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Xing J. Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology. Phys Biol 2022; 19:10.1088/1478-3975/ac8c16. [PMID: 35998617 PMCID: PMC9585661 DOI: 10.1088/1478-3975/ac8c16] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/23/2022] [Indexed: 11/11/2022]
Abstract
Cells with the same genome can exist in different phenotypes and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming for induced pluripotent stem cells and transdifferentiation, cancer metastasis and fibrosis progression. The regulation and dynamics of cell phenotypic conversion is a fundamental problem in biology, and has a long history of being studied within the formalism of dynamical systems. A main challenge for mechanism-driven modeling studies is acquiring sufficient amount of quantitative information for constraining model parameters. Advances in quantitative experimental approaches, especially high throughput single-cell techniques, have accelerated the emergence of a new direction for reconstructing the governing dynamical equations of a cellular system from quantitative single-cell data, beyond the dominant statistical approaches. Here I review a selected number of recent studies using live- and fixed-cell data and provide my perspective on future development.
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Affiliation(s)
- Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15232, USA
- UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
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2
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Xing J. Reconstructing data-driven governing equations for cell phenotypic transitions: integration of data science and systems biology. Phys Biol 2022. [PMID: 35998617 DOI: 10.48550/arxiv.2203.14964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cells with the same genome can exist in different phenotypes and can change between distinct phenotypes when subject to specific stimuli and microenvironments. Some examples include cell differentiation during development, reprogramming for induced pluripotent stem cells and transdifferentiation, cancer metastasis and fibrosis progression. The regulation and dynamics of cell phenotypic conversion is a fundamental problem in biology, and has a long history of being studied within the formalism of dynamical systems. A main challenge for mechanism-driven modeling studies is acquiring sufficient amount of quantitative information for constraining model parameters. Advances in quantitative experimental approaches, especially high throughput single-cell techniques, have accelerated the emergence of a new direction for reconstructing the governing dynamical equations of a cellular system from quantitative single-cell data, beyond the dominant statistical approaches. Here I review a selected number of recent studies using live- and fixed-cell data and provide my perspective on future development.
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Affiliation(s)
- Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15232, United States of America.,Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15232, United States of America.,UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, United States of America
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3
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Exploiting Cancer's Tactics to Make Cancer a Manageable Chronic Disease. Cancers (Basel) 2020; 12:cancers12061649. [PMID: 32580319 PMCID: PMC7352192 DOI: 10.3390/cancers12061649] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
The history of modern oncology started around eighty years ago with the introduction of cytotoxic agents such as nitrogen mustard into the clinic, followed by multi-agent chemotherapy protocols. Early success in radiation therapy in Hodgkin lymphoma gave birth to the introduction of radiation therapy into different cancer treatment protocols. Along with better understanding of cancer biology, we developed drugs targeting cancer-related cellular and genetic aberrancies. Discovery of the crucial role of vasculature in maintenance, survival, and growth of a tumor opened the way to the development of anti-angiogenic agents. A better understanding of T-cell regulatory pathways advanced immunotherapy. Awareness of stem-like cancer cells and their role in cancer metastasis and local recurrence led to the development of drugs targeting them. At the same time, sequential and rapidly accelerating advances in imaging and surgical technology have markedly increased our ability to safely remove ≥90% of tumor cells. While we have advanced our ability to kill cells from multiple directions, we have still failed to stop most types of cancer from recurring. Here we analyze the tactics employed in cancer evolution; namely, chromosomal instability (CIN), intra-tumoral heterogeneity (ITH), and cancer-specific metabolism. These tactics govern the resistance to current cancer therapeutics. It is time to focus on maximally delaying the time to recurrence, with drugs that target these fundamental tactics of cancer evolution. Understanding the control of CIN and the optimal state of ITH as the most important tactics in cancer evolution could facilitate the development of improved cancer therapeutic strategies designed to transform cancer into a manageable chronic disease.
