-regulated kinase (p-ERK) with immunohistochemistry. Angiosarcoma cell lines were treated with the mitogen-activated protein kinase kinase (MEK) inhibitor trametinib, pan-VEGFR inhibitor cediranib, or combined trametinib and cediranib and viability was assessed. Reverse phase protein array (RPPA) was performed to assess multiple oncogenic protein pathways. SVR angiosarcoma cells were grown in vivo and gene expression effects of treatment were assessed with whole exome RNA sequencing. MAPK signaling was found active in over half of clinical angiosarcoma samples. Inhibition of MAPK signaling with the MEK inhibitor trametinib decreased the viability of angiosarcoma cells. Combined inhibition of the VEGF and MAPK pathways with cediranib and trametinib had an additive effect in in vitro models, and a combinatorial effect in an in vivo model. Combined treatment led to smaller tumors than treatment with either agent alone. RNA-seq demonstrated distinct expression signatures between the trametinib treated tumors and those treated with both trametinib and cediranib. These results indicate a clinical study of combined VEGFR and MEK inhibition in angiosarcoma is warranted.
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Affiliation(s)
- Michael J Wagner
- Division of Medical Oncology, University of Washington, 825 Eastlake Ave E, Seattle, WA, 98109, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
| | - Yasmin A Lyons
- Department of Gynecologic Oncology and Reproductive Medicine and Center for RNA Interference and Non-Coding RNA, UT MD Anderson Cancer Center, Houston, USA
| | - Jean H Siedel
- Department of Gynecologic Oncology and Reproductive Medicine and Center for RNA Interference and Non-Coding RNA, UT MD Anderson Cancer Center, Houston, USA
| | - Robert Dood
- Department of Gynecologic Oncology and Reproductive Medicine and Center for RNA Interference and Non-Coding RNA, UT MD Anderson Cancer Center, Houston, USA
| | - Archana S Nagaraja
- Department of Gynecologic Oncology and Reproductive Medicine and Center for RNA Interference and Non-Coding RNA, UT MD Anderson Cancer Center, Houston, USA
| | - Monika Haemmerle
- Department of Gynecologic Oncology and Reproductive Medicine and Center for RNA Interference and Non-Coding RNA, UT MD Anderson Cancer Center, Houston, USA
- Section for Experimental Pathology, Medical Faculty, Institute of Pathology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Lingegowda S Mangala
- Department of Gynecologic Oncology and Reproductive Medicine and Center for RNA Interference and Non-Coding RNA, UT MD Anderson Cancer Center, Houston, USA
| | - Pritha Chanana
- Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Alexander J Lazar
- Department of Pathology, UT MD Anderson Cancer Center, Houston, USA
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, USA
| | - Wei-Lien Wang
- Department of Pathology, UT MD Anderson Cancer Center, Houston, USA
| | - Vinod Ravi
- Sarcoma Medical Oncology, UT MD Anderson Cancer Center, Houston, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine and Center for RNA Interference and Non-Coding RNA, UT MD Anderson Cancer Center, Houston, USA
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28
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Ene CI, Kreuser SA, Jung M, Zhang H, Arora S, White Moyes K, Szulzewsky F, Barber J, Cimino PJ, Wirsching HG, Patel A, Kong P, Woodiwiss TR, Durfy SJ, Houghton AM, Pierce RH, Parney IF, Crane CA, Holland EC. Anti-PD-L1 antibody direct activation of macrophages contributes to a radiation-induced abscopal response in glioblastoma. Neuro Oncol 2021; 22:639-651. [PMID: 31793634 DOI: 10.1093/neuonc/noz226] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 12/24/2022] Open
Abstract
BACKGROUND Most glioblastomas recur near prior radiation treatment sites. Future clinical success will require achieving and optimizing an "abscopal effect," whereby unirradiated neoplastic cells outside treatment sites are recognized and attacked by the immune system. Radiation combined with anti-programmed cell death ligand 1 (PD-L1) demonstrated modest efficacy in phase II human glioblastoma clinical trials, but the mechanism and relevance of the abscopal effect during this response remain unknown. METHODS We modified an immune-competent, genetically driven mouse glioma model (forced platelet derived growth factor [PDGF] expression + phosphatase and tensin homolog loss) where a portion of the tumor burden is irradiated (PDGF) and another unirradiated luciferase-expressing tumor (PDGF + luciferase) is used as a readout of the abscopal effect following systemic anti-PD-L1 immunotherapy. We assessed relevance of tumor neoepitope during the abscopal response by inducing expression of epidermal growth factor receptor variant III (EGFRvIII) (PDGF + EGFRvIII). Statistical tests were two-sided. RESULTS Following radiation of one lesion, anti-PD-L1 immunotherapy enhanced the abscopal response to the unirradiated lesion. In PDGF-driven gliomas without tumor neoepitope (PDGF + luciferase, n = 8), the abscopal response occurred via anti-PD-L1 driven, extracellular signal-regulated kinase-mediated, bone marrow-derived macrophage phagocytosis of adjacent unirradiated tumor cells, with modest survival implications (median survival 41 days vs radiation alone 37.5 days, P = 0.03). In PDGF-driven gliomas with tumor neoepitope (PDGF + EGFRvIII, n = 8), anti-PD-L1 enhanced abscopal response was associated with macrophage and T-cell infiltration and increased survival benefit (median survival 36 days vs radiation alone 28 days, P = 0.001). CONCLUSION Our results indicate that anti-PD-L1 immunotherapy enhances a radiation- induced abscopal response via canonical T-cell activation and direct macrophage activation in glioblastoma.
