1
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Schulte D, Snijder J. A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics. J Proteome Res 2024; 23:3552-3559. [PMID: 38932690 PMCID: PMC11301774 DOI: 10.1021/acs.jproteome.4c00188] [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: 03/11/2024] [Revised: 05/29/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Antibody sequences can be determined at 99% accuracy directly from the polypeptide product by using bottom-up proteomics techniques. Sequencing accuracy at the peptide level is limited by the isobaric residues leucine and isoleucine, incomplete fragmentation spectra in which the order of two or more residues remains ambiguous due to lacking fragment ions for the intermediate positions, and isobaric combinations of amino acids, of potentially different lengths, for example, GG = N and GA = Q. Here, we present several updates to Stitch (v1.5), which performs template-based assembly of de novo peptides to reconstruct antibody sequences. This version introduces a mass-based alignment algorithm that explicitly accounts for mass coincidence errors. In addition, it incorporates a postprocessing procedure to assign I/L residues based on secondary fragments (satellite ions, i.e., w-ions). Moreover, evidence for sequence assignments can now be directly evaluated with the addition of an integrated spectrum viewer. Lastly, input data from a wider selection of de novo peptide sequencing algorithms are allowed, now including Casanovo, PEAKS, Novor.Cloud, pNovo, and MaxNovo, in addition to flat text and FASTA. Combined, these changes make Stitch compatible with a larger range of data processing pipelines and improve its tolerance to peptide-level sequencing errors.
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Affiliation(s)
- Douwe Schulte
- Biomolecular Mass Spectrometry
and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht
Institute of Pharmaceutical Sciences, Utrecht
University, Padualaan 8, Utrecht 3584
CH, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry
and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht
Institute of Pharmaceutical Sciences, Utrecht
University, Padualaan 8, Utrecht 3584
CH, The Netherlands
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2
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Angelo M, Zhang W, Vilseck JZ, Aoki ST. In silico λ-dynamics predicts protein binding specificities to modified RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577511. [PMID: 38328125 PMCID: PMC10849657 DOI: 10.1101/2024.01.26.577511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
RNA modifications shape gene expression through a smorgasbord of chemical changes to canonical RNA bases. Although numbering in the hundreds, only a few RNA modifications are well characterized, in part due to the absence of methods to identify modification sites. Antibodies remain a common tool to identify modified RNA and infer modification sites through straightforward applications. However, specificity issues can result in off-target binding and confound conclusions. This work utilizes in silico λ-dynamics to efficiently estimate binding free energy differences of modification-targeting antibodies between a variety of naturally occurring RNA modifications. Crystal structures of inosine and N6-methyladenosine (m6A) targeting antibodies bound to their modified ribonucleosides were determined and served as structural starting points. λ-Dynamics was utilized to predict RNA modifications that permit or inhibit binding to these antibodies. In vitro RNA-antibody binding assays supported the accuracy of these in silico results. High agreement between experimental and computed binding propensities demonstrated that λ-dynamics can serve as a predictive screen for antibody specificity against libraries of RNA modifications. More importantly, this strategy is an innovative way to elucidate how hundreds of known RNA modifications interact with biological molecules without the limitations imposed by in vitro or in vivo methodologies.
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Affiliation(s)
- Murphy Angelo
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
| | - Jonah Z. Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Scott T. Aoki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
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3
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Schulte D, Peng W, Snijder J. Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling. Anal Chem 2022; 94:10391-10399. [PMID: 35834437 PMCID: PMC9330293 DOI: 10.1021/acs.analchem.2c01300] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Antibodies can target a vast molecular diversity of antigens.
This
is achieved by generating a complementary diversity of antibody sequences
through somatic recombination and hypermutation. A full understanding
of the antibody repertoire in health and disease therefore requires
dedicated de novo sequencing methods. Next-generation
cDNA sequencing methods have laid the foundation of our current understanding
of the antibody repertoire, but these methods share one major limitation
in that they target the antibody-producing B-cells, rather than the
functional secreted product in bodily fluids. Mass spectrometry-based
methods offer an opportunity to bridge this gap between antibody repertoire
profiling and bulk serological assays, as they can access antibody
sequence information straight from the secreted polypeptide products.
In a step to meeting the challenge of mass spectrometry (MS)-based
antibody sequencing, we present a fast and simple software tool (Stitch)
to map proteomic short reads to user-defined templates with dedicated
features for both monoclonal antibody sequencing and profiling of
polyclonal antibody repertoires. We demonstrate the use of Stitch
by fully reconstructing two monoclonal antibody sequences with >98%
accuracy (including I/L assignment); sequencing a Fab from patient
serum isolated by reversed-phase liquid chromatography (LC) fractionation
against a high background of homologous antibody sequences; sequencing
antibody light chains from the urine of multiple-myeloma patients;
and profiling the IgG repertoire in sera from patients hospitalized
with COVID-19. We demonstrate that Stitch assembles a comprehensive
overview of the antibody sequences that are represented in the dataset
and provides an important first step toward analyzing polyclonal antibodies
and repertoire profiling.
