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Ray R, Nait Mohamed FA, Maurer DP, Huang J, Alpay BA, Ronsard L, Xie Z, Han J, Fernandez-Quintero M, Phan QA, Ursin RL, Vu M, Kirsch KH, Prum T, Rosado VC, Bracamonte-Moreno T, Okonkwo V, Bals J, McCarthy C, Nair U, Kanekiyo M, Ward AB, Schmidt AG, Batista FD, Lingwood D. Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses. Immunity 2024; 57:1141-1159.e11. [PMID: 38670113 PMCID: PMC11096021 DOI: 10.1016/j.immuni.2024.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]
Abstract
Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
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Affiliation(s)
- Rashmi Ray
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
| | - Daniel P Maurer
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Jiachen Huang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Berk A Alpay
- Systems, Synthetic, and Quantitative Biology Program, Harvard University, Cambridge, MA 02138, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Larance Ronsard
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Zhenfei Xie
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Monica Fernandez-Quintero
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82/III, 6020 Innsbruck, Austria
| | - Quynh Anh Phan
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Rebecca L Ursin
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mya Vu
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thavaleak Prum
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Victoria C Rosado
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thalia Bracamonte-Moreno
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Vintus Okonkwo
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Julia Bals
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Caitlin McCarthy
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Usha Nair
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Aaron G Schmidt
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Department of Biology, The Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel Lingwood
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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2
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Wamhoff EC, Ronsard L, Feldman J, Knappe GA, Hauser BM, Romanov A, Case JB, Sanapala S, Lam EC, Denis KJS, Boucau J, Barczak AK, Balazs AB, Diamond MS, Schmidt AG, Lingwood D, Bathe M. Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds. Nat Commun 2024; 15:795. [PMID: 38291019 PMCID: PMC10828404 DOI: 10.1038/s41467-024-44869-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024] Open
Abstract
Protein-based virus-like particles (P-VLPs) are commonly used to spatially organize antigens and enhance humoral immunity through multivalent antigen display. However, P-VLPs are thymus-dependent antigens that are themselves immunogenic and can induce B cell responses that may neutralize the platform. Here, we investigate thymus-independent DNA origami as an alternative material for multivalent antigen display using the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, the primary target of neutralizing antibody responses. Sequential immunization of mice with DNA-based VLPs (DNA-VLPs) elicits protective neutralizing antibodies to SARS-CoV-2 in a manner that depends on the valency of the antigen displayed and on T cell help. Importantly, the immune sera do not contain boosted, class-switched antibodies against the DNA scaffold, in contrast to P-VLPs that elicit strong B cell memory against both the target antigen and the scaffold. Thus, DNA-VLPs enhance target antigen immunogenicity without generating scaffold-directed immunity and thereby offer an important alternative material for particulate vaccine design.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Larance Ronsard
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - Jared Feldman
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Blake M Hauser
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shilpa Sanapala
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Evan C Lam
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - Kerri J St Denis
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - Julie Boucau
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - Amy K Barczak
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - Alejandro B Balazs
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aaron G Schmidt
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Daniel Lingwood
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, 02139, USA.
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02139, USA.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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3
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Peabody J, Core SB, Ronsard L, Lingwood D, Peabody DS, Chackerian B. An Approach for Antigen-Agnostic Identification of Virus-Like Particle-Displayed Epitopes that Engage Specific Antibody V Gene Regions. Methods Mol Biol 2024; 2720:55-74. [PMID: 37775657 DOI: 10.1007/978-1-0716-3469-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
Antibody complementarity determining regions (CDRs) participate in antigen recognition, but not all participate equally in antigen binding. Here we describe a technique for discovering strong, specific binding partners to defined motifs within the CDRs of chimeric, engineered antibodies using affinity selection and counter-selection of epitopes displayed on bacteriophage MS2-based virus-like particles (VLPs). As an example, we show how this technique can be used to identify families of VLPs that interact with antibodies displaying the CDRs encoded by the germline precursor of a broadly neutralizing monoclonal antibody against HIV-1.
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Affiliation(s)
- Julianne Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Susan B Core
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - David S Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA.
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4
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Ronsard L, Yousif AS, Nait Mohamed FA, Feldman J, Okonkwo V, McCarthy C, Schnabel J, Caradonna T, Barnes RM, Rohrer D, Lonberg N, Schmidt A, Lingwood D. Engaging an HIV vaccine target through the acquisition of low B cell affinity. Nat Commun 2023; 14:5249. [PMID: 37640732 PMCID: PMC10462694 DOI: 10.1038/s41467-023-40918-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
Low affinity is common for germline B cell receptors (BCR) seeding development of broadly neutralizing antibodies (bnAbs) that engage hypervariable viruses, including HIV. Antibody affinity selection is also non-homogenizing, insuring the survival of low affinity B cell clones. To explore whether this provides a natural window for expanding human B cell lineages against conserved vaccine targets, we deploy transgenic mice mimicking human antibody diversity and somatic hypermutation (SHM) and immunize with simple monomeric HIV glycoprotein envelope immunogens. We report an immunization regimen that focuses B cell memory upon the conserved CD4 binding site (CD4bs) through both conventional affinity maturation and reproducible expansion of low affinity BCR clones with public patterns in SHM. In the latter instance, SHM facilitates target acquisition by decreasing binding strength. This suggests that permissive B cell selection enables the discovery of antibody epitopes, in this case an HIV bnAb site.
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Affiliation(s)
- Larance Ronsard
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Ashraf S Yousif
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Jared Feldman
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Vintus Okonkwo
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Caitlin McCarthy
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Julia Schnabel
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Timothy Caradonna
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063-2478, USA
| | - Aaron Schmidt
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Lingwood
- The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA, 02139, USA.