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Affiliation(s)
- Chibawanye I Ene
- Department of Neurological Surgery, University of Washington, Seattle, Washington.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Shannon A Kreuser
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Miyeon Jung
- Department of Neurological Surgery, University of Washington, Seattle, Washington.,Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota
| | - Huajia Zhang
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kara White Moyes
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jason Barber
- Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Patrick J Cimino
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, Washington
| | - Hans-Georg Wirsching
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Anoop Patel
- Department of Neurological Surgery, University of Washington, Seattle, Washington.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Paul Kong
- Experimental Histopathology, Fred Hutchinson Cancer Research Center, Seattle Washington
| | - Timothy R Woodiwiss
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sharon J Durfy
- Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - A McGarry Houghton
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Robert H Pierce
- Experimental Histopathology, Fred Hutchinson Cancer Research Center, Seattle Washington
| | - Ian F Parney
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota
| | - Courtney A Crane
- Department of Neurological Surgery, University of Washington, Seattle, Washington.,Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington.,Alvord Brain Tumor Center, University of Washington, Seattle, Washington
| | - Eric C Holland
- Department of Neurological Surgery, University of Washington, Seattle, Washington.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Alvord Brain Tumor Center, University of Washington, Seattle, Washington
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29
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Randles A, Wirsching HG, Dean JA, Cheng YK, Emerson S, Pattwell SS, Holland EC, Michor F. Computational modelling of perivascular-niche dynamics for the optimization of treatment schedules for glioblastoma. Nat Biomed Eng 2021; 5:346-359. [PMID: 33864039 PMCID: PMC8054983 DOI: 10.1038/s41551-021-00710-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 03/04/2021] [Indexed: 01/05/2023]
Abstract
Glioblastoma stem-like cells dynamically transition between a chemoradiation-resistant state and a chemoradiation-sensitive state. However, physical barriers in the tumour microenvironment restrict the delivery of chemotherapy to tumour compartments that are distant from blood vessels. Here, we show that a massively parallel computational model of the spatiotemporal dynamics of the perivascular niche that incorporates glioblastoma stem-like cells and differentiated tumour cells as well as relevant tissue-level phenomena can be used to optimize the administration schedules of concurrent radiation and temozolomide-the standard-of-care treatment for glioblastoma. In mice with platelet-derived growth factor (PDGF)-driven glioblastoma, the model-optimized treatment schedule increased the survival of the animals. For standard radiation fractionation in patients, the model predicts that chemotherapy may be optimally administered about one hour before radiation treatment. Computational models of the spatiotemporal dynamics of the tumour microenvironment could be used to predict tumour responses to a broader range of treatments and to optimize treatment regimens.
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Affiliation(s)
- Amanda Randles
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Hans-Georg Wirsching
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Jamie A Dean
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Yu-Kang Cheng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Samuel Emerson
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Siobhan S Pattwell
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- The Ludwig Center, Harvard University, Boston, MA, USA.
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30
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Ozawa T, Kaneko S, Szulzewsky F, Qiao Z, Takadera M, Narita Y, Kondo T, Holland EC, Hamamoto R, Ichimura K. C11orf95-RELA fusion drives aberrant gene expression through the unique epigenetic regulation for ependymoma formation. Acta Neuropathol Commun 2021; 9:36. [PMID: 33685520 PMCID: PMC7941712 DOI: 10.1186/s40478-021-01135-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 12/13/2022] Open
Abstract
Recurrent C11orf95-RELA fusions (RELAFUS) are the hallmark of supratentorial ependymomas. The presence of RELA as the fusion partner indicates a close association of aberrant NF-κB activity with tumorigenesis. However, the oncogenic role of the C11orf95 has not been determined. Here, we performed ChIP-seq analyses to explore genomic regions bound by RELAFUS and H3K27ac proteins in human 293T and mouse ependymoma cells. We then utilized published RNA-Seq data from human and mouse RELAFUS tumors and identified target genes that were directly regulated by RELAFUS in these tumors. Subsequent transcription factor motif analyses of RELAFUS target genes detected a unique GC-rich motif recognized by the C11orf95 moiety, that is present in approximately half of RELAFUS target genes. Luciferase assays confirmed that a promoter carrying this motif is sufficient to drive RELAFUS-dependent gene expression. Further, the RELAFUS target genes were found to be overlapped with Rela target genes primarily via non-canonical NF-κB binding sites. Using a series of truncation and substitution mutants of RELAFUS, we also show that the activation domain in the RELAFUS moiety is necessary for the regulation of gene expression of these RELAFUS target genes. Lastly, we performed an anti-cancer drug screening with mouse ependymoma cells and identified potential anti-ependymoma drugs that are related to the oncogenic mechanism of RELAFUS. These findings suggested that RELAFUS might induce ependymoma formation through oncogenic pathways orchestrated by both C11orf95 and RELA target genes. Thus, our study unveils a complex gene function of RELAFUS as an oncogenic transcription factor in RELAFUS positive ependymomas.
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31
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Kanvinde PP, Malla AP, Connolly NP, Szulzewsky F, Anastasiadis P, Ames HM, Kim AJ, Winkles JA, Holland EC, Woodworth GF. Leveraging the replication-competent avian-like sarcoma virus/tumor virus receptor-A system for modeling human gliomas. Glia 2021; 69:2059-2076. [PMID: 33638562 PMCID: PMC8591561 DOI: 10.1002/glia.23984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 01/07/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022]
Abstract
Gliomas are the most common primary intrinsic brain tumors occurring in adults. Of all malignant gliomas, glioblastoma (GBM) is considered the deadliest tumor type due to diffuse brain invasion, immune evasion, cellular, and molecular heterogeneity, and resistance to treatments resulting in high rates of recurrence. An extensive understanding of the genomic and microenvironmental landscape of gliomas gathered over the past decade has renewed interest in pursuing novel therapeutics, including immune checkpoint inhibitors, glioma-associated macrophage/microglia (GAMs) modulators, and others. In light of this, predictive animal models that closely recreate the conditions and findings found in human gliomas will serve an increasingly important role in identifying new, effective therapeutic strategies. Although numerous syngeneic, xenograft, and transgenic rodent models have been developed, few include the full complement of pathobiological features found in human tumors, and therefore few accurately predict bench-to-bedside success. This review provides an update on how genetically engineered rodent models based on the replication-competent avian-like sarcoma (RCAS) virus/tumor virus receptor-A (tv-a) system have been used to recapitulate key elements of human gliomas in an immunologically intact host microenvironment and highlights new approaches using this model system as a predictive tool for advancing translational glioma research.
