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Copperman J, Mclean IC, Gross SM, Singh J, Chang YH, Zuckerman DM, Heiser LM. Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576248. [PMID: 38293173 PMCID: PMC10827140 DOI: 10.1101/2024.01.18.576248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Extracellular signals induce changes to molecular programs that modulate multiple cellular phenotypes, including proliferation, motility, and differentiation status. The connection between dynamically adapting phenotypic states and the molecular programs that define them is not well understood. Here we develop data-driven models of single-cell phenotypic responses to extracellular stimuli by linking gene transcription levels to "morphodynamics" - changes in cell morphology and motility observable in time-lapse image data. We adopt a dynamics-first view of cell state by grouping single-cell trajectories into states with shared morphodynamic responses. The single-cell trajectories enable development of a first-of-its-kind computational approach to map live-cell dynamics to snapshot gene transcript levels, which we term MMIST, Molecular and Morphodynamics-Integrated Single-cell Trajectories. The key conceptual advance of MMIST is that cell behavior can be quantified based on dynamically defined states and that extracellular signals alter the overall distribution of cell states by altering rates of switching between states. We find a cell state landscape that is bound by epithelial and mesenchymal endpoints, with distinct sequences of epithelial to mesenchymal transition (EMT) and mesenchymal to epithelial transition (MET) intermediates. The analysis yields predictions for gene expression changes consistent with curated EMT gene sets and provides a prediction of thousands of RNA transcripts through extracellular signal-induced EMT and MET with near-continuous time resolution. The MMIST framework leverages true single-cell dynamical behavior to generate molecular-level omics inferences and is broadly applicable to other biological domains, time-lapse imaging approaches and molecular snapshot data.
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Affiliation(s)
- Jeremy Copperman
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland OR 97239, U.S.A
| | - Ian C. Mclean
- Department of Biomedical Engineering, Oregon Health and Science University, Portland OR 97239, U.S.A
| | | | - Jalim Singh
- Knight Cancer Institute, Oregon Health and Science University, Portland OR 97239, U.S.A
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland OR 97239, U.S.A
- Knight Cancer Institute, Oregon Health and Science University, Portland OR 97239, U.S.A
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland OR 97239, U.S.A
- Knight Cancer Institute, Oregon Health and Science University, Portland OR 97239, U.S.A
| | - Laura M. Heiser
- Department of Biomedical Engineering, Oregon Health and Science University, Portland OR 97239, U.S.A
- Knight Cancer Institute, Oregon Health and Science University, Portland OR 97239, U.S.A
- Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland OR 97239, U.S.A
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2
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Dave U, Narain P, Mishra D, Gomes J. Aggregation of E121K mutant D-amino acid oxidase and ubiquitination-mediated autophagy mechanisms leading to amyotrophic lateral sclerosis. J Neurol Sci 2024; 456:122845. [PMID: 38134563 DOI: 10.1016/j.jns.2023.122845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 11/04/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a terminal adult-onset neuromuscular disorder. Our group has been studying this illness and previously reported novel mutations and rare mutations in a study using next-generation sequencing of DNA samples from Indian ALS patients. In this paper, we focus on the E121K mutation in the DAO gene to understand how it leads to ALS. Our experiments in SH-SY5Y cells indicate that the E121K mutation results in the accumulation of mutant protein aggregates, a change in cell morphology, and the death of neuronal cells. These protein aggregates get ubiquitinated and cause an imbalance in autophagy regulation. We observed an increase in the cellular concentrations of p62, OPTN, and LC3II. Through confocal microscopy studies, we show that the binding of p62 with ubiquitinated aggregates and its recruitment to LC3II mediates autophagosome generation. These relative changes in the key partners in autophagy increase cell death in cells harboring the E121K mutation and is a probable mechanism leading to ALS.
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Affiliation(s)
- Upma Dave
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Priyam Narain
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Dibyakanti Mishra
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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3
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Abdelmessih R, Xu J, Hung FR, Auguste DT. Integration of an LPAR1 Antagonist into Liposomes Enhances Their Internalization and Tumor Accumulation in an Animal Model of Human Metastatic Breast Cancer. Mol Pharm 2023; 20:5500-5514. [PMID: 37844135 PMCID: PMC10631474 DOI: 10.1021/acs.molpharmaceut.3c00348] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/29/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023]
Abstract
Lysophosphatidic acid receptor 1 (LPAR1) is elevated in breast cancer. The deregulation of LPAR1, including the function and level of expression, is linked to cancer initiation, progression, and metastasis. LPAR1 antagonists, AM095 or Ki16425, may be effective therapeutic molecules, yet their limited water solubility hinders in vivo delivery. In this study, we report on the synthesis of two liposomal formulations incorporating AM095 or Ki16425, embedded within the lipid bilayer, as targeted nanocarriers for metastatic breast cancer (MBC). The data show that the Ki16425 liposomal formulation exhibited a 50% increase in internalization by MBC mouse epithelial cells (4T1) and a 100% increase in tumor accumulation in a mouse model of MBC compared with that of a blank liposomal formulation (control). At the same time, normal mouse epithelial cells (EpH-4Ev) internalized the Ki16425 liposomal formulation 25% lesser than the control formulation. Molecular dynamics simulations show that the integration of AM095 or Ki16425 modified the physical and mechanical properties of the lipid bilayer, making it more flexible in these liposomal formulations compared with liposomes without drug. The incorporation of an LPAR1 antagonist within a liposomal drug delivery system represents a viable therapeutic approach for targeting the LPA-LPAR1 axis, which may hinder the progression of MBC.
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Affiliation(s)
- Rudolf
G. Abdelmessih
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jiaming Xu
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Francisco R. Hung
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Debra T. Auguste
- Department of Chemical Engineering, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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4
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Dave U, Khan S, Gomes J. Characterization of E121K mutation of D-amino acid oxidase - Insights into mechanisms leading to amyotrophic lateral sclerosis. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140947. [PMID: 37558109 DOI: 10.1016/j.bbapap.2023.140947] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/29/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
D-amino acid oxidase (DAO) maintains the intracellular d-serine level which modulates the activity of the N-methyl-d-aspartate receptor and its dysfunction has been linked to several neurodegenerative disorders. In targeted next-generation sequencing study by our group, E121K mutation in DAO was associated with amyotrophic lateral sclerosis (ALS) in patients from India. However, variations in molecular mechanisms caused by this mutation which leads to ALS have not been studied. Hence, we carried out comparative biophysical characterization and assay studies of the wildtype- and mutant E121K-DAO. We observed that the purified E121K-DAO was inactive and exhibited a lower affinity for the FAD cofactor and benzoate inhibitor. Structural studies revealed that the E121K mutant has higher beta-sheet content, melting temperature, and oligomeric states compared to the wildtype. Kinetic study of aggregation of the variants using thioflavin-T confirmed that the E121K-DAO was more prone to aggregation. Microscopic visualization showed that the aggregation proceeds through an intermediate step involving the formation of fibrillar structures in the E121K mutant. Our results give insights into the underlying mechanisms leading to ALS pathogenesis.
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Affiliation(s)
- Upma Dave
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shumayila Khan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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5
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Liedig C, Neupane P, Lashnits E, Breitschwerdt EB, Maggi RG. Blood Supplementation Enhances Bartonella henselae Growth and Molecular Detection of Bacterial DNA in Liquid Culture. Microbiol Spectr 2023; 11:e0512622. [PMID: 37227273 PMCID: PMC10269525 DOI: 10.1128/spectrum.05126-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/07/2023] [Indexed: 05/26/2023] Open
Abstract
Bacteria of the genus Bartonella, a member of the Alphaproteobacteria, are fastidious, Gram-negative, aerobic bacilli that comprise numerous species, subspecies, and genotypes. Bartonella henselae, with a worldwide distribution, infects cats, dogs, horses, humans, and other mammals. Diagnostically, direct detection of Bartonella henselae in patient blood specimens by culture or molecular methods is required to confirm infection with this bacterium. Enrichment blood culture combined with quantitative PCR (qPCR) or ddPCR enhances the sensitivity of direct detection. The addition of sheep blood to liquid culture media increased the Bartonella henselae DNA concentration compared to controls, additionally improving PCR direct detection sensitivity. IMPORTANCE This study aims to improve diagnostic detection of Bartonella henselae. Patient samples are combined with enriched bacterial cultures aimed at growing Bartonella henselae for the best possible chance at detection. However, current Bartonella growth methods could be improved. The DNA extraction method used by most laboratories should also be optimized. Sheep blood was added to increase the growth of Bartonella henselae and multiple DNA extraction methods were to be compared to each other.
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Affiliation(s)
- Chance Liedig
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, and the Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Pradeep Neupane
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Erin Lashnits
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Edward B. Breitschwerdt
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, and the Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Ricardo G. Maggi
- Intracellular Pathogens Research Laboratory, Department of Clinical Sciences, and the Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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6
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Gross SM, Dane MA, Smith RL, Devlin KL, McLean IC, Derrick DS, Mills CE, Subramanian K, London AB, Torre D, Evangelista JE, Clarke DJB, Xie Z, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn DF, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe JD, Ma’ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM. A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Commun Biol 2022; 5:1066. [PMID: 36207580 PMCID: PMC9546880 DOI: 10.1038/s42003-022-03975-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/12/2022] [Indexed: 02/01/2023] Open
Abstract
The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.
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Affiliation(s)
- Sean M. Gross
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Mark A. Dane
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Rebecca L. Smith
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Kaylyn L. Devlin
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Ian C. McLean
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Daniel S. Derrick
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Caitlin E. Mills
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Kartik Subramanian
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Alexandra B. London
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Denis Torre
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - John Erol Evangelista
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Daniel J. B. Clarke
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Zhuorui Xie
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Cemal Erdem
- grid.26090.3d0000 0001 0665 0280Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC USA
| | - Nicholas Lyons
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ted Natoli
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Sarah Pessa
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Xiaodong Lu
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - James Mullahoo
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jonathan Li
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Miriam Adam
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Brook Wassie
- grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Moqing Liu
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - David F. Kilburn
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Tiera A. Liby
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Elmar Bucher
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Crystal Sanchez-Aguila
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA
| | - Kenneth Daily
- grid.430406.50000 0004 6023 5303Sage Bionetworks, Seattle, WA USA
| | - Larsson Omberg
- grid.430406.50000 0004 6023 5303Sage Bionetworks, Seattle, WA USA
| | - Yunguan Wang
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Connor Jacobson
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Clarence Yapp
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Mirra Chung
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - Dusica Vidovic
- grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Institute for Data Science & Computing, University of Miami, Miami, FL 33136 USA
| | - Yiling Lu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Stephan Schurer
- grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Institute for Data Science & Computing, University of Miami, Miami, FL 33136 USA
| | - Albert Lee
- grid.94365.3d0000 0001 2297 5165Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA
| | - Ajay Pillai
- grid.94365.3d0000 0001 2297 5165Human Genome Research Institute, National Institutes of Health, Bethesda, USA
| | - Aravind Subramanian
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Malvina Papanastasiou
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Ernest Fraenkel
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Heidi S. Feiler
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Gordon B. Mills
- grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Division of Oncological Sciences, OHSU, Portland, OR USA
| | - Jake D. Jaffe
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Avi Ma’ayan
- grid.59734.3c0000 0001 0670 2351Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Marc R. Birtwistle
- grid.26090.3d0000 0001 0665 0280Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC USA
| | - Peter K. Sorger
- grid.38142.3c000000041936754XLaboratory of Systems Pharmacology, Department of Systems Biology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA USA
| | - James E. Korkola
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Joe W. Gray
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
| | - Laura M. Heiser
- grid.5288.70000 0000 9758 5690Department of Biomedical Engineering, OHSU, Portland, OR USA ,grid.5288.70000 0000 9758 5690Knight Cancer Institute, OHSU, Portland, OR USA
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7
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Anderson KS, Erick TK, Chen M, Daley H, Campbell M, Colson Y, Mihm M, Zakka LR, Hopper M, Barry W, Winer EP, Dranoff G, Overmoyer B. The feasibility of using an autologous GM-CSF-secreting breast cancer vaccine to induce immunity in patients with stage II-III and metastatic breast cancers. Breast Cancer Res Treat 2022; 194:65-78. [PMID: 35482127 PMCID: PMC9046531 DOI: 10.1007/s10549-022-06562-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/02/2022] [Indexed: 12/12/2022]
Abstract
PURPOSE The antigenic targets of immunity and the role of vaccination in breast cancer are unknown. We performed a phase I study of an autologous GM-CSF-secreting breast cancer vaccine in patients with metastatic and stage II-III breast cancer. METHODS Tumor cells from patients with metastatic (n = 15) and stage II-III (n = 7) disease were transduced with a replication-defective adenoviral vector encoding GM-CSF, and then irradiated. Twelve and seven patients with metastatic and stage II-III disease, respectively, received weekly vaccination for three weeks, followed by every other week until disease progression or vaccine supply was exhausted (metastatic) or until six total vaccine doses were administered (stage II-III). RESULTS Among those patients with metastatic disease who received vaccinations, eight had progressive disease at two months, three had stable disease for 4-13 months, and one has had no evidence of disease for 13 years. Of the patients with stage II-III disease, five died of metastatic disease between 1.16 and 8.49 years after the start of vaccinations (median 6.24 years) and two are alive as of September 2021. Toxicities included injection site reactions, fatigue, fever, upper respiratory symptoms, joint pain, nausea, and edema. Four of five evaluable patients with metastatic disease developed a skin reaction with immune cell infiltration after the fifth injection of unmodified, irradiated tumor cells. CONCLUSION We conclude that tumor cells can be harvested from patients with metastatic or stage II-III breast cancer to prepare autologous GM-CSF-secreting vaccines that induce coordinated immune responses with limited toxicity. TRIAL REGISTRATION AND DATE OF REGISTRATION: clinicaltrials.gov, NCT00317603 (April 25, 2006) and NCT00880464 (April 13, 2009).
