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Wilson JJ, Wei J, Daamen AR, Sears JD, Bechtel E, Mayberry CL, Stafford GA, Bechtold L, Grammer AC, Lipsky PE, Roopenian DC, Chang CH. Glucose oxidation-dependent survival of activated B cells provides a putative novel therapeutic target for lupus treatment. iScience 2023; 26:107487. [PMID: 37636066 PMCID: PMC10448027 DOI: 10.1016/j.isci.2023.107487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/27/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Aberrant metabolic demand is observed in immune/inflammatory disorders, yet the role in pathogenesis remains unclear. Here, we discover that in lupus, activated B cells, including germinal center B (GCB) cells, have remarkably high glycolytic requirement for survival over T cell populations, as demonstrated by increased metabolic activity in lupus-activated B cells compared to immunization-induced cells. The augmented reliance on glucose oxidation makes GCB cells vulnerable to mitochondrial ROS-induced oxidative stress and apoptosis. Short-term glycolysis inhibition selectively reduces pathogenic activated B in lupus-prone mice, extending their lifespan, without affecting T follicular helper cells. Particularly, BCMA-expressing GCB cells rely heavily on glucose oxidation. Depleting BCMA-expressing activated B cells with APRIL-based CAR-T cells significantly prolongs the lifespan of mice with severe autoimmune disease. These results reveal that glycolysis-dependent activated B and GCB cells, especially those expressing BCMA, are potentially key lupus mediators, and could be targeted to improve disease outcomes.
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Affiliation(s)
- John J. Wilson
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA
| | - Jian Wei
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Andrea R. Daamen
- AMPEL BioSolutions and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | - John D. Sears
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Elaine Bechtel
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA
| | | | | | | | - Amrie C. Grammer
- AMPEL BioSolutions and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | - Peter E. Lipsky
- AMPEL BioSolutions and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | | | - Chih-Hao Chang
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA 02111, USA
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2
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Woo XY, Srivastava A, Mack PC, Graber JH, Sanderson BJ, Lloyd MW, Chen M, Domanskyi S, Gandour-Edwards R, Tsai RA, Keck J, Cheng M, Bundy M, Jocoy EL, Riess JW, Holland W, Grubb SC, Peterson JG, Stafford GA, Paisie C, Neuhauser SB, Karuturi RKM, George J, Simons AK, Chavaree M, Tepper CG, Goodwin N, Airhart SD, Lara PN, Openshaw TH, Liu ET, Gandara DR, Bult CJ. A Genomically and Clinically Annotated Patient-Derived Xenograft Resource for Preclinical Research in Non-Small Cell Lung Cancer. Cancer Res 2022; 82:4126-4138. [PMID: 36069866 PMCID: PMC9664138 DOI: 10.1158/0008-5472.can-22-0948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/22/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022]
Abstract
Patient-derived xenograft (PDX) models are an effective preclinical in vivo platform for testing the efficacy of novel drugs and drug combinations for cancer therapeutics. Here we describe a repository of 79 genomically and clinically annotated lung cancer PDXs available from The Jackson Laboratory that have been extensively characterized for histopathologic features, mutational profiles, gene expression, and copy-number aberrations. Most of the PDXs are models of non-small cell lung cancer (NSCLC), including 37 lung adenocarcinoma (LUAD) and 33 lung squamous cell carcinoma (LUSC) models. Other lung cancer models in the repository include four small cell carcinomas, two large cell neuroendocrine carcinomas, two adenosquamous carcinomas, and one pleomorphic carcinoma. Models with both de novo and acquired resistance to targeted therapies with tyrosine kinase inhibitors are available in the collection. The genomic profiles of the LUAD and LUSC PDX models are consistent with those observed in patient tumors from The Cancer Genome Atlas and previously characterized gene expression-based molecular subtypes. Clinically relevant mutations identified in the original patient tumors were confirmed in engrafted PDX tumors. Treatment studies performed in a subset of the models recapitulated the responses expected on the basis of the observed genomic profiles. These models therefore serve as a valuable preclinical platform for translational cancer research. SIGNIFICANCE Patient-derived xenografts of lung cancer retain key features observed in the originating patient tumors and show expected responses to treatment with standard-of-care agents, providing experimentally tractable and reproducible models for preclinical investigations.