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Affiliation(s)
- Pranjali P Kanvinde
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Adarsha P Malla
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Nina P Connolly
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Pavlos Anastasiadis
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Heather M Ames
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anthony J Kim
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jeffrey A Winkles
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Center for Vascular and Inflammatory Diseases, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Graeme F Woodworth
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Nuechterlein N, Li B, Feroze A, Holland EC, Shapiro L, Haynor D, Fink J, Cimino PJ. Radiogenomic modeling predicts survival-associated prognostic groups in glioblastoma. Neurooncol Adv 2021; 3:vdab004. [PMID: 33615222 PMCID: PMC7883769 DOI: 10.1093/noajnl/vdab004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Combined whole-exome sequencing (WES) and somatic copy number alteration (SCNA) information can separate isocitrate dehydrogenase (IDH)1/2-wildtype glioblastoma into two prognostic molecular subtypes, which cannot be distinguished by epigenetic or clinical features. The potential for radiographic features to discriminate between these molecular subtypes has yet to be established. Methods Radiologic features (n = 35 340) were extracted from 46 multisequence, pre-operative magnetic resonance imaging (MRI) scans of IDH1/2-wildtype glioblastoma patients from The Cancer Imaging Archive (TCIA), all of whom have corresponding WES/SCNA data. We developed a novel feature selection method that leverages the structure of extracted MRI features to mitigate the dimensionality challenge posed by the disparity between a large number of features and the limited patients in our cohort. Six traditional machine learning classifiers were trained to distinguish molecular subtypes using our feature selection method, which was compared to least absolute shrinkage and selection operator (LASSO) feature selection, recursive feature elimination, and variance thresholding. Results We were able to classify glioblastomas into two prognostic subgroups with a cross-validated area under the curve score of 0.80 (±0.03) using ridge logistic regression on the 15-dimensional principle component analysis (PCA) embedding of the features selected by our novel feature selection method. An interrogation of the selected features suggested that features describing contours in the T2 signal abnormality region on the T2-weighted fluid-attenuated inversion recovery (FLAIR) MRI sequence may best distinguish these two groups from one another. Conclusions We successfully trained a machine learning model that allows for relevant targeted feature extraction from standard MRI to accurately predict molecularly-defined risk-stratifying IDH1/2-wildtype glioblastoma patient groups.
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Affiliation(s)
- Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Beibin Li
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Abdullah Feroze
- Department of Neurological Surgery, University of Washington, Seattle, Washington, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Linda Shapiro
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - David Haynor
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - James Fink
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - Patrick J Cimino
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Pathology, Division of Neuropathology, University of Washington, Seattle, Washington, USA
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Szulzewsky F, Holland EC, Vasioukhin V. YAP1 and its fusion proteins in cancer initiation, progression and therapeutic resistance. Dev Biol 2021; 475:205-221. [PMID: 33428889 DOI: 10.1016/j.ydbio.2020.12.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/14/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023]
Abstract
YAP1 is a transcriptional co-activator whose activity is controlled by the Hippo signaling pathway. In addition to important functions in normal tissue homeostasis and regeneration, YAP1 has also prominent functions in cancer initiation, aggressiveness, metastasis, and therapy resistance. In this review we are discussing the molecular functions of YAP1 and its roles in cancer, with a focus on the different mechanisms of de-regulation of YAP1 activity in human cancers, including inactivation of upstream Hippo pathway tumor suppressors, regulation by intersecting pathways, miRNAs, and viral oncogenes. We are also discussing new findings on the function and biology of the recently identified family of YAP1 gene fusions, that constitute a new type of activating mutation of YAP1 and that are the likely oncogenic drivers in several subtypes of human cancers. Lastly, we also discuss different strategies of therapeutic inhibition of YAP1 functions.
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Affiliation(s)
- Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA; Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Valeri Vasioukhin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
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Horne EA, Diaz P, Cimino PJ, Jung E, Xu C, Hamel E, Wagenbach M, Kumasaka D, Wageling NB, Azorín DD, Winkler F, Wordeman LG, Holland EC, Stella N. A brain-penetrant microtubule-targeting agent that disrupts hallmarks of glioma tumorigenesis. Neurooncol Adv 2020; 3:vdaa165. [PMID: 33506204 PMCID: PMC7813200 DOI: 10.1093/noajnl/vdaa165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Glioma is sensitive to microtubule-targeting agents (MTAs), but most MTAs do not cross the blood brain barrier (BBB). To address this limitation, we developed the new chemical entity, ST-401, a brain-penetrant MTA. METHODS Synthesis of ST-401. Measures of MT assembly and dynamics. Cell proliferation and viability of patient-derived (PD) glioma in culture. Measure of tumor microtube (TM) parameters using immunofluorescence analysis and machine learning-based workflow. Pharmacokinetics (PK) and experimental toxicity in mice. In vivo antitumor activity in the RCAS/tv-a PDGFB-driven glioma (PDGFB-glioma) mouse model. RESULTS We discovered that ST-401 disrupts microtubule (MT) function through gentle and reverisible reduction in MT assembly that triggers mitotic delay and cell death in interphase. ST-401 inhibits the formation of TMs, MT-rich structures that connect glioma to a network that promotes resistance to DNA damage. PK analysis of ST-401 in mice shows brain penetration reaching antitumor concentrations, and in vivo testing of ST-401 in a xenograft flank tumor mouse model demonstrates significant antitumor activity and no over toxicity in mice. In the PDGFB-glioma mouse model, ST-401 enhances the therapeutic efficacies of temozolomide (TMZ) and radiation therapy (RT). CONCLUSION Our study identifies hallmarks of glioma tumorigenesis that are sensitive to MTAs and reports ST-401 as a promising chemical scaffold to develop brain-penetrant MTAs.
