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Wang L, Li W, Yang W, Sun X, Ding Y, Zhao Q, Liu W, Xie X, Xu J, Wei R, Zhu S, Ge Y, Wu PY, Song B. MRI Manifestations of Breast Cancer Stroma and their Role in Predicting Molecular Subtype: A Case-control Study. Curr Med Imaging 2024; 20:CMIR-EPUB-138768. [PMID: 38415486 DOI: 10.2174/0115734056287368240213135143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVE This study explored whether breast MRI manifestations could be used to predict the stroma distribution of breast cancer (BC) and the role of tumor stroma-based MRI manifestations in molecular subtype prediction. METHODS 57 patients with pathologically confirmed invasive BC (non-special type) who had lumpy BC on MRI within one week before surgery were retrospectively collected in the study. Stroma distributions were classified according to their characteristics in the pathological sections. The stromal distribution patterns among molecular subtypes were compared with the MRI manifestations of BC with different stroma distribution types (SDTs). RESULTS SDTs were significantly different and depended on the BC hormone receptor (HR) (P<0.001). There were also significant differences among five SDTs on T2WI, ADC map, internal delayed enhanced features (IDEF), marginal delayed enhanced features (MDEF), and time signal intensity (TSI) curves. Spiculated margin and the absence of type-I TSI were independent predictors for BC with star grid type stroma. The appearance frequency of hypo-intensity on T2WI in HR- BCs was significantly lower (P=0.043) than in HR+ BCs. Star grid stroma and spiculated margin were key factors in predicting HR+ BCs, and the AUC was 0.927 (95% CI: 0.867-0.987). CONCLUSION Breast MRI can be used to predict BC's stromal distribution and molecular subtypes.
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Affiliation(s)
- Lanyun Wang
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
| | - Wenjing Li
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
| | - Wenjun Yang
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
| | - Xilin Sun
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
| | - Yi Ding
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
| | - Qian Zhao
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
| | - Weiyan Liu
- Department of General Surgery, Minhang Hospital, Fudan University, Shanghai, China
| | - Xiaoli Xie
- Department of Pathology, Minhang Hospital, Fudan University, Shanghai, China
| | - Jingjing Xu
- Department of Medical Examination Center, Minhang Hospital, Fudan University, Shanghai, China
| | - Ran Wei
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
| | - Shizhen Zhu
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
| | | | - Pu-Yeh Wu
- GE Healthcare, MR Research China, Beijing, China
| | - Bin Song
- Department of Radiology, Minhang Hospital, Fudan University, Shanghai, China
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Xianyu Z, Correia C, Ung CY, Zhu S, Billadeau DD, Li H. The Rise of Hypothesis-Driven Artificial Intelligence in Oncology. Cancers (Basel) 2024; 16:822. [PMID: 38398213 PMCID: PMC10886811 DOI: 10.3390/cancers16040822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Cancer is a complex disease involving the deregulation of intricate cellular systems beyond genetic aberrations and, as such, requires sophisticated computational approaches and high-dimensional data for optimal interpretation. While conventional artificial intelligence (AI) models excel in many prediction tasks, they often lack interpretability and are blind to the scientific hypotheses generated by researchers to enable cancer discoveries. Here we propose that hypothesis-driven AI, a new emerging class of AI algorithm, is an innovative approach to uncovering the complex etiology of cancer from big omics data. This review exemplifies how hypothesis-driven AI is different from conventional AI by citing its application in various areas of oncology including tumor classification, patient stratification, cancer gene discovery, drug response prediction, and tumor spatial organization. Our aim is to stress the feasibility of incorporating domain knowledge and scientific hypotheses to craft the design of new AI algorithms. We showcase the power of hypothesis-driven AI in making novel cancer discoveries that can be overlooked by conventional AI methods. Since hypothesis-driven AI is still in its infancy, open questions such as how to better incorporate new knowledge and biological perspectives to ameliorate bias and improve interpretability in the design of AI algorithms still need to be addressed. In conclusion, hypothesis-driven AI holds great promise in the discovery of new mechanistic and functional insights that explain the complexity of cancer etiology and potentially chart a new roadmap to improve treatment regimens for individual patients.
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Affiliation(s)
- Zilin Xianyu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (Z.X.); (C.C.); (C.Y.U.); (S.Z.); (D.D.B.)
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (Z.X.); (C.C.); (C.Y.U.); (S.Z.); (D.D.B.)
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (Z.X.); (C.C.); (C.Y.U.); (S.Z.); (D.D.B.)
| | - Shizhen Zhu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (Z.X.); (C.C.); (C.Y.U.); (S.Z.); (D.D.B.)
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Daniel D. Billadeau
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (Z.X.); (C.C.); (C.Y.U.); (S.Z.); (D.D.B.)
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (Z.X.); (C.C.); (C.Y.U.); (S.Z.); (D.D.B.)
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3
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Ung CY, Correia C, Li H, Adams CM, Westendorf JJ, Zhu S. Multiorgan locked-state model of chronic diseases and systems pharmacology opportunities. Drug Discov Today 2024; 29:103825. [PMID: 37967790 DOI: 10.1016/j.drudis.2023.103825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/29/2023] [Accepted: 11/08/2023] [Indexed: 11/17/2023]
Abstract
With increasing human life expectancy, the global medical burden of chronic diseases is growing. Hence, chronic diseases are a pressing health concern and will continue to be in decades to come. Chronic diseases often involve multiple malfunctioning organs in the body. An imminent question is how interorgan crosstalk contributes to the etiology of chronic diseases. We conceived the locked-state model (LoSM), which illustrates how interorgan communication can give rise to body-wide memory-like properties that 'lock' healthy or pathological conditions. Next, we propose cutting-edge systems biology and artificial intelligence strategies to decipher chronic multiorgan locked states. Finally, we discuss the clinical implications of the LoSM and assess the power of systems-based therapies to dismantle pathological multiorgan locked states while improving treatments for chronic diseases.
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Affiliation(s)
- Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Christopher M Adams
- Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jennifer J Westendorf
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA; Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Shizhen Zhu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
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4
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Meng-Lin K, Ung CY, Zhang C, Weiskittel TM, Wisniewski P, Zhang Z, Tan SH, Yeo KS, Zhu S, Correia C, Li H. SPIN-AI: A Deep Learning Model That Identifies Spatially Predictive Genes. Biomolecules 2023; 13:895. [PMID: 37371475 PMCID: PMC10296445 DOI: 10.3390/biom13060895] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Spatially resolved sequencing technologies help us dissect how cells are organized in space. Several available computational approaches focus on the identification of spatially variable genes (SVGs), genes whose expression patterns vary in space. The detection of SVGs is analogous to the identification of differentially expressed genes and permits us to understand how genes and associated molecular processes are spatially distributed within cellular niches. However, the expression activities of SVGs fail to encode all information inherent in the spatial distribution of cells. Here, we devised a deep learning model, Spatially Informed Artificial Intelligence (SPIN-AI), to identify spatially predictive genes (SPGs), whose expression can predict how cells are organized in space. We used SPIN-AI on spatial transcriptomic data from squamous cell carcinoma (SCC) as a proof of concept. Our results demonstrate that SPGs not only recapitulate the biology of SCC but also identify genes distinct from SVGs. Moreover, we found a substantial number of ribosomal genes that were SPGs but not SVGs. Since SPGs possess the capability to predict spatial cellular organization, we reason that SPGs capture more biologically relevant information for a given cellular niche than SVGs. Thus, SPIN-AI has broad applications for detecting SPGs and uncovering which biological processes play important roles in governing cellular organization.
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Affiliation(s)
- Kevin Meng-Lin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Choong-Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Taylor M. Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Philip Wisniewski
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Zhuofei Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Shyang-Hong Tan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Kok-Siong Yeo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (K.-S.Y.); (S.Z.)
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (K.-S.Y.); (S.Z.)
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA; (K.M.-L.); (C.-Y.U.); (C.Z.); (T.M.W.); (P.W.); (Z.Z.); (S.-H.T.)
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5
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Weiskittel TM, Cao A, Meng-Lin K, Lehmann Z, Feng B, Correia C, Zhang C, Wisniewski P, Zhu S, Yong Ung C, Li H. Network Biology-Inspired Machine Learning Features Predict Cancer Gene Targets and Reveal Target Coordinating Mechanisms. Pharmaceuticals (Basel) 2023; 16:752. [PMID: 37242535 PMCID: PMC10223789 DOI: 10.3390/ph16050752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Anticipating and understanding cancers' need for specific gene activities is key for novel therapeutic development. Here we utilized DepMap, a cancer gene dependency screen, to demonstrate that machine learning combined with network biology can produce robust algorithms that both predict what genes a cancer is dependent on and what network features coordinate such gene dependencies. Using network topology and biological annotations, we constructed four groups of novel engineered machine learning features that produced high accuracies when predicting binary gene dependencies. We found that in all examined cancer types, F1 scores were greater than 0.90, and model accuracy remained robust under multiple hyperparameter tests. We then deconstructed these models to identify tumor type-specific coordinators of gene dependency and identified that in certain cancers, such as thyroid and kidney, tumors' dependencies are highly predicted by gene connectivity. In contrast, other histologies relied on pathway-based features such as lung, where gene dependencies were highly predictive by associations with cell death pathway genes. In sum, we show that biologically informed network features can be a valuable and robust addition to predictive pharmacology models while simultaneously providing mechanistic insights.
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Affiliation(s)
- Taylor M. Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
- Mayo Clinic Alix School of Medicine, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Andrew Cao
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Kevin Meng-Lin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Zachary Lehmann
- Department of Chemistry, Biochemistry and Physics, South Dakota State University, Brookings, SD 57006, USA
| | - Benjamin Feng
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Philip Wisniewski
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; (T.M.W.)
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic predisposition to neuroblastoma results from a regulatory polymorphism that promotes the adrenergic cell state. J Clin Invest 2023; 133:e166919. [PMID: 37183825 PMCID: PMC10178836 DOI: 10.1172/jci166919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/14/2023] [Indexed: 05/16/2023] Open
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like mesenchymal cell state and a more differentiated sympathetic adrenergic cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional cofactor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism, G/T, that affects a GATA motif in the first intron of LMO1. Here, we showed that WT zebrafish with the GATA genotype developed adrenergic neuroblastoma, while knock-in of the protective TATA allele at this locus reduced the penetrance of MYCN-driven tumors, which were restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrated that TATA/TATA tumors also exhibited a mesenchymal cell state and were low risk at diagnosis. Thus, conversion of the regulatory GATA to a TATA allele in the first intron of LMO1 reduced the neuroblastoma-initiation rate by preventing formation of the adrenergic cell state. This mechanism was conserved over 400 million years of evolution, separating zebrafish and humans.
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Affiliation(s)
- Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Hui Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- National Clinical Research Center for Child Health, National Children’s Regional Medical Center, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Derek A. Oldridge
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Adam D. Durbin
- Department of Oncology and Comprehensive Cancer Center, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Brian J. Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mark W. Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota, USA
| | - Andrew C. Wood
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Science, University of Auckland, Auckland, New Zealand
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - J. Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Biology Department, MIT, Cambridge, Massachusetts, USA
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Pediatric Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts, USA
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Weichert-Leahey N, Shi H, Tao T, Oldridge DA, Durbin AD, Abraham BJ, Zimmerman MW, Zhu S, Wood AC, Reyon D, Joung JK, Young RA, Diskin SJ, Maris JM, Look AT. Genetic Predisposition to Neuroblastoma Results from a Regulatory Polymorphism that Promotes the Adrenergic Cell State. bioRxiv 2023:2023.02.28.530457. [PMID: 36909587 PMCID: PMC10002714 DOI: 10.1101/2023.02.28.530457] [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: 03/06/2023]
Abstract
Childhood neuroblastomas exhibit plasticity between an undifferentiated neural crest-like "mesenchymal" cell state and a more differentiated sympathetic "adrenergic" cell state. These cell states are governed by autoregulatory transcriptional loops called core regulatory circuitries (CRCs), which drive the early development of sympathetic neuronal progenitors from migratory neural crest cells during embryogenesis. The adrenergic cell identity of neuroblastoma requires LMO1 as a transcriptional co-factor. Both LMO1 expression levels and the risk of developing neuroblastoma in children are associated with a single nucleotide polymorphism G/T that affects a G ATA motif in the first intron of LMO1. Here we show that wild-type zebrafish with the G ATA genotype develop adrenergic neuroblastoma, while knock-in of the protective T ATA allele at this locus reduces the penetrance of MYCN-driven tumors, which are restricted to the mesenchymal cell state. Whole genome sequencing of childhood neuroblastomas demonstrates that T ATA/ T ATA tumors also exhibit a mesenchymal cell state and are low risk at diagnosis. Thus, conversion of the regulatory G ATA to a T ATA allele in the first intron of LMO1 reduces the neuroblastoma initiation rate by preventing formation of the adrenergic cell state, a mechanism that is conserved over 400 million years of evolution separating zebrafish and humans.
