1
|
Kahn RA, Virk H, Laflamme C, Houston DW, Polinski NK, Meijers R, Levey AI, Saper CB, Errington TM, Turn RE, Bandrowski A, Trimmer JS, Rego M, Freedman LP, Ferrara F, Bradbury ARM, Cable H, Longworth S. Antibody characterization is critical to enhance reproducibility in biomedical research. eLife 2024; 13:e100211. [PMID: 39140332 DOI: 10.7554/elife.100211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/06/2024] [Indexed: 08/15/2024] Open
Abstract
Antibodies are used in many areas of biomedical and clinical research, but many of these antibodies have not been adequately characterized, which casts doubt on the results reported in many scientific papers. This problem is compounded by a lack of suitable control experiments in many studies. In this article we review the history of the 'antibody characterization crisis', and we document efforts and initiatives to address the problem, notably for antibodies that target human proteins. We also present recommendations for a range of stakeholders - researchers, universities, journals, antibody vendors and repositories, scientific societies and funders - to increase the reproducibility of studies that rely on antibodies.
Collapse
Affiliation(s)
- Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, United States
| | - Harvinder Virk
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Douglas W Houston
- The Development Studies Hybridoma Databank, University of Iowa, Iowa City, United States
| | - Nicole K Polinski
- The Michael J Fox Foundation for Parkinson's Research, New York, United States
| | - Rob Meijers
- Institute for Protein Innovation, Boston, United States
| | - Allan I Levey
- Department of Neurology, Emory University School of Medicine, Atlanta, United States
| | - Clifford B Saper
- Department of Neurology and Program in Neuroscience, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, United States
| | | | - Rachel E Turn
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Anita Bandrowski
- Department of Neuroscience, University of California, San Diego, La Jolla, United States
| | - James S Trimmer
- Department of Physiology and Membrane Biology, University of California, Davis School of Medicine, Davis, United States
| | | | - Leonard P Freedman
- Frederick National Laboratory for Cancer Research, Frederick, United States
| | | | | | - Hannah Cable
- Department of Research and Development, Abcam, Cambridge, United Kingdom
| | | |
Collapse
|
2
|
Kumar R, Zemaitis KJ, Fulcher JM, Paša-Tolić L. Advances in mass spectrometry-enabled multiomics at single-cell resolution. Curr Opin Biotechnol 2024; 87:103096. [PMID: 38432187 DOI: 10.1016/j.copbio.2024.103096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Biological organisms are multifaceted, intricate systems where slight perturbations can result in extensive changes in gene expression, protein abundance and/or activity, and metabolic flux. These changes occur at different timescales, spatially across cells of heterogeneous origins, and within single-cells. Hence, multimodal measurements at the smallest biological scales are necessary to capture dynamic changes in heterogeneous biological systems. Of the analytical techniques used to measure biomolecules, mass spectrometry (MS) has proven to be a powerful option due to its sensitivity, robustness, and flexibility with regard to the breadth of biomolecules that can be analyzed. Recently, many studies have coupled MS to other analytical techniques with the goal of measuring multiple modalities from the same single-cell. It is with these concepts in mind that we focus this review on MS-enabled multiomic measurements at single-cell or near-single- cell resolution.
Collapse
Affiliation(s)
- Rashmi Kumar
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kevin J Zemaitis
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - James M Fulcher
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| |
Collapse
|
3
|
Ayoubi R, Ryan J, Biddle MS, Alshafie W, Fotouhi M, Bolivar SG, Ruiz Moleon V, Eckmann P, Worrall D, McDowell I, Southern K, Reintsch W, Durcan TM, Brown C, Bandrowski A, Virk H, Edwards AM, McPherson P, Laflamme C. Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications. eLife 2023; 12:RP91645. [PMID: 37995198 PMCID: PMC10666931 DOI: 10.7554/elife.91645] [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] [Indexed: 11/25/2023] Open
Abstract
Antibodies are critical reagents to detect and characterize proteins. It is commonly understood that many commercial antibodies do not recognize their intended targets, but information on the scope of the problem remains largely anecdotal, and as such, feasibility of the goal of at least one potent and specific antibody targeting each protein in a proteome cannot be assessed. Focusing on antibodies for human proteins, we have scaled a standardized characterization approach using parental and knockout cell lines (Laflamme et al., 2019) to assess the performance of 614 commercial antibodies for 65 neuroscience-related proteins. Side-by-side comparisons of all antibodies against each target, obtained from multiple commercial partners, have demonstrated that: (i) more than 50% of all antibodies failed in one or more applications, (ii) yet, ~50-75% of the protein set was covered by at least one high-performing antibody, depending on application, suggesting that coverage of human proteins by commercial antibodies is significant; and (iii) recombinant antibodies performed better than monoclonal or polyclonal antibodies. The hundreds of underperforming antibodies identified in this study were found to have been used in a large number of published articles, which should raise alarm. Encouragingly, more than half of the underperforming commercial antibodies were reassessed by the manufacturers, and many had alterations to their recommended usage or were removed from the market. This first study helps demonstrate the scale of the antibody specificity problem but also suggests an efficient strategy toward achieving coverage of the human proteome; mine the existing commercial antibody repertoire, and use the data to focus new renewable antibody generation efforts.
Collapse
Affiliation(s)
- Riham Ayoubi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Joel Ryan
- Advanced BioImaging Facility (ABIF), McGill UniversityMontrealCanada
| | - Michael S Biddle
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of LeicesterLeicesterUnited Kingdom
| | - Walaa Alshafie
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Maryam Fotouhi
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Sara Gonzalez Bolivar
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Vera Ruiz Moleon
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Peter Eckmann
- Department of Neuroscience, UC San DiegoLa JollaUnited States
| | - Donovan Worrall
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Ian McDowell
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Kathleen Southern
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Wolfgang Reintsch
- The Neuro's Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill UniversityMontrealCanada
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), Structural Genomics Consortium, McGill UniversityMontrealCanada
| | - Claire Brown
- Advanced BioImaging Facility (ABIF), McGill UniversityMontrealCanada
| | | | - Harvinder Virk
- NIHR Respiratory BRC, Department of Respiratory Sciences, University of LeicesterLeicesterUnited Kingdom
| | - Aled M Edwards
- Structural Genomics Consortium, University of TorontoTorontoCanada
| | - Peter McPherson
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| | - Carl Laflamme
- Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill UniversityMontrealCanada
| |
Collapse
|
4
|
Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
Collapse
Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| |
Collapse
|
5
|
Wu PS, Lin MH, Hsiao JC, Lin PY, Pan SH, Chen YJ. EGFR-T790M Mutation-Derived Interactome Rerouted EGFR Translocation Contributing to Gefitinib Resistance in Non-Small Cell Lung Cancer. Mol Cell Proteomics 2023; 22:100624. [PMID: 37495186 PMCID: PMC10545940 DOI: 10.1016/j.mcpro.2023.100624] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 05/20/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
Secondary mutation, T790M, conferring tyrosine kinase inhibitors (TKIs) resistance beyond oncogenic epidermal growth factor receptor (EGFR) mutations presents a challenging unmet need. Although TKI-resistant mechanisms are intensively investigated, the underlying responses of cancer cells adapting drug perturbation are largely unknown. To illuminate the molecular basis linking acquired mutation to TKI resistance, affinity purification coupled mass spectrometry was adopted to dissect EGFR interactome in TKI-sensitive and TKI-resistant non-small cell lung cancer cells. The analysis revealed TKI-resistant EGFR-mutant interactome allocated in diverse subcellular distribution and enriched in endocytic trafficking, in which gefitinib intervention activated autophagy-mediated EGFR degradation and thus autophagy inhibition elevated gefitinib susceptibility. Alternatively, gefitinib prompted TKI-sensitive EGFR translocating toward cell periphery through Rab7 ubiquitination which may favor efficacy to TKIs suppression. This study revealed that T790M mutation rewired EGFR interactome that guided EGFR to autophagy-mediated degradation to escape treatment, suggesting that combination therapy with TKI and autophagy inhibitor may overcome acquired resistance in non-small cell lung cancer.
Collapse
Affiliation(s)
- Pei-Shan Wu
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan; Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Miao-Hsia Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | | | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Szu-Hua Pan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan; Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan; Doctoral Degree Program of Translational Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Yu-Ju Chen
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan; Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
6
|
Keskitalo S, Varjosalo M. Single-cell omics techniques to elucidate cell-to-cell variability in signalling cascades involved in human diseases. Expert Rev Proteomics 2023; 20:247-250. [PMID: 37804136 DOI: 10.1080/14789450.2023.2268836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Affiliation(s)
- Salla Keskitalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| |
Collapse
|
7
|
Tuncay A, Crabtree DR, Muggeridge DJ, Husi H, Cobley JN. Performance benchmarking microplate-immunoassays for quantifying target-specific cysteine oxidation reveals their potential for understanding redox-regulation and oxidative stress. Free Radic Biol Med 2023; 204:252-265. [PMID: 37192685 DOI: 10.1016/j.freeradbiomed.2023.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023]
Abstract
The antibody-linked oxi-state assay (ALISA) for quantifying target-specific cysteine oxidation can benefit specialist and non-specialist users. Specialists can benefit from time-efficient analysis and high-throughput target and/or sample n-plex capacities. The simple and accessible "off-the-shelf" nature of ALISA brings the benefits of oxidative damage assays to non-specialists studying redox-regulation. Until performance benchmarking establishes confidence in the "unseen" microplate results, ALISA is unlikely to be widely adopted. Here, we implemented pre-set pass/fail criteria to benchmark ALISA by evaluating immunoassay performance in diverse contexts. ELISA-mode ALISA assays were accurate, reliable, and sensitive. For example, the average inter-assay CV for detecting 20%- and 40%-oxidised PRDX2 or GAPDH standards was 4.6% (range: 3.6-7.4%). ALISA displayed target-specificity. Immunodepleting the target decreased the signal by ∼75%. Single-antibody formatted ALISA failed to quantify the matrix-facing alpha subunit of the mitochondrial ATP synthase. However, RedoxiFluor quantified the alpha subunit displaying exceptional performance in the single-antibody format. ALISA discovered that (1) monocyte-to-macrophage differentiation amplified PRDX2-oxidation in THP-1 cells and (2) exercise increased GAPDH-specific oxidation in human erythrocytes. The "unseen" microplate data were "seen-to-be-believed" via orthogonal visually displayed immunoassays like the dimer method. Finally, we established target (n = 3) and sample (n = 100) n-plex capacities in ∼4 h with 50-70 min hands-on time. Our work showcases the potential of ALISA to advance our understanding of redox-regulation and oxidative stress.