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Affiliation(s)
- Xing Yi Woo
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA,Current affiliation: Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Philip C. Mack
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA,Current affiliation: Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joel H. Graber
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA,Current affiliation: MDI Biological Laboratory, Bar Harbor, Maine, USA
| | - Brian J. Sanderson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Michael W. Lloyd
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Mandy Chen
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Sergii Domanskyi
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | | | - Rebekah A. Tsai
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - James Keck
- The Jackson Laboratory, Sacramento, California, USA
| | | | | | | | - Jonathan W. Riess
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - William Holland
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Stephen C. Grubb
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - James G. Peterson
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Grace A. Stafford
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Carolyn Paisie
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | | | | | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Allen K. Simons
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Margaret Chavaree
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA,Eastern Maine Medical Center, Lafayette Family Cancer Center, Brewer, Maine, USA
| | - Clifford G. Tepper
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Neal Goodwin
- The Jackson Laboratory, Sacramento, California, USA,Current affiliation: Teknova, Hollister, California USA
| | - Susan D. Airhart
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - Primo N. Lara
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Thomas H. Openshaw
- Eastern Maine Medical Center, Lafayette Family Cancer Center, Brewer, Maine, USA,Current affiliation: Cape Cod Hospital, Hyannis, Massachusetts, USA
| | - Edison T. Liu
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA
| | - David R. Gandara
- University of California Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Carol J. Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, Maine, USA,Corresponding author: Carol J. Bult, The Jackson Laboratory, 600 Main Street, RL13, Bar Harbor, ME 04609; (tel) 207-288-6324,
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3
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Dwyer JR, Racine JJ, Chapman HD, Quinlan A, Presa M, Stafford GA, Schmitz I, Serreze DV. Nfkbid Overexpression in Nonobese Diabetic Mice Elicits Complete Type 1 Diabetes Resistance in Part Associated with Enhanced Thymic Deletion of Pathogenic CD8 T Cells and Increased Numbers and Activity of Regulatory T Cells. J Immunol 2022; 209:227-237. [PMID: 35760520 PMCID: PMC9365269 DOI: 10.4049/jimmunol.2100558] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Type 1 diabetes (T1D) in both humans and NOD mice is caused by T cell-mediated autoimmune destruction of pancreatic β cells. Increased frequency or activity of autoreactive T cells and failures of regulatory T cells (Tregs) to control these pathogenic effectors have both been implicated in T1D etiology. Due to the expression of MHC class I molecules on β cells, CD8 T cells represent the ultimate effector population mediating T1D. Developing autoreactive CD8 T cells normally undergo extensive thymic negative selection, but this process is impaired in NOD mice and also likely T1D patients. Previous studies identified an allelic variant of Nfkbid, a NF-κB signal modulator, as a gene strongly contributing to defective thymic deletion of autoreactive CD8 T cells in NOD mice. These previous studies found ablation of Nfkbid in NOD mice using the clustered regularly interspaced short palindromic repeats system resulted in greater thymic deletion of pathogenic CD8 AI4 and NY8.3 TCR transgenic T cells but an unexpected acceleration of T1D onset. This acceleration was associated with reductions in the frequency of peripheral Tregs. In this article, we report transgenic overexpression of Nfkbid in NOD mice also paradoxically results in enhanced thymic deletion of autoreactive CD8 AI4 T cells. However, transgenic elevation of Nfkbid expression also increased the frequency and functional capacity of peripheral Tregs, in part contributing to the induction of complete T1D resistance. Thus, future identification of a pharmaceutical means to enhance Nfkbid expression might ultimately provide an effective T1D intervention approach.