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8
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Ung CY, Correia C, Billadeau DD, Zhu S, Li H. Manifold epigenetics: A conceptual model that guides engineering strategies to improve whole-body regenerative health. Front Cell Dev Biol 2023; 11:1122422. [PMID: 36866271 PMCID: PMC9971008 DOI: 10.3389/fcell.2023.1122422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Despite the promising advances in regenerative medicine, there is a critical need for improved therapies. For example, delaying aging and improving healthspan is an imminent societal challenge. Our ability to identify biological cues as well as communications between cells and organs are keys to enhance regenerative health and improve patient care. Epigenetics represents one of the major biological mechanisms involving in tissue regeneration, and therefore can be viewed as a systemic (body-wide) control. However, how epigenetic regulations concertedly lead to the development of biological memories at the whole-body level remains unclear. Here, we review the evolving definitions of epigenetics and identify missing links. We then propose our Manifold Epigenetic Model (MEMo) as a conceptual framework to explain how epigenetic memory arises and discuss what strategies can be applied to manipulate the body-wide memory. In summary we provide a conceptual roadmap for the development of new engineering approaches to improve regenerative health.
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Affiliation(s)
- Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | | | - Shizhen Zhu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States,*Correspondence: Shizhen Zhu, ; Hu Li,
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States,*Correspondence: Shizhen Zhu, ; Hu Li,
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Shen MY, Zhang L, Zhu SZ, Pan JJ, Tang YM, Li Q, Zhou MG, He TJ. [Associations between different levels of blood pressure and risk of prediabetes]. Zhonghua Liu Xing Bing Xue Za Zhi 2022; 43:1939-1944. [PMID: 36572467 DOI: 10.3760/cma.j.cn112338-20220505-00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Objective: To explore sex and rural-urban differences in the associations of different blood pressure levels with the risk of prediabetes. Methods: We used a multi-stage stratified cluster random sampling method to investigate 21 637 residents aged ≥18 years from 10 survey areas in Hubei province in 2020. The data on questionnaire, physical measurements, and laboratory indicators of the participants were collected. The associations of different blood pressure levels with risk of prediabetes by sex and regions were analyzed using multivariate logistic regressions after complex weighting. Results: A total of 16 111 subjects were included. The prevalence (95%CI) of prediabetes, impaired fasting glucose (IFG), impaired glucose tolerance (IGT), and IFG complicated with IGT were 25.1% (14.4%-35.9%), 12.7% (3.2%-22.1%), 8.1% (6.3%-9.8%), and 4.4% (2.3%-6.5%), respectively. After multivariate adjustment, the risk of prediabetes, IFG, IGT, and IFG complicated with IGT increased with the increment of blood pressure (both P for trend <0.05). The positive dose-response relationships between blood pressure levels and risk of prediabetes were also significant among male, urban, and rural residents (both P for trend <0.05), and the interactions between sex and blood pressure showed significant associations for risk of prediabetes and IGT (both P for interaction <0.05). Conclusions: Higher blood pressure levels were associated with an increased risk of prediabetes. The association with prediabetes was stronger in males, but no significant difference was found between urban and rural residents. More distinctive and effective prevention and control strategies should be developed for different populations.
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Affiliation(s)
- M Y Shen
- Department of Disease Surveillance, Institute of Chronic Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - L Zhang
- Department of Disease Surveillance, Institute of Chronic Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - S Z Zhu
- Department of Disease Surveillance, Institute of Chronic Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - J J Pan
- Department of Disease Surveillance, Institute of Chronic Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Y M Tang
- Department of Disease Surveillance, Institute of Chronic Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Q Li
- Department of Disease Surveillance, Institute of Chronic Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - M G Zhou
- Department of Disease Surveillance, Institute of Chronic Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - T J He
- Department of Disease Surveillance, Institute of Chronic Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
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10
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Zhang C, Correia C, Weiskittel TM, Tan SH, Meng-Lin K, Yu GT, Yao J, Yeo KS, Zhu S, Ung CY, Li H. A Knowledge-Based Discovery Approach Couples Artificial Neural Networks With Weight Engineering to Uncover Immune-Related Processes Underpinning Clinical Traits of Breast Cancer. Front Immunol 2022; 13:920669. [PMID: 35911770 PMCID: PMC9330471 DOI: 10.3389/fimmu.2022.920669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022] Open
Abstract
Immune-related processes are important in underpinning the properties of clinical traits such as prognosis and drug response in cancer. The possibility to extract knowledge learned by artificial neural networks (ANNs) from omics data to explain cancer clinical traits is a very attractive subject for novel discovery. Recent studies using a version of ANNs called autoencoders revealed their capability to store biologically meaningful information indicating that autoencoders can be utilized as knowledge discovery platforms aside from their initial assigned use for dimensionality reduction. Here, we devise an innovative weight engineering approach and ANN platform called artificial neural network encoder (ANNE) using an autoencoder and apply it to a breast cancer dataset to extract knowledge learned by the autoencoder model that explains clinical traits. Intriguingly, the extracted biological knowledge in the form of gene–gene associations from ANNE shows immune-related components such as chemokines, carbonic anhydrase, and iron metabolism that modulate immune-related processes and the tumor microenvironment play important roles in underpinning breast cancer clinical traits. Our work shows that biological “knowledge” learned by an ANN model is indeed encoded as weights throughout its neuronal connections, and it is possible to extract learned knowledge via a novel weight engineering approach to uncover important biological insights.
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Affiliation(s)
- Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Taylor M. Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Shyang Hong Tan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Kevin Meng-Lin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Grace T. Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Jingwen Yao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Kok Siong Yeo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- *Correspondence: Hu Li, ; Choong Yong Ung,
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- *Correspondence: Hu Li, ; Choong Yong Ung,
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11
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Zhang Z, Zhu S, Liu Y, Liu L, Ma Z. Enthalpy driving force and chemical bond weakening: the solid-solution formation mechanism and densification behavior of high-entropy diborides (Hf1-x/4Zr1-x/4Nb1-x/4Ta1-x/4Scx)B2. Ann Ital Chir 2022. [DOI: 10.1016/j.jeurceramsoc.2022.03.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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12
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Ung CY, Levee TM, Zhang C, Correia C, Yeo KS, Li H, Zhu S. Gene utility recapitulates chromosomal aberrancies in advanced stage neuroblastoma. Comput Struct Biotechnol J 2022; 20:3291-3303. [PMID: 35832612 PMCID: PMC9251784 DOI: 10.1016/j.csbj.2022.06.024] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/11/2022] [Indexed: 11/03/2022] Open
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in children. Although only a few recurrent somatic mutations have been identified, chromosomal abnormalities, including the loss of heterozygosity (LOH) at the chromosome 1p and gains of chromosome 17q, are often seen in the high-risk cases. The biological basis and evolutionary forces that drive such genetic abnormalities remain enigmatic. Here, we conceptualize the Gene Utility Model (GUM) that seeks to identify genes driving biological signaling via their collective gene utilities and apply it to understand the impact of those differentially utilized genes on constraining the evolution of NB karyotypes. By employing a computational process-guided flow algorithm to model gene utility in protein–protein networks that built based on transcriptomic data, we conducted several pairwise comparative analyses to uncover genes with differential utilities in stage 4 NBs with distinct classification. We then constructed a utility karyotype by mapping these differentially utilized genes to their respective chromosomal loci. Intriguingly, hotspots of the utility karyotype, to certain extent, can consistently recapitulate the major chromosomal abnormalities of NBs and also provides clues to yet identified predisposition sites. Hence, our study not only provides a new look, from a gene utility perspective, into the known chromosomal abnormalities detected by integrative genomic sequencing efforts, but also offers new insights into the etiology of NB and provides a framework to facilitate the identification of novel therapeutic targets for this devastating childhood cancer.
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13
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Anderson NM, Qin X, Finan JM, Lam A, Athoe J, Missiaen R, Skuli N, Kennedy A, Saini AS, Tao T, Zhu S, Nissim I, Look AT, Qing G, Simon MC, Feng H. Metabolic Enzyme DLST Promotes Tumor Aggression and Reveals a Vulnerability to OXPHOS Inhibition in High-Risk Neuroblastoma. Cancer Res 2021; 81:4417-4430. [PMID: 34233924 DOI: 10.1158/0008-5472.can-20-2153] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/13/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022]
Abstract
High-risk neuroblastoma remains therapeutically challenging to treat, and the mechanisms promoting disease aggression are poorly understood. Here, we show that elevated expression of dihydrolipoamide S-succinyltransferase (DLST) predicts poor treatment outcome and aggressive disease in patients with neuroblastoma. DLST is an E2 component of the α-ketoglutarate (αKG) dehydrogenase complex, which governs the entry of glutamine into the tricarboxylic acid cycle (TCA) for oxidative decarboxylation. During this irreversible step, αKG is converted into succinyl-CoA, producing NADH for oxidative phosphorylation (OXPHOS). Utilizing a zebrafish model of MYCN-driven neuroblastoma, we demonstrate that even modest increases in DLST expression promote tumor aggression, while monoallelic dlst loss impedes disease initiation and progression. DLST depletion in human MYCN-amplified neuroblastoma cells minimally affected glutamine anaplerosis and did not alter TCA cycle metabolites other than αKG. However, DLST loss significantly suppressed NADH production and impaired OXPHOS, leading to growth arrest and apoptosis of neuroblastoma cells. In addition, multiple inhibitors targeting the electron transport chain, including the potent IACS-010759 that is currently in clinical testing for other cancers, efficiently reduced neuroblastoma proliferation in vitro. IACS-010759 also suppressed tumor growth in zebrafish and mouse xenograft models of high-risk neuroblastoma. Together, these results demonstrate that DLST promotes neuroblastoma aggression and unveils OXPHOS as an essential contributor to high-risk neuroblastoma. SIGNIFICANCE: These findings demonstrate a novel role for DLST in neuroblastoma aggression and identify the OXPHOS inhibitor IACS-010759 as a potential therapeutic strategy for this deadly disease.
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Affiliation(s)
- Nicole M Anderson
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xiaodan Qin
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, The Center for Cancer Research, Boston University School of Medicine, Boston, Massachusetts
| | - Jennifer M Finan
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Andrew Lam
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, The Center for Cancer Research, Boston University School of Medicine, Boston, Massachusetts
| | - Jacob Athoe
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, The Center for Cancer Research, Boston University School of Medicine, Boston, Massachusetts
| | - Rindert Missiaen
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Nicolas Skuli
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Annie Kennedy
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Amandeep S Saini
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, The Center for Cancer Research, Boston University School of Medicine, Boston, Massachusetts
| | - Ting Tao
- National Clinical Research Center for Child Health, National Children's Regional Medical Center, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Itzhak Nissim
- Division of Genetics and Metabolism, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Biochemistry, and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Guoliang Qing
- Frontier Science Center for Immunology & Metabolism, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania. .,Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hui Feng
- Departments of Pharmacology and Medicine, Section of Hematology and Medical Oncology, The Center for Cancer Research, Boston University School of Medicine, Boston, Massachusetts.
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14
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Cheung BB, Kleynhans A, Mittra R, Kim PY, Holien JK, Nagy Z, Ciampa OC, Seneviratne JA, Mayoh C, Raipuria M, Gadde S, Massudi H, Wong IPL, Tan O, Gong A, Suryano A, Diakiw SM, Liu B, Arndt GM, Liu T, Kumar N, Sangfelt O, Zhu S, Norris MD, Haber M, Carter DR, Parker MW, Marshall GM. A novel combination therapy targeting ubiquitin-specific protease 5 in MYCN-driven neuroblastoma. Oncogene 2021; 40:2367-2381. [PMID: 33658627 PMCID: PMC8016666 DOI: 10.1038/s41388-021-01712-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 01/31/2023]
Abstract
Histone deacetylase (HDAC) inhibitors are effective in MYCN-driven cancers, because of a unique need for HDAC recruitment by the MYCN oncogenic signal. However, HDAC inhibitors are much more effective in combination with other anti-cancer agents. To identify novel compounds which act synergistically with HDAC inhibitor, such as suberanoyl hydroxamic acid (SAHA), we performed a cell-based, high-throughput drug screen of 10,560 small molecule compounds from a drug-like diversity library and identified a small molecule compound (SE486-11) which synergistically enhanced the cytotoxic effects of SAHA. Effects of drug combinations on cell viability, proliferation, apoptosis and colony forming were assessed in a panel of neuroblastoma cell lines. Treatment with SAHA and SE486-11 increased MYCN ubiquitination and degradation, and markedly inhibited tumorigenesis in neuroblastoma xenografts, and, MYCN transgenic zebrafish and mice. The combination reduced ubiquitin-specific protease 5 (USP5) levels and increased unanchored polyubiquitin chains. Overexpression of USP5 rescued neuroblastoma cells from the cytopathic effects of the combination and reduced unanchored polyubiquitin, suggesting USP5 is a therapeutic target of the combination. SAHA and SE486-11 directly bound to USP5 and the drug combination exhibited a 100-fold higher binding to USP5 than individual drugs alone in microscale thermophoresis assays. MYCN bound to the USP5 promoter and induced USP5 gene expression suggesting that USP5 and MYCN expression created a forward positive feedback loop in neuroblastoma cells. Thus, USP5 acts as an oncogenic cofactor with MYCN in neuroblastoma and the novel combination of HDAC inhibitor with SE486-11 represents a novel therapeutic approach for the treatment of MYCN-driven neuroblastoma.