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Roberts CM, Cardenas C, Tedja R. The Role of Intra-Tumoral Heterogeneity and Its Clinical Relevance in Epithelial Ovarian Cancer Recurrence and Metastasis. Cancers (Basel) 2019; 11:cancers11081083. [PMID: 31366178 PMCID: PMC6721439 DOI: 10.3390/cancers11081083] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/22/2019] [Accepted: 07/27/2019] [Indexed: 12/14/2022] Open
Abstract
Epithelial ovarian cancer is the deadliest gynecologic cancer, due in large part to recurrent tumors. Recurrences tend to have metastasized, mainly in the peritoneal cavity and developed resistance to the first line chemotherapy. Key to the progression and ultimate lethality of ovarian cancer is the existence of extensive intra-tumoral heterogeneity (ITH). In this review, we describe the genetic and epigenetic changes that have been reported to give rise to different cell populations in ovarian cancer. We also describe at length the contributions made to heterogeneity by both linear and parallel models of clonal evolution and the existence of cancer stem cells. We dissect the key biological signals from the tumor microenvironment, both directly from other cell types in the vicinity and soluble or circulating factors. Finally, we discuss the impact of tumor heterogeneity on the choice of therapeutic approaches in the clinic. Variability in ovarian tumors remains a major barrier to effective therapy, but by leveraging future research into tumor heterogeneity, we may be able to overcome this barrier and provide more effective, personalized therapy to patients.
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Affiliation(s)
- Cai M Roberts
- Obstetrics, Gynecology and Reproductive Sciences Department, Yale School of Medicine, New Haven, CT 06520, USA
| | - Carlos Cardenas
- Obstetrics, Gynecology and Reproductive Sciences Department, Yale School of Medicine, New Haven, CT 06520, USA
| | - Roslyn Tedja
- Obstetrics, Gynecology and Reproductive Sciences Department, Yale School of Medicine, New Haven, CT 06520, USA.
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Jusino S, Fernández-Padín FM, Saavedra HI. Centrosome aberrations and chromosome instability contribute to tumorigenesis and intra-tumor heterogeneity. ACTA ACUST UNITED AC 2018; 4. [PMID: 30381801 PMCID: PMC6205736 DOI: 10.20517/2394-4722.2018.24] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Centrosomes serve as the major microtubule organizing centers in cells and thereby contribute to cell shape, polarity, and motility. Also, centrosomes ensure equal chromosome segregation during mitosis. Centrosome aberrations arise when the centrosome cycle is deregulated, or as a result of cytokinesis failure. A long-standing postulate is that centrosome aberrations are involved in the initiation and progression of cancer. However, this notion has been a subject of controversy because until recently the relationship has been correlative. Recently, it was shown that numerical or structural centrosome aberrations can initiate tumors in certain tissues in mice, as well as invasion. Particularly, we will focus on centrosome amplification and chromosome instability as drivers of intra-tumor heterogeneity and their consequences in cancer. We will also discuss briefly the controversies surrounding this theory to highlight the fact that the role of both centrosome amplification and chromosome instability in cancer is highly context-dependent. Further, we will discuss single-cell sequencing as a novel technique to understand intra-tumor heterogeneity and some therapeutic approaches to target chromosome instability.
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Affiliation(s)
- Shirley Jusino
- Basic Sciences Department, Division of Pharmacology and Toxicology, Ponce Health Sciences University, Ponce Research Institute, Ponce, PR 00732, USA
| | - Fabiola M Fernández-Padín
- Basic Sciences Department, Division of Pharmacology and Toxicology, Ponce Health Sciences University, Ponce Research Institute, Ponce, PR 00732, USA
| | - Harold I Saavedra
- Basic Sciences Department, Division of Pharmacology and Toxicology, Ponce Health Sciences University, Ponce Research Institute, Ponce, PR 00732, USA
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Trinh AL, Chen H, Chen Y, Hu Y, Li Z, Siegel ER, Linskey ME, Wang PH, Digman MA, Zhou YH. Tracking Functional Tumor Cell Subpopulations of Malignant Glioma by Phasor Fluorescence Lifetime Imaging Microscopy of NADH. Cancers (Basel) 2017; 9:cancers9120168. [PMID: 29211022 PMCID: PMC5742816 DOI: 10.3390/cancers9120168] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/27/2017] [Accepted: 12/01/2017] [Indexed: 12/29/2022] Open
Abstract
Intra-tumoral heterogeneity is associated with therapeutic resistance of cancer and there exists a need to non-invasively identify functional tumor subpopulations responsible for tumor recurrence. Reduced nicotinamide adenine dinucleotide (NADH) is a metabolic coenzyme essential in cellular respiration. Fluorescence lifetime imaging microscopy (FLIM) of NADH has been demonstrated to be a powerful label-free indicator for inferring metabolic states of living cells. Using FLIM, we identified a significant shift towards longer NADH fluorescence lifetimes, suggesting an increase in the fraction of protein-bound NADH, in the invasive stem-like tumor-initiating cell (STIC) subpopulation relative to the tumor mass-forming cell (TMC) subpopulation of malignant gliomas. By applying our previously studied model to transition glioma from a majority of STIC to a majority of TMC in serum-adherent culture conditions following serial passages, we compared changes in NADH states, cellular respirations (oxidative phosphorylation and glycolysis), EGFR expression, and cell-growth speed over passages. We identified a significant positive correlation between free-NADH fraction and cell growth, which was related to an increase of TMC fraction. In comparison, the increase of EGFR and cellular respirations preceded all these changes. In conclusion, FLIM of NADH provides a non-invasive method to monitor the dynamics of tumor heterogeneity before and after treatment.