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Affiliation(s)
- Douwe Schulte
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Weiwei Peng
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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4
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Gadush MV, Sautto GA, Chandrasekaran H, Bensussan A, Ross TM, Ippolito GC, Person MD. Template-Assisted De Novo Sequencing of SARS-CoV-2 and Influenza Monoclonal Antibodies by Mass Spectrometry. J Proteome Res 2022; 21:1616-1627. [PMID: 35653804 DOI: 10.1021/acs.jproteome.1c00913] [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] [Indexed: 11/29/2022]
Abstract
In this study, we used multiple enzyme digestions, coupled with higher-energy collisional dissociation (HCD) and electron-transfer/higher-energy collision dissociation (EThcD) fragmentation to develop a mass-spectrometric (MS) method for determining the complete protein sequence of monoclonal antibodies (mAbs). The method was refined on an mAb of a known sequence, a SARS-CoV-1 antireceptor binding domain (RBD) spike monoclonal antibody. The data were searched using Supernovo to generate a complete template-assisted de novo sequence for this and two SARS-CoV-2 mAbs of known sequences resulting in correct sequences for the variable regions and correct distinction of Ile and Leu residues. We then used the method on a set of 25 antihemagglutinin (HA) influenza antibodies of unknown sequences and determined high confidence sequences for >99% of the complementarity determining regions (CDRs). The heavy-chain and light-chain genes were cloned and transfected into cells for recombinant expression followed by affinity purification. The recombinant mAbs displayed binding curves matching the original mAbs with specificity to the HA influenza antigen. Our findings indicate that this methodology results in almost complete antibody sequence coverage with high confidence results for CDR regions on diverse mAb sequences.
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Affiliation(s)
- Michelle V Gadush
- Center for Biomedical Research Support, Biological Mass Spectrometry Facility, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Giuseppe A Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia 30602, United States
| | - Hamssika Chandrasekaran
- Center for Biomedical Research Support, Biological Mass Spectrometry Facility, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Alena Bensussan
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ted M Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia 30602, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Maria D Person
- Center for Biomedical Research Support, Biological Mass Spectrometry Facility, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Irani V, Soliman C, Raftis MA, Guy AJ, Elbourne A, Ramsland PA. Expression of monoclonal antibodies for functional and structural studies. METHODS IN MICROBIOLOGY 2022. [DOI: 10.1016/bs.mim.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Peng W, Pronker MF, Snijder J. Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme. J Proteome Res 2021; 20:3559-3566. [PMID: 34121409 PMCID: PMC8256418 DOI: 10.1021/acs.jproteome.1c00169] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/20/2022]
Abstract
Antibody sequence information is crucial to understanding the structural basis for antigen binding and enables the use of antibodies as therapeutics and research tools. Here, we demonstrate a method for direct de novo sequencing of monoclonal IgG from the purified antibody products. The method uses a panel of multiple complementary proteases to generate suitable peptides for de novo sequencing by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in a bottom-up fashion. Furthermore, we apply a dual fragmentation scheme, using both stepped high-energy collision dissociation (stepped HCD) and electron-transfer high-energy collision dissociation (EThcD), on all peptide precursors. The method achieves full sequence coverage of the monoclonal antibody herceptin, with an accuracy of 99% in the variable regions. We applied the method to sequence the widely used anti-FLAG-M2 mouse monoclonal antibody, which we successfully validated by remodeling a high-resolution crystal structure of the Fab and demonstrating binding to a FLAG-tagged target protein in Western blot analysis. The method thus offers robust and reliable sequences of monoclonal antibodies.
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Affiliation(s)
| | | | - Joost Snijder
- Biomolecular Mass Spectrometry
and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht
Institute of Pharmaceutical Sciences, Utrecht
University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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7
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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8
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Gonzales Hurtado PA, Morrison R, Ribeiro JMC, Magale H, Attaher O, Diarra BS, Mahamar A, Barry A, Dicko A, Duffy PE, Fried M. Proteomics Pipeline for Identifying Variant Proteins in Plasmodium falciparum Parasites Isolated from Children Presenting with Malaria. J Proteome Res 2019; 18:3831-3839. [PMID: 31549843 PMCID: PMC11097108 DOI: 10.1021/acs.jproteome.9b00169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Plasmodium falciparum variant antigens named erythrocyte membrane protein 1 (PfEMP1) are important targets for developing a protective immunity to malaria caused by P. falciparum. One of the major challenges in P. falciparum proteomics studies is identifying PfEMP1s at the protein level due to antigenic variation. To identify these PfEMP1s using shotgun proteomics, we developed a pipeline that searches high-resolution mass spectrometry spectra against a custom protein sequence database. A local alignment algorithm, LAX, was developed as a part of the pipeline that matches peptide sequences to the most similar PfEMP1 and calculates a weight value based on peptide's uniqueness used for PfEMP1 protein inference. The pipeline was first validated in the analysis of a laboratory strain with a known PfEMP1, then it was implemented on the analysis of parasite isolates from malaria-infected pregnant women and finally on the analysis of parasite isolates from malaria-infected children where there was an increase of PfEMP1s identified in 27 out of 31 isolates using the expanded database.