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5
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Wamhoff EC, Ronsard L, Feldman J, Knappe GA, Hauser BM, Romanov A, Lam E, Denis KS, Boucau J, Barczak AK, Balazs AB, Schmidt A, Lingwood D, Bathe M. Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds. bioRxiv 2023:2022.08.16.504128. [PMID: 36032975 PMCID: PMC9413718 DOI: 10.1101/2022.08.16.504128] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Multivalent antigen display is a well-established principle to enhance humoral immunity. Protein-based virus-like particles (VLPs) are commonly used to spatially organize antigens. However, protein-based VLPs are limited in their ability to control valency on fixed scaffold geometries and are thymus-dependent antigens that elicit neutralizing B cell memory themselves, which can distract immune responses. Here, we investigated DNA origami as an alternative material for multivalent antigen display in vivo, applied to the receptor binding domain (RBD) of SARS-CoV2 that is the primary antigenic target of neutralizing antibody responses. Icosahedral DNA-VLPs elicited neutralizing antibodies to SARS-CoV-2 in a valency-dependent manner following sequential immunization in mice, quantified by pseudo- and live-virus neutralization assays. Further, induction of B cell memory against the RBD required T cell help, but the immune sera did not contain boosted, class-switched antibodies against the DNA scaffold. This contrasted with protein-based VLP display of the RBD that elicited B cell memory against both the target antigen and the scaffold. Thus, DNA-based VLPs enhance target antigen immunogenicity without generating off-target, scaffold-directed immune memory, thereby offering a potentially important alternative material for particulate vaccine design.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Larance Ronsard
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Jared Feldman
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Blake M. Hauser
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Evan Lam
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Kerri St. Denis
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Julie Boucau
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Amy K Barczak
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Alejandro B. Balazs
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Aaron Schmidt
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, United States
| | - Daniel Lingwood
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, United States
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, United States
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6
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Abdelsalam SA, Renu K, Zahra HA, Abdallah BM, Ali EM, Veeraraghavan VP, Sivalingam K, Ronsard L, Ammar RB, Vidya DS, Karuppaiya P, Al-Ramadan SY, Rajendran P. Polyphenols Mediate Neuroprotection in Cerebral Ischemic Stroke-An Update. Nutrients 2023; 15:nu15051107. [PMID: 36904106 PMCID: PMC10005012 DOI: 10.3390/nu15051107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/18/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Stroke is one of the main causes of mortality and disability, and it is due to be included in monetary implications on wellbeing frameworks around the world. Ischemic stroke is caused by interference in cerebral blood flow, leading to a deficit in the supply of oxygen to the affected region. It accounts for nearly 80-85% of all cases of stroke. Oxidative stress has a significant impact on the pathophysiologic cascade in brain damage leading to stroke. In the acute phase, oxidative stress mediates severe toxicity, and it initiates and contributes to late-stage apoptosis and inflammation. Oxidative stress conditions occur when the antioxidant defense in the body is unable to counteract the production and aggregation of reactive oxygen species (ROS). The previous literature has shown that phytochemicals and other natural products not only scavenge oxygen free radicals but also improve the expressions of cellular antioxidant enzymes and molecules. Consequently, these products protect against ROS-mediated cellular injury. This review aims to give an overview of the most relevant data reported in the literature on polyphenolic compounds, namely, gallic acid, resveratrol, quercetin, kaempferol, mangiferin, epigallocatechin, and pinocembrin, in terms of their antioxidant effects and potential protective activity against ischemic stroke.
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Affiliation(s)
- Salaheldin Abdelraouf Abdelsalam
- Department of Biological Sciences, College of Science, King Faisal University, Chennai 31982, Saudi Arabia
- Department of Zoology, Faculty of Science, Assiut University, Assiut 71515, Egypt
| | - Kaviyarasi Renu
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College & Hospitals, Saveetha University, Chennai 600077, India
| | - Hamad Abu Zahra
- Department of Biological Sciences, College of Science, King Faisal University, Chennai 31982, Saudi Arabia
| | - Basem M. Abdallah
- Department of Biological Sciences, College of Science, King Faisal University, Chennai 31982, Saudi Arabia
| | - Enas M. Ali
- Department of Biological Sciences, College of Science, King Faisal University, Chennai 31982, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Cairo 12613, Egypt
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College & Hospitals, Saveetha University, Chennai 600077, India
| | - Kalaiselvi Sivalingam
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Larance Ronsard
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Rebai Ben Ammar
- Department of Biological Sciences, College of Science, King Faisal University, Chennai 31982, Saudi Arabia
- Laboratory of Aromatic and Medicinal Plants, Center of Biotechnology of Borj-Cedria, Technopole of Borj-Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Devanathadesikan Seshadri Vidya
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdul Aziz University, Al-Kharj 11942, Saudi Arabia
| | - Palaniyandi Karuppaiya
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - S. Y. Al-Ramadan
- Department of Anatomy, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Peramaiyan Rajendran
- Department of Biological Sciences, College of Science, King Faisal University, Chennai 31982, Saudi Arabia
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College & Hospitals, Saveetha University, Chennai 600077, India
- Correspondence: ; Tel.: +966-0135899543
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7
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Hauser BM, Feldman J, Sangesland M, Ronsard L, St Denis KJ, Sheehan ML, Cao Y, Boucau J, Windsor IW, Cheng AH, Vu ML, Cardoso MR, Kannegieter T, Balazs AB, Lingwood D, Garcia-Beltran WF, Schmidt AG. Cross-reactive SARS-CoV-2 epitope targeted across donors informs immunogen design. Cell Rep Med 2022; 3:100834. [PMID: 36423634 PMCID: PMC9663748 DOI: 10.1016/j.xcrm.2022.100834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/14/2022] [Revised: 09/07/2022] [Accepted: 11/08/2022] [Indexed: 11/17/2022]
Abstract
The emergence of the antigenically distinct and highly transmissible Omicron variant highlights the possibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune escape due to viral evolution. This continued evolution, along with the possible introduction of new sarbecoviruses from zoonotic reservoirs, may evade host immunity elicited by current SARS-CoV-2 vaccines. Identifying cross-reactive antibodies and defining their epitope(s) can provide templates for rational immunogen design strategies for next-generation vaccines. Here, we characterize the receptor-binding-domain-directed, cross-reactive humoral repertoire across 10 human vaccinated donors. We identify cross-reactive antibodies from diverse gene rearrangements targeting two conserved receptor-binding domain epitopes. An engineered immunogen enriches antibody responses to one of these conserved epitopes in mice with pre-existing SARS-CoV-2 immunity; elicited responses neutralize SARS-CoV-2, variants, and related sarbecoviruses. These data show how immune focusing to a conserved epitope targeted by human cross-reactive antibodies may guide pan-sarbecovirus vaccine development, providing a template for identifying such epitopes and translating to immunogen design.
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Affiliation(s)
- Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kerri J St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Maegan L Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Yi Cao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ian W Windsor
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Agnes H Cheng
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mya L Vu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Ty Kannegieter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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8
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Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep 2022; 41:111628. [PMID: 36351401 PMCID: PMC9883670 DOI: 10.1016/j.celrep.2022.111628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 02/04/2022] [Revised: 08/22/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
Pathogens evade host humoral responses by accumulating mutations in surface antigens. While variable, there are conserved regions that cannot mutate without compromising fitness. Antibodies targeting these conserved epitopes are often broadly protective but remain minor components of the repertoire. Rational immunogen design leverages a structural understanding of viral antigens to modulate humoral responses to favor these responses. Here, we report an epitope-enriched immunogen presenting a higher copy number of the influenza hemagglutinin (HA) receptor-binding site (RBS) epitope relative to other B cell epitopes. Immunization in a partially humanized murine model imprinted with an H1 influenza shows H1-specific serum and >99% H1-specific B cells being RBS-directed. Single B cell analyses show a genetically restricted response that structural analysis defines as RBS-directed antibodies engaging the RBS with germline-encoded contacts. These data show how epitope enrichment expands B cell responses toward conserved epitopes and advances immunogen design approaches for next-generation viral vaccines.