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Affiliation(s)
- Andrew L Trinh
- Laboratory for Fluorescence Dynamics and Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.
| | - Hongtao Chen
- Laboratory for Fluorescence Dynamics and Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.
| | - Yumay Chen
- UC Irvine Diabetes Center and Department of Medicine, University of California, Irvine, CA 92697, USA.
| | - Yuanjie Hu
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California, Irvine, CA 92697, USA.
| | - Zhenzhi Li
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California, Irvine, CA 92697, USA.
| | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Mark E Linskey
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California, Irvine, CA 92697, USA.
| | - Ping H Wang
- UC Irvine Diabetes Center and Department of Medicine, University of California, Irvine, CA 92697, USA.
| | - Michelle A Digman
- Laboratory for Fluorescence Dynamics and Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA.
| | - Yi-Hong Zhou
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California, Irvine, CA 92697, USA.
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Li Y, Hu Y, Liu C, Wang Q, Han X, Han Y, Xie XS, Chen XH, Li X, Siegel ER, Afrasiabi K, Linskey ME, Zhou YX, Zhou YH. Human fibulin-3 protein variant expresses anti-cancer effects in the malignant glioma extracellular compartment in intracranial xenograft models. Oncotarget 2017; 8:106311-106323. [PMID: 29290950 PMCID: PMC5739735 DOI: 10.18632/oncotarget.22344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/25/2017] [Indexed: 01/01/2023] Open
Abstract
Background Decades of cytotoxic and more recently immunotherapy treatments for malignant glioma have had limited success due to dynamic intra-tumoral heterogeneity. The dynamic interplay of cancer cell subpopulations has been found to be under the control of proteins in the cancer microenvironment. EGF-containing fibulin-like extracellular matrix protein (EFEMP1) (also fibulin-3) has the multiple functions of suppressing cancer growth and angiogenesis, while promoting cancer cell invasion. EFEMP1-derived tumor suppressor protein (ETSP) retains EFEMP1’s anti-growth and anti-angiogenic functions while actually inhibiting cancer cell invasion. Methods In this study, we examined the therapeutic effect on glioblastoma multiforme (GBM) of an in vitro synthesized protein, ZR30, which is based on the sequence of ETSP, excluding the signaling peptide. Results ZR30 showed the same effects as ETSP in blocking EGFR/NOTCH/AKT signaling pathways, when applied to cultures of multiple GBM cell lines and primary cultures. ZR30’s inhibition of MMP2 activation was shown not only for GBM cells, but also for other types of cancer cells having overexpression of MMP2. A significant improvement in survival of mice with orthotopic human GBM xenografts was observed after a single, intra-tumoral injection of ZR30. Using a model mimicking the intra-tumoral heterogeneity of GBM with cell subpopulations carrying different invasive and proliferative phenotypes, we demonstrated an equal and simultaneous tumor suppressive effect of ZR30 on both tumor cell subpopulations, with suppression of FOXM1 and activation of SEMA3B expressions in the xenografts. Conclusion Overall, the data support a complementary pleiotrophic therapeutic effect of ZR30 acting in the extracellular compartment of GBM.
