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Kaczmarczyk JA, Roberts RR, Luke BT, Chan KC, Van Wagoner CM, Felder RA, Saul RG, Simona C, Blonder J. Comparative microsomal proteomics of a model lung cancer cell line NCI-H23 reveals distinct differences between molecular profiles of 3D and 2D cultured cells. Oncotarget 2021; 12:2022-2038. [PMID: 34611477 PMCID: PMC8487723 DOI: 10.18632/oncotarget.28072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/15/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths in the USA and worldwide. Yet, about 95% of new drug candidates validated in preclinical phase eventually fail in clinical trials. Such a high attrition rate is attributed mostly to the inability of conventional two-dimensionally (2D) cultured cancer cells to mimic native three-dimensional (3D) growth of malignant cells in human tumors. To ascertain phenotypical differences between these two distinct culture conditions, we carried out a comparative proteomic analysis of a membrane fraction obtained from 3D- and 2D-cultured NSCLC model cell line NCI-H23. This analysis revealed a map of 1,166 (24%) protein species regulated in culture dependent manner, including differential regulation of a subset of cell surface-based CD molecules. We confirmed exclusive expression of CD99, CD146 and CD239 in 3D culture. Furthermore, label-free quantitation, targeting KRas proteoform-specific peptides, revealed upregulation of both wild type and monoallelic KRas4BG12C mutant at the surface of 3D cultured cells. In order to reduce the high attrition rate of new drug candidates, the results of this study strongly suggests exploiting base-line molecular profiling of a large number of patient-derived NSCLC cell lines grown in 2D and 3D culture, prior to actual drug candidate testing.
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Affiliation(s)
- Jan A. Kaczmarczyk
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Rhonda R. Roberts
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Brian T. Luke
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - King C. Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Current address: The Center for Cell Clearance, University of Virginia, Charlottesville, VA 22908, USA
| | - Carly M. Van Wagoner
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Current address: The Center for Cell Clearance, University of Virginia, Charlottesville, VA 22908, USA
| | - Robin A. Felder
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Richard G. Saul
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Colantonio Simona
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Josip Blonder
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
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Schoenherr RM, Huang D, Voytovich UJ, Ivey RG, Kennedy JJ, Saul RG, Colantonio S, Roberts RR, Knotts JG, Kaczmarczyk JA, Perry C, Hewitt SM, Bocik W, Whiteley GR, Hiltke T, Boja ES, Rodriguez H, Whiteaker JR, Paulovich AG. A dataset describing a suite of novel antibody reagents for the RAS signaling network. Sci Data 2019; 6:160. [PMID: 31467290 PMCID: PMC6715692 DOI: 10.1038/s41597-019-0166-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
RAS genes are frequently mutated in cancer and have for decades eluded effective therapeutic attack. The National Cancer Institute's RAS Initiative has a focus on understanding pathways and discovering therapies for RAS-driven cancers. Part of these efforts is the generation of novel reagents to enable the quantification of RAS network proteins. Here we present a dataset describing the development, validation (following consensus principles developed by the broader research community), and distribution of 104 monoclonal antibodies (mAbs) enabling detection of 27 phosphopeptides and 69 unmodified peptides from 20 proteins in the RAS network. The dataset characterizes the utility of the antibodies in a variety of applications, including Western blotting, immunoprecipitation, protein array, immunohistochemistry, and targeted mass spectrometry. All antibodies and characterization data are publicly available through the CPTAC Antibody Portal, Panorama Public Repository, and/or PRIDE databases. These reagents will aid researchers in discerning pathways and measuring expression changes in the RAS signaling network.
