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Turkarslan S, He Y, Hothi P, Murie C, Nicolas A, Kannan K, Park JH, Pan M, Awawda A, Cole ZD, Shapiro MA, Stuhlmiller TJ, Lee H, Patel AP, Cobbs C, Baliga NS. An atlas of causal and mechanistic drivers of interpatient heterogeneity in glioma. medRxiv 2024:2024.04.05.24305380. [PMID: 38633778 PMCID: PMC11023657 DOI: 10.1101/2024.04.05.24305380] [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: 04/19/2024]
Abstract
Grade IV glioma, formerly known as glioblastoma multiforme (GBM) is the most aggressive and lethal type of brain tumor, and its treatment remains challenging in part due to extensive interpatient heterogeneity in disease driving mechanisms and lack of prognostic and predictive biomarkers. Using mechanistic inference of node-edge relationship (MINER), we have analyzed multiomics profiles from 516 patients and constructed an atlas of causal and mechanistic drivers of interpatient heterogeneity in GBM (gbmMINER). The atlas has delineated how 30 driver mutations act in a combinatorial scheme to causally influence a network of regulators (306 transcription factors and 73 miRNAs) of 179 transcriptional "programs", influencing disease progression in patients across 23 disease states. Through extensive testing on independent patient cohorts, we share evidence that a machine learning model trained on activity profiles of programs within gbmMINER significantly augments risk stratification, identifying patients who are super-responders to standard of care and those that would benefit from 2 nd line treatments. In addition to providing mechanistic hypotheses regarding disease prognosis, the activity of programs containing targets of 2 nd line treatments accurately predicted efficacy of 28 drugs in killing glioma stem-like cells from 43 patients. Our findings demonstrate that interpatient heterogeneity manifests from differential activities of transcriptional programs, providing actionable strategies for mechanistically characterizing GBM from a systems perspective and developing better prognostic and predictive biomarkers for personalized medicine.
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2
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Park JH, Hothi P, Lopez Garcia de Lomana A, Pan M, Calder R, Turkarslan S, Wu WJ, Lee H, Patel AP, Cobbs C, Huang S, Baliga NS. Gene regulatory network topology governs resistance and treatment escape in glioma stem-like cells. bioRxiv 2024:2024.02.02.578510. [PMID: 38370784 PMCID: PMC10871280 DOI: 10.1101/2024.02.02.578510] [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: 02/20/2024]
Abstract
Poor prognosis and drug resistance in glioblastoma (GBM) can result from cellular heterogeneity and treatment-induced shifts in phenotypic states of tumor cells, including dedifferentiation into glioma stem-like cells (GSCs). This rare tumorigenic cell subpopulation resists temozolomide, undergoes proneural-to-mesenchymal transition (PMT) to evade therapy, and drives recurrence. Through inference of transcriptional regulatory networks (TRNs) of patient-derived GSCs (PD-GSCs) at single-cell resolution, we demonstrate how the topology of transcription factor interaction networks drives distinct trajectories of cell state transitions in PD-GSCs resistant or susceptible to cytotoxic drug treatment. By experimentally testing predictions based on TRN simulations, we show that drug treatment drives surviving PD-GSCs along a trajectory of intermediate states, exposing vulnerability to potentiated killing by siRNA or a second drug targeting treatment-induced transcriptional programs governing non-genetic cell plasticity. Our findings demonstrate an approach to uncover TRN topology and use it to rationally predict combinatorial treatments that disrupts acquired resistance in GBM.
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Affiliation(s)
| | - Parvinder Hothi
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA
| | | | - Min Pan
- Institute for Systems Biology, Seattle, WA
| | | | | | - Wei-Ju Wu
- Institute for Systems Biology, Seattle, WA
| | - Hwahyung Lee
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA
| | - Anoop P Patel
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC
- Center for Advanced Genomic Technologies, Duke University, Durham, NC
| | - Charles Cobbs
- Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA
- Departments of Microbiology, Biology, and Molecular Engineering Sciences, University of Washington, Seattle, WA
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3
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Hothi P, Cobbs C. The potential role of human endogenous retrovirus K in glioblastoma. J Clin Invest 2023; 133:e170885. [PMID: 37395278 DOI: 10.1172/jci170885] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
The most active human endogenous retrovirus K (HERV-K) subtype, HML-2, has been implicated as a driver of oncogenesis in several cancers. However, the presence and function of HML-2 in malignant gliomas has remained unclear. In this issue of the JCI, Shah and colleagues demonstrate HML-2 overexpression in glioblastoma (GBM) and its role in maintaining the cancer stem cell phenotype. Given that stem-like cells are considered responsible for GBM heterogeneity and treatment resistance, targeting the stem cell niche may reduce tumor recurrence and improve clinical outcomes. The findings provide a foundation for future studies to determine whether antiretroviral and/or immunotherapy approaches targeting HML-2 could be used as therapeutics for GBM.
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Park JH, de Lomana ALG, Marzese DM, Juarez T, Feroze A, Hothi P, Cobbs C, Patel AP, Kesari S, Huang S, Baliga NS. A Systems Approach to Brain Tumor Treatment. Cancers (Basel) 2021; 13:3152. [PMID: 34202449 PMCID: PMC8269017 DOI: 10.3390/cancers13133152] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 05/11/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
Brain tumors are among the most lethal tumors. Glioblastoma, the most frequent primary brain tumor in adults, has a median survival time of approximately 15 months after diagnosis or a five-year survival rate of 10%; the recurrence rate is nearly 90%. Unfortunately, this prognosis has not improved for several decades. The lack of progress in the treatment of brain tumors has been attributed to their high rate of primary therapy resistance. Challenges such as pronounced inter-patient variability, intratumoral heterogeneity, and drug delivery across the blood-brain barrier hinder progress. A comprehensive, multiscale understanding of the disease, from the molecular to the whole tumor level, is needed to address the intratumor heterogeneity resulting from the coexistence of a diversity of neoplastic and non-neoplastic cell types in the tumor tissue. By contrast, inter-patient variability must be addressed by subtyping brain tumors to stratify patients and identify the best-matched drug(s) and therapies for a particular patient or cohort of patients. Accomplishing these diverse tasks will require a new framework, one involving a systems perspective in assessing the immense complexity of brain tumors. This would in turn entail a shift in how clinical medicine interfaces with the rapidly advancing high-throughput (HTP) technologies that have enabled the omics-scale profiling of molecular features of brain tumors from the single-cell to the tissue level. However, several gaps must be closed before such a framework can fulfill the promise of precision and personalized medicine for brain tumors. Ultimately, the goal is to integrate seamlessly multiscale systems analyses of patient tumors and clinical medicine. Accomplishing this goal would facilitate the rational design of therapeutic strategies matched to the characteristics of patients and their tumors. Here, we discuss some of the technologies, methodologies, and computational tools that will facilitate the realization of this vision to practice.
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Affiliation(s)
- James H. Park
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
| | | | - Diego M. Marzese
- Balearic Islands Health Research Institute (IdISBa), 07010 Palma, Spain;
| | - Tiffany Juarez
- St. John’s Cancer Institute, Santa Monica, CA 90401, USA; (T.J.); (S.K.)
| | - Abdullah Feroze
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA; (A.F.); (A.P.P.)
| | - Parvinder Hothi
- Swedish Neuroscience Institute, Seattle, WA 98122, USA; (P.H.); (C.C.)
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Seattle, WA 98122, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle, WA 98122, USA; (P.H.); (C.C.)
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Seattle, WA 98122, USA
| | - Anoop P. Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA; (A.F.); (A.P.P.)
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Santosh Kesari
- St. John’s Cancer Institute, Santa Monica, CA 90401, USA; (T.J.); (S.K.)
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, WA 98109, USA; (J.H.P.); (S.H.)
