1
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Neagu AN, Josan CL, Jayaweera TM, Morrissiey H, Johnson KR, Darie CC. Bio-Pathological Functions of Posttranslational Modifications of Histological Biomarkers in Breast Cancer. Molecules 2024; 29:4156. [PMID: 39275004 PMCID: PMC11397409 DOI: 10.3390/molecules29174156] [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: 08/12/2024] [Revised: 08/23/2024] [Accepted: 08/29/2024] [Indexed: 09/16/2024] Open
Abstract
Proteins are the most common types of biomarkers used in breast cancer (BC) theranostics and management. By definition, a biomarker must be a relevant, objective, stable, and quantifiable biomolecule or other parameter, but proteins are known to exhibit the most variate and profound structural and functional variation. Thus, the proteome is highly dynamic and permanently reshaped and readapted, according to changing microenvironments, to maintain the local cell and tissue homeostasis. It is known that protein posttranslational modifications (PTMs) can affect all aspects of protein function. In this review, we focused our analysis on the different types of PTMs of histological biomarkers in BC. Thus, we analyzed the most common PTMs, including phosphorylation, acetylation, methylation, ubiquitination, SUMOylation, neddylation, palmitoylation, myristoylation, and glycosylation/sialylation/fucosylation of transcription factors, proliferation marker Ki-67, plasma membrane proteins, and histone modifications. Most of these PTMs occur in the presence of cellular stress. We emphasized that these PTMs interfere with these biomarkers maintenance, turnover and lifespan, nuclear or subcellular localization, structure and function, stabilization or inactivation, initiation or silencing of genomic and non-genomic pathways, including transcriptional activities or signaling pathways, mitosis, proteostasis, cell-cell and cell-extracellular matrix (ECM) interactions, membrane trafficking, and PPIs. Moreover, PTMs of these biomarkers orchestrate all hallmark pathways that are dysregulated in BC, playing both pro- and/or antitumoral and context-specific roles in DNA damage, repair and genomic stability, inactivation/activation of tumor-suppressor genes and oncogenes, phenotypic plasticity, epigenetic regulation of gene expression and non-mutational reprogramming, proliferative signaling, endocytosis, cell death, dysregulated TME, invasion and metastasis, including epithelial-mesenchymal/mesenchymal-epithelial transition (EMT/MET), and resistance to therapy or reversal of multidrug therapy resistance. PTMs occur in the nucleus but also at the plasma membrane and cytoplasmic level and induce biomarker translocation with opposite effects. Analysis of protein PTMs allows for the discovery and validation of new biomarkers in BC, mainly for early diagnosis, like extracellular vesicle glycosylation, which may be considered as a potential source of circulating cancer biomarkers.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iași, Carol I bvd. 20A, 700505 Iasi, Romania
| | - Claudiu-Laurentiu Josan
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iași, Carol I bvd. 20A, 700505 Iasi, Romania
| | - Taniya M Jayaweera
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Kaya R Johnson
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA
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2
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Zhao X, Hu Y, Zhao J, Liu Y, Ma X, Chen H, Xing Y. Role of protein Post-translational modifications in enterovirus infection. Front Microbiol 2024; 15:1341599. [PMID: 38596371 PMCID: PMC11002909 DOI: 10.3389/fmicb.2024.1341599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/18/2024] [Indexed: 04/11/2024] Open
Abstract
Enteroviruses (EVs) are the main cause of a number of neurological diseases. Growing evidence has revealed that successful infection with enteroviruses is highly dependent on the host machinery, therefore, host proteins play a pivotal role in viral infections. Both host and viral proteins can undergo post-translational modification (PTM) which can regulate protein activity, stability, solubility and interactions with other proteins; thereby influencing various biological processes, including cell metabolism, metabolic, signaling pathways, cell death, and cancer development. During viral infection, both host and viral proteins regulate the viral life cycle through various PTMs and different mechanisms, including the regulation of host cell entry, viral protein synthesis, genome replication, and the antiviral immune response. Therefore, protein PTMs play important roles in EV infections. Here, we review the role of various host- and virus-associated PTMs during enterovirus infection.
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Affiliation(s)
- Xiaohui Zhao
- Department of Pathogen Biology, School of Medicine, Qinghai University, Qinghai, China
| | - Yibo Hu
- Department of Orthopaedic Trauma, The Affiliated Hospital of Qinghai University, Qinghai, China
| | - Jun Zhao
- Department of Pathogen Biology, School of Medicine, Qinghai University, Qinghai, China
| | - Yan Liu
- Department of Immunology, School of Medicine, Qinghai, China
| | - Xueman Ma
- Department of Traditional Chinese Medicine, School of Medicine, Qinghai University, Qinghai, China
| | - Hongru Chen
- Department of Public Health, School of Medicine, Qinghai University, Qinghai, China
| | - Yonghua Xing
- Department of Genetics, School of Medicine, Qinghai University, Qinghai, China
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3
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Liang M, Ran F, Li L, Hang H, An L. In vitro evolution of diagnostic antibodies targeting native antigens in plasma by sandwich flow cytometry. Biotechnol J 2024; 19:e2300492. [PMID: 38403438 DOI: 10.1002/biot.202300492] [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: 09/17/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 02/27/2024]
Abstract
Monoclonal antibodies (mAbs) that recognize and bind to specific antigens (Ags) have a wide range of applications in research, therapy, and diagnostics. However, many of these antibodies cannot bind well to the native Ags. In this study, based on the Chinese hamster ovary (CHO) cell display platform developed previously in our lab, we reported a novel artificial evolution procedure to improve the affinity of mAb against the native Ag directly using the plasma samples without purification of the native Ag. In this procedure, a pair of antibodies able to bind the Ag in sandwich manner are first confirmed (Ab1/Ab2) and the antibody (Ab) to be affinity-improved (Ab1) is displayed on CHO cells for Ab mutation. Then the cells were detected and sorted with flow cytometry in the form of Ab1-Ag-fluorescence labeled Ab2, which we named sandwich flow cytometry. Here, we used soluble isoform of suppression of tumorigenicity 2 (sST2) protein as model Ag, carried out "sandwich" maturation directly using the plasma samples containing the native sST2 protein and optimized a pair of antibodies with significantly improved sensitivity in the detection of the native sST2 in plasma. This method could be very useful in optimization of the diagnostic Ab pairs working in a "sandwich" manner if more antibodies were also successfully affinity-matured with this method.