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Affiliation(s)
- Yanyan Li
- Neurosurgery & Brain and Nerve Research Laboratory
| | - Yuan Hu
- Neurosurgery & Brain and Nerve Research Laboratory
| | - Chuanjin Liu
- Neurosurgery & Brain and Nerve Research Laboratory
| | - Qingyue Wang
- Neurosurgery & Brain and Nerve Research Laboratory
| | - Xiaoxiao Han
- Neurosurgery & Brain and Nerve Research Laboratory
| | - Yong Han
- Neurosurgery & Brain and Nerve Research Laboratory
| | - Xue-Shun Xie
- Neurosurgery & Brain and Nerve Research Laboratory
| | - Xiong-Hui Chen
- Department of Emergency Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiang Li
- Neuroepigenetic Reseach Lab, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
| | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kambiz Afrasiabi
- Brain Tumor Research Laboratory, Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Mark E Linskey
- Brain Tumor Research Laboratory, Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - You-Xin Zhou
- Neurosurgery & Brain and Nerve Research Laboratory
| | - Yi-Hong Zhou
- Neurosurgery & Brain and Nerve Research Laboratory.,Brain Tumor Research Laboratory, Department of Surgery, University of California Irvine, Irvine, CA, USA.,Ziren Research, Irvine, CA, USA
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8
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Zhou YH, Chen Y, Hu Y, Yu L, Tran K, Giedzinski E, Ru N, Gau A, Pan F, Qiao J, Atkin N, Ly KC, Lee N, Siegel ER, Linskey ME, Wang P, Limoli C. The role of EGFR double minutes in modulating the response of malignant gliomas to radiotherapy. Oncotarget 2017; 8:80853-80868. [PMID: 29113349 PMCID: PMC5655244 DOI: 10.18632/oncotarget.20714] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/04/2017] [Indexed: 01/05/2023] Open
Abstract
EGFR amplification in cells having double minute chromosomes (DM) is commonly found in glioblastoma multiforme (GBM); however, how much it contributes to the current failure to treat GBM successfully is unknown. We studied two syngeneic primary cultures derived from a GBM with and without cells carrying DM, for their differential molecular and metabolic profiles, in vivo growth patterns, and responses to irradiation (IR). Each cell line has a distinct molecular profile consistent with an invasive “go” (with DM) or angiogenic “grow” phenotype (without DM) demonstrated in vitro and in intracranial xenograft models. Cells with DM were relatively radio-resistant and used higher glycolytic respiration and lower oxidative phosphorylation in comparison to cells without them. The DM-containing cell was able to restore tumor heterogeneity by mis-segregation of the DM-chromosomes, giving rise to cell subpopulations without them. As a response to IR, DM-containing cells switched their respiration from glycolic metabolism to oxidative phosphorylation and shifted molecular profiles towards that of cells without DM. Irradiated cells with DM showed the capacity to alter their extracellular microenvironment to not only promote invasiveness of the surrounding cells, regardless of DM status, but also to create a pro-angiogenic tumor microenvironment. IR of cells without DM was found primarily to increase extracellular MMP2 activity. Overall, our data suggest that the DM-containing cells of GBM are responsible for tumor recurrence due to their high invasiveness and radio-resistance and the mis-segregation of their DM chromosomes, to give rise to fast-growing cells lacking DM chromosomes.
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Affiliation(s)
- Yi-Hong Zhou
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Yumay Chen
- UC Irvine Diabetes Center and Department of Medicine, University of California Irvine, Irvine, CA, USA
| | - Yuanjie Hu
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Liping Yu
- Department of Radiation Oncology, University of California Irvine, Irvine, CA, USA
| | - Katherine Tran
- Department of Radiation Oncology, University of California Irvine, Irvine, CA, USA
| | - Erich Giedzinski
- Department of Radiation Oncology, University of California Irvine, Irvine, CA, USA
| | - Ning Ru
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Alex Gau
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Francine Pan
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Jiao Qiao
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Naomi Atkin
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Khang Chi Ly
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Nathan Lee
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Eric R Siegel
- Departments of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mark E Linskey
- UC Irvine Brain Tumor Laboratory and Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Ping Wang
- UC Irvine Diabetes Center and Department of Medicine, University of California Irvine, Irvine, CA, USA
| | - Charles Limoli
- Department of Radiation Oncology, University of California Irvine, Irvine, CA, USA
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Hu Y, Ke C, Ru N, Chen Y, Yu L, Siegel ER, Linskey ME, Wang P, Zhou YH. Cell context-dependent dual effects of EFEMP1 stabilizes subpopulation equilibrium in responding to changes of in vivo growth environment. Oncotarget 2016; 6:30762-72. [PMID: 26307682 PMCID: PMC4741566 DOI: 10.18632/oncotarget.5220] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/08/2015] [Indexed: 12/27/2022] Open
Abstract
Conflicting functions of EFEMP1 in cancer have been reported. Using two syngeneic glioma cell lines (U251 and U251-NS) carrying two different principal cell subpopulations that express high or low EGFR, and that are able to interconvert via mis-segregation of chromosome 7 (Chr7), we studied EFEMP1's cell-context-dependent functions in regulating subpopulation equilibrium, here defined by the percentage of cells carrying different copies of Chr7. We found that EFEMP1 attenuated levels of EGFR and cellular respiration in high-EGFR-expressing cells, but increased levels of NOTCH1, MMP2, cell invasiveness, and both oxidative phosphorylation and glycolytic respiration in low-EGFR-expressing cells. Consistently, EFEMP1 suppressed intracranial xenograft formation in U251 and promoted its formation in U251-NS. Interestingly, subpopulation equilibria in xenografts of U251-NS without EFEMP1 overexpression were responsive to inoculum size (1, 10 and 100 thousand cells), which may change the tumor-onset environment. It was not observed in xenografts of U251-NS with EFEMP1 overexpression. The anti-EGFR function of EFEMP1 suppressed acceleration of growth of U251-NS, but not the subpopulation equilibrium, when serially passed under a different (serum-containing adherent) culture condition. Overall, the data suggest that the orthotopic environment of the brain tumor supports EFEMP1 in carrying out both its anti-EGFR and pro-invasive/cancer stem cell-transforming functions in the two glioma cell subpopulations during formation of a single tumor, where EFEMP1 stabilizes the subpopulation equilibrium in response to alterations of the growth environment. This finding implies that EFEMP1 may restrain cancer plasticity in coping with ever-changing tumor microenvironments and/or therapeutic-intervention stresses.