Collapse
Affiliation(s)
- Ahmet Tuncay
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | - Daniel R Crabtree
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | | | - Holger Husi
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | - James N Cobley
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK; Cysteine Redox Technology Group, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK.
| |
Collapse
|
8
|
Fabbrizi E, Fiorentino F, Carafa V, Altucci L, Mai A, Rotili D. Emerging Roles of SIRT5 in Metabolism, Cancer, and SARS-CoV-2 Infection. Cells 2023; 12:cells12060852. [PMID: 36980194 PMCID: PMC10047932 DOI: 10.3390/cells12060852] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Sirtuin 5 (SIRT5) is a predominantly mitochondrial enzyme catalyzing the removal of glutaryl, succinyl, malonyl, and acetyl groups from lysine residues through a NAD+-dependent deacylase mechanism. SIRT5 is an important regulator of cellular homeostasis and modulates the activity of proteins involved in different metabolic pathways such as glycolysis, tricarboxylic acid (TCA) cycle, fatty acid oxidation, electron transport chain, generation of ketone bodies, nitrogenous waste management, and reactive oxygen species (ROS) detoxification. SIRT5 controls a wide range of aspects of myocardial energy metabolism and plays critical roles in heart physiology and stress responses. Moreover, SIRT5 has a protective function in the context of neurodegenerative diseases, while it acts as a context-dependent tumor promoter or suppressor. In addition, current research has demonstrated that SIRT5 is implicated in the SARS-CoV-2 infection, although opposing conclusions have been drawn in different studies. Here, we review the current knowledge on SIRT5 molecular actions under both healthy and diseased settings, as well as its functional effects on metabolic targets. Finally, we revise the potential of SIRT5 as a therapeutic target and provide an overview of the currently reported SIRT5 modulators, which include both activators and inhibitors.
Collapse
Affiliation(s)
- Emanuele Fabbrizi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Vincenzo Carafa
- Department of Precision Medicine, Università degli Studi della Campania “L. Vanvitelli”, 80138 Naples, Italy
- BIOGEM, 83031 Ariano Irpino, Italy
| | - Lucia Altucci
- Department of Precision Medicine, Università degli Studi della Campania “L. Vanvitelli”, 80138 Naples, Italy
- BIOGEM, 83031 Ariano Irpino, Italy
- IEOS—Istituto per l’Endocrinologia e Oncologia Sperimentale, CNR, 80131 Naples, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
- Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (A.M.); (D.R.); Tel.: +39-0649913392 (A.M.); +39-0649913237 (D.R.); Fax: +39-0649693268 (A.M.)
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: (A.M.); (D.R.); Tel.: +39-0649913392 (A.M.); +39-0649913237 (D.R.); Fax: +39-0649693268 (A.M.)
| |
Collapse
|
9
|
Zhao Y, Hu J, Wu J, Li Z. ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, Bactrocera dorsalis. Front Genet 2023; 14:1108104. [PMID: 36911387 PMCID: PMC9996634 DOI: 10.3389/fgene.2023.1108104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction: While it has been suggested that histone modifications can facilitate animal responses to rapidly changing environments, few studies have profiled whole-genome histone modification patterns in invasive species, leaving the regulatory landscape of histone modifications in invasive species unclear. Methods: Here, we screen genome-wide patterns of two important histone modifications, trimethylated Histone H3 Lysine 4 (H3K4me3) and trimethylated Histone H3 Lysine 27 (H3K27me3), in adult thorax muscles of a notorious invasive pest, the Oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), using Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). Results: We identified promoters featured by the occupancy of H3K4me3, H3K27me3 or bivalent histone modifications that were respectively annotated with unique genes key to muscle development and structure maintenance. In addition, we found H3K27me3 occupied the entire body of genes, where the average enrichment was almost constant. Transcriptomic analysis indicated that H3K4me3 is associated with active gene transcription, and H3K27me3 is mostly associated with transcriptional repression. Importantly, we identified genes and putative motifs modified by distinct histone modification patterns that may possibly regulate flight activity. Discussion: These findings provide the first evidence of histone modification signature in B. dorsalis, and will be useful for future studies of epigenetic signature in other invasive insect species.
Collapse
Affiliation(s)
- Yan Zhao
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiajiao Wu
- Technology Center of Guangzhou Customs, Guangzhou, China
| | - Zhihong Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
| |
Collapse
|
10
|
Tcf12 is required to sustain myogenic genes synergism with MyoD by remodelling the chromatin landscape. Commun Biol 2022; 5:1201. [DOI: 10.1038/s42003-022-04176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractMuscle stem cells (MuSCs) are essential for skeletal muscle development and regeneration, ensuring muscle integrity and normal function. The myogenic proliferation and differentiation of MuSCs are orchestrated by a cascade of transcription factors. In this study, we elucidate the specific role of transcription factor 12 (Tcf12) in muscle development and regeneration based on loss-of-function studies. Muscle-specific deletion of Tcf12 cause muscle weight loss owing to the reduction of myofiber size during development. Inducible deletion of Tcf12 specifically in adult MuSCs delayed muscle regeneration. The examination of MuSCs reveal that Tcf12 deletion resulted in cell-autonomous defects during myogenesis and Tcf12 is necessary for proper myogenic gene expression. Mechanistically, TCF12 and MYOD work together to stabilise chromatin conformation and sustain muscle cell fate commitment-related gene and chromatin architectural factor expressions. Altogether, our findings identify Tcf12 as a crucial regulator of MuSCs chromatin remodelling that regulates muscle cell determination and participates in skeletal muscle development and regeneration.
Collapse
|
11
|
Jiang M, Li X, Dong X, Zu Y, Zhan Z, Piao Z, Lang H. Research Advances and Prospects of Orphan Genes in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:947129. [PMID: 35874010 PMCID: PMC9305701 DOI: 10.3389/fpls.2022.947129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.
Collapse
Affiliation(s)
- Mingliang Jiang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiangshu Dong
- School of Agriculture, Yunnan University, Kunming, China
| | - Ye Zu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hong Lang
- School of Agriculture, Jilin Agricultural Science and Technology College, Jilin, China
| |
Collapse
|
12
|
Ura M, Mukherjee S, Marcon E, Koestler SA, Kossiakoff AA. Synthetic Antibodies Detect Distinct Cellular States of Chromosome Passenger Complex Proteins. J Mol Biol 2022; 434:167602. [PMID: 35469831 PMCID: PMC9862951 DOI: 10.1016/j.jmb.2022.167602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 01/25/2023]
Abstract
High performance affinity reagents are essential tools to enable biologists to profile the cellular location and composition of macromolecular complexes undergoing dynamic reorganization. To support further development of such tools, we have assembled a high-throughput phage display pipeline to generate Fab-based affinity reagents that target different dynamic forms of a large macromolecular complex, using the Chromosomal Passenger Complex (CPC), as an example. The CPC is critical for the maintenance of chromosomal and cytoskeleton processes during cell division. The complex contains 4 protein components: Aurora B kinase, survivin, borealin and INCENP. The CPC acts as a node to dynamically organize other partnering subcomplexes to build multiple functional structures during mitotic progression. Using phage display mutagenesis, a cohort of synthetic antibodies (sABs) were generated against different domains of survivin, borealin and INCENP. Immunofluorescence established that a set of these sABs can discriminate between the form of the CPC complex in the midbody versus the spindle. Others localize to targets, which appear to be less organized, in the nucleus or cytoplasm. This differentiation suggests that different CPC epitopes have dynamic accessibility depending upon the mitotic state of the cell. An Immunoprecipitation/Mass Spectrometry analysis was performed using sABs that bound specifically to the CPC in either the midbody or MT spindle macromolecular assemblies. Thus, sABs can be exploited as high performance reagents to profile the accessibility of different components of the CPC within macromolecular assemblies during different stages of mitosis suggesting this high throughput approach will be applicable to other complex macromolecular systems.
Collapse
Affiliation(s)
- Marcin Ura
- Department of Biochemistry and Molecular Biology. The University of Chicago, United States
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology. The University of Chicago, United States
| | - Edyta Marcon
- Terrence Donnelly Centre for Cellular and Biomolecular Research, The University of Toronto, ON, Canada
| | - Stefan A. Koestler
- Department of Physiology, Development and Neuroscience. University of Cambridge, UK
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology. The University of Chicago, United States,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, United States,Correspondence to Anthony A. Kossiakoff: Department of Biochemistry and Molecular Biology. The University of Chicago, United States. (A.A. Kossiakoff)
| |
Collapse
|
13
|
Overview of SIRT5 as a potential therapeutic target: Structure, function and inhibitors. Eur J Med Chem 2022; 236:114363. [DOI: 10.1016/j.ejmech.2022.114363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 01/21/2023]
|
14
|
Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin. Biochem Soc Trans 2022; 50:199-212. [PMID: 35166326 PMCID: PMC9847230 DOI: 10.1042/bst20210959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/30/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023]
Abstract
Defining the genome-wide chromatin landscape has been a goal of experimentalists for decades. Here we review highlights of these efforts, from seminal experiments showing discontinuities in chromatin structure related to gene activation to extensions of these methods elucidating general features of chromatin related to gene states by exploiting deep sequencing methods. We also review chromatin conformational capture methods to identify patterns in long-range interactions between genomic loci.