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Affiliation(s)
- Karen S Anderson
- Center for Personalized Diagnostics, School of Life Sciences, Biodesign Institute, Arizona State University, PO Box 876401, Tempe, AZ, 85287-6401, USA.
- Department of Medical Oncology, Mayo Clinic, Scottsdale, AZ, USA.
| | - Timothy K Erick
- Department of Medical Oncology, Dana-Farber Cancer Institute, MB, Boston, USA
| | - Meixuan Chen
- Center for Personalized Diagnostics, School of Life Sciences, Biodesign Institute, Arizona State University, PO Box 876401, Tempe, AZ, 85287-6401, USA
| | - Heather Daley
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Margaret Campbell
- Department of Medical Oncology, Dana-Farber Cancer Institute, MB, Boston, USA
| | - Yolonda Colson
- Department of Thoracic Surgery, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Martin Mihm
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA, USA
| | - Labib R Zakka
- Department of Dermatology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marika Hopper
- Center for Personalized Diagnostics, School of Life Sciences, Biodesign Institute, Arizona State University, PO Box 876401, Tempe, AZ, 85287-6401, USA
| | - William Barry
- Department of Medical Oncology, Dana-Farber Cancer Institute, MB, Boston, USA
| | - Eric P Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, MB, Boston, USA
| | - Glenn Dranoff
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Beth Overmoyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, MB, Boston, USA
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8
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Deb S, Felix DA, Koch P, Deb MK, Szafranski K, Buder K, Sannai M, Groth M, Kirkpatrick J, Pietsch S, Gollowitzer A, Groß A, Riemenschneider P, Koeberle A, González‐Estévez C, Rudolph KL. Tnfaip2/exoc3-driven lipid metabolism is essential for stem cell differentiation and organ homeostasis. EMBO Rep 2021; 22:e49328. [PMID: 33300287 PMCID: PMC7788457 DOI: 10.15252/embr.201949328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 01/07/2023] Open
Abstract
Lipid metabolism influences stem cell maintenance and differentiation but genetic factors that control these processes remain to be delineated. Here, we identify Tnfaip2 as an inhibitor of reprogramming of mouse fibroblasts into induced pluripotent stem cells. Tnfaip2 knockout impairs differentiation of embryonic stem cells (ESCs), and knockdown of the planarian para-ortholog, Smed-exoc3, abrogates in vivo tissue homeostasis and regeneration-processes that are driven by somatic stem cells. When stimulated to differentiate, Tnfaip2-deficient ESCs fail to induce synthesis of cellular triacylglycerol (TAG) and lipid droplets (LD) coinciding with reduced expression of vimentin (Vim)-a known inducer of LD formation. Smed-exoc3 depletion also causes a strong reduction of TAGs in planarians. The study shows that Tnfaip2 acts epistatically with and upstream of Vim in impairing cellular reprogramming. Supplementing palmitic acid (PA) and palmitoyl-L-carnitine (the mobilized form of PA) restores the differentiation capacity of Tnfaip2-deficient ESCs and organ maintenance in Smed-exoc3-depleted planarians. Together, these results identify a novel role of Tnfaip2 and exoc3 in controlling lipid metabolism, which is essential for ESC differentiation and planarian organ maintenance.
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Affiliation(s)
- Sarmistha Deb
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Daniel A Felix
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Philipp Koch
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | | | - Karol Szafranski
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Katrin Buder
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Mara Sannai
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - Marco Groth
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | | | - Stefan Pietsch
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
| | - André Gollowitzer
- Institute of PharmacyFriedrich‐Schiller‐UniversityJenaGermany
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Alexander Groß
- Institute of Medical Systems BiologyUlm UniversityUlmGermany
| | | | - Andreas Koeberle
- Institute of PharmacyFriedrich‐Schiller‐UniversityJenaGermany
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | | | - Karl Lenhard Rudolph
- Leibniz Institute on Aging – Fritz Lipmann Institute e.V.JenaGermany
- University Hospital JenaFriedrich Schiller UniversityJenaGermany
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9
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Rushing AW, Rushing B, Hoang K, Sanders SV, Péloponèse JM, Polakowski N, Lemasson I. HTLV-1 basic leucine zipper factor protects cells from oxidative stress by upregulating expression of Heme Oxygenase I. PLoS Pathog 2019; 15:e1007922. [PMID: 31251786 PMCID: PMC6623464 DOI: 10.1371/journal.ppat.1007922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 07/11/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022] Open
Abstract
Adult T-cell Leukemia (ATL) is a lymphoproliferative disease of CD4+ T-cells infected with Human T-cell Leukemia Virus type I (HTLV-1). With the exception of allogeneic hematopoietic stem cell transplantation, there are no effective treatments to cure ATL, and ATL cells often acquire resistance to conventional chemotherapeutic agents. Accumulating evidence shows that development and maintenance of ATL requires key contributions from the viral protein, HTLV-1 basic leucine zipper factor (HBZ). In this study we found that HBZ activates expression of Heme Oxygenase 1 (HMOX-1), a component of the oxidative stress response that functions to detoxify free heme. Transcription of HMOX1 and other antioxidant genes is regulated by the small Mafs. These cellular basic leucine zipper (bZIP) factors control transcription by forming homo- or heterodimers among themselves or with other cellular bZIP factors that then bind Maf responsive elements (MAREs) in promoters or enhancers of antioxidant genes. Our data support a model in which HBZ activates HMOX1 transcription by forming heterodimers with the small Mafs that bind MAREs located in an upstream enhancer region. Consistent with this model, we found that HMOX-1 is upregulated in HTLV-1-transformed T-cell lines and confers these cells with resistance to heme-induced cytotoxicity. In this context, HBZ-mediated activation of HMOX-1 expression may contribute to resistance of ATL cells to certain chemotherapeutic agents. We also provide evidence that HBZ counteracts oxidative stress caused by two other HTLV-1-encoded proteins, Tax and p13. Tax induces oxidative stress as a byproduct of driving mitotic expansion of infected cells, and p13 is believed to induce oxidative stress to eliminate infected cells that have become transformed. Therefore, in this context, HBZ-mediated activation of HMOX-1 expression may facilitate transformation. Overall, this study characterizes a novel function of HBZ that may support the development and maintenance of ATL.
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Affiliation(s)
- Amanda W. Rushing
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
- * E-mail: (AWR); (IL)
| | - Blake Rushing
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Kimson Hoang
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Stephanie V. Sanders
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Jean-Marie Péloponèse
- Institut de Recherche en Infectiologie de Montpellier, Centre National de la Recherche Scientifique, Université de Montpellier, Montpellier, France
| | - Nicholas Polakowski
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
| | - Isabelle Lemasson
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, United States of America
- * E-mail: (AWR); (IL)
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10
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Ashenden M, van Weverwijk A, Murugaesu N, Fearns A, Campbell J, Gao Q, Iravani M, Isacke CM. An In Vivo Functional Screen Identifies JNK Signaling As a Modulator of Chemotherapeutic Response in Breast Cancer. Mol Cancer Ther 2017; 16:1967-1978. [PMID: 28611109 DOI: 10.1158/1535-7163.mct-16-0731] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 04/15/2017] [Accepted: 05/18/2017] [Indexed: 11/16/2022]
Abstract
Chemotherapy remains the mainstay of treatment for advanced breast cancer; however, resistance is an inevitable event for the majority of patients with metastatic disease. Moreover, there is little information available to guide stratification of first-line chemotherapy, crucial given the common development of multidrug resistance. Here, we describe an in vivo screen to interrogate the response to anthracycline-based chemotherapy in a syngeneic metastatic breast cancer model and identify JNK signaling as a key modulator of chemotherapy response. Combining in vitro and in vivo functional analyses, we demonstrate that JNK inhibition both promotes tumor cell cytostasis and blocks activation of the proapoptotic protein Bax, thereby antagonizing chemotherapy-mediated cytotoxicity. To investigate the clinical relevance of this dual role of JNK signaling, we developed a proliferation-independent JNK activity signature and demonstrate high JNK activity to be enriched in triple-negative and basal-like breast cancer subtypes. Consistent with the dual role of JNK signaling in vitro, high-level JNK pathway activation in triple-negative breast cancers is associated both with poor patient outcome in the absence of chemotherapy treatment and, in neoadjuvant clinical studies, is predictive of enhanced chemotherapy response. These data highlight the potential of monitoring JNK activity as early biomarker of response to chemotherapy and emphasize the importance of rational treatment regimes, particularly when combining cytostatic and chemotherapeutic agents. Mol Cancer Ther; 16(9); 1967-78. ©2017 AACR.
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Affiliation(s)
- Matthew Ashenden
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Antoinette van Weverwijk
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nirupa Murugaesu
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Antony Fearns
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - James Campbell
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Qiong Gao
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Marjan Iravani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Clare M Isacke
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom.