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Affiliation(s)
- Eric A Horne
- Department of Pharmacology, University of Washington, Seattle, Washington, USA,Stella Therapeutics, Inc., Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Philippe Diaz
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA,DermaXon LLC, Missoula, Montana, USA
| | - Patrick J Cimino
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Erik Jung
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Cong Xu
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
| | - Ernest Hamel
- Developmental Therapeutics Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Michael Wagenbach
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
| | - Debra Kumasaka
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Daniel D Azorín
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Linda G Wordeman
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, Washington, USA,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA,Corresponding Author: Nephi Stella, PhD, Department of Psychiatry and Behavioral Sciences, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-5280, USA ()
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Peeters S, Owens G, Sun MZ, Lee A, Kienzler JC, Orpilla J, Contreras E, Treger J, Odesa S, Everson RG, Becher O, Holland EC, Nathanson D, Xing Y, Liau LM, Prins RM, Wang AC. Dendritic Cell Vaccination is Effective Against H3.3G34R Mutant Glioblastoma in a Novel Syngeneic Genetically Engineered Mouse Model. Neurosurgery 2020. [DOI: 10.1093/neuros/nyaa447_795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Wang AC, Owens G, Lee A, Sun MZ, Peeters S, Kienzler JC, Orpilla J, Contreras E, Treger J, Odesa SK, Everson RG, Holland EC, Becher O, Nathanson D, Xing Y, Liau LM, Prins RM. Engineering T Cell Receptors to Target H3.3G34 Mutant Glioblastoma. Neurosurgery 2020. [DOI: 10.1093/neuros/nyaa447_794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Alexander J, LaPlant QC, Pattwell SS, Szulzewsky F, Cimino PJ, Caruso FP, Pugliese P, Chen Z, Chardon F, Hill AJ, Spurrell C, Ahrendsen D, Pietras A, Starita LM, Hambardzumyan D, Iavarone A, Shendure J, Holland EC. Multimodal single-cell analysis reveals distinct radioresistant stem-like and progenitor cell populations in murine glioma. Glia 2020; 68:2486-2502. [PMID: 32621641 PMCID: PMC7586969 DOI: 10.1002/glia.23866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/30/2020] [Accepted: 05/17/2020] [Indexed: 11/22/2022]
Abstract
Radiation therapy is part of the standard of care for gliomas and kills a subset of tumor cells, while also altering the tumor microenvironment. Tumor cells with stem-like properties preferentially survive radiation and give rise to glioma recurrence. Various techniques for enriching and quantifying cells with stem-like properties have been used, including the fluorescence activated cell sorting (FACS)-based side population (SP) assay, which is a functional assay that enriches for stem-like tumor cells. In these analyses, mouse models of glioma have been used to understand the biology of this disease and therapeutic responses, including the radiation response. We present combined SP analysis and single-cell RNA sequencing of genetically-engineered mouse models of glioma to show a time course of cellular response to radiation. We identify and characterize two distinct tumor cell populations that are inherently radioresistant and also distinct effects of radiation on immune cell populations within the tumor microenvironment.
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Affiliation(s)
- Jes Alexander
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
- Department of Radiation OncologyUniversity of Washington School of MedicineSeattleWashingtonUSA
| | - Quincey C. LaPlant
- Department of Radiation OncologyMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Siobhan S. Pattwell
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Frank Szulzewsky
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Patrick J. Cimino
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleWashingtonUSA
| | - Francesca P. Caruso
- Dipartimento di Scienze e TecnologieUniversità degli Studi del SannioBeneventoItaly
- Bioinformatics Lab, BIOGEMAriano IrpinoItaly
| | - Pietro Pugliese
- Dipartimento di Scienze e TecnologieUniversità degli Studi del SannioBeneventoItaly
- Bioinformatics Lab, BIOGEMAriano IrpinoItaly
| | - Zhihong Chen
- Department of Oncological SciencesTisch Cancer Institute, and Department of Neurosurgery, Mount Sinai Icahn School of MedicineNew YorkNew YorkUSA
| | - Florence Chardon
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Andrew J. Hill
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Cailyn Spurrell
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Dakota Ahrendsen
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | | | - Lea M. Starita
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Dolores Hambardzumyan
- Department of Oncological SciencesTisch Cancer Institute, and Department of Neurosurgery, Mount Sinai Icahn School of MedicineNew YorkNew YorkUSA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology, Department of Pathology and Cell BiologyColumbia University Medical CenterNew YorkNew YorkUSA
| | - Jay Shendure
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
- Allen Discovery Center for Cell LineageSeattleWashingtonUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleWashingtonUSA
| | - Eric C. Holland
- Human Biology DivisionFred Hutchinson Cancer Research CenterSeattleWashingtonUSA
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Ene CI, Brempelis K, Cowan C, Kreuser S, Chinn H, Holland EC, Crane C. Macrophages Programmed to Secrete Interleukin-12 Induce an Anti-Tumor Immune Response Within Glioblastoma. Neurosurgery 2020. [DOI: 10.1093/neuros/nyaa447_832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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39
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Takadera M, Satomi K, Szulzewsky F, Cimino PJ, Holland EC, Yamamoto T, Ichimura K, Ozawa T. Phenotypic characterization with somatic genome editing and gene transfer reveals the diverse oncogenicity of ependymoma fusion genes. Acta Neuropathol Commun 2020; 8:203. [PMID: 33228790 PMCID: PMC7684901 DOI: 10.1186/s40478-020-01080-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/11/2020] [Indexed: 11/10/2022] Open
Abstract
Recurrent RELA and YAP1 fusions are intimately associated with tumorigenesis in supratentorial ependymomas. Chromothripsis and focal copy number alterations involving 11q are hallmarks of these tumors. However, it is unknown whether the chromosomal alterations are a direct causal event resulting in fusion transcripts. In addition, the biological significance of the RELA fusion variants and YAP1 fusions is not yet fully characterized. In this study, we generated gene rearrangements on 11q with the CRISPR/Cas9 system and investigated the formation of oncogenic ependymoma fusion genes. Further, we examined the oncogenic potential of RELA fusion variants and YAP1 fusions in a lentiviral gene transfer model. We observed that endogenous RELA fusion events were successfully induced by CRISPR/Cas9-mediated genome rearrangement in cultured cells. In vivo genome editing in mouse brain resulted in the development of ependymoma-like brain tumors that harbored the Rela fusion gene. All RELA fusion variants tested, except a variant lacking the Rel homology domain, were able to induce tumor formation, albeit with different efficacy. Furthermore, expression of YAP1-FAM118B and YAP1-MAMLD1 fusions induced the formation of spindle-cell-like tumors at varying efficacy. Our results indicate that chromosomal rearrangements involving the Rela locus are the causal event for the formation of Rela fusion-driven ependymomas in mice. Furthermore, the type of RELA. fusion might affect the aggressiveness of tumors and that the Rel homology domain is essential for the oncogenic functions of RELA. fusions. The YAP1 fusion genes are also oncogenic when expressed in mice.