Collapse
|
15
|
Frauenstein A, Ebner S, Hansen FM, Sinha A, Phulphagar K, Swatek K, Hornburg D, Mann M, Meissner F. Identification of covalent modifications regulating immune signaling complex composition and phenotype. Mol Syst Biol 2021; 17:e10125. [PMID: 34318608 PMCID: PMC8447602 DOI: 10.15252/msb.202010125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 11/23/2022] Open
Abstract
Cells signal through rearrangements of protein communities governed by covalent modifications and reversible interactions of distinct sets of proteins. A method that identifies those post‐transcriptional modifications regulating signaling complex composition and functional phenotypes in one experimental setup would facilitate an efficient identification of novel molecular signaling checkpoints. Here, we devised modifications, interactions and phenotypes by affinity purification mass spectrometry (MIP‐APMS), comprising the streamlined cloning and transduction of tagged proteins into functionalized reporter cells as well as affinity chromatography, followed by MS‐based quantification. We report the time‐resolved interplay of more than 50 previously undescribed modification and hundreds of protein–protein interactions of 19 immune protein complexes in monocytes. Validation of interdependencies between covalent, reversible, and functional protein complex regulations by knockout or site‐specific mutation revealed ISGylation and phosphorylation of TRAF2 as well as ARHGEF18 interaction in Toll‐like receptor 2 signaling. Moreover, we identify distinct mechanisms of action for small molecule inhibitors of p38 (MAPK14). Our method provides a fast and cost‐effective pipeline for the molecular interrogation of protein communities in diverse biological systems and primary cells.
Collapse
Affiliation(s)
- Annika Frauenstein
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefan Ebner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ankit Sinha
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kshiti Phulphagar
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kirby Swatek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Hornburg
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Martinsried, Germany.,Institute of Innate Immunity, Department of Systems Immunology and Proteomics, Medical Faculty, University of Bonn, Bonn, Germany
| |
Collapse
|
16
|
Pandey S, Tuma Z, Smrhova T, Cedikova M, Macanova T, Chottova Dvorakova M. Laser Capture Microdissection Coupled Capillary Immunoassay to Study the Expression of PCK-2 on Spatially-Resolved Islets of Rat Langerhans. Pharmaceutics 2021; 13:pharmaceutics13060883. [PMID: 34203686 PMCID: PMC8232303 DOI: 10.3390/pharmaceutics13060883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 11/25/2022] Open
Abstract
The platform for precise proteomic profiling of targeted cell populations from heterogeneous tissue sections is developed. We demonstrate a seamless and systematic integration of LCM with an automated cap-IA for the handling of a very small-sized dissected tissues section from the kidney, liver and pancreatic Langerhans islet of rats. Our analysis reveals that the lowest LCM section area ≥ 0.125 mm2 with 10 µm thickness can be optimized for the detection of proteins through LCM-cap-IA integration. We detect signals ranging from a highly-abundant protein, β-actin, to a low-abundance protein, LC-3AB, using 0.125 mm2 LCM section from rat kidney, but, so far, a relatively large section is required for good quality of results. This integration is applicable for a highly-sensitive and accurate assessment of microdissected tissue sections to decipher hidden proteomic information of pure targeted cells. To validate this integration, PCK2 protein expression is studied within Langerhans islets of normal and diabetic rats. Our results show significant overexpression of PCK2 in Langerhans islets of rats with long-term diabetes.
Collapse
Affiliation(s)
- Shashank Pandey
- Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic; (Z.T.); (M.C.); (M.C.D.)
- Correspondence:
| | - Zdenek Tuma
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic; (Z.T.); (M.C.); (M.C.D.)
| | - Tereza Smrhova
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic;
| | - Miroslava Cedikova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic; (Z.T.); (M.C.); (M.C.D.)
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic;
| | - Tereza Macanova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic;
| | - Magdalena Chottova Dvorakova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic; (Z.T.); (M.C.); (M.C.D.)
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic;
| |
Collapse
|
17
|
Hill CA, Fernandez DM, Giannarelli C. Single cell analyses to understand the immune continuum in atherosclerosis. Atherosclerosis 2021; 330:85-94. [PMID: 33934886 DOI: 10.1016/j.atherosclerosis.2021.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/22/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Atherosclerosis is initiated by the accumulation of lipids in the arterial wall that trigger a complex and poorly understood network of inflammatory processes. At the same time, recent clinical findings reveal that targeting specific immune alterations in patients with cardiovascular disease (CVD) represents a promising approach to preventing recurrent cardiovascular events. In order to achieve these tailored therapies, it is critical to resolve the heterogenous environment of the atherosclerotic lesion and decipher the complex structural and functional changes which immune cells undergo throughout disease progression. Recently, single-cell approaches including single cell mass cytometry by time of flight (CyTOF), single cell RNA sequencing (scRNA-seq) and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) have emerged as valuable tools in resolving cellular plasticity within atherosclerotic lesions. In this review, we will discuss the most important insights that have been gleaned from the application of these single-cell approaches to validated experimental models of atherosclerosis. Additionally, as clinical progress in treatment of the disease depends on the translation of discoveries to human tissues, we will also examine the challenges associated with the application of single-cell approaches to human vascular tissue and the discoveries made by the initial efforts in this direction. Finally, we will analyze the advantages and limitations of dissociative single-cell approaches and how novel in-situ technologies could advance the field by allowing for the investigation of individual cells while preserving the heterogenous architecture of the atherosclerotic lesion.
Collapse
Affiliation(s)
| | | | - Chiara Giannarelli
- Department of Medicine, Cardiovascular Research Center, USA; Department of Genetics and Genomic Sciences, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Cardiology and Cardiovascular Research Center at NYU Langone NYU Grossman School of Medicine, New York, NY, USA.
| |
Collapse
|
18
|
Xin JW, Chai ZX, Zhang CF, Yang YM, Zhang Q, Zhu Y, Cao HW, YangJi C, Zhong JC, Ji QM. Comparative Analysis of Skeleton Muscle Proteome Profile between Yak and Cattle Provides Insight into High-Altitude Adaptation. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666200127151931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background::
Mechanisms underlying yak adaptation to high-altitude environments have
been investigated at the levels of morphology, anatomy, physiology, genome and transcriptome, but
have not been explored at the proteome level.
Objective:
The protein profiles were compared between yak and cattle to explore molecular mechanisms
underlying yak adaptation to high altitude conditions.
Methods:
In the present study, an antibody microarray chip was developed, which included 6,500
mouse monoclonal antibodies. Immunoprecipitation and mass spectrometry were performed on 12
selected antibodies which showed that the chip was highly specific. Using this chip, muscle tissue proteome
was compared between yak and cattle, and 12 significantly Differentially Expressed Proteins (DEPs)
between yak and cattle were identified. Their expression levels were validated using Western blot.
Results:
ompared with cattle, higher levels of Rieske Iron-Sulfur Protein (RISP), Cytochrome C oxidase
subunit 4 isoform 1, mitochondrial (COX4I1), ATP synthase F1 subunit beta (ATP5F1B), Sarcoplasmic/
Endoplasmic Reticulum Calcium ATPase1 (SERCA1) and Adenosine Monophosphate Deaminase1
(AMPD1) in yak might improve oxygen utilization and energy metabolism. Pyruvate Dehydrogenase
protein X component (PDHX) and Acetyltransferase component of pyruvate dehydrogenase
complex (DLAT) showed higher expression levels and L-lactate dehydrogenase A chain (LDHA)
showed lower expression level in yak, which might help yak reduce the accumulation of lactic acid. In
addition, higher expression levels of Filamin C (FLNC) and low levels of AHNAK and Four and a half
LIM domains 1 (FHL1) in yak might reduce the risks of pulmonary arteries vasoconstriction, remodeling
and hypertension.
Conclusion:
Overall, the present study reported the differences in protein profile between yak and cattle,
which might be helpful to further understand molecular mechanisms underlying yak adaptation to
high altitude environments.
Collapse
Affiliation(s)
- Jin-Wei Xin
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Zhi-Xin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Cheng-Fu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Yu-Mei Yang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Qiang Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Yong Zhu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Han-Wen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Cidan YangJi
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| | - Jin-Cheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Qiu-Mei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, China
| |
Collapse
|
19
|
Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci 2021; 78:469-495. [PMID: 32710154 PMCID: PMC11073434 DOI: 10.1007/s00018-020-03602-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
Stem cells and their derivatives are novel pharmaceutics that have the potential for use as tissue replacement therapies. However, the heterogeneous characteristics of stem cell cultures have hindered their biomedical applications. In theory and practice, when cell type-specific or stage-specific cell surface proteins are targeted by unique antibodies, they become highly efficient in detecting and isolating specific cell populations. There is a growing demand to identify reliable and actionable cell surface markers that facilitate purification of particular cell types at specific developmental stages for use in research and clinical applications. The identification of these markers as very important members of plasma membrane proteins, ion channels, transporters, and signaling molecules has directly benefited from proteomics and tools for proteomics-derived data analyses. Here, we review the methodologies that have played a role in the discovery of cell surface markers and introduce cutting edge single cell proteomics as an advanced tool. We also discuss currently available specific cell surface markers for stem cells and their lineages, with emphasis on the nervous system, heart, pancreas, and liver. The remaining gaps that pertain to the discovery of these markers and how single cell proteomics and identification of surface markers associated with the progenitor stages of certain terminally differentiated cells may pave the way for their use in regenerative medicine are also discussed.
Collapse
Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem St, P.O. Box: 16635-148, 1665659911, Tehran, Iran.
| |
Collapse
|
20
|
Sivertsson Å, Lindström E, Oksvold P, Katona B, Hikmet F, Vuu J, Gustavsson J, Sjöstedt E, von Feilitzen K, Kampf C, Schwenk JM, Uhlén M, Lindskog C. Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins. J Proteome Res 2020; 19:4766-4781. [PMID: 33170010 PMCID: PMC7723238 DOI: 10.1021/acs.jproteome.0c00486] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The localization of proteins at a
tissue- or cell-type-specific
level is tightly linked to the protein function. To better understand
each
protein’s role in cellular systems, spatial information constitutes
an important complement to quantitative data. The standard methods
for determining the spatial distribution of proteins in single cells
of complex tissue samples make use of antibodies. For a stringent
analysis of the human proteome, we used orthogonal methods and independent
antibodies to validate 5981 antibodies that show the expression of
3775 human proteins across all major human tissues. This enhanced
validation uncovered 56 proteins corresponding to the group of “missing
proteins” and 171 proteins of unknown function. The presented
strategy will facilitate further discussions around criteria for evidence
of protein existence based on immunohistochemistry and serves as a
useful guide to identify candidate proteins for integrative studies
with quantitative proteomics methods.