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Affiliation(s)
- Yuanjie Hu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Chao Ke
- Department of Surgery, University of California Irvine, Irvine, CA, USA.,State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Ning Ru
- Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Yumay Chen
- UC Irvine Diabetes Center and Department of Medicine, University of California Irvine, Irvine, CA, USA
| | | | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mark E Linskey
- Department of Surgery, University of California Irvine, Irvine, CA, USA
| | - Ping Wang
- UC Irvine Diabetes Center and Department of Medicine, University of California Irvine, Irvine, CA, USA
| | - Yi-Hong Zhou
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA.,Department of Surgery, University of California Irvine, Irvine, CA, USA
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10
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Baulch JE, Geidzinski E, Tran KK, Yu L, Zhou YH, Limoli CL. Irradiation of primary human gliomas triggers dynamic and aggressive survival responses involving microvesicle signaling. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:405-415. [PMID: 26602180 DOI: 10.1002/em.21988] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/04/2015] [Indexed: 06/05/2023]
Abstract
Malignant gliomas are heterogeneous populations of dynamically interacting cells. Genomic and transcriptional changes define this cellular hierarchy and allow certain tumor cells to co-opt metabolic machinery and adopt gene expression profiles that promote cellular reprogramming. Resultant expansion of privileged subpopulations can then rapidly adapt to microenvironmental stress that ultimately influence tumor response to therapeutic intervention. In this study, primary gliomas were subjected to acute or chronic irradiation and analyzed for changes in survival parameters, oxidative stress, gene expression, and cell invasion before and after treatment with secreted microvesicles isolated from irradiated and nonirradiated glioma cells. We found that primary gliomas exposed to ionizing radiation undergo metabolic changes that increase oxidative stress, alter gene expression, and affect the contents of and response to cellular secreted microvesicles. Radiation-induced changes were exacerbated under chronic as compared to acute irradiation paradigms and promoted cellular reprogramming through enhanced expression of key transcription factors and regulators involved in differentiation and pluripotency (SOX2, POU3F2, SALL2, OLIG2, NANOG, POU5F1v1, MSI1). Irradiation also affected changes in paracrine signaling mediated by cellular secreted microvesicles that significantly altered target cell phenotype. Primary gliomas treated with microvesicles exhibited increased radioresistance and treatment with microvesicles from chronically irradiated gliomas promoted invasion via induction of increased matrix metalloproteinase II activity. Together, our data describe a complex radiation response of primary glioma cells involving metabolic and transcriptional changes that alter radiation sensitivity and induce invasive behavior. These important changes can contribute to tumor growth and recurrence, and confound interventions designed to forestall disease progression. Environ. Mol. Mutagen. 57:405-415, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Janet E Baulch
- Department of Radiation Oncology, University of California, Irvine, California
| | - Erich Geidzinski
- Department of Radiation Oncology, University of California, Irvine, California
| | - Katherine K Tran
- Department of Radiation Oncology, University of California, Irvine, California
| | - Liping Yu
- Department of Radiation Oncology, University of California, Irvine, California
| | - Yi-Hong Zhou
- Department of Medicine, University of California, Irvine, California
| | - Charles L Limoli
- Department of Radiation Oncology, University of California, Irvine, California
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11
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Zhou YH, Hu Y, Yu L, Ke C, Vo C, Hsu H, Li Z, Di Donato AT, Chaturbedi A, Hwang JW, Siegel ER, Linskey ME. Weaponizing human EGF-containing fibulin-like extracellular matrix protein 1 (EFEMP1) for 21 st century cancer therapeutics. Oncoscience 2016; 3:208-219. [PMID: 27713911 PMCID: PMC5043071 DOI: 10.18632/oncoscience.306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/13/2016] [Indexed: 12/26/2022] Open
Abstract