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40
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Brempelis KJ, Cowan CM, Kreuser SA, Labadie KP, Prieskorn BM, Lieberman NAP, Ene CI, Moyes KW, Chinn H, DeGolier KR, Matsumoto LR, Daniel SK, Yokoyama JK, Davis AD, Hoglund VJ, Smythe KS, Balcaitis SD, Jensen MC, Ellenbogen RG, Campbell JS, Pierce RH, Holland EC, Pillarisetty VG, Crane CA. Genetically engineered macrophages persist in solid tumors and locally deliver therapeutic proteins to activate immune responses. J Immunother Cancer 2020; 8:jitc-2020-001356. [PMID: 33115946 PMCID: PMC7594542 DOI: 10.1136/jitc-2020-001356] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background Though currently approved immunotherapies, including chimeric antigen receptor T cells and checkpoint blockade antibodies, have been successfully used to treat hematological and some solid tumor cancers, many solid tumors remain resistant to these modes of treatment. In solid tumors, the development of effective antitumor immune responses is hampered by restricted immune cell infiltration and an immunosuppressive tumor microenvironment (TME). An immunotherapy that infiltrates and persists in the solid TME, while providing local, stable levels of therapeutic to activate or reinvigorate antitumor immunity could overcome these challenges faced by current immunotherapies. Methods Using lentivirus-driven engineering, we programmed human and murine macrophages to express therapeutic payloads, including Interleukin (IL)-12. In vitro coculture studies were used to evaluate the effect of genetically engineered macrophages (GEMs) secreting IL-12 on T cells and on the GEMs themselves. The effects of IL-12 GEMs on gene expression profiles within the TME and tumor burden were evaluated in syngeneic mouse models of glioblastoma and melanoma and in human tumor slices isolated from patients with advanced gastrointestinal malignancies. Results Here, we present a cellular immunotherapy platform using lentivirus-driven genetic engineering of human and mouse macrophages to constitutively express proteins, including secreted cytokines and full-length checkpoint antibodies, as well as cytoplasmic and surface proteins that overcomes these barriers. GEMs traffic to, persist in, and express lentiviral payloads in xenograft mouse models of glioblastoma, and express a non-signaling truncated CD19 surface protein for elimination. IL-12-secreting GEMs activated T cells and induced interferon-gamma (IFNγ) in vitro and slowed tumor growth resulting in extended survival in vivo. In a syngeneic glioblastoma model, IFNγ signaling cascades were also observed in mice treated with mouse bone-marrow-derived GEMs secreting murine IL-12. These findings were reproduced in ex vivo tumor slices comprised of intact MEs. In this setting, IL-12 GEMs induced tumor cell death, chemokines and IFNγ-stimulated genes and proteins. Conclusions Our data demonstrate that GEMs can precisely deliver titratable doses of therapeutic proteins to the TME to improve safety, tissue penetrance, targeted delivery and pharmacokinetics.
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Affiliation(s)
- Katherine J Brempelis
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Courtney M Cowan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Shannon A Kreuser
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Kevin P Labadie
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Brooke M Prieskorn
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nicole A P Lieberman
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Chibawanye I Ene
- Department of Neurological Surgery, University of Washington, Seattle, Washington, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kara W Moyes
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Harrison Chinn
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Kole R DeGolier
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Lisa R Matsumoto
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sara K Daniel
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Jason K Yokoyama
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Immunotherapy Integration Hub, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Amira D Davis
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Virginia J Hoglund
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Kimberly S Smythe
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Stephanie D Balcaitis
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Michael C Jensen
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Immunotherapy Integration Hub, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, Washington, USA
| | - Jean S Campbell
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Robert H Pierce
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eric C Holland
- Department of Neurological Surgery, University of Washington, Seattle, Washington, USA.,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Courtney A Crane
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington, USA .,Discovery and Translational Sciences, Mozart Therapeutics, Seattle, WA, 98119
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41
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De Boeck A, Ahn BY, D'Mello C, Lun X, Menon SV, Alshehri MM, Szulzewsky F, Shen Y, Khan L, Dang NH, Reichardt E, Goring KA, King J, Grisdale CJ, Grinshtein N, Hambardzumyan D, Reilly KM, Blough MD, Cairncross JG, Yong VW, Marra MA, Jones SJM, Kaplan DR, McCoy KD, Holland EC, Bose P, Chan JA, Robbins SM, Senger DL. Glioma-derived IL-33 orchestrates an inflammatory brain tumor microenvironment that accelerates glioma progression. Nat Commun 2020; 11:4997. [PMID: 33020472 PMCID: PMC7536425 DOI: 10.1038/s41467-020-18569-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [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: 10/25/2018] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Despite a deeper molecular understanding, human glioblastoma remains one of the most treatment refractory and fatal cancers. It is known that the presence of macrophages and microglia impact glioblastoma tumorigenesis and prevent durable response. Herein we identify the dual function cytokine IL-33 as an orchestrator of the glioblastoma microenvironment that contributes to tumorigenesis. We find that IL-33 expression in a large subset of human glioma specimens and murine models correlates with increased tumor-associated macrophages/monocytes/microglia. In addition, nuclear and secreted functions of IL-33 regulate chemokines that collectively recruit and activate circulating and resident innate immune cells creating a pro-tumorigenic environment. Conversely, loss of nuclear IL-33 cripples recruitment, dramatically suppresses glioma growth, and increases survival. Our data supports the paradigm that recruitment and activation of immune cells, when instructed appropriately, offer a therapeutic strategy that switches the focus from the cancer cell alone to one that includes the normal host environment.
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Affiliation(s)
- Astrid De Boeck
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bo Young Ahn
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Charlotte D'Mello
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Xueqing Lun
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Shyam V Menon
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mana M Alshehri
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Frank Szulzewsky
- Divison of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Lubaba Khan
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ngoc Ha Dang
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Elliott Reichardt
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kimberly-Ann Goring
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer King
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Natalie Grinshtein
- Department of Molecular Genetics, University of Toronto and Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute and the Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Karlyne M Reilly
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Michael D Blough
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - J Gregory Cairncross
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - V Wee Yong
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - David R Kaplan
- Department of Molecular Genetics, University of Toronto and Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto, ON, Canada
| | - Kathy D McCoy
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Eric C Holland
- Divison of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Pinaki Bose
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer A Chan
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pathology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Stephen M Robbins
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Donna L Senger
- Clark Smith Brain Tumour Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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Ene CI, Cimino PJ, Fine HA, Holland EC. Incorporating genomic signatures into surgical and medical decision-making for elderly glioblastoma patients. Neurosurg Focus 2020; 49:E11. [PMID: 33002863 DOI: 10.3171/2020.7.focus20418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/17/2020] [Indexed: 11/06/2022]
Abstract
Glioblastoma (GBM) is the most common type of malignant primary brain tumor in adults. It is a uniformly fatal disease (median overall survival 16 months) even with aggressive resection and an adjuvant temozolomide-based chemoradiation regimen. Age remains an independent risk factor for a poor prognosis. Several factors contribute to the dismal outcomes in the elderly population with GBM, including poor baseline health status, differences in underlying genomic alterations, and variability in the surgical and medical management of this subpopulation. The latter arises from a lack of adequate representation of elderly patients in clinical trials, resulting in limited data on the response of this subpopulation to standard treatment. Results from retrospective and some prospective studies have indicated that resection of only contrast-enhancing lesions and administration of hypofractionated radiotherapy in combination with temozolomide are effective strategies for optimizing survival while maintaining baseline quality of life in elderly GBM patients; however, survival remains dismal relative to that in a younger cohort. Here, the authors present historical context for the current strategies used for the multimodal management (surgical and medical) of elderly patients with GBM. Furthermore, they provide insights into elderly GBM patient-specific genomic signatures such as isocitrate dehydrogenase 1/2 (IDH1/2) wildtype status, telomerase reverse transcriptase promoter (TERTp) mutations, and somatic copy number alterations including CDK4/MDM2 coamplification, which are becoming better understood and could be utilized in a clinical trial design and patient stratification to guide the development of more effective adjuvant therapies specifically for elderly GBM patients.