Collapse
Affiliation(s)
- Åsa Sivertsson
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Emil Lindström
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Per Oksvold
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Borbala Katona
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Jimmy Vuu
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Jonas Gustavsson
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Evelina Sjöstedt
- Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden.,Atlas Antibodies AB, 16869 Bromma, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, 17121 Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 75185 Uppsala, Sweden
| |
Collapse
|
21
|
Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| |
Collapse
|
22
|
Heo M, Chenon G, Castrillon C, Bibette J, Bruhns P, Griffiths AD, Baudry J, Eyer K. Deep phenotypic characterization of immunization-induced antibacterial IgG repertoires in mice using a single-antibody bioassay. Commun Biol 2020; 3:614. [PMID: 33106526 PMCID: PMC7589517 DOI: 10.1038/s42003-020-01296-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Antibodies with antibacterial activity need to bind to the bacterial surface with affinity, specificity, and sufficient density to induce efficient elimination. To characterize the anti-bacterial antibody repertoire, we developed an in-droplet bioassay with single-antibody resolution. The assay not only allowed us to identify whether the secreted antibodies recognized a bacterial surface antigen, but also to estimate the apparent dissociation constant (KD app) of the interaction and the density of the recognized epitope on the bacteria. Herein, we found substantial differences within the KD app/epitope density profiles in mice immunized with various species of heat-killed bacteria. The experiments further revealed a high cross-reactivity of the secreted IgG repertoires, binding to even unrelated bacteria with high affinity. This application confirmed the ability to quantify the anti-bacterial antibody repertoire and the utility of the developed bioassay to study the interplay between bacteria and the humoral response.
Collapse
Affiliation(s)
- Millie Heo
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Guilhem Chenon
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Carlos Castrillon
- Unit of Antibodies in Therapy and Pathology, Institute Pasteur, UMR1222 INSERM, F-75015, Paris, France
- 'Laboratoire de Biochimie' (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Jérôme Bibette
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Pierre Bruhns
- Unit of Antibodies in Therapy and Pathology, Institute Pasteur, UMR1222 INSERM, F-75015, Paris, France
| | - Andrew D Griffiths
- 'Laboratoire de Biochimie' (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Jean Baudry
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France
| | - Klaus Eyer
- 'Laboratoire Colloïdes et Matériaux Divisés' (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, F-75005, Paris, France.
- Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland.
| |
Collapse
|
23
|
MacNeil T, Vathiotis IA, Martinez-Morilla S, Yaghoobi V, Zugazagoitia J, Liu Y, Rimm DL. Antibody validation for protein expression on tissue slides: a protocol for immunohistochemistry. Biotechniques 2020; 69:460-468. [PMID: 32852223 PMCID: PMC7807291 DOI: 10.2144/btn-2020-0095] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antibodies play a crucial role in basic research and clinical decision-making. However, there are no standardized algorithms or guidelines to ensure their accuracy and validity. There have been efforts to generate consensus, but, with the exception of clinical labs, antibody validation remains variable in the literature and sometimes in clinical practice. Here we focus on immunohistochemistry, an example of a scientific and clinical tool where validation of antibodies is critical. We describe a protocol that we use to validate antibodies specifically for immunohistochemistry, including some of the pillars of antibody validation from Uhlen et al. 2016, as an example of a rigorous approach to build antibody-based tests for both basic and translational science labs and for the clinic.
Collapse
Affiliation(s)
- Tyler MacNeil
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | | | | | - Vesal Yaghoobi
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jon Zugazagoitia
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yuting Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - David L Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
24
|
ROBO2-mediated RALDH2 signaling is required for common nephric duct fusion with primitive bladder. Dev Biol 2020; 464:103-110. [PMID: 32562756 DOI: 10.1016/j.ydbio.2020.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 05/11/2020] [Accepted: 06/04/2020] [Indexed: 11/20/2022]
Abstract
Congenital anomalies of the urinary tract are a significant cause of morbidity in infancy, and many congenital anomalies are linked to ureter development; however, the mechanism by which congenital anomalies control ureter development remains unknown. The loss of Robo2 can cause ureter defects and vesicoureteral reflux. However, how Robo2 impacts ureter development is unclear. We found that ROBO2 is expressed in the common nephric duct (CND) and primitive bladder, and impacts CND migration and fusion with the primitive bladder via its novel binding partner retinaldehyde dehydrogenase-2 (RALDH2). Delayed apoptosis that is due to the failure of CND fusion with the primitive bladder in the Robo2-/-embryo results in an abnormal ureter connection to the CND, which is required for ureter development. We define a novel pathway in which the CND is remodeled by ROBO2 and retinoic acid rescued the ureter anomalies in the Robo2-/-embryo. These findings may be relevant to diverse disease conditions that are associated with altered signaling in the primitive bladder.
Collapse
|
25
|
Preger C, Wigren E, Ossipova E, Marks C, Lengqvist J, Hofström C, Andersson O, Jakobsson PJ, Gräslund S, Persson H. Generation and validation of recombinant antibodies to study human aminoacyl-tRNA synthetases. J Biol Chem 2020; 295:13981-13993. [PMID: 32817337 DOI: 10.1074/jbc.ra120.012893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/10/2020] [Indexed: 11/06/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) have long been viewed as mere housekeeping proteins and have therefore often been overlooked in drug discovery. However, recent findings have revealed that many aaRSs have noncanonical functions, and several of the aaRSs have been linked to autoimmune diseases, cancer, and neurological disorders. Deciphering these roles has been challenging because of a lack of tools to enable their study. To help solve this problem, we have generated recombinant high-affinity antibodies for a collection of thirteen cytoplasmic and one mitochondrial aaRSs. Selected domains of these proteins were produced recombinantly in Escherichia coli and used as antigens in phage display selections using a synthetic human single-chain fragment variable library. All targets yielded large sets of antibody candidates that were validated through a panel of binding assays against the purified antigen. Furthermore, the top-performing binders were tested in immunoprecipitation followed by MS for their ability to capture the endogenous protein from mammalian cell lysates. For antibodies targeting individual members of the multi-tRNA synthetase complex, we were able to detect all members of the complex, co-immunoprecipitating with the target, in several cell types. The functionality of a subset of binders for each target was also confirmed using immunofluorescence. The sequences of these proteins have been deposited in publicly available databases and repositories. We anticipate that this open source resource, in the form of high-quality recombinant proteins and antibodies, will accelerate and empower future research of the role of aaRSs in health and disease.
Collapse
Affiliation(s)
- Charlotta Preger
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Edvard Wigren
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elena Ossipova
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Carolyn Marks
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Camilla Hofström
- Science for Life Laboratory, Drug Discovery and Development, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Oskar Andersson
- Science for Life Laboratory, Drug Discovery and Development, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Susanne Gräslund
- Structural Genomics Consortium, Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development, Stockholm, Sweden .,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| |
Collapse
|
26
|
Detecting protein and post-translational modifications in single cells with iDentification and qUantification sEparaTion (DUET). Commun Biol 2020; 3:420. [PMID: 32747637 PMCID: PMC7400673 DOI: 10.1038/s42003-020-01132-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/09/2020] [Indexed: 11/08/2022] Open
Abstract
While technologies for measuring transcriptomes in single cells have matured, methods for measuring proteins and their post-translational modification (PTM) states in single cells are still being actively developed. Unlike nucleic acids, proteins cannot be amplified, making detection of minute quantities from single cells difficult. Here, we develop a strategy to detect targeted protein and its PTM isoforms in single cells. We barcode the proteins from single cells by tagging them with oligonucleotides, pool barcoded cells together, run bulk gel electrophoresis to separate protein and its PTM isoform and quantify their abundances by sequencing the oligonucleotides associated with each protein species. We used this strategy, iDentification and qUantification sEparaTion (DUET), to measure histone protein H2B and its monoubiquitination isoform, H2Bub, in single yeast cells. Our results revealed the heterogeneities of H2B ubiquitination levels in single cells from different cell-cycle stages, which is obscured in ensemble measurements.
Collapse
|
27
|
Deeg CA, Degroote RL, Giese IM, Hirmer S, Amann B, Weigand M, Wiedemann C, Hauck SM. CD11d is a novel antigen on chicken leukocytes. J Proteomics 2020; 225:103876. [PMID: 32534212 DOI: 10.1016/j.jprot.2020.103876] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/11/2020] [Accepted: 06/06/2020] [Indexed: 01/02/2023]
Abstract
In life sciences, antibodies are among the most commonly used tools for identifying, tracking, quantifying and isolating molecules, mainly proteins. However, it has recently become clear that antibodies often fall short with respect to specificity and selectivity and in many cases target proteins are not even known. When commercial availability of antibodies is scarce, e.g. for targeting proteins from farm animals, researchers face additional challenges: they often have to rely on cross-reactive antibodies, which are poorly characterized for their exact target, their actual cross-reactivity and the desired application. In this study, we aimed at identifying the true target of mouse monoclonal antibody 8F2, which was generated against chicken PBMC and used for decades in research, while it's actual target molecule remained unknown. We used 8F2 antibody for immunoprecipitation in chicken PBMC and subsequently identified its true target as CD11d, which was never described in chicken lymphocytes before, by quantitative LC-MSMS. The most abundant interactor of CD11d was identified as integrin beta 2. The existence of this alpha integrin was therefore clearly proven on protein level and provides a first basis to further assess the role of CD11d in chickens in future studies. Data are available via ProteomeXchange with identifier PXD017248. SIGNIFICANCE: Our studies determined CD11d as the true target of a previously uncharacterized mouse monoclonal antibody 8F2, generated against chicken peripheral blood derived mononuclear cells (PBMC). This is therefore now first member of alpha integrins in chickens, that existence was now clearly identified on protein level. The additional identification of CD11d interactors provides information on integrin-dependent regulation of signaling networks, allowing further functional studies.