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Affiliation(s)
- Mingxia Liang
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, Beijing, China
- University of Chinese Academy of Sciences, Beijing, Beijing, China
| | - Fanlei Ran
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, Beijing, China
- University of Chinese Academy of Sciences, Beijing, Beijing, China
| | - Li Li
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Haiying Hang
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, Beijing, China
- University of Chinese Academy of Sciences, Beijing, Beijing, China
| | - Lili An
- Key Laboratory of Protein and Peptide Drugs, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, Beijing, China
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4
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van der Zon AAM, Verduin J, van den Hurk RS, Gargano AFG, Pirok BWJ. Sample transformation in online separations: how chemical conversion advances analytical technology. Chem Commun (Camb) 2023; 60:36-50. [PMID: 38053451 PMCID: PMC10729587 DOI: 10.1039/d3cc03599a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023]
Abstract
While the advent of modern analytical technology has allowed scientists to determine the complexity of mixtures, it also spurred the demand to understand these sophisticated mixtures better. Chemical transformation can be used to provide insights into properties of complex samples such as degradation pathways or molecular heterogeneity that are otherwise unaccessible. In this article, we explore how sample transformation is exploited across different application fields to empower analytical methods. Transformation mechanisms include molecular-weight reduction, controlled degradation, and derivatization. Both offline and online transformation methods have been explored. The covered studies show that sample transformation facilitates faster reactions (e.g. several hours to minutes), reduces sample complexity, unlocks new sample dimensions (e.g. functional groups), provides correlations between multiple sample dimensions, and improves detectability. The article highlights the state-of-the-art and future prospects, focusing in particular on the characterization of protein and nucleic-acid therapeutics, nanoparticles, synthetic polymers, and small molecules.
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Affiliation(s)
- Annika A M van der Zon
- University of Amsterdam, van't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Joshka Verduin
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Vrije Universiteit Amsterdam, Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Rick S van den Hurk
- University of Amsterdam, van't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Andrea F G Gargano
- University of Amsterdam, van't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bob W J Pirok
- University of Amsterdam, van't Hoff Institute for Molecular Sciences, Analytical Chemistry Group, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Centre of Analytical Sciences Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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5
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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6
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Mendez Q, Driscoll HA, Mirando GR, Acca F, Chapados CD, Jones KS, Weiner M, Li X, Ferguson MR. MILKSHAKE Western blot and Sundae ELISA: We all scream for better antibody validation. J Immunol Methods 2023; 521:113540. [PMID: 37597727 PMCID: PMC10568614 DOI: 10.1016/j.jim.2023.113540] [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: 06/28/2023] [Revised: 08/15/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Knowing that an antibody's sensitivity and specificity is accurate is crucial for reliable data collection. This certainty is especially difficult to achieve for antibodies (Abs) which bind post-translationally modified proteins. Here we describe two validation methods using surrogate proteins in western blot and ELISA. The first method, which we termed "MILKSHAKE" is a modified maltose binding protein, hence the name, that is enzymatically conjugated to a peptide from the chosen target which is either modified or non-modified at the residue of interest. The surety of the residue's modification status can be used to confirm Ab specificity to the target's post-translational modification (PTM). The second method uses a set of surrogate proteins, which we termed "Sundae". Sundae consists of a set of modified maltose binding proteins with a genetically encoded target sequence, each of which contains a single amino acid substitution at one position of interest. With Sundae, Abs can be evaluated for binding specificities to all twenty amino acids at a single position. Combining MILKSHAKE and Sundae methods, Ab specificity can be determined at a single-residue resolution. These data improve evaluation of commercially available Abs and identify off-target effects for Research-Use-Only and therapeutic Abs.
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Affiliation(s)
- Qiana Mendez
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Holland A Driscoll
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Gregory R Mirando
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Felicity Acca
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Cassandra D Chapados
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Kezzia S Jones
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Michael Weiner
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Xiaofeng Li
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
| | - Mary R Ferguson
- Department of Molecular Sciences, Abbratech, 25 Business Park Drive Branford, CT, USA.
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7
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Yang M, Unsihuay D, Hu H, Meke FN, Qu Z, Zhang ZY, Laskin J. Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. Anal Chem 2023; 95:5214-5222. [PMID: 36917636 PMCID: PMC11330692 DOI: 10.1021/acs.analchem.2c04795] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool for label-free mapping of the spatial distribution of proteins in biological tissues. We have previously demonstrated imaging of individual proteoforms in biological tissues using nanospray desorption electrospray ionization (nano-DESI), an ambient liquid extraction-based MSI technique. Nano-DESI MSI generates multiply charged protein ions, which is advantageous for their identification using top-down proteomics analysis. In this study, we demonstrate proteoform mapping in biological tissues with a spatial resolution down to 7 μm using nano-DESI MSI. A substantial decrease in protein signals observed in high-spatial-resolution MSI makes these experiments challenging. We have enhanced the sensitivity of nano-DESI MSI experiments by optimizing the design of the capillary-based probe and the thickness of the tissue section. In addition, we demonstrate that oversampling may be used to further improve spatial resolution at little or no expense to sensitivity. These developments represent a new step in MSI-based spatial proteomics, which complements targeted imaging modalities widely used for studying biological systems.