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11
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Hong JH, Kwak Y, Woo Y, Park C, Lee SA, Lee H, Park SJ, Suh Y, Suh BK, Goo BS, Mun DJ, Sanada K, Nguyen MD, Park SK. Regulation of the actin cytoskeleton by the Ndel1-Tara complex is critical for cell migration. Sci Rep 2016; 6:31827. [PMID: 27546710 PMCID: PMC4992831 DOI: 10.1038/srep31827] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/27/2016] [Indexed: 11/16/2022] Open
Abstract
Nuclear distribution element-like 1 (Ndel1) plays pivotal roles in diverse biological processes and is implicated in the pathogenesis of multiple neurodevelopmental disorders. Ndel1 function by regulating microtubules and intermediate filaments; however, its functional link with the actin cytoskeleton is largely unknown. Here, we show that Ndel1 interacts with TRIO-associated repeat on actin (Tara), an actin-bundling protein, to regulate cell movement. In vitro wound healing and Boyden chamber assays revealed that Ndel1- or Tara-deficient cells were defective in cell migration. Moreover, Tara overexpression induced the accumulation of Ndel1 at the cell periphery and resulted in prominent co-localization with F-actin. This redistribution of Ndel1 was abolished by deletion of the Ndel1-interacting domain of Tara, suggesting that the altered peripheral localization of Ndel1 requires a physical interaction with Tara. Furthermore, co-expression of Ndel1 and Tara in SH-SY5Y cells caused a synergistic increase in F-actin levels and filopodia formation, suggesting that Tara facilitates cell movement by sequestering Ndel1 at peripheral structures to regulate actin remodeling. Thus, we demonstrated that Ndel1 interacts with Tara to regulate cell movement. These findings reveal a novel role of the Ndel1-Tara complex in actin reorganization during cell movement.
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Affiliation(s)
- Ji-Ho Hong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Yongdo Kwak
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Youngsik Woo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Cana Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Seol-Ae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Haeryun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Sung Jin Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Yeongjun Suh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Bo Kyoung Suh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Bon Seong Goo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Dong Jin Mun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
| | - Kamon Sanada
- Molecular Genetics Research Laboratory, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Minh Dang Nguyen
- Hotchkiss Brain Institute, Departments of Clinical Neurosciences, Cell Biology and Anatomy, and Biochemistry and Molecular Biology, University of Calgary, Calgary T2N 4N1, Canada
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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12
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Liu Y, An S, Ward R, Yang Y, Guo XX, Li W, Xu TR. G protein-coupled receptors as promising cancer targets. Cancer Lett 2016; 376:226-39. [PMID: 27000991 DOI: 10.1016/j.canlet.2016.03.031] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) regulate an array of fundamental biological processes, such as growth, metabolism and homeostasis. Specifically, GPCRs are involved in cancer initiation and progression. However, compared with the involvement of the epidermal growth factor receptor in cancer, that of GPCRs have been largely ignored. Recent findings have implicated many GPCRs in tumorigenesis, tumor progression, invasion and metastasis. Moreover, GPCRs contribute to the establishment and maintenance of a microenvironment which is permissive for tumor formation and growth, including effects upon surrounding blood vessels, signaling molecules and the extracellular matrix. Thus, GPCRs are considered to be among the most useful drug targets against many solid cancers. Development of selective ligands targeting GPCRs may provide novel and effective treatment strategies against cancer and some anticancer compounds are now in clinical trials. Here, we focus on tumor related GPCRs, such as G protein-coupled receptor 30, the lysophosphatidic acid receptor, angiotensin receptors 1 and 2, the sphingosine 1-phosphate receptors and gastrin releasing peptide receptor. We also summarize their tissue distributions, activation and roles in tumorigenesis and discuss the potential use of GPCR agonists and antagonists in cancer therapy.
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Affiliation(s)
- Ying Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Su An
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Richard Ward
- Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Yang Yang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Xiao-Xi Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Wei Li
- Kidney Cancer Research, Diagnosis and Translational Technology Center of Yunnan Province, Department of Urology, The People's Hospital of Yunnan Province, Kunming, Yunnan 650032, China.
| | - Tian-Rui Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
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13
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Doss JF, Corcoran DL, Jima DD, Telen MJ, Dave SS, Chi JT. A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes. BMC Genomics 2015; 16:952. [PMID: 26573221 PMCID: PMC4647483 DOI: 10.1186/s12864-015-2156-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 10/27/2015] [Indexed: 12/30/2022] Open
Abstract
Background Human erythrocytes are terminally differentiated, anucleate cells long thought to lack RNAs. However, previous studies have shown the persistence of many small-sized RNAs in erythrocytes. To comprehensively define the erythrocyte transcriptome, we used high-throughput sequencing to identify both short (18–24 nt) and long (>200 nt) RNAs in mature erythrocytes. Results Analysis of the short RNA transcriptome with miRDeep identified 287 known and 72 putative novel microRNAs. Unexpectedly, we also uncover an extensive repertoire of long erythrocyte RNAs that encode many proteins critical for erythrocyte differentiation and function. Additionally, the erythrocyte long RNA transcriptome is significantly enriched in the erythroid progenitor transcriptome. Joint analysis of both short and long RNAs identified several loci with co-expression of both microRNAs and long RNAs spanning microRNA precursor regions. Within the miR-144/451 locus previously implicated in erythroid development, we observed unique co-expression of several primate-specific noncoding RNAs, including a lncRNA, and miR-4732-5p/-3p. We show that miR-4732-3p targets both SMAD2 and SMAD4, two critical components of the TGF-β pathway implicated in erythropoiesis. Furthermore, miR-4732-3p represses SMAD2/4-dependent TGF-β signaling, thereby promoting cell proliferation during erythroid differentiation. Conclusions Our study presents the most extensive profiling of erythrocyte RNAs to date, and describes primate-specific interactions between the key modulator miR-4732-3p and TGF-β signaling during human erythropoiesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2156-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer F Doss
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
| | - David L Corcoran
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
| | - Dereje D Jima
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Medicine, Duke University, Durham, NC, 27710, USA.
| | - Marilyn J Telen
- Division of Hematology, Department of Medicine, and Duke Comprehensive Sickle Cell Center, Duke University, Durham, NC, 27710, USA.
| | - Sandeep S Dave
- Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Medicine, Duke University, Durham, NC, 27710, USA.
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA.
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14
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Hicks MJ, Hu Q, Macrae E, DeWille J. Mitogen-activated protein kinase signaling controls basal and oncostatin M-mediated JUNB gene expression. Mol Cell Biochem 2015; 403:115-24. [PMID: 25662951 DOI: 10.1007/s11010-015-2342-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/30/2015] [Indexed: 12/22/2022]
Abstract
The mitogen-activated protein kinase (MAPK) pathway is aberrantly activated in many human cancers, including breast cancer. Activation of MAPK signaling is associated with the increased expression of a wide range of genes that promote cell survival, proliferation, and migration. This report investigated the influence of MAPK signaling on the regulation and expression of JUNB in human breast cancer cell lines. JUNB has been associated with tumor suppressor and oncogenic functions, with most reports describing JUNB as an oncogene in breast cancer. Our results indicated that JUNB expression is elevated in MCF10A(met), SKBR3, and MDA-MB-231 human breast cancer cell lines compared to nontransformed MCF10A mammary epithelial cells. Increased RAS/MAPK signaling in MCF10A(met) cells correlates with the increased association of RNA polymerase II (Pol II) phosphorylated on serine 5 (Pol IIser5p) with the JUNB proximal promoter. Pol IIser5p is the "transcription initiating" form of Pol II. Treatment with U0126, a MAPK pathway inhibitor, reduces Pol IIser5p association with the JUNB proximal promoter and reduces JUNB expression. Oncostatin M (OSM) enhances MAPK and STAT3 signaling and significantly induces JUNB expression. U0126 treatment reduces OSM-induced Pol IIser5p binding to the JUNB proximal promoter and JUNB expression, but does not reduce pSTAT3 levels or the association of pSTAT3 with the JUNB proximal promoter. These results demonstrate that the MAPK pathway plays a primary role in the control of JUNB gene expression by promoting the association of Pol IIser5p with the JUNB proximal promoter.
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Affiliation(s)
- Mellissa J Hicks
- Department of Veterinary Biosciences, College of Veterinary Medicine, Ohio State University, Columbus, OH, 43210, USA
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15
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Anderson KS, Cramer DW, Sibani S, Wallstrom G, Wong J, Park J, Qiu J, Vitonis A, LaBaer J. Autoantibody signature for the serologic detection of ovarian cancer. J Proteome Res 2014; 14:578-86. [PMID: 25365139 PMCID: PMC4334299 DOI: 10.1021/pr500908n] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sera from patients with ovarian cancer contain autoantibodies (AAb) to tumor-derived proteins that are potential biomarkers for early detection. To detect AAb, we probed high-density programmable protein microarrays (NAPPA) expressing 5177 candidate tumor antigens with sera from patients with serous ovarian cancer (n = 34 cases/30 controls) and measured bound IgG. Of these, 741 antigens were selected and probed with an independent set of ovarian cancer sera (n = 60 cases/60 controls). Twelve potential autoantigens were identified with sensitivities ranging from 13 to 22% at >93% specificity. These were retested using a Luminex bead array using 60 cases and 60 controls, with sensitivities ranging from 0 to 31.7% at 95% specificity. Three AAb (p53, PTPRA, and PTGFR) had area under the curve (AUC) levels >60% (p < 0.01), with the partial AUC (SPAUC) over 5 times greater than for a nondiscriminating test (p < 0.01). Using a panel of the top three AAb (p53, PTPRA, and PTGFR), if at least two AAb were positive, then the sensitivity was 23.3% at 98.3% specificity. AAb to at least one of these top three antigens were also detected in 7/20 sera (35%) of patients with low CA 125 levels and 0/15 controls. AAb to p53, PTPRA, and PTGFR are potential biomarkers for the early detection of ovarian cancer.
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Affiliation(s)
- Karen S Anderson
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287-6401, United States
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16
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Doi A, Ishikawa K, Shibata N, Ito E, Fujimoto J, Yamamoto M, Shiga H, Mochizuki H, Kawamura Y, Goshima N, Semba K, Watanabe S. Enhanced expression of retinoic acid receptor alpha (RARA) induces epithelial-to-mesenchymal transition and disruption of mammary acinar structures. Mol Oncol 2014; 9:355-64. [PMID: 25300573 DOI: 10.1016/j.molonc.2014.09.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/15/2014] [Accepted: 09/15/2014] [Indexed: 01/01/2023] Open
Abstract
The early steps of mammary tumorigenesis include loss of epithelial cell polarity, escape from anoikis, and acquisition of proliferative capacity. The genes responsible for these processes are predicted to be early diagnostic markers or new therapeutic targets. Here we tested 51 genes coamplified with ERBB2 in the 17q12-21 amplicon for these tumorigenic activities using an MCF10A 3D culture-based screening system. We found that overexpression of retinoic acid receptor α (RARA) disrupted normal acinar structure and induced epithelial-to-mesenchymal transition (EMT). The mRNA levels of known EMT-inducing factors, including SLUG, FOXC2, ZEB1, and ZEB2, were significantly increased upon RARA overexpression. Knockdown of ZEB1 suppressed the RARA-mediated EMT phenotype. These results suggest that overexpression of RARA enhances malignant transformation during mammary tumorigenesis.