- Departments of Microbiology, Biology, and Molecular Engineering Sciences, University of Washington, Seattle, WA 98105, USA
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5
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Salomon MP, Orozco JIJ, Wilmott JS, Hothi P, Manughian-Peter AO, Cobbs CS, Scolyer RA, Hoon DSB, Marzese DM. Brain metastasis DNA methylomes, a novel resource for the identification of biological and clinical features. Sci Data 2018; 5:180245. [PMID: 30398472 PMCID: PMC6219670 DOI: 10.1038/sdata.2018.245] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/03/2018] [Indexed: 12/20/2022] Open
Abstract
Brain metastases (BM) are one the most lethal and poorly managed clinical complications in cancer patients. These secondary tumors represent the most common intracranial neoplasm in adults, most frequently originating from lung cancer, breast cancer, and cutaneous melanoma. In primary brain tumors, such as gliomas, recent advances in DNA methylation profiling have allowed for a comprehensive molecular classification. Such data provide prognostic information, in addition to helping predict patient response to specific systemic therapies. However, epigenetic alterations of metastatic brain tumors with specific biological and translational relevance still require much further exploration. Using the widely employed Illumina Infinium HumanMethylation 450K platform, we have generated a cohort of genome-wide DNA methylomes from ninety-six needle-dissected BM specimens from patients with lung cancer, breast cancer, and cutaneous melanoma with clinical, pathological, and demographic annotations. This resource offers an unprecedented and unique opportunity to identify novel DNA methylation features influencing the behavior of brain metastasis, and thus accelerate the discovery of BM-specific theranostic epigenetic alterations.
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Affiliation(s)
- Matthew P. Salomon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA
| | - Javier I. J. Orozco
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA
| | - James S. Wilmott
- Melanoma Institute Australia, The University of Sydney, Camperdown, NSW, 2065, Australia
| | - Parvinder Hothi
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Ayla O. Manughian-Peter
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA
| | - Charles S. Cobbs
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Camperdown, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, 2006, Australia
- Royal Prince Alfred Hospital, Sydney, New South Wales, 2050, Australia
| | - Dave S. B. Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA
| | - Diego M. Marzese
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John’s Health Center, Santa Monica, CA 90404, USA
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6
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Orozco JIJ, Knijnenburg TA, Manughian-Peter AO, Salomon MP, Barkhoudarian G, Jalas JR, Wilmott JS, Hothi P, Wang X, Takasumi Y, Buckland ME, Thompson JF, Long GV, Cobbs CS, Shmulevich I, Kelly DF, Scolyer RA, Hoon DSB, Marzese DM. Epigenetic profiling for the molecular classification of metastatic brain tumors. Nat Commun 2018; 9:4627. [PMID: 30401823 PMCID: PMC6219520 DOI: 10.1038/s41467-018-06715-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 09/19/2018] [Indexed: 01/29/2023] Open
Abstract
Optimal treatment of brain metastases is often hindered by limitations in diagnostic capabilities. To meet this challenge, here we profile DNA methylomes of the three most frequent types of brain metastases: melanoma, breast, and lung cancers (n = 96). Using supervised machine learning and integration of DNA methylomes from normal, primary, and metastatic tumor specimens (n = 1860), we unravel epigenetic signatures specific to each type of metastatic brain tumor and constructed a three-step DNA methylation-based classifier (BrainMETH) that categorizes brain metastases according to the tissue of origin and therapeutically relevant subtypes. BrainMETH predictions are supported by routine histopathologic evaluation. We further characterize and validate the most predictive genomic regions in a large cohort of brain tumors (n = 165) using quantitative-methylation-specific PCR. Our study highlights the importance of brain tumor-defining epigenetic alterations, which can be utilized to further develop DNA methylation profiling as a critical tool in the histomolecular stratification of patients with brain metastases.
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Affiliation(s)
- Javier I J Orozco
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | | | - Ayla O Manughian-Peter
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Matthew P Salomon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Garni Barkhoudarian
- Pacific Neuroscience Institute, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - John R Jalas
- Department of Pathology, Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
| | - Parvinder Hothi
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, 98122, USA
| | - Xiaowen Wang
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Yuki Takasumi
- Department of Pathology, Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Michael E Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, the Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Royal North Shore Hospital, Sydney, NSW, 2065, Australia
| | - Charles S Cobbs
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, 98122, USA
| | | | - Daniel F Kelly
- Pacific Neuroscience Institute, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, 2065, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, 2006, Australia
- Royal Prince Alfred Hospital, Sydney, NSW, 2050, Australia
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
- Sequencing Center, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Diego M Marzese
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA.
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7
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Diaz P, Horne E, Xu C, Hamel E, Wagenbach M, Petrov RR, Uhlenbruck B, Haas B, Hothi P, Wordeman L, Gussio R, Stella N. Modified carbazoles destabilize microtubules and kill glioblastoma multiform cells. Eur J Med Chem 2018; 159:74-89. [PMID: 30268825 DOI: 10.1016/j.ejmech.2018.09.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 11/26/2022]
Abstract
Small molecules that target microtubules (MTs) represent promising therapeutics to treat certain types of cancer, including glioblastoma multiform (GBM). We synthesized modified carbazoles and evaluated their antitumor activity in GBM cells in culture. Modified carbazoles with an ethyl moiety linked to the nitrogen of the carbazole and a carbonyl moiety linked to distinct biaromatic rings exhibited remarkably different killing activities in human GBM cell lines and patient-derived GBM cells, with IC50 values from 67 to >10,000 nM. Measures of the activity of modified carbazoles with tubulin and microtubules coupled to molecular docking studies show that these compounds bind to the colchicine site of tubulin in a unique low interaction space that inhibits tubulin assembly. The modified carbazoles reported here represent novel chemical tools to better understand how small molecules disrupt MT functions and kill devastating cancers such as GBM.
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Affiliation(s)
- Philippe Diaz
- Department of Biomedical and Pharmaceutical Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA; DermaXon LLC, 32 Campus Drive, Missoula, MT, 59812, USA.
| | - Eric Horne
- Stella Therapeutics, Inc., Pacific Northwest Research Institute, 720 Broadway, Seattle, WA, 98122, USA
| | - Cong Xu
- Department of Pharmacology (CX, BH and NS), Department of Physiology and Biophysics (MW and LW), Department of Psychiatry and Behavioral Sciences (NS), The University of Washington, Seattle, WA, 98195, USA
| | - Ernest Hamel
- Screening Technologies Branch (EH) and Computational Drug Development Group (RG), Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Michael Wagenbach
- Department of Pharmacology (CX, BH and NS), Department of Physiology and Biophysics (MW and LW), Department of Psychiatry and Behavioral Sciences (NS), The University of Washington, Seattle, WA, 98195, USA
| | - Ravil R Petrov
- Department of Biomedical and Pharmaceutical Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Benjamin Uhlenbruck
- Department of Biomedical and Pharmaceutical Sciences, The University of Montana, 32 Campus Drive, Missoula, MT, 59812, USA
| | - Brian Haas
- Department of Pharmacology (CX, BH and NS), Department of Physiology and Biophysics (MW and LW), Department of Psychiatry and Behavioral Sciences (NS), The University of Washington, Seattle, WA, 98195, USA
| | - Parvinder Hothi
- Ivy Center for Advance Brain Tumor Treatment, Swedish Neuroscience Institute, 550 17th Ave, Seattle, WA, 98122, USA
| | - Linda Wordeman
- Department of Pharmacology (CX, BH and NS), Department of Physiology and Biophysics (MW and LW), Department of Psychiatry and Behavioral Sciences (NS), The University of Washington, Seattle, WA, 98195, USA
| | - Rick Gussio
- Screening Technologies Branch (EH) and Computational Drug Development Group (RG), Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Nephi Stella
- Stella Therapeutics, Inc., Pacific Northwest Research Institute, 720 Broadway, Seattle, WA, 98122, USA; Department of Pharmacology (CX, BH and NS), Department of Physiology and Biophysics (MW and LW), Department of Psychiatry and Behavioral Sciences (NS), The University of Washington, Seattle, WA, 98195, USA.