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Affiliation(s)
| | | | | | | | | | | | - Ingo Schmitz
- Department of Molecular Immunology, Ruhr-University, Bochum, Germany
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4
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Hosur V, Low BE, Li D, Stafford GA, Kohar V, Shultz LD, Wiles MV. Genes adapt to outsmart gene-targeting strategies in mutant mouse strains by skipping exons to reinitiate transcription and translation. Genome Biol 2020; 21:168. [PMID: 32646486 PMCID: PMC7350591 DOI: 10.1186/s13059-020-02086-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Gene disruption in mouse embryonic stem cells or zygotes is a conventional genetics approach to identify gene function in vivo. However, because different gene disruption strategies use different mechanisms to disrupt genes, the strategies can result in diverse phenotypes in the resulting mouse model. To determine whether different gene disruption strategies affect the phenotype of resulting mutant mice, we characterized Rhbdf1 mouse mutant strains generated by three commonly used strategies-definitive-null, targeted knockout (KO)-first, and CRISPR/Cas9. RESULTS We find that Rhbdf1 responds differently to distinct KO strategies, for example, by skipping exons and reinitiating translation to potentially yield gain-of-function alleles rather than the expected null or severe hypomorphic alleles. Our analysis also revealed that at least 4% of mice generated using the KO-first strategy show conflicting phenotypes. CONCLUSIONS Exon skipping is a widespread phenomenon occurring across the genome. These findings have significant implications for the application of genome editing in both basic research and clinical practice.
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Affiliation(s)
- Vishnu Hosur
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | - Benjamin E. Low
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | - Daniel Li
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery at Weill Cornell Medicine, New York, NY 10021 USA
| | | | - Vivek Kohar
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
| | | | - Michael V. Wiles
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME USA
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5
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Mockus SM, Ananda G, Lundquist M, Spotlow V, Simons A, Mitchell T, Stafford GA, Potter CS, Philip V, Stearns T, Srivastava A, Barter M, Rowe L, Malcolm J, Bult C, Katuturi RKM, Rasmussen K, Hinerfeld D. Abstract 4816: Design, validation, and interpretation of an NGS assay for actionable variants in solid tumors. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The Jackson Laboratory Cancer Treatment Profile™ (JAX-CTP™) is a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable gene variants in solid tumors to inform the selection of targeted therapeutics for cancer treatment. We will describe the design of the 358- gene panel, analytical validation, and the curation and clinical reporting of actionable variants. Selection of the gene panel was based on known drug targets, casual implications in cancer, and a thorough pathway analysis. DNA is extracted from FFPE tumor samples and using hybrid capture, the genes of interest are enriched and sequenced on Illumina HiSeq 2500 or MiSeq sequencers. FASTQ files generated from Illumina's CASAVA software are submitted to the JAX Clinical Genome Analytics (CGA) data analysis pipeline to perform automated read quality assessment, alignment, and variant calling. Identified variants are then submitted for clinical curation using a combination of the in-house JAX Clinical Knowledgebase (CKB) and the external Genetic Variant Annotation (GVA) from CollabRx. Once clinically annotated, the variants are graded relative to their clinical utility for the specific tumor type and compiled into a clinical report to inform patient treatment. Extensive analytical validation, following CAP guidelines, was conducted to assess limit of detection, accuracy, precision, sensitivity, and specificity of the assay. The summarized optimized sensitivity of the assay is a minimum coverage of samples at 300X, a limit of detection of 10% for SNP’s/indels and ≥6 copies for CNV’s, and an average of 3-4 actionable variants per sample. The challenges of interpreting gene variants for clinical actionability and for establishing an analytically valid bioinformatic pipeline will be discussed in-depth.