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Affiliation(s)
- Ayano Doi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Kosuke Ishikawa
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Japan Biological Informatics Consortium (JBiC), 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan.
| | - Nao Shibata
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Emi Ito
- Division of Gene Expression Analysis, Translational Research Center (Tokyo Branch), Fukushima Medical University, Shibuya-ku, Tokyo 151-0051, Japan
| | - Jiro Fujimoto
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Japan Biological Informatics Consortium (JBiC), 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan
| | - Mizuki Yamamoto
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hatsuki Shiga
- Japan Biological Informatics Consortium (JBiC), 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan
| | - Hiromi Mochizuki
- Japan Biological Informatics Consortium (JBiC), 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan
| | - Yoshifumi Kawamura
- Japan Biological Informatics Consortium (JBiC), 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan
| | - Naoki Goshima
- Quantitative Proteomics Team, Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Division of Gene Function Analysis, Translational Research Center, Fukushima Medical University, 1 Hikarigaoka, Fukushima-city, Fukushima 960-1295, Japan.
| | - Shinya Watanabe
- Division of Gene Expression Analysis, Translational Research Center (Tokyo Branch), Fukushima Medical University, Shibuya-ku, Tokyo 151-0051, Japan
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17
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Sun K, Cai H, Duan X, Yang Y, Li M, Qu J, Zhang X, Wang J. Aberrant expression and potential therapeutic target of lysophosphatidic acid receptor 3 in triple-negative breast cancers. Clin Exp Med 2014; 15:371-80. [PMID: 25209561 PMCID: PMC4522273 DOI: 10.1007/s10238-014-0306-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 07/28/2014] [Indexed: 01/22/2023]
Abstract
Triple receptor-negative breast cancers (TNBCs) generally have poor prognoses because of the loss of therapeutic targets. As lysophosphatidic acid (LPA) receptor signaling has been shown to affect breast cancer initiation and progression, we try to evaluate the potential roles of LPA receptors in TNBCs. We examined mRNA and protein expressions of LPA receptors 1-3, using quantitative real-time PCR and immunohistochemical analyses in normal (n = 37), benign disease (n = 55), and breast cancer tissues (n = 82). Carcinomas expressed higher levels of LPA2 and LPA3 mRNAs (0.17 ± 0.070 and 0.05 ± 0.023, respectively) than did normal breast tissue (0.13 ± 0.072 and 0.02 ± 0.002, respectively). Enhanced immunohistochemical staining for LPA2 and LPA3 protein was also consistently observed in carcinomas. The LPA3 overexpression was associated with lymph node metastases, and absence of estrogen receptor, progesterone receptors, and human epidermal growth factor receptor 2 expression. TNBC tissues and cell lines showed the highest LPA3 expression compared with luminal-type A and B breast cancers. Suppression of LPA3 by shRNA did not influence cell growth in breast cancer cells. However, the migration and invasion of TNBC cells were significantly inhibited by LPA3-shRNA or inhibitor, which had no or less effect on normal and non-TNBC breast cells. In conclusion, our data indicated that the expression of LPA receptor 3 was increased in human TNBCs and is associated with tumor metastatic ability, and this implies that LPA3 is a potential therapeutic target for the treatment of TNBCs.
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Affiliation(s)
- Kai Sun
- The Second Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
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18
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Surana R, Wang S, Xu W, Jablonski SA, Weiner LM. IL4 limits the efficacy of tumor-targeted antibody therapy in a murine model. Cancer Immunol Res 2014; 2:1103-12. [PMID: 25204776 DOI: 10.1158/2326-6066.cir-14-0103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Tumor-targeted antibody therapy has had a major impact on reducing morbidity and mortality in a wide range of cancers. Antibodies mediate their antitumor activity in part by activating immune effector cells; however, the tumor microenvironment (TME) is enriched with cellular and soluble mediators that actively suppress generation of antitumor immunity. Here, we investigate the potential of prospectively identifying and neutralizing an immunomodulatory soluble mediator within the TME to enhance therapeutic efficacy of the HER2-directed antibody trastuzumab. Using the D5-HER2 cell line and an immunocompetent human HER2 transgenic animal (hmHER2Tg) in which human HER2 is a self-antigen, we determined that IL4 was present in the TME and produced by both tumor and stromal cells. A siRNA-based screening approach identified STAT5A as a novel negative regulator of IL4 production by D5-HER2 tumor cells. Furthermore, IL4 neutralization using the anti-IL4 antibody 11B11 enhanced the efficacy of trastuzumab and modulated the TME. For example, IL4 neutralization resulted in reduced levels of myeloid chemoattractants CCL2, CCL11, and CXCL5 in the TME. Combination therapy with 11B11 and trastuzumab resulted in a reduction of tumor-infiltrating CD11b(+)CD206(+) myeloid cells compared with monotherapy. These data suggest that IL4 neutralization enhances the efficacy of trastuzumab by influencing the phenotype of myeloid cells within the TME and provide further rationale for combining tumor-targeted antibody therapy with agents that neutralize factors in the TME that suppress generation of productive antitumor immune responses.
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Affiliation(s)
- Rishi Surana
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Shangzi Wang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Wei Xu
- Department of Pathology, Georgetown University Medical Center, Washington, District of Columbia
| | - Sandra A Jablonski
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Louis M Weiner
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia.
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19
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Zheng X, Zhai B, Koivunen P, Shin SJ, Lu G, Liu J, Geisen C, Chakraborty AA, Moslehi JJ, Smalley DM, Wei X, Chen X, Chen Z, Beres JM, Zhang J, Tsao JL, Brenner MC, Zhang Y, Fan C, DePinho RA, Paik J, Gygi SP, Kaelin WG, Zhang Q. Prolyl hydroxylation by EglN2 destabilizes FOXO3a by blocking its interaction with the USP9x deubiquitinase. Genes Dev 2014; 28:1429-44. [PMID: 24990963 PMCID: PMC4083087 DOI: 10.1101/gad.242131.114] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The three EglN prolyl hydroxylases (EglN1, EglN2, and EglN3) regulate the stability of the HIF transcription factor. We recently showed that loss of EglN2, however, also leads to down-regulation of Cyclin D1 and decreased cell proliferation in a HIF-independent manner. Here we report that EglN2 can hydroxylate FOXO3a on two specific prolyl residues in vitro and in vivo. Hydroxylation of these sites prevents the binding of USP9x deubiquitinase, thereby promoting the proteasomal degradation of FOXO3a. FOXO transcription factors can repress Cyclin D1 transcription. Failure to hydroxylate FOXO3a promotes its accumulation in cells, which in turn suppresses Cyclin D1 expression. These findings provide new insights into post-transcriptional control of FOXO3a and provide a new avenue for pharmacologically altering Cyclin D1 activity.
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Affiliation(s)
- Xingnan Zheng
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Bo Zhai
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, Oulu Center for Cell-Matrix Research, University of Oulu, FIN-90014 Oulu, Finland
| | - Sandra J Shin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Gang Lu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jiayun Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Christoph Geisen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Abhishek A Chakraborty
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Javid J Moslehi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - David M Smalley
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Xin Wei
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Zhengming Chen
- Department of Public Health, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York, New York 10065, USA
| | - Justine M Beres
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Jing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Jen Lan Tsao
- Fibrogen, Incorporated, San Francisco, California 94158, USA
| | | | - Yuqing Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
| | - Ronald A DePinho
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jihye Paik
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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20
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Cox N, Pilling D, Gomer RH. Distinct Fcγ receptors mediate the effect of serum amyloid p on neutrophil adhesion and fibrocyte differentiation. THE JOURNAL OF IMMUNOLOGY 2014; 193:1701-8. [PMID: 25024390 DOI: 10.4049/jimmunol.1400281] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The plasma protein serum amyloid P (SAP) reduces neutrophil adhesion, inhibits the differentiation of monocytes into fibroblast-like cells called fibrocytes, and promotes phagocytosis of cell debris by macrophages. Together, these effects of SAP reduce key aspects of inflammation and fibrosis, and SAP injections improve lung function in pulmonary fibrosis patients. SAP functions are mediated, in part, by FcγRs, but the contribution of each FcγR is not fully understood. We found that aa Q55 and E126 in human SAP affect human fibrocyte differentiation and SAP binding to FcγRI. E126, K130, and Q128 affect neutrophil adhesion and SAP affinity for FcγRIIa. Q128 also affects phagocytosis by macrophages and SAP affinity for FcγRI. All the identified functionally significant amino acids in SAP form a binding site that is distinct from the previously described SAP-FcγRIIa binding site. Blocking FcγRI with an IgG-blocking Ab reduces the SAP effect on fibrocyte differentiation, and ligating FcγRIIa with Abs reduces neutrophil adhesion. Together, these results suggest that SAP binds to FcγRI on monocytes to inhibit fibrocyte differentiation, and binds to FcγRIIa on neutrophils to reduce neutrophil adhesion.
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Affiliation(s)
- Nehemiah Cox
- Department of Biology, Texas A&M University, College Station, TX 77843
| | - Darrell Pilling
- Department of Biology, Texas A&M University, College Station, TX 77843
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843
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21
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Yu X, Bian X, Throop A, Song L, Moral LD, Park J, Seiler C, Fiacco M, Steel J, Hunter P, Saul J, Wang J, Qiu J, Pipas JM, LaBaer J. Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions. Am J Cancer Res 2014; 4:808-22. [PMID: 24955142 PMCID: PMC4063979 DOI: 10.7150/thno.8255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/27/2014] [Indexed: 12/24/2022] Open
Abstract
Throughout the long history of virus-host co-evolution, viruses have developed delicate strategies to facilitate their invasion and replication of their genome, while silencing the host immune responses through various mechanisms. The systematic characterization of viral protein-host interactions would yield invaluable information in the understanding of viral invasion/evasion, diagnosis and therapeutic treatment of a viral infection, and mechanisms of host biology. With more than 2,000 viral genomes sequenced, only a small percent of them are well investigated. The access of these viral open reading frames (ORFs) in a flexible cloning format would greatly facilitate both in vitro and in vivo virus-host interaction studies. However, the overall progress of viral ORF cloning has been slow. To facilitate viral studies, we are releasing the initiation of our panviral proteome collection of 2,035 ORF clones from 830 viral genes in the Gateway® recombinational cloning system. Here, we demonstrate several uses of our viral collection including highly efficient production of viral proteins using human cell-free expression system in vitro, global identification of host targets for rubella virus using Nucleic Acid Programmable Protein Arrays (NAPPA) containing 10,000 unique human proteins, and detection of host serological responses using micro-fluidic multiplexed immunoassays. The studies presented here begin to elucidate host-viral protein interactions with our systemic utilization of viral ORFs, high-throughput cloning, and proteomic technologies. These valuable plasmid resources will be available to the research community to enable continued viral functional studies.
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22
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Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Nat Methods 2013; 11:149-55. [PMID: 24317253 PMCID: PMC3922286 DOI: 10.1038/nmeth.2763] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 10/15/2013] [Indexed: 02/07/2023]
Abstract
Multiple reaction monitoring (MRM) mass spectrometry has been successfully applied to monitor targeted proteins in biological specimens, raising the possibility that assays could be configured to measure all human proteins. We report the results of a pilot study designed to test the feasibility of a large-scale, international effort for MRM assay generation. We have configured, validated across three laboratories and made publicly available as a resource to the community 645 novel MRM assays representing 319 proteins expressed in human breast cancer. Assays were multiplexed in groups of >150 peptides and deployed to quantify endogenous analytes in a panel of breast cancer-related cell lines. The median assay precision was 5.4%, with high interlaboratory correlation (R(2) > 0.96). Peptide measurements in breast cancer cell lines were able to discriminate among molecular subtypes and identify genome-driven changes in the cancer proteome. These results establish the feasibility of a large-scale effort to develop an MRM assay resource.
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23
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Zhang M, Taylor CE, Piao L, Datta J, Bruno PA, Bhave S, Su T, Lang JC, Xie X, Teknos TN, Mapp AK, Pan Q. Genetic and chemical targeting of epithelial-restricted with serine box reduces EGF receptor and potentiates the efficacy of afatinib. Mol Cancer Ther 2013; 12:1515-25. [PMID: 23723125 DOI: 10.1158/1535-7163.mct-12-1110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
EGF receptor (EGFR) is elevated in more than 90% of head and neck squamous cell carcinoma (HNSCC). However, a majority of patients with HNSCC do not respond to anti-EGFR therapeutics. Insensitivity to EGFR inhibitors may be due to kinase-independent actions of EGFR and/or activation of Her2. Strategies to reduce EGFR and Her2 protein levels in concert may be an optimal approach to enhance the efficacy of current anti-EGFR molecules. In this study, knockdown of epithelial-restricted with serine box (ESX) decreased EGFR and Her2 promoter activity, expression, and levels. ESX was elevated in primary HNSCC tumors and associated with increased EGFR and Her2. Genetic ablation of ESX decreased EGFR and Her2 levels and enhanced the antiproliferative effects of EGFR/Her2 tyrosine kinase inhibitors (TKI), lapatinib and afatinib. Biphenyl isoxazolidine, a novel small-molecule ESX inhibitor, reduced EGFR and Her2 levels and potentiated the antiproliferative efficacy of afatinib. Single-agent biphenyl isoxazolidine retarded the in vivo tumorigenicity of CAL27 cells. Importantly, the combination of biphenyl isoxazolidine and afatinib was significantly superior in vivo and resulted in a 100% response rate with a 94% reduction in tumor volume. Targeting EGFR/Her2 levels with an ESX inhibitor and EGFR/Her2 kinase activity with a TKI simultaneously is a highly active therapeutic approach to manage HNSCC. Our work provides evidence to support the further development of ESX inhibitors as an adjuvant to enhance the response rate of patients with HNSCC to current anti-EGFR/Her2 therapeutics.