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8
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Puchalski RB, Shah N, Miller J, Dalley R, Nomura SR, Yoon JG, Smith KA, Lankerovich M, Bertagnolli D, Bickley K, Boe AF, Brouner K, Butler S, Caldejon S, Chapin M, Datta S, Dee N, Desta T, Dolbeare T, Dotson N, Ebbert A, Feng D, Feng X, Fisher M, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Hejazinia N, Hohmann J, Hothi P, Howard R, Joines K, Kriedberg A, Kuan L, Lau C, Lee F, Lee H, Lemon T, Long F, Mastan N, Mott E, Murthy C, Ngo K, Olson E, Reding M, Riley Z, Rosen D, Sandman D, Shapovalova N, Slaughterbeck CR, Sodt A, Stockdale G, Szafer A, Wakeman W, Wohnoutka PE, White SJ, Marsh D, Rostomily RC, Ng L, Dang C, Jones A, Keogh B, Gittleman HR, Barnholtz-Sloan JS, Cimino PJ, Uppin MS, Keene CD, Farrokhi FR, Lathia JD, Berens ME, Iavarone A, Bernard A, Lein E, Phillips JW, Rostad SW, Cobbs C, Hawrylycz MJ, Foltz GD. An anatomic transcriptional atlas of human glioblastoma. Science 2018; 360:660-663. [PMID: 29748285 DOI: 10.1126/science.aaf2666] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/30/2018] [Indexed: 12/20/2022]
Abstract
Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment.
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Affiliation(s)
- Ralph B Puchalski
- Allen Institute for Brain Science, Seattle, WA 98109, USA. .,Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Nameeta Shah
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA. .,Mazumdar Shaw Center for Translational Research, Bangalore 560099, India
| | - Jeremy Miller
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Steve R Nomura
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jae-Guen Yoon
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Michael Lankerovich
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Kris Bickley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Andrew F Boe
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Mike Chapin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Suvro Datta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tsega Desta
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Amanda Ebbert
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Feng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xu Feng
- Radia Inc., Lynnwood, WA 98036, USA
| | - Michael Fisher
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Garrett Gee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Guangyu Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Nika Hejazinia
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - John Hohmann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Parvinder Hothi
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Robert Howard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kevin Joines
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ali Kriedberg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chris Lau
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Felix Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hwahyung Lee
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Tracy Lemon
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Fuhui Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Naveed Mastan
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Erika Mott
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chantal Murthy
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Eric Olson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Melissa Reding
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zack Riley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Rosen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Sandman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Andrew Sodt
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wayne Wakeman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Don Marsh
- White Marsh Forests, Seattle, WA 98119, USA
| | - Robert C Rostomily
- Department of Neurosurgery, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.,Department of Neurological Surgery, Houston Methodist Hospital and Research Institute, Houston, TX 77030, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Chinh Dang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Allan Jones
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Haley R Gittleman
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Patrick J Cimino
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | - Megha S Uppin
- Nizam's Institute of Medical Sciences, Punjagutta, Hyderabad 500082, India
| | - C Dirk Keene
- Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, WA 98104, USA
| | | | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Michael E Berens
- TGen, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Neurology, Columbia University, New York, NY 10032, USA.,Department of Pathology, Columbia University, New York, NY 10032, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Charles Cobbs
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | | | - Greg D Foltz
- Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
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9
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Ulasov IV, Foster H, Butters M, Yoon JG, Ozawa T, Nicolaides T, Figueroa X, Hothi P, Prados M, Butters J, Cobbs C. Precision knockdown of EGFR gene expression using radio frequency electromagnetic energy. J Neurooncol 2017; 133:257-264. [PMID: 28434113 DOI: 10.1007/s11060-017-2440-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/15/2017] [Indexed: 10/19/2022]
Abstract
Electromagnetic fields (EMF) in the radio frequency energy (RFE) range can affect cells at the molecular level. Here we report a technology that can record the specific RFE signal of a given molecule, in this case the siRNA of epidermal growth factor receptor (EGFR). We demonstrate that cells exposed to this EGFR siRNA RFE signal have a 30-70% reduction of EGFR mRNA expression and ~60% reduction in EGFR protein expression vs. control treated cells. Specificity for EGFR siRNA effect was confirmed via RNA microarray and antibody dot blot array. The EGFR siRNA RFE decreased cell viability, as measured by Calcein-AM measures, LDH release and Caspase 3 cleavage, and increased orthotopic xenograft survival. The outcomes of this study demonstrate that an RFE signal can induce a specific siRNA-like effect on cells. This technology opens vast possibilities of targeting a broader range of molecules with applications in medicine, agriculture and other areas.
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Affiliation(s)
- Ilya V Ulasov
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, 550 17th Avenue, Seattle, WA, 98122, USA.
| | - Haidn Foster
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, 550 17th Avenue, Seattle, WA, 98122, USA
| | - Mike Butters
- Nativis Inc., 219 Terry Avenue North, Seattle, WA, 98109, USA
| | - Jae-Geun Yoon
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, 550 17th Avenue, Seattle, WA, 98122, USA
| | - Tomoko Ozawa
- Department of Neurosurgery, Brain Tumor Research Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Theodore Nicolaides
- Department of Neurosurgery, Brain Tumor Research Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Xavier Figueroa
- Nativis Inc., 219 Terry Avenue North, Seattle, WA, 98109, USA
| | - Parvinder Hothi
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, 550 17th Avenue, Seattle, WA, 98122, USA
| | - Michael Prados
- Department of Neurosurgery, Brain Tumor Research Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - John Butters
- Nativis Inc., 219 Terry Avenue North, Seattle, WA, 98109, USA
| | - Charles Cobbs
- Ben & Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, 550 17th Avenue, Seattle, WA, 98122, USA.
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10
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Ghosh D, Ulasov IV, Chen L, Harkins LE, Wallenborg K, Hothi P, Rostad S, Hood L, Cobbs CS. TGFβ-Responsive HMOX1 Expression Is Associated with Stemness and Invasion in Glioblastoma Multiforme. Stem Cells 2016; 34:2276-89. [PMID: 27354342 DOI: 10.1002/stem.2411] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [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: 10/07/2015] [Revised: 04/09/2016] [Accepted: 05/03/2016] [Indexed: 01/06/2023]
Abstract
Glioblastoma multiforme (GBM) is the most common and lethal adult brain tumor. Resistance to standard radiation and chemotherapy is thought to involve survival of GBM cancer stem cells (CSCs). To date, no single marker for identifying GBM CSCs has been able to capture the diversity of CSC populations, justifying the needs for additional CSC markers for better characterization. Employing targeted mass spectrometry, here we present five cell-surface markers HMOX1, SLC16A1, CADM1, SCAMP3, and CLCC1 which were found to be elevated in CSCs relative to healthy neural stem cells (NSCs). Transcriptomic analyses of REMBRANDT and TCGA compendiums also indicated elevated expression of these markers in GBM relative to controls and non-GBM diseases. Two markers SLC16A1 and HMOX1 were found to be expressed among pseudopalisading cells that reside in the hypoxic region of GBM, substantiating the histopathological hallmarks of GBM. In a prospective study (N = 8) we confirmed the surface expression of HMOX1 on freshly isolated primary GBM cells (P0). Employing functional assays that are known to evaluate stemness, we demonstrate that elevated HMOX1 expression is associated with stemness in GBM and can be modulated through TGFβ. siRNA-mediated silencing of HMOX1 impaired GBM invasion-a phenomenon related to poor prognosis. In addition, surgical resection of GBM tumors caused declines (18% ± 5.1SEM) in the level of plasma HMOX1 as measured by ELISA, in 8/10 GBM patients. These findings indicate that HMOX1 is a robust predictor of GBM CSC stemness and pathogenesis. Further understanding of the role of HMOX1 in GBM may uncover novel therapeutic approaches. Stem Cells 2016;34:2276-2289.