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Affiliation(s)
- Patricia A. Gonzales Hurtado
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland 20852, United States
| | - Robert Morrison
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland 20852, United States
| | - Jose M. C. Ribeiro
- Laboratory of Malaria Vector Research, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland 20852, United States
| | - Hussein Magale
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland 20852, United States
| | - Oumar Attaher
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences Techniques and Technologies of Bamako, P.O. Box 1805, Bamako, 1. 20892, Mali
| | - Bacary S. Diarra
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences Techniques and Technologies of Bamako, P.O. Box 1805, Bamako, 1. 20892, Mali
| | - Almahamoudou Mahamar
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences Techniques and Technologies of Bamako, P.O. Box 1805, Bamako, 1. 20892, Mali
| | - Amadou Barry
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences Techniques and Technologies of Bamako, P.O. Box 1805, Bamako, 1. 20892, Mali
| | - Alassane Dicko
- Malaria Research & Training Center, Faculty of Medicine, Pharmacy and Dentistry, University of Sciences Techniques and Technologies of Bamako, P.O. Box 1805, Bamako, 1. 20892, Mali
| | - Patrick E. Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland 20852, United States
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Disease, NIH, Bethesda, Maryland 20852, United States
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9
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Meyer L, López T, Espinosa R, Arias CF, Vollmers C, DuBois RM. A simplified workflow for monoclonal antibody sequencing. PLoS One 2019; 14:e0218717. [PMID: 31233538 PMCID: PMC6590890 DOI: 10.1371/journal.pone.0218717] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/07/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of antibody variable regions makes cDNA sequencing challenging, and conventional monoclonal antibody cDNA amplification requires the use of degenerate primers. Here, we describe a simplified workflow for amplification of IgG antibody variable regions from hybridoma RNA by a specialized RT-PCR followed by Sanger sequencing. We perform three separate reactions for each hybridoma: one each for kappa, lambda, and heavy chain transcripts. We prime reverse transcription with a primer specific to the respective constant region and use a template-switch oligonucleotide, which creates a custom sequence at the 5’ end of the antibody cDNA. This template-switching circumvents the issue of low sequence homology and the need for degenerate primers. Instead, subsequent PCR amplification of the antibody cDNA molecules requires only two primers: one primer specific for the template-switch oligonucleotide sequence and a nested primer to the respective constant region. We successfully sequenced the variable regions of five mouse monoclonal IgG antibodies using this method, which enabled us to design chimeric mouse/human antibody expression plasmids for recombinant antibody production in mammalian cell culture expression systems. All five recombinant antibodies bind their respective antigens with high affinity, confirming that the amino acid sequences determined by our method are correct and demonstrating the high success rate of our method. Furthermore, we also designed RT-PCR primers and amplified the variable regions from RNA of cells transfected with chimeric mouse/human antibody expression plasmids, showing that our approach is also applicable to IgG antibodies of human origin. Our monoclonal antibody sequencing method is highly accurate, user-friendly, and very cost-effective.
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Affiliation(s)
- Lena Meyer
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rafaela Espinosa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (RMD); (CV)
| | - Rebecca M. DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (RMD); (CV)
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10
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Rickert KW, Grinberg L, Woods RM, Wilson S, Bowen MA, Baca M. Combining phage display with de novo protein sequencing for reverse engineering of monoclonal antibodies. MAbs 2016; 8:501-12. [PMID: 26852694 DOI: 10.1080/19420862.2016.1145865] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The enormous diversity created by gene recombination and somatic hypermutation makes de novo protein sequencing of monoclonal antibodies a uniquely challenging problem. Modern mass spectrometry-based sequencing will rarely, if ever, provide a single unambiguous sequence for the variable domains. A more likely outcome is computation of an ensemble of highly similar sequences that can satisfy the experimental data. This outcome can result in the need for empirical testing of many candidate sequences, sometimes iteratively, to identity one which can replicate the activity of the parental antibody. Here we describe an improved approach to antibody protein sequencing by using phage display technology to generate a combinatorial library of sequences that satisfy the mass spectrometry data, and selecting for functional candidates that bind antigen. This approach was used to reverse engineer 2 commercially-obtained monoclonal antibodies against murine CD137. Proteomic data enabled us to assign the majority of the variable domain sequences, with the exception of 3-5% of the sequence located within or adjacent to complementarity-determining regions. To efficiently resolve the sequence in these regions, small phage-displayed libraries were generated and subjected to antigen binding selection. Following enrichment of antigen-binding clones, 2 clones were selected for each antibody and recombinantly expressed as antigen-binding fragments (Fabs). In both cases, the reverse-engineered Fabs exhibited identical antigen binding affinity, within error, as Fabs produced from the commercial IgGs. This combination of proteomic and protein engineering techniques provides a useful approach to simplifying the technically challenging process of reverse engineering monoclonal antibodies from protein material.