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Affiliation(s)
| | - Dongqing Huang
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Richard G Ivey
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Richard G Saul
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rhonda R Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph G Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jan A Kaczmarczyk
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Candice Perry
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gordon R Whiteley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tara Hiltke
- National Cancer Institute, Bethesda, MD, USA
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3
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Smith TC, Saul RG, Barton ER, Luna EJ. Generation and characterization of monoclonal antibodies that recognize human and murine supervillin protein isoforms. PLoS One 2018; 13:e0205910. [PMID: 30332471 PMCID: PMC6192639 DOI: 10.1371/journal.pone.0205910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/02/2018] [Accepted: 10/02/2018] [Indexed: 01/06/2023] Open
Abstract
Supervillin isoforms have been implicated in cell proliferation, actin filament-based motile processes, vesicle trafficking, and signal transduction. However, an understanding of the roles of these proteins in cancer metastasis and physiological processes has been limited by the difficulty of obtaining specific antibodies against these highly conserved membrane-associated proteins. To facilitate research into the biological functions of supervillin, monoclonal antibodies were generated against the bacterially expressed human supervillin N-terminus. Two chimeric monoclonal antibodies with rabbit Fc domains (clones 1E2/CPTC-SVIL-1; 4A8/CPTC-SVIL-2) and two mouse monoclonal antibodies (clones 5A8/CPTC-SVIL-3; 5G3/CPTC-SVIL-4) were characterized with respect to their binding sites, affinities, and for efficacy in immunoblotting, immunoprecipitation, immunofluorescence microscopy and immunohistochemical staining. Two antibodies (1E2, 5G3) recognize a sequence found only in primate supervillins, whereas the other two antibodies (4A8, 5A8) are specific for a more broadly conserved conformational epitope(s). All antibodies function in immunoblotting, immunoprecipitation and in immunofluorescence microscopy under the fixation conditions identified here. We also show that the 5A8 antibody works on immunohistological sections. These antibodies should provide useful tools for the study of mammalian supervillins.
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Affiliation(s)
- Tara C. Smith
- Department of Radiology, Division of Cell Biology & Imaging, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Richard G. Saul
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD, United States of America
| | - Elisabeth R. Barton
- Applied Physiology & Kinesiology, College of Health & Human Performance, University of Florida, Gainesville, FL, United States of America
| | - Elizabeth J. Luna
- Department of Radiology, Division of Cell Biology & Imaging, University of Massachusetts Medical School, Worcester, MA, United States of America
- * E-mail:
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4
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Navas T, Pfister TD, Colantonio S, Aziz A, Dieckman L, Saul RG, Kaczmarczyk J, Borgel S, Alcoser SY, Hollingshead MG, Lee YH, Bottaro DP, Hiltke T, Whiteley G, Takebe N, Kinders RJ, Parchment RE, Tomaszewski JE, Doroshow JH. Novel antibody reagents for characterization of drug- and tumor microenvironment-induced changes in epithelial-mesenchymal transition and cancer stem cells. PLoS One 2018; 13:e0199361. [PMID: 29928062 PMCID: PMC6013203 DOI: 10.1371/journal.pone.0199361] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/06/2018] [Indexed: 01/10/2023] Open
Abstract
The presence of cancer stem cells (CSCs) and the induction of epithelial-to-mesenchymal transition (EMT) in tumors are associated with tumor aggressiveness, metastasis, drug resistance, and poor prognosis, necessitating the development of reagents for unambiguous detection of CSC- and EMT-associated proteins in tumor specimens. To this end, we generated novel antibodies to EMT- and CSC-associated proteins, including Goosecoid, Sox9, Slug, Snail, and CD133. Importantly, unlike several widely used antibodies to CD133, the anti-CD133 antibodies we generated recognize epitopes distal to known glycosylation sites, enabling analyses that are not confounded by differences in CD133 glycosylation. For all target proteins, we selected antibodies that yielded the expected target protein molecular weights by Western analysis and the correct subcellular localization patterns by immunofluorescence microscopy assay (IFA); binding selectivity was verified by immunoprecipitation−mass spectrometry and by immunohistochemistry and IFA peptide blocking experiments. Finally, we applied these reagents to assess modulation of the respective markers of EMT and CSCs in xenograft tumor models by IFA. We observed that the constitutive presence of human hepatocyte growth factor (hHGF) in the tumor microenvironment of H596 non-small cell lung cancer tumors implanted in homozygous hHGF knock-in transgenic mice induced a more mesenchymal-like tumor state (relative to the epithelial-like state when implanted in control SCID mice), as evidenced by the elevated expression of EMT-associated transcription factors detected by our novel antibodies. Similarly, our new anti-CD133 antibody enabled detection and quantitation of drug-induced reductions in CD133-positive tumor cells following treatment of SUM149PT triple-negative breast cancer xenograft models with the CSC/focal adhesion kinase (FAK) inhibitor VS-6063. Thus, our novel antibodies to CSC- and EMT-associated factors exhibit sufficient sensitivity and selectivity for immunofluorescence microscopy studies of these processes in preclinical xenograft tumor specimens and the potential for application with clinical samples.