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Affiliation(s)
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Rachel Hecht
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Anne A Roffler
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Max J Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Daniel P Maurer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elisa Marchiori
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Thomas H Oguin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham NC 27703, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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9
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Sangesland M, Torrents de la Peña A, Boyoglu-Barnum S, Ronsard L, Mohamed FAN, Moreno TB, Barnes RM, Rohrer D, Lonberg N, Ghebremichael M, Kanekiyo M, Ward A, Lingwood D. Allelic polymorphism controls autoreactivity and vaccine elicitation of human broadly neutralizing antibodies against influenza virus. Immunity 2022; 55:1693-1709.e8. [PMID: 35952670 PMCID: PMC9474600 DOI: 10.1016/j.immuni.2022.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/08/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023]
Abstract
Human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin stalk of group 1 influenza A viruses (IAVs) are biased for IGHV1-69 alleles that use phenylalanine (F54) but not leucine (L54) within their CDRH2 loops. Despite this, we demonstrated that both alleles encode for human IAV bnAbs that employ structurally convergent modes of contact to the same epitope. To resolve differences in lineage expandability, we compared F54 versus L54 as substrate within humanized mice, where antibodies develop with human-like CDRH3 diversity but are restricted to single VH genes. While both alleles encoded for bnAb precursors, only F54 IGHV1-69 supported elicitation of heterosubtypic serum bnAbs following immunization with a stalk-only nanoparticle vaccine. L54 IGHV1-69 was unproductive, co-encoding for anergic B cells and autoreactive stalk antibodies that were cleared from B cell memory. Moreover, human stalk antibodies also demonstrated L54-dependent autoreactivity. Therefore, IGHV1-69 polymorphism, which is skewed ethnically, gates tolerance and vaccine expandability of influenza bnAbs.
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Affiliation(s)
- Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thalia Bracamonte Moreno
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA 94063-2478, USA
| | - Musie Ghebremichael
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Andrew Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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10
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Dobson CS, Reich AN, Gaglione S, Smith BE, Kim EJ, Dong J, Ronsard L, Okonkwo V, Lingwood D, Dougan M, Dougan SK, Birnbaum ME. Antigen identification and high-throughput interaction mapping by reprogramming viral entry. Nat Methods 2022; 19:449-460. [PMID: 35396484 PMCID: PMC9012700 DOI: 10.1038/s41592-022-01436-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 03/01/2022] [Indexed: 01/11/2023]
Abstract
Deciphering immune recognition is critical for understanding a broad range of diseases and for the development of effective vaccines and immunotherapies. Efforts to do so are limited by a lack of technologies capable of simultaneously capturing the complexity of adaptive immunoreceptor repertoires and the landscape of potential antigens. To address this, we present receptor-antigen pairing by targeted retroviruses, which combines viral pseudotyping and molecular engineering approaches to enable one-pot library-on-library interaction screens by displaying antigens on the surface of lentiviruses and encoding their identity in the viral genome. Antigen-specific viral infection of cell lines expressing human T or B cell receptors allows readout of both antigen and receptor identities via single-cell sequencing. The resulting system is modular, scalable and compatible with any cell type. These techniques provide a suite of tools for targeted viral entry, molecular engineering and interaction screens with broad potential applications.
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Affiliation(s)
- Connor S. Dobson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anna N. Reich
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Stephanie Gaglione
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Blake E. Smith
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA,Program in Immunology, Harvard Medical School, Boston, MA, USA
| | - Ellen J. Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Jiayi Dong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Vintus Okonkwo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Michael Dougan
- Program in Immunology, Harvard Medical School, Boston, MA, USA,Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephanie K. Dougan
- Program in Immunology, Harvard Medical School, Boston, MA, USA,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael E. Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Koch Institute for Integrative Cancer Research, Cambridge, MA, USA,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA,Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602, Singapore,
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11
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Feldman J, Bals J, Altomare CG, St. Denis K, Lam EC, Hauser BM, Ronsard L, Sangesland M, Moreno TB, Okonkwo V, Hartojo N, Balazs AB, Bajic G, Lingwood D, Schmidt AG. Naive human B cells engage the receptor binding domain of SARS-CoV-2, variants of concern, and related sarbecoviruses. Sci Immunol 2021; 6:eabl5842. [PMID: 34648356 PMCID: PMC8720485 DOI: 10.1126/sciimmunol.abl5842] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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] [Indexed: 12/26/2022]
Abstract
Initial exposure to a pathogen elicits an adaptive immune response to control and eradicate the threat. Interrogating the abundance and specificity of the naive B cell repertoire drives understanding of how to mount protective responses. Here, we isolated naive B cells from eight seronegative human donors targeting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD). Single-cell B cell receptor (BCR) sequencing identified diverse gene usage and no restriction on complementarity determining region length. A subset of recombinant antibodies produced by naive B cell precursors bound to SARS-CoV-2 RBD and engaged circulating variants including B.1.1.7, B.1.351, and B.1.617.2, as well as preemergent bat-derived coronaviruses RaTG13, SHC104, and WIV1. By structural characterization of a naive antibody in complex with SARS-CoV-2 spike, we identified a conserved mode of recognition shared with infection-induced antibodies. We found that representative naive antibodies could signal in a B cell activation assay, and by using directed evolution, we could select for a higher-affinity RBD interaction, conferred by a single amino acid change. The minimally mutated, affinity-matured antibodies also potently neutralized SARS-CoV-2. Understanding the SARS-CoV-2 RBD–specific naive repertoire may inform potential responses capable of recognizing future SARS-CoV-2 variants or emerging coronaviruses, enabling the development of pan-coronavirus vaccines aimed at engaging protective germline responses.
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Affiliation(s)
- Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Clara G. Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kerri St. Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Evan C. Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Vintus Okonkwo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Nathania Hartojo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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12
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Ronsard L, Yousif AS, Peabody J, Okonkwo V, Devant P, Mogus AT, Barnes RM, Rohrer D, Lonberg N, Peabody D, Chackerian B, Lingwood D. Engineering an Antibody V Gene-Selective Vaccine. Front Immunol 2021; 12:730471. [PMID: 34566992 PMCID: PMC8459710 DOI: 10.3389/fimmu.2021.730471] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022] Open
Abstract
The ligand-binding surface of the B cell receptor (BCR) is formed by encoded and non-encoded antigen complementarity determining regions (CDRs). Genetically reproducible or ‘public’ antibodies can arise when the encoded CDRs play deterministic roles in antigen recognition, notably within human broadly neutralizing antibodies against HIV and influenza virus. We sought to exploit this by engineering virus-like-particle (VLP) vaccines that harbor multivalent affinity against gene-encoded moieties of the BCR antigen binding site. As proof of concept, we deployed a library of RNA bacteriophage VLPs displaying random peptides to identify a multivalent antigen that selectively triggered germline BCRs using the human VH gene IGVH1-2*02. This VLP selectively primed IGHV1-2*02 BCRs that were present within a highly diversified germline antibody repertoire within humanized mice. Our approach thus provides methodology to generate antigens that engage specific BCR configurations of interest, in the absence of structure-based information.