Collapse
Affiliation(s)
- Cornelia A Deeg
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany.
| | - Roxane L Degroote
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Isabella M Giese
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Sieglinde Hirmer
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Barbara Amann
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Maria Weigand
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Carmen Wiedemann
- Chair of Physiology, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, 80939 Munich, Germany
| |
Collapse
|
28
|
Tans R, van Rijswijck DMH, Davidson A, Hannam R, Ricketts B, Tack CJ, Wessels HJCT, Gloerich J, van Gool AJ. Affimers as an alternative to antibodies for protein biomarker enrichment. Protein Expr Purif 2020; 174:105677. [PMID: 32461183 DOI: 10.1016/j.pep.2020.105677] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Assessing the specificity of protein binders is an essential first step in protein biomarker assay development. Affimers are novel protein binders and can potentially replace antibodies in multiple protein capture-based assays. Affimers are selected for their high specificity against the target protein and have benefits over antibodies like batch-to-batch reproducibility and are stable across a wide range of chemical conditions. Here we mimicked a typical initial screening of affimers and commercially available monoclonal antibodies against two non-related proteins, IL-37b and proinsulin, to assess the potential of affimers as alternative to antibodies. METHODS Binding specificity of anti-IL-37b and anti-proinsulin affimers and antibodies was investigated via magnetic bead-based capture of their recombinant protein targets in human plasma. Captured proteins were analyzed using SDS-PAGE, Coomassie blue staining, Western blotting and LC-MS/MS-based proteomics. RESULTS All affimers and antibodies were able to bind their target protein in human plasma. Gel and LC-MS/MS analysis showed that both affimer and antibody-based captures resulted in co-purified background proteins. However, affimer-based captures showed the highest relative enrichment of IL-37b and proinsulin. CONCLUSIONS For both proteins tested, affimers show higher specificity in purifying their target proteins from human plasma compared to monoclonal antibodies. These results indicate that affimers are promising antibody-replacement tools for protein biomarker assay development.
Collapse
Affiliation(s)
- Roel Tans
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Danique M H van Rijswijck
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Alex Davidson
- Avacta Life Sciences, Unit 20, Ash Way, Thorp Arch Estate & Retail Park, Wetherby, LS23 7FA, United Kingdom
| | - Ryan Hannam
- Avacta Life Sciences, Unit 20, Ash Way, Thorp Arch Estate & Retail Park, Wetherby, LS23 7FA, United Kingdom
| | - Bryon Ricketts
- Avacta Life Sciences, Unit 20, Ash Way, Thorp Arch Estate & Retail Park, Wetherby, LS23 7FA, United Kingdom
| | - Cees J Tack
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Jolein Gloerich
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands
| | - Alain J van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525, GA, Nijmegen, the Netherlands.
| |
Collapse
|
29
|
Neves K, Amaral OB. Addressing selective reporting of experiments through predefined exclusion criteria. eLife 2020; 9:e56626. [PMID: 32441650 PMCID: PMC7244322 DOI: 10.7554/elife.56626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
The pressure for every research article to tell a clear story often leads researchers in the life sciences to exclude experiments that 'did not work' when they write up their results. However, this practice can lead to reporting bias if the decisions about which experiments to exclude are taken after data have been collected and analyzed. Here we discuss how to balance clarity and thoroughness when reporting the results of research, and suggest that predefining the criteria for excluding experiments might help researchers to achieve this balance.
Collapse
Affiliation(s)
- Kleber Neves
- Institute of Medical Biochemistry Leopoldo de Meis, Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Olavo B Amaral
- Institute of Medical Biochemistry Leopoldo de Meis, Universidade Federal do Rio de JaneiroRio de JaneiroBrazil
| |
Collapse
|
30
|
Moshkovskii SA, Lobas AA, Gorshkov MV. Single Cell Proteogenomics - Immediate Prospects. BIOCHEMISTRY (MOSCOW) 2020; 85:140-146. [PMID: 32093591 DOI: 10.1134/s0006297920020029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recent technical advances in genomic technology have led to the explosive growth of transcriptome-wide studies at the level of single cells. The review describes the first steps of the single cell proteomics that has originated soon after development of transcriptomics methods. The first studies on the shotgun proteomics of single cells that used liquid chromatography/mass spectrometry have been already published. In these works, the cells were separated by the methods used in transcriptomics studies (e.g., cell sorting) and analyzed by modified mass spectrometry with tandem mass tags. The new proteogenomics approach involving integration of single cell transcriptomics and proteomics data will provide better understanding of the mechanisms of cell interactions in normal development and disease.
Collapse
Affiliation(s)
- S A Moshkovskii
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia. .,Orekhovich Institute of Biomedical Chemistry, Moscow, 119121, Russia
| | - A A Lobas
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| | - M V Gorshkov
- Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Research Center of Chemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
| |
Collapse
|
31
|
Lombard-Banek C, Schiel JE. Mass Spectrometry Advances and Perspectives for the Characterization of Emerging Adoptive Cell Therapies. Molecules 2020; 25:E1396. [PMID: 32204371 PMCID: PMC7144572 DOI: 10.3390/molecules25061396] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Adoptive cell therapy is an emerging anti-cancer modality, whereby the patient's own immune cells are engineered to express T-cell receptor (TCR) or chimeric antigen receptor (CAR). CAR-T cell therapies have advanced the furthest, with recent approvals of two treatments by the Food and Drug Administration of Kymriah (trisagenlecleucel) and Yescarta (axicabtagene ciloleucel). Recent developments in proteomic analysis by mass spectrometry (MS) make this technology uniquely suited to enable the comprehensive identification and quantification of the relevant biochemical architecture of CAR-T cell therapies and fulfill current unmet needs for CAR-T product knowledge. These advances include improved sample preparation methods, enhanced separation technologies, and extension of MS-based proteomic to single cells. Innovative technologies such as proteomic analysis of raw material quality attributes (MQA) and final product quality attributes (PQA) may provide insights that could ultimately fuel development strategies and lead to broad implementation.
Collapse
Affiliation(s)
- Camille Lombard-Banek
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA;
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - John E. Schiel
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA;
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| |
Collapse
|
32
|
Wang Z, Li Y, Hou B, Pronobis MI, Wang M, Wang Y, Cheng G, Weng W, Wang Y, Tang Y, Xu X, Pan R, Lin F, Wang N, Chen Z, Wang S, Ma LZ, Li Y, Huang D, Jiang L, Wang Z, Zeng W, Zhang Y, Du X, Lin Y, Li Z, Xia Q, Geng J, Dai H, Yu Y, Zhao XD, Yuan Z, Yan J, Nie Q, Zhang X, Wang K, Chen F, Zhang Q, Zhu Y, Zheng S, Poss KD, Tao SC, Meng X. An array of 60,000 antibodies for proteome-scale antibody generation and target discovery. SCIENCE ADVANCES 2020; 6:eaax2271. [PMID: 32195335 PMCID: PMC7065887 DOI: 10.1126/sciadv.aax2271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 12/13/2019] [Indexed: 05/28/2023]
Abstract
Antibodies are essential for elucidating gene function. However, affordable technology for proteome-scale antibody generation does not exist. To address this, we developed Proteome Epitope Tag Antibody Library (PETAL) and its array. PETAL consists of 62,208 monoclonal antibodies (mAbs) against 15,199 peptides from diverse proteomes. PETAL harbors binders for a great multitude of proteins in nature due to antibody multispecificity, an intrinsic antibody feature. Distinctive combinations of 10,000 to 20,000 mAbs were found to target specific proteomes by array screening. Phenotype-specific mAb-protein pairs were found for maize and zebrafish samples. Immunofluorescence and flow cytometry mAbs for membrane proteins and chromatin immunoprecipitation-sequencing mAbs for transcription factors were identified from respective proteome-binding PETAL mAbs. Differential screening of cell surface proteomes of tumor and normal tissues identified internalizing tumor antigens for antibody-drug conjugates. By finding high-affinity mAbs at a fraction of current time and cost, PETAL enables proteome-scale antibody generation and target discovery.
Collapse
Affiliation(s)
- Zhaohui Wang
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Hou
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Mira I. Pronobis
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Yuemeng Wang
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | | | - Weining Weng
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Yiqiang Wang
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Yanfang Tang
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Xuefan Xu
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Rong Pan
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Fei Lin
- Abmart, 333 Guiping Road, Shanghai 200033, China
| | - Nan Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ziqing Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiwei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Luyan zulie Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yangrui Li
- Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi 530007, China
| | - Dongliang Huang
- Guangxi Key Laboratory of Sugarcane Genetic Improvement/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, Guangxi 530007, China
| | - Li Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhiqiang Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
| | - Wenfang Zeng
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
| | - Ying Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, Henan 450009, China
| | - Xuemei Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100083, China
| | - Ying Lin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Zhiqing Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Jing Geng
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Beijing 100029, China
| | - Huaping Dai
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Beijing 100029, China
| | - Yuan Yu
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
| | - Xiao-dong Zhao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zheng Yuan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jian Yan
- Ludwig Institute for Cancer Research, 9500 Gilman Dr., La Jolla, CA 92093, USA
- Department of Medical Biochemistry and Biophysics, Division of Functional Genomics and Systems Biology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Qinghua Nie
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xiquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, China
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Kun Wang
- Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China
| | - Fulin Chen
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
| | - Qin Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yuxian Zhu
- Institute for Advanced Studies and College of Life Sciences, Wuhan University, Wuhan, China
| | - Susan Zheng
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D. Poss
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Sheng-ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai 200240, China
| | - Xun Meng
- School of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
- Abmart, 333 Guiping Road, Shanghai 200033, China
| |
Collapse
|
33
|
van Kruijsbergen I, Mulder MPC, Uckelmann M, van Welsem T, de Widt J, Spanjaard A, Jacobs H, El Oualid F, Ovaa H, van Leeuwen F. Strategy for Development of Site-Specific Ubiquitin Antibodies. Front Chem 2020; 8:111. [PMID: 32154221 PMCID: PMC7047734 DOI: 10.3389/fchem.2020.00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Protein ubiquitination is a key post-translational modification regulating a wide range of biological processes. Ubiquitination involves the covalent attachment of the small protein ubiquitin to a lysine of a protein substrate. In addition to its well-established role in protein degradation, protein ubiquitination plays a role in protein-protein interactions, DNA repair, transcriptional regulation, and other cellular functions. Understanding the mechanisms and functional relevance of ubiquitin as a signaling system requires the generation of antibodies or alternative reagents that specifically detect ubiquitin in a site-specific manner. However, in contrast to other post-translational modifications such as acetylation, phosphorylation, and methylation, the instability and size of ubiquitin-76 amino acids-complicate the preparation of suitable antigens and the generation antibodies detecting such site-specific modifications. As a result, the field of ubiquitin research has limited access to specific antibodies. This severely hampers progress in understanding the regulation and function of site-specific ubiquitination in many areas of biology, specifically in epigenetics and cancer. Therefore, there is a high demand for antibodies recognizing site-specific ubiquitin modifications. Here we describe a strategy for the development of site-specific ubiquitin antibodies. Based on a recently developed antibody against site-specific ubiquitination of histone H2B, we provide detailed protocols for chemical synthesis methods for antigen preparation and discuss considerations for screening and quality control experiments.