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Affiliation(s)
- Manchao Zhang
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
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24
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Festa F, Steel J, Bian X, Labaer J. High-throughput cloning and expression library creation for functional proteomics. Proteomics 2013; 13:1381-99. [PMID: 23457047 DOI: 10.1002/pmic.201200456] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 01/11/2013] [Accepted: 01/31/2013] [Indexed: 12/11/2022]
Abstract
The study of protein function usually requires the use of a cloned version of the gene for protein expression and functional assays. This strategy is particularly important when the information available regarding function is limited. The functional characterization of the thousands of newly identified proteins revealed by genomics requires faster methods than traditional single-gene experiments, creating the need for fast, flexible, and reliable cloning systems. These collections of ORF clones can be coupled with high-throughput proteomics platforms, such as protein microarrays and cell-based assays, to answer biological questions. In this tutorial, we provide the background for DNA cloning, discuss the major high-throughput cloning systems (Gateway® Technology, Flexi® Vector Systems, and Creator(TM) DNA Cloning System) and compare them side-by-side. We also report an example of high-throughput cloning study and its application in functional proteomics. This tutorial is part of the International Proteomics Tutorial Programme (IPTP12).
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Affiliation(s)
- Fernanda Festa
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6401, USA
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25
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Alvarez-Calderon F, Gregory MA, DeGregori J. Using functional genomics to overcome therapeutic resistance in hematological malignancies. Immunol Res 2013; 55:100-15. [PMID: 22941562 PMCID: PMC3673782 DOI: 10.1007/s12026-012-8353-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite great advances in our understanding of the driving events involved in malignant transformation, only a small number of oncogenic drivers have been targeted and translated into tangible clinical benefit. Moreover, even when a targeted therapy can be shown to effectively inhibit an oncogenic driver, leading to cancer remission, disease persistence and/or relapse is typically inevitable. Reemergence of the cancer can result from either intrinsic or acquired resistance mechanisms that result in failure to eliminate all cancer cells. Intrinsic mechanisms of resistance include tumor heterogeneity and pathways that can compensate for the inhibition of the oncogenic driver. Acquired resistance mechanisms include mutation of the oncogenic driver to directly prevent drug-mediated inhibition and the activation of compensatory survival pathways. RNA interference (RNAi)-based screening provides a powerful approach for the interrogation of both intrinsic and acquired resistance mechanisms. The availability of short interfering (si)RNA libraries targeting all human and mouse genes has made it possible to perform large-scale unbiased screens to identify pathways that are specifically required in cancer cells of particular genotypes or following particular treatments, facilitating the design of potential new therapeutic strategies that may limit resistance mechanisms. In this review, we will discuss how RNAi screens can be used to uncover critical growth and survival pathways and aid in the identification of novel therapeutic targets for improved treatment of hematological malignancies.
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Affiliation(s)
- Francesca Alvarez-Calderon
- Integrated Department of Immunology, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
- Medical Scientist Training Program, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
| | - Mark A. Gregory
- Department of Biochemistry and Molecular Genetics, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
| | - James DeGregori
- Integrated Department of Immunology, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
- Department of Biochemistry and Molecular Genetics, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
- Department of Pediatrics, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
- Program in Molecular Biology, University of Colorado – Anschutz Medical Campus, Aurora CO and National Jewish Health, Denver CO
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26
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Kittler R, Zhou J, Hua S, Ma L, Liu Y, Pendleton E, Cheng C, Gerstein M, White KP. A comprehensive nuclear receptor network for breast cancer cells. Cell Rep 2013; 3:538-51. [PMID: 23375374 DOI: 10.1016/j.celrep.2013.01.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/26/2012] [Accepted: 01/04/2013] [Indexed: 01/16/2023] Open
Abstract
In breast cancer, nuclear receptors (NRs) play a prominent role in governing gene expression, have prognostic utility, and are therapeutic targets. We built a regulatory map for 24 NRs, six chromatin state markers, and 14 breast-cancer-associated transcription factors (TFs) that are expressed in the breast cancer cell line MCF-7. The resulting network reveals a highly interconnected regulatory matrix where extensive crosstalk occurs among NRs and other breast -cancer-associated TFs. We show that large numbers of factors are coordinately bound to highly occupied target regions throughout the genome, and these regions are associated with active chromatin state and hormone-responsive gene expression. This network also provides a framework for stratifying and predicting patient outcomes, and we use it to show that the peroxisome proliferator-activated receptor delta binds to a set of genes also regulated by the retinoic acid receptors and whose expression is associated with poor prognosis in breast cancer.
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Affiliation(s)
- Ralf Kittler
- Institute of Genomics and Systems Biology, Argonne National Laboratory, Chicago, IL 60637, USA
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27
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Mouneimne G, Hansen SD, Selfors LM, Petrak L, Hickey MM, Gallegos LL, Simpson KJ, Lim J, Gertler FB, Hartwig JH, Mullins RD, Brugge JS. Differential remodeling of actin cytoskeleton architecture by profilin isoforms leads to distinct effects on cell migration and invasion. Cancer Cell 2012; 22:615-30. [PMID: 23153535 PMCID: PMC3500527 DOI: 10.1016/j.ccr.2012.09.027] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/06/2012] [Accepted: 09/28/2012] [Indexed: 01/17/2023]
Abstract
Dynamic actin cytoskeletal reorganization is integral to cell motility. Profilins are well-characterized regulators of actin polymerization; however, functional differences among coexpressed profilin isoforms are not well defined. Here, we demonstrate that profilin-1 and profilin-2 differentially regulate membrane protrusion, motility, and invasion; these processes are promoted by profilin-1 and suppressed by profilin-2. Compared to profilin-1, profilin-2 preferentially drives actin polymerization by the Ena/VASP protein, EVL. Profilin-2 and EVL suppress protrusive activity and cell motility by an actomyosin contractility-dependent mechanism. Importantly, EVL or profilin-2 downregulation enhances invasion in vitro and in vivo. In human breast cancer, lower EVL expression correlates with high invasiveness and poor patient outcome. We propose that profilin-2/EVL-mediated actin polymerization enhances actin bundling and suppresses breast cancer cell invasion.
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Affiliation(s)
- Ghassan Mouneimne
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Scott D. Hansen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Laura M. Selfors
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Lara Petrak
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Michele M. Hickey
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Lisa L. Gallegos
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Kaylene J. Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, 3002
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, 3050
| | - James Lim
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Frank B. Gertler
- The Koch Institute for integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - John H. Hartwig
- Division of Translational Medicine at Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - R. Dyche Mullins
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158
| | - Joan S. Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Corresponding author: , Phone: 617 432 3974, Fax: 617 432 3969
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28
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David M, Ribeiro J, Descotes F, Serre CM, Barbier M, Murone M, Clézardin P, Peyruchaud O. Targeting lysophosphatidic acid receptor type 1 with Debio 0719 inhibits spontaneous metastasis dissemination of breast cancer cells independently of cell proliferation and angiogenesis. Int J Oncol 2011; 40:1133-41. [PMID: 22200658 PMCID: PMC3584523 DOI: 10.3892/ijo.2011.1309] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 09/23/2011] [Indexed: 01/26/2023] Open
Abstract
Metastasis is the main cause of death for cancer patients. Targeting factors that control metastasis formation is a major challenge for clinicians. Lysophosphatidic acid (LPA) is a bioactive phospholipid involved in cancer. LPA activates at least six independent G protein-coupled receptors (LPA1–6). Tumor cells frequently co-express multiple LPA receptors, puzzling the contribution of each one to cancer progression. All three receptors, LPA1, LPA2 and LPA3, act as oncogenes and prometastatic factors in the mouse mammary gland. The competitive inhibitor of LPA1 and LPA3 receptors, Ki16425, inhibits efficiently breast cancer bone metastases in animal models. We showed here that Debio 0719, which corresponds to the R-stereoisomer of Ki16425 exhibited highest antagonist activities at LPA1 (IC50=60 nM) and LPA3 (IC50=660 nM) than Ki16425 [IC50=130 nM (LPA1); IC50=2.3 μM (LPA3)]. In vitro, Debio 0719, inhibited LPA-dependent invasion of the 4T1 mouse mammary cancer cells. In vivo, early but not late administration of Debio 0719 (50 mg/kg p.o. twice daily) to BALB/c mice during the course of orthotopic 4T1 primary tumor growth reduced the number of spontaneously disseminated tumor cells to bone and lungs without affecting the growth of primary tumors and tumor-induced angiogenesis. We found that increased LPA1 mRNA expression in primary tumors of breast cancer patients correlated significantly with their positive lymph node status (p<0.001). Altogether, our results suggest that LPA1 controls early events of metastasis independently of cell proliferation and angiogenesis. Therefore, targeting this receptor with Debio 0719 has a high therapeutic potential against metastasis formation for breast cancer patients.
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Affiliation(s)
- Marion David
- INSERM, UMR1033, Université de Lyon, Faculté de Médecine Lyon Est, Lyon, France
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29
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Hu Y, Flockhart I, Vinayagam A, Bergwitz C, Berger B, Perrimon N, Mohr SE. An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinformatics 2011; 12:357. [PMID: 21880147 PMCID: PMC3179972 DOI: 10.1186/1471-2105-12-357] [Citation(s) in RCA: 509] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 08/31/2011] [Indexed: 12/12/2022] Open
Abstract
Background Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the functions of orthologs in other species. Several tools for predicting orthologous gene relationships are available. However, these tools can give different results and identification of predicted orthologs is not always straightforward. Results We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt), for rapid identification of orthologs. DIOPT integrates existing approaches, facilitating rapid identification of orthologs among human, mouse, zebrafish, C. elegans, Drosophila, and S. cerevisiae. As compared to individual tools, DIOPT shows increased sensitivity with only a modest decrease in specificity. Moreover, the flexibility built into the DIOPT graphical user interface allows researchers with different goals to appropriately 'cast a wide net' or limit results to highest confidence predictions. DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. This helps users identify the most appropriate matches among multiple possible orthologs. To facilitate using model organisms for functional analysis of human disease-associated genes, we used DIOPT to predict high-confidence orthologs of disease genes in Online Mendelian Inheritance in Man (OMIM) and genes in genome-wide association study (GWAS) data sets. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist). Conclusions DIOPT and DIOPT-DIST are useful resources for researchers working with model organisms, especially those who are interested in exploiting model organisms such as Drosophila to study the functions of human disease genes.