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Affiliation(s)
- Belamy B Cheung
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia.
| | - Ane Kleynhans
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Rituparna Mittra
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Patrick Y Kim
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Jessica K Holien
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
| | - Zsuzsanna Nagy
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Olivia C Ciampa
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Janith A Seneviratne
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Mukesh Raipuria
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Satyanarayana Gadde
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Chemistry, UNSW Sydney, Sydney, NSW, Australia
| | - Hassina Massudi
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Sydney, NSW, Australia
| | - Iris Poh Ling Wong
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Owen Tan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew Gong
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Aldwin Suryano
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Sonya M Diakiw
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Bing Liu
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Greg M Arndt
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Tao Liu
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Naresh Kumar
- School of Chemistry, UNSW Sydney, Sydney, NSW, Australia
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Cancer Center and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, Sydney, NSW, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Daniel R Carter
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW, Australia
| | - Michael W Parker
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia.
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15
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Abstract
Zebrafish has emerged as an important animal model to study human diseases, especially cancer. Along with the robust transgenic and genome editing technologies applied in zebrafish modeling, the ease of maintenance, high-yield productivity, and powerful live imaging altogether make the zebrafish a valuable model system to study metastasis and cellular and molecular bases underlying this process in vivo. The first zebrafish neuroblastoma (NB) model of metastasis was developed by overexpressing two oncogenes, MYCN and LMO1, under control of the dopamine-beta-hydroxylase (dβh) promoter. Co-overexpressed MYCN and LMO1 led to the reduced latency and increased penetrance of neuroblastomagenesis, as well as accelerated distant metastasis of tumor cells. This new model reliably reiterates many key features of human metastatic NB, including involvement of clinically relevant and metastasis-associated genetic alterations; natural and spontaneous development of metastasis in vivo; and conserved sites of metastases. Therefore, the zebrafish model possesses unique advantages to dissect the complex process of tumor metastasis in vivo.
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Affiliation(s)
- Zuag Paj Her
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center
| | - Kok Siong Yeo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center
| | - Cassie Howe
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center
| | - Taylor Levee
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center;
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16
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Li S, Yeo KS, Levee TM, Howe CJ, Her ZP, Zhu S. Zebrafish as a Neuroblastoma Model: Progress Made, Promise for the Future. Cells 2021; 10:cells10030580. [PMID: 33800887 PMCID: PMC8001113 DOI: 10.3390/cells10030580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/24/2022] Open
Abstract
For nearly a decade, researchers in the field of pediatric oncology have been using zebrafish as a model for understanding the contributions of genetic alternations to the pathogenesis of neuroblastoma (NB), and exploring the molecular and cellular mechanisms that underlie neuroblastoma initiation and metastasis. In this review, we will enumerate and illustrate the key advantages of using the zebrafish model in NB research, which allows researchers to: monitor tumor development in real-time; robustly manipulate gene expression (either transiently or stably); rapidly evaluate the cooperative interactions of multiple genetic alterations to disease pathogenesis; and provide a highly efficient and low-cost methodology to screen for effective pharmaceutical interventions (both alone and in combination with one another). This review will then list some of the common challenges of using the zebrafish model and provide strategies for overcoming these difficulties. We have also included visual diagram and figures to illustrate the workflow of cancer model development in zebrafish and provide a summary comparison of commonly used animal models in cancer research, as well as key findings of cooperative contributions between MYCN and diverse singling pathways in NB pathogenesis.
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Affiliation(s)
- Shuai Li
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; (S.L.); (K.S.Y.); (T.M.L.); (C.J.H.); (Z.P.H.)
| | - Kok Siong Yeo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; (S.L.); (K.S.Y.); (T.M.L.); (C.J.H.); (Z.P.H.)
| | - Taylor M. Levee
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; (S.L.); (K.S.Y.); (T.M.L.); (C.J.H.); (Z.P.H.)
| | - Cassie J. Howe
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; (S.L.); (K.S.Y.); (T.M.L.); (C.J.H.); (Z.P.H.)
| | - Zuag Paj Her
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; (S.L.); (K.S.Y.); (T.M.L.); (C.J.H.); (Z.P.H.)
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; (S.L.); (K.S.Y.); (T.M.L.); (C.J.H.); (Z.P.H.)
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
- Correspondence:
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17
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Dong Z, Yeo KS, Lopez G, Zhang C, Dankert Eggum EN, Rokita JL, Ung CY, Levee TM, Her ZP, Howe CJ, Hou X, van Ree JH, Li S, He S, Tao T, Fritchie K, Torres-Mora J, Lehman JS, Meves A, Razidlo GL, Rathi KS, Weroha SJ, Look AT, van Deursen JM, Li H, Westendorf JJ, Maris JM, Zhu S. GAS7 Deficiency Promotes Metastasis in MYCN-Driven Neuroblastoma. Cancer Res 2021; 81:2995-3007. [PMID: 33602789 DOI: 10.1158/0008-5472.can-20-1890] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/04/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022]
Abstract
One of the greatest barriers to curative treatment of neuroblastoma is its frequent metastatic outgrowth prior to diagnosis, especially in cases driven by amplification of the MYCN oncogene. However, only a limited number of regulatory proteins that contribute to this complex MYCN-mediated process have been elucidated. Here we show that the growth arrest-specific 7 (GAS7) gene, located at chromosome band 17p13.1, is preferentially deleted in high-risk MYCN-driven neuroblastoma. GAS7 expression was also suppressed in MYCN-amplified neuroblastoma lacking 17p deletion. GAS7 deficiency led to accelerated metastasis in both zebrafish and mammalian models of neuroblastoma with overexpression or amplification of MYCN. Analysis of expression profiles and the ultrastructure of zebrafish neuroblastoma tumors with MYCN overexpression identified that GAS7 deficiency led to (i) downregulation of genes involved in cell-cell interaction, (ii) loss of contact among tumor cells as critical determinants of accelerated metastasis, and (iii) increased levels of MYCN protein. These results provide the first genetic evidence that GAS7 depletion is a critical early step in the cascade of events culminating in neuroblastoma metastasis in the context of MYCN overexpression. SIGNIFICANCE: Heterozygous deletion or MYCN-mediated repression of GAS7 in neuroblastoma releases an important brake on tumor cell dispersion and migration to distant sites, providing a novel mechanism underlying tumor metastasis in MYCN-driven neuroblastoma.See related commentary by Menard, p. 2815.
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Affiliation(s)
- Zhiwei Dong
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Kok Siong Yeo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Gonzalo Lopez
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Cheng Zhang
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Erin N Dankert Eggum
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Choong Yong Ung
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Taylor M Levee
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Zuag Paj Her
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Cassie J Howe
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Xiaonan Hou
- Departments of Oncology, Radiation Oncology, and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Janine H van Ree
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Shuai Li
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ting Tao
- Children's Hospital, Zhejiang University School of Medicine; National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, China
| | - Karen Fritchie
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jorge Torres-Mora
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Julia S Lehman
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
| | - Alexander Meves
- Department of Dermatology, Mayo Clinic, Rochester, Minnesota
| | - Gina L Razidlo
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Komal S Rathi
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - S John Weroha
- Departments of Oncology, Radiation Oncology, and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jan M van Deursen
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Hu Li
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Jennifer J Westendorf
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota.,Department of Orthopedic Surgery, Mayo Clinic, Rochester, Minnesota
| | - John M Maris
- Department of Bioinformatics and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, Minnesota. .,Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota
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18
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Tang YM, Zhang L, Zhu SZ, Pan JJ, Zhou SH, He TJ, Li Q. Gout in China, 1990-2017: the Global Burden of Disease Study 2017. Public Health 2021; 191:33-38. [PMID: 33482625 DOI: 10.1016/j.puhe.2020.06.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 04/27/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The aim of the study was to estimate the gout burden and risk factors in China from 1990 to 2017. STUDY DESIGN The Global Burden of Disease (GBD) Study uses various analytical tools and a diverse set of data sources to generate comparable estimates of deaths and mortality rates broken down by age, sex, cause, year, and geography. METHODS We used the results from the GBD Study 2017 to compare disability-adjusted life years (DALYs), prevalence, incidence, and risk factors of gout in China. The median of the percentage change and 95% uncertainty intervals were determined for the period between 1990 and 2017. RESULTS The age-standardized DALY rate, prevalence, and incidence increased 6.92%, 6.88%, and 6.16%, respectively, in China from 1990 to 2017. Although the rates of gout both globally and in China were increasing, the range of change for males in China was larger than that of the global level. All risk factors combined accounted for 30.04% of gout DALYs in 2017. The leading risk factors for gout DALYs were high body mass index and impaired kidney function, and the proportion of high body mass index increased significantly from 10.67% to 24.31%, whereas the proportion of impaired kidney function remained basically unchanged. CONCLUSIONS The age-standardized DALY rate, prevalence, and incidence in China have increased progressively since 1990. Increasing attention on body weight management should be prioritized for controlling the rising prevalence of gout in the young and middle-aged population.
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Affiliation(s)
- Y M Tang
- Institute of Chronic and Non-communicable Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Hubei, China
| | - L Zhang
- Institute of Chronic and Non-communicable Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Hubei, China
| | - S Z Zhu
- Institute of Chronic and Non-communicable Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Hubei, China
| | - J J Pan
- Institute of Chronic and Non-communicable Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Hubei, China
| | - S H Zhou
- Institute of Chronic and Non-communicable Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Hubei, China
| | - T J He
- Institute of Chronic and Non-communicable Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Hubei, China
| | - Q Li
- Institute of Chronic and Non-communicable Disease Control and Prevention, Hubei Provincial Center for Disease Control and Prevention, Hubei, China.
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19
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Sun S, Liu Y, Ma Z, Zhu S, Hong C, Chen H, Ma K. Fabrication of ZrB2-SiC powder with a eutectic phase for sintering or plasma spraying. POWDER TECHNOL 2020. [DOI: 10.1016/j.powtec.2020.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Xu F, Zhu S, Hu J, Ma Z, Liu Y. Ablation Behavior of a Carbon Fabric Reinforced Phenolic Composite Modified by Surface-Decorated ZrB 2/SiC. Materials (Basel) 2020; 13:ma13020256. [PMID: 31936016 PMCID: PMC7014342 DOI: 10.3390/ma13020256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/29/2019] [Accepted: 01/03/2020] [Indexed: 11/16/2022]
Abstract
Carbon fabric reinforced phenolic composites were widely used as TPSs (thermal protection system) material in the aerospace industry. However, their limited oxidative ablation resistance restricted their further utility in more serious service conditions. In this study, the surface-decorated ZrB2/SiC and its modified carbon fabric reinforced phenolic composites have been successfully prepared. The self-modification mechanism of the surface-decorated ZrB2/SiC particles were characterized. The mechanical performance and ablation behavior of the composites were investigated. Results showed that the ZrB2/SiC particles possessed a good surface-decorated effect, which achieved good compatibility with the phenolic resin. The mechanical performance of the modified phenolic composite was effectively improved. The anti-oxidative ablation performance of the composite was improved. The mass ablation rate of the surface-decorated ZrB2–SiC-modified carbon fabric reinforced phenolic composites was 25% lower than that of the unmodified composites. The formed ZrO2 ceramic layer attached to the surface of the residual chars prevented the heat energy and oxygen from the inner material. Meanwhile, the volatilization of SiO2 and B2O3 effectively increased the heat dissipation. All these results confirmed that the ZrB2–SiC particles can effectively improve the ablation resistance of the composite, which provided a basis for the application of the composites to more serious service environments.