Collapse
Affiliation(s)
- Ila van Kruijsbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Monique P C Mulder
- Leiden Institute for Chemical Immunology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Michael Uckelmann
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - John de Widt
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Huib Ovaa
- Leiden Institute for Chemical Immunology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
34
|
Abstract
The existence of cellular heterogeneity and its central relevance to biological phenomena provides a strong rationale for a need for analytical methods that enable analysis at the single-cell level. Analysis of the genome and transcriptome is possible at the single-cell level, but the comprehensive interrogation of the proteome with this level of resolution remains challenging. Single-cell protein analysis tools are advancing rapidly, however, and providing insights into collections of proteins with great relevance to cell and disease biology. Here, we review single-cell protein analysis technologies and assess their advantages and limitations. The emerging technologies presented have the potential to reveal new insights into tumour heterogeneity and therapeutic resistance, elucidate mechanisms of immune response and immunotherapy, and accelerate drug discovery.
Collapse
|
35
|
Li ASM, Li F, Eram MS, Bolotokova A, Dela Seña CC, Vedadi M. Chemical probes for protein arginine methyltransferases. Methods 2019; 175:30-43. [PMID: 31809836 DOI: 10.1016/j.ymeth.2019.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/29/2019] [Accepted: 11/29/2019] [Indexed: 12/28/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the transfer of methyl groups to specific arginine residues of their substrates using S-adenosylmethionine as a methyl donor, contributing to regulation of many biological processes including transcription, and DNA damage repair. Dysregulation of PRMT expression is often associated with various diseases including cancers. Different methods have been used to characterize the activities of PRMTs and determine their kinetic parameters including mass spectrometry, radiometric, and antibody-based assays. Here, we present kinetic characterization of PRMTs using a radioactivity-based assay for better comparison along with previously reported values. We also report on full characterization of PRMT9 activity with SAP145 peptide as substrate. We further review the potent, selective and cell-active PRMT inhibitors discovered in recent years to provide a better understanding of available tools to investigate the roles these proteins play in health and disease.
Collapse
Affiliation(s)
- Alice Shi Ming Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Albina Bolotokova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Carlo C Dela Seña
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
36
|
Slezak T, Bailey LJ, Jaskolowski M, Nahotko DA, Filippova EV, Davydova EK, Kossiakoff AA. An engineered ultra-high affinity Fab-Protein G pair enables a modular antibody platform with multifunctional capability. Protein Sci 2019; 29:141-156. [PMID: 31622515 DOI: 10.1002/pro.3751] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/21/2022]
Abstract
Engineered recombinant antibody-based reagents are rapidly supplanting traditionally derived antibodies in many cell biological applications. A particularly powerful aspect of these engineered reagents is that other modules having myriad functions can be attached to them either chemically or through molecular fusions. However, these processes can be cumbersome and do not lend themselves to high throughput applications. Consequently, we have endeavored to develop a platform that can introduce multiple functionalities into a class of Fab-based affinity reagents in a "plug and play" fashion. This platform exploits the ultra-tight binding interaction between affinity matured variants of a Fab scaffold (FabS ) and a domain of an immunoglobulin binding protein, protein G (GA1). GA1 is easily genetically manipulatable facilitating the ability to link these modules together like beads on a string with adjustable spacing to produce multivalent and bi-specific entities. GA1 can also be fused to other proteins or be chemically modified to engage other types of functional components. To demonstrate the utility for the Fab-GA1 platform, we applied it to a detection proximity assay based on the β-lactamase (BL) split enzyme system. We also show the bi-specific capabilities of the module by using it in context of a Bi-specific T-cell engager (BiTE), which is a therapeutic assemblage that induces cell killing by crosslinking T-cells to cancer cells. We show that GA1-Fab modules are easily engineered into potent cell-killing BiTE-like assemblages and have the advantage of interchanging Fabs directed against different cell surface cancer-related targets in a plug and play fashion.
Collapse
Affiliation(s)
- Tomasz Slezak
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Lucas J Bailey
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Mateusz Jaskolowski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois.,Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Dominik A Nahotko
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Ekaterina V Filippova
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Elena K Davydova
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
| |
Collapse
|
37
|
Laflamme C, McKeever PM, Kumar R, Schwartz J, Kolahdouzan M, Chen CX, You Z, Benaliouad F, Gileadi O, McBride HM, Durcan TM, Edwards AM, Healy LM, Robertson J, McPherson PS. Implementation of an antibody characterization procedure and application to the major ALS/FTD disease gene C9ORF72. eLife 2019; 8:e48363. [PMID: 31612854 PMCID: PMC6794092 DOI: 10.7554/elife.48363] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/26/2019] [Indexed: 01/02/2023] Open
Abstract
Antibodies are a key resource in biomedical research yet there are no community-accepted standards to rigorously characterize their quality. Here we develop a procedure to validate pre-existing antibodies. Human cell lines with high expression of a target, determined through a proteomics database, are modified with CRISPR/Cas9 to knockout (KO) the corresponding gene. Commercial antibodies against the target are purchased and tested by immunoblot comparing parental and KO. Validated antibodies are used to definitively identify the most highly expressing cell lines, new KOs are generated if needed, and the lines are screened by immunoprecipitation and immunofluorescence. Selected antibodies are used for more intensive procedures such as immunohistochemistry. The pipeline is easy to implement and scalable. Application to the major ALS disease gene C9ORF72 identified high-quality antibodies revealing C9ORF72 localization to phagosomes/lysosomes. Antibodies that do not recognize C9ORF72 have been used in highly cited papers, raising concern over previously reported C9ORF72 properties.
Collapse
Affiliation(s)
- Carl Laflamme
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Paul M McKeever
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoCanada
| | - Rahul Kumar
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Julie Schwartz
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Mahshad Kolahdouzan
- Neuroimmunology Unit, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Carol X Chen
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Zhipeng You
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Faiza Benaliouad
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Opher Gileadi
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | - Heidi M McBride
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Thomas M Durcan
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Aled M Edwards
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
- Structural Genomics Consortium, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Luke M Healy
- Neuroimmunology Unit, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoCanada
- Department of Laboratory Medicine and PathobiologyUniversity of TorontoTorontoCanada
| | - Peter S McPherson
- Tanenbaum Open Science Institute, Montreal Neurological InstituteMcGill UniversityMontrealCanada
| |
Collapse
|
38
|
Abstract
Antibodies can be developed to directly inhibit almost any protein, but their inability to enter the cytosol limits inhibitory antibodies to membrane-associated or extracellular targets. Developing a cytosolic antibody delivery system would offer unique opportunities to directly inhibit and study intracellular protein function. Here we demonstrate that IgG antibodies that are conjugated with anionic polypeptides (ApPs) can be complexed with cationic lipids originally designed for nucleic acid delivery through electrostatic interactions, enabling close to 90% cytosolic delivery efficiency with only 500 nM IgG. The ApP is fused to a small photoreactive antibody-binding domain (pAbBD) that can be site-specifically photocrosslinked to nearly all off-the-shelf IgGs, enabling easy exchange of cargo IgGs. We show that cytosolically delivered IgGs can inhibit the drug efflux pump multidrug resistance-associated protein 1 (MRP1) and the transcription factor NFκB. This work establishes an approach for using existing antibody collections to modulate intracellular protein function.
Collapse
|
39
|
Kwon JH, Kim HH, Cho HB, Cha YJ, Lee J. Viral antigen nanoparticles for discriminated and quantitative detection of different subtypes of anti-virus immunoglobulins. NANOSCALE 2019; 11:18282-18289. [PMID: 31573015 DOI: 10.1039/c9nr06160f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The aim of this study is to develop a novel method for the accurate diagnosis of the infection status of viral diseases, which requires discriminated and quantitative detection of different anti-virus immunoglubulin subtypes. Considering hepatitis A as a representative model disease, viral antigen nanoparticles (vAgNPs) were designed and synthesized by genetically presenting hepatitis A virus (HAV) antigens on the surface of human heavy chain ferritin (hFTH) nanoparticles to detect anti-HAV antibodies with discriminating immunoglobulin subtypes M and G (IgM and IgG, respectively). The vAgNPs also display multi-copies of hexa-histidine peptide (H6) on their surface to chemisorb gold ions (Au3+), which is vital for the autonomous generation of quantitatively meaningful detection signals. The quantitative level of anti-HAV IgM or IgG in 30 patient sera was successfully analyzed using the vAgNPs of HAV, which was performed through label-free one-step-immunoassay based on the self-enhancement of optical signals from gold nanoparticles clustered on the viral antigen nanoparticles. The diagnostic performance was compared with that of enzyme-linked immunosorbent assay (ELISA), which did not enable accurate quantitative assay due to the poor linearity between the antibody concentration and detection signal. Furthermore, these vAgNP-based immunoassays did not produce any false negative/positive signals, indicating 100% sensitivity and 100% specificity.