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Affiliation(s)
- Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Daisy Unsihuay
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Hang Hu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Frederick Nguele Meke
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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8
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Antonarelli G, Pieri V, Porta FM, Fusco N, Finocchiaro G, Curigliano G, Criscitiello C. Targeting Post-Translational Modifications to Improve Combinatorial Therapies in Breast Cancer: The Role of Fucosylation. Cells 2023; 12:cells12060840. [PMID: 36980181 PMCID: PMC10047715 DOI: 10.3390/cells12060840] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/03/2023] [Accepted: 03/05/2023] [Indexed: 03/30/2023] Open
Abstract
Various tumors rely on post-translational modifications (PTMs) to promote invasiveness and angiogenesis and to reprogram cellular energetics to abate anti-cancer immunity. Among PTMs, fucosylation is a particular type of glycosylation that has been linked to different aspects of immune and hormonal physiological functions as well as hijacked by many types of tumors. Multiple tumors, including breast cancer, have been linked to dismal prognoses and increased metastatic potential due to fucosylation of the glycan core, namely core-fucosylation. Pre-clinical studies have examined the molecular mechanisms regulating core-fucosylation in breast cancer models, its negative prognostic value across multiple disease stages, and the activity of in vivo pharmacological inhibition, instructing combinatorial therapies and translation into clinical practice. Throughout this review, we describe the role of fucosylation in solid tumors, with a particular focus on breast cancer, as well as physiologic conditions on the immune system and hormones, providing a view into its potential as a biomarker for predicating or predicting cancer outcomes, as well as a potential clinical actionability as a biomarker.
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Affiliation(s)
- Gabriele Antonarelli
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology (DIPO), University of Milan, 20122 Milan, Italy
| | - Valentina Pieri
- Neural Stem Cell Biology Unit, Division of Neuroscience, IRCCS San Raffaele Hospital, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesca Maria Porta
- Division of Pathology, European Institute of Oncology (IEO), IRCCS, 20141 Milan, Italy
- School of Pathology, University of Milan, 20122 Milan, Italy
| | - Nicola Fusco
- Department of Oncology and Hemato-Oncology (DIPO), University of Milan, 20122 Milan, Italy
- Division of Pathology, European Institute of Oncology (IEO), IRCCS, 20141 Milan, Italy
| | | | - Giuseppe Curigliano
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology (DIPO), University of Milan, 20122 Milan, Italy
| | - Carmen Criscitiello
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology (DIPO), University of Milan, 20122 Milan, Italy
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9
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Waury K, Willemse EAJ, Vanmechelen E, Zetterberg H, Teunissen CE, Abeln S. Bioinformatics tools and data resources for assay development of fluid protein biomarkers. Biomark Res 2022; 10:83. [DOI: 10.1186/s40364-022-00425-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
AbstractFluid protein biomarkers are important tools in clinical research and health care to support diagnosis and to monitor patients. Especially within the field of dementia, novel biomarkers could address the current challenges of providing an early diagnosis and of selecting trial participants. While the great potential of fluid biomarkers is recognized, their implementation in routine clinical use has been slow. One major obstacle is the often unsuccessful translation of biomarker candidates from explorative high-throughput techniques to sensitive antibody-based immunoassays. In this review, we propose the incorporation of bioinformatics into the workflow of novel immunoassay development to overcome this bottleneck and thus facilitate the development of novel biomarkers towards clinical laboratory practice. Due to the rapid progress within the field of bioinformatics many freely available and easy-to-use tools and data resources exist which can aid the researcher at various stages. Current prediction methods and databases can support the selection of suitable biomarker candidates, as well as the choice of appropriate commercial affinity reagents. Additionally, we examine methods that can determine or predict the epitope - an antibody’s binding region on its antigen - and can help to make an informed choice on the immunogenic peptide used for novel antibody production. Selected use cases for biomarker candidates help illustrate the application and interpretation of the introduced tools.
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10
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Mann G, Sulkshane P, Sadhu P, Ziv T, Glickman MH, Brik A. Antibody for Serine 65 Phosphorylated Ubiquitin Identifies PLK1-Mediated Phosphorylation of Mitotic Proteins and APC1. Molecules 2022; 27:molecules27154867. [PMID: 35956818 PMCID: PMC9369648 DOI: 10.3390/molecules27154867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022] Open
Abstract
Deciphering the protein posttranslational modification (PTM) code is one of the greatest biochemical challenges of our time. Phosphorylation and ubiquitylation are key PTMs that dictate protein function, recognition, sub-cellular localization, stability, turnover and fate. Hence, failures in their regulation leads to various disease. Chemical protein synthesis allows preparation of ubiquitinated and phosphorylated proteins to study their biochemical properties in great detail. However, monitoring these modifications in intact cells or in cell extracts mostly depends on antibodies, which often have off-target binding. Here, we report that the most widely used antibody for ubiquitin (Ub) phosphorylated at serine 65 (pUb) has significant off-targets that appear during mitosis. These off-targets are connected to polo-like kinase 1 (PLK1) mediated phosphorylation of cell cycle-related proteins and the anaphase promoting complex subunit 1 (APC1).
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Affiliation(s)
- Guy Mann
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000, Israel; (G.M.); (P.S.)
| | - Prasad Sulkshane
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel;
| | - Pradeep Sadhu
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000, Israel; (G.M.); (P.S.)
| | - Tamar Ziv
- The Smoler Protein Research Center, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion Israel Institute of Technology, Haifa 32000, Israel;
| | - Michael H. Glickman
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa 32000, Israel;
- Correspondence: (M.H.G.); (A.B.)
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000, Israel; (G.M.); (P.S.)
- Correspondence: (M.H.G.); (A.B.)