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Affiliation(s)
- Feng Xu
- School of Material Science and Engineering, Beijing Institute of Technology, Beijing 100081, China; (F.X.); (J.H.); (Z.M.); (Y.L.)
- National Key Laboratory of Science and Technology on Material under Shock and Impact, Beijing 100081, China
| | - Shizhen Zhu
- School of Material Science and Engineering, Beijing Institute of Technology, Beijing 100081, China; (F.X.); (J.H.); (Z.M.); (Y.L.)
- National Key Laboratory of Science and Technology on Material under Shock and Impact, Beijing 100081, China
- Correspondence: ; Tel.: +86-010-68911144
| | - Jingdan Hu
- School of Material Science and Engineering, Beijing Institute of Technology, Beijing 100081, China; (F.X.); (J.H.); (Z.M.); (Y.L.)
| | - Zhuang Ma
- School of Material Science and Engineering, Beijing Institute of Technology, Beijing 100081, China; (F.X.); (J.H.); (Z.M.); (Y.L.)
- National Key Laboratory of Science and Technology on Material under Shock and Impact, Beijing 100081, China
| | - Yanbo Liu
- School of Material Science and Engineering, Beijing Institute of Technology, Beijing 100081, China; (F.X.); (J.H.); (Z.M.); (Y.L.)
- National Key Laboratory of Science and Technology on Material under Shock and Impact, Beijing 100081, China
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21
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Koach J, Holien JK, Massudi H, Carter DR, Ciampa OC, Herath M, Lim T, Seneviratne JA, Milazzo G, Murray JE, McCarroll JA, Liu B, Mayoh C, Keenan B, Stevenson BW, Gorman MA, Bell JL, Doughty L, Hüttelmaier S, Oberthuer A, Fischer M, Gifford AJ, Liu T, Zhang X, Zhu S, Gustafson WC, Haber M, Norris MD, Fletcher JI, Perini G, Parker MW, Cheung BB, Marshall GM. Drugging MYCN Oncogenic Signaling through the MYCN-PA2G4 Binding Interface. Cancer Res 2019; 79:5652-5667. [PMID: 31501192 DOI: 10.1158/0008-5472.can-19-1112] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/17/2019] [Accepted: 09/03/2019] [Indexed: 11/16/2022]
Abstract
MYCN is a major driver for the childhood cancer, neuroblastoma, however, there are no inhibitors of this target. Enhanced MYCN protein stability is a key component of MYCN oncogenesis and is maintained by multiple feedforward expression loops involving MYCN transactivation target genes. Here, we reveal the oncogenic role of a novel MYCN target and binding protein, proliferation-associated 2AG4 (PA2G4). Chromatin immunoprecipitation studies demonstrated that MYCN occupies the PA2G4 gene promoter, stimulating transcription. Direct binding of PA2G4 to MYCN protein blocked proteolysis of MYCN and enhanced colony formation in a MYCN-dependent manner. Using molecular modeling, surface plasmon resonance, and mutagenesis studies, we mapped the MYCN-PA2G4 interaction site to a 14 amino acid MYCN sequence and a surface crevice of PA2G4. Competitive chemical inhibition of the MYCN-PA2G4 protein-protein interface had potent inhibitory effects on neuroblastoma tumorigenesis in vivo. Treated tumors showed reduced levels of both MYCN and PA2G4. Our findings demonstrate a critical role for PA2G4 as a cofactor in MYCN-driven neuroblastoma and highlight competitive inhibition of the PA2G4-MYCN protein binding as a novel therapeutic strategy in the disease. SIGNIFICANCE: Competitive chemical inhibition of the PA2G4-MYCN protein interface provides a basis for drug design of small molecules targeting MYC and MYCN-binding partners in malignancies driven by MYC family oncoproteins.
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Affiliation(s)
- Jessica Koach
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia.,Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Jessica K Holien
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Hassina Massudi
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Daniel R Carter
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia.,School of Women's & Children's Health, UNSW Sydney, Randwick New South Wales, Australia.,School of Biomedical Engineering, University of Technology Sydney, Australia
| | - Olivia C Ciampa
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Mika Herath
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Taylor Lim
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Janith A Seneviratne
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Jayne E Murray
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Joshua A McCarroll
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia.,Australian Centre for NanoMedicine, ARC Centre for Excellence in Convergent Bio-Nano Science and Technology, UNSW, Australia
| | - Bing Liu
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Bryce Keenan
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Brendan W Stevenson
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Michael A Gorman
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Jessica L Bell
- The Section for Molecular Cell Biology, Institute of Molecular Medicine, Martin Luther University of Halle, Halle, Germany
| | - Larissa Doughty
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Stefan Hüttelmaier
- The Section for Molecular Cell Biology, Institute of Molecular Medicine, Martin Luther University of Halle, Halle, Germany
| | - Andre Oberthuer
- Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, Cologne, Germany.,Department of Neonatology and Pediatric Intensive Care Medicine, Children's Hospital, University of Cologne, Cologne, Germany
| | - Matthias Fischer
- Department of Pediatric Oncology and Hematology, Children's Hospital, University of Cologne, Cologne, Germany.,Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Andrew J Gifford
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia.,Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Xiaoling Zhang
- Department of Biochemistry and Molecular Biology, Cancer Center and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Cancer Center and Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - W Clay Gustafson
- Department of Pediatrics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Michelle Haber
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Murray D Norris
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Michael W Parker
- ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Belamy B Cheung
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia. .,School of Women's & Children's Health, UNSW Sydney, Randwick New South Wales, Australia.,School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Glenn M Marshall
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, UNSW Sydney, Kensington, New South Wales, Australia. .,School of Women's & Children's Health, UNSW Sydney, Randwick New South Wales, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia
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22
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Zimmerman MW, Liu Y, He S, Durbin AD, Abraham BJ, Easton J, Shao Y, Xu B, Zhu S, Zhang X, Weichert-Leahey N, Young RA, Zhang J, Look AT. Abstract IA19: MYC activation through enhancer hijacking or focal enhancer amplification drives a subset of high-risk pediatric neuroblastoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.pedca17-ia19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The amplified MYCN gene serves as an oncogenic driver in approximately 20% of high-risk pediatric neuroblastomas. Here we show that MYC itself is a potent transforming gene in a separate subset of high-risk neuroblastoma cases (~10%), based on (i) its upregulation by focal enhancer amplification or genomic rearrangements leading to enhancer hijacking, and (ii) its ability to transform neuroblastoma precursor cells in a transgenic animal model. The aberrant regulatory elements associated with oncogenic MYC activation include focally amplified distal enhancers or translocation of highly active enhancers from other genes to within topologically associating domains containing the MYC gene locus. The clinical outcome for patients with high levels of MYC expression is virtually identical to that of patients with amplification of the MYCN gene, a known high-risk feature of this disease. Together, these findings establish MYC as a bona fide oncogene in a clinically significant group of high-risk childhood neuroblastomas.
Citation Format: Mark W. Zimmerman, Yu Liu, Shuning He, Adam D. Durbin, Brian J. Abraham, John Easton, Ying Shao, Beisi Xu, Shizhen Zhu, Xiaoling Zhang, Nina Weichert-Leahey, Richard A. Young, Jinghui Zhang, A. Thomas Look. MYC activation through enhancer hijacking or focal enhancer amplification drives a subset of high-risk pediatric neuroblastoma [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr IA19.
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Affiliation(s)
- Mark W. Zimmerman
- 1Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA,
- *These authors contributed equally to this work
| | - Yu Liu
- 2Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN,
- *These authors contributed equally to this work
| | - Shuning He
- 1Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA,
| | - Adam D. Durbin
- 1Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA,
| | | | - John Easton
- 2Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN,
| | - Ying Shao
- 2Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN,
| | - Beisi Xu
- 2Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN,
| | - Shizhen Zhu
- 4Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN,
| | - Xiaoling Zhang
- 4Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN,
| | | | - Richard A. Young
- 3Whitehead Institute for Biomedical Research, Cambridge, MA,
- 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- †These authors supervised the study
| | - Jinghui Zhang
- 2Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN,
- †These authors supervised the study
| | - A. Thomas Look
- 1Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA,
- †These authors supervised the study
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23
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Zimmerman MW, Liu Y, He S, Durbin AD, Abraham BJ, Easton J, Shao Y, Xu B, Zhu S, Zhang X, Li Z, Weichert-Leahey N, Young RA, Zhang J, Look AT. MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification. Cancer Discov 2018; 8:320-335. [PMID: 29284669 PMCID: PMC5856009 DOI: 10.1158/2159-8290.cd-17-0993] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/11/2017] [Accepted: 12/21/2017] [Indexed: 11/16/2022]
Abstract
The amplified MYCN gene serves as an oncogenic driver in approximately 20% of high-risk pediatric neuroblastomas. Here, we show that the family member MYC is a potent transforming gene in a separate subset of high-risk neuroblastoma cases (∼10%), based on (i) its upregulation by focal enhancer amplification or genomic rearrangements leading to enhancer hijacking, and (ii) its ability to transform neuroblastoma precursor cells in a transgenic animal model. The aberrant regulatory elements associated with oncogenic MYC activation include focally amplified distal enhancers and translocation of highly active enhancers from other genes to within topologically associating domains containing the MYC gene locus. The clinical outcome for patients with high levels of MYC expression is virtually identical to that of patients with amplification of the MYCN gene, a known high-risk feature of this disease. Together, these findings establish MYC as a bona fide oncogene in a clinically significant group of high-risk childhood neuroblastomas.Significance: Amplification of the MYCN oncogene is a recognized hallmark of high-risk pediatric neuroblastoma. Here, we demonstrate that MYC is also activated as a potent oncogene in a distinct subset of neuroblastoma cases through either focal amplification of distal enhancers or enhancer hijacking mediated by chromosomal translocation. Cancer Discov; 8(3); 320-35. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 253.
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Affiliation(s)
- Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yu Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Adam D Durbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Xiaoling Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Zhaodong Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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24
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Dankert EN, Look AT, Zhu S. Unraveling Neuroblastoma Pathogenesis with the Zebrafish. Cell Cycle 2017; 17:395-396. [PMID: 29231124 DOI: 10.1080/15384101.2017.1414683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Erin N Dankert
- a Department of Biochemistry and Molecular Biology , Mayo Clinic College of Medicine, Mayo Clinic Cancer Center , Rochester , MN , USA
| | - A Thomas Look
- b Department of Pediatric Oncology , Dana-Farber Cancer Institute, Harvard Medical School , Boston , MA , USA
| | - Shizhen Zhu
- a Department of Biochemistry and Molecular Biology , Mayo Clinic College of Medicine, Mayo Clinic Cancer Center , Rochester , MN , USA
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25
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Zhang X, Dong Z, Zhang C, Ung CY, He S, Tao T, Oliveira AM, Meves A, Ji B, Look AT, Li H, Neel BG, Zhu S. Critical Role for GAB2 in Neuroblastoma Pathogenesis through the Promotion of SHP2/MYCN Cooperation. Cell Rep 2017; 18:2932-2942. [PMID: 28329685 DOI: 10.1016/j.celrep.2017.02.065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/17/2017] [Accepted: 02/21/2017] [Indexed: 11/26/2022] Open
Abstract
Growing evidence suggests a major role for Src-homology-2-domain-containing phosphatase 2 (SHP2/PTPN11) in MYCN-driven high-risk neuroblastoma, although biologic confirmation and a plausible mechanism for this contribution are lacking. Using a zebrafish model of MYCN-overexpressing neuroblastoma, we demonstrate that mutant ptpn11 expression in the adrenal gland analog of MYCN transgenic fish promotes the proliferation of hyperplastic neuroblasts, accelerates neuroblastomagenesis, and increases tumor penetrance. We identify a similar mechanism in tumors with wild-type ptpn11 and dysregulated Gab2, which encodes a Shp2 activator that is overexpressed in human neuroblastomas. In MYCN transgenic fish, Gab2 overexpression activated the Shp2-Ras-Erk pathway, enhanced neuroblastoma induction, and increased tumor penetrance. We conclude that MYCN cooperates with either GAB2-activated or mutant SHP2 in human neuroblastomagenesis. Our findings further suggest that combined inhibition of MYCN and the SHP2-RAS-ERK pathway could provide effective targeted therapy for high-risk neuroblastoma patients with MYCN amplification and aberrant SHP2 activation.
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Affiliation(s)
- Xiaoling Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Zhiwei Dong
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andre M Oliveira
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Alexander Meves
- Department of Dermatology, Mayo Clinic, Rochester, MN 55902, USA
| | - Baoan Ji
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Benjamin G Neel
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA.