Collapse
Affiliation(s)
- J-H Kwon
- Department of Chemical and Biological Engineering, College of Engineering, Korea University, Anam-Ro 145, Seoul 136-713, Republic of Korea.
| | | | | | | | | |
Collapse
|
40
|
Li Q, Cui S, Ma Q, Liu Y, Yu H, Geng G, Agborbesong E, Ren C, Wei K, Zhang Y, Yang J, Bai X, Cai G, Xie Y, Li X, Chen X. Disruption of Robo2-Baiap2 integrated signaling drives cystic disease. JCI Insight 2019; 4:127602. [PMID: 31534052 DOI: 10.1172/jci.insight.127602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/21/2019] [Indexed: 11/17/2022] Open
Abstract
Hereditary renal cystic diseases are characterized by defects in primary cilia of renal tubular epithelial cells and abnormality of tubular epithelium, which ultimately result in the development of renal cysts. However, the mechanism leading from abnormality of the tubular epithelium to cystogenesis is not well understood. In this report, we demonstrate a critical role for Robo2 in regulating epithelial development, including ciliogenesis, polarization, and differentiation. We found that Robo2 deficiency results in cystic kidneys, and the cyst cells showed defective cilia and polarity defects in tubular epithelium. The cyst cells, less than terminally differentiated, continue to proliferate. We further established that Robo2 works with p53 as well as polarity and ciliary proteins (Par3, PKCς, ZO-2, and Claudin-2) to regulate these processes. Robo2 binds to Baiap2 (also known as IRSp53) through the IRSp53/MIM homology domain in renal epithelial cells. This binding allows Robo2 to phosphorylate MDM2 at Ser166 via Baiap2 and maintain p53 homeostasis. Disruption of the Robo2-Baiap2 complex causes MDM2 to be subjected to dephosphorylation, leading to a high level of active p53, and initiated p53-mediated cellular senescence via p21 and decreased the expression of ZO-1, ZO-2, PKCς, Par3, and Claudin-2 proteins, resulting in defects in epithelial development, including ciliogenesis, polarization, and differentiation. Importantly, double knockout of Robo2 and p53 rescued all the epithelial defects in kidneys compared with those in Robo2-knockout kidneys. Taken together, the present results demonstrate that Robo2 deficiency causes renal cystic disease, which is largely dependent on defective Robo2-Baiap2 integrated signaling in kidneys.
Collapse
Affiliation(s)
- Qinggang Li
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Shaoyuan Cui
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Qian Ma
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Ying Liu
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Hongyu Yu
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - GuangRui Geng
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Ewud Agborbesong
- Department of Internal Medicine, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Chongyu Ren
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kai Wei
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Yingjie Zhang
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Jurong Yang
- Department of Urology, Third Affiliated Hospital of Chongqing Medical University (General Hospital), Chongqing, China
| | - Xueyuan Bai
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Guangyan Cai
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Yuansheng Xie
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Xiangmei Chen
- Department of Nephrology, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| |
Collapse
|
41
|
Fredolini C, Byström S, Sanchez-Rivera L, Ioannou M, Tamburro D, Pontén F, Branca RM, Nilsson P, Lehtiö J, Schwenk JM. Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles. Sci Rep 2019; 9:8324. [PMID: 31171813 PMCID: PMC6554399 DOI: 10.1038/s41598-019-43552-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 04/27/2019] [Indexed: 11/16/2022] Open
Abstract
There is a strong need for procedures that enable context and application dependent validation of antibodies. Here, we applied a magnetic bead assisted workflow and immunoprecipitation mass spectrometry (IP-MS/MS) to assess antibody selectivity for the detection of proteins in human plasma. A resource was built on 414 IP experiments using 157 antibodies (targeting 120 unique proteins) in assays with heat-treated or untreated EDTA plasma. For each protein we determined their antibody related degrees of enrichment using z-scores and their frequencies of identification across all IP assays. Out of 1,313 unique endogenous proteins, 426 proteins (33%) were detected in >20% of IPs, and these background components were mainly comprised of proteins from the complement system. For 45% (70/157) of the tested antibodies, the expected target proteins were enriched (z-score ≥ 3). Among these 70 antibodies, 59 (84%) co-enriched other proteins beside the intended target and mainly due to sequence homology or protein abundance. We also detected protein interactions in plasma, and for IGFBP2 confirmed these using several antibodies and sandwich immunoassays. The protein enrichment data with plasma provide a very useful and yet lacking resource for the assessment of antibody selectivity. Our insights will contribute to a more informed use of affinity reagents for plasma proteomics assays.
Collapse
Affiliation(s)
- Claudia Fredolini
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Sanna Byström
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Laura Sanchez-Rivera
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Marina Ioannou
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Davide Tamburro
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | - Rui M Branca
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Janne Lehtiö
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Jochen M Schwenk
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden.
| |
Collapse
|
42
|
Idborg H, Zandian A, Ossipova E, Wigren E, Preger C, Mobarrez F, Checa A, Sohrabian A, Pucholt P, Sandling JK, Fernandes-Cerqueira C, Rönnelid J, Oke V, Grosso G, Kvarnström M, Larsson A, Wheelock CE, Syvänen AC, Rönnblom L, Kultima K, Persson H, Gräslund S, Gunnarsson I, Nilsson P, Svenungsson E, Jakobsson PJ. Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients. Front Immunol 2019; 10:1029. [PMID: 31156624 PMCID: PMC6533644 DOI: 10.3389/fimmu.2019.01029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Systemic Lupus Erythematosus (SLE) is a heterogeneous autoimmune disease, which currently lacks specific diagnostic biomarkers. The diversity within the patients obstructs clinical trials but may also reflect differences in underlying pathogenesis. Our objective was to obtain protein profiles to identify potential general biomarkers of SLE and to determine molecular subgroups within SLE for patient stratification. Plasma samples from a cross-sectional study of well-characterized SLE patients (n = 379) and matched population controls (n = 316) were analyzed by antibody suspension bead array targeting 281 proteins. To investigate the differences between SLE and controls, Mann–Whitney U-test with Bonferroni correction, generalized linear modeling and receiver operating characteristics (ROC) analysis were performed. K-means clustering was used to identify molecular SLE subgroups. We identified Interferon regulating factor 5 (IRF5), solute carrier family 22 member 2 (SLC22A2) and S100 calcium binding protein A12 (S100A12) as the three proteins with the largest fold change between SLE patients and controls (SLE/Control = 1.4, 1.4, and 1.2 respectively). The lowest p-values comparing SLE patients and controls were obtained for S100A12, Matrix metalloproteinase-1 (MMP1) and SLC22A2 (padjusted = 3 × 10−9, 3 × 10−6, and 5 × 10−6 respectively). In a set of 15 potential biomarkers differentiating SLE patients and controls, two of the proteins were transcription factors, i.e., IRF5 and SAM pointed domain containing ETS transcription factor (SPDEF). IRF5 was up-regulated while SPDEF was found to be down-regulated in SLE patients. Unsupervised clustering of all investigated proteins identified three molecular subgroups among SLE patients, characterized by (1) high levels of rheumatoid factor-IgM, (2) low IRF5, and (3) high IRF5. IRF5 expressing microparticles were analyzed by flow cytometry in a subset of patients to confirm the presence of IRF5 in plasma and detection of extracellular IRF5 was further confirmed by immunoprecipitation-mass spectrometry (IP-MS). Interestingly IRF5, a known genetic risk factor for SLE, was detected extracellularly and suggested by unsupervised clustering analysis to differentiate between SLE subgroups. Our results imply a set of circulating molecules as markers of possible pathogenic importance in SLE. We believe that these findings could be of relevance for understanding the pathogenesis and diversity of SLE, as well as for selection of patients in clinical trials.
Collapse
Affiliation(s)
- Helena Idborg
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Arash Zandian
- SciLifeLab, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Elena Ossipova
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Edvard Wigren
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Charlotta Preger
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Fariborz Mobarrez
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Sciences, Akademiska Hospital, Uppsala University, Uppsala, Sweden
| | - Antonio Checa
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Azita Sohrabian
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Cátia Fernandes-Cerqueira
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Vilija Oke
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Giorgia Grosso
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marika Kvarnström
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Kim Kultima
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development & School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Susanne Gräslund
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Nilsson
- SciLifeLab, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
43
|
HiBiT-qIP, HiBiT-based quantitative immunoprecipitation, facilitates the determination of antibody affinity under immunoprecipitation conditions. Sci Rep 2019; 9:6895. [PMID: 31053795 PMCID: PMC6499798 DOI: 10.1038/s41598-019-43319-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/31/2019] [Indexed: 12/23/2022] Open
Abstract
The affinity of an antibody for its antigen serves as a critical parameter for antibody evaluation. The evaluation of antibody-antigen affinity is essential for a successful antibody-based assay, particularly immunoprecipitation (IP), due to its strict dependency on antibody performance. However, the determination of antibody affinity or its quantitative determinant, the dissociation constant (Kd), under IP conditions is difficult. In the current study, we used a NanoLuc-based HiBiT system to establish a HiBiT-based quantitative immunoprecipitation (HiBiT-qIP) assay for determining the Kd of antigen-antibody interactions in solution. The HiBiT-qIP method measures the amount of immunoprecipitated proteins tagged with HiBiT in a simple yet quantitative manner. We used this method to measure the Kd values of epitope tag-antibody interactions. To accomplish this, FLAG, HA, V5, PA and Ty1 epitope tags in their monomeric, dimeric or trimeric form were fused with glutathione S-transferase (GST) and the HiBiT peptide, and these tagged GST proteins were mixed with cognate monoclonal antibodies in IP buffer for the assessment of the apparent Kd values. This HiBiT-qIP assay showed a considerable variation in the Kd values among the examined antibody clones. Additionally, the use of epitope tags in multimeric form revealed a copy number-dependent increase in the apparent affinity.
Collapse
|
44
|
Steentoft C, Fuhrmann M, Battisti F, Van Coillie J, Madsen TD, Campos D, Halim A, Vakhrushev SY, Joshi HJ, Schreiber H, Mandel U, Narimatsu Y. A strategy for generating cancer-specific monoclonal antibodies to aberrant O-glycoproteins: identification of a novel dysadherin-Tn antibody. Glycobiology 2019; 29:307-319. [PMID: 30726901 PMCID: PMC6430981 DOI: 10.1093/glycob/cwz004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/25/2022] Open
Abstract
Successful application of potent antibody-based T-cell engaging immunotherapeutic strategies is currently limited mainly to hematological cancers. One major reason is the lack of well-characterized antigens on solid tumors with sufficient cancer specific expression. Aberrantly O-glycosylated proteins contain promising cancer-specific O-glycopeptide epitopes suitable for immunotherapeutic applications, but currently only few examples of such antibody epitopes have been identified. We previously showed that chimeric antigen receptor T-cells directed towards aberrantly O-glycosylated MUC1 can control malignant growth in a mouse model. Here, we present a discovery platform for the generation of cancer-specific monoclonal antibodies targeting aberrant O-glycoproteins. The strategy is based on cancer cell lines engineered to homogeneously express the truncated Tn O-glycoform, the so-called SimpleCells. We used SimpleCells of different cancer origin to elicit monoclonal antibodies with selectivity for aberrant O-glycoproteins. For validation we selected and characterized one monoclonal antibody (6C5) directed to a Tn-glycopeptide in dysadherin (FXYD5), known to be upregulated in cancer and promote metastasis. While dysadherin is widely expressed also in normal cells, we demonstrated that the 6C5 epitope is specifically expressed in cancer.
