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Beguir K, Skwark MJ, Fu Y, Pierrot T, Carranza NL, Laterre A, Kadri I, Korched A, Lowegard AU, Lui BG, Sänger B, Liu Y, Poran A, Muik A, Şahin U. Early computational detection of potential high-risk SARS-CoV-2 variants. Comput Biol Med 2023; 155:106618. [PMID: 36774893 PMCID: PMC9892295 DOI: 10.1016/j.compbiomed.2023.106618] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
The ongoing COVID-19 pandemic is leading to the discovery of hundreds of novel SARS-CoV-2 variants daily. While most variants do not impact the course of the pandemic, some variants pose an increased risk when the acquired mutations allow better evasion of antibody neutralisation or increased transmissibility. Early detection of such high-risk variants (HRVs) is paramount for the proper management of the pandemic. However, experimental assays to determine immune evasion and transmissibility characteristics of new variants are resource-intensive and time-consuming, potentially leading to delays in appropriate responses by decision makers. Presented herein is a novel in silico approach combining spike (S) protein structure modelling and large protein transformer language models on S protein sequences to accurately rank SARS-CoV-2 variants for immune escape and fitness potential. Both metrics were experimentally validated using in vitro pseudovirus-based neutralisation test and binding assays and were subsequently combined to explore the changing landscape of the pandemic and to create an automated Early Warning System (EWS) capable of evaluating new variants in minutes and risk-monitoring variant lineages in near real-time. The system accurately pinpoints the putatively dangerous variants by selecting on average less than 0.3% of the novel variants each week. The EWS flagged all 16 variants designated by the World Health Organization (WHO) as variants of interest (VOIs) if applicable or variants of concern (VOCs) otherwise with an average lead time of more than one and a half months ahead of their designation as such.
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Affiliation(s)
- Karim Beguir
- InstaDeep Ltd, 5 Merchant Square, London, W2 1AY, UK.
| | | | - Yunguan Fu
- InstaDeep Ltd, 5 Merchant Square, London, W2 1AY, UK
| | | | | | | | | | - Abir Korched
- InstaDeep Ltd, 5 Merchant Square, London, W2 1AY, UK
| | | | | | - Bianca Sänger
- BioNTech SE, An der Goldgrube 12, 55131, Mainz, Germany
| | - Yunpeng Liu
- BioNTech US, 40 Erie Street, Cambridge, MA, 02139, USA
| | - Asaf Poran
- BioNTech US, 40 Erie Street, Cambridge, MA, 02139, USA
| | | | - Uğur Şahin
- BioNTech SE, An der Goldgrube 12, 55131, Mainz, Germany.
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2
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Muik A, Adams Iii HC, Gieseke F, Altintas I, Schoedel KB, Blum JM, Sänger B, Burm SM, Stanganello E, Verzijl D, Spires VM, Vascotto F, Toker A, Quinkhardt J, Fereshteh M, Diken M, Satijn DPE, Kreiter S, Ahmadi T, Breij ECW, Türeci Ö, Sasser K, Sahin U, Jure-Kunkel M. DuoBody-CD40x4-1BB induces dendritic-cell maturation and enhances T-cell activation through conditional CD40 and 4-1BB agonist activity. J Immunother Cancer 2022; 10:jitc-2021-004322. [PMID: 35688554 PMCID: PMC9189854 DOI: 10.1136/jitc-2021-004322] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
Background Despite the preclinical promise of CD40 and 4-1BB as immuno-oncology targets, clinical efforts evaluating CD40 and 4-1BB agonists as monotherapy have found limited success. DuoBody-CD40×4-1BB (GEN1042/BNT312) is a novel investigational Fc-inert bispecific antibody for dual targeting and conditional stimulation of CD40 and 4-1BB to enhance priming and reactivation of tumor-specific immunity in patients with cancer. Methods Characterization of DuoBody-CD40×4-1BB in vitro was performed in a broad range of functional immune cell assays, including cell-based reporter assays, T-cell proliferation assays, mixed-lymphocyte reactions and tumor-infiltrating lymphocyte assays, as well as live-cell imaging. The in vivo activity of DuoBody-CD40×4-1BB was assessed in blood samples from patients with advanced solid tumors that were treated with DuoBody-CD40×4-1BB in the dose-escalation phase of the first-in-human clinical trial (NCT04083599). Results DuoBody-CD40×4-1BB exhibited conditional CD40 and 4-1BB agonist activity that was strictly dependent on crosslinking of both targets. Thereby, DuoBody-CD40×4-1BB strengthened the dendritic cell (DC)/T-cell immunological synapse, induced DC maturation, enhanced T-cell proliferation and effector functions in vitro and enhanced expansion of patient-derived tumor-infiltrating lymphocytes ex vivo. The addition of PD-1 blocking antibodies resulted in potentiation of T-cell activation and effector functions in vitro compared with either monotherapy, providing combination rationale. Furthermore, in a first-in-human clinical trial, DuoBody-CD40×4-1BB mediated clear immune modulation of peripheral antigen presenting cells and T cells in patients with advanced solid tumors. Conclusion DuoBody-CD40×4-1BB is capable of enhancing antitumor immunity by modulating DC and T-cell functions and shows biological activity in patients with advanced solid tumors. These findings demonstrate that targeting of these two pathways with an Fc-inert bispecific antibody may be an efficacious approach to (re)activate tumor-specific immunity and support the clinical investigation of DuoBody-CD40×4-1BB for the treatment of cancer.