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Affiliation(s)
- Dhiman Ghosh
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle. .,Institute for Systems Biology, Seattle.
| | - Ilya V Ulasov
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle
| | - LiPing Chen
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle
| | - Lualhati E Harkins
- Department of Pathology and Laboratory Medicine, Birmingham Veterans Hospital, Birmingham
| | | | - Parvinder Hothi
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle
| | - Steven Rostad
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle.,CellNetix Pathology and Laboratories, Seattle
| | | | - Charles S Cobbs
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle. .,Institute for Systems Biology, Seattle.
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11
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Ulasov IV, Shah N, Kaverina NV, Lee H, Lin B, Lieber A, Kadagidze ZG, Yoon JG, Schroeder B, Hothi P, Ghosh D, Baryshnikov AY, Cobbs CS. Tamoxifen improves cytopathic effect of oncolytic adenovirus in primary glioblastoma cells mediated through autophagy. Oncotarget 2016; 6:3977-87. [PMID: 25738357 PMCID: PMC4414167 DOI: 10.18632/oncotarget.2897] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 12/11/2014] [Indexed: 11/25/2022] Open
Abstract
Oncolytic gene therapy using viral vectors may provide an attractive therapeutic option for malignant gliomas. These viral vectors are designed in a way to selectively target tumor cells and spare healthy cells. To determine the translational impact, it is imperative to assess the factors that interfere with the anti-glioma effects of the oncolytic adenoviral vectors. In the current study, we evaluated the efficacy of survivin-driven oncolytic adenoviruses pseudotyping with adenoviral fiber knob belonging to the adenoviral serotype 3, 11 and 35 in their ability to kill glioblastoma (GBM) cells selectively without affecting normal cells. Our results indicate that all recombinant vectors used in the study can effectively target GBM in vitro with high specificity, especially the 3 knob-modified vector. Using intracranial U87 and U251 GBM xenograft models we have also demonstrated that treatment with Conditionally Replicative Adenovirus (CRAd-S-5/3) vectors can effectively regress tumor. However, in several patient-derived GBM cell lines, cells exhibited resistance to the CRAd infection as evident from the diminishing effects of autophagy. To improve therapeutic response, tumor cells were pretreated with tamoxifen. Our preliminary data suggest that tamoxifen sensitizes glioblastoma cells towards oncolytic treatment with CRAd-S-5/3, which may prove useful for GBM in future experimental therapy.
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Affiliation(s)
- Ilya V Ulasov
- Swedish Neuroscience Institute, Seattle, WA, 98122, USA.,Institute of Experimental Diagnostic and Biotherapy, NN. Blokhin Cancer Research Center, RAMN, Moscow, Russia, 115478
| | - Nameeta Shah
- Swedish Neuroscience Institute, Seattle, WA, 98122, USA
| | - Natalya V Kaverina
- NN. Blokhin Cancer Research Center, RAMN, Moscow, Russia, 115478.,Current address: Division of Nephrology, University of Washington, Seattle, 98109, USA
| | - Hwahyang Lee
- Swedish Neuroscience Institute, Seattle, WA, 98122, USA
| | - Biaoyang Lin
- Swedish Neuroscience Institute, Seattle, WA, 98122, USA
| | - Andre Lieber
- University of Washington, Seattle, WA, 98122, USA
| | | | - Jae-Guen Yoon
- Swedish Neuroscience Institute, Seattle, WA, 98122, USA
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12
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Lin B, Lee H, Yoon JG, Madan A, Wayner E, Tonning S, Hothi P, Schroeder B, Ulasov I, Foltz G, Hood L, Cobbs C. Global analysis of H3K4me3 and H3K27me3 profiles in glioblastoma stem cells and identification of SLC17A7 as a bivalent tumor suppressor gene. Oncotarget 2016; 6:5369-81. [PMID: 25749033 PMCID: PMC4467155 DOI: 10.18632/oncotarget.3030] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/01/2015] [Indexed: 01/21/2023] Open
Abstract
Epigenetic changes, including H3K4me3 and H3K27me3 histone modification, play an important role in carcinogenesis. However, no genome-wide histone modification map has been generated for gliomas. Here, we report a genome-wide map of H3K4me3 and H3K27me3 histone modifications for 8 glioma stem cell (GSC) lines, together with the associated gene activation or repression patterns. In addition, we compared the genome-wide histone modification maps of GSC lines to those of astrocytes to identify unique gene activation or repression profiles in GSCs and astrocytes. We also identified a set of bivalent genes, which are genes that are associated with both H3K4me3 and H3K27me3 marks and are poised for action in embryonic stem cells. These bivalent genes are potential targets for inducing differentiation in glioblastoma (GBM) as a therapeutic approach. Finally, we identified SLC17A7 as a bivalent tumor suppressor gene in GBM, as it is down-regulated at both the protein and RNA levels in GBM tissues compared with normal brain tissues, and it inhibits GBM cell proliferation, migration and invasion.
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Affiliation(s)
- Biaoyang Lin
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China.,Dept. of Urology, University of Washington, Seattle, WA 98195, USA.,System Biology Division, Zhejiang-California International Nanosystem Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hwahyung Lee
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Jae-Geun Yoon
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Anup Madan
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA.,LabCorp Clinical Trials (Genomics Laboratory), Seattle, WA 98109, USA
| | - Elizabeth Wayner
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Sanja Tonning
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Parvinder Hothi
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Brett Schroeder
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Ilya Ulasov
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Gregory Foltz
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
| | - Leroy Hood
- The Institute for Systems Biology, Seattle, WA 98109, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Swedish Medical Center, Seattle, WA 98122, USA
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13
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Pham K, Luo D, Siemann DW, Law BK, Reynolds BA, Hothi P, Foltz G, Harrison JK. VEGFR inhibitors upregulate CXCR4 in VEGF receptor-expressing glioblastoma in a TGFβR signaling-dependent manner. Cancer Lett 2015; 360:60-7. [PMID: 25676691 DOI: 10.1016/j.canlet.2015.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/03/2015] [Accepted: 02/03/2015] [Indexed: 11/16/2022]
Abstract
The failure of standard treatment for patients diagnosed with glioblastoma (GBM) coupled with the highly vascularized nature of this solid tumor has led to the consideration of agents targeting VEGF or VEGFRs, as alternative therapeutic strategies for this disease. Despite modest achievements in survival obtained with such treatments, failure to maintain an enduring survival benefit and more invasive relapsing tumors are evident. Our study suggests a potential mechanism by which anti-VEGF/VEGFR therapies regulate the enhanced invasive phenotype through a pathway that involves TGFβR and CXCR4. VEGFR signaling inhibitors (Cediranib and Vandetanib) elevated the expression of CXCR4 in VEGFR-expressing GBM cell lines and tumors, and enhanced the in vitro migration of these lines toward CXCL12. The combination of VEGFR inhibitor and CXCR4 antagonist provided a greater survival benefit to tumor-bearing animals. The upregulation of CXCR4 by VEGFR inhibitors was dependent on TGFβ/TGFβR, but not HGF/MET, signaling activity, suggesting a mechanism of crosstalk among VEGF/VEGFR, TGFβ/TGFβR, and CXCL12/CXCR4 pathways in the malignant phenotype of recurrent tumors after anti-VEGF/VEGFR therapies. Thus, the combination of VEGFR, CXCR4, and TGFβR inhibitors could provide an alternative strategy to halt GBM progression.