De-regulated EFEMP1 gene expression in solid tumors has been widely reported with conflicting roles. We dissected EFEMP1 to identify domains responsible for its cell context-dependent dual functions, with the goal being to construct an EFEMP1-derived tumor-suppressor protein (ETSP) that lacked tumor-promoting function. Exon/intron boundaries of EFEMP1 were used as boundaries of functional modules in constructing EFEMP1 variants, with removal of various module(s), and/or mutating an amino acid residue to convert a weak integrin binding-site into a strong one. A series of in vitro assays on cancerous features, and subcutaneous and intracranial xenograft-formation assays, were carried out for effects from overexpression of wild-type and variant forms of EFEMP1 in two glioma subpopulations characterized as tumor mass-forming cells (TMCs) or stem-like tumor initiating cells (STICs), where EFEMP1 showed cellcontext- dependent dual functions. One of the EFEMP1 variants was identified as the sought-after ETSP, which had a stronger tumor-suppression function in TMCs by targeting EGFR and angiogenesis, and a new tumor-suppression function in STICs by targeting NOTCH signaling and MMP2-mediated cell invasion. Therefore, ETSP may form the basis for further important research to develop a novel cancer therapy to treat many types of cancer by its tumor suppressor effect in the extracellular matrix compartment.
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Affiliation(s)
- Yi-Hong Zhou
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
| | - Yuanjie Hu
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
| | - Liping Yu
- Real-Time PCR, Ziren Research LLC, Irvine, CA, USA
| | - Chao Ke
- Neurosurgery, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Christopher Vo
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
| | - Hao Hsu
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
| | - Zhenzhi Li
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
| | - Anne T Di Donato
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
| | - Abhishek Chaturbedi
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
| | - Ji Won Hwang
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
| | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mark E Linskey
- Neurosurgery, Brain Tumor Research Laboratory, University of California Irvine, Irvine, CA, USA
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Chappell G, Silva GO, Uehara T, Pogribny IP, Rusyn I. Characterization of copy number alterations in a mouse model of fibrosis-associated hepatocellular carcinoma reveals concordance with human disease. Cancer Med 2016; 5:574-85. [PMID: 26778414 PMCID: PMC4799957 DOI: 10.1002/cam4.606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/22/2015] [Accepted: 11/16/2015] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a prevalent human cancer with rising incidence worldwide. Human HCC is frequently associated with chronic liver inflammation and cirrhosis, pathophysiological processes that are a consequence of chronic viral infection, disturbances in metabolism, or exposure to chemical toxicants. To better characterize the pathogenesis of HCC, we used a human disease‐relevant mouse model of fibrosis‐associated hepatocarcinogenesis. In this model, marked liver tumor response caused by the promutagenic chemical N‐nitrosodiethylamine in the presence of liver fibrosis was associated with epigenetic events indicative of genomic instability. Therefore, we hypothesized that DNA copy number alterations (CNAs), a feature of genomic instability and a common characteristic of cancer, are concordant between human HCC and mouse models of fibrosis‐associated hepatocarcinogenesis. We evaluated DNA CNAs and changes in gene expression in the mouse liver (normal, tumor, and nontumor fibrotic tissues). Additionally, we compared our findings to DNA CNAs in human HCC cases (tumor and nontumor cirrhotic/fibrotic tissues) using publicly available data from The Cancer Genome Atlas (TCGA). We observed that while fibrotic liver tissue is largely devoid of DNA CNAs, highly frequently occurring DNA CNAs are found in mouse tumors, which is indicative of a profound increase in chromosomal instability in HCC. The cross‐species gene‐level comparison of CNAs identified shared regions of CNAs between human fibrosis‐ and cirrhosis‐associated liver tumors and mouse fibrosis‐associated HCC. Our results suggest that CNAs most commonly arise in neoplastic tissue rather than in fibrotic or cirrhotic liver, and demonstrate the utility of this mouse model in replicating the molecular features of human HCC.