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Affiliation(s)
- Keith W Rickert
- a Department of Antibody Discovery and Protein Engineering , MedImmune, LLC , Gaithersburg , MD , USA
| | - Luba Grinberg
- a Department of Antibody Discovery and Protein Engineering , MedImmune, LLC , Gaithersburg , MD , USA
| | - Robert M Woods
- a Department of Antibody Discovery and Protein Engineering , MedImmune, LLC , Gaithersburg , MD , USA
| | - Susan Wilson
- a Department of Antibody Discovery and Protein Engineering , MedImmune, LLC , Gaithersburg , MD , USA
| | - Michael A Bowen
- a Department of Antibody Discovery and Protein Engineering , MedImmune, LLC , Gaithersburg , MD , USA
| | - Manuel Baca
- a Department of Antibody Discovery and Protein Engineering , MedImmune, LLC , Gaithersburg , MD , USA
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11
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Zucchelli S, Patrucco L, Persichetti F, Gustincich S, Cotella D. Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs. Comput Struct Biotechnol J 2016; 14:404-410. [PMID: 27872686 PMCID: PMC5107644 DOI: 10.1016/j.csbj.2016.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.
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Affiliation(s)
- Silvia Zucchelli
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Area of Neuroscience, SISSA, Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Neuroscience and Brain Technologies, Italian Institute of Technology (IIT), Genova, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
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12
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Xiao Y, Vecchi MM, Wen D. Distinguishing between Leucine and Isoleucine by Integrated LC–MS Analysis Using an Orbitrap Fusion Mass Spectrometer. Anal Chem 2016; 88:10757-10766. [DOI: 10.1021/acs.analchem.6b03409] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yongsheng Xiao
- Analytical
Biochemistry,
Department of Cell and Protein Sciences, Biogen, 250 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Malgorzata M. Vecchi
- Analytical
Biochemistry,
Department of Cell and Protein Sciences, Biogen, 250 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Dingyi Wen
- Analytical
Biochemistry,
Department of Cell and Protein Sciences, Biogen, 250 Binney Street, Cambridge, Massachusetts 02142, United States
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13
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Díez P, Fuentes M. Proteogenomics for the Comprehensive Analysis of Human Cellular and Serum Antibody Repertoires. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 926:153-162. [PMID: 27686811 DOI: 10.1007/978-3-319-42316-6_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The vast repertoire of immunoglobulins produced by the immune system is a consequence of the huge amount of antigens to which we are exposed every day. The diversity of these immunoglobulins is due to different mechanisms (including VDJ recombination, somatic hypermutation, and antigen selection). Understanding how the immune system is capable of generating this diversity and which are the molecular bases of the composition of immunoglobulins are key challenges in the immunological field. During the last decades, several techniques have emerged as promising strategies to achieve these goals, but it is their combination which appears to be the fruitful solution for increasing the knowledge about human cellular and serum antibody repertoires.In this chapter, we address the diverse strategies focused on the analysis of immunoglobulin repertoires as well as the characterization of the genomic and peptide sequences. Moreover, the advantages of combining various -omics approaches are discussed through review different published studies, showing the benefits in clinical areas.
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain. .,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra, S/N 37007, Salamanca, Spain.
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14
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Abreu TF, Sumitomo BN, Nishiyama MY, Oliveira UC, Souza GHMF, Kitano ES, Zelanis A, Serrano SMT, Junqueira-de-Azevedo I, Silva PI, Tashima AK. Peptidomics of Acanthoscurria gomesiana spider venom reveals new toxins with potential antimicrobial activity. J Proteomics 2016; 151:232-242. [PMID: 27436114 DOI: 10.1016/j.jprot.2016.07.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 06/22/2016] [Accepted: 07/13/2016] [Indexed: 12/24/2022]
Abstract
Acanthoscurria gomesiana is a Brazilian spider from the Theraphosidae family inhabiting regions of Southeastern Brazil. Potent antimicrobial peptides as gomesin and acanthoscurrin have been discovered from the spider hemolymph in previous works. Spider venoms are also recognized as sources of biologically active peptides, however the venom peptidome of A. gomesiana remained unexplored to date. In this work, a MS-based workflow was applied to the investigation of the spider venom peptidome. Data-independent and data-dependent LC-MS/MS acquisitions of intact peptides and of peptides submitted to multiple enzyme digestions, followed by automated chromatographic alignment, de novo analysis, database and homology searches with manual validations showed that the venom is composed by <165 features, with masses ranging from 0.4-15.8kDa. From digestions, 135 peptides were identified from 17 proteins, including three new mature peptides: U1-TRTX-Agm1a, U1-TRTX-Agm2a and U1-TRTX-Agm3a, containing 3, 4 and 3 disulfide bonds, respectively. The toxins U1-TRTX-Agm1a differed by only one amino acid from U1-TRTX-Ap1a from A. paulensis and U1-TRTX-Agm2a was derived from the genicutoxin-D1 precursor from A. geniculata. These toxins have potential applications as antimicrobial agents, as the peptide fraction of A. gomesiana showed activity against Escherichia coli, Enterobacter cloacae and Candida albicans strains. MS data are available via ProteomeXchange Consortium with identifier PXD003884. BIOLOGICAL SIGNIFICANCE Biological fluids of the Acanthoscurria gomesiana spider are sources of active molecules, as is the case of antimicrobial peptides and acylpolyamines found in the hemolymphs. The venom is also a potential source of toxins with pharmacological and biotechnological applications. However, to our knowledge no A. gomesiana venom toxin structure has been determined to date. Using a combination of high resolution mass spectrometry, transcriptomics and bioinformatics, we employed a workflow to fully sequence, determine the number of disulfide bonds of mature peptides and we found new potential antimicrobial peptides. This workflow is suitable for complete peptide toxin sequencing when handling limited amount of venom samples and can accelerate the discovery of peptides with potential biotechnological applications.