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Affiliation(s)
- Kien Pham
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Defang Luo
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Dietmar W Siemann
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA; Department of Radiation Oncology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Brian K Law
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Brent A Reynolds
- Department of Neurosurgery, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Parvinder Hothi
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Gregory Foltz
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jeffrey K Harrison
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
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14
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Pham K, Luo D, Siemann D, Law B, Reynolds B, Hothi P, Foltz G, Harrison J. AI-24 * VEGFR INHIBITORS ENHANCE PROGRESSION OF GLIOBLASTOMA BY UPREGULATING CXCR4 IN A TGF R SIGNALING-DEPENDENT MANNER. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou238.24] [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: 11/14/2022] Open
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15
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Pham K, Luo D, Siemann D, Reynolds BA, Hothi P, Foltz G, Harrison JK. Abstract 1425: Impact of VEGFR pathway inhibition on the expression and function of CXCR4 in primary patient derived glioblastoma cell lines. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Glioblastoma (GBM) is one of the most malignant and aggressive forms of primary brain tumors. Current standard treatment options for patients diagnosed with GBM include surgical resection, radiation, and chemotherapy. Since GBM features an extensively vascularized solid tumor, anti-angiogenic agents have also been considered as a treatment regimen for GBM patients. Indeed, evidence from clinical trials has shown that Bevacizumab (Avastin®), an anti-VEGF monoclonal antibody, successfully reduces the development of tumor microvascular networks and prolongs the progression-free survival rate of GBM patients. In a subset of patients, however, tumors become resistant to this treatment and exhibit a more infiltrative phenotype after anti-angiogenic therapy. A recent published study (Lu et. al., Cancer Cell, 22:21; 2012) proposed that the HGF/c-MET signaling pathway may be involved in this enhanced invasive phenotype post anti-angiogenic therapy targeting VEGFRs. These data suggest that integrating VEGFR and c-MET inhibitors will prevent tumor recurrence from anti-angiogenic therapy. Because of the heterogeneity of the tumor microenvironment and complexity in signaling communication among cancer cells, we are interested in the contribution of chemokines and chemokine receptors in this phenomenon. Characterization of several primary patient-derived glioblastoma cell lines indicated heterogeneity in the level of expression of VEGFRs: some lines were VEGFR positive while others were VEGFR negative. VEGF and c-MET mRNAs were detected in all lines. Flow cytometry analysis of chemokine receptors indicated that levels of CXCR4 were elevated after VEGF/VEGFR inhibitor treatment (Bevacizumab, Cediranib or Vandetanib) only in VEGFR-expressing GBM cell lines, while CXCR7 was not affected by VEGFR pathway inhibition. In addition, VEGFR inhibitor treatment enhanced the migration of VEGFR-expressing lines to CXCL12. c-MET inhibitors did not impact VEGFR inhibitor-stimulated CXCR4 expression, suggesting that this regulation is independent of c-MET. Together, our data suggest that the CXCL12/CXCR4 axis may be an additional potential factor contributing to the invasive phenotype in recurrent tumors after anti-angiogenic therapy. Thus, the combination of VEGFR pathway inhibitors and CXCR4 antagonists may provide an alternative strategy to halt tumor progression and provide benefit to patients with GBM.
Citation Format: Kien Pham, Defang Luo, Dietmar Siemann, Brent A. Reynolds, Parvinder Hothi, Gregory Foltz, Jeffrey K. Harrison. Impact of VEGFR pathway inhibition on the expression and function of CXCR4 in primary patient derived glioblastoma cell lines. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1425. doi:10.1158/1538-7445.AM2013-1425
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Affiliation(s)
- Kien Pham
- 1Univ. of Florida College of Medicine, Gainesville, FL
| | - Defang Luo
- 1Univ. of Florida College of Medicine, Gainesville, FL
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16
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Liu C, Pham K, Luo D, Reynolds BA, Hothi P, Foltz G, Harrison JK. Expression and functional heterogeneity of chemokine receptors CXCR4 and CXCR7 in primary patient-derived glioblastoma cells. PLoS One 2013; 8:e59750. [PMID: 23555768 PMCID: PMC3605406 DOI: 10.1371/journal.pone.0059750] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [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: 09/27/2012] [Accepted: 02/18/2013] [Indexed: 12/25/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary brain tumor in adults. The poor prognosis and minimally successful treatments of these tumors indicates a need to identify new therapeutic targets. Therapy resistance of GBMs is attributed to heterogeneity of the glioblastoma due to genetic alterations and functional subpopulations. Chemokine receptors CXCR4 and CXCR7 play important roles in progression of various cancers although the specific functions of the CXCL12-CXCR4-CXCR7 axis in GBM are less characterized. In this study we examined the expression and function of CXCR4 and CXCR7 in four primary patient-derived GBM cell lines of the proliferative subclass, investigating their roles in in vitro growth, migration, sphere and tube formation. CXCR4 and CXCR7 cell surface expression was heterogeneous both between and within each cell line examined, which was not reflected by RT-PCR analysis. Variable percentages of CXCR4+CXCR7- (CXCR4 single positive), CXCR4-CXCR7+ (CXCR7 single positive), CXCR4+CXCR7+ (double positive), and CXCR4-CXCR7- (double negative) subpopulations were evident across the lines examined. A subpopulation of slow cell cycling cells was enriched in CXCR4 and CXCR7. CXCR4+, CXCR7+, and CXCR4+/CXCR7+ subpopulations were able to initiate intracranial tumors in vivo. CXCL12 stimulated in vitro cell growth, migration, sphere formation and tube formation in some lines and, depending on the response, the effects were mediated by either CXCR4 or CXCR7. Collectively, our results indicate a high level of heterogeneity in both the surface expression and functions of CXCR4 and CXCR7 in primary human GBM cells of the proliferative subclass. Should targeting of CXCR4 and CXCR7 provide clinical benefits to GBM patients, a personalized treatment approach should be considered given the differential expression and functions of these receptors in GBM.
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Affiliation(s)
- Che Liu
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Kien Pham
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Defang Luo
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Brent A. Reynolds
- Department of Neurosurgery, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Parvinder Hothi
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, Washington, United States of America
| | - Gregory Foltz
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, Washington, United States of America
| | - Jeffrey K. Harrison
- Department of Pharmacology & Therapeutics, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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17
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Hothi P, Martins TJ, Chen L, Deleyrolle L, Yoon JG, Reynolds B, Foltz G. High-throughput chemical screens identify disulfiram as an inhibitor of human glioblastoma stem cells. Oncotarget 2013; 3:1124-36. [PMID: 23165409 PMCID: PMC3717950 DOI: 10.18632/oncotarget.707] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [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] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma Multiforme (GBM) continues to have a poor patient prognosis despite optimal standard of care. Glioma stem cells (GSCs) have been implicated as the presumed cause of tumor recurrence and resistance to therapy. With this in mind, we screened a diverse chemical library of 2,000 compounds to identify therapeutic agents that inhibit GSC proliferation and therefore have the potential to extend patient survival. High-throughput screens (HTS) identified 78 compounds that repeatedly inhibited cellular proliferation, of which 47 are clinically approved for other indications and 31 are experimental drugs. Several compounds (such as digitoxin, deguelin, patulin and phenethyl caffeate) exhibited high cytotoxicity, with half maximal inhibitory concentrations (IC50) in the low nanomolar range. In particular, the FDA approved drug for the treatment of alcoholism, disulfiram (DSF), was significantly potent across multiple patient samples (IC50 of 31.1 nM). The activity of DSF was potentiated by copper (Cu), which markedly increased GSC death. DSF–Cu inhibited the chymotrypsin-like proteasomal activity in cultured GSCs, consistent with inactivation of the ubiquitin-proteasome pathway and the subsequent induction of tumor cell death. Given that DSF is a relatively non-toxic drug that can penetrate the blood-brain barrier, we suggest that DSF should be tested (as either a monotherapy or as an adjuvant) in pre-clinical models of human GBM. Data also support targeting of the ubiquitin-proteasome pathway as a therapeutic approach in the treatment of GBM.