Citation Format: Susan M. Mockus, Guruprasad Ananda, Micaela Lundquist, Vanessa Spotlow, Al Simons, Talia Mitchell, Grace A. Stafford, Christopher S. Potter, Vivek Philip, Timothy Stearns, Anuj Srivastava, Mary Barter, Lucy Rowe, Joan Malcolm, Carol Bult, Radha Krishna Murthy Katuturi, Karen Rasmussen, Douglas Hinerfeld. Design, validation, and interpretation of an NGS assay for actionable variants in solid tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4816. doi:10.1158/1538-7445.AM2015-4816
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Affiliation(s)
- Susan M. Mockus
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | | | - Vanessa Spotlow
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Al Simons
- 2The Jackson Laboratory for Mammalian Genomics, Bar Harbor, ME
| | - Talia Mitchell
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | | | - Vivek Philip
- 2The Jackson Laboratory for Mammalian Genomics, Bar Harbor, ME
| | - Timothy Stearns
- 2The Jackson Laboratory for Mammalian Genomics, Bar Harbor, ME
| | - Anuj Srivastava
- 2The Jackson Laboratory for Mammalian Genomics, Bar Harbor, ME
| | - Mary Barter
- 2The Jackson Laboratory for Mammalian Genomics, Bar Harbor, ME
| | - Lucy Rowe
- 2The Jackson Laboratory for Mammalian Genomics, Bar Harbor, ME
| | - Joan Malcolm
- 1The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Carol Bult
- 2The Jackson Laboratory for Mammalian Genomics, Bar Harbor, ME
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6
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Potter CS, Patterson SE, Woo XY, Stafford GA, Tsongalis GJ, Mockus SM. Ranking therapies for clinical trial selection based on somatic mutation profiles. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.e22089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | - Gregory J. Tsongalis
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
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7
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Patterson SE, Potter CS, Stafford GA, Woo XY, Spotlow V, Mitchell T, Liu R, Ananda G, Tsongalis GJ, Mockus SM. Solid tumor profiling via next-generation sequencing to identify tumor-specific actionable variants. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.1539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | - Talia Mitchell
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Roger Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | - Gregory J. Tsongalis
- The Geisel School of Medicine at Dartmouth and Dartmouth Hitchcock Medical Center, Lebanon, NH
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8
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Rasmussen KE, Nehring R, Ananda G, Stafford GA, Phillip V, Mockus S, Srivastava A, Simons A, Donnelly C, Karuturi K, Hinerfeld D, Spotlow V, Lundquist M, Ruan X, Bult CJ, Scott S, Love T, Richards DR, Liu ET. Utilization of a 358-gene panel to molecularly profile solid tumors for association with target-based therapeutic agents. J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.e22117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Sean Scott
- Ingenuity, a QIAGEN Company, Redwood City, CA
| | - Tara Love
- Ingenuity, a QIAGEN Company, Redwood City, CA
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9
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Thomas DG, Gaheen S, Harper SL, Fritts M, Klaessig F, Hahn-Dantona E, Paik D, Pan S, Stafford GA, Freund ET, Klemm JD, Baker NA. ISA-TAB-Nano: a specification for sharing nanomaterial research data in spreadsheet-based format. BMC Biotechnol 2013; 13:2. [PMID: 23311978 PMCID: PMC3598649 DOI: 10.1186/1472-6750-13-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 12/11/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND AND MOTIVATION The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials. RESULTS We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata. CONCLUSION The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.
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Affiliation(s)
- Dennis G Thomas
- Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sharon Gaheen
- SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA
| | - Stacey L Harper
- Department of Environmental and Molecular Toxicology, School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - Martin Fritts
- SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA
| | - Fred Klaessig
- Pennsylvania Bio Nano Systems, LLC, Doylestown, PA, USA
| | | | - David Paik
- Department of Radiology, Stanford University, Stanford, CA 94305, USA
| | - Sue Pan
- SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Information Systems Program, Rockville, MD 20852, USA
| | | | | | - Juli D Klemm
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20852, USA
| | - Nathan A Baker
- Knowledge Discovery and Informatics, Pacific Northwest National Laboratory, PO Box 999, MSID K7-28, Richland, WA 99352, USA
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10
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Freimuth RR, Freund ET, Schick L, Sharma MK, Stafford GA, Suzek BE, Hernandez J, Hipp J, Kelley JM, Rokicki K, Pan S, Buckler A, Stokes TH, Fernandez A, Fore I, Buetow KH, Klemm JD. Life sciences domain analysis model. J Am Med Inform Assoc 2012; 19:1095-102. [PMID: 22744959 PMCID: PMC3486731 DOI: 10.1136/amiajnl-2011-000763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Objective Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. Materials and methods The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. Results The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. Discussion The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. Conclusions The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science.