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Affiliation(s)
- Tony Navas
- Clinical Pharmacodynamics Biomarker Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Thomas D. Pfister
- Clinical Pharmacodynamics Biomarker Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Simona Colantonio
- Antibody Characterization Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Amina Aziz
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Lynda Dieckman
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois, United States of America
| | - Richard G. Saul
- Antibody Characterization Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Jan Kaczmarczyk
- Antibody Characterization Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Suzanne Borgel
- Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Sergio Y. Alcoser
- Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Melinda G. Hollingshead
- Biological Testing Branch, Developmental Therapeutics Program, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Young H. Lee
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Donald P. Bottaro
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, Center for Strategic Scientific Initiatives, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Naoko Takebe
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Robert J. Kinders
- Clinical Pharmacodynamics Biomarker Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Ralph E. Parchment
- Clinical Pharmacodynamics Biomarker Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, Maryland, United States of America
| | - Joseph E. Tomaszewski
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
| | - James H. Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland, United States of America
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
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5
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Ye X, Luke BT, Wei BR, Kaczmarczyk JA, Loncarek J, Dwyer JE, Johann DJ, Saul RG, Nissley DV, McCormick F, Whiteley GR, Blonder J. Direct molecular dissection of tumor parenchyma from tumor stroma in tumor xenograft using mass spectrometry-based glycoproteomics. Oncotarget 2018; 9:26431-26452. [PMID: 29899869 PMCID: PMC5995176 DOI: 10.18632/oncotarget.25449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/02/2018] [Indexed: 12/18/2022] Open
Abstract
The most widely used cancer animal model is the human-murine tumor xenograft. Unbiased molecular dissection of tumor parenchyma versus stroma in human-murine xenografts is critical for elucidating dysregulated protein networks/pathways and developing therapeutics that may target these two functionally codependent compartments. Although antibody-reliant technologies (e.g., immunohistochemistry, imaging mass cytometry) are capable of distinguishing tumor-proper versus stromal proteins, the breadth or extent of targets is limited. Here, we report an antibody-free targeted cross-species glycoproteomic (TCSG) approach that enables direct dissection of human tumor parenchyma from murine tumor stroma at the molecular/protein level in tumor xenografts at a selectivity rate presently unattainable by other means. This approach was used to segment/dissect and obtain the protein complement phenotype of the tumor stroma and parenchyma of the metastatic human lung adenocarcinoma A549 xenograft, with no need for tissue microdissection prior to mass-spectrometry analysis. An extensive molecular map of the tumor proper and the associated microenvironment was generated along with the top functional N-glycosylated protein networks enriched in each compartment. Importantly, immunohistochemistry-based cross-validation of selected parenchymal and stromal targets applied on human tissue samples of lung adenocarcinoma and normal adjacent tissue is indicative of a noteworthy translational capacity for this unique approach that may facilitate identifications of novel targets for next generation antibody therapies and development of real time preclinical tumor models.
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Affiliation(s)
- Xiaoying Ye
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Brian T. Luke
- Advanced Biomedical Computing Center, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Bih-Rong Wei
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jan A. Kaczmarczyk
- Cancer Research Technology Program, Antibody Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Jadranka Loncarek
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jennifer E. Dwyer
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Donald J. Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72209, USA
| | - Richard G. Saul
- Cancer Research Technology Program, Antibody Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Dwight V. Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Gordon R. Whiteley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Josip Blonder
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
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6
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Frieling JS, Shay G, Izumi V, Aherne ST, Saul RG, Budzevich M, Koomen J, Lynch CC. Matrix metalloproteinase processing of PTHrP yields a selective regulator of osteogenesis, PTHrP 1-17. Oncogene 2017; 36:4498-4507. [PMID: 28368420 DOI: 10.1038/onc.2017.70] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/19/2017] [Accepted: 02/21/2017] [Indexed: 01/02/2023]
Abstract
Parathyroid hormone-related protein (PTHrP) is a critical regulator of bone resorption and augments osteolysis in skeletal malignancies. Here we report that the mature PTHrP1-36 hormone is processed by matrix metalloproteinases to yield a stable product, PTHrP1-17. PTHrP1-17 retains the ability to signal through PTH1R to induce calcium flux and ERK phosphorylation but not cyclic AMP production or CREB phosphorylation. Notably, PTHrP1-17 promotes osteoblast migration and mineralization in vitro, and systemic administration of PTHrP1-17 augments ectopic bone formation in vivo. Further, in contrast to PTHrP1-36, PTHrP1-17 does not affect osteoclast formation/function in vitro or in vivo. Finally, immunoprecipitation-mass spectrometry analyses using PTHrP1-17-specific antibodies establish that PTHrP1-17 is indeed generated by cancer cells. Thus, matrix metalloproteinase-directed processing of PTHrP disables the osteolytic functions of the mature hormone to promote osteogenesis, indicating important roles for this circuit in bone remodelling in normal and disease contexts.