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Affiliation(s)
| | | | | | - Isil Altintas
- Translational Research and Precision Medicine, Genmab BV, Utrecht, The Netherlands
| | | | | | | | - Saskia M Burm
- Translational Research and Precision Medicine, Genmab BV, Utrecht, The Netherlands
| | - Eliana Stanganello
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Dennis Verzijl
- Translational Research and Precision Medicine, Genmab BV, Utrecht, The Netherlands
| | | | - Fulvia Vascotto
- TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | | | | | | | | | | | | | - Tahamtan Ahmadi
- Experimental Medicine, Genmab US Inc, Plainsboro, New Jersey, USA
| | - Esther C W Breij
- Translational Research and Precision Medicine, Genmab BV, Utrecht, The Netherlands
| | | | | | - Ugur Sahin
- BioNTech SE, Mainz, Germany.,TRON-Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
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3
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Muik A, Garralda E, Altintas I, Gieseke F, Geva R, Ben-Ami E, Maurice-Dror C, Calvo E, LoRusso PM, Alonso G, Rodriguez-Ruiz ME, Schoedel KB, Blum JM, Sänger B, Salcedo TW, Burm SM, Stanganello E, Verzijl D, Vascotto F, Sette A, Quinkhardt J, Plantinga TS, Toker A, van den Brink EN, Fereshteh M, Diken M, Satijn D, Kreiter S, Breij EC, Bajaj G, Lagkadinou E, Sasser K, Türeci Ö, Forssmann U, Ahmadi T, Şahin U, Jure-Kunkel M, Melero I. Preclinical Characterization and Phase I Trial Results of a Bispecific Antibody Targeting PD-L1 and 4-1BB (GEN1046) in Patients with Advanced Refractory Solid Tumors. Cancer Discov 2022; 12:1248-1265. [PMID: 35176764 PMCID: PMC9662884 DOI: 10.1158/2159-8290.cd-21-1345] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/23/2021] [Accepted: 02/11/2022] [Indexed: 01/07/2023]
Abstract
Checkpoint inhibitors (CPI) have revolutionized the treatment paradigm for advanced solid tumors; however, there remains an opportunity to improve response rates and outcomes. In preclinical models, 4-1BB costimulation synergizes with CPIs targeting the programmed cell death protein 1 (PD-1)/programmed cell death ligand 1 (PD-L1) axis by activating cytotoxic T-cell-mediated antitumor immunity. DuoBody-PD-L1×4-1BB (GEN1046) is an investigational, first-in-class bispecific immunotherapy agent designed to act on both pathways by combining simultaneous and complementary PD-L1 blockade and conditional 4-1BB stimulation in one molecule. GEN1046 induced T-cell proliferation, cytokine production, and antigen-specific T-cell-mediated cytotoxicity superior to clinically approved PD-(L)1 antibodies in human T-cell cultures and exerted potent antitumor activity in transplantable mouse tumor models. In dose escalation of the ongoing first-in-human study in heavily pretreated patients with advanced refractory solid tumors (NCT03917381), GEN1046 demonstrated pharmacodynamic immune effects in peripheral blood consistent with its mechanism of action, manageable safety, and early clinical activity [disease control rate: 65.6% (40/61)], including patients resistant to prior PD-(L)1 immunotherapy. SIGNIFICANCE DuoBody-PD-L1×4-1BB (GEN1046) is a first-in-class bispecific immunotherapy with a manageable safety profile and encouraging preclinical and early clinical activity. With its ability to confer clinical benefit in tumors typically less sensitive to CPIs, GEN1046 may fill a clinical gap in CPI-relapsed or refractory disease or as a combination therapy with CPIs. See related commentary by Li et al., p. 1184. This article is highlighted in the In This Issue feature, p. 1171.