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
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26
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Zhu S, Zhang X, Weichert-Leahey N, Dong Z, Zhang C, Lopez G, Tao T, He S, Wood AC, Oldridge D, Ung CY, van Ree JH, Khan A, Salazar BM, Lummertz da Rocha E, Zimmerman MW, Guo F, Cao H, Hou X, Weroha SJ, Perez-Atayde AR, Neuberg DS, Meves A, McNiven MA, van Deursen JM, Li H, Maris JM, Look AT. LMO1 Synergizes with MYCN to Promote Neuroblastoma Initiation and Metastasis. Cancer Cell 2017; 32:310-323.e5. [PMID: 28867147 PMCID: PMC5605802 DOI: 10.1016/j.ccell.2017.08.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 06/01/2017] [Accepted: 08/07/2017] [Indexed: 11/28/2022]
Abstract
A genome-wide association study identified LMO1, which encodes an LIM-domain-only transcriptional cofactor, as a neuroblastoma susceptibility gene that functions as an oncogene in high-risk neuroblastoma. Here we show that dβh promoter-mediated expression of LMO1 in zebrafish synergizes with MYCN to increase the proliferation of hyperplastic sympathoadrenal precursor cells, leading to a reduced latency and increased penetrance of neuroblastomagenesis. The transgenic expression of LMO1 also promoted hematogenous dissemination and distant metastasis, which was linked to neuroblastoma cell invasion and migration, and elevated expression levels of genes affecting tumor cell-extracellular matrix interaction, including loxl3, itga2b, itga3, and itga5. Our results provide in vivo validation of LMO1 as an important oncogene that promotes neuroblastoma initiation, progression, and widespread metastatic dissemination.
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Affiliation(s)
- Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA.
| | - Xiaoling Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zhiwei Dong
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew C Wood
- Department of Molecular Medicine, University of Auckland, Auckland, New Zealand
| | - Derek Oldridge
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Choong Yong Ung
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Janine H van Ree
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Amish Khan
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Brittany M Salazar
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Edroaldo Lummertz da Rocha
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Feng Guo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hong Cao
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Xiaonan Hou
- Departments of Oncology, Radiation Oncology, and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55902, USA
| | - S John Weroha
- Departments of Oncology, Radiation Oncology, and Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55902, USA
| | - Antonio R Perez-Atayde
- Department of Pathology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115, USA
| | - Donna S Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander Meves
- Department of Dermatology, Mayo Clinic, Rochester, MN 55902, USA
| | - Mark A McNiven
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Jan M van Deursen
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic Cancer Center, Rochester, MN 55902, USA
| | - Hu Li
- Department of Molecular Pharmacology & Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Philadelphia, PA 19104, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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27
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Ghanat Bari M, Ung CY, Zhang C, Zhu S, Li H. Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks. Sci Rep 2017; 7:6993. [PMID: 28765560 PMCID: PMC5539301 DOI: 10.1038/s41598-017-07481-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/27/2017] [Indexed: 12/25/2022] Open
Abstract
Emerging evidence indicates the existence of a new class of cancer genes that act as "signal linkers" coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed genes, which we term Class I cancer genes, are readily detected by most analytical tools, the new class of cancer-related genes, i.e., Class II, escape detection because they are neither mutated nor differentially expressed. Given this hypothesis, we developed a Machine Learning-Assisted Network Inference (MALANI) algorithm, which assesses all genes regardless of expression or mutational status in the context of cancer etiology. We used 8807 expression arrays, corresponding to 9 cancer types, to build more than 2 × 108 Support Vector Machine (SVM) models for reconstructing a cancer network. We found that ~3% of ~19,000 not differentially expressed genes are Class II cancer gene candidates. Some Class II genes that we found, such as SLC19A1 and ATAD3B, have been recently reported to associate with cancer outcomes. To our knowledge, this is the first study that utilizes both machine learning and network biology approaches to uncover Class II cancer genes in coordinating functionality in cancer networks and will illuminate our understanding of how genes are modulated in a tissue-specific network contribute to tumorigenesis and therapy development.
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Affiliation(s)
- Mehrab Ghanat Bari
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Choong Yong Ung
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA.
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Tao T, Powers JT, Shi H, Missios P, Perez-Atayde AR, Zhu S, Daley GQ, Look TA. Abstract 1040: LIN28B-mediated let-7 independent activation of AKT promotes neuroblastoma pathogenesis. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1040] [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
LIN28 is well known as a RNA-binding protein and a suppressor of microRNA biogenesis, by selectively blocking the processing of let-7 precursors. It plays diverse functions in cellular reprogramming, development, metabolism and tumorigenesis. Many of these functions are executed through its ability to inhibit let-7 maturation. However, little is known about its function independent of let-7. Here we made zebrafish transgenic lines expressing high levels of either wild-type or mutant LIN28B (does not block the maturation of let-7) in the peripheral sympathetic nervous system driven by the dopamine beta-hydroxylase promoter. We bred these lines with a transgenic zebrafish line overexpressing the MYCN oncogene in these cells. Either wild-type or mutant LIN28B overexpression accelerated the onset and increased the penetrance of MYCN-induced neuroblastoma, despite the fact that only wild-type LIN28B blocked let-7 maturation compared to MYCN-only tumors. Mechanistically, both wild-type and mutant LIN28B overexpression enhanced MYCN-induced hyperplasia by increasing cell proliferation in the sympathoadrenal lineage. Further studies revealed that overexpression of either wild-type or mutant LIN28B resulted in hyperphosphorylation of AKT on both Ser473 and Thr308 in zebrafish tumors and also serum-deprived human neuroblastoma cell lines. Both wild-type and mutant LIN28B interacted with IGF2BP1, a known interactor that increases stability and translation of a subset of RNAs. We found IGF2 RNA levels to be increased in response to either form of LIN28B. Coincident with IGF2 overexpression, IGF1R was phosphorylated, providing an explanation for PI3K-AKT activation in LIN28B overexpressing cells. Finally, overexpression of a constitutively active, myristoylated murine Akt2 (myr-mAkt2) alone in zebrafish induced ganglioneuroma in the interregnal gland (the zebrafish equivalent of the human adrenal medulla), without a requirement for MCYN overexpression. Thus, our studies indicate that overexpression of LIN28B leads to AKT activation mediated through its interaction with IGF2BP1 and subsequent upregulation of IGF2. This pathway provides a mechanism underlying enhanced transformation in LIN28B overexpressing neuroblastomas, which is independent of the inhibitory activity of LIN28B on let-7 maturation.
Citation Format: Ting Tao, John T. Powers, Hui Shi, Pavlos Missios, Antonio R. Perez-Atayde, Shizhen Zhu, George Q. Daley, Thomas A. Look. LIN28B-mediated let-7 independent activation of AKT promotes neuroblastoma pathogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1040. doi:10.1158/1538-7445.AM2017-1040
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Affiliation(s)
- Ting Tao
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Hui Shi
- 1Dana-Farber Cancer Institute, Boston, MA
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29
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Zimmerman MW, He S, Zhu S, Yang S, Zhou Y, Zon LI, Look AT. Abstract 3871: Modeling the chromatin and transcriptional landscape of MYC and MYCN driven neuroblastoma in zebrafish. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3871] [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
Elevated expression levels of MYC family genes are frequently observed in human cancer cells and correlate with tumor aggressiveness and poor prognosis. In neuroblastoma 40% of all cases are high-risk, of which 20% harbor amplification of the MYCN proto-oncogene. In high-risk cases lacking MYCN gene amplification, high expression levels of c-MYC (MYC) are often present and are associated with unfavorable histology and a poor survival. Unlike MYCN amplification, which is frequently observed in the presence of segmental chromosomal aberrations, MYC overexpression is not associated with genetic abnormalities or somatic mutations. In order to study this newly defined subgroup, we have created a novel transgenic zebrafish model in which overexpression of MYC alone in the peripheral sympathetic nervous system (PSNS) drives early-onset neuroblastoma in nearly every fish by seven weeks of age. The tumors resulting from MYC overexpression arise in the interrenal gland, which is the fish counterpart of the adrenal medulla, and are histologically identical to human neuroblastoma. We next performed the Assay for Transposase Accessible Chromatin (ATAC) sequencing and RNA-seq to identify open chromatin regions that correlate with activation of gene transcription. Lineage specific genes essential for neuronal precursor cell identity, such as PHOX2B, HAND2, and TFAP2A are highly expressed in both MYC-expressing and MYCN-amplified human neuroblastoma cell lines and are actively transcribed in zebrafish models of MYC and MYCN driven neuroblastoma. Furthermore, these studies reveal shared and differential regulatory of effects of MYC relative to MYCN activity in maintaining the malignant phenotype of neuroblastoma in vivo. Additional insight into the mechanisms of aberrant transcriptional regulation will inform the future design and use of therapeutic strategies targeting transcription in this high-risk malignancy of childhood.
Citation Format: Mark W. Zimmerman, Shuning He, Shizhen Zhu, Song Yang, Yi Zhou, Leonard I. Zon, A Thomas Look. Modeling the chromatin and transcriptional landscape of MYC and MYCN driven neuroblastoma in zebrafish [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3871. doi:10.1158/1538-7445.AM2017-3871
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Affiliation(s)
| | - Shuning He
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Song Yang
- 3Boston Children's Hospital, Boston, MA
| | - Yi Zhou
- 3Boston Children's Hospital, Boston, MA
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Zimmerman MW, He S, Shin J, Zhu S, Guo F, Mansour M, Reyon D, Joung JK, Quan J, Yusufzai T, Look AT. Abstract 2433: Loss of chd5-mediated gene repression synergizes with MYCN to accelerate neuroblastoma tumorigenesis in zebrafish. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2433] [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
Neuroblastoma is a malignancy of the peripheral sympathetic nervous system (PSNS) and accounts for 10-15% of cancer deaths among children. For the 40% of patients presenting with high-risk disease, current therapeutic approaches are insufficient and long-term survival is less than 50%. Along with genomic amplification of the MYCN oncogene, hemizygous loss of the 1p36 chromosomal region is a major risk factor in neuroblastoma. The human CHD5 gene is a neuronal specific chromatin remodeling helicase that maps to 1p36, and is thus frequently lost in high-risk neuroblastoma. Our laboratory has previously generated a faithful model of pediatric neuroblastoma in the zebrafish driven by overexpression of the MYCN oncogene in the PSNS (dbh:MYCN). Additionally, zebrafish chd5 mutant alleles were created using the newly developed gene editing technologies TALEN and CRISPR-Cas9. The resulting chd5 mutant fish exhibit abnormal development of the PSNS in the form of expansion of the superior cervical ganglia and enlargement of the interrenal gland (adrenal medulla). Haploinsufficiency for Chd5 combined with dbh:MYCN expression accelerates the onset and increases the penetrance of neuroblastoma tumorigenesis in zebrafish, indicating a tumor suppressive function. Elevated p-ERK and PCNA+ cells in tumor tissue indicates that loss of Chd5, cooperates with MYCN overexpression to accelerate neuroblast proliferation in vivo. Chd5 (in addition to Chd3 and Chd4) is a core member of the epigenetic regulatory NuRD complex, which also contains HDAC1-2, MTA1-3, MBD2-3, GATAD2A/B and RBBP4/7. The conserved biological function of Chd5 is to silence gene expression through the maintenance of a repressed chromatin state. Tumors deficient for Chd5 expression exhibit reduced levels of the H3K27me3 histone modification, a marker of facultatively repressed genes. Future studies will further explore the mechanism and function of Chd5 so that the pathways mediating tumor suppression can be elucidated and that essential proteins in these pathways can be targeted in ways that exploit the synthetic lethal relationships that are established.
Citation Format: Mark W. Zimmerman, Shuning He, Jimann Shin, Shizhen Zhu, Feng Guo, Marc Mansour, Deepak Reyon, J Keith Joung, Jinhua Quan, Timur Yusufzai, A Thomas Look. Loss of chd5-mediated gene repression synergizes with MYCN to accelerate neuroblastoma tumorigenesis in zebrafish. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2433.