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Affiliation(s)
- Robert R Freimuth
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
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11
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Boyd LB, Hunicke-Smith SP, Stafford GA, Freund ET, Ehlman M, Chandran U, Dennis R, Fernandez AT, Goldstein S, Steffen D, Tycko B, Klemm JD. The caBIG® Life Science Business Architecture Model. Bioinformatics 2011; 27:1429-35. [PMID: 21450709 PMCID: PMC3087952 DOI: 10.1093/bioinformatics/btr141] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 01/31/2011] [Accepted: 03/12/2011] [Indexed: 11/28/2022] Open
Abstract
MOTIVATION Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG®) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research. RESULTS LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. AVAILABILITY AND IMPLEMENTATION The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ).
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Affiliation(s)
- Lauren Becnel Boyd
- Department of Medicine, Hematology/Oncology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
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12
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Cimino JJ, Hayamizu TF, Bodenreider O, Davis B, Stafford GA, Ringwald M. The caBIG terminology review process. J Biomed Inform 2009; 42:571-80. [PMID: 19154797 PMCID: PMC2729758 DOI: 10.1016/j.jbi.2008.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 10/23/2008] [Accepted: 12/14/2008] [Indexed: 10/21/2022]
Abstract
The National Cancer Institute (NCI) is developing an integrated biomedical informatics infrastructure, the cancer Biomedical Informatics Grid (caBIG), to support collaboration within the cancer research community. A key part of the caBIG architecture is the establishment of terminology standards for representing data. In order to evaluate the suitability of existing controlled terminologies, the caBIG Vocabulary and Data Elements Workspace (VCDE WS) working group has developed a set of criteria that serve to assess a terminology's structure, content, documentation, and editorial process. This paper describes the evolution of these criteria and the results of their use in evaluating four standard terminologies: the Gene Ontology (GO), the NCI Thesaurus (NCIt), the Common Terminology for Adverse Events (known as CTCAE), and the laboratory portion of the Logical Objects, Identifiers, Names and Codes (LOINC). The resulting caBIG criteria are presented as a matrix that may be applicable to any terminology standardization effort.
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Affiliation(s)
- James J Cimino
- National Institutes of Health, Laboratory for Informatics Development, Clinical Center, Room 6-2551, 10 Center Drive, Bethesda, MD 20892, USA.
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Abstract
Chromatin-modifying enzymes such as the histone acetyltransferase GCN5 can contribute to transcriptional activation at steps subsequent to the initial binding of transcriptional activators. However, few studies have directly examined dependence of chromatin remodeling in vivo on GCN5 or other acetyltransferases, and none have examined remodeling via nucleosomal activator binding sites. In this study, we have monitored chromatin perturbation via nucleosomal binding sites in the yeast episome TALS by GAL4 derivatives in GCN5(+) and gcn5Delta yeast cells. The strong activator GAL4 shows no dependence on GCN5 for remodeling TALS chromatin, whereas GAL4-estrogen receptor-VP16 shows substantial, albeit not complete, GCN5 dependence. Mini-GAL4 derivatives having weakened interactions with TATA-binding protein and TFIIB exhibit a strong dependence on GCN5 for both transcriptional activation and TALS remodeling not seen for native GAL4. These results indicate that GCN5 can contribute to chromatin remodeling at activator binding sites and that dependence on coactivator function for a given activator can vary according to the type and strength of contacts that it makes with other factors. We also found a weaker dependence for chromatin remodeling on SPT7 than on GCN5, indicating that GCN5 can function via pathways independent of the SAGA complex. Finally, we examine dependence on GCN5 and SWI-SNF at two model promoters and find that although these two chromatin-remodeling and/or modification activities may sometimes work together, in other instances they act in complementary fashion.