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Affiliation(s)
| | - Elena Garralda
- Medical Oncology Department, Vall d'Hebron University Hospital and Institute of Oncology, Barcelona, Spain
| | | | | | - Ravit Geva
- Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Eytan Ben-Ami
- Department of Oncology, Chaim Sheba Medical Center, Ramat Gan, Israel
| | | | - Emiliano Calvo
- START Madrid-CIOCC, Clara Campal Comprehensive Cancer Center, Madrid, Spain
| | | | - Guzman Alonso
- Medical Oncology Department, Vall d'Hebron University Hospital and Institute of Oncology, Barcelona, Spain
| | | | | | | | | | | | | | - Eliana Stanganello
- TRON gGmbH, Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | | | - Fulvia Vascotto
- TRON gGmbH, Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | | | | | | | | | | | - Mark Fereshteh
- TRON gGmbH, Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ignacio Melero
- Department of Immunology, Clínica Universidad de Navarra and CIBERONC, Pamplona, Spain.,Corresponding Author: Ignacio Melero, Division of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), University of Navarra and Instituto de Investigacion Sanitaria de Navarra (IdISNA), Av. Pio XII, 55, Pamplona, Navarra 31008, Spain. Phone: 346-5357-4014; E-mail:
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4
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Vogel AB, Kanevsky I, Che Y, Swanson KA, Muik A, Vormehr M, Kranz LM, Walzer KC, Hein S, Güler A, Loschko J, Maddur MS, Ota-Setlik A, Tompkins K, Cole J, Lui BG, Ziegenhals T, Plaschke A, Eisel D, Dany SC, Fesser S, Erbar S, Bates F, Schneider D, Jesionek B, Sänger B, Wallisch AK, Feuchter Y, Junginger H, Krumm SA, Heinen AP, Adams-Quack P, Schlereth J, Schille S, Kröner C, de la Caridad Güimil Garcia R, Hiller T, Fischer L, Sellers RS, Choudhary S, Gonzalez O, Vascotto F, Gutman MR, Fontenot JA, Hall-Ursone S, Brasky K, Griffor MC, Han S, Su AAH, Lees JA, Nedoma NL, Mashalidis EH, Sahasrabudhe PV, Tan CY, Pavliakova D, Singh G, Fontes-Garfias C, Pride M, Scully IL, Ciolino T, Obregon J, Gazi M, Carrion R, Alfson KJ, Kalina WV, Kaushal D, Shi PY, Klamp T, Rosenbaum C, Kuhn AN, Türeci Ö, Dormitzer PR, Jansen KU, Sahin U. BNT162b vaccines protect rhesus macaques from SARS-CoV-2. Nature 2021; 592:283-289. [PMID: 33524990 DOI: 10.1038/s41586-021-03275-y] [Citation(s) in RCA: 400] [Impact Index Per Article: 133.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/20/2021] [Indexed: 01/16/2023]
Abstract
A safe and effective vaccine against COVID-19 is urgently needed in quantities that are sufficient to immunize large populations. Here we report the preclinical development of two vaccine candidates (BNT162b1 and BNT162b2) that contain nucleoside-modified messenger RNA that encodes immunogens derived from the spike glycoprotein (S) of SARS-CoV-2, formulated in lipid nanoparticles. BNT162b1 encodes a soluble, secreted trimerized receptor-binding domain (known as the RBD-foldon). BNT162b2 encodes the full-length transmembrane S glycoprotein, locked in its prefusion conformation by the substitution of two residues with proline (S(K986P/V987P); hereafter, S(P2) (also known as P2 S)). The flexibly tethered RBDs of the RBD-foldon bind to human ACE2 with high avidity. Approximately 20% of the S(P2) trimers are in the two-RBD 'down', one-RBD 'up' state. In mice, one intramuscular dose of either candidate vaccine elicits a dose-dependent antibody response with high virus-entry inhibition titres and strong T-helper-1 CD4+ and IFNγ+CD8+ T cell responses. Prime-boost vaccination of rhesus macaques (Macaca mulatta) with the BNT162b candidates elicits SARS-CoV-2-neutralizing geometric mean titres that are 8.2-18.2× that of a panel of SARS-CoV-2-convalescent human sera. The vaccine candidates protect macaques against challenge with SARS-CoV-2; in particular, BNT162b2 protects the lower respiratory tract against the presence of viral RNA and shows no evidence of disease enhancement. Both candidates are being evaluated in phase I trials in Germany and the USA1-3, and BNT162b2 is being evaluated in an ongoing global phase II/III trial (NCT04380701 and NCT04368728).