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Affiliation(s)
- Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
| | - Ashraf S Yousif
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
| | - Julianne Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Vintus Okonkwo
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
| | - Pascal Devant
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
| | - Alemu Tekewe Mogus
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | | | - Daniel Rohrer
- Bristol-Myers Squibb, Redwood City, CA, United States
| | - Nils Lonberg
- Bristol-Myers Squibb, Redwood City, CA, United States
| | - David Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, Cambridge, MA, United States
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13
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Das Adhikari U, Eng G, Farcasanu M, Avena LE, Choudhary MC, Triant VA, Flagg M, Schiff AE, Gomez I, Froehle LM, Diefenbach TJ, Ronsard L, Lingwood D, Lee GC, Rabi SA, Erstad D, Velmahos G, Li JZ, Hodin R, Stone JR, Honko AN, Griffiths A, Yilmaz O, Kwon DS. Fecal SARS-CoV-2 RNA is associated with decreased COVID-19 survival. Clin Infect Dis 2021; 74:1081-1084. [PMID: 34245255 PMCID: PMC8406863 DOI: 10.1093/cid/ciab623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
The clinical significance of SARS CoV-2 RNA in stool remains uncertain. We found that extrapulmonary dissemination of infection to the gastrointestinal (GI) tract, assessed by the presence of SARS-CoV-2 RNA in stool, is associated with decreased COVID-19 survival. Measurement of SARS-CoV-2 RNA in stool may have utility for clinical risk assessment.
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Affiliation(s)
- Upasana Das Adhikari
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - George Eng
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114 USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Mara Farcasanu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Laura E Avena
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118 United States
| | - Manish C Choudhary
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115 USA
| | - Virginia A Triant
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Meaghan Flagg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Abigail E Schiff
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Isabella Gomez
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Leah M Froehle
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | | | - Larance Ronsard
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA
| | - Grace C Lee
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Seyed Alireza Rabi
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Derek Erstad
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - George Velmahos
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Jonathan Z Li
- Harvard Medical School, Boston, MA 02114 USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115 USA
| | - Richard Hodin
- Division of Surgery, Massachusetts General Hospital, Boston, MA 02114 USA
| | - James R Stone
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Anna N Honko
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118 United States
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118 United States
| | - Omer Yilmaz
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114 USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139 USA.,Harvard Medical School, Boston, MA 02114 USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114 USA
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14
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Feldman J, Bals J, Altomare CG, St Denis K, Lam EC, Hauser BM, Ronsard L, Sangesland M, Moreno TB, Okonkwo V, Hartojo N, Balazs AB, Bajic G, Lingwood D, Schmidt AG. Naive human B cells engage the receptor binding domain of SARS-CoV-2, variants of concern, and related sarbecoviruses. bioRxiv 2021. [PMID: 33594359 PMCID: PMC7885909 DOI: 10.1101/2021.02.02.429458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exposure to a pathogen elicits an adaptive immune response aimed to control and eradicate. Interrogating the abundance and specificity of the naive B cell repertoire contributes to understanding how to potentially elicit protective responses. Here, we isolated naive B cells from 8 seronegative human donors targeting the SARS-CoV-2 receptor-binding domain (RBD). Single B cell analysis showed diverse gene usage with no restricted complementarity determining region lengths. We show that recombinant antibodies engage SARS-CoV-2 RBD, circulating variants, and pre-emergent coronaviruses. Representative antibodies signal in a B cell activation assay and can be affinity matured through directed evolution. Structural analysis of a naive antibody in complex with spike shows a conserved mode of recognition shared with infection-induced antibodies. Lastly, both naive and affinity-matured antibodies can neutralize SARS-CoV-2. Understanding the naive repertoire may inform potential responses recognizing variants or emerging coronaviruses enabling the development of pan-coronavirus vaccines aimed at engaging germline responses. Isolation of antibody germline precursors targeting the receptor binding domain of coronaviruses.
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Affiliation(s)
- Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Clara G Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kerri St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Evan C Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Vintus Okonkwo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Nathania Hartojo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.,Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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15
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Sangesland M, Yousif AS, Ronsard L, Kazer SW, Zhu AL, Gatter GJ, Hayward MR, Barnes RM, Quirindongo-Crespo M, Rohrer D, Lonberg N, Kwon D, Shalek AK, Lingwood D. A Single Human V H-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood. Cell Rep 2021; 32:108065. [PMID: 32846123 PMCID: PMC7446668 DOI: 10.1016/j.celrep.2020.108065] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 04/08/2020] [Revised: 06/05/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023] Open
Abstract
B cell receptors (BCRs) display a combination of variable (V)-gene-encoded complementarity determining regions (CDRs) and adaptive/hypervariable CDR3 loops to engage antigens. It has long been proposed that the former tune for recognition of pathogens or groups of pathogens. To experimentally evaluate this within the human antibody repertoire, we perform immune challenges in transgenic mice that bear diverse human CDR3 and light chains but are constrained to different human VH-genes. We find that, of six commonly deployed VH sequences, only those CDRs encoded by IGHV1-2∗02 enable polyclonal antibody responses against bacterial lipopolysaccharide (LPS) when introduced to the bloodstream. The LPS is from diverse strains of gram-negative bacteria, and the VH-gene-dependent responses are directed against the non-variable and universal saccrolipid substructure of this antigen. This reveals a broad-spectrum anti-LPS response in which germline-encoded CDRs naturally hardwire the human antibody repertoire for recognition of a conserved microbial target.
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Affiliation(s)
- Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Samuel W Kazer
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Alex Lee Zhu
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - G James Gatter
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Matthew R Hayward
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Rd., Redwood City, CA 94063-2478, USA
| | | | - Daniel Rohrer
- Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Rd., Redwood City, CA 94063-2478, USA
| | - Douglas Kwon
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Division of Infectious Diseases, Massachusetts General Hospital. 55 Fruit St., Boston, MA 02114, USA
| | - Alex K Shalek
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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16
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Sangesland M, de la Pena AT, Ronsard L, Ghebremichael M, Ward AB, Lingwood D. Allelic polymorphism gates vaccine amplification of a human broadly neutralizing response against influenza virus. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.59.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
A major goal of universal influenza vaccine design is to elicit high titer antibody responses against functionally conserved but immunologically subdominant sites of vulnerability. Using a transgenic mouse model where antibodies develop with human-like CDRH3 diversity but are otherwise restricted to single VH-genes of interest, we have demonstrated that human IGHV1-69 endows for pathway-amplifiable broadly neutralizing antibody (bnAb) responses targeting the hemagglutinin (HA) stalk of group 1 influenza A viruses following vaccination with an engineered HA nanoparticle. However, IGHV1-69 is polymorphic with alleles containing either a phenylalanine (F54) or leucine (L54) within the contacting CDRH2 loop at germline, the latter which is correlated with dampened IGHV1-69 usage in human stalk bnAbs. To experimentally test the consequence of this, we applied our transgenic model to assess the capacity for both alleles to vaccine expand bnAbs through pathway-amplification. We found that while both VH forms endow germline targeting solutions to the same bnAb site on HA, only the F54 allele is productive following sequential immunization with a stalk-only nanoparticle immunogen. By contrast, L54 BCRs, while initially expanded, were autoreactive and rapidly tolerized upon boosting. While globally most humans utilize at least one copy of the F54 allele and would be predicted to support bnAb expansion, certain ethnicities show heightened usage of the L54 allele and may be unable to support such pathway-amplification. Thus, we find that allele usage gates the ability to pathway expand productive bnAb responses through immune tolerance.