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Affiliation(s)
- Thiago F Abreu
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Bianca N Sumitomo
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Milton Y Nishiyama
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, SP, Brazil
| | - Ursula C Oliveira
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, SP, Brazil
| | - Gustavo H M F Souza
- Mass Spectrometry Applications Research & Development Laboratory, Waters Corporation, Sāo Paulo, SP, Brazil
| | - Eduardo S Kitano
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, SP, Brazil
| | - André Zelanis
- Departamento de Ciência e Tecnologia, Universidade Federal de São Paulo, ICT-UNIFESP, São José dos Campos, SP, Brazil
| | - Solange M T Serrano
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, SP, Brazil
| | - Inácio Junqueira-de-Azevedo
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, SP, Brazil
| | - Pedro I Silva
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, SP, Brazil
| | - Alexandre K Tashima
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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15
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Sheynkman GM, Shortreed MR, Cesnik AJ, Smith LM. Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2016; 9:521-45. [PMID: 27049631 PMCID: PMC4991544 DOI: 10.1146/annurev-anchem-071015-041722] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Mass spectrometry-based proteomics has emerged as the leading method for detection, quantification, and characterization of proteins. Nearly all proteomic workflows rely on proteomic databases to identify peptides and proteins, but these databases typically contain a generic set of proteins that lack variations unique to a given sample, precluding their detection. Fortunately, proteogenomics enables the detection of such proteomic variations and can be defined, broadly, as the use of nucleotide sequences to generate candidate protein sequences for mass spectrometry database searching. Proteogenomics is experiencing heightened significance due to two developments: (a) advances in DNA sequencing technologies that have made complete sequencing of human genomes and transcriptomes routine, and (b) the unveiling of the tremendous complexity of the human proteome as expressed at the levels of genes, cells, tissues, individuals, and populations. We review here the field of human proteogenomics, with an emphasis on its history, current implementations, the types of proteomic variations it reveals, and several important applications.
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Affiliation(s)
- Gloria M Sheynkman
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Anthony J Cesnik
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706; ,
- Genome Center of Wisconsin, University of Wisconsin, Madison, Wisconsin 53706;
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16
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Bogdanoff WA, Morgenstern D, Bern M, Ueberheide BM, Sanchez-Fauquier A, DuBois RM. De Novo Sequencing and Resurrection of a Human Astrovirus-Neutralizing Antibody. ACS Infect Dis 2016; 2:313-321. [PMID: 27213181 PMCID: PMC4869151 DOI: 10.1021/acsinfecdis.6b00026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Indexed: 11/29/2022]
Abstract
Monoclonal antibody (mAb) therapeutics targeting cancer, autoimmune diseases, inflammatory diseases, and infectious diseases are growing exponentially. Although numerous panels of mAbs targeting infectious disease agents have been developed, their progression into clinically useful mAbs is often hindered by the lack of sequence information and/or loss of hybridoma cells that produce them. Here we combine the power of crystallography and mass spectrometry to determine the amino acid sequence and glycosylation modification of the Fab fragment of a potent human astrovirus-neutralizing mAb. We used this information to engineer a recombinant antibody single-chain variable fragment that has the same specificity as the parent monoclonal antibody to bind to the astrovirus capsid protein. This antibody can now potentially be developed as a therapeutic and diagnostic agent.