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Affiliation(s)
| | - Shuning He
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Feng Guo
- 1Dana-Farber Cancer Institute, Boston, MA
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31
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He S, Mansour MR, Zimmerman MW, Ki DH, Layden HM, Akahane K, de Groh ED, Perez-Atayde AR, Zhu S, Epstein JA, Look AT. Abstract 2456: Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2456] [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
Earlier reports indicated that the role of Nf1 tumor suppressor gene in limiting sympathoadrenal cell growth during embryologic development is independent of its ability to down-modulate RAS-MAPK signaling. This finding raised the question of whether neuroblastoma pathogenesis was also accelerated by loss of a similar non-canonical function of NF1. To elucidate how loss of the NF1 tumor suppressor gene contributes to the development of high-risk neuroblastoma, we relied on a transgenic zebrafish model that overexpresses MYCN and harbors loss-of-function nf1 mutations. We show here that loss of nf1 leads to aberrant activation of RAS signaling in MYCN-induced neuroblastoma, promoting both increased tumor cell survival and rapid tumor cell proliferation. We demonstrate further that the GTPase-activating protein (GAP) activity of the (GAP)-related domain (GRD) is sufficient to suppress accelerated initiation of neuroblastoma in nf1-deficient zebrafish, even though this transgene is unable to restrict abnormal sympathoadrenal cell growth during embryologic development. Hence NF1 exhibits different activities in vivo in the normal development and tumorigenesis of the peripheral sympathetic nervous system. Our findings establish nf1-deficient zebrafish that overexpress MYCN as an ideal animal model system for investigating new strategies to improve treatment of very high risk neuroblastomas with aberrant RAS-MAPK activation. We are currently performing high-throughput in vivo drug analysis using these zebrafish with primary tumors.
Citation Format: Shuning He, Marc R. Mansour, Mark W. Zimmerman, Dong Hyuk Ki, Hillary M. Layden, Koshi Akahane, Eric D. de Groh, Antonio R. Perez-Atayde, Shizhen Zhu, Jonathan A. Epstein, A Thomas Look. Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2456.
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Affiliation(s)
- Shuning He
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Eric D. de Groh
- 3Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | - Shizhen Zhu
- 5Mayo Clinic Cancer Center and Mayo Clinic Center for Individualized Medicine, Rochester, MN
| | - Jonathan A. Epstein
- 3Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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32
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He S, Mansour MR, Zimmerman MW, Ki DH, Layden HM, Akahane K, Gjini E, de Groh ED, Perez-Atayde AR, Zhu S, Epstein JA, Look AT. Synergy between loss of NF1 and overexpression of MYCN in neuroblastoma is mediated by the GAP-related domain. eLife 2016; 5. [PMID: 27130733 PMCID: PMC4900799 DOI: 10.7554/elife.14713] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 01/26/2016] [Accepted: 04/26/2016] [Indexed: 11/20/2022] Open
Abstract
Earlier reports showed that hyperplasia of sympathoadrenal cell precursors during embryogenesis in Nf1-deficient mice is independent of Nf1’s role in down-modulating RAS-MAPK signaling. We demonstrate in zebrafish that nf1 loss leads to aberrant activation of RAS signaling in MYCN-induced neuroblastomas that arise in these precursors, and that the GTPase-activating protein (GAP)-related domain (GRD) is sufficient to suppress the acceleration of neuroblastoma in nf1-deficient fish, but not the hypertrophy of sympathoadrenal cells in nf1 mutant embryos. Thus, even though neuroblastoma is a classical “developmental tumor”, NF1 relies on a very different mechanism to suppress malignant transformation than it does to modulate normal neural crest cell growth. We also show marked synergy in tumor cell killing between MEK inhibitors (trametinib) and retinoids (isotretinoin) in primary nf1a-/- zebrafish neuroblastomas. Thus, our model system has considerable translational potential for investigating new strategies to improve the treatment of very high-risk neuroblastomas with aberrant RAS-MAPK activation. DOI:http://dx.doi.org/10.7554/eLife.14713.001 Neuroblastoma is one of the most common childhood cancers and is responsible for about 15% of childhood deaths due to cancer. The neuroblastoma tumors arise in cells that develop into and form part of the body’s nervous system. Many researchers have studied the genetics of this disease and have recognised common patterns. In particular, neuroblastomas can occur when a protein called MYCN is over-produced and a tumor suppressor protein called NF1 is lost. NF1 is a large protein with several distinct parts or domains. The most studied domain of NF1 is called the GRD, and it is mainly responsible for dampening down signals that cause cells to grow, specialize and survive. However, experiments in mice have revealed that this protein uses its other domains to control the normal development of part of the nervous system. He et al. wanted to know which domains of NF1 are important for suppressing the growth of neuroblastomas. The experiments were conducted in zebrafish that had been engineered to produce an excess of the human version of MYCN. When He et al. also deleted the gene for the zebrafish’s version of NF1, the fish quickly developed neuroblastomas. Supplying the zebrafish with just the GRD of NF1 was enough to supress the growth of the tumors. These experiments show that NF1 uses different domains and signalling pathways to regulate the normal development of part of the nervous system and to prevent formation of neuroblastoma. These engineered zebrafish represent an animal model of neuroblastoma that mimics the human disease in many ways. This model will make it possible to test new drug combinations and to find more effective treatments for neuroblastoma patients. DOI:http://dx.doi.org/10.7554/eLife.14713.002
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Affiliation(s)
- Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Marc R Mansour
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Hematology, UCL Cancer Institute, University College London, London, United Kingdom
| | - Mark W Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Dong Hyuk Ki
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Hillary M Layden
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Koshi Akahane
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Evisa Gjini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Eric D de Groh
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - Antonio R Perez-Atayde
- Department of Pathology, Children's Hospital Boston, Harvard Medical School, Boston, United States
| | - Shizhen Zhu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, United States.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, United States
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Penn Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States.,Institute for Regenerative Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, United States
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
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Abstract
Neuroblastoma, an important developmental tumor arising in the peripheral sympathetic nervous system (PSNS), accounts for approximately 10 % of all cancer-related deaths in children. Recent genomic analyses have identified a spectrum of genetic alterations in this tumor. Amplification of the MYCN oncogene is found in 20 % of cases and is often accompanied by mutational activation of the ALK (anaplastic lymphoma kinase) gene, suggesting their cooperation in tumor initiation and spread. Understanding how complex genetic changes function together in oncogenesis has been a continuing and daunting task in cancer research. This challenge was addressed in neuroblastoma by generating a transgenic zebrafish model that overexpresses human MYCN and activated ALK in the PSNS, leading to tumors that closely resemble human neuroblastoma and new opportunities to probe the mechanisms that underlie the pathogenesis of this tumor. For example, coexpression of activated ALK with MYCN in this model triples the penetrance of neuroblastoma and markedly accelerates tumor onset, demonstrating the interaction of these modified genes in tumor development. Further, MYCN overexpression induces adrenal sympathetic neuroblast hyperplasia, blocks chromaffin cell differentiation, and ultimately triggers a developmentally-timed apoptotic response in the hyperplastic sympathoadrenal cells. In the context of MYCN overexpression, activated ALK provides prosurvival signals that block this apoptotic response, allowing continued expansion and oncogenic transformation of hyperplastic neuroblasts, thus promoting progression to neuroblastoma. This application of the zebrafish model illustrates its value in rational assessment of the multigenic changes that define neuroblastoma pathogenesis and points the way to future studies to identify novel targets for therapeutic intervention.
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Affiliation(s)
- Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Cancer Center and Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55902, USA.
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
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34
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Liu L, Ma Z, Yan Z, Zhu S, Gao L. The ZrO₂ Formation in ZrB₂/SiC Composite Irradiated by Laser. Materials (Basel) 2015; 8:8745-8750. [PMID: 28793742 PMCID: PMC5458866 DOI: 10.3390/ma8125475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/30/2015] [Accepted: 12/03/2015] [Indexed: 11/29/2022]
Abstract
In order to clearly understand the details of ZrO2 formation during ablation, high intensity continuous laser was chosen to irradiate ZrB2/SiC. The results reveal that there are two different modes of ZrO2 formation depending on whether liquid SiO2 is present. When liquid SiO2 is present, ZrO2 generated by the oxidation of ZrB2 is firstly dissolved into SiO2. Then, ZrO2 will precipitate again, the temperature will decrease and the SiO2 will evaporate. Otherwise, the ZrB2 will be oxidized to ZrO2 directly.
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Affiliation(s)
- Ling Liu
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China.
- National Key Laboratory of Science and Technology on Materials under Shock and Impact, Beijing 100081, China.
| | - Zhuang Ma
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China.
- National Key Laboratory of Science and Technology on Materials under Shock and Impact, Beijing 100081, China.
| | - Zhenyu Yan
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China.
- National Key Laboratory of Science and Technology on Materials under Shock and Impact, Beijing 100081, China.
| | - Shizhen Zhu
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China.
- National Key Laboratory of Science and Technology on Materials under Shock and Impact, Beijing 100081, China.
| | - Lihong Gao
- School of Materials Science and Engineering, Beijing Institute of Technology, Beijing 100081, China.
- National Key Laboratory of Science and Technology on Materials under Shock and Impact, Beijing 100081, China.
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35
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Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, Anders L, Tian L, Zhang S, Wei JS, Khan J, Bramlett K, Rahman N, Capasso M, Iolascon A, Gerhard DS, Guidry Auvil JM, Young RA, Hakonarson H, Diskin SJ, Look AT, Maris JM. Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. Nature 2015; 528:418-21. [PMID: 26560027 DOI: 10.1038/nature15540] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 09/02/2015] [Indexed: 12/30/2022]
Abstract
Neuroblastoma is a paediatric malignancy that typically arises in early childhood, and is derived from the developing sympathetic nervous system. Clinical phenotypes range from localized tumours with excellent outcomes to widely metastatic disease in which long-term survival is approximately 40% despite intensive therapy. A previous genome-wide association study identified common polymorphisms at the LMO1 gene locus that are highly associated with neuroblastoma susceptibility and oncogenic addiction to LMO1 in the tumour cells. Here we investigate the causal DNA variant at this locus and the mechanism by which it leads to neuroblastoma tumorigenesis. We first imputed all possible genotypes across the LMO1 locus and then mapped highly associated single nucleotide polymorphism (SNPs) to areas of chromatin accessibility, evolutionary conservation and transcription factor binding sites. We show that SNP rs2168101 G>T is the most highly associated variant (combined P = 7.47 × 10(-29), odds ratio 0.65, 95% confidence interval 0.60-0.70), and resides in a super-enhancer defined by extensive acetylation of histone H3 lysine 27 within the first intron of LMO1. The ancestral G allele that is associated with tumour formation resides in a conserved GATA transcription factor binding motif. We show that the newly evolved protective TATA allele is associated with decreased total LMO1 expression (P = 0.028) in neuroblastoma primary tumours, and ablates GATA3 binding (P < 0.0001). We demonstrate allelic imbalance favouring the G-containing strand in tumours heterozygous for this SNP, as demonstrated both by RNA sequencing (P < 0.0001) and reporter assays (P = 0.002). These findings indicate that a recently evolved polymorphism within a super-enhancer element in the first intron of LMO1 influences neuroblastoma susceptibility through differential GATA transcription factor binding and direct modulation of LMO1 expression in cis, and this leads to an oncogenic dependency in tumour cells.
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Affiliation(s)
- Derek A Oldridge
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Medical Scientist Training Program, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew C Wood
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, Auckland Region 1142, New Zealand
| | - Nina Weichert-Leahey
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Ian Crimmins
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Robyn Sussman
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Cynthia Winter
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lee D McDaniel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Maura Diamond
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Lori S Hart
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Shizhen Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Adam D Durbin
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA
| | - Lars Anders
- Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA
| | - Lifeng Tian
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Shile Zhang
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Jun S Wei
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Javed Khan
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
| | | | | | - Mario Capasso
- University of Naples Federico II, 80131 Naples, Italy.,CEINGE Biotecnologie Avanzate, 80131 Naples, Italy
| | - Achille Iolascon
- University of Naples Federico II, 80131 Naples, Italy.,CEINGE Biotecnologie Avanzate, 80131 Naples, Italy
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Jaime M Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research and MIT, Boston, Massachusetts 02142, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Sharon J Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104, USA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA.,Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,Abramson Family Cancer Research Institute, Philadelphia, Pennsylvania 19104, USA
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Zimmerman MW, He S, Shin J, Zhu S, Mansour M, Joung K, Quan J, Yusufzai T, Look AT. Abstract 476: Loss of chd5-mediated tumor suppression accelerates MYCN-driven neuroblastoma tumorigenesis in zebrafish. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-476] [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
Neuroblastoma is a childhood tumor of the peripheral sympathetic nervous system (PSNS) that originates from cells of the primitive neural crest. For the 40% of patients with high-risk disease, current therapies are often ineffective and long-term survival remains obstinately low. A major risk factor in neuroblastoma is hemizygous loss of the 1p36 chromosomal region, which has long been suspected to harbor one or more powerful tumor suppressor genes. Our studies indicate that loss of Chromodomain helicase DNA-binding protein 5 (chd5), which is in this deleted region, cooperates with MYCN overexpression to accelerate in vivo neuroblastoma tumorigenesis. Zebrafish chd5-null alleles were created utilizing both zinc-finger nuclease and TALEN technology. The resulting chd5 mutant fish exhibit abnormal development of the PSNS in the form of expansion of the superior cervical ganglia and enlargement of the interrenal gland (adrenal medulla). In order to examine the effect of chd5 haploinsuficiency on in vivo neuroblastoma tumorigenesis, chd5 mutant fish were crossed with the dbh:MYCN transgenic model resulting in neuroblastoma tumors. Consistent with a tumor suppressor function, chd5 haploinsufficient fish exhibit an accelerated neuroblastoma phenotype with tumors present beginning as early as 6 weeks compared to 15 weeks observed in wildtype fish. The chd5 protein can serve as one of two enzymatic components of the nucleosome remodeling and histone deacetylase (NuRD) complex, which is a repressor of gene expression and is reported to have diverse roles in regulating chromatin organization, developmental signaling and gene stability. Future studies will examine the mechanism and function of chd5 so that the pathways mediating tumor suppression can be elucidated and that essential proteins in these pathways can be targeted in ways that exploit the synthetic lethal relationships that are established.