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17
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Singh J, Ronsard L, Pandey M, Kapoor R, Ramachandran VG, Banerjea AC. Molecular and Genetic Characterization of Natural Variants of HIV-1 Nef Gene from North India and its Functional Implication in Down-Regulation of MHC-I and CD-4. Curr HIV Res 2021; 19:172-187. [PMID: 32981506 DOI: 10.2174/1570162x18666200925160755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND HIV-1 Nef is an important accessory protein with multiple effector functions. Genetic studies of the HIV-1 Nef gene show extensive genetic diversity and the functional studies have been carried out mostly with Nef derived from regions dominated by subtype B (North America & Europe). OBJECTIVE This study was carried out to characterize genetic variations of the Nef gene from HIV-1 infected individuals from North India and to find out their functional implications. METHODS The unique representative variants were sub-cloned in a eukaryotic expression vector and further characterized with respect to their ability to downregulate cell surface expression of CD4 and MHC-1 molecules. RESULTS The phylogenetic analysis of Nef variants revealed sequence similarity with either consensus subtype B or B/C recombinants. Boot scan analysis of some of our variants showed homology to B/C recombinant and some to wild type Nef B. Extensive variations were observed in most of the variants. The dN/dS ratio revealed 80% purifying selection and 20% diversifying selection implying the importance of mutations in Nef variants. Intracellular stability of Nef variants differed greatly when compared with wild type Nef B and C. There were some variants that possessed mutations in the functional domains of Nef and responsible for its differential CD4 and MHC-1 downregulation activity. CONCLUSION We observed enhanced biological activities in some of the variants, perhaps arising from amino acid substitutions in their functional domains. The CD4 and MHC-1 down-regulation activity of Nef is likely to confer immense survival advantage allowing the most rare genotype in a population to become the most abundant after a single selection event.
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Affiliation(s)
- J Singh
- National Institute of Immunology, New Delhi, India
| | - L Ronsard
- National Institute of Immunology, New Delhi, India
| | - M Pandey
- King George`s Medical University, India
| | - R Kapoor
- National Institute of Immunology, New Delhi, India
| | - V G Ramachandran
- Department of Virology, National Institute of Immunology, New Delhi-110067, India
| | - A C Banerjea
- Department of Virology, National Institute of Immunology, New Delhi-110067, India
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18
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Yousif AS, Ronsard L, Shah P, Omatsu T, Sangesland M, Bracamonte Moreno T, Lam EC, Vrbanac VD, Balazs AB, Reinecker HC, Lingwood D. The persistence of interleukin-6 is regulated by a blood buffer system derived from dendritic cells. Immunity 2020; 54:235-246.e5. [PMID: 33357409 PMCID: PMC7836640 DOI: 10.1016/j.immuni.2020.12.001] [Citation(s) in RCA: 22] [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] [Received: 04/06/2020] [Revised: 10/17/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022]
Abstract
The interleukin-6 (IL-6) membrane receptor and its circulating soluble form, sIL-6R, can be targeted by antibody therapy to reduce deleterious immune signaling caused by chronic overexpression of the pro-inflammatory cytokine IL-6. This strategy may also hold promise for treating acute hyperinflammation, such as observed in coronavirus disease 2019 (COVID-19), highlighting a need to define regulators of IL-6 homeostasis. We found that conventional dendritic cells (cDCs), defined in mice via expression of the transcription factor Zbtb46, were a major source of circulating sIL-6R and, thus, systemically regulated IL-6 signaling. This was uncovered through identification of a cDC-dependent but T cell-independent modality that naturally adjuvants plasma cell differentiation and antibody responses to protein antigens. This pathway was then revealed as part of a broader biological buffer system in which cDC-derived sIL-6R set the in-solution persistence of IL-6. This control axis may further inform the development of therapeutic agents to modulate pro-inflammatory immune reactions.
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Affiliation(s)
- Ashraf S Yousif
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Pankaj Shah
- The Center for the Study of Inflammatory Bowel Disease, Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Tatsushi Omatsu
- The Center for the Study of Inflammatory Bowel Disease, Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thalia Bracamonte Moreno
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Evan C Lam
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Vladimir D Vrbanac
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Alejandro B Balazs
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Hans-Christian Reinecker
- The Center for the Study of Inflammatory Bowel Disease, Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA; The Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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19
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Sangesland M, Ghebremichael M, Ronsard L, Lingwood D. The human antibody repertoire genetically encodes for both productive and non-productive targeting solutions against the same broadly neutralizing antibody epitope on influenza virus. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.245.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
A major obstacle to universal influenza vaccine development centers on the ability to elicit high titer responses against functionally conserved but immunologically subdominant features of this virus. Using a transgenic mouse vaccine model wherein antibodies develop with human CDRH3 diversity but are constrained to user defined antibody V genes, we have recently demonstrated that the human VH gene IGHV1-69 encodes for germline B cell receptors (BCRs) that naturally engage a conserved broadly neutralizing epitope on the hemagglutinin (HA) stalk of Group 1 influenza A viruses (IAV). Importantly, this VH endowment enables elicitation of an immunodominant bnAb response against IAV following vaccination with an engineered HA vaccine nanoparticle. However, IGHV1-69 is polymorphic with ~15% of the global population homozygous for alleles that bear a single nucleotide polymorphism (SNP) in CDRH2 (F54L) which confers germline binding to the bnAb target. To test the consequences of this, we applied our transgenic vaccine model to compare the capacity of IGHV1-69 vs IGHV1-69 SNP to elicit bnAb responses following immunization with our HA nanoparticle. We found that while both VH forms endow germline BCR targeting solutions to the same IAV bnAb site, only the WT form is productive following immunization. Germline competition within heterozygous animals (F54/L54) suggests that the capacity for pathway expansion arises via differences in the germline-endowed affinity for the same bnAb target. While globally, most humans utilize at least one copy of IGHV1-69 and would be predicted to support a bnAb response to our vaccine antigen, certain ethnicities show heightened usage of IGHV1-69 SNP and may therefore be limited by non-productive responses.
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20
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Keating CL, Kuhn E, Bals J, Cocco AR, Yousif AS, Matysiak C, Sangesland M, Ronsard L, Smoot M, Moreno TB, Okonkwo V, Setliff I, Georgiev I, Balazs AB, Carr SA, Lingwood D. Spontaneous Glycan Reattachment Following N-Glycanase Treatment of Influenza and HIV Vaccine Antigens. J Proteome Res 2020; 19:733-743. [PMID: 31913636 DOI: 10.1021/acs.jproteome.9b00620] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In cells, asparagine/N-linked glycans are added to glycoproteins cotranslationally, in an attachment process that supports proper folding of the nascent polypeptide. We found that following pruning of N-glycan by the amidase PNGase F, the principal influenza vaccine antigen and major viral spike protein hemagglutinin (HA) spontaneously reattached N-glycan to its de-N-glycosylated positions when the amidase was removed from solution. This reaction, which we term N-glycanation, was confirmed by site-specific analysis of HA glycoforms by mass spectrometry prior to PNGase F exposure, during exposure to PNGase F, and after amidase removal. Iterative rounds of de-N-glycosylation followed by N-glycanation could be repeated at least three times and were observed for other viral glycoproteins/vaccine antigens, including the envelope glycoprotein (Env) from HIV. Covalent N-glycan reattachment was nonenzymatic as it occurred in the presence of metal ions that inhibit PNGase F activity. Rather, N-glycanation relied on a noncovalent assembly between protein and glycan, formed in the presence of the amidase, where linearization of the glycoprotein prevented this retention and subsequent N-glycanation. This reaction suggests that under certain experimental conditions, some glycoproteins can organize self-glycan addition, highlighting a remarkable self-assembly principle that may prove useful for re-engineering therapeutic glycoproteins such as influenza HA or HIV Env, where glycan sequence and structure can markedly affect bioactivity and vaccine efficacy.