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Affiliation(s)
- Walter A. Bogdanoff
- Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa
Cruz, California 95064, United States
| | - David Morgenstern
- Department of Biochemistry and Molecular
Pharmacology, New York University School of Medicine, New York, New York 10016, United States
| | - Marshall Bern
- Protein Metrics, San Carlos, California 94070, United States
| | - Beatrix M. Ueberheide
- Department of Biochemistry and Molecular
Pharmacology, New York University School of Medicine, New York, New York 10016, United States
| | - Alicia Sanchez-Fauquier
- Viral Gastroenteritis
Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Rebecca M. DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa
Cruz, California 95064, United States
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17
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Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics 2015; 31:i53-61. [PMID: 26072509 PMCID: PMC4542777 DOI: 10.1093/bioinformatics/btv238] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. AVAILABILITY AND IMPLEMENTATION IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools. CONTACT ppevzner@ucsd.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yana Safonova
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Stefano Bonissone
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Eugene Kurpilyansky
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Ekaterina Starostina
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Alla Lapidus
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Jeremy Stinson
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Laura DePalatis
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Wendy Sandoval
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Jennie Lill
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Pavel A Pevzner
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
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18
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Dasari S, Theis JD, Vrana JA, Meureta OM, Quint PS, Muppa P, Zenka RM, Tschumper RC, Jelinek DF, Davila JI, Sarangi V, Kurtin PJ, Dogan A. Proteomic detection of immunoglobulin light chain variable region peptides from amyloidosis patient biopsies. J Proteome Res 2015; 14:1957-67. [PMID: 25734799 DOI: 10.1021/acs.jproteome.5b00015] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Immunoglobulin light chain (LC) amyloidosis (AL) is caused by deposition of clonal LCs produced by an underlying plasma cell neoplasm. The clonotypic LC sequences are unique to each patient, and they cannot be reliably detected by either immunoassays or standard proteomic workflows that target the constant regions of LCs. We addressed this issue by developing a novel sequence template-based workflow to detect LC variable (LCV) region peptides directly from AL amyloid deposits. The workflow was implemented in a CAP/CLIA compliant clinical laboratory dedicated to proteomic subtyping of amyloid deposits extracted from either formalin-fixed paraffin-embedded tissues or subcutaneous fat aspirates. We evaluated the performance of the workflow on a validation cohort of 30 AL patients, whose amyloidogenic clone was identified using a novel proteogenomics method, and 30 controls. The recall and negative predictive values of the workflow, when identifying the gene family of the AL clone, were 93 and 98%, respectively. Application of the workflow on a clinical cohort of 500 AL amyloidosis samples highlighted a bias in the LCV gene families used by the AL clones. We also detected similarity between AL clones deposited in multiple organs of systemic AL patients. In summary, AL proteomic data sets are rich in LCV region peptides of potential clinical significance that are recoverable with advanced bioinformatics.
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Affiliation(s)
- Surendra Dasari
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Jason D Theis
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Julie A Vrana
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Oana M Meureta
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Patrick S Quint
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Prasuna Muppa
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Roman M Zenka
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Renee C Tschumper
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Diane F Jelinek
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Jaime I Davila
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Vivekananda Sarangi
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Paul J Kurtin
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
| | - Ahmet Dogan
- †Department of Health Sciences Research, ‡Department of Laboratory Medicine and Pathology, §Information Technology Administration, and ∥Department of Immunology and Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, United States
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19
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Bainbridge TW, DeAlmeida VI, Izrael-Tomasevic A, Chalouni C, Pan B, Goldsmith J, Schoen AP, Quiñones GA, Kelly R, Lill JR, Sandoval W, Costa M, Polakis P, Arnott D, Rubinfeld B, Ernst JA. Evolutionary divergence in the catalytic activity of the CAM-1, ROR1 and ROR2 kinase domains. PLoS One 2014; 9:e102695. [PMID: 25029443 PMCID: PMC4100928 DOI: 10.1371/journal.pone.0102695] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/23/2014] [Indexed: 12/15/2022] Open
Abstract
Receptor tyrosine kinase-like orphan receptors (ROR) 1 and 2 are atypical members of the receptor tyrosine kinase (RTK) family and have been associated with several human diseases. The vertebrate RORs contain an ATP binding domain that deviates from the consensus amino acid sequence, although the impact of this deviation on catalytic activity is not known and the kinase function of these receptors remains controversial. Recently, ROR2 was shown to signal through a Wnt responsive, β-catenin independent pathway and suppress a canonical Wnt/β-catenin signal. In this work we demonstrate that both ROR1 and ROR2 kinase domains are catalytically deficient while CAM-1, the C. elegans homolog of ROR, has an active tyrosine kinase domain, suggesting a divergence in the signaling processes of the ROR family during evolution. In addition, we show that substitution of the non-consensus residues from ROR1 or ROR2 into CAM-1 and MuSK markedly reduce kinase activity, while restoration of the consensus residues in ROR does not restore robust kinase function. We further demonstrate that the membrane-bound extracellular domain alone of either ROR1 or ROR2 is sufficient for suppression of canonical Wnt3a signaling, and that this domain can also enhance Wnt5a suppression of Wnt3a signaling. Based on these data, we conclude that human ROR1 and ROR2 are RTK-like pseudokinases.
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Affiliation(s)
- Travis W. Bainbridge
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Venita I. DeAlmeida
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - Anita Izrael-Tomasevic
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Cécile Chalouni
- Center for Advanced Light Microscopy, Genentech, Inc., South San Francisco, California, United States of America
| | - Borlan Pan
- Department of Structural Biology, Genentech, Inc., South San Francisco, California, United States of America
| | - Joshua Goldsmith
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - Alia P. Schoen
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Gabriel A. Quiñones
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Ryan Kelly
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Jennie R. Lill
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Wendy Sandoval
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Mike Costa
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - Paul Polakis
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - David Arnott
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
| | - Bonnee Rubinfeld
- Department of Cancer Targets, Genentech, Inc., South San Francisco, California, United States of America
| | - James A. Ernst
- Department of Protein Chemistry, Genentech, Inc., South San Francisco, California, United States of America
- * E-mail:
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20
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Murray D, Barnidge D. Characterization of immunoglobulin by mass spectrometry with applications for the clinical laboratory. Crit Rev Clin Lab Sci 2014; 50:91-102. [PMID: 24156651 DOI: 10.3109/10408363.2013.838206] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Studies monitoring immunoglobulin (Ig) antigen specificity have brought to light key Ig biomarkers for immunity, autoimmunity, cancer detection, and immune system function evaluation. A fundamentally new approach to the detection of Igs based on the primary structure of the Ig is beginning to emerge in the literature. This approach has only become feasible in light of advances in proteomics and rapid improvements in mass spectrometry (MS). Driven primarily by the development of Ig pharmaceuticals, Ig MS-based proteomic methods are revealing structural features which were previously unavailable with other characterization techniques. The task of adapting these techniques to clinical chemistry is in its infancy, but these methods have the potential to dramatically alter testing for Ig biomarkers. The purpose of this article is to review the advances that have been made in proteomic characterization of Igs by MS and the early attempts to apply these methods to clinical samples.