Citation Format: Mark W. Zimmerman, Shuning He, Jimann Shin, Shizhen Zhu, Marc Mansour, Keith Joung, Jinhua Quan, Timur Yusufzai, A. Thomas Look. Loss of chd5-mediated tumor suppression accelerates MYCN-driven neuroblastoma tumorigenesis in zebrafish. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 476. doi:10.1158/1538-7445.AM2015-476
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Affiliation(s)
| | - Shuning He
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | - Keith Joung
- 2Massachusetts General Hospital, Charlestown, MA
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Ung CY, Guo F, Zhang X, Zhu Z, Zhu S. Mosaic zebrafish transgenesis for functional genomic analysis of candidate cooperative genes in tumor pathogenesis. J Vis Exp 2015:52567. [PMID: 25867597 PMCID: PMC4401404 DOI: 10.3791/52567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comprehensive genomic analysis has uncovered surprisingly large numbers of genetic alterations in various types of cancers. To robustly and efficiently identify oncogenic "drivers" among these tumors and define their complex relationships with concurrent genetic alterations during tumor pathogenesis remains a daunting task. Recently, zebrafish have emerged as an important animal model for studying human diseases, largely because of their ease of maintenance, high fecundity, obvious advantages for in vivo imaging, high conservation of oncogenes and their molecular pathways, susceptibility to tumorigenesis and, most importantly, the availability of transgenic techniques suitable for use in the fish. Transgenic zebrafish models of cancer have been widely used to dissect oncogenic pathways in diverse tumor types. However, developing a stable transgenic fish model is both tedious and time-consuming, and it is even more difficult and more time-consuming to dissect the cooperation of multiple genes in disease pathogenesis using this approach, which requires the generation of multiple transgenic lines with overexpression of the individual genes of interest followed by complicated breeding of these stable transgenic lines. Hence, use of a mosaic transient transgenic approach in zebrafish offers unique advantages for functional genomic analysis in vivo. Briefly, candidate transgenes can be coinjected into one-cell-stage wild-type or transgenic zebrafish embryos and allowed to integrate together into each somatic cell in a mosaic pattern that leads to mixed genotypes in the same primarily injected animal. This permits one to investigate in a faster and less expensive manner whether and how the candidate genes can collaborate with each other to drive tumorigenesis. By transient overexpression of activated ALK in the transgenic fish overexpressing MYCN, we demonstrate here the cooperation of these two oncogenes in the pathogenesis of a pediatric cancer, neuroblastoma that has resisted most forms of contemporary treatment.
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Affiliation(s)
- Choong Yong Ung
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic College of Medicine, Center for Individualized Medicine
| | - Feng Guo
- Tufts University School of Medicine
| | - Xiaoling Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic
| | - Zhihui Zhu
- Department of Biochemistry and Molecular Biology, Mayo Clinic
| | - Shizhen Zhu
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic College of Medicine, Center for Individualized Medicine; Department of Biochemistry and Molecular Biology, Mayo Clinic;
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Zhu S, Wood A, He S, Stanton R, Guo F, Maris J, Look AT. Abstract 356: Role of the LMO1 oncogene in neuroblastoma pathogenesis. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-356] [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
Neuroblastoma, an embryonic tumor of the peripheral sympathetic nervous system (PSNS), accounts for 10% of all childhood cancer deaths. We recently developed a robust zebrafish model of neuroblastoma and demonstrated that activated ALK synergizes with MYCN by inhibiting a developmentally-timed apoptotic response that is otherwise induced by MYCN (Zhu et.al. Cancer Cell, 2012). We have now used this model to provide evidence in support of the results of a neuroblastoma genome-wide association study (GWAS) showing that common variation within the LIM domain-only 1 (LMO1) gene locus is highly associated with the development of advanced neuroblastoma and may function as an oncogene in established disease (Wang K et.al. Nature, 2011). We are collaborating because our zebrafish system provides a robust in vivo tumor model to investigate the underlying mechanisms through which LMO1 overexpression contributes to malignant transformation. Here we developed transgenic lines in which LMO1 is overexpressed in the PSNS under control of the dopamine-beta-hydroxylase (dβh) promoter. We observed that overexpression of LMO1 in three individual transgenic lines synergized with MYCN to accelerate the onset of neuroblastoma in the interrenal gland (IRG), the zebrafish analogue of the adrenal medulla. Tumors began to appear at 13 weeks in transgenic fish overexpressing MYCN alone and this latency was shortened dramatically to 5 weeks (p=0.02) and the penetrance was increased more than three-fold in the transgenic fish coexpressing both MYCN and LMO1. In addition, we found that coexpression of LMO1 with activated ALK induced neuroblastoma, which is the first time in our model system that neuroblastoma has been induced without MYCN overexpression. Thus, the zebrafish model system appears to be robust for “functional genomics analysis” to provide in vivo evidence and investigate mechanisms and pathways underlying new associations emerging from GWAS, tumor genome resequencing and other genome-wide technologies that are currently under intense investigation in human cancers.
Citation Format: Shizhen Zhu, Andrew Wood, Shuning He, Rebecca Stanton, Feng Guo, John Maris, A. Thomas Look. Role of the LMO1 oncogene in neuroblastoma pathogenesis. [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 356. doi:10.1158/1538-7445.AM2013-356
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Affiliation(s)
| | - Andrew Wood
- 2Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Feng Guo
- 1Dana-Farber Cancer Inst., Boston, MA
| | - John Maris
- 2Children's Hospital of Philadelphia, Philadelphia, PA
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Zhu S, Lee JS, Guo F, Shin J, Perez-Atayde AR, Kutok JL, Rodig SJ, Neuberg DS, Helman D, Feng H, Stewart RA, Wang W, George RE, Kanki J, Look AT. Abstract 4252: Activated ALK collaborates with MYCN in neuroblastoma pathogenesis. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4252] [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
Neuroblastoma is a developmental tumor that arises in the peripheral sympathetic nervous system and accounts for 10% of all cancer-related deaths in children. The anaplastic lymphoma kinase (ALK) gene is mutationally activated in a subset of primary neuroblastomas, including those with MYCN gene amplification, suggesting pathogenic cooperation. Because the mechanism underlying this cooperation is unclear, we generated a novel transgenic zebrafish model that overexpresses human MYCN and activated ALK in the peripheral sympathetic nervous system to analyze their interaction. The expression of MYCN in this model induces neuroblastomas in the inter-renal gland, the zebrafish analogue of the adrenal medulla, which is the site of origin observed in approximately half of childhood neuroblastomas. Furthermore, the tumors resemble human neuroblastomas histologically, immunohistochemically and ultrastructurally. Concomitant expression of activated ALK with MYCN in this model profoundly accelerates the onset of neuroblastoma and markedly increases disease penetrance. Detailed in vivo analyses show that MYCN overexpression induces adrenal sympathetic neuroblast hyperplasia, blocks chromaffin cell differentiation, and triggers a developmentally-timed apoptotic response in the hyperplastic sympathoadrenal cells. Coexpression of activated ALK with MYCN provides prosurvival signals that block this apoptotic response and allow continued expansion and oncogenic transformation of hyperplastic neuroblasts. Taken together, these findings provide a mechanism for the synergistic interplay of MYCN with activated ALK in neuroblastoma pathogenesis and demonstrate the utility of the zebrafish model in understanding human disease processes that may aid the development of improved therapeutic strategies.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4252. doi:1538-7445.AM2012-4252
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Affiliation(s)
| | | | - Feng Guo
- 1Dana-Farber Cancer Inst., Boston, MA
| | | | | | | | | | | | | | - Hui Feng
- 1Dana-Farber Cancer Inst., Boston, MA
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Zhu S, Lee JS, Guo F, Shin J, Perez-Atayde AR, Kutok JL, Rodig SJ, Neuberg DS, Helman D, Feng H, Stewart RA, Wang W, George RE, Kanki JP, Look AT. Activated ALK collaborates with MYCN in neuroblastoma pathogenesis. Cancer Cell 2012; 21:362-73. [PMID: 22439933 PMCID: PMC3315700 DOI: 10.1016/j.ccr.2012.02.010] [Citation(s) in RCA: 245] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 11/23/2011] [Accepted: 02/07/2012] [Indexed: 12/14/2022]
Abstract
Amplification of the MYCN oncogene in childhood neuroblastoma is often accompanied by mutational activation of ALK (anaplastic lymphoma kinase), suggesting their pathogenic cooperation. We generated a transgenic zebrafish model of neuroblastoma in which MYCN-induced tumors arise from a subpopulation of neuroblasts that migrate into the adrenal medulla analog following organogenesis. Coexpression of activated ALK with MYCN in this model triples the disease penetrance and markedly accelerates tumor onset. MYCN overexpression induces adrenal sympathetic neuroblast hyperplasia, blocks chromaffin cell differentiation, and ultimately triggers a developmentally-timed apoptotic response in the hyperplastic sympathoadrenal cells. Coexpression of activated ALK with MYCN provides prosurvival signals that block this apoptotic response and allow continued expansion and oncogenic transformation of hyperplastic neuroblasts, thus promoting progression to neuroblastoma.
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Affiliation(s)
- Shizhen Zhu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Jeong-Soo Lee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Feng Guo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Jimann Shin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Antonio R. Perez-Atayde
- Department of Pathology, Children's Hospital Boston, Harvard Medical School, Boston MA, 02115, USA
| | - Jeffery L. Kutok
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston MA, 02115, USA
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston MA, 02115, USA
| | - Donna S. Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Daniel Helman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Hui Feng
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Rodney A. Stewart
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Wenchao Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - Rani E. George
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - John P. Kanki
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA, 02115, USA
- Correspondence: (A.T.L.)
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Abstract
Rho small GTPases play pivotal roles in a variety of dynamic cellular processes including cytoskeleton rearrangement, cell migration, cell proliferation, cell survival, and gene regulation. However, their functions in vivo are much less understood. Recently, the zebrafish, Danio rerio has emerged as a powerful model organism for developmental and genetic studies. Zebrafish embryos have many unique characteristics, such as optical transparency, external fertilization and development, and amenability for various molecular manipulations including morpholino oligo-mediated gene knockdown, mRNA or DNA overexpression-induced gain of function or rescue, in situ hybridization (ISH) with riboprobes for gene expression, western blot for protein analysis, small-molecule inhibition on signaling pathways, and bioimaging for tracking of molecular events. Taking many of such advantages, we have demonstrated the role of rhoA small GTPase in the control of gastrulation cell movements and cell survival during early zebrafish embryogenesis, linking RhoA functions to at least the noncanonical Wnt, Mek/Erk, and Bcl2 signaling nodes in vivo. Here, we describe the use of such techniques, including gene knockdown by morpholino oligo, functional rescue by mRNA overexpression, microinjection, ISH, western blot analysis and pharmacological inhibition of signaling pathways by small molecule inhibitors, with special considerations on their merits, potential drawbacks, and adaptation which could pave the way to our better understanding of the roles of various classes of small GTPases in regulating cell dynamics and development in vivo.