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11
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Tyrosine O-sulfation proteoforms affect HIV-1 monoclonal antibody potency. Sci Rep 2022; 12:8433. [PMID: 35589938 PMCID: PMC9120178 DOI: 10.1038/s41598-022-12423-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/05/2022] [Indexed: 11/08/2022] Open
Abstract
CAP256V2LS, a broadly neutralizing monoclonal antibody (bNAb), is being pursued as a promising drug for HIV-1 prevention. The total level of tyrosine-O-sulfation, a post-translational modification, was known to play a key role for antibody biological activity. More importantly, here wedescribe for the first time the significance of the tyrosine-O-sulfation proteoforms. We developed a hydrophobic interaction chromatography (HIC) method to separate and quantify different sulfation proteoforms, which led to the direct functionality assessment of tyrosine-sulfated species. The fully sulfated (4-SO3) proteoform demonstrated the highest in vitro relative antigen binding potency and neutralization efficiency against a panel of HIV-1 viruses. Interestingly, highly variable levels of 4-SO3 were produced by different clonal CHO cell lines, which helped the bNAb process development towards production of a highly potent CAP256V2LS clinical product with high 4-SO3 proteoform. This study presents powerful insight for any biotherapeutic protein development where sulfation may play an important role in product efficacy.
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12
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Suraritdechachai S, Lakkanasirorat B, Uttamapinant C. Molecular probes for cellular imaging of post-translational proteoforms. RSC Chem Biol 2022; 3:201-219. [PMID: 35360891 PMCID: PMC8826509 DOI: 10.1039/d1cb00190f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.
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Affiliation(s)
- Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Benya Lakkanasirorat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
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13
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Hermann J, Schurgers L, Jankowski V. Identification and characterization of post-translational modifications: Clinical implications. Mol Aspects Med 2022; 86:101066. [PMID: 35033366 DOI: 10.1016/j.mam.2022.101066] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
Post-translational modifications (PTMs) generate marginally modified isoforms of native peptides, proteins and lipoproteins thereby regulating protein functions, molecular interactions, and localization. With a key role in functional proteomics, post-translational modifications are recently also associated with the onsets and progressions of various diseases, such as cancer, cardiovascular, renal, and metabolic diseases. With the impact of post-translational modifications becoming increasingly clear, its reliable detection and quantification remain a major obstacle in the translation of these novel pathological markers into clinical diagnosis. While current antibody-based clinical diagnostics struggle to detect and quantify these marginal protein and lipoprotein alterations, state-of-the-art mass spectrometric, proteomic approaches provide the mass accuracy and resolving power necessary to isolate, identify and quantify novel and pathological post-translational modifications; however clinical translation of mass spectrometric applications are still facing major challenges. Here we review the status quo of the clinical translation of mass-spectrometric applications as novel diagnostic tools for the identification and quantification of post-translational modifications and focus on the emerging role of mass spectrometric methods in the clinical assessment of PTMs in disease states.
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Affiliation(s)
- Juliane Hermann
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Leon Schurgers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6200, MD, Maastricht, the Netherlands
| | - Vera Jankowski
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074, Aachen, Germany.
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14
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Hershman RL, Li Y, Ma F, Xu Q, Van Deventer J. Intracellular Delivery of Antibodies for Selective Cell Signaling Interference. ChemMedChem 2021; 17:e202100678. [PMID: 34890114 DOI: 10.1002/cmdc.202100678] [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: 10/25/2021] [Indexed: 11/11/2022]
Abstract
Many intracellular signaling events remain poorly characterized due to a general lack of tools to interfere with "undruggable" targets. Antibodies have the potential to elucidate intracellular mechanisms via targeted disruption of cell signaling cascades because of their ability to bind to a target with high specificity and affinity. However, due to their size and chemical composition, antibodies cannot innately cross the cell membrane, and thus access to the cytosol with these macromolecules has been limited. Here, we describe strategies for accessing the intracellular space with recombinant antibodies mediated by cationic lipid nanoparticles to selectively disrupt intracellular signaling events. Together, our results demonstrate the use of recombinantly produced antibodies, delivered at concentrations of 10 nM, to selectively interfere with signaling driven by a single posttranslational modification. Efficient intracellular delivery of engineered antibodies opens up possibilities for modulation of previously "undruggable" targets, including for potential therapeutic applications.
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Affiliation(s)
| | - Yamin Li
- Tufts University, Biomedical Engineering, UNITED STATES
| | - Feihe Ma
- Tufts University, Biomedical Engineering, UNITED STATES
| | - Qioabing Xu
- Tufts University, Biomedical Engineering, UNITED STATES
| | - James Van Deventer
- Tufts University, Chemical and Biological Engineering, 4 Colby St. Room 148, 02155, Medford, UNITED STATES
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15
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Shen C, Zhang Z, Tian Y, Li F, Zhou L, Jiang W, Yang L, Zhang B, Wang L, Zhang Y. Sulforaphane enhances the antitumor response of chimeric antigen receptor T cells by regulating PD-1/PD-L1 pathway. BMC Med 2021; 19:283. [PMID: 34819055 PMCID: PMC8614004 DOI: 10.1186/s12916-021-02161-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/13/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Chimeric antigen receptor T (CAR-T) cell therapy has limited effects in the treatment of solid tumors. Sulforaphane (SFN) is known to play an important role in inhibiting tumor growth, but its effect on CAR-T cells remains unclear. The goal of the current study was to determine whether combined CAR-T cells and SFN could provide antitumor efficacy against solid tumors. METHODS The effect of combined SFN and CAR-T cells was determined in vitro using a co-culture system and in vivo using a xenograft mouse model. We further validated the effects of combination therapy in patients with cancer. RESULTS In vitro, the combination of SFN and CAR-T cells resulted in enhanced cytotoxicity and increased lysis of tumor cells. We found that SFN suppressed programmed cell death 1 (PD-1) expression in CAR-T cells and potentiated antitumor functions in vitro and in vivo. As a ligand of PD-1, programmed cell death ligand 1 (PD-L1) expression was also decreased in tumor cells after SFN treatment. In addition, β-TrCP was increased by SFN, resulting in higher activation of ubiquitination-mediated proteolysis of PD-L1, which induced PD-L1 degradation. The combination of SFN and CAR-T cell therapy acted synergistically to promote better immune responses in vivo compared with monotherapy. In clinical treatments, PD-1 expression was lower, and proinflammatory cytokine levels were higher in patients with various cancers who received CAR-T cells and took SFN orally than that in the control group. CONCLUSION SFN improves the cytotoxicity of CAR-T cells by modulating the PD-1/PD-L1 pathway, which may provide a promising strategy for the combination of SFN with CAR-T cells for cancer immunotherapy.