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Affiliation(s)
- G A Stafford
- Department of Biomedical Sciences, State University of New York at Albany School of Public Health, Albany, New York 12201-2002, USA
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14
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Ryan MP, Stafford GA, Yu L, Morse RH. Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling. Mol Cell Biol 2000; 20:5847-57. [PMID: 10913168 PMCID: PMC86062 DOI: 10.1128/mcb.20.16.5847-5857.2000] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional activators are believed to work in part by recruiting general transcription factors, such as TATA-binding protein (TBP) and the RNA polymerase II holoenzyme. Activation domains also contribute to remodeling of chromatin in vivo. To determine whether these two activities represent distinct functions of activation domains, we have examined transcriptional activation and chromatin remodeling accompanying artificial recruitment of TBP in yeast (Saccharomyces cerevisiae). We measured transcription of reporter genes with defined chromatin structure by artificial recruitment of TBP and found that a reporter gene whose TATA element was relatively accessible could be activated by artificially recruited TBP, whereas two promoters, GAL10 and CHA1, that have accessible activator binding sites, but nucleosomal TATA elements, could not. A third reporter gene containing the HIS4 promoter could be activated by GAL4-TBP only when a RAP1 binding site was present, although RAP1 alone could not activate the reporter, suggesting that RAP1 was needed to open the chromatin structure to allow activation. Consistent with this interpretation, artificially recruited TBP was unable to perturb nucleosome positioning via a nucleosomal binding site, in contrast to a true activator such as GAL4, or to perturb the TATA-containing nucleosome at the CHA1 promoter. Finally, we show that activation of the GAL10 promoter by GAL4, which requires chromatin remodeling, can occur even in swi gcn5 yeast, implying that remodeling pathways independent of GCN5, the SWI-SNF complex, and TFIID can operate during transcriptional activation in vivo.
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Affiliation(s)
- M P Ryan
- Molecular Genetics Program, Wadsworth Center, New York State Department of Health, Albany, New York 12201-2002, USA
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15
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Affiliation(s)
- M P Ryan
- Wadsworth Center, New York State Department of Health, Albany 12208, USA
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16
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Stafford GA, Morse RH. Mutations in the AF-2/hormone-binding domain of the chimeric activator GAL4.estrogen receptor.VP16 inhibit hormone-dependent transcriptional activation and chromatin remodeling in yeast. J Biol Chem 1998; 273:34240-6. [PMID: 9852087 DOI: 10.1074/jbc.273.51.34240] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
GAL4.estrogen receptor.VP16 (GAL4.ER.VP16), which contains the GAL4 DNA-binding domain, the human ER hormone binding (AF-2) domain, and the VP16 activation domain, functions as a hormone-dependent transcriptional activator in yeast (Louvion, J.-F., Havaux-Copf, B., and Picard, D. (1993) Gene (Amst.) 131, 129-134). Previously, we showed that this activator can remodel chromatin in yeast in a hormone-dependent manner. In this work, we show that a weakened VP16 activation domain in GAL4.ER.VP16 still allows hormone-dependent chromatin remodeling, but mutations in the AF-2 domain that abolish activity in the native ER also eliminate the ability of GAL4.ER.VP16 to activate transcription and to remodel chromatin. These findings suggest that an important role of the AF-2 domain in the native ER is to mask the activation potential of the AF-1 activation domain in the unliganded state; upon ligand activation, a conformational change releases AF-2-mediated repression and transcriptional activation ensues. We also show that the AF-2 domain, although inactive at simple promoters on its own in yeast, can enhance transcription by the MCM1 activator in hormone-dependent manner, consistent with its having a role in activation as well as repression in the native ER.