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Affiliation(s)
- Yanhui Hu
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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30
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Prescott JD, Poczobutt JM, Tentler JJ, Walker DM, Gutierrez-Hartmann A. Mapping of ESE-1 subdomains required to initiate mammary epithelial cell transformation via a cytoplasmic mechanism. Mol Cancer 2011; 10:103. [PMID: 21871131 PMCID: PMC3183030 DOI: 10.1186/1476-4598-10-103] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2010] [Accepted: 08/28/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The ETS family transcription factor ESE-1 is often overexpressed in human breast cancer. ESE-1 initiates transformation of MCF-12A cells via a non-transcriptional, cytoplasmic process that is mediated by a unique 40-amino acid serine and aspartic acid rich (SAR) subdomain, whereas, ESE-1's nuclear transcriptional property is required to maintain the transformed phenotype of MCF7, ZR-75-1 and T47D breast cancer cells. RESULTS To map the minimal functional nuclear localization (NLS) and nuclear export (NES) signals, we fused in-frame putative NLS and NES motifs between GFP and the SAR domain. Using these GFP constructs as reporters of subcellular localization, we mapped a single NLS to six basic amino acids (242 HGKRRR 247) in the AT-hook and two CRM1-dependent NES motifs, one to the pointed domain (NES1: 102 LCNCALEELRL 112) and another to the DNA binding domain (DBD), (NES2: 275 LWEFIRDILI 284). Moreover, analysis of a putative NLS located in the DBD (316 GQKKKNSN 323) by a similar GFP-SAR reporter or by internal deletion of the DBD, revealed this sequence to lack NLS activity. To assess the role of NES2 in regulating ESE-1 subcellular localization and subsequent transformation potency, we site-specifically mutagenized NES2, within full-length GFP-ESE-1 and GFP-NES2-SAR reporter constructs. These studies show that site-specific mutation of NES2 completely abrogates ESE-1 transforming activity. Furthermore, we show that exclusive cytoplasmic targeting of the SAR domain is sufficient to initiate transformation, and we report that an intact SAR domain is required, since block mutagenesis reveals that an intact SAR domain is necessary to maintain its full transforming potency. Finally, using a monoclonal antibody targeting the SAR domain, we demonstrate that the SAR domain contains a region accessible for protein - protein interactions. CONCLUSIONS These data highlight that ESE-1 contains NLS and NES signals that play a critical role in regulating its subcellular localization and function, and that an intact SAR domain mediates MEC transformation exclusively in the cytoplasm, via a novel nontranscriptional mechanism, whereby the SAR motif is accessible for ligand and/or protein interactions. These findings are significant, since they provide novel molecular insights into the functions of ETS transcription factors in mammary cell transformation.
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Affiliation(s)
- Jason D Prescott
- Medical Scientist Training Program, University of Colorado Denver, Aurora, CO 80045, USA
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Cormier CY, Park JG, Fiacco M, Steel J, Hunter P, Kramer J, Singla R, LaBaer J. PSI:Biology-materials repository: a biologist's resource for protein expression plasmids. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2011; 12:55-62. [PMID: 21360289 PMCID: PMC3184641 DOI: 10.1007/s10969-011-9100-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 02/02/2011] [Indexed: 01/08/2023]
Abstract
The Protein Structure Initiative:Biology-Materials Repository (PSI:Biology-MR; MR; http://psimr.asu.edu ) sequence-verifies, annotates, stores, and distributes the protein expression plasmids and vectors created by the Protein Structure Initiative (PSI). The MR has developed an informatics and sample processing pipeline that manages this process for thousands of samples per month from nearly a dozen PSI centers. DNASU ( http://dnasu.asu.edu ), a freely searchable database, stores the plasmid annotations, which include the full-length sequence, vector information, and associated publications for over 130,000 plasmids created by our laboratory, by the PSI and other consortia, and by individual laboratories for distribution to researchers worldwide. Each plasmid links to external resources, including the PSI Structural Biology Knowledgebase ( http://sbkb.org ), which facilitates cross-referencing of a particular plasmid to additional protein annotations and experimental data. To expedite and simplify plasmid requests, the MR uses an expedited material transfer agreement (EP-MTA) network, where researchers from network institutions can order and receive PSI plasmids without institutional delays. As of March 2011, over 39,000 protein expression plasmids and 78 empty vectors from the PSI are available upon request from DNASU. Overall, the MR's repository of expression-ready plasmids, its automated pipeline, and the rapid process for receiving and distributing these plasmids more effectively allows the research community to dissect the biological function of proteins whose structures have been studied by the PSI.
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Affiliation(s)
- Catherine Y. Cormier
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Jin G. Park
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Michael Fiacco
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Jason Steel
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Preston Hunter
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Jason Kramer
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Rajeev Singla
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics at the Biodesign Institute at Arizona State University, Tempe, AZ 85287-6401
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32
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Du J, Sun C, Hu Z, Yang Y, Zhu Y, Zheng D, Gu L, Lu X. Lysophosphatidic acid induces MDA-MB-231 breast cancer cells migration through activation of PI3K/PAK1/ERK signaling. PLoS One 2010; 5:e15940. [PMID: 21209852 PMCID: PMC3012724 DOI: 10.1371/journal.pone.0015940] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 11/30/2010] [Indexed: 01/28/2023] Open
Abstract
Background Enhanced motility of cancer cells is a critical step in promoting tumor metastasis. Lysophosphatidic acid (LPA), representing the major mitogenic activity in serum, stimulates migration in various types of cancer cells. However, the underlying signaling mechanisms for LPA-induced motility of cancer cells remain to be elucidated. Methodology/Principal Findings In this study, we found that LPA dose-dependently stimulated migration of MDA-MB-231 breast cancer cells, with 10 µM being the most effective. LPA also increased ERK activity and the MEK inhibitor U0126 could block LPA-induced ERK activity and cell migration. In addition, LPA induced PAK1 activation while ERK activation and cell migration were inhibited by ectopic expression of an inactive mutant form of PAK1 in MDA-MB-231 cells. Furthermore, LPA increased PI3K activity, and the PI3K inhibitor LY294002 inhibited both LPA-induced PAK1/ERK activation and cell migration. Moreover, in the breast cancer cell, LPA treatment resulted in remarkable production of reactive oxygen species (ROS), while LPA-induced ROS generation, PI3K/PAK1/ERK activation and cell migration could be inhibited by N-acetyl-L-Cysteine, a scavenger of ROS. Conclusions/Significance Taken together, this study identifies a PI3K/PAK1/ERK signaling pathway for LPA-stimulated breast cancer cell migration. These data also suggest that ROS generation plays an essential role in the activation of LPA-stimulated PI3K/PAK1/ERK signaling and breast cancer cell migration. These findings may provide a basis for designing future therapeutic strategy for blocking breast cancer metastasis.
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Affiliation(s)
- Jun Du
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Chongqi Sun
- Kangda College, Nanjing Medical University, Nanjing, China
| | - Zhenzhen Hu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yu Yang
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yichao Zhu
- Cancer Center, Nanjing Medical University, Nanjing, China
| | - Datong Zheng
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Luo Gu
- Cancer Center, Nanjing Medical University, Nanjing, China
- * E-mail: (LG); (XL)
| | - Xiang Lu
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- * E-mail: (LG); (XL)
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Anderson KS, Sibani S, Wallstrom G, Qiu J, Mendoza EA, Raphael J, Hainsworth E, Montor WR, Wong J, Park JG, Lokko N, Logvinenko T, Ramachandran N, Godwin AK, Marks J, Engstrom P, Labaer J. Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer. J Proteome Res 2010; 10:85-96. [PMID: 20977275 DOI: 10.1021/pr100686b] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cancer patients spontaneously generate autoantibodies (AAb) to tumor-derived proteins. To detect AAb, we have probed novel high-density custom protein microarrays (NAPPA) expressing 4988 candidate tumor antigens with sera from patients with early stage breast cancer (IBC), and bound IgG was measured. We used a three-phase serial screening approach. First, a prescreen was performed to eliminate uninformative antigens. Sera from stage I-III IBC (n = 53) and healthy women (n = 53) were screened for AAb to all 4988 protein antigens. Antigens were selected if the 95th percentile of signal of cases and controls were significantly different (p < 0.05) and if the number of cases with signals above the 95th percentile of controls was significant (p < 0.05). These 761 antigens were screened using an independent set of IBC sera (n = 51) and sera from women with benign breast disease (BBD) (n = 39). From these, 119 antigens had a partial area under the ROC curve (p < 0.05), with sensitivities ranging from 9-40% at >91% specificity. Twenty-eight of these antigens were confirmed using an independent serum cohort (n = 51 cases/38 controls, p < 0.05). Using all 28 AAb, a classifier was identified with a sensitivity of 80.8% and a specificity of 61.6% (AUC = 0.756). These are potential biomarkers for the early detection of breast cancer.
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Affiliation(s)
- Karen S Anderson
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.
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Heyer J, Kwong LN, Lowe SW, Chin L. Non-germline genetically engineered mouse models for translational cancer research. Nat Rev Cancer 2010; 10:470-80. [PMID: 20574449 PMCID: PMC4602412 DOI: 10.1038/nrc2877] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genetically engineered mouse models (GEMMs) of cancer have affected virtually all areas of cancer research. However, the accelerated discovery of new cancer genes emerging from large-scale cancer genomics and new chemical entities pouring from the drug discovery pipeline have strained the capacity of traditional germline mouse models to provide crucial insights. This Review introduces new approaches to modelling cancer, with emphasis on a growing collection of non-germline GEMMs (nGEMMs). These offer flexibility, speed and uniformity at reduced costs, thus paving the way for much needed throughput and practical preclinical therapeutic testing models.
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Affiliation(s)
- Joerg Heyer
- AVEO Pharmaceuticals, 75 Sidney Street, 4th floor, Cambridge, MA 02139, USA
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35
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Reinke AW, Grigoryan G, Keating AE. Identification of bZIP interaction partners of viral proteins HBZ, MEQ, BZLF1, and K-bZIP using coiled-coil arrays. Biochemistry 2010; 49:1985-97. [PMID: 20102225 DOI: 10.1021/bi902065k] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Basic-region leucine-zipper transcription factors (bZIPs) contain a segment rich in basic amino acids that can bind DNA, followed by a leucine zipper that can interact with other leucine zippers to form coiled-coil homo- or heterodimers. Several viruses encode proteins containing bZIP domains, including four that encode bZIPs lacking significant homology to any human protein. We investigated the interaction specificity of these four viral bZIPs by using coiled-coil arrays to assess self-associations as well as heterointeractions with 33 representative human bZIPs. The arrays recapitulated reported viral-human interactions and also uncovered new associations. MEQ and HBZ interacted with multiple human partners and had unique interaction profiles compared to any human bZIPs, whereas K-bZIP and BZLF1 displayed homospecificity. New interactions detected included HBZ with MAFB, MAFG, ATF2, CEBPG, and CREBZF and MEQ with NFIL3. These were confirmed in solution using circular dichroism. HBZ can heteroassociate with MAFB and MAFG in the presence of MARE-site DNA, and this interaction is dependent on the basic region of HBZ. NFIL3 and MEQ have different yet overlapping DNA-binding specificities and can form a heterocomplex with DNA. Computational design considering both affinity for MEQ and specificity with respect to other undesired bZIP-type interactions was used to generate a MEQ dimerization inhibitor. This peptide, anti-MEQ, bound MEQ both stably and specifically, as assayed using coiled-coil arrays and circular dichroism in solution. Anti-MEQ also inhibited MEQ binding to DNA. These studies can guide further investigation of the function of viral and human bZIP complexes.
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Affiliation(s)
- Aaron W Reinke
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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36
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Lysophosphatidic acid production and action: critical new players in breast cancer initiation and progression. Br J Cancer 2010; 102:941-6. [PMID: 20234370 PMCID: PMC2844037 DOI: 10.1038/sj.bjc.6605588] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Lysophosphatidic acid (LPA) is a potent lipid mediator that acts on a series of specific G protein-coupled receptors, leading to diverse biological actions. Lysophosphatidic acid induces cell proliferation, survival and migration, which are critically required for tumour formation and metastasis. This bioactive lipid is produced by the ectoenzyme lysophospholipase D or autotaxin (ATX), earlier known as an autocrine motility factor. The ATX-LPA signalling axis has emerged as an important player in many types of cancer. Indeed, aberrant expression of ATX and LPA receptors occurs during the development and progression of breast cancer. Importantly, expression of either ATX or LPA receptors in the mammary gland of transgenic mice is sufficient to induce the development of a high frequency of invasive and metastatic mammary cancers. The focus of research now turns to understanding the mechanisms by which ATX and LPA promote mammary tumourigenesis and metastasis. Targeting the ATX-LPA signalling axis for drug development may further improve outcomes in patients with breast cancer.