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Affiliation(s)
- Celina L Keating
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Eric Kuhn
- The Broad Institute of The Massachusetts Institute of Technology and Harvard University , 415 Main Street , Cambridge , Massachusetts 02142 , United States of America
| | - Julia Bals
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Alexandra R Cocco
- The Broad Institute of The Massachusetts Institute of Technology and Harvard University , 415 Main Street , Cambridge , Massachusetts 02142 , United States of America
| | - Ashraf S Yousif
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Colette Matysiak
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Matthew Smoot
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Thalia Bracamonte Moreno
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Vintus Okonkwo
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Ian Setliff
- Program in Chemical & Physical Biology , Vanderbilt University Medical Center , 340 Light Hall , Nashville 37232-0301 , United States of America.,Vanderbilt Vaccine Center , Vanderbilt University , 2213 Garland Avenue , Nashville , Tennessee 37232-0417 , United States of America
| | - Ivelin Georgiev
- Program in Chemical & Physical Biology , Vanderbilt University Medical Center , 340 Light Hall , Nashville 37232-0301 , United States of America.,Vanderbilt Vaccine Center , Vanderbilt University , 2213 Garland Avenue , Nashville , Tennessee 37232-0417 , United States of America.,Department of Pathology, Microbiology, and Immunology , Vanderbilt University Medical Center , C-3322 Medical Center North , Nashville , Tennessee 37232-2561 , United States of America.,Department of Electrical Engineering and Computer Science , Vanderbilt University , 2301 Vanderbilt Place , Nashville , Tennessee 37235-1826 , United States of America
| | - Alejandro B Balazs
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
| | - Steven A Carr
- The Broad Institute of The Massachusetts Institute of Technology and Harvard University , 415 Main Street , Cambridge , Massachusetts 02142 , United States of America
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital , The Massachusetts Institute of Technology and Harvard University , 400 Technology Square , Cambridge , Massachusetts 02139 , United States of America
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21
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Setliff I, Shiakolas AR, Pilewski KA, Murji AA, Mapengo RE, Janowska K, Richardson S, Oosthuysen C, Raju N, Ronsard L, Kanekiyo M, Qin JS, Kramer KJ, Greenplate AR, McDonnell WJ, Graham BS, Connors M, Lingwood D, Acharya P, Morris L, Georgiev IS. High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity. Cell 2019; 179:1636-1646.e15. [PMID: 31787378 DOI: 10.1016/j.cell.2019.11.003] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/28/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022]
Abstract
B cell receptor (BCR) sequencing is a powerful tool for interrogating immune responses to infection and vaccination, but it provides limited information about the antigen specificity of the sequenced BCRs. Here, we present LIBRA-seq (linking B cell receptor to antigen specificity through sequencing), a technology for high-throughput mapping of paired heavy- and light-chain BCR sequences to their cognate antigen specificities. B cells are mixed with a panel of DNA-barcoded antigens so that both the antigen barcode(s) and BCR sequence are recovered via single-cell next-generation sequencing. Using LIBRA-seq, we mapped the antigen specificity of thousands of B cells from two HIV-infected subjects. The predicted specificities were confirmed for a number of HIV- and influenza-specific antibodies, including known and novel broadly neutralizing antibodies. LIBRA-seq will be an integral tool for antibody discovery and vaccine development efforts against a wide range of antigen targets.
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Affiliation(s)
- Ian Setliff
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrea R Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kelsey A Pilewski
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Amyn A Murji
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rutendo E Mapengo
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Katarzyna Janowska
- Division of Structural Biology, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Simone Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Charissa Oosthuysen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Nagarajan Raju
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Larance Ronsard
- Ragon Institute of Massachusetts General Hospital, Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Juliana S Qin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kevin J Kramer
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Allison R Greenplate
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wyatt J McDonnell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Translational and Clinical Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Mark Connors
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Daniel Lingwood
- Ragon Institute of Massachusetts General Hospital, Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Priyamvada Acharya
- Division of Structural Biology, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lynn Morris
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4041, South Africa
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.
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22
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Sangesland M, Ronsard L, Kazer SW, Bals J, Boyoglu-Barnum S, Yousif AS, Barnes R, Feldman J, Quirindongo-Crespo M, McTamney PM, Rohrer D, Lonberg N, Chackerian B, Graham BS, Kanekiyo M, Shalek AK, Lingwood D. Germline-Encoded Affinity for Cognate Antigen Enables Vaccine Amplification of a Human Broadly Neutralizing Response against Influenza Virus. Immunity 2019; 51:735-749.e8. [PMID: 31563464 PMCID: PMC6801110 DOI: 10.1016/j.immuni.2019.09.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 05/27/2019] [Accepted: 08/30/2019] [Indexed: 12/27/2022]
Abstract
Antibody paratopes are formed by hypervariable complementarity-determining regions (CDRH3s) and variable gene-encoded CDRs. The latter show biased usage in human broadly neutralizing antibodies (bnAbs) against both HIV and influenza virus, suggesting the existence of gene-endowed targeting solutions that may be amenable to pathway amplification. To test this, we generated transgenic mice with human CDRH3 diversity but simultaneously constrained to individual user-defined human immunoglobulin variable heavy-chain (VH) genes, including IGHV1-69, which shows biased usage in human bnAbs targeting the hemagglutinin stalk of group 1 influenza A viruses. Sequential immunization with a stalk-only hemagglutinin nanoparticle elicited group 1 bnAbs, but only in IGHV1-69 mice. This VH-endowed response required minimal affinity maturation, was elicited alongside pre-existing influenza immunity, and when IGHV1-69 B cells were diluted to match the frequency measured in humans. These results indicate that the human repertoire could, in principle, support germline-encoded bnAb elicitation using a single recombinant hemagglutinin immunogen.
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Affiliation(s)
- Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Samuel W Kazer
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main St, Cambridge, MA 02142, USA
| | - Julia Bals
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Ashraf S Yousif
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ralston Barnes
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Jared Feldman
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | | | | | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Road, Redwood City, CA 94063-2478, USA
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, 2425 Camino de Salud, Albuquerque, NM 87106, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Alex K Shalek
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main St, Cambridge, MA 02142, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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23
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Ronsard L, Sood V, Yousif AS, Ramesh J, Shankar V, Das J, Sumi N, Rai T, Mohankumar K, Sridharan S, Dorschel A, Ramachandran VG, Banerjea AC. Genetic Polymorphisms in the Open Reading Frame of the CCR5 gene From HIV-1 Seronegative and Seropositive Individuals From National Capital Regions of India. Sci Rep 2019; 9:7594. [PMID: 31110236 PMCID: PMC6527560 DOI: 10.1038/s41598-019-44136-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/10/2019] [Indexed: 11/19/2022] Open
Abstract
C-C chemokine receptor type 5 (CCR5) serves as a co-receptor for Human immunodeficiency virus (HIV), enabling the virus to enter human CD4 T cells and macrophages. In the absence of CCR5, HIV strains that require CCR5 (R5 or M-tropic HIV) fail to successfully initiate infection. Various natural mutations of the CCR5 gene have been reported to interfere with the HIV-CCR5 interaction, which influences the rate of AIDS progression. Genetic characterization of the CCR5 gene in individuals from the National Capital Regions (NCRs) of India revealed several natural point mutations in HIV seropositive/negative individuals. Furthermore, we identified novel frame-shifts mutations in the CCR5 gene in HIV seronegative individuals, as well as the well reported CCR5Δ32 mutation. Additionally, we observed a number of mutations present only in HIV seropositive individuals. This is the first report to describe the genetic variations of CCR5 in individuals from the NCRs of India and demonstrates the utility of investigating understudied populations to identify novel CCR5 polymorphisms.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of Immunology, New Delhi, India. .,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India. .,Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA, USA.