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Affiliation(s)
- Chunyi Shen
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Zhen Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Yonggui Tian
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Feng Li
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Lingxiao Zhou
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Wenyi Jiang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Li Yang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China
| | - Bin Zhang
- Robert H. Lurie Comprehensive Cancer Center, Department of Medicine-Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Liping Wang
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China.
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China. .,Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East Road, Zhengzhou, 450052, Henan, China. .,School of Life Sciences, Zhengzhou University, Zhengzhou, China. .,Henan Key Laboratory for Tumor Immunology and Biotherapy, Zhengzhou, China. .,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China.
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16
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Vimer S, Ben-Nissan G, Marty M, Fleishman SJ, Sharon M. Direct-MS analysis of antibody-antigen complexes. Proteomics 2021; 21:e2000300. [PMID: 34310051 PMCID: PMC8595693 DOI: 10.1002/pmic.202000300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/04/2021] [Accepted: 07/15/2021] [Indexed: 11/05/2022]
Abstract
In recent decades, antibodies (Abs) have attracted the attention of academia and the biopharmaceutical industry due to their therapeutic properties and versatility in binding a vast spectrum of antigens. Different engineering strategies have been developed for optimizing Ab specificity, efficacy, affinity, stability and production, enabling systematic screening and analysis procedures for selecting lead candidates. This quality assessment is critical but usually demands time-consuming and labor-intensive purification procedures. Here, we harnessed the direct-mass spectrometry (direct-MS) approach, in which the analysis is carried out directly from the crude growth media, for the rapid, structural characterization of designed Abs. We demonstrate that properties such as stability, specificity and interactions with antigens can be defined, without the need for prior purification.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Marty
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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17
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The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins. Biochem J 2021; 478:3575-3596. [PMID: 34624072 DOI: 10.1042/bcj20210533] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 01/12/2023]
Abstract
Histidine phosphorylation is an important and ubiquitous post-translational modification. Histidine undergoes phosphorylation on either of the nitrogens in its imidazole side chain, giving rise to 1- and 3- phosphohistidine (pHis) isomers, each having a phosphoramidate linkage that is labile at high temperatures and low pH, in contrast with stable phosphomonoester protein modifications. While all organisms routinely use pHis as an enzyme intermediate, prokaryotes, lower eukaryotes and plants also use it for signal transduction. However, research to uncover additional roles for pHis in higher eukaryotes is still at a nascent stage. Since the discovery of pHis in 1962, progress in this field has been relatively slow, in part due to a lack of the tools and techniques necessary to study this labile modification. However, in the past ten years the development of phosphoproteomic techniques to detect phosphohistidine (pHis), and methods to synthesize stable pHis analogues, which enabled the development of anti-phosphohistidine (pHis) antibodies, have accelerated our understanding. Recent studies that employed anti-pHis antibodies and other advanced techniques have contributed to a rapid expansion in our knowledge of histidine phosphorylation. In this review, we examine the varied roles of pHis-containing proteins from a chemical and structural perspective, and present an overview of recent developments in pHis proteomics and antibody development.
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18
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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19
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Bonfiglio JJ, Leidecker O, Dauben H, Longarini EJ, Colby T, San Segundo-Acosta P, Perez KA, Matic I. An HPF1/PARP1-Based Chemical Biology Strategy for Exploring ADP-Ribosylation. Cell 2021; 183:1086-1102.e23. [PMID: 33186521 DOI: 10.1016/j.cell.2020.09.055] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/27/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022]
Abstract
Strategies for installing authentic ADP-ribosylation (ADPr) at desired positions are fundamental for creating the tools needed to explore this elusive post-translational modification (PTM) in essential cellular processes. Here, we describe a phospho-guided chemoenzymatic approach based on the Ser-ADPr writer complex for rapid, scalable preparation of a panel of pure, precisely modified peptides. Integrating this methodology with phage display technology, we have developed site-specific as well as broad-specificity antibodies to mono-ADPr. These recombinant antibodies have been selected and characterized using multiple ADP-ribosylated peptides and tested by immunoblotting and immunofluorescence for their ability to detect physiological ADPr events. Mono-ADPr proteomics and poly-to-mono comparisons at the modification site level have revealed the prevalence of mono-ADPr upon DNA damage and illustrated its dependence on PARG and ARH3. These and future tools created on our versatile chemical biology-recombinant antibody platform have broad potential to elucidate ADPr signaling pathways in health and disease.