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Affiliation(s)
- Parvinder Hothi
- The Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment, Swedish Neuroscience Institute, Seattle, WA, USA
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18
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Hay S, Johannissen LO, Hothi P, Sutcliffe MJ, Scrutton NS. Pressure Effects on Enzyme-Catalyzed Quantum Tunneling Events Arise from Protein-Specific Structural and Dynamic Changes. J Am Chem Soc 2012; 134:9749-54. [DOI: 10.1021/ja3024115] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sam Hay
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Linus O. Johannissen
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Parvinder Hothi
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Michael J. Sutcliffe
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Manchester
Interdisciplinary Biocentre, ‡Faculty of Life Sciences, and §School of Chemical Engineering and
Analytical Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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19
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Bowsher CG, Eyres LM, Gummadova JO, Hothi P, McLean KJ, Munro AW, Scrutton NS, Hanke GT, Sakakibara Y, Hase T. Identification of N-terminal regions of wheat leaf ferredoxin NADP+ oxidoreductase important for interactions with ferredoxin. Biochemistry 2011; 50:1778-87. [PMID: 21265508 DOI: 10.1021/bi1014562] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Wheat leaves contain two isoproteins of the photosynthetic ferredoxin:NADP(+) reductase (pFNRI and pFNRII). Truncated forms of both enzymes have been detected in vivo, but only pFNRII displays N-terminal length-dependent changes in activity. To investigate the impact of N-terminal truncation on interaction with ferredoxin (Fd), recombinant pFNRII proteins, differing by deletions of up to 25 amino acids, were generated. During purification of the isoproteins found in vivo, the longer forms of pFNRII bound more strongly to a Fd affinity column than did the shorter forms, pFNRII(ISKK) and pFNRII[N-2](KKQD). Further truncation of the N-termini resulted in a pFNRII protein which failed to bind to a Fd column. Similar k(cat) values (104-140 s(-1)) for cytochrome c reduction were measured for all but the most truncated pFNRII[N-5](DEGV), which had a k(cat) of 38 s(-1). Stopped-flow kinetic studies, examining the impact of truncation on electron flow between mutant pFNRII proteins and Fd, showed there was a variation in k(obs) from 76 to 265 s(-1) dependent on the pFNRII partner. To analyze the sites which contribute to Fd binding at the pFNRII N-terminal, three mutants were generated, in which a single or double lysine residue was changed to glutamine within the in vivo N-terminal truncation region. The mutations affected binding of pFNRII to the Fd column. Based on activity measurements, the double lysine residue change resulted in a pFNRII enzyme with decreased Fd affinity. The results highlight the importance of this flexible N-terminal region of the pFNRII protein in binding the Fd partner.
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Affiliation(s)
- C G Bowsher
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Manchester M13 9PT, UK.
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Hay S, Pudney CR, Hothi P, Scrutton NS. Correction of pre-steady-state KIEs for isotopic impurities and the consequences of kinetic isotope fractionation. J Phys Chem A 2009; 112:13109-15. [PMID: 18847184 DOI: 10.1021/jp805107n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We show, both experimentally and by kinetic modeling, that enzymatic single-turnover (pre-steady-state) H-transfer reactions can be significantly complicated by kinetic isotope fractionation. This fractionation results in the formation of more protiated than deuterated product and is a unique problem for pre-steady-state reactions. When observed rate constants are measured using rapid-mixing (e.g., stopped flow) methodologies, kinetic isotope fractionation can lead to a large underestimation of both the magnitude and temperature dependence of kinetic isotope effects (KIEs). This fractionation is related to the isotopic purity of the substrates used and highlights a major problem with experimental studies which measure KIEs with substrates that are not isotopically pure. As it is not always possible to prepare isotopically pure substrates, we describe two general methods for the correction, for known isotope impurities, of KIEs calculated from pre-steady-state measurements.
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Affiliation(s)
- Sam Hay
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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21
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Abstract
The reaction of PQQ (2,7,9-tricarboxypyrroloquinoline quinone)-dependent MDH (methanol dehydrogenase) from Methylophilus methylotrophus has been studied under steady-state conditions in the presence of an alternative activator [GEE (glycine ethyl ester)] and compared with similar reactions performed with ammonium (used more generally as an activator in steady-state analysis of MDH). Studies of initial velocity with methanol (protiated methanol, C1H3O1H) and [2H]methanol (deuteriated methanol, C2H3O2H) as substrate, performed with different concentrations of GEE and PES (phenazine ethosulphate), indicate competitive binding effects for substrate and PES on the stimulation and inhibition of enzyme activity by GEE. GEE is more effective at stimulating activity than ammonium at low concentrations, suggesting tighter binding of GEE to the active site. Inhibition of activity at high GEE concentration is less pronounced than at high ammonium concentration. This suggests a close spatial relationship between the stimulatory (KS) and inhibitory (KI) binding sites in that binding of GEE to the KS site sterically impairs the binding of GEE to the KI site. The binding of GEE is also competitive with the binding of PES, and GEE is more effective than ammonium in competing with PES. This competitive binding of GEE and PES lowers the effective concentration of PES at the site competent for electron transfer. Accordingly, the oxidative half-reaction, which is second-order with respect to PES concentration, is more rate-limiting in steady-state turnover with GEE than with ammonium. The smaller methanol C-1H/C-2H kinetic isotope effects observed with GEE are consistent with a larger contribution made by the oxidative half-reaction to rate limitation. Cyanide is much less effective at suppressing 'endogenous' activity in the presence of GEE than with ammonium, which is attributed to impaired binding of cyanide to the catalytic site through steric interaction with GEE bound at the KS site. The kinetic model developed previously for reactions of MDH with ammonium [Hothi, Basran, Sutcliffe and Scrutton (2003) Biochemistry 42, 3966-3978] is consistent with data obtained with GEE, although a more detailed structural interpretation is given here. Molecular-modelling studies rationalize the kinetic observations in terms of a complex binding scenario at the molecular level involving two spatially distinct inhibitory sites (KI and KI'). The KI' site caps the entrance to the active site and is interpreted as the PES binding site. The KI site is adjacent to, and, for GEE, overlaps with, the KS site, and is located in the active-site cavity close to the PQQ cofactor and the catalytic site for methanol oxidation.
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Affiliation(s)
- Parvinder Hothi
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Michael J. Sutcliffe
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
- †Department of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
| | - Nigel S. Scrutton
- *Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, U.K
- To whom correspondence should be addressed (email )
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Hothi P, Hay S, Roujeinikova A, Sutcliffe MJ, Lee M, Leys D, Cullis PM, Scrutton NS. Driving Force Analysis of Proton Tunnelling Across a Reactivity Series for an Enzyme-Substrate Complex. Chembiochem 2008; 9:2839-45. [DOI: 10.1002/cbic.200800408] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hothi P, Lee M, Cullis PM, Leys D, Scrutton NS. Catalysis by the isolated tryptophan tryptophylquinone-containing subunit of aromatic amine dehydrogenase is distinct from native enzyme and synthetic model compounds and allows further probing of TTQ mechanism. Biochemistry 2007; 47:183-94. [PMID: 18052255 DOI: 10.1021/bi701690u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Para-substituted benzylamines are poor reactivity probes for structure-reactivity studies with TTQ-dependent aromatic amine dehydrogenase (AADH). In this study, we combine kinetic isotope effects (KIEs) with structure-reactivity studies to show that para-substituted benzylamines are good reactivity probes of TTQ mechanism with the isolated TTQ-containing subunit of AADH. Contrary to the TTQ-containing subunit of methylamine dehydrogenase (MADH), which is catalytically inactive, the small subunit of AADH catalyzes the oxidative deamination of a variety of amine substrates. Observed rate constants are second order with respect to substrate and inhibitor (phenylhydrazine) concentration. Kinetic studies with para-substituted benzylamines and their dideuterated counterparts reveal KIEs (>6) larger than those observed with native AADH (KIEs approximately unity). This is attributed to formation of the benzylamine-derived iminoquinone requiring structural rearrangement of the benzyl side chain in the active site of the native enzyme. This structural reorganization requires motions from the side chains of adjacent residues (which are absent in the isolated small subunit). The position of Phealpha97 in particular is responsible for the conformational gating (and hence deflated KIEs) observed with para-substituted benzylamines in the native enzyme. Hammett plots for the small subunit exhibit a strong correlation of structure-reactivity data with electronic substituent effects for para-substituted benzylamines and phenethylamines, unlike native AADH for which a poor correlation is observed. TTQ reduction in the isolated subunit is enhanced by electron withdrawing substituents, contrary to structure-reactivity studies reported for synthetic TTQ model compounds in which rate constants are enhanced by electron donating substituents. We infer that para-substituted benzylamines are good reactivity probes of TTQ mechanism with the isolated small subunit. This is attributed to the absence of structural rearrangement prior to H-transfer that limits the rate of TTQ reduction by para-substituted benzylamines in native enzyme.