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Affiliation(s)
- J S Frieling
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - G Shay
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - V Izumi
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - S T Aherne
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - R G Saul
- Antibody Characterization Lab, Leidos Biomedical Research, Frederick, MD, USA
| | - M Budzevich
- Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Koomen
- Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - C C Lynch
- Departments of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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7
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Schoenherr RM, Saul RG, Whiteaker JR, Yan P, Whiteley GR, Paulovich AG. Anti-peptide monoclonal antibodies generated for immuno-multiple reaction monitoring-mass spectrometry assays have a high probability of supporting Western blot and ELISA. Mol Cell Proteomics 2014; 14:382-98. [PMID: 25512614 DOI: 10.1074/mcp.o114.043133] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Immunoaffinity enrichment of peptides coupled to targeted, multiple reaction monitoring-mass spectrometry (immuno-MRM) has recently been developed for quantitative analysis of peptide and protein expression. As part of this technology, antibodies are generated to short, linear, tryptic peptides that are well-suited for detection by mass spectrometry. Despite its favorable analytical performance, a major obstacle to widespread adoption of immuno-MRM is a lack of validated affinity reagents because commercial antibody suppliers are reluctant to commit resources to producing anti-peptide antibodies for immuno-MRM while the market is much larger for conventional technologies, especially Western blotting and ELISA. Part of this reluctance has been the concern that affinity reagents generated to short, linear, tryptic peptide sequences may not perform well in traditional assays that detect full-length proteins. In this study, we test the feasibility and success rates of generating immuno-MRM monoclonal antibodies (mAbs) (targeting tryptic peptide antigens) that are also compatible with conventional, protein-based immuno-affinity technologies. We generated 40 novel, peptide immuno-MRM assays and determined that the cross-over success rates for using immuno-MRM monoclonals for Western blotting is 58% and for ELISA is 43%, which compare favorably to cross-over success rates amongst conventional immunoassay technologies. These success rates could most likely be increased if conventional and immuno-MRM antigen design strategies were combined, and we suggest a workflow for such a comprehensive approach. Additionally, the 40 novel immuno-MRM assays underwent fit-for-purpose analytical validation, and all mAbs and assays have been made available as a resource to the community via the Clinical Proteomic Tumor Analysis Consortium's (CPTAC) Antibody (http://antibodies.cancer.gov) and Assay Portals (http://assays.cancer.gov), respectively. This study also represents the first determination of the success rate (92%) for generating mAbs for immuno-MRM using a recombinant B cell cloning approach, which is considerably faster than the traditional hybridoma approach.
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Affiliation(s)
- Regine M Schoenherr
- From the ‡Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., P.O. Box 19024, Seattle, Washington 98109-1024
| | - Richard G Saul
- §Leidos Biochemical Research, Inc., Frederick National Laboratory for Cancer Research ATRF, C1014, 8560 Progress Drive, Frederick, Maryland 21701
| | - Jeffrey R Whiteaker
- From the ‡Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., P.O. Box 19024, Seattle, Washington 98109-1024
| | - Ping Yan
- From the ‡Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., P.O. Box 19024, Seattle, Washington 98109-1024
| | - Gordon R Whiteley
- §Leidos Biochemical Research, Inc., Frederick National Laboratory for Cancer Research ATRF, C1014, 8560 Progress Drive, Frederick, Maryland 21701
| | - Amanda G Paulovich
- From the ‡Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., P.O. Box 19024, Seattle, Washington 98109-1024;
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8
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Abstract
The potential of using mass spectrometry profiling as a diagnostic tool has been demonstrated for a wide variety of diseases. Various cancers and cancer-related diseases have been the focus of much of this work because of both the paucity of good diagnostic markers and the knowledge that early diagnosis is the most powerful weapon in treating cancer. The implementation of mass spectrometry as a routine diagnostic tool has proved to be difficult, however, primarily because of the stringent controls that are required for the method to be reproducible. The method is evolving as a powerful guide to the discovery of biomarkers that could, in turn, be used either individually or in an array or panel of tests for early disease detection. Using proteomic patterns to guide biomarker discovery and the possibility of deployment in the clinical laboratory environment on current instrumentation or in a hybrid technology has the possibility of being the early diagnosis tool that is needed.