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Affiliation(s)
- David Murray
- Department of Laboratory Medicine and Pathology, Mayo Clinic , Rochester, MN , USA
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21
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Guthals A, Clauser KR, Frank AM, Bandeira N. Sequencing-grade de novo analysis of MS/MS triplets (CID/HCD/ETD) from overlapping peptides. J Proteome Res 2013; 12:2846-57. [PMID: 23679345 DOI: 10.1021/pr400173d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Full-length de novo sequencing of unknown proteins remains a challenging open problem. Traditional methods that sequence spectra individually are limited by short peptide length, incomplete peptide fragmentation, and ambiguous de novo interpretations. We address these issues by determining consensus sequences for assembled tandem mass (MS/MS) spectra from overlapping peptides (e.g., by using multiple enzymatic digests). We have combined electron-transfer dissociation (ETD) with collision-induced dissociation (CID) and higher-energy collision-induced dissociation (HCD) fragmentation methods to boost interpretation of long, highly charged peptides and take advantage of corroborating b/y/c/z ions in CID/HCD/ETD. Using these strategies, we show that triplet CID/HCD/ETD MS/MS spectra from overlapping peptides yield de novo sequences of average length 70 AA and as long as 200 AA at up to 99% sequencing accuracy.
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Affiliation(s)
- Adrian Guthals
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
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22
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Yun Lee D, Arnott D, Brown EJ. Ubiquilin4 is an adaptor protein that recruits Ubiquilin1 to the autophagy machinery. EMBO Rep 2013; 14:373-81. [PMID: 23459205 PMCID: PMC3615663 DOI: 10.1038/embor.2013.22] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 01/13/2023] Open
Abstract
Ubiquilins (Ubqlns)-a family of ubiquitin-binding proteins-are involved in several protein degradation pathways and have been implicated in various neurodegenerative diseases. Ubqln1 regulates autophagosome maturation during autophagy-mediated degradation. We now show that Ubqln4 mediates the interaction between Ubqln1 and the autophagy machinery by recruiting Ubqln1 to LC3. This targeting of Ubqln1 to autophagosomes requires the Ubqln4 UBL domain and the Ubqln1 UBA domain. This study identifies a new role for Ubqln4, expanding the role for Ubqlns in protein degradation.
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Affiliation(s)
- Dong Yun Lee
- Department of Infectious Disease, South San Francisco, California 94080, USA
| | - David Arnott
- Department of Protein Chemistry, Genentech Inc., South San Francisco, California 94080, USA
| | - Eric J Brown
- Department of Infectious Disease, South San Francisco, California 94080, USA
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23
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Guthals A, Watrous JD, Dorrestein PC, Bandeira N. The spectral networks paradigm in high throughput mass spectrometry. MOLECULAR BIOSYSTEMS 2013; 8:2535-44. [PMID: 22610447 DOI: 10.1039/c2mb25085c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
High-throughput proteomics is made possible by a combination of modern mass spectrometry instruments capable of generating many millions of tandem mass (MS(2)) spectra on a daily basis and the increasingly sophisticated associated software for their automated identification. Despite the growing accumulation of collections of identified spectra and the regular generation of MS(2) data from related peptides, the mainstream approach for peptide identification is still the nearly two decades old approach of matching one MS(2) spectrum at a time against a database of protein sequences. Moreover, database search tools overwhelmingly continue to require that users guess in advance a small set of 4-6 post-translational modifications that may be present in their data in order to avoid incurring substantial false positive and negative rates. The spectral networks paradigm for analysis of MS(2) spectra differs from the mainstream database search paradigm in three fundamental ways. First, spectral networks are based on matching spectra against other spectra instead of against protein sequences. Second, spectral networks find spectra from related peptides even before considering their possible identifications. Third, spectral networks determine consensus identifications from sets of spectra from related peptides instead of separately attempting to identify one spectrum at a time. Even though spectral networks algorithms are still in their infancy, they have already delivered the longest and most accurate de novo sequences to date, revealed a new route for the discovery of unexpected post-translational modifications and highly-modified peptides, enabled automated sequencing of cyclic non-ribosomal peptides with unknown amino acids and are now defining a novel approach for mapping the entire molecular output of biological systems that is suitable for analysis with tandem mass spectrometry. Here we review the current state of spectral networks algorithms and discuss possible future directions for automated interpretation of spectra from any class of molecules.