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Affiliation(s)
- Parvinder Hothi
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, UK
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24
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Roujeinikova A, Hothi P, Masgrau L, Sutcliffe MJ, Scrutton NS, Leys D. New Insights into the Reductive Half-reaction Mechanism of Aromatic Amine Dehydrogenase Revealed by Reaction with Carbinolamine Substrates. J Biol Chem 2007; 282:23766-77. [PMID: 17475620 DOI: 10.1074/jbc.m700677200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aromatic amine dehydrogenase uses a tryptophan tryptophylquinone (TTQ) cofactor to oxidatively deaminate primary aromatic amines. In the reductive half-reaction, a proton is transferred from the substrate C1 to betaAsp-128 O-2, in a reaction that proceeds by H-tunneling. Using solution studies, kinetic crystallography, and computational simulation we show that the mechanism of oxidation of aromatic carbinolamines is similar to amine oxidation, but that carbinolamine oxidation occurs at a substantially reduced rate. This has enabled us to determine for the first time the structure of the intermediate prior to the H-transfer/reduction step. The proton-betaAsp-128 O-2 distance is approximately 3.7A, in contrast to the distance of approximately 2.7A predicted for the intermediate formed with the corresponding primary amine substrate. This difference of approximately 1.0 A is due to an unexpected conformation of the substrate moiety, which is supported by molecular dynamic simulations and reflected in the approximately 10(7)-fold slower TTQ reduction rate with phenylaminoethanol compared with that with primary amines. A water molecule is observed near TTQ C-6 and is likely derived from the collapse of the preceding carbinolamine TTQ-adduct. We suggest this water molecule is involved in consecutive proton transfers following TTQ reduction, and is ultimately repositioned near the TTQ O-7 concomitant with protein rearrangement. For all carbinolamines tested, highly stable amide-TTQ adducts are formed following proton abstraction and TTQ reduction. Slow hydrolysis of the amide occurs after, rather than prior to, TTQ oxidation and leads ultimately to a carboxylic acid product.
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Affiliation(s)
- Anna Roujeinikova
- Manchester Interdisciplinary Biocenter, University of Manchester, Manchester M17DN, United Kingdom
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25
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Hothi P, Roujeinikova A, Khadra KA, Lee M, Cullis P, Leys D, Scrutton NS. Isotope Effects Reveal That Para-Substituted Benzylamines Are Poor Reactivity Probes of the Quinoprotein Mechanism for Aromatic Amine Dehydrogenase,. Biochemistry 2007; 46:9250-9. [PMID: 17636875 DOI: 10.1021/bi7007239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity correlations have been employed previously in the mechanistic interpretation of TTQ-dependent amine dehydrogenases using a series of para-substituted benzylamines. However, by combining the use of kinetic isotope effects (KIEs) and crystallographic analysis, in conjunction with structure-reactivity correlation studies, we show that para-substituted benzylamines are poor reactivity probes for TTQ-dependent aromatic amine dehydrogenase (AADH). Stopped-flow kinetic studies of the reductive half-reaction, with para-substituted benzylamines and their dideuterated counterparts, demonstrate that C-H or C-D bond breakage is not fully rate limiting (KIEs approximately unity). Contrary to previous reports, Hammett plots exhibit a poor correlation of structure-reactivity data with electronic substituent effects for para-substituted benzylamines and phenylethylamines. Crystallographic studies of enzyme-substrate complexes reveal that the observed structure-reactivity correlations are not attributed to distinct binding modes for para-substituted benzylamines in the active site, although two binding sites for p-nitrobenzylamine are identified. We identify structural rearrangements, prior to the H-transfer step, which are likely to limit the rate of TTQ reduction by benzylamines. This work emphasizes (i) the need for caution when applying structure-activity correlations to enzyme-catalyzed reactions and (ii) the added benefit of using both isotope effects and structural analysis, in conjunction with structure-reactivity relationships, to study chemical steps in enzyme reaction cycles.
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Affiliation(s)
- Parvinder Hothi
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, UK
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26
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Sutcliffe MJ, Masgrau L, Roujeinikova A, Johannissen LO, Hothi P, Basran J, Ranaghan KE, Mulholland AJ, Leys D, Scrutton NS. Hydrogen tunnelling in enzyme-catalysed H-transfer reactions: flavoprotein and quinoprotein systems. Philos Trans R Soc Lond B Biol Sci 2006; 361:1375-86. [PMID: 16873125 PMCID: PMC1647315 DOI: 10.1098/rstb.2006.1878] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is now widely accepted that enzyme-catalysed C-H bond breakage occurs by quantum mechanical tunnelling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (TST, i.e. including zero-point energy, but with no tunnelling correction) has been driven over the recent years by experimental studies of the temperature dependence of kinetic isotope effects (KIEs) for these reactions in a range of enzymes, including the tryptophan tryptophylquinone-dependent enzymes such as methylamine dehydrogenase and aromatic amine dehydrogenase, and the flavoenzymes such as morphinone reductase and pentaerythritol tetranitrate reductase, which produced observations that are also inconsistent with the simple Bell-correction model of tunnelling. However, these data-especially, the strong temperature dependence of reaction rates and the variable temperature dependence of KIEs-are consistent with other tunnelling models (termed full tunnelling models), in which protein and/or substrate fluctuations generate a configuration compatible with tunnelling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate nuclear quantum states and, when necessary, motion required to increase the probability of tunnelling in these states. Furthermore, tunnelling mechanisms in enzymes are supported by atomistic computational studies performed within the framework of modern TST, which incorporates quantum nuclear effects.
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Affiliation(s)
- Michael J Sutcliffe
- Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Science, Faculty of Life Sciences, University of Manchester, UK.