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Affiliation(s)
- Chibawanye I Ene
- 1Department of Neurological Surgery, University of Washington School of Medicine
| | - Patrick J Cimino
- 2Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, Washington
| | - Howard A Fine
- 3Meyer Cancer Center, Division of Neuro-Oncology, Department of Neurology, NewYork-Presbyterian Hospital/Weill Cornell Medicine, New York, New York; and
| | - Eric C Holland
- 4Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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43
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Glorioso JC, Cohen JB, Goins WF, Hall B, Jackson JW, Kohanbash G, Amankulor N, Kaur B, Caligiuri MA, Chiocca EA, Holland EC, Quéva C. Oncolytic HSV Vectors and Anti-Tumor Immunity. Curr Issues Mol Biol 2020; 41:381-468. [PMID: 32938804 DOI: 10.21775/cimb.041.381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The therapeutic promise of oncolytic viruses (OVs) rests on their ability to both selectively kill tumor cells and induce anti-tumor immunity. The potential of tumors to be recognized and eliminated by an effective anti-tumor immune response has been spurred on by the discovery that immune checkpoint inhibition can overcome tumor-specific cytotoxic T cell (CTL) exhaustion and provide durable responses in multiple tumor indications. OV-mediated tumor destruction is now recognized as a powerful means to assist in the development of anti-tumor immunity for two important reasons: (i) OVs, through the elicitation of an anti-viral response and the production of type I interferon, are potent stimulators of inflammation and can be armed with transgenes to further enhance anti-tumor immune responses; and (ii) lytic activity can promote the release of tumor-associated antigens (TAAs) and tumor neoantigens that function as in situ tumor-specific vaccines to elicit adaptive immunity. Oncolytic herpes simplex viruses (oHSVs) are among the most widely studied OVs for the treatment of solid malignancies, and Amgen's oHSV Imlygic® for the treatment of melanoma is the only OV approved in major markets. Here we describe important biological features of HSV that make it an attractive OV, clinical experience with HSV-based vectors, and strategies to increase applicability to cancer treatment.
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Affiliation(s)
- Joseph C Glorioso
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA , USA
| | - Justus B Cohen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA , USA
| | - William F Goins
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA , USA
| | - Bonnie Hall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA , USA
| | - Joseph W Jackson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA , USA
| | - Gary Kohanbash
- Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Nduka Amankulor
- Department of Neurological Surgery, Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Balveen Kaur
- Department of Neurosurgery, McGovern Medical School at UTHealth, Houston, TX, USA
| | | | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric C Holland
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA, USA
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44
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Wirsching HG, Arora S, Zhang H, Szulzewsky F, Cimino PJ, Quéva C, Houghton AM, Glorioso JC, Weller M, Holland EC. Cooperation of oncolytic virotherapy with VEGF-neutralizing antibody treatment in IDH wildtype glioblastoma depends on MMP9. Neuro Oncol 2020; 21:1607-1609. [PMID: 31412117 DOI: 10.1093/neuonc/noz145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Hans-Georg Wirsching
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Seattle Translational Tumor Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Huajia Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Patrick J Cimino
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Pathology, Division of Neuropathology, University of Washington, Seattle, Washington, USA
| | | | - A McGarry Houghton
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joseph C Glorioso
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Neurosurgery, University of Washington, Seattle, Washington, USA.,Alvord Brain Tumor Center, University of Washington, Seattle, Washington, USA
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45
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Szulzewsky F, Arora S, Hoellerbauer P, King C, Nathan E, Chan M, Cimino PJ, Ozawa T, Kawauchi D, Pajtler KW, Gilbertson RJ, Paddison PJ, Vasioukhin V, Gujral TS, Holland EC. Comparison of tumor-associated YAP1 fusions identifies a recurrent set of functions critical for oncogenesis. Genes Dev 2020; 34:1051-1064. [PMID: 32675324 PMCID: PMC7397849 DOI: 10.1101/gad.338681.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
YAP1 is a transcriptional coactivator and the principal effector of the Hippo signaling pathway, which is causally implicated in human cancer. Several YAP1 gene fusions have been identified in various human cancers and identifying the essential components of this family of gene fusions has significant therapeutic value. Here, we show that the YAP1 gene fusions YAP1-MAMLD1, YAP1-FAM118B, YAP1-TFE3, and YAP1-SS18 are oncogenic in mice. Using reporter assays, RNA-seq, ChIP-seq, and loss-of-function mutations, we can show that all of these YAP1 fusion proteins exert TEAD-dependent YAP activity, while some also exert activity of the C'-terminal fusion partner. The YAP activity of the different YAP1 fusions is resistant to negative Hippo pathway regulation due to constitutive nuclear localization and resistance to degradation of the YAP1 fusion proteins. Genetic disruption of the TEAD-binding domain of these oncogenic YAP1 fusions is sufficient to inhibit tumor formation in vivo, while pharmacological inhibition of the YAP1-TEAD interaction inhibits the growth of YAP1 fusion-expressing cell lines in vitro. These results highlight TEAD-dependent YAP activity found in these gene fusions as critical for oncogenesis and implicate these YAP functions as potential therapeutic targets in YAP1 fusion-positive tumors.