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Affiliation(s)
- Juan José Bonfiglio
- Research Group of Proteomics and ADP-ribosylation Signaling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Orsolya Leidecker
- Research Group of Proteomics and ADP-ribosylation Signaling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Helen Dauben
- Research Group of Proteomics and ADP-ribosylation Signaling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Edoardo José Longarini
- Research Group of Proteomics and ADP-ribosylation Signaling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Thomas Colby
- Research Group of Proteomics and ADP-ribosylation Signaling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Pablo San Segundo-Acosta
- Research Group of Proteomics and ADP-ribosylation Signaling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Kathryn A Perez
- Protein Expression and Purification Core Facility, EMBL Heidelberg, 69126 Heidelberg, Germany
| | - Ivan Matic
- Research Group of Proteomics and ADP-ribosylation Signaling, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany.
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20
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A Novel Mouse Monoclonal Antibody C42 against C-Terminal Peptide of Alpha-1-Antitrypsin. Int J Mol Sci 2021; 22:ijms22042141. [PMID: 33670003 PMCID: PMC7926790 DOI: 10.3390/ijms22042141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/17/2022] Open
Abstract
The C-terminal-fragments of alpha1-antitrypsin (AAT) have been identified and their diverse biological roles have been reported in vitro and in vivo. These findings prompted us to develop a monoclonal antibody that specifically recognizes C-36 peptide (corresponding to residues 359–394) resulting from the protease-associated cleavage of AAT. The C-36-targeting mouse monoclonal Immunoglobulin M (IgM) antibody (containing κ light chains, clone C42) was generated and enzyme-linked immunosorbent assay (ELISA)-tested by Davids Biotechnologie GmbH, Germany. Here, we addressed the effectiveness of the novel C42 antibody in different immunoassay formats, such as dot- and Western blotting, confocal laser microscopy, and flow cytometry. According to the dot-blot results, our novel C42 antibody detects the C-36 peptide at a range of 0.1–0.05 µg and shows no cross-reactivity with native, polymerized, or oxidized forms of full-length AAT, the AAT-elastase complex mixture, as well as with shorter C-terminal fragments of AAT. However, the C42 antibody does not detect denatured peptide in SDS-PAGE/Western blotting assays. On the other hand, our C42 antibody, unconjugated as well as conjugated to DyLight488 fluorophore, when applied for immunofluorescence microscopy and flow cytometry assays, specifically detected the C-36 peptide in human blood cells. Altogether, we demonstrate that our novel C42 antibody successfully recognizes the C-36 peptide of AAT in a number of immunoassays and has potential to become an important tool in AAT-related studies.
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21
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Combinations of histone post-translational modifications. Biochem J 2021; 478:511-532. [DOI: 10.1042/bcj20200170] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
Abstract
Histones are essential proteins that package the eukaryotic genome into its physiological state of nucleosomes, chromatin, and chromosomes. Post-translational modifications (PTMs) of histones are crucial to both the dynamic and persistent regulation of the genome. Histone PTMs store and convey complex signals about the state of the genome. This is often achieved by multiple variable PTM sites, occupied or unoccupied, on the same histone molecule or nucleosome functioning in concert. These mechanisms are supported by the structures of ‘readers’ that transduce the signal from the presence or absence of PTMs in specific cellular contexts. We provide background on PTMs and their complexes, review the known combinatorial function of PTMs, and assess the value and limitations of common approaches to measure combinatorial PTMs. This review serves as both a reference and a path forward to investigate combinatorial PTM functions, discover new synergies, and gather additional evidence supporting that combinations of histone PTMs are the central currency of chromatin-mediated regulation of the genome.
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22
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Misincorporation Proteomics Technologies: A Review. Proteomes 2021; 9:proteomes9010002. [PMID: 33494504 PMCID: PMC7924376 DOI: 10.3390/proteomes9010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Proteinopathies are diseases caused by factors that affect proteoform conformation. As such, a prevalent hypothesis is that the misincorporation of noncanonical amino acids into a proteoform results in detrimental structures. However, this hypothesis is missing proteomic evidence, specifically the detection of a noncanonical amino acid in a peptide sequence. This review aims to outline the current state of technology that can be used to investigate mistranslations and misincorporations whilst framing the pursuit as Misincorporation Proteomics (MiP). The current availability of technologies explored herein is mass spectrometry, sample enrichment/preparation, data analysis techniques, and the hyphenation of approaches. While many of these technologies show potential, our review reveals a need for further development and refinement of approaches is still required.
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23
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Roychowdhury T, Chattopadhyay S. Chemical Decorations of "MARs" Residents in Orchestrating Eukaryotic Gene Regulation. Front Cell Dev Biol 2020; 8:602994. [PMID: 33409278 PMCID: PMC7779526 DOI: 10.3389/fcell.2020.602994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/19/2020] [Indexed: 01/19/2023] Open
Abstract
Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure–function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein–protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA–protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.
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Affiliation(s)
- Tanaya Roychowdhury
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, India.,Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
| | - Samit Chattopadhyay
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, India.,Cancer Biology and Inflammatory Disorder Division, Indian Institute of Chemical Biology, Kolkata, India
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24
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Ishii M, Nakakido M, Caaveiro JMM, Kuroda D, Okumura CJ, Maruyama T, Entzminger K, Tsumoto K. Structural basis for antigen recognition by methylated lysine-specific antibodies. J Biol Chem 2020; 296:100176. [PMID: 33303630 PMCID: PMC7948472 DOI: 10.1074/jbc.ra120.015996] [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: 09/10/2020] [Revised: 12/05/2020] [Accepted: 12/10/2020] [Indexed: 12/05/2022] Open
Abstract
Proteins are modulated by a variety of posttranslational modifications including methylation. Despite its importance, the majority of protein methylation modifications discovered by mass spectrometric analyses are functionally uncharacterized, partly owing to the difficulty in obtaining reliable methylsite-specific antibodies. To elucidate how functional methylsite-specific antibodies recognize the antigens and lead to the development of a novel method to create such antibodies, we use an immunized library paired with phage display to create rabbit monoclonal antibodies recognizing trimethylated Lys260 of MAP3K2 as a representative substrate. We isolated several methylsite-specific antibodies that contained unique complementarity determining region sequence. We characterized the mode of antigen recognition by each of these antibodies using structural and biophysical analyses, revealing the molecular details, such as binding affinity toward methylated/nonmethylated antigens and structural motif that is responsible for recognition of the methylated lysine residue, by which each antibody recognized the target antigen. In addition, the comparison with the results of Western blotting analysis suggests a critical antigen recognition mode to generate cross-reactivity to protein and peptide antigen of the antibodies. Computational simulations effectively recapitulated our biophysical data, capturing the antibodies of differing affinity and specificity. Our exhaustive characterization provides molecular architectures of functional methylsite-specific antibodies and thus should contribute to the development of a general method to generate functional methylsite-specific antibodies by de novo design.