| | - Vikas Sood
- Laboratory of Virology, National Institute of Immunology, New Delhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Ashraf S Yousif
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA, USA
| | - Janani Ramesh
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vijay Shankar
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Jishnu Das
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA, USA
| | - N Sumi
- Endocrinology & Toxicology Lab, Department of Zoology, University of Calicut, Kerala, India
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, Delhi, India
| | | | - Subhashree Sridharan
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
| | | | | | - Akhil C Banerjea
- Laboratory of Virology, National Institute of Immunology, New Delhi, India.
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Ramesh J, Ronsard L, Gao A, Venugopal B. Autophagy Intertwines with Different Diseases-Recent Strategies for Therapeutic Approaches. Diseases 2019; 7:diseases7010015. [PMID: 30717078 PMCID: PMC6473623 DOI: 10.3390/diseases7010015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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] [Received: 12/06/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 12/12/2022] Open
Abstract
Autophagy is a regular and substantial “clear-out process” that occurs within the cell and that gets rid of debris that accumulates in membrane-enclosed vacuoles by using enzyme-rich lysosomes, which are filled with acids that degrade the contents of the vacuoles. This machinery is well-connected with many prevalent diseases, including cancer, HIV, and Parkinson’s disease. Considering that autophagy is well-known for its significant connections with a number of well-known fatal diseases, a thorough knowledge of the current findings in the field is essential in developing therapies to control the progression rate of diseases. Thus, this review summarizes the critical events comprising autophagy in the cellular system and the significance of its key molecules in manifesting this pathway in various diseases for down- or upregulation. We collectively reviewed the role of autophagy in various diseases, mainly neurodegenerative diseases, cancer, inflammatory diseases, and renal disorders. Here, some collective reports on autophagy showed that this process might serve as a dual performer: either protector or contributor to certain diseases. The aim of this review is to help researchers to understand the role of autophagy-regulating genes encoding functional open reading frames (ORFs) and its connection with diseases, which will eventually drive better understanding of both the progression and suppression of different diseases at various stages. This review also focuses on certain novel therapeutic strategies which have been published in the recent years based on targeting autophagy key proteins and its interconnecting signaling cascades.
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Affiliation(s)
- Janani Ramesh
- Department of Medical Biochemistry, Dr. A.L.M. Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai 600113, India.
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02140, USA.
| | - Anthony Gao
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Bhuvarahamurthy Venugopal
- Department of Medical Biochemistry, Dr. A.L.M. Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai 600113, India.
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Ronsard L, Rai T, Rai D, Ramachandran VG, Banerjea AC. In silico Analyses of Subtype Specific HIV-1 Tat-TAR RNA Interaction Reveals the Structural Determinants for Viral Activity. Front Microbiol 2017; 8:1467. [PMID: 28848502 PMCID: PMC5550727 DOI: 10.3389/fmicb.2017.01467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/20/2017] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Tat transactivates viral genes through strong interaction with TAR RNA. The stem-loop bulged region of TAR consisting of three nucleotides at the position 23–25 and the loop region consisting of six nucleotides at the position 30–35 are essential for viral transactivation. The arginine motif of Tat (five arginine residues on subtype TatC) is critically important for TAR interaction. Any mutations in this motif could lead to reduce transactivation ability and pathogenesis. Here, we identified structurally important residues (arginine and lysine residues) of Tat in this motif could bind to TAR via hydrogen bond interactions which is critical for transactivation. Natural mutant Ser46Phe in the core motif could likely led to conformational change resulting in more hydrogen bond interactions than the wild type Tat making it highly potent transactivator. Importantly, we report the possible probabilities of number of hydrogen bond interactions in the wild type Tat and the mutants with TAR complexes. This study revealed the differential transactivation of subtype B and C Tat could likely be due to the varying number of hydrogen bonds with TAR. Our data support that the N-terminal and the C-terminal domains of Tat is involved in the TAR interactions through hydrogen bonds which is important for transactivation. This study highlights the evolving pattern of structurally important determinants of Tat in the arginine motif for viral transactivation.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of ImmunologyNew Delhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical SciencesNew Delhi, India
| | - Devesh Rai
- Department of Microbiology, All India Institute of Medical SciencesNew Delhi, India
| | - Vishnampettai G Ramachandran
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Akhil C Banerjea
- Laboratory of Virology, National Institute of ImmunologyNew Delhi, India
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Chaudhuri S, Singh MK, Bhattacharya D, Datta A, Hazra I, Mondal S, Faruk Sk Md O, Ronsard L, Ghosh TK, Chaudhuri S. T11TS immunotherapy repairs PI3K-AKT signaling in T-cells: Clues toward enhanced T-cell survival in rat glioma model. J Cell Physiol 2017; 233:759-770. [PMID: 28608562 DOI: 10.1002/jcp.26047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 06/12/2017] [Indexed: 01/20/2023]
Abstract
Malignant glioma is the most fatal of astrocytic lineage tumors despite therapeutic advances. Onset and progression of gliomas is accompanied by severe debilitation of T-cell defense and T-cell survival. One of the chief contributors to T-cell survival downstream of activation is the PI3K-AKT pathway. Our prior studies showed that the novel immunotherapeutic molecule T11-target structure (T11TS) blocks T-cell apoptosis in glioma. We also showed activation of immunological synapse components and calcineurin-NFAT pathway following T11TS immunotherapy of glioma-bearing rats. This lead to investigations whether such T-cell activation upon T11TS therapy translates into activation of downstream PI3K/AKT signals which may be related to observed blockade of T-cell apoptosis. For the purpose, we assessed by flowcytometry and immunoblotting, expressions of PI3K, PDK1, AKT, p-AKT, and PTEN in splenic T-cells of normal, experimentally-induced glioma-bearing rats and glioma-bearing rats receiving first, second and third doses of T11TS. We also determined comparative nuclear translocation of NF-κB across groups. We found significant increases in T-cell expressions of PDK1, PI3K, and p-AKT in T11TS-treated animal groups compared to sharp downregulations in glioma. AKT levels remained unchanged across groups. PTEN levels declined sharply after T11TS immunotherapy. T11TS also caused enhanced NF-κB translocation to the T-cell nucleus compared to glioma group. Results showed heightened activation of the PI3K-AKT pathway in glioma-bearing rats following T11TS immunotherapy. These results illustrate the novel role of T11TS immunotherapy in ameliorating the PI3K pathway in T-cells in glioma-bearing animals to enhance T-cell survival, according greater defense against glioma. The study thus has far-reaching clinical outcomes.