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Affiliation(s)
- Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
| | - Claire King
- Department of Oncology, Cambridge Cancer Center, Cambridge CB2 0RE, England
| | - Erica Nathan
- Department of Oncology, Cambridge Cancer Center, Cambridge CB2 0RE, England
| | - Marina Chan
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Patrick J Cimino
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104, USA
| | - Tatsuya Ozawa
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Daisuke Kawauchi
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | | | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
| | - Valeri Vasioukhin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Taranjit S Gujral
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
- Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Cimino PJ, Holland EC. Targeted copy number analysis outperforms histologic grading in predicting patient survival for WHO grades II/III IDH-mutant astrocytomas. Neuro Oncol 2020; 21:819-821. [PMID: 30918961 DOI: 10.1093/neuonc/noz052] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Patrick J Cimino
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, Washington
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
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Niu B, Zeng X, Phan TA, Szulzewsky F, Holte S, Holland EC, Tian JP. Mathematical modeling of PDGF-driven glioma reveals the dynamics of immune cells infiltrating into tumors. Neoplasia 2020; 22:323-332. [PMID: 32585427 PMCID: PMC7322103 DOI: 10.1016/j.neo.2020.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Tumor-infiltrated immune cells compose a significant component of many cancers. They have been observed to have contradictory impacts on tumors. Although the primary reasons for these observations remain elusive, it is important to understand how immune cells infiltrating into tumors is regulated. Recently our group conducted a series of experimental studies, which showed that muIDH1 gliomas have a significant global reduction of immune cells and suggested that the longer survival time of mice with CIMP gliomas may be due to the IDH mutation and its effect on reducing of the tumor-infiltrated immune cells. However, to comprehend how IDH1 mutants regulate infiltration of immune cells into gliomas and how they affect the aggressiveness of gliomas, it is necessary to integrate our experimental data into a dynamical system to acquire a much deeper understanding of subtle regulation of immune cell infiltration. Methods: The method is integration of mathematical modeling and experiments. According to mass conservation laws and assumption that immune cells migrate into the tumor site along a chemotactic gradient field, a mathematical model is formulated. Parameters are estimated from our experiments. Numerical methods are developed to solve the problem. Numerical predictions are compared with experimental results. Results: Our analysis shows that the net rate of increase of immune cells infiltrated into the tumor is approximately proportional to the 4/5 power of the chemoattractant production rate, and it is an increasing function of time while the percentage of immune cells infiltrated into the tumor is a decreasing function of time. Our model predicts that wtIDH1 mice will survive longer if the immune cells are blocked by reducing chemotactic coefficient. For more aggressive gliomas, our model shows that there is little difference in their survivals between wtIDH1 and muIDH1 tumors, and the percentage of immune cells infiltrated into the tumor is much lower. These predictions are verified by our experimental results. In addition, wtIDH1 and muIDH1 can be quantitatively distinguished by their chemoattractant production rates, and the chemotactic coefficient determines possibilities of immune cells migration along chemoattractant gradient fields. Conclusions: The chemoattractant gradient field produced by tumor cells may facilitate immune cells migration to the tumor cite. The chemoattractant production rate may be utilized to classify wtIDH1 and muIDH1 tumors. The dynamics of immune cells infiltrating into tumors is largely determined by tumor cell chemoattractant production rate and chemotactic coefficient.
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Affiliation(s)
- Ben Niu
- Department of Mathematical Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM 88003, United States; Department of Mathematics, Harbin Institute of Technology at Weihai, 2 West Wenhua Road, Weihai, Shandong 264209, PR China
| | - Xianyi Zeng
- Department of Mathematical Sciences, University of Texas at El Paso, 500 West University Avenue, El Paso, TX 79968, United States
| | - Tuan Anh Phan
- Department of Mathematical Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM 88003, United States
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA 98109, United States
| | - Sarah Holte
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA 98109, United States
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA 98109, United States; Solid Tumor Translational Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA 98109, United States.
| | - Jianjun Paul Tian
- Department of Mathematical Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM 88003, United States.
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Pattwell SS, Arora S, Cimino PJ, Ozawa T, Szulzewsky F, Hoellerbauer P, Bonifert T, Hoffstrom BG, Boiani NE, Bolouri H, Correnti CE, Oldrini B, Silber JR, Squatrito M, Paddison PJ, Holland EC. A kinase-deficient NTRK2 splice variant predominates in glioma and amplifies several oncogenic signaling pathways. Nat Commun 2020; 11:2977. [PMID: 32532995 PMCID: PMC7293284 DOI: 10.1038/s41467-020-16786-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 10/16/2019] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Independent scientific achievements have led to the discovery of aberrant splicing patterns in oncogenesis, while more recent advances have uncovered novel gene fusions involving neurotrophic tyrosine receptor kinases (NTRKs) in gliomas. The exploration of NTRK splice variants in normal and neoplastic brain provides an intersection of these two rapidly evolving fields. Tropomyosin receptor kinase B (TrkB), encoded NTRK2, is known for critical roles in neuronal survival, differentiation, molecular properties associated with memory, and exhibits intricate splicing patterns and post-translational modifications. Here, we show a role for a truncated NTRK2 splice variant, TrkB.T1, in human glioma. TrkB.T1 enhances PDGF-driven gliomas in vivo, augments PDGF-induced Akt and STAT3 signaling in vitro, while next generation sequencing broadly implicates TrkB.T1 in the PI3K signaling cascades in a ligand-independent fashion. These TrkB.T1 findings highlight the importance of expanding upon whole gene and gene fusion analyses to include splice variants in basic and translational neuro-oncology research. Tropomyosin receptor kinase B (TrkB), encoded by the neurotrophic tyrosine receptor kinase 2 (NTRK2) gene, exhibits intricate splicing patterns and post-translational modifications. Here, the authors perform whole gene and transcript-level analyses and report the TrkB.T1 splice variant enhances PDGF-driven gliomas in vivo and augments PI3K signaling cascades in vitro.