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37
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Jedeszko C, Victor BC, Podgorski I, Sloane BF. Fibroblast hepatocyte growth factor promotes invasion of human mammary ductal carcinoma in situ. Cancer Res 2009; 69:9148-55. [PMID: 19920187 PMCID: PMC2789178 DOI: 10.1158/0008-5472.can-09-1043] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stromal-derived hepatocyte growth factor (HGF) acting through its specific proto-oncogene receptor c-Met has been suggested to play a paracrine role in the regulation of tumor cell migration and invasion. The transition from preinvasive ductal carcinoma in situ (DCIS) to invasive breast carcinoma is marked by infiltration of stromal fibroblasts and the loss of basement membrane. We hypothesized that HGF produced by the infiltrating fibroblasts may alter proteolytic pathways in DCIS cells, and, to study this hypothesis, established three-dimensional reconstituted basement membrane overlay cocultures with two human DCIS cell lines, MCF10.DCIS and SUM102. Both cell lines formed large dysplastic structures in three-dimensional cultures that resembled DCIS in vivo and occasionally developed invasive outgrowths. In coculture with HGF-secreting mammary fibroblasts, the percentage of DCIS structures with invasive outgrowths was increased. Activation of c-Met with conditioned medium from HGF-secreting fibroblasts or with recombinant HGF increased the percentage of DCIS structures with invasive outgrowths, their degradation of collagen IV, and their secretion of urokinase-type plasminogen activator and its receptor. In agreement with the in vitro findings, coinjection with HGF-secreting fibroblasts increased invasiveness of MCF10.DCIS xenografts in severe combined immunodeficient mice. Our study shows that paracrine HGF/c-Met signaling between fibroblasts and preinvasive DCIS cells enhances the transition to invasive carcinomas and suggests that three-dimensional cocultures are appropriate models for testing therapeutics that target tumor microenvironment-enhanced invasiveness.
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Liu S, Murph M, Panupinthu N, Mills GB. ATX-LPA receptor axis in inflammation and cancer. Cell Cycle 2009; 8:3695-701. [PMID: 19855166 PMCID: PMC4166520 DOI: 10.4161/cc.8.22.9937] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lysophosphatidic acid (LPA, 1- or 2-acyl-sn-glycerol 3-phosphate) mediates a plethora of physiological and pathological activities via interactions with a series of high affinity G protein-coupled receptors (GPCR). Both LPA receptor family members and autotaxin (ATX/LysoPLD), the primary LPA-producing enzyme, are aberrantly expressed in many human breast cancers and several other cancer lineages. Using transgenic mice expressing either an LPA receptor or ATX, we recently demonstrated that the ATX-LPA receptor axis plays a causal role in breast tumorigenesis and cancer-related inflammation, further validating the ATX-LPA receptor axis as a rich therapeutic target in cancer.
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Affiliation(s)
- Shuying Liu
- Department of Systems Biology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77230, USA
| | - Mandi Murph
- University of Georgia College of Pharmacy, Athens, GA 30602
| | - Nattapon Panupinthu
- Department of Systems Biology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77230, USA
| | - Gordon B. Mills
- Department of Systems Biology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77230, USA,Correspondence: Dr. Gordon B. Mills, Department of Systems Biology, Division of Cancer Medicine, 1515 Holcombe Blvd., Houston, TX 77030, USA, , Tel (713) 563-4200, Fax (713) 563-4235
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39
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Bric A, Miething C, Bialucha CU, Scuoppo C, Zender L, Krasnitz A, Xuan Z, Zuber J, Wigler M, Hicks J, McCombie RW, Hemann MT, Hannon GJ, Powers S, Lowe SW. Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model. Cancer Cell 2009; 16:324-35. [PMID: 19800577 PMCID: PMC2829755 DOI: 10.1016/j.ccr.2009.08.015] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 07/13/2009] [Accepted: 08/07/2009] [Indexed: 12/11/2022]
Abstract
Short hairpin RNAs (shRNAs) capable of stably suppressing gene function by RNA interference (RNAi) can mimic tumor-suppressor-gene loss in mice. By selecting for shRNAs capable of accelerating lymphomagenesis in a well-characterized mouse lymphoma model, we identified over ten candidate tumor suppressors, including Sfrp1, Numb, Mek1, and Angiopoietin 2. Several components of the DNA damage response machinery were also identified, including Rad17, which acts as a haploinsufficient tumor suppressor that responds to oncogenic stress and whose loss is associated with poor prognosis in human patients. Our results emphasize the utility of in vivo RNAi screens, identify and validate a diverse set of tumor suppressors, and have therapeutic implications.
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MESH Headings
- Angiopoietin-2/genetics
- Animals
- Cell Cycle Proteins/genetics
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- DNA Damage
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- Genes, myc
- Genes, p53
- Genetic Testing/methods
- Hematopoietic Stem Cell Transplantation
- Hematopoietic Stem Cells/metabolism
- Humans
- Intercellular Signaling Peptides and Proteins/genetics
- Lymphoma/genetics
- Lymphoma/metabolism
- Lymphoma/pathology
- MAP Kinase Kinase 1/genetics
- Membrane Proteins/genetics
- Mice
- Mice, Inbred C57BL
- Nerve Tissue Proteins/genetics
- Prognosis
- RNA Interference
- Reproducibility of Results
- Time Factors
- Transduction, Genetic
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Affiliation(s)
- Anka Bric
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | | | - Claudio Scuoppo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA
| | - Lars Zender
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Zhenyu Xuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Johannes Zuber
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - James Hicks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | | | - Gregory J. Hannon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
| | - Scott Powers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Scott W. Lowe
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
- Contact information: Scott Lowe, PhD, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, Phone: 516-367-8406, Fax: 516-367-8454,
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Hua S, Kittler R, White KP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell 2009; 137:1259-71. [PMID: 19563758 PMCID: PMC3374131 DOI: 10.1016/j.cell.2009.04.043] [Citation(s) in RCA: 237] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 02/17/2009] [Accepted: 04/15/2009] [Indexed: 01/23/2023]
Abstract
Retinoic acid (RA) triggers antiproliferative effects in tumor cells, and therefore RA and its synthetic analogs have great potential as anticarcinogenic agents. Retinoic acid receptors (RARs) mediate RA effects by directly regulating gene expression. To define the genetic network regulated by RARs in breast cancer, we identified RAR genomic targets using chromatin immunoprecipitation and expression analysis. We found that RAR binding throughout the genome is highly coincident with estrogen receptor alpha (ERalpha) binding, resulting in a widespread crosstalk of RA and estrogen signaling to antagonistically regulate breast cancer-associated genes. ERalpha- and RAR-binding sites appear to be coevolved on a large scale throughout the human genome, often resulting in competitive binding activity at nearby or overlapping cis-regulatory elements. The highly coordinated intersection between these two critical nuclear hormone receptor signaling pathways provides a global mechanism for balancing gene expression output via local regulatory interactions dispersed throughout the genome.
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Affiliation(s)
- Sujun Hua
- Institute of Genomics and Systems Biology and Department of Human Genetics, The University of Chicago, 920 East 58 Street, Illinois 60637, USA
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Ralf Kittler
- Institute of Genomics and Systems Biology and Department of Human Genetics, The University of Chicago, 920 East 58 Street, Illinois 60637, USA
| | - Kevin P. White
- Institute of Genomics and Systems Biology and Department of Human Genetics, The University of Chicago, 920 East 58 Street, Illinois 60637, USA
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Abstract
A protocol for ligation-dependent cloning using the Flexi Vector method in a 96-well format is described. The complete protocol includes PCR amplification of the desired gene to append Flexi Vector cloning sequences, restriction digestion of the PCR products, ligation of the digested PCR products into a similarly digested acceptor vector, transformation and growth of host cells, analysis of the transformed clones, and storage of a sequence-verified clone. The protocol also includes transfer of the sequence-verified clones into another Flexi Vector plasmid backbone. Smaller numbers of cloning reactions can be undertaken by appropriate scaling of the indicated reaction volumes.
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Murph M, Nguyen G, Radhakrishna H, Mills GB. Sharpening the edges of understanding the structure/function of the LPA1 receptor: expression in cancer and mechanisms of regulation. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1781:547-57. [PMID: 18501205 PMCID: PMC2565514 DOI: 10.1016/j.bbalip.2008.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Revised: 04/11/2008] [Accepted: 04/19/2008] [Indexed: 02/03/2023]
Abstract
Since the molecular cloning of the vzg-1/Edg-2/LPA1 gene, studies have attempted to characterize LPA1 receptor functionality into a single categorical role, different from the other Edg-family LPA receptors. The desire to categorize LPA1 function has highlighted its complexity and demonstrated that the LPA1 receptor does not have one absolute function throughout every system. The central nervous system is highly enriched in the LPA1 receptor, suggesting an integral role in neuronal processes. Metastatic and invasive breast cancer also appears to have LPA-mediated LPA1 receptor functions that enhance phenotypes associated with tumorigenesis. LPA1 possesses a number of motifs conserved among G protein-coupled receptors (GPCRs): a DRY-like motif, a PDZ domain, Ser/Thr predicted sites of phosphorylation, a di-leucine motif, double cysteines in the tail and conserved residues that stabilize structure and determine ligand binding. The third intracellular loop of the LPA1 receptor may be the crux of receptor signaling and attenuation with phosphorylation of Thr-236 potentially a key determinant of basal LPA1 signaling. Mutagenesis data supports the notion that Thr-236 regulates this process since mutating Thr-236 to Ala-236 increased basal and LPA-mediated serum response factor (SRF) signaling activity and Lys-236 further increased this basal signaling. Here we describe progress on defining the major functions of the LPA1 receptor, discuss a context dependent dualistic role as both a negative regulator in cancer and a proto-oncogene, outline its structural components at the molecular amino acid level and present mutagenesis data on the third intracellular loop of the receptor.
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Affiliation(s)
- Mandi Murph
- Department of Systems Biology, MD Anderson Cancer Center, Houston, Texas 77030
| | - Giang Nguyen
- School of Biology and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, Georgia 30332
| | - Harish Radhakrishna
- School of Biology and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, Georgia 30332,The Coca-Cola Company, One Coca-Cola Plaza, TEC-437, Atlanta, GA 30301
| | - Gordon B. Mills
- Department of Systems Biology, MD Anderson Cancer Center, Houston, Texas 77030
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43
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Burgess DJ, Doles J, Zender L, Xue W, Ma B, McCombie WR, Hannon GJ, Lowe SW, Hemann MT. Topoisomerase levels determine chemotherapy response in vitro and in vivo. Proc Natl Acad Sci U S A 2008; 114:689-94. [PMID: 18574145 DOI: 10.3171/2010.2.jns09719] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Topoisomerase poisons are chemotherapeutic agents that are used extensively for treating human malignancies. These drugs can be highly effective, yet tumors are frequently refractory to treatment or become resistant upon tumor relapse. Using a pool-based RNAi screening approach and a well characterized mouse model of lymphoma, we explored the genetic basis for heterogeneous responses to topoisomerase poisons in vitro and in vivo. These experiments identified Top2A expression levels as major determinants of response to the topoisomerase 2 poison doxorubicin and showed that suppression of Top2A produces resistance to doxorubicin in vitro and in vivo. Analogously, using a targeted RNAi approach, we demonstrated that suppression of Top1 produces resistance to the topoisomerase 1 poison camptothecin yet hypersensitizes cancer cells to doxorubicin. Importantly, lymphomas relapsing after treatment display spontaneous changes in topoisomerase levels as predicted by in vitro gene knockdown studies. These results highlight the utility of pooled shRNA screens for identifying genetic determinants of chemotherapy response and suggest strategies for improving the effectiveness of topoisomerase poisons in the clinic.