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MESH Headings
- Aging/immunology
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- BNT162 Vaccine
- COVID-19/blood
- COVID-19/immunology
- COVID-19/prevention & control
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/chemistry
- COVID-19 Vaccines/genetics
- COVID-19 Vaccines/immunology
- Cell Line
- Clinical Trials as Topic
- Disease Models, Animal
- Female
- Humans
- Immunization, Passive
- Internationality
- Macaca mulatta/immunology
- Macaca mulatta/virology
- Male
- Mice
- Mice, Inbred BALB C
- Models, Molecular
- Protein Multimerization
- RNA, Viral/analysis
- Respiratory System/immunology
- Respiratory System/virology
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Solubility
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- T-Lymphocytes/immunology
- Vaccination
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/chemistry
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- COVID-19 Serotherapy
- mRNA Vaccines
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Journey Cole
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Olga Gonzalez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Fulvia Vascotto
- TRON-Translational Oncology at the University Medical Centre of the Johannes Gutenberg University, Mainz, Germany
| | - Matthew R Gutman
- VCA SouthPaws Veterinary Specialists and Emergency Center, Fairfax, VA, USA
| | | | - Shannan Hall-Ursone
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Kathleen Brasky
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michal Gazi
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ricardo Carrion
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | | | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Pei-Yong Shi
- University of Texas Medical Branch, Galveston, TX, USA
| | | | | | | | | | | | | | - Ugur Sahin
- BioNTech, Mainz, Germany.
- TRON-Translational Oncology at the University Medical Centre of the Johannes Gutenberg University, Mainz, Germany.
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5
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Muik A, Wallisch AK, Sänger B, Swanson KA, Mühl J, Chen W, Cai H, Maurus D, Sarkar R, Türeci Ö, Dormitzer PR, Şahin U. Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine-elicited human sera. Science 2021; 371:1152-1153. [PMID: 33514629 DOI: 10.1101/2021.01.18.426984] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 05/18/2023]
Abstract
Recently, a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage called B.1.1.7 (variant of concern: VOC 202012/01), which is reported to spread more efficiently and faster than other strains, emerged in the United Kingdom. This variant has an unusually large number of mutations, with 10 amino acid changes in the spike (S) protein, raising concerns that its recognition by neutralizing antibodies may be affected. In this study, we tested SARS-CoV-2-S pseudoviruses bearing either the Wuhan reference strain or the B.1.1.7 lineage spike protein with sera of 40 participants who were vaccinated in a previously reported trial with the messenger RNA-based COVID-19 vaccine BNT162b2. The immune sera had slightly reduced but overall largely preserved neutralizing titers against the B.1.1.7 lineage pseudovirus. These data indicate that the B.1.1.7 lineage will not escape BNT162b2-mediated protection.
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Affiliation(s)
| | | | | | - Kena A Swanson
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | - Julia Mühl
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | - Wei Chen
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | - Hui Cai
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | | | - Ritu Sarkar
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | - Özlem Türeci
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | | | - Uğur Şahin
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany.
- TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Freiligrathstraße 12, 55131 Mainz, Germany
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6
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Muik A, Wallisch AK, Sänger B, Swanson KA, Mühl J, Chen W, Cai H, Maurus D, Sarkar R, Türeci Ö, Dormitzer PR, Şahin U. Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine-elicited human sera. Science 2021; 371:1152-1153. [PMID: 33514629 PMCID: PMC7971771 DOI: 10.1126/science.abg6105] [Citation(s) in RCA: 399] [Impact Index Per Article: 133.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022]
Abstract
Recently, a new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage called B.1.1.7 (variant of concern: VOC 202012/01), which is reported to spread more efficiently and faster than other strains, emerged in the United Kingdom. This variant has an unusually large number of mutations, with 10 amino acid changes in the spike (S) protein, raising concerns that its recognition by neutralizing antibodies may be affected. In this study, we tested SARS-CoV-2-S pseudoviruses bearing either the Wuhan reference strain or the B.1.1.7 lineage spike protein with sera of 40 participants who were vaccinated in a previously reported trial with the messenger RNA-based COVID-19 vaccine BNT162b2. The immune sera had slightly reduced but overall largely preserved neutralizing titers against the B.1.1.7 lineage pseudovirus. These data indicate that the B.1.1.7 lineage will not escape BNT162b2-mediated protection.
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Affiliation(s)
| | | | | | - Kena A Swanson
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | - Julia Mühl
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | - Wei Chen
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | - Hui Cai
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | | | - Ritu Sarkar
- Pfizer, 401 N. Middletown Rd., Pearl River, NY 10960, USA
| | - Özlem Türeci
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany
| | | | - Uğur Şahin
- BioNTech, An der Goldgrube 12, 55131 Mainz, Germany. .,TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Freiligrathstraße 12, 55131 Mainz, Germany
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