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Affiliation(s)
- Grace Chappell
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, 77843.,Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Grace O Silva
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, 27599.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina, 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Takeki Uehara
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Igor P Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, 72079
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, 77843
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Rahmatpanah FB, Jia Z, Chen X, Char JE, Men B, Franke AC, Jones FE, McClelland M, Mercola D. A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors. Oncotarget 2015; 6:1286-301. [PMID: 25428913 PMCID: PMC4359233 DOI: 10.18632/oncotarget.2676] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/04/2014] [Indexed: 01/06/2023] Open
Abstract
HER2-positive breast cancer accounts for 25% of all cases and has a poor prognosis. Although progress has been made in understanding signal transduction, little is known of how HER2 achieves gene regulation. We performed whole genome expression analysis on a HER2+ and HER2− breast cancer cell lines and compared these results to expression in 812 primary tumors stratified by their HER2 expression level. Chip-on-chip with anti-RNA polymerase II was compared among breast cancer cell lines to identify genes that are potentially activated by HER2. The expression levels of these HER2-dependent POL II binding genes were determined for the 812 HER2+/− breast cancer tissues. Genes differentially expressed between HER2+/− cell lines were generally regulated in the same direction as in breast cancer tissues. We identified genes that had POLII binding in HER2+ cell lines, but without significant gene expression. Of 737 such genes “poised” for expression in cell lines, 113 genes were significantly differentially expressed in breast tumors in a HER2-dependent manner. Pathway analysis of these 113 genes revealed that a large group of genes were associated with stem cell and progenitor cell control as indicated by networks centered on NANOG, SOX2, OCT3/4. HER2 directs POL II binding to a large number of genes in breast cancer cells. A “poised” class of genes in HER2+ cell lines with POLII binding and low RNA expression but is differentially expressed in primary tumors, strongly suggests a role of the microenvironment and further suggests a role for stem cells proliferation in HER2-regulated breast cancer tissue.
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Affiliation(s)
- Farah B Rahmatpanah
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Zhenyu Jia
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.,Department of Statistics, University of Akron, Akron, Ohio, USA.,Department of Family and Community Medicine, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Xin Chen
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Jessica E Char
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Bozhao Men
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Anna-Clara Franke
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
| | - Frank E Jones
- Department of Cell and Molecular Biology, Tulane University, New Orleans, Louisiana, USA
| | - Michael McClelland
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA.,Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, USA
| | - Dan Mercola
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
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14
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Ke C, Tran K, Chen Y, Di Donato AT, Yu L, Hu Y, Linskey ME, Wang PH, Limoli CL, Zhou YH. Linking differential radiation responses to glioma heterogeneity. Oncotarget 2015; 5:1657-65. [PMID: 24722169 PMCID: PMC4039238 DOI: 10.18632/oncotarget.1823] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The phenotypic and genetic diversity that define tumor subpopulations within high-grade glioma can lead to therapeutic resistance and tumor recurrence. Given that cranial irradiation is a frontline treatment for malignant glioma, understanding how irradiation selectively effects different cellular subpopulations within these heterogeneous cancers should help identify interventions targeted to better combat this deadly disease. To analyze the radiation response of distinct glioma subpopulations, 2 glioma cells lines (U251, A172) were cultured under conditions that promoted either adherence or non-adherent spheroids. Past work has demonstrated that subpopulations derived from defined culture conditions exhibit differences in karyotype, proliferation, gene expression and tumorigenicity. Spheroid cultures from each of the glioma cell lines were found to be more radiosensitive, which was consistent with higher levels of oxidative stress and lower levels of both oxidative phosphorylation and glycolytic metabolism 1 week following irradiation. In contrast, radioresistant non-spheroid parental cultures showed increased glycolytic activity in response to irradiation, while oxidative phosphorylation was affected to a lesser extent. Overall these data suggest that prolonged radiation-induced oxidative stress can compromise the metabolic state of certain glioma subpopulations thereby altering their sensitivity to an important therapeutic intervention used routinely for the control of glioma.