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Affiliation(s)
- Misaki Ishii
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Jose M M Caaveiro
- Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | | | | | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan; Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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25
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Monoclonal Anti-AMP Antibodies Are Sensitive and Valuable Tools for Detecting Patterns of AMPylation. iScience 2020; 23:101800. [PMID: 33299971 PMCID: PMC7704405 DOI: 10.1016/j.isci.2020.101800] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/16/2020] [Accepted: 11/10/2020] [Indexed: 12/29/2022] Open
Abstract
AMPylation is a post-translational modification that modifies amino acid side chains with adenosine monophosphate (AMP). Recently, a role of AMPylation as a universal regulatory mechanism in infection and cellular homeostasis has emerged, driving the demand for universal tools to study this modification. Here, we describe three monoclonal anti-AMP antibodies (mAbs) from mouse that are capable of protein backbone-independent recognition of AMPylation, in denatured (western blot) as well as native (ELISA, IP) applications, thereby outperforming previously reported tools. These antibodies are highly sensitive and specific for AMP modifications, highlighting their potential as tools for new target identification, as well as for validation of known targets. Interestingly, applying the anti-AMP mAbs to various cancer cell lines reveals a previously undescribed broad and diverse AMPylation pattern. In conclusion, these anti-AMP mABs will further advance the current understanding of AMPylation and the spectrum of modified targets. Generation of murine monoclonal anti-AMP antibodies via synthetic AMPylated peptide Characterization in the applications western blot, ELISA, and immunoprecipitation Sensitive and specific recognition of AMPylation independent of protein backbone Expansion of toolbox for the detection and enrichment of AMPylation
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26
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Zhou XX, Bracken CJ, Zhang K, Zhou J, Mou Y, Wang L, Cheng Y, Leung KK, Wells JA. Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. J Am Chem Soc 2020; 142:17703-17713. [PMID: 32924468 DOI: 10.1021/jacs.0c08458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Engineering sequence-specific antibodies (Abs) against phosphotyrosine (pY) motifs embedded in folded polypeptides remains highly challenging because of the stringent requirement for simultaneous recognition of the pY motif and the surrounding folded protein epitope. Here, we present a method named phosphotyrosine Targeting by Recombinant Ab Pair, or pY-TRAP, for in vitro engineering of binders for native pY proteins. Specifically, we create the pY protein by unnatural amino acid misincorporation, mutagenize a universal pY-binding Ab to create a first binder B1 for the pY motif on the pY protein, and then select against the B1-pY protein complex for a second binder B2 that recognizes the composite epitope of B1 and the pY-containing protein complex. We applied pY-TRAP to create highly specific binders to folded Ub-pY59, a rarely studied Ub phosphoform exclusively observed in cancerous tissues, and ZAP70-pY248, a kinase phosphoform regulated in feedback signaling pathways in T cells. The pY-TRAPs do not have detectable binding to wild-type proteins or to other pY peptides or proteins tested. This pY-TRAP approach serves as a generalizable method for engineering sequence-specific Ab binders to native pY proteins.
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Affiliation(s)
- Xin X Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Colton J Bracken
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Kaihua Zhang
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States
| | - Jie Zhou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Yun Mou
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Lei Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, United States.,Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, United States
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27
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Scott WA, Campos EI. Interactions With Histone H3 & Tools to Study Them. Front Cell Dev Biol 2020; 8:701. [PMID: 32850821 PMCID: PMC7411163 DOI: 10.3389/fcell.2020.00701] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/10/2020] [Indexed: 01/12/2023] Open
Abstract
Histones are an integral part of chromatin and thereby influence its structure, dynamics, and functions. The effects of histone variants, posttranslational modifications, and binding proteins is therefore of great interest. From the moment that they are deposited on chromatin, nucleosomal histones undergo dynamic changes in function of the cell cycle, and as DNA is transcribed and replicated. In the process, histones are not only modified and bound by various proteins, but also shuffled, evicted, or replaced. Technologies and tools to study such dynamic events continue to evolve and better our understanding of chromatin and of histone proteins proper. Here, we provide an overview of H3.1 and H3.3 histone dynamics throughout the cell cycle, while highlighting some of the tools used to study their protein–protein interactions. We specifically discuss how histones are chaperoned, modified, and bound by various proteins at different stages of the cell cycle. Established and select emerging technologies that furthered (or have a high potential of furthering) our understanding of the dynamic histone–protein interactions are emphasized. This includes experimental tools to investigate spatiotemporal changes on chromatin, the role of histone chaperones, histone posttranslational modifications, and histone-binding effector proteins.