Collapse
Affiliation(s)
- Catharina Steentoft
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Max Fuhrmann
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Federico Battisti
- Department of Experimental Medicine, “Sapienza” University of Rome, Viale Regina Elena 324 Rome, Italy
| | - Julie Van Coillie
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Thomas D Madsen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Diana Campos
- Instituto de Investigação e Inovação e Saúde, Universidade do Porto, Rua Júlio Amaral de Carvalho 45, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Júlio Amaral de Carvalho 45, Porto, Portugal
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Hans Schreiber
- Department of Pathology, Committee on Immunology, Committee on Cancer Biology, The University of Chicago, 5841 S. Maryland Avenue, Chicago, IL, USA
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, Copenhagen N, Denmark
| |
Collapse
|
45
|
Demarest TG, Babbar M, Okur MN, Dan X, Croteau DL, Fakouri NB, Mattson MP, Bohr VA. NAD+Metabolism in Aging and Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2019. [DOI: 10.1146/annurev-cancerbio-030518-055905] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aging is a major risk factor for many types of cancer, and the molecular mechanisms implicated in aging, progeria syndromes, and cancer pathogenesis display considerable similarities. Maintaining redox homeostasis, efficient signal transduction, and mitochondrial metabolism is essential for genome integrity and for preventing progression to cellular senescence or tumorigenesis. NAD+is a central signaling molecule involved in these and other cellular processes implicated in age-related diseases and cancer. Growing evidence implicates NAD+decline as a major feature of accelerated aging progeria syndromes and normal aging. Administration of NAD+precursors such as nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN) offer promising therapeutic strategies to improve health, progeria comorbidities, and cancer therapies. This review summarizes insights from the study of aging and progeria syndromes and discusses the implications and therapeutic potential of the underlying molecular mechanisms involved in aging and how they may contribute to tumorigenesis.
Collapse
Affiliation(s)
- Tyler G. Demarest
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
- Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Mansi Babbar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Mustafa N. Okur
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Xiuli Dan
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Deborah L. Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Nima B. Fakouri
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Mark P. Mattson
- Laboratory of Neurosciences, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Vilhelm A. Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| |
Collapse
|
46
|
Teyra J, Singer AU, Schmitges FW, Jaynes P, Kit Leng Lui S, Polyak MJ, Fodil N, Krieger JR, Tong J, Schwerdtfeger C, Brasher BB, Ceccarelli DFJ, Moffat J, Sicheri F, Moran MF, Gros P, Eichhorn PJA, Lenter M, Boehmelt G, Sidhu SS. Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure 2019; 27:590-605.e5. [PMID: 30713027 DOI: 10.1016/j.str.2019.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/23/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022]
Abstract
The multi-domain deubiquitinase USP15 regulates diverse eukaryotic processes and has been implicated in numerous diseases. We developed ubiquitin variants (UbVs) that targeted either the catalytic domain or each of three adaptor domains in USP15, including the N-terminal DUSP domain. We also designed a linear dimer (diUbV), which targeted the DUSP and catalytic domains, and exhibited enhanced specificity and more potent inhibition of catalytic activity than either UbV alone. In cells, the UbVs inhibited the deubiquitination of two USP15 substrates, SMURF2 and TRIM25, and the diUbV inhibited the effects of USP15 on the transforming growth factor β pathway. Structural analyses revealed that three distinct UbVs bound to the catalytic domain and locked the active site in a closed, inactive conformation, and one UbV formed an unusual strand-swapped dimer and bound two DUSP domains simultaneously. These inhibitors will enable the study of USP15 function in oncology, neurology, immunology, and inflammation.
Collapse
Affiliation(s)
- Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Alex U Singer
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frank W Schmitges
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sarah Kit Leng Lui
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Maria J Polyak
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Nassima Fodil
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Jonathan R Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jiefei Tong
- Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | | | - Bradley B Brasher
- Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA
| | - Derek F J Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael F Moran
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Pieter J A Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Martin Lenter
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | | | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
47
|
Wang YX, Feige P, Brun CE, Hekmatnejad B, Dumont NA, Renaud JM, Faulkes S, Guindon DE, Rudnicki MA. EGFR-Aurka Signaling Rescues Polarity and Regeneration Defects in Dystrophin-Deficient Muscle Stem Cells by Increasing Asymmetric Divisions. Cell Stem Cell 2019; 24:419-432.e6. [PMID: 30713094 DOI: 10.1016/j.stem.2019.01.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/20/2018] [Accepted: 01/07/2019] [Indexed: 12/17/2022]
Abstract
Loss of dystrophin expression in Duchenne muscular dystrophy (DMD) causes progressive degeneration of skeletal muscle, which is exacerbated by reduced self-renewing asymmetric divisions of muscle satellite cells. This, in turn, affects the production of myogenic precursors and impairs regeneration and suggests that increasing such divisions may be beneficial. Here, through a small-molecule screen, we identified epidermal growth factor receptor (EGFR) and Aurora kinase A (Aurka) as regulators of asymmetric satellite cell divisions. Inhibiting EGFR causes a substantial shift from asymmetric to symmetric division modes, whereas EGF treatment increases asymmetric divisions. EGFR activation acts through Aurka to orient mitotic centrosomes, and inhibiting Aurka blocks EGF stimulation-induced asymmetric division. In vivo EGF treatment markedly activates asymmetric divisions of dystrophin-deficient satellite cells in mdx mice, increasing progenitor numbers, enhancing regeneration, and restoring muscle strength. Therefore, activating an EGFR-dependent polarity pathway promotes functional rescue of dystrophin-deficient satellite cells and enhances muscle force generation.
Collapse
Affiliation(s)
- Yu Xin Wang
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Peter Feige
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Caroline E Brun
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Bahareh Hekmatnejad
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Nicolas A Dumont
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jean-Marc Renaud
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Sharlene Faulkes
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Daniel E Guindon
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Michael A Rudnicki
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Regenerative Medicine Program, Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Department of Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
| |
Collapse
|
48
|
Vandemoortele G, De Sutter D, Moliere A, Pauwels J, Gevaert K, Eyckerman S. A Well-Controlled BioID Design for Endogenous Bait Proteins. J Proteome Res 2018; 18:95-106. [PMID: 30525648 DOI: 10.1021/acs.jproteome.8b00367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate the overexpression of bait proteins. Control cell lines are typically nonengineered cells or engineered clones, implying a considerable risk for artifacts because of clonal variation. Genome engineering can also transform BioID, a proximity labeling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bicistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A autocleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over the classical ectopic expression of p53-BirA*, and we provide a first well-controlled view of the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.
Collapse
Affiliation(s)
- Giel Vandemoortele
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Aline Moliere
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| |
Collapse
|
49
|
|
50
|
Li J, Levitan B, Gomez-Jimenez S, Kültz D. Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks ( Gasterosteus aculeatus). Mol Cell Proteomics 2018; 17:2146-2163. [PMID: 30093419 PMCID: PMC6210217 DOI: 10.1074/mcp.ra118.000973] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/07/2018] [Indexed: 12/31/2022] Open
Abstract
A data-independent acquisition (DIA) assay library for quantitative analyses of proteome dynamics has been developed for gills of threespine sticklebacks (Gasterosteus aculeatus). A raw spectral library was generated by data-dependent acquisition (DDA) and annotation of tryptic peptides to MSMS spectra and protein database identifiers. The assay library was constructed from the raw spectral library by removal of low-quality, ambiguous, and low-signal peptides. Only unique proteins represented by at least two peptides are included in the assay library, which consists of 1506 proteins, 5074 peptides, 5104 precursors, and 25,322 transitions. This assay library was used with DIA data to identify biochemical differences in gill proteomes of four populations representing different eco- and morpho-types of threespine sticklebacks. The assay library revealed unique and reproducible proteome signatures. Warm-adapted, low-plated, brackish-water fish from Laguna de la Bocana del Rosario (Mexico) show elevated HSP47, extracellular matrix, and innate immunity proteins whereas several immunoglobulins, interferon-induced proteins, ubiquitins, proteolytic enzymes, and nucleic acid remodeling proteins are reduced. Fully-plated, brackish-water fish from Westchester Lagoon (Alaska) display elevated ion regulation, GTPase signaling, and contractile cytoskeleton proteins, altered abundances of many ribosomal, calcium signaling and immunity proteins, and depleted transcriptional regulators and metabolic enzymes. Low-plated freshwater fish from Lake Solano (California) have elevated inflammasomes and proteolytic proteins whereas several iron containing and ion regulatory proteins are reduced. Gills of fully-plated, marine fish from Bodega Harbor (California) have elevated oxidative metabolism enzymes and reduced transglutaminase 2, collagens, and clathrin heavy chains. These distinct proteome signatures represent targets for testing ecological and evolutionary influences on molecular mechanisms of gill function in threespine sticklebacks. Furthermore, the gill assay library represents a model for other tissues and paves the way for accurate and reproducible network analyses of environmental context-dependent proteome dynamics in complex organisms.
Collapse
Affiliation(s)
- Johnathon Li
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616
| | - Bryn Levitan
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616
| | - Silvia Gomez-Jimenez
- §Centro de Investigación en Alimentación y Desarrollo, Carretera a la Victoria Km. 0.6, Apartado, Hermosillo, Sonora, México C.P. 83000
| | - Dietmar Kültz
- From the ‡Department of Animal Sciences, University of California Davis, Meyer Hall, One Shields Ave., Davis, CA 95616;
- ¶Coastal Marine Sciences Institute, University of California, Davis
| |
Collapse
|