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Gilchuk P, Guthals A, Bonissone SR, Shaw JB, Ilinykh PA, Huang K, Bombardi RG, Liang J, Grinyo A, Davidson E, Chen EC, Gunn BM, Alter G, Saphire EO, Doranz BJ, Bukreyev A, Zeitlin L, Castellana N, Crowe JE. Proteo-Genomic Analysis Identifies Two Major Sites of Vulnerability on Ebolavirus Glycoprotein for Neutralizing Antibodies in Convalescent Human Plasma. Front Immunol 2021; 12:706757. [PMID: 34335620 PMCID: PMC8322977 DOI: 10.3389/fimmu.2021.706757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
Three clinically relevant ebolaviruses - Ebola (EBOV), Bundibugyo (BDBV), and Sudan (SUDV) viruses, are responsible for severe disease and occasional deadly outbreaks in Africa. The largest Ebola virus disease (EVD) epidemic to date in 2013-2016 in West Africa highlighted the urgent need for countermeasures, leading to the development and FDA approval of the Ebola virus vaccine rVSV-ZEBOV (Ervebo®) in 2020 and two monoclonal antibody (mAb)-based therapeutics (Inmazeb® [atoltivimab, maftivimab, and odesivimab-ebgn] and Ebanga® (ansuvimab-zykl) in 2020. The humoral response plays an indispensable role in ebolavirus immunity, based on studies of mAbs isolated from the antibody genes in peripheral blood circulating ebolavirus-specific human memory B cells. However, antibodies in the body are not secreted by circulating memory B cells in the blood but rather principally by plasma cells in the bone marrow. Little is known about the protective polyclonal antibody responses in convalescent plasma. Here we exploited both single-cell antibody gene sequencing and proteomic sequencing approaches to assess the composition of the ebolavirus glycoprotein (GP)-reactive antibody repertoire in the plasma of an EVD survivor. We first identified 1,512 GP-specific mAb variable gene sequences from single cells in the memory B cell compartment. Using mass spectrometric analysis of the corresponding GP-specific plasma IgG, we found that only a portion of the large B cell antibody repertoire was represented in the plasma. Molecular and functional analysis of proteomics-identified mAbs revealed recognition of epitopes in three major antigenic sites - the GP head domain, the glycan cap, and the base region, with a high prevalence of neutralizing and protective mAb specificities that targeted the base and glycan cap regions on the GP. Polyclonal plasma antibodies from the survivor reacted broadly to EBOV, BDBV, and SUDV GP, while reactivity of the potently neutralizing mAbs we identified was limited mostly to the homologous EBOV GP. Together these results reveal a restricted diversity of neutralizing humoral response in which mAbs targeting two antigenic sites on GP - glycan cap and base - play a principal role in plasma-antibody-mediated protective immunity against EVD.
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Affiliation(s)
- Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Adrian Guthals
- Mapp Biopharmaceutical, Inc. San Diego, CA, United States
| | - Stefano R. Bonissone
- Abterra Biosciences (formerly Digital Proteomics LLC), San Diego, CA, United States
| | - Jared B. Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Philipp A. Ilinykh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
| | - Kai Huang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
| | - Robin G. Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jenny Liang
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Ariadna Grinyo
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Edgar Davidson
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Elaine C. Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bronwyn M. Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc. San Diego, CA, United States
| | - Natalie Castellana
- Abterra Biosciences (formerly Digital Proteomics LLC), San Diego, CA, United States
| | - James E. Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
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Archer TC, Ehrenberger T, Mundt F, Gold MP, Krug K, Mah CK, Mahoney EL, Daniel CJ, LeNail A, Ramamoorthy D, Mertins P, Mani DR, Zhang H, Gillette MA, Clauser K, Noble M, Tang LC, Pierre-François J, Silterra J, Jensen J, Tamayo P, Korshunov A, Pfister SM, Kool M, Northcott PA, Sears RC, Lipton JO, Carr SA, Mesirov JP, Pomeroy SL, Fraenkel E. Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Cancer Cell 2018; 34:396-410.e8. [PMID: 30205044 PMCID: PMC6372116 DOI: 10.1016/j.ccell.2018.08.004] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/28/2018] [Accepted: 08/03/2018] [Indexed: 12/18/2022]
Abstract
There is a pressing need to identify therapeutic targets in tumors with low mutation rates such as the malignant pediatric brain tumor medulloblastoma. To address this challenge, we quantitatively profiled global proteomes and phospho-proteomes of 45 medulloblastoma samples. Integrated analyses revealed that tumors with similar RNA expression vary extensively at the post-transcriptional and post-translational levels. We identified distinct pathways associated with two subsets of SHH tumors, and found post-translational modifications of MYC that are associated with poor outcomes in group 3 tumors. We found kinases associated with subtypes and showed that inhibiting PRKDC sensitizes MYC-driven cells to radiation. Our study shows that proteomics enables a more comprehensive, functional readout, providing a foundation for future therapeutic strategies.