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Affiliation(s)
- Darren J Burgess
- Cold Spring Harbor Laboratory and Howard Hughes Medical Institute, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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Topoisomerase levels determine chemotherapy response in vitro and in vivo. Proc Natl Acad Sci U S A 2008; 105:9053-8. [PMID: 18574145 DOI: 10.1073/pnas.0803513105] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Topoisomerase poisons are chemotherapeutic agents that are used extensively for treating human malignancies. These drugs can be highly effective, yet tumors are frequently refractory to treatment or become resistant upon tumor relapse. Using a pool-based RNAi screening approach and a well characterized mouse model of lymphoma, we explored the genetic basis for heterogeneous responses to topoisomerase poisons in vitro and in vivo. These experiments identified Top2A expression levels as major determinants of response to the topoisomerase 2 poison doxorubicin and showed that suppression of Top2A produces resistance to doxorubicin in vitro and in vivo. Analogously, using a targeted RNAi approach, we demonstrated that suppression of Top1 produces resistance to the topoisomerase 1 poison camptothecin yet hypersensitizes cancer cells to doxorubicin. Importantly, lymphomas relapsing after treatment display spontaneous changes in topoisomerase levels as predicted by in vitro gene knockdown studies. These results highlight the utility of pooled shRNA screens for identifying genetic determinants of chemotherapy response and suggest strategies for improving the effectiveness of topoisomerase poisons in the clinic.
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Production and sequence validation of a complete full length ORF collection for the pathogenic bacterium Vibrio cholerae. Proc Natl Acad Sci U S A 2008; 105:4364-9. [PMID: 18337508 DOI: 10.1073/pnas.0712049105] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cholera, an infectious disease with global impact, is caused by pathogenic strains of the bacterium Vibrio cholerae. High-throughput functional proteomics technologies now offer the opportunity to investigate all aspects of the proteome, which has led to an increased demand for comprehensive protein expression clone resources. Genome-scale reagents for cholera would encourage comprehensive analyses of immune responses and systems-wide functional studies that could lead to improved vaccine and therapeutic strategies. Here, we report the production of the FLEXGene clone set for V. cholerae O1 biovar eltor str. N16961: a complete-genome collection of ORF clones. This collection includes 3,761 sequence-verified clones from 3,887 targeted ORFs (97%). The ORFs were captured in a recombinational cloning vector to facilitate high-throughput transfer of ORF inserts into suitable expression vectors. To demonstrate its application, approximately 15% of the collection was transferred into the relevant expression vector and used to produce a protein microarray by transcribing, translating, and capturing the proteins in situ on the array surface with 92% success. In a second application, a method to screen for protein triggers of Toll-like receptors (TLRs) was developed. We tested in vitro-synthesized proteins for their ability to stimulate TLR5 in A549 cells. This approach appropriately identified FlaC, and previously uncharacterized TLR5 agonist activities. These data suggest that the genome-scale, fully sequenced ORF collection reported here will be useful for high-throughput functional proteomic assays, immune response studies, structure biology, and other applications.
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Meaburn KJ, Misteli T. Locus-specific and activity-independent gene repositioning during early tumorigenesis. ACTA ACUST UNITED AC 2008; 180:39-50. [PMID: 18195100 PMCID: PMC2213600 DOI: 10.1083/jcb.200708204] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mammalian genome is highly organized within the cell nucleus. The nuclear position of many genes and genomic regions changes during physiological processes such as proliferation, differentiation, and disease. It is unclear whether disease-associated positioning changes occur specifically or are part of more global genome reorganization events. Here, we have analyzed the spatial position of a defined set of cancer-associated genes in an established mammary epithelial three-dimensional cell culture model of the early stages of breast cancer. We find that the genome is globally reorganized during normal and tumorigenic epithelial differentiation. Systematic mapping of changes in spatial positioning of cancer-associated genes reveals gene-specific positioning behavior and we identify several genes that are specifically repositioned during tumorigenesis. Alterations of spatial positioning patterns during differentiation and tumorigenesis were unrelated to gene activity. Our results demonstrate the existence of activity-independent genome repositioning events in the early stages of tumor formation.
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Affiliation(s)
- Karen J Meaburn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Rolfs A, Hu Y, Ebert L, Hoffmann D, Zuo D, Ramachandran N, Raphael J, Kelley F, McCarron S, Jepson DA, Shen B, Baqui MMA, Pearlberg J, Taycher E, DeLoughery C, Hoerlein A, Korn B, LaBaer J. A biomedically enriched collection of 7000 human ORF clones. PLoS One 2008; 3:e1528. [PMID: 18231609 PMCID: PMC2211400 DOI: 10.1371/journal.pone.0001528] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 11/28/2007] [Indexed: 01/21/2023] Open
Abstract
We report the production and availability of over 7000 fully sequence verified plasmid ORF clones representing over 3400 unique human genes. These ORF clones were derived using the human MGC collection as template and were produced in two formats: with and without stop codons. Thus, this collection supports the production of either native protein or proteins with fusion tags added to either or both ends. The template clones used to generate this collection were enriched in three ways. First, gene redundancy was removed. Second, clones were selected to represent the best available GenBank reference sequence. Finally, a literature-based software tool was used to evaluate the list of target genes to ensure that it broadly reflected biomedical research interests. The target gene list was compared with 4000 human diseases and over 8500 biological and chemical MeSH classes in ∼15 Million publications recorded in PubMed at the time of analysis. The outcome of this analysis revealed that relative to the genome and the MGC collection, this collection is enriched for the presence of genes with published associations with a wide range of diseases and biomedical terms without displaying a particular bias towards any single disease or concept. Thus, this collection is likely to be a powerful resource for researchers who wish to study protein function in a set of genes with documented biomedical significance.
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Affiliation(s)
- Andreas Rolfs
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Yanhui Hu
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Lars Ebert
- Deutsches Ressourcenzentrum fuer Genomforschung (RZPD), Heidelberg, Germany
| | - Dietmar Hoffmann
- Sanofi-Aventis, Cambridge, Massachusetts, United States of America
| | - Dongmei Zuo
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Niro Ramachandran
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Jacob Raphael
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Fontina Kelley
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Seamus McCarron
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Daniel A. Jepson
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Binghua Shen
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Munira M. A. Baqui
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Joseph Pearlberg
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Elena Taycher
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Craig DeLoughery
- Sanofi-Aventis, Cambridge, Massachusetts, United States of America
| | - Andreas Hoerlein
- Deutsches Ressourcenzentrum fuer Genomforschung (RZPD), Heidelberg, Germany
| | - Bernhard Korn
- Deutsches Ressourcenzentrum fuer Genomforschung (RZPD), Heidelberg, Germany
| | - Joshua LaBaer
- Harvard Institute of Proteomics, Harvard Medical School, Cambridge, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Naffar-Abu-Amara S, Shay T, Galun M, Cohen N, Isakoff SJ, Kam Z, Geiger B. Identification of novel pro-migratory, cancer-associated genes using quantitative, microscopy-based screening. PLoS One 2008; 3:e1457. [PMID: 18213366 PMCID: PMC2195451 DOI: 10.1371/journal.pone.0001457] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2007] [Accepted: 12/18/2007] [Indexed: 01/22/2023] Open
Abstract
Background Cell migration is a highly complex process, regulated by multiple genes, signaling pathways and external stimuli. To discover genes or pharmacological agents that can modulate the migratory activity of cells, screening strategies that enable the monitoring of diverse migratory parameters in a large number of samples are necessary. Methodology In the present study, we describe the development of a quantitative, high-throughput cell migration assay, based on a modified phagokinetic tracks (PKT) procedure, and apply it for identifying novel pro-migratory genes in a cancer-related gene library. In brief, cells are seeded on fibronectin-coated 96-well plates, covered with a monolayer of carboxylated latex beads. Motile cells clear the beads, located along their migratory paths, forming tracks that are visualized using an automated, transmitted-light screening microscope. The tracks are then segmented and characterized by multi-parametric, morphometric analysis, resolving a variety of morphological and kinetic features. Conclusions In this screen we identified 4 novel genes derived from breast carcinoma related cDNA library, whose over-expression induces major alteration in the migration of the stationary MCF7 cells. This approach can serve for high throughput screening for novel ways to modulate cellular migration in pathological states such as tumor metastasis and invasion.
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Affiliation(s)
- Suha Naffar-Abu-Amara
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Shay
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Meirav Galun
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Cohen
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Steven J. Isakoff
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, United States of America
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zvi Kam
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Benjamin Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * To whom correspondence should be addressed. E-mail:
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Karantza-Wadsworth V, White E. A mouse mammary epithelial cell model to identify molecular mechanisms regulating breast cancer progression. Methods Enzymol 2008; 446:61-76. [PMID: 18603116 PMCID: PMC2857708 DOI: 10.1016/s0076-6879(08)01604-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Breast cancer, like any other human cancer, results from the accumulation of mutations that deregulate critical cellular processes, such as cell proliferation and death. Activation of oncogenes and inactivation of tumor suppressor genes are common events during cancer initiation and progression and often determine treatment responsiveness. Thus, recapitulating these events in mouse cancer models is critical for unraveling the molecular mechanisms involved in tumorigenesis and for interrogating their possible impact on response to anticancer drugs. We have developed a novel mouse mammary epithelial cell model, which replicates the steps of epithelial tumor progression and takes advantage of the power of mouse genetics and the ability to assess three-dimensional morphogenesis in the presence of extracellular matrix to model human breast cancer.
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Affiliation(s)
- Vassiliki Karantza-Wadsworth
- Division of Medical Oncology, Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
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Liu Y, Shu XZ, Prestwich GD. Tumor engineering: orthotopic cancer models in mice using cell-loaded, injectable, cross-linked hyaluronan-derived hydrogels. ACTA ACUST UNITED AC 2007; 13:1091-101. [PMID: 17582839 DOI: 10.1089/ten.2006.0297] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Current cancer xenograft models used to evaluate new anticancer therapies are limited to "good take" cell lines, fail to mimic normal human disease, and poorly predict clinical outcomes. We now describe the use of an injectable, in situ cross-linkable synthetic extracellular matrix (sECM) to deliver and grow cancer cells in vivo. The hyaluronan (HA)-derived sECMs were seeded with breast, colon, and ovarian cancer cells prior to gelation, and then injected subcutaneously into mammary fat pads, subserosally in colons, and intracapsularly in ovaries, respectively. Two cell lines were used for each type of cancer, and results were compared with orthotopic injection of cells in serum-free medium. At 4 weeks postinjection, four parameters were measured: (i) incidence and size of cancer at the injection site, (ii) vascularization or necrosis of new cancer tissue, (iii) cancer seeding in adjacent tissues, and (iv) metastasis to lymph nodes and other vital organs. In addition, the activation of the phosphoinositide 3-kinase (PI 3-K) signaling pathway was analyzed immunohistochemically. Overall, orthotopic delivery of cancer cells in sECM hydrogels showed clear advantages: (i) increased incidence of cancer formation and reduced variability in tumor size, (ii) enhanced growth of organ-specific cancers with good tumor-tissue integration, (iii) improved vascularization and reduced necrosis within the tumor, (iv) reduced cancer seeding on adjacent tissues, and (v) better general health of animals. Thus, engineered tumors represent an improved approach to traditional tumor xenografts, and facilitate studies in cancer biology, invasion and metastasis, as well as the investigation of new therapeutic and diagnostic protocols.
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Affiliation(s)
- Yanchun Liu
- Center for Therapeutic Biomaterials and Department of Medicinal Chemistry, The University of Utah, Salt Lake City 84108-1257, USA
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