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27
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Combe JP, Basran J, Hothi P, Leys D, Rigby SEJ, Munro AW, Scrutton NS. Lys-D48 is required for charge stabilization, rapid flavin reduction, and internal electron transfer in the catalytic cycle of dihydroorotate dehydrogenase B of Lactococcus lactis. J Biol Chem 2006; 281:17977-88. [PMID: 16624811 DOI: 10.1074/jbc.m601417200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydroorotate dehydrogenase B (DHODB) catalyzes the oxidation of dihydroorotate (DHO) to orotate and is found in the pyrimidine biosynthetic pathway. The Lactococcus lactis enzyme is a dimer of heterodimers containing FMN, FAD, and a 2Fe-2S center. Lys-D48 is found in the catalytic subunit and its side-chain adopts different positions, influenced by ligand binding. Based on crystal structures of DHODB in the presence and absence of orotate, we hypothesized that Lys-D48 has a role in facilitating electron transfer in DHODB, specifically in stabilizing negative charge in the reduced FMN isoalloxazine ring. We show that mutagenesis of Lys-D48 to an alanine, arginine, glutamine, or glutamate residue (mutants K38A, K48R, K48Q, and K48E) impairs catalytic turnover substantially (approximately 50-500-fold reduction in turnover number). Stopped-flow studies demonstrate that loss of catalytic activity is attributed to poor rates of FMN reduction by substrate. Mutation also impairs electron transfer from the 2Fe-2S center to FMN. Addition of methylamine leads to partial rescue of flavin reduction activity. Nicotinamide coenzyme oxidation and reduction at the distal FAD site is unaffected by the mutations. Formation of the spin-interacting state between the FMN semiquinone-reduced 2Fe-2S centers observed in wild-type enzyme is retained in the mutant proteins, consistent with there being little perturbation of the superexchange paths that contribute to the efficiency of electron transfer between these cofactors. Our data suggest a key charge-stabilizing role for Lys-D48 during reduction of FMN by dihydroorotate, or by electron transfer from the 2Fe-2S center, and establish a common mechanism of FMN reduction in the single FMN-containing A-type and the complex multicenter B-type DHOD enzymes.
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Affiliation(s)
- Jonathan P Combe
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Jackson's Mill, Sackville Street, Manchester M60 1QD, United Kingdom
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28
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Masgrau L, Roujeinikova A, Johannissen LO, Hothi P, Basran J, Ranaghan KE, Mulholland AJ, Sutcliffe MJ, Scrutton NS, Leys D. Atomic Description of an Enzyme Reaction Dominated by Proton Tunneling. Science 2006; 312:237-41. [PMID: 16614214 DOI: 10.1126/science.1126002] [Citation(s) in RCA: 265] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp(128)beta in a reaction dominated by tunneling over approximately 0.6 angstroms. The role of long-range coupled motions in promoting tunneling is controversial. We show that, in this enzyme system, tunneling is promoted by a short-range motion modulating proton-acceptor distance and no long-range coupled motion is required.
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Affiliation(s)
- Laura Masgrau
- Manchester Interdisciplinary Biocentre, University of Manchester, Jackson's Mill, Post Office Box 88, Manchester M60 1QD, UK
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29
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Abstract
The heterologous expression of tryptophan trytophylquinone (TTQ)-dependent aromatic amine dehydrogenase (AADH) has been achieved in Paracoccus denitrificans. The aauBEDA genes and orf-2 from the aromatic amine utilization (aau) gene cluster of Alcaligenes faecalis were placed under the regulatory control of the mauF promoter from P. denitrificans and introduced into P. denitrificans using a broad-host-range vector. The physical, spectroscopic and kinetic properties of the recombinant AADH were indistinguishable from those of the native enzyme isolated from A. faecalis. TTQ biogenesis in recombinant AADH is functional despite the lack of analogues in the cloned aau gene cluster for mauF, mauG, mauL, mauM and mauN that are found in the methylamine utilization (mau) gene cluster of a number of methylotrophic organisms. Steady-state reaction profiles for recombinant AADH as a function of substrate concentration differed between 'fast' (tryptamine) and 'slow' (benzylamine) substrates, owing to a lack of inhibition by benzylamine at high substrate concentrations. A deflated and temperature-dependent kinetic isotope effect indicated that C-H/C-D bond breakage is only partially rate-limiting in steady-state reactions with benzylamine. Stopped-flow studies of the reductive half-reaction of recombinant AADH with benzylamine demonstrated that the KIE is elevated over the value observed in steady-state turnover and is independent of temperature, consistent with (a) previously reported studies with native AADH and (b) breakage of the substrate C-H bond by quantum mechanical tunnelling. The limiting rate constant (k(lim)) for TTQ reduction is controlled by a single ionization with pK(a) value of 6.0, with maximum activity realized in the alkaline region. Two kinetically influential ionizations were identified in plots of k(lim)/K(d) of pK(a) values 7.1 and 9.3, again with the maximum value realized in the alkaline region. The potential origin of these kinetically influential ionizations is discussed.
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Affiliation(s)
- Parvinder Hothi
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, UK
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30
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Abstract
It is now widely accepted that substrate C-H bond breakage by quinoprotein enzymes occurs by quantum mechanical tunneling. This paradigm shift in the conceptual framework for these reactions away from semi-classical transition state theory (i.e., including zero-point energy but with no tunneling correction) has been driven over recent years by experimental studies of the temperature dependence of kinetic isotope effects for these reactions in the TTQ-dependent enzymes methylamine dehydrogenase and aromatic amine dehydrogenase, which produced observations also inconsistent with the simple Bell correction model of tunneling. However, these data-specifically, the strong temperature dependence of reaction rates and the variable temperature dependence of kinetic isotope effects-are consistent with other tunneling models (denoted full tunneling models) in which protein and/or substrate fluctuations generate a configuration compatible with tunneling. These models accommodate substrate/protein (environment) fluctuations required to attain a configuration with degenerate quantum states and, when necessary, motion required to increase the probability of tunneling in these states. Furthermore, tunneling mechanisms in quinoproteins are supported by computational studies employing variational transition state theory with multidimensional tunneling corrections; these studies are also discussed in this review. Potential pitfalls in analyzing the temperature dependence of kinetic isotope effects as probes of tunneling are also discussed with reference to PQQ-dependent methanol dehydrogenase.
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Affiliation(s)
- Laura Masgrau
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, UK
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Hothi P, Basran J, Sutcliffe MJ, Scrutton NS. Effects of multiple ligand binding on kinetic isotope effects in PQQ-dependent methanol dehydrogenase. Biochemistry 2003; 42:3966-78. [PMID: 12667088 DOI: 10.1021/bi027282v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of PQQ-dependent methanol dehydrogenase (MDH) from Methylophilus methylotrophus has been studied by steady-state and stopped-flow kinetic methods, with particular reference to multiple ligand binding and the kinetic isotope effect (KIE) for PQQ reduction. Phenazine ethosulfate (PES; an artificial electron acceptor) and cyanide (a suppressant of endogenous activity), but not ammonium (an activator of MDH), compete for binding at the catalytic methanol-binding site. Cyanide does not activate turnover in M. methylotrophus MDH, as reported previously for the Paracoccus denitrificans enzyme. Activity is dependent on activation by ammonium but is inhibited at high ammonium concentrations. PES and methanol also influence the stimulatory and inhibitory effects of ammonium through competitive binding. Reaction profiles as a function of ammonium and PES concentration differ between methanol and deuterated methanol, owing to force constant effects on the binding of methanol to the stimulatory and inhibitory ammonium binding sites. Differential binding gives rise to unusual KIEs for PQQ reduction as a function of ammonium and PES concentration. The observed KIEs at different ligand concentrations are independent of temperature, consistent with their origin in differential binding affinities of protiated and deuterated substrate at the ammonium binding sites. Stopped-flow studies indicate that enzyme oxidation is not rate-limiting at low ammonium concentrations (<4 mM) during steady-state turnover. At higher ammonium concentrations (>20 mM), the low effective concentration of PES in the active site owing to the competitive binding of ammonium lowers the second-order rate constant for enzyme oxidation, and the oxidative half-reaction becomes more rate limiting. A sequential stopped-flow method is reported that has enabled, for the first time, a detailed study of the reductive half-reaction of MDH and comparison with steady-state data. The limiting rate of PQQ reduction (0.48 s(-1)) is less than the steady-state turnover number, and the observed KIE in stopped-flow studies is unity. Although catalytically active, we propose reduction of the oxidized enzyme generated in stopped-flow analyses is gated by conformational change or ligand exchange. Slow recovery from this trapped state on mixing with methanol accounts for the slow reduction of PQQ and a KIE of 1. This study emphasizes the need for caution in using inflated KIEs, and the temperature dependence of KIEs, as a probe for hydrogen tunneling.
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Affiliation(s)
- Parvinder Hothi
- Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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