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Affiliation(s)
- Adrian Guthals
- Dept. Computer Science and Engineering, University of California, San Diego, USA
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24
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Phosphorylation of NLRC4 is critical for inflammasome activation. Nature 2012; 490:539-42. [PMID: 22885697 DOI: 10.1038/nature11429] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 07/24/2012] [Indexed: 01/04/2023]
Abstract
NLRC4 is a cytosolic member of the NOD-like receptor family that is expressed in innate immune cells. It senses indirectly bacterial flagellin and type III secretion systems, and responds by assembling an inflammasome complex that promotes caspase-1 activation and pyroptosis. Here we use knock-in mice expressing NLRC4 with a carboxy-terminal 3×Flag tag to identify phosphorylation of NLRC4 on a single, evolutionarily conserved residue, Ser 533, following infection of macrophages with Salmonella enterica serovar Typhimurium (also known as Salmonella typhimurium). Western blotting with a NLRC4 phospho-Ser 533 antibody confirmed that this post-translational modification occurs only in the presence of stimuli known to engage NLRC4 and not the related protein NLRP3 or AIM2. Nlrc4(-/-) macrophages reconstituted with NLRC4 mutant S533A, unlike those reconstituted with wild-type NLRC4, did not activate caspase-1 and pyroptosis in response to S. typhimurium, indicating that S533 phosphorylation is critical for NLRC4 inflammasome function. Conversely, phosphomimetic NLRC4 S533D caused rapid macrophage pyroptosis without infection. Biochemical purification of the NLRC4-phosphorylating activity and a screen of kinase inhibitors identified PRKCD (PKCδ) as a candidate NLRC4 kinase. Recombinant PKCδ phosphorylated NLRC4 S533 in vitro, immunodepletion of PKCδ from macrophage lysates blocked NLRC4 S533 phosphorylation in vitro, and Prkcd(-/-) macrophages exhibited greatly attenuated caspase-1 activation and IL-1β secretion specifically in response to S. typhimurium. Phosphorylation-defective NLRC4 S533A failed to recruit procaspase-1 and did not assemble inflammasome specks during S. typhimurium infection, so phosphorylation of NLRC4 S533 probably drives conformational changes necessary for NLRC4 inflammasome activity and host innate immunity.
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25
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A proteomics approach for the identification and cloning of monoclonal antibodies from serum. Nat Biotechnol 2012; 30:447-52. [DOI: 10.1038/nbt.2167] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/21/2012] [Indexed: 11/09/2022]
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Chiang EY, Kolumam G, McCutcheon KM, Young J, Lin Z, Balazs M, Grogan JL. In vivo depletion of lymphotoxin-alpha expressing lymphocytes inhibits xenogeneic graft-versus-host-disease. PLoS One 2012; 7:e33106. [PMID: 22427961 PMCID: PMC3299734 DOI: 10.1371/journal.pone.0033106] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/03/2012] [Indexed: 12/23/2022] Open
Abstract
Graft-versus-host disease (GVHD) is a major barrier to successful allogeneic hematopoietic cell transplantation and is largely mediated by activated donor lymphocytes. Lymphotoxin (LT)-α is expressed by subsets of activated T and B cells, and studies in preclinical models demonstrated that targeted depletion of these cells with a mouse anti-LT-α monoclonal antibody (mAb) was efficacious in inhibiting inflammation and autoimmune disease. Here we demonstrate that LT-α is also upregulated on activated human donor lymphocytes in a xenogeneic model of GVHD and targeted depletion of these donor cells ameliorated GVHD. A depleting humanized anti-LT-α mAb, designated MLTA3698A, was generated that specifically binds to LT-α in both the soluble and membrane-bound forms, and elicits antibody-dependent cellular cytotoxicity (ADCC) activity in vitro. Using a human peripheral blood mononuclear cell transplanted SCID (Hu-SCID) mouse model of GVHD, the anti-human LT-α mAb specifically depleted activated LT-expressing human donor T and B cells, resulting in prolonged survival of the mice. A mutation in the Fc region, rendering the mAb incapable of mediating ADCC, abolished all in vitro and in vivo effects. These data support a role for using a depleting anti-LT-α antibody in treating immune diseases such as GVHD and autoimmune diseases.
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Affiliation(s)
- Eugene Y. Chiang
- Department of Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Ganesh Kolumam
- Department of Tumor Biology and Angiogenesis, Genentech Inc., South San Francisco, California, United States of America
| | - Krista M. McCutcheon
- Department of Antibody Engineering, Genentech Inc., South San Francisco, California, United States of America
| | - Judy Young
- Department of Assay and Automation Technology, Genentech Inc., South San Francisco, California, United States of America
| | - Zhonghua Lin
- Department of Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Mercedesz Balazs
- Department of Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Jane L. Grogan
- Department of Immunology, Genentech Inc., South San Francisco, California, United States of America
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