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Affiliation(s)
- Tenley C Archer
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA; Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tobias Ehrenberger
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Filip Mundt
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Maxwell P Gold
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Karsten Krug
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clarence K Mah
- Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Elizabeth L Mahoney
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Colin J Daniel
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Alexander LeNail
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Divya Ramamoorthy
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Philipp Mertins
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - D R Mani
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hailei Zhang
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael A Gillette
- Harvard Medical School, Boston, MA, USA; Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital (MGH), Boston, MA, USA
| | - Karl Clauser
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Noble
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lauren C Tang
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jessica Pierre-François
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Jacob Silterra
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James Jensen
- Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Pablo Tamayo
- Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA
| | - Andrey Korshunov
- CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neuropathology, Heidelberg University, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Paul A Northcott
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Rosalie C Sears
- Department of Molecular and Medical Genetics, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Jonathan O Lipton
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Steven A Carr
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego (UCSD), La Jolla, CA, USA; Moores Cancer Center, University of California San Diego (UCSD), La Jolla, CA, USA.
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ernest Fraenkel
- Eli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
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Cintas C, Douché T, Therville N, Arcucci S, Ramos-Delgado F, Basset C, Thibault B, Guillermet-Guibert J. Signal-Targeted Therapies and Resistance Mechanisms in Pancreatic Cancer: Future Developments Reside in Proteomics. Cancers (Basel) 2018; 10:E174. [PMID: 29865155 DOI: 10.3390/cancers10060174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 12/18/2022] Open
Abstract
For patients with metastatic pancreatic cancer that are not eligible for surgery, signal-targeted therapies have so far failed to significantly improve survival. These therapeutic options have been tested in phase II/III clinical trials mostly in combination with the reference treatment gemcitabine. Innovative therapies aim to annihilate oncogenic dependency, or to normalize the tumoural stroma to allow immune cells to function and/or re-vascularisation to occur. Large scale transcriptomic and genomic analysis revealed that pancreatic cancers display great heterogeneity but failed to clearly delineate specific oncogene dependency, besides oncogenic Kras. Beyond these approaches, proteomics appears to be an appropriate approach to classify signal dependency and to identify specific alterations at the targetable level. However, due to difficulties in sampling, proteomic data for this pathology are scarce. In this review, we will discuss the current state of clinical trials for targeted therapies against pancreatic cancer. We will then highlight the most recent proteomic data for pancreatic tumours and their metastasis, which could help to identify major oncogenic signalling dependencies, as well as provide future leads to explain why pancreatic tumours are intrinsically resistant to signal-targeted therapies. We will finally discuss how studies on phosphatidylinositol-3-kinase (PI3K) signalling, as the paradigmatic pro-tumoural signal downstream of oncogenic Kras in pancreatic cancer, would benefit from exploratory proteomics to increase the efficiency of targeted therapies.
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