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Affiliation(s)
- Chao Ke
- Neurological Surgery, University of California, Irvine, CA, USA
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15
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Ge L, Hoa NT, Wilson Z, Arismendi-Morillo G, Kong XT, Tajhya RB, Beeton C, Jadus MR. Big Potassium (BK) ion channels in biology, disease and possible targets for cancer immunotherapy. Int Immunopharmacol 2014; 22:427-43. [PMID: 25027630 PMCID: PMC5472047 DOI: 10.1016/j.intimp.2014.06.040] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/27/2014] [Accepted: 06/30/2014] [Indexed: 11/18/2022]
Abstract
The Big Potassium (BK) ion channel is commonly known by a variety of names (Maxi-K, KCNMA1, slo, stretch-activated potassium channel, KCa1.1). Each name reflects a different physical property displayed by this single ion channel. This transmembrane channel is found on nearly every cell type of the body and has its own distinctive roles for that tissue type. The BKα channel contains the pore that releases potassium ions from intracellular stores. This ion channel is found on the cell membrane, endoplasmic reticulum, Golgi and mitochondria. Complex splicing pathways produce different isoforms. The BKα channels can be phosphorylated, palmitoylated and myristylated. BK is composed of a homo-tetramer that interacts with β and γ chains. These accessory proteins provide a further modulating effect on the functions of BKα channels. BK channels play important roles in cell division and migration. In this review, we will focus on the biology of the BK channel, especially its role, and its immune response towards cancer. Recent proteomic studies have linked BK channels with various proteins. Some of these interactions offer further insight into the role that BK channels have with cancers, especially with brain tumors. This review shows that BK channels have a complex interplay with intracellular components of cancer cells and still have plenty of secrets to be discovered.
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Affiliation(s)
- Lisheng Ge
- Research Service, VA Long Beach Healthcare System, 5901 E. 7th Street, Long Beach, CA 90822, USA
| | - Neil T Hoa
- Research Service, VA Long Beach Healthcare System, 5901 E. 7th Street, Long Beach, CA 90822, USA
| | - Zechariah Wilson
- Research Service, VA Long Beach Healthcare System, 5901 E. 7th Street, Long Beach, CA 90822, USA
| | | | - Xiao-Tang Kong
- Department of Neuro-Surgery, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rajeev B Tajhya
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine Beeton
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin R Jadus
- Research Service, VA Long Beach Healthcare System, 5901 E. 7th Street, Long Beach, CA 90822, USA; Pathology and Laboratory Medicine Service, VA Long Beach Healthcare System, 5901 E. 7th Street, Long Beach, CA 90822, USA; Neuro-Oncology Program, Chao Comprehensive Cancer Center, University of California, Irvine, Orange, CA 92868, USA; Pathology and Laboratory Medicine, Med Sci I, University of California, Irvine, CA 92697, USA.
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Hu Y, Gao H, Vo C, Ke C, Pan F, Yu L, Siegel E, Hess KR, Linskey ME, Zhou YH. Anti-EGFR function of EFEMP1 in glioma cells and patient prognosis. Oncoscience 2014; 1:205-15. [PMID: 25594013 PMCID: PMC4278290 DOI: 10.18632/oncoscience.24] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/24/2014] [Indexed: 12/15/2022] Open
Abstract
EGFR is one of the key oncogenes subjected to targeted therapy for several cancers, as it is known to be amplified and/or mutated in up to 40% of malignant gliomas. EFEMP1, a fibulin-like extracellular protein, exerts both tumor suppressive and oncogenic effects in various cancers and glioma cell models. Although EFEMP1's anti-cancer activity has most commonly been attributed to its anti-angiogenic effects, we showed for gliomas that EFEMP1's binding to EGFR accounts for its suppression of the intracranial tumorigenicity of glioma cells expressing high levels of EGFR. In gliomas where EFEMP1 expression, and thus the anti-EGFR effect of EFEMP1, was suppressed, heightened levels of EGFR expression were associated with unfavorable patient outcomes in prognostic models. Results from the current study clearly demonstrate the impact that the anti-EGFR function of EFEMP1 has on the expression of EGFR and patient prognosis. A glioma prognostic model also suggests EFEMP1's context-dependent oncogenic function in gliomas expressing low levels of EGFR. Hence the level of EFEMP1 expression may have a predictive value for choosing patients for anti-EGFR therapy.
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Affiliation(s)
- Yuanjie Hu
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA
| | - Hengjun Gao
- Institute of Digestive Disease, Tongji University, Shanghai, China ; National Engineering Center for Biochip at Shanghai, Shanghai, China
| | - Christopher Vo
- Neurological Surgery, University of California Irvine, Irvine, CA, USA
| | - Chao Ke
- Neurological Surgery, University of California Irvine, Irvine, CA, USA ; State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Francine Pan
- Neurological Surgery, University of California Irvine, Irvine, CA, USA
| | | | - Eric Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kenneth R Hess
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark E Linskey
- Neurological Surgery, University of California Irvine, Irvine, CA, USA
| | - Yi-Hong Zhou
- Department of Biological Chemistry, University of California Irvine, Irvine, CA, USA ; Neurological Surgery, University of California Irvine, Irvine, CA, USA
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