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Affiliation(s)
- William A Scott
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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28
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Gutiérrez-Sánchez M, Carrasco-Yepez MM, Herrera-Díaz J, Rojas-Hernández S. Identification of differential protein recognition pattern between Naegleria fowleri and Naegleria lovaniensis. Parasite Immunol 2020; 42:e12715. [PMID: 32191816 DOI: 10.1111/pim.12715] [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: 10/23/2019] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 12/15/2022]
Abstract
Many pathogenicity factors are involved in the development of primary amoebic meningoencephalitis (PAM) caused by N fowleri. However, most of them are not exclusive for N fowleri and they have not even been described in other nonpathogenic Naegleria species. Therefore, the objective of this work was to identify differential proteins and protein pattern recognition between Naegleria fowleri and Naegleria lovaniensis using antibodies anti-N fowleri as strategy to find vaccine candidates against meningoencephalitis. Electrophoresis and Western blots conventional and 2-DE were performed for the identification of antigenic proteins, and these were analysed by the mass spectrometry technique. The results obtained in 2-DE gels and Western blot showed very notable differences in spot intensity between these two species, specifically those with relative molecular weight of 100, 75, 50 and 19 kDa. Some spots corresponding to these molecular weights were identified as actin fragment, myosin II, heat shock protein, membrane protein Mp2CL5 among others, with differences in theoretical post-translational modifications. In this work, we found differences in antigenic proteins between both species, proteins that could be used for a further development of vaccines against N fowleri infection.
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Affiliation(s)
- Mara Gutiérrez-Sánchez
- Laboratorio de Inmunobiología Molecular y Celular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico
| | - Maria Maricela Carrasco-Yepez
- Laboratorio de Microbiología, Grupo CyMA, Unidad de Investigación Interdisciplinaria en Ciencias de la Salud y la Educación, Universidad Nacional Autónoma de México, UNAM FES Iztacala, Tlalnepantla, Mexico
| | - Jorge Herrera-Díaz
- Unidad de Servicios de Apoyo a la Investigación y la Industria, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Saul Rojas-Hernández
- Laboratorio de Inmunobiología Molecular y Celular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico
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29
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Schmidt FI. From atoms to physiology: what it takes to really understand inflammasomes. J Physiol 2019; 597:5335-5348. [PMID: 31490557 DOI: 10.1113/jp277027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/29/2019] [Indexed: 12/22/2022] Open
Abstract
Rapid inflammatory responses to cytosolic threats are mediated by inflammasomes - large macromolecular signalling complexes that control the activation of the pro-inflammatory cytokines interleukin (IL)-1β and IL-18, as well as cell death by pyroptosis. Different inflammasome sensors are activated by diverse direct and indirect signals, and subsequently nucleate the polymerization of the adaptor molecule ASC to form signalling platforms macroscopically observed as ASC specks. Caspase-1 is autocatalytically activated at these sites and subsequently matures pro-inflammatory cytokines and the pore-forming effector molecule gasdermin D. While most molecules and basic assembly principles have been deduced from reductionist experimental systems, we still lack fundamental information on the structure and regulation of these complexes in their physiological environment and in the interplay with other signalling pathways. In this review, novel experimental approaches are proposed, including some that rely on nanobodies and single domain antibodies, to understand inflammasome assembly and regulation in the context of the relevant tissues or cells.
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30
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Antfolk D, Antila C, Kemppainen K, Landor SKJ, Sahlgren C. Decoding the PTM-switchboard of Notch. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118507. [PMID: 31301363 PMCID: PMC7116576 DOI: 10.1016/j.bbamcr.2019.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/03/2019] [Accepted: 07/06/2019] [Indexed: 01/08/2023]
Abstract
The developmentally indispensable Notch pathway exhibits a high grade of pleiotropism in its biological output. Emerging evidence supports the notion of post-translational modifications (PTMs) as a modus operandi controlling dynamic fine-tuning of Notch activity. Although, the intricacy of Notch post-translational regulation, as well as how these modifications lead to multiples of divergent Notch phenotypes is still largely unknown, numerous studies show a correlation between the site of modification and the output. These include glycosylation of the extracellular domain of Notch modulating ligand binding, and phosphorylation of the PEST domain controlling half-life of the intracellular domain of Notch. Furthermore, several reports show that multiple PTMs can act in concert, or compete for the same sites to drive opposite outputs. However, further investigation of the complex PTM crosstalk is required for a complete understanding of the PTM-mediated Notch switchboard. In this review, we aim to provide a consistent and up-to-date summary of the currently known PTMs acting on the Notch signaling pathway, their functions in different contexts, as well as explore their implications in physiology and disease. Furthermore, we give an overview of the present state of PTM research methodology, and allude to a future with PTM-targeted Notch therapeutics.
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Affiliation(s)
- Daniel Antfolk
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Christian Antila
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Kati Kemppainen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Sebastian K-J Landor
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland.
| | - Cecilia Sahlgren
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland; Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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31
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Zhang J, Dang F, Ren J, Wei W. Biochemical Aspects of PD-L1 Regulation in Cancer Immunotherapy. Trends Biochem Sci 2018; 43:1014-1032. [PMID: 30287140 DOI: 10.1016/j.tibs.2018.09.004] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/04/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022]
Abstract
PD-L1, frequently expressed in human cancers, engages with PD-1 on immune cells and contributes to cancer immune evasion. As such, antibodies blocking the PD-1/PD-L1 interaction reactivate cytotoxic T cells to eradicate cancer cells. However, a majority of cancer patients fail to respond to PD-1/PD-L1 blockade with unclear underlying mechanism(s). Recent studies revealed that PD-L1 expression levels on tumor cells might affect the clinical response to anti-PD-1/PD-L1 therapies. Hence, understanding molecular mechanisms for controlling PD-L1 expression will be important to improve the clinical response rate and efficacy of PD-1/PD-L1 blockade. In this review, we primarily focus on summarizing PD-L1 regulation and its potential roles in regulating antitumor immune response, with purpose to optimize anti-PD-1/PD-L1 therapies, benefiting a wider cancer patient population.
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Affiliation(s)
- Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; These authors contributed equally to this work
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; These authors contributed equally to this work
| | - Junming Ren
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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