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Affiliation(s)
- G A Stafford
- Molecular Genetics Program, Wadsworth Center, New York State Department of Health, and State University of New York School of Public Health, Albany, New York 12201-2002, USA
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17
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Stafford GA, Oswald RE, Figl A, Cohen BN, Weiland GA. Two domains of the beta subunit of neuronal nicotinic acetylcholine receptors contribute to the affinity of substance P. J Pharmacol Exp Ther 1998; 286:619-26. [PMID: 9694912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Substance P is known to noncompetitively inhibit activation of muscle and neuronal nicotinic acetylcholine receptors. Neuronal nicotinic receptors formed from different combinations of alpha and beta subunits exhibited differential sensitivity to substance P, with those containing beta-4 subunits having a 25-fold higher affinity than those having beta-2 subunits. To identify the regions and/or amino acid residues of the beta subunit responsible for this difference, chimeric beta subunits were coexpressed with alpha-3 in Xenopus oocytes and the IC50 values for substance P were determined. Amino acid residues between 105 and 109 (beta4 numbering), in the middle of the N-terminal domain, and between 214 and 301, between the extracellular side of M1 and the intracellular side of M3, were identified as major contributors to the apparent affinity of substance P. The affinity of acetylcholine was only affected by residue changes between 105 and 109. Site-directed mutagenesis revealed two amino acids that are important determinants of the affinity of substance P, beta4(V108)/beta2(F106), which is in the middle of the first extracellular domain, and beta4(F255)/beta2(V253), which is within the putative channel lining transmembrane domain M2. However, other residues within these domains must be making subtle but significant contributions, since simultaneous mutation of both these amino acids did not cause complete interconversion of the beta subunit-dependent differences in the receptor affinity for substance P.
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Affiliation(s)
- G A Stafford
- Department of Pharmacology, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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18
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Abstract
We examine the generality of transcription factor-mediated chromatin remodeling by monitoring changes in chromatin structure in a yeast (Saccharomyces cerevisiae) episome outside of the context of a natural promoter. The episome has a well defined chromatin structure and a binding site for the transcription factor GAL4 but lacks a nearby functional TATA element or transcription start site, so that changes in chromatin structure are unlikely to be caused by transcription. To separate changes caused by binding and by activation domains, we use both GAL4 and a chimeric, hormone-dependent activator consisting of the GAL4 DNA-binding domain, an estrogen receptor (ER) hormone-binding domain, and a VP16 activation domain (Louvion, J.-F., Havaux-Copf, B. and Picard, D. (1993) Gene (Amst.) 131, 129-134). Both GAL4 and GAL4.ER.VP16 show very little perturbation of chromatin structure in their nonactivating configurations. Substantial additional perturbation occurs upon activation. This additional perturbation is marked by changes in micrococcal nuclease cleavage patterns, restriction endonuclease accessibility, and DNA topology and is not seen with the nonactivating derivative GAL4.ER. Remodeling by GAL4.ER.VP16 is detectable within 15 min following hormone addition and is complete within 45 min, suggesting that replication is not required. We conclude that activation domains can exert a major influence on chromatin remodeling by increasing binding affinity and/or by recruitment of other chromatin remodeling activities and that this remodeling can occur outside the context of a bona fide promoter.