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Affiliation(s)
- Siobhan S Pattwell
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA
| | - Patrick J Cimino
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA.,Department of Pathology, University of Washington School of Medicine, 325 9th Avenue, Box 359791, Seattle, WA, 98104, USA
| | - Tatsuya Ozawa
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA
| | - Pia Hoellerbauer
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Tobias Bonifert
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA
| | - Benjamin G Hoffstrom
- Antibody Technology Resource, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, 98109, USA
| | - Norman E Boiani
- Antibody Technology Resource, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, 98109, USA
| | - Hamid Bolouri
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA.,Systems Immunology, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA, 98101, USA
| | - Colin E Correnti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, 98109, USA
| | - Barbara Oldrini
- Seve Ballesteros Foundation Brain Tumor Group, Spanish National Cancer Research Centre, 28209, Madrid, Spain
| | - John R Silber
- Department of Neurological Surgery, Alvord Brain Tumor Center, University of Washington School of Medicine, Seattle, WA, 98104, USA
| | - Massimo Squatrito
- Seve Ballesteros Foundation Brain Tumor Group, Spanish National Cancer Research Centre, 28209, Madrid, Spain
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Mailstop C3-168, Seattle, WA, 98109, USA. .,Department of Neurological Surgery, Alvord Brain Tumor Center, University of Washington School of Medicine, Seattle, WA, 98104, USA. .,Seattle Tumor Translational Research Center, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, 98109, USA.
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49
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Ma Z, Niu B, Phan TA, Stensjøen AL, Ene C, Woodiwiss T, Wang T, Maini PK, Holland EC, Tian JP. Stochastic growth pattern of untreated human glioblastomas predicts the survival time for patients. Sci Rep 2020; 10:6642. [PMID: 32313150 PMCID: PMC7171128 DOI: 10.1038/s41598-020-63394-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/30/2020] [Indexed: 12/01/2022] Open
Abstract
Glioblastomas are highly malignant brain tumors. Knowledge of growth rates and growth patterns is useful for understanding tumor biology and planning treatment logistics. Based on untreated human glioblastoma data collected in Trondheim, Norway, we first fit the average growth to a Gompertz curve, then find a best fitted white noise term for the growth rate variance. Combining these two fits, we obtain a new type of Gompertz diffusion dynamics, which is a stochastic differential equation (SDE). Newly collected untreated human glioblastoma data in Seattle, US, re-verify our model. Instead of growth curves predicted by deterministic models, our SDE model predicts a band with a center curve as the tumor size average and its width as the tumor size variance over time. Given the glioblastoma size in a patient, our model can predict the patient survival time with a prescribed probability. The survival time is approximately a normal random variable with simple formulas for its mean and variance in terms of tumor sizes. Our model can be applied to studies of tumor treatments. As a demonstration, we numerically investigate different protocols of surgical resection using our model and provide possible theoretical strategies.
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Affiliation(s)
- Ziwei Ma
- Department of Mathematical Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM, 88003, USA.,College of Sciences, Northwest A&F University, 22 Xinong Rd, Yangling, Shaanxi, 712100, China
| | - Ben Niu
- Department of Mathematical Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM, 88003, USA.,Department of Mathematics, Harbin Institute of Technology at Weihai, 2 West Wenhua Road, Weihai, Shandong, 264209, P.R. China
| | - Tuan Anh Phan
- Department of Mathematical Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM, 88003, USA
| | - Anne Line Stensjøen
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health sciences, NTNU - Norwegian University of Science and Technology, Post Box 8905, N-7491, Trondheim, Norway
| | - Chibawanye Ene
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA, 98109, USA
| | - Timothy Woodiwiss
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA, 98109, USA
| | - Tonghui Wang
- Department of Mathematical Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM, 88003, USA
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Woodstock Road, Oxford, OX2 6GG, UK
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA, 98109, USA. .,Solid Tumor Translational Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., PO Box 19024, Seattle, WA, 98109, USA.
| | - Jianjun Paul Tian
- Department of Mathematical Sciences, New Mexico State University, 1780 E University Ave, Las Cruces, NM, 88003, USA.
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Kaley TJ, Panageas KS, Pentsova EI, Mellinghoff IK, Nolan C, Gavrilovic I, DeAngelis LM, Abrey LE, Holland EC, Omuro A, Lacouture ME, Ludwig E, Lassman AB. Phase I clinical trial of temsirolimus and perifosine for recurrent glioblastoma. Ann Clin Transl Neurol 2020; 7:429-436. [PMID: 32293798 PMCID: PMC7187704 DOI: 10.1002/acn3.51009] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 11/13/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 11/29/2022] Open
Abstract
Purpose Malignant glioma (MG) is the most deadly primary brain cancer. Signaling though the PI3K/AKT/mTOR axis is activated in most MGs and therefore a potential therapeutic target. The mTOR inhibitor temsirolimus and the AKT inhibitor perifosine are each well‐tolerated as single agents but with limited activity reclinical data demonstrate synergistic anti‐tumor effects from combined treatment. Therefore, we initiated a phase I trial of combined therapy in recurrent MGs to determine safety and a recommended phase II dose. Methods Adults with recurrent MG, Karnofsky Performance Status ≥ 60 were enrolled, with no limit on the number of prior therapies. Temsirolimus dose was escalated using standard 3 + 3 design from 15 mg to 170 mg administered once weekly. Perifosine was fixed as a 600 mg load on day 1 followed by 100 mg nightly (single agent MTD) until dose level 7 when the load increased to 900 mg. Results We treated 35 patients with with glioblastoma (17) or other MGs (18; including nine anaplastic astrocytoma, nine anaplastic oligodendroglioma, one anaplastic oligoastrocytoma, and two low grade astrocytomas with radiographic transformation to MG). We observed five dose‐limiting toxicities (DLTs): one at dose level 3 (50mg temsirolimus), then two at dose level 7 expansion (170 mg temsirolimus), and then two more at dose level 6 expansion (170 mg temsirolimus). DLTs included thrombocytopenia (n = 3), intracerebral hemorrhage (n = 1) and lung infection (n = 1). Conclusion Combining the mTOR inhibitor temsirolimus dosed at 115 mg weekly and the AKT inhibitor perifosine dosed at 100 mg daily (following 600 mg load) is tolerable in heavily pretreated adults with recurrent MGs.
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Affiliation(s)
- Thomas J Kaley
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katherine S Panageas
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elena I Pentsova
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ingo K Mellinghoff
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Craig Nolan
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Igor Gavrilovic
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lisa M DeAngelis
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lauren E Abrey
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric C Holland
- Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Antonio Omuro
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mario E Lacouture
- Department of Dermatology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emmy Ludwig
- Gastroenterology and Nutrition Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew B Lassman
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York.,Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, New York
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