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Affiliation(s)
- Shizhen Zhu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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42
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Gutierrez A, Grebliunaite R, Feng H, Kozakewich E, Zhu S, Guo F, Payne E, Mansour M, Dahlberg SE, Neuberg DS, den Hertog J, Prochownik EV, Testa JR, Harris M, Kanki JP, Look AT. Pten mediates Myc oncogene dependence in a conditional zebrafish model of T cell acute lymphoblastic leukemia. J Biophys Biochem Cytol 2011. [DOI: 10.1083/jcb1941oia4] [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: 11/22/2022] Open
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Gutierrez A, Grebliunaite R, Feng H, Kozakewich E, Zhu S, Guo F, Payne E, Mansour M, Dahlberg SE, Neuberg DS, den Hertog J, Prochownik EV, Testa JR, Harris M, Kanki JP, Look AT. Pten mediates Myc oncogene dependence in a conditional zebrafish model of T cell acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2011; 208:1595-603. [PMID: 21727187 PMCID: PMC3149218 DOI: 10.1084/jem.20101691] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Loss-of-function mutations in pten genes, or expression of a constitutively active version of Akt2, render T-ALL cell survival and disease progression independent of Myc. The MYC oncogenic transcription factor is overexpressed in most human cases of T cell acute lymphoblastic leukemia (T-ALL), often downstream of mutational NOTCH1 activation. Genetic alterations in the PTEN–PI3K–AKT pathway are also common in T-ALL. We generated a conditional zebrafish model of T-ALL in which 4-hydroxytamoxifen (4HT) treatment induces MYC activation and disease, and withdrawal of 4HT results in T-ALL apoptosis and tumor regression. However, we found that loss-of-function mutations in zebrafish pten genes, or expression of a constitutively active Akt2 transgene, rendered tumors independent of the MYC oncogene and promoted disease progression after 4HT withdrawal. Moreover, MYC suppresses pten mRNA levels, suggesting that Akt pathway activation downstream of MYC promotes tumor progression. Our findings indicate that Akt pathway activation is sufficient for tumor maintenance in this model, even after loss of survival signals driven by the MYC oncogene.
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Affiliation(s)
- Alejandro Gutierrez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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Zhu S, Lee JS, Shin J, Perez-Atayde AR, Kutok JL, Rodig SJ, Neuberg DS, Guo F, Helman D, Feng H, Stewart RA, Wang W, George RE, Kanki JP, Look AT. Abstract 4296: Activated ALK accelerates the onset of neuroblastoma in MYCN-transgenic zebrafish. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-4296] [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
Neuroblastoma is the most common extracranial solid tumor in children and originates during development of the peripheral sympathetic nervous system. Advanced-stage disease and a poor outcome are associated with amplification of the MYCN oncogene, often in combination with mutational activation or amplification of another oncogene ALK (anaplastic lymphoma kinase), suggesting that they cooperate in neuroblastoma pathogenesis. To investigate this possibility, we generated a transgenic zebrafish model of neuroblastoma in which human MYCN is expressed under the control of the dopamine-beta-hydroxylase promoter, and show that the resultant tumors recapitulate childhood neuroblastomas histologically, immunohistochemically, and ultrastructurally. Surprisingly, the tumors arise from a subpopulation of neuroblasts that migrate into the adrenal analogue (interrenal gland) in the zebrafish after organogenesis is complete. Coexpression of activated ALK with MYCN markedly increased the frequency of neuroblastoma and accelerated the time of onset, providing conclusive evidence for synergistic interplay between these two oncogenes in neuroblastoma pathogenesis.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4296. doi:10.1158/1538-7445.AM2011-4296
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Affiliation(s)
| | | | | | | | | | | | | | - Feng Guo
- 1Dana-Farber Cancer Inst., Boston, MA
| | | | - Hui Feng
- 1Dana-Farber Cancer Inst., Boston, MA
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Lee JS, Padmanabhan A, Shin J, Zhu S, Guo F, Kanki JP, Epstein JA, Look AT. Oligodendrocyte progenitor cell numbers and migration are regulated by the zebrafish orthologs of the NF1 tumor suppressor gene. Hum Mol Genet 2010; 19:4643-53. [PMID: 20858602 DOI: 10.1093/hmg/ddq395] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Neurofibromatosis type 1 is the most commonly inherited human cancer predisposition syndrome. Neurofibromin (NF1) gene mutations lead to increased risk of neurofibromas, schwannomas, low grade, pilocytic optic pathway gliomas, as well as malignant peripheral nerve sheath tumors and glioblastomas. Despite the evidence for NF1 tumor suppressor function in glial cell tumors, the mechanisms underlying transformation remain poorly understood. In this report, we used morpholinos to knockdown the two nf1 orthologs in zebrafish and show that oligodendrocyte progenitor cell (OPC) numbers are increased in the developing spinal cord, whereas neurons are unaffected. The increased OPC numbers in nf1 morphants resulted from increased proliferation, as detected by increased BrdU labeling, whereas TUNEL staining for apoptotic cells was unaffected. This phenotype could be rescued by the forced expression of the GTPase-activating protein (GAP)-related domain of human NF1. In addition, the in vivo analysis of OPC migration following nf1 loss using time-lapse microscopy demonstrated that olig2-EGFP(+) OPCs exhibit enhanced cell migration within the developing spinal cord. OPCs pause intermittently as they migrate, and in nf1 knockdown animals, they covered greater distances due to a decrease in average pause duration, rather than an increase in velocity while in motion. Interestingly, nf1 knockdown also leads to an increase in ERK signaling, principally in the neurons of the spinal cord. Together, these results show that negative regulation of the Ras pathway through the GAP activity of NF1 limits OPC proliferation and motility during development, providing insight into the oncogenic mechanisms through which NF1 loss contributes to human glial tumors.
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Affiliation(s)
- Jeong-Soo Lee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
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Lee JS, Zhu S, Shin J, Perez-Atayde AR, Feng H, Guo F, Helman D, Wang W, Stewart RA, George R, Kanki J, Look AT. Abstract LB-162: The onset of MYCN overexpression-induced neuroblastoma is accelerated by ALK mutation in zebrafish. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-lb-162] [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
Neuroblastoma (NB) is the most common extracranial solid tumor in infancy and originates in the peripheral sympathetic nervous system (PSNS). High-risk NB is fatal in the majority of patients, despite intensive myeloablative chemotherapy. The MYCN oncogene is amplified in over 20% of NB, particularly in those with highest risk treatment failure. We have developed a zebrafish NB model by overexpressing human MYCN under the control of the dopamine-beta-hydroxylase (D) promoter specific for noradrenergic cells in the PSNS. Fish from this stable transgenic line developed tumors as early as 4 months of age with approximately 20% penetrance at 8 months of age. The tumors resemble human NB histologically, immunohistochemically, and ultrastructurally. The expression of MYCN suppressed the normal development of PSNS neurons and chromaffin cells in the head kidney during embryogenesis and in young adult fish. In some fish, tumor cells began to repopulate the interrenal gland of the head kidney by 2 months of age. Germline and somatic activating mutations have been identified in the ALK gene, which encodes a receptor tyrosine kinase, in human NB, including those with MYCN amplification. To assess cooperativity between amplified MYCN and mutant ALK genes in transformation, we generated a zebrafish stable transgenic line in which the activated mutant form of ALK (F1174L) was expressed under the control of the DßH promoter. These transgenic animals did not display an abnormal phenotype nor did they develop tumors during the first 6 months of life. In contrast, mutant ALK expression accelerated the onset of MYCN-induced neuroblastoma when the 2 genes were co-expressed in double transgenic fish, indicating that MYCN over-expression and activating ALK mutations can cooperate in tumorigenesis. Although co-expression of mutant ALK accelerated the onset of tumors, it did not rescue the MYCN-induced suppression of PSNS development, suggesting that an as-yet-unidentified tumor suppressor gene, possibly located on distal 1p in the human genome, may be lost to fulfill this role in NB tumorigenesis.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-162.
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Affiliation(s)
| | | | | | | | - Hui Feng
- 1Dana-Farber Cancer Inst., Boston, MA
| | - Feng Guo
- 1Dana-Farber Cancer Inst., Boston, MA
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47
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Zhu S, Liu L, Korzh V, Gong Z, Low BC. RhoA acts downstream of Wnt5 and Wnt11 to regulate convergence and extension movements by involving effectors Rho Kinase and Diaphanous: Use of zebrafish as an in vivo model for GTPase signaling. Cell Signal 2006; 18:359-72. [PMID: 16019189 DOI: 10.1016/j.cellsig.2005.05.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Accepted: 05/06/2005] [Indexed: 01/09/2023]
Abstract
Gastrulation shapes the early embryos by forming three germ layers, ectoderm, mesoderm and endoderm. In vertebrates, this process requires massive cell rearrangement including convergence and extension (CE) movements that involve narrowing and lengthening of embryonic tissues as well as cell elongation. Such polarization and movements require precise reorganization and regulation of the cytoskeleton network and cell adhesion. Rho small GTPases are key regulators for dynamic actin cytoskeleton. However, the signaling mechanisms underlying their functions in CE remain to be further elucidated. We have cloned the zebrafish Danio rerio rhoA and by capitalizing on the specific functional knockdown using morpholinos against rhoA and the availability of CE mutants defective in Wnt signaling, we showed that rhoA morphants were reminiscent to noncanonical wnt mutants with serious disruption in CE movements. Injection of rhoA mRNA effectively rescued such defects in wnt5 and wnt11 mutants. Furthermore, CE defects in rhoA knockdown or wnt mutants can be suppressed through functional bypass after ectopic expression of the two mammalian Rho effectors, the Rho kinase and Diaphanous (mDia). These results provide the first evidence that the RhoA in vivo acts downstream of Wnt5 and Wnt11 to effect, without affecting cell fates, on the CE movements in zebrafish embryos. Significantly, it elicits such effect via both effectors, Rho kinase and Dia. These findings also support the versatility of the zebrafish as a model to further investigate the roles of various classes of small GTPases in regulating cell dynamics in vivo.
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Affiliation(s)
- Shizhen Zhu
- Cell Signaling and Developmental Biology Laboratory, National University of Singapore, 14 Science Drive 4, Singapore 117543, The Republic of Singapore
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Shi ZJ, Sun DJ, Wang ZJ, Tao ZH, Pan SX, Liu XJ, Zhang SQ, Ou ZY, Zhu SZ, Li QJ, Chang J, Wu RZ, Deng SS, Zheng XQ. A brief introduction to the research achievement on the strategy and technical measures for interrupting the transmission of lymphatic filariasis in China. Zhongguo Ji Sheng Chong Xue Yu Ji Sheng Chong Bing Za Zhi 2003; 19:110-2. [PMID: 12572001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
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Abstract
By mimicking the partial spatial structure of the dimer of the l-aspartase subunit, the central ten-helix bundle, and an "active site" between the cleft of domain 1 (D1) and domain 3 (D3) from different subunits, we designed l-aspartase variants, in which D1D2 and D2D3 were ligated with a random hexapeptide loop. As expected, we obtained the variant with the highest activity (relative activity is 21.3% of the native enzyme, named as drAsp017) by in vitro selection. The molecular weight of this variant, obtained from size-exclusion column chromatography, is about 81 kDa, which indicates that it is indeed a monomer, whereas native l-aspartase is a tetramer. The activity-reversibility of drAsp017 (10(-7) m) was 80% after incubation for 30 min at 50 degrees C, while native enzyme only retained about 17% under the same conditions. Reactivation of drAsp017 denatured in 4 m guanidine HCl was independent of protein concentration at up to 20 x 10(-8) m at 25 degrees C, whereas the protein concentration of native enzyme strongly affected its reactivation under the above conditions. The sensitivity of drAsp017 (10(-7) m) to effective factors in the fumarate-amination reaction compared with native enzyme was also determined. Half-saturating concentrations of the activator l-aspartate and Mg2+ for drAsp017 (0.8 and 0.5 mm, respectively) are much higher than that of the native enzyme (0.10 and 0.15 mm, respectively). The data show that a monomeric l-aspartase is obtained by in vitro selection. Thus, the conversion of oligomeric proteins into their functional monomers could have important applications.
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Affiliation(s)
- Xiangduo Kong
- Key Lab for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130023, Peoples Republic of China
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Abstract
A circular RNA-DNA enzyme with higher activity to target RNA cleavage and higher stability than that of the hammerhead ribozyme in the presence of RNase A was obtained by in vitro selection. The molecule is composed of a catalytic domain of 22-mer ribonucleotides derived from the hammerhead ribozyme and a fragment of 55-mer deoxyribonucleotides. The DNA fragment contains two substrate-binding domains (9-mer and 6-mer, respectively) and a "regulation domain" (assistant 40-mer DNA with 20-mer random deoxyribonucleotides sequence), which probably play the role in the regulation of flexibility and rigidity of the circular RNA-DNA enzyme. The above results suggest that the circular RNA-DNA enzyme will have a great prospect in gene-targeting therapies.
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Affiliation(s)
- Xiang-duo Kong
- Key Lab for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, 130023, People's Republic of China
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