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Affiliation(s)
- G A Stafford
- Molecular Genetics Program, Wadsworth Center, New York State Department of Health and State University of New York School of Public Health, Albany, New York 12201-2002, USA
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19
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Stafford GA, Oswald RE, Weiland GA. The beta subunit of neuronal nicotinic acetylcholine receptors is a determinant of the affinity for substance P inhibition. Mol Pharmacol 1994; 45:758-62. [PMID: 7514262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Substance P is known to inhibit nicotinic acetylcholine receptors from neuronal tissue, skeletal muscle, and electroplaque. The interaction of substance P with specific combinations of neuronal nicotinic acetylcholine receptor subunits was studied by expressing various combinations of subunits in Xenopus oocytes. The response to acetylcholine was inhibited by substance P with all subunit combinations tested; however, the apparent affinity for substance P varied by 20-30-fold. The affinity seemed to be dependent on the beta subtype expressed (beta 4 or beta 2). This suggests that the beta subunit may contribute, at least partially, to the substance P binding site. In the case of the alpha 7 subtype, which forms a homooligomeric receptor, the apparent affinity for substance P was intermediate between those of the two beta subtypes coexpressed with either alpha 3 or alpha 4. As previously found, the inhibition was noncompetitive. Furthermore, the inhibition was not voltage dependent and, therefore, is unlikely to be due to substance P blocking the channel within the transmembrane portion of the pore.
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Affiliation(s)
- G A Stafford
- Department of Pharmacology, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853
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Bigger CA, Cheh A, Latif F, Fishel R, Canella KA, Stafford GA, Yagi H, Jerina DM, Dipple A. DNA strand breaks induced by configurationally isomeric hydrocarbon diol epoxides. Drug Metab Rev 1994; 26:287-99. [PMID: 8082571 DOI: 10.3109/03602539409029798] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- C A Bigger
- Chemistry of Carcinogenesis Laboratory, NCI-Frederick Cancer Research and Development Center, Maryland 21702
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21
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Yaney GC, Stafford GA, Henstenberg JD, Sharp GW, Weiland GA. Binding of the dihydropyridine calcium channel blocker (+)-[3H] isopropyl-4-(2,1,3-benzoxadiazol-4-yl)-1,4-dihydro-5-methoxycarbonyl-2, 6-dimethyl-3-pyridinecarboxylate (PN200-110) to RINm5F membranes and cells: characterization and functional significance. J Pharmacol Exp Ther 1991; 258:652-62. [PMID: 1713965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
This report provides direct evidence for a dihydropyridine receptor/calcium channel in the insulin-secreting beta-cell line RINm5F. The receptor/channel can modulate the intracellular Ca++ concentration and the resultant insulin secretion by regulating the influx of extracellular Ca++ through dihydropyridine-sensitive voltage-dependent L-type Ca++ channels. Elevated extracellular K+ or the dihydropyridine Ca++ channel agonist, BAY k 8644 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(2-trifluoromethyl- phenyl)pyridine-5-carboxylate], stimulated the uptake of 45Ca++, raised [Ca++]i, and increased insulin secretion in a concentration-dependent manner. These actions were inhibited by L-type Ca++ channel blockers including nitrendipine, verapamil and diltiazem. (+)-[3H]PN200-110 bound specifically with high affinity to RINm5F cell membranes (Kd approximately 200 pM). Specific binding was inhibited competitively by dihydropyridines whereas phenylalkylamines inhibited incompletely (+)-[3H]PN200-110 binding, consistent with an allosteric interaction. The benzothiazepine diltiazem had no effect on (+)-[3H]PN200-110 binding in the presence of Ca++, but increased binding allosterically in the absence of Ca++ (in the presence of EGTA). Maximal (+)-[3H]PN200-110 binding required divalent cations, with Mg++, Mn++ and Ba++ essentially as effective as Ca++ in reversing the effects of EGTA, whereas binding was not supported by Cd++ or La . Specific high affinity (+)-[3H]PN200-110 binding was also demonstrated in intact RINm5F cells and shown to be modulated by membrane potential. Depolarization of the cells by raising extracellular K+ from 5 to 80 mM increased the affinity of (+)-[3H]PN200-110 4- to 5-fold (decreased Kd) with no significant effect on the maximum number of binding sites.
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Affiliation(s)
- G C Yaney
- Department of Pharmacology, New York State College of Veterinary Medicine, Cornell University, Ithaca
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