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Affiliation(s)
- Gordon R Whiteley
- Clinical Proteomics Reference Lab, Advanced Technology Program, SAIC-Frederick, NCI-Frederick, PO Box B, Frederick, MD 21702, USA.
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9
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Abstract
Abstract
Starburst dendrimers are novel, water-soluble polymeric materials, with a well-defined composition and structure. In our application, we used dendrimers composed of poly(amidoamine) groups to which we coupled several specific antibodies, to investigate potential formats based on radial partition immunoassay. The coupled antibodies have retained their stability and immunological binding after coupling, both in solution and when immobilized onto a solid support. On the basis of our feasibility studies with model systems, we conclude that immunoassays can be developed with performance equivalent to or better than that in many established systems. By application of a mixture of the dendrimer-coupled antibody and the analyte of interest to the solid phase, we have investigated the performance characteristics of solution-phase immunoassays. Our experiments demonstrate enhanced sensitivity for creatine kinase MB isoenzyme (CKMB), thyrotropin, and myoglobin assays and reduced instrumental analysis time for the CKMB assay.
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Affiliation(s)
- P Singh
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
| | - F Moll
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
| | - S H Lin
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
| | - C Ferzli
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
| | - K S Yu
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
| | - R K Koski
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
| | - R G Saul
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
| | - P Cronin
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
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10
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Singh P, Moll F, Lin SH, Ferzli C, Yu KS, Koski RK, Saul RG, Cronin P. Starburst dendrimers: enhanced performance and flexibility for immunoassays. Clin Chem 1994; 40:1845-9. [PMID: 8070111] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Starburst dendrimers are novel, water-soluble polymeric materials, with a well-defined composition and structure. In our application, we used dendrimers composed of poly(amidoamine) groups to which we coupled several specific antibodies, to investigate potential formats based on radial partition immunoassay. The coupled antibodies have retained their stability and immunological binding after coupling, both in solution and when immobilized onto a solid support. On the basis of our feasibility studies with model systems, we conclude that immunoassays can be developed with performance equivalent to or better than that in many established systems. By application of a mixture of the dendrimer-coupled antibody and the analyte of interest to the solid phase, we have investigated the performance characteristics of solution-phase immunoassays. Our experiments demonstrate enhanced sensitivity for creatine kinase MB isoenzyme (CKMB), thyrotropin, and myoglobin assays and reduced instrumental analysis time for the CKMB assay.
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Affiliation(s)
- P Singh
- Baxter Diagnostics, Inc., Miami, FL 33152-0672
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11
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Abstract
Axolemma-enriched fractions were isolated from the white matter of bovine corpus callosum via a purified preparation of myelinated axons which were osmotically shocked and fractionated on a discontinuous density gradient. Two membrane fractions of differing density were obtained: both were somewhat enriched over white matter whole homogenate in specific activity of acetylcholinesterase and 5'-nucleotidase and maximal binding capacity for saxitoxin. Both membrane fractions contained appreciable amounts of 2', 3'-cyclic nucleotide 3'-phosphohydrolase; the specific activity of antimycin-sensitive NAPH-cytochrome c reductase and cytochrome c oxidase indicated low levels of contamination by microsomal and mitochondrial membrane. The myelin which is concomitantly isolated with the axolemma-enriched fractions has a lipid and protein composition comparable to that of myelin isolated by other procedures. Both axolemma-enriched fractions contain about one half of their dry weight as lipid comprised of approximately 25% cholesterol, 25% galactolipid (cerebrosides and sulfatides in a molar ratio of about 4:1) and 50% phospholipid, mostly choline phosphatides and ethanolamine phospholes in an equimolar ratio. The axolemma fractions are also enriched in ganglioside content relative to the myelin fraction. The polypeptides of the axolemma-enriched fractions range from 20,000 to over 200,000 in molecular weight; the predominant proteins are in the range from 50,000 to 69,000. The most dense axolemma-enriched fraction is over fourfold enriched in glycoprotein content compared with myelin, with at least 10 different molecular-weight classes of glycoproteins as identified by Schiff stain of polyacrylamide gel protein profiles. The differences and similarities in the molecular composition of axolemma-enriched preparations which have been characterized to date are discussed.
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Stanley J, Saul RG, Hadfield MG, De Vries GH. Mammalian central nervous system axolemma: histochemical evidence for axonal plasma membrane origin of bovine and rat axolemma-enriched membrane fractions. Neuroscience 1979; 4:155-67. [PMID: 759984 DOI: 10.1016/0306-4522(79)90225-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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