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Affiliation(s)
- Suhnrita Chaudhuri
- Department of Laboratory Medicine, Cellular and Molecular Immunology Lab, School of Tropical Medicine, Kolkata, West Bengal 700073, India.,Department of Physiology, University of Calcutta, Kolkata, West Bengal 700009, India
| | - Manoj K Singh
- Department of Laboratory Medicine, Cellular and Molecular Immunology Lab, School of Tropical Medicine, Kolkata, West Bengal 700073, India
| | - Debanjan Bhattacharya
- Department of Laboratory Medicine, Cellular and Molecular Immunology Lab, School of Tropical Medicine, Kolkata, West Bengal 700073, India
| | - Ankur Datta
- Department of Laboratory Medicine, Cellular and Molecular Immunology Lab, School of Tropical Medicine, Kolkata, West Bengal 700073, India
| | - Iman Hazra
- Department of Laboratory Medicine, Cellular and Molecular Immunology Lab, School of Tropical Medicine, Kolkata, West Bengal 700073, India
| | - Somnath Mondal
- Department of Laboratory Medicine, Cellular and Molecular Immunology Lab, School of Tropical Medicine, Kolkata, West Bengal 700073, India
| | - Omar Faruk Sk Md
- Department of Laboratory Medicine, Cellular and Molecular Immunology Lab, School of Tropical Medicine, Kolkata, West Bengal 700073, India
| | - Larance Ronsard
- Virology Lab, National Institute of Immunology, New Delhi 110067, India
| | - Tushar K Ghosh
- Department of Physiology, University of Calcutta, Kolkata, West Bengal 700009, India
| | - Swapna Chaudhuri
- Department of Laboratory Medicine, Cellular and Molecular Immunology Lab, School of Tropical Medicine, Kolkata, West Bengal 700073, India
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Ronsard L, Ganguli N, Singh VK, Mohankumar K, Rai T, Sridharan S, Pajaniradje S, Kumar B, Rai D, Chaudhuri S, Coumar MS, Ramachandran VG, Banerjea AC. Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction. Front Microbiol 2017; 8:706. [PMID: 28484443 PMCID: PMC5399533 DOI: 10.3389/fmicb.2017.00706] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/05/2017] [Indexed: 01/10/2023] Open
Abstract
HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR) RNA. In this study, HIV-1 infected patients (n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities. Molecular dynamics simulation data verified that the variants with this mutation had a higher binding affinity for TAR than both the wild-type Tat and other variants that lacked Ser46Phe and Ser61Arg. Other mutations in Tat conferred varying affinities for TAR interaction leading to differential transactivation abilities. This is the first report from North India with a clinical validation of CD4 counts to demonstrate the influence of Tat genetic variations affecting the stability of Tat and its interaction with TAR. This study highlights the co-evolution pattern of Tat and predominant nucleotides for Tat activity, facilitating the identification of genetic determinants for the attenuation of viral gene expression.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of ImmunologyDelhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalDelhi, India
| | - Nilanjana Ganguli
- Laboratory of Virology, National Institute of ImmunologyDelhi, India
| | - Vivek K Singh
- Centre for Bioinformatics, School of Life Sciences, Pondicherry UniversityPondicherry, India
| | - Kumaravel Mohankumar
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India.,Department of Veterinary Physiology and Pharmacology, Texas A&M University, College StationTX, USA
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical SciencesDelhi, India
| | - Subhashree Sridharan
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India.,Department of Symptom Research, The University of Texas MD Anderson Cancer Center, HoustonTX, USA
| | - Sankar Pajaniradje
- Department of Biochemistry and Molecular Biology, Pondicherry UniversityPondicherry, India
| | - Binod Kumar
- Department of Microbiology and Immunology, Rosalind Franklin University of Medicine and Science, ChicagoIL, USA
| | - Devesh Rai
- Department of Microbiology, All India Institute of Medical SciencesDelhi, India
| | - Suhnrita Chaudhuri
- Department of Neurological Surgery, Northwestern University, ChicagoIL, USA
| | - Mohane S Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry UniversityPondicherry, India
| | | | - Akhil C Banerjea
- Laboratory of Virology, National Institute of ImmunologyDelhi, India
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Padmapriya R, Gayathri L, Ronsard L, Akbarsha MA, Raveendran R. In vitro Anti-Proliferative Effect of Tephrosia purpurea on Human Hepatocellular Carcinoma Cells. Pharmacogn Mag 2017; 13:S16-S21. [PMID: 28479720 PMCID: PMC5407109 DOI: 10.4103/0973-1296.203981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/11/2016] [Indexed: 12/23/2022] Open
Abstract
Background: Tephrosia purpurea is an Indian herb used in traditional medicine to treat various diseases such as jaundice, asthma, liver and urinary disorders. However, the anti-cancer potential of T. purpurea on hepatocellular carcinoma (HCC) is poorly understood. Therefore, this study aims to investigate the anti-cancer activity of T. purpurea in HepG2 hepatocellular carcinoma cells. Methods: The leaves and root of T. purpurea were extracted with methanol using soxhlet apparatus. The cytotoxicity of the T. purpurea extracts in HepG2 cells was evaluated using MTT assay whereas the mode of cell death was examined by AOEB, Hoechst and JC1 staining under a fluorescence microscope. T. purpurea extracts-induced caspase-3 expression was investigated using colorimetric assay. Results: The leaves and root extracts inhibited HepG2 cell growth at the IC50 of 102.33 ± 10.26 µg/mL and 276.67 ± 20.43 µg/mL respectively at 24 h. Chromatin condensation, nuclear fragmentation, apoptotic bodies formation and mitochondrial membrane depolarization were observed in HepG2 cells treated with both extracts. The caspase-3 expression was significantly (p < 0.05) increased in extracts treated cells when compared to control. Conclusion: The leaves and root extracts of T. purpurea induce apoptosis mediated cell death in HepG2 cells. SUMMARY The leaves and root extracts of T. purpurea exhibited anticancer activity in HepG2 hepatocellular carcinoma cells. These extracts induced cell shrinkage, DNA condensation and fragmentation, mitochondrial membrane depolarization and upregulated caspase-3 expression indicating T. purpurea extracts induce apoptosis in HepG2 cells.
Abbreviation used: AO: acridine orange, DMSO: dimethyl sulfoxide, EB: ethidium bromide, IC50: the concentration at which 50% of cancer cells are dead, JC-1: 5, 5’, 6, 6’-tetrachloro-1, 1’, 3, 3’-tetraethyl-imidacarbocyanine iodide, MTT: 3-4, 5-dimethylthiazole-2-yl, 2,5-diphenyl tetrazolium bromide, PBS: phosphate-buffered saline, ΔΨm: mitochondrial trans-membrane potential.
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Affiliation(s)
| | - Loganathan Gayathri
- Mahatma Gandhi-Doerenkamp Center, Bharathidasan University, Tiruchirappalli, India
| | - Larance Ronsard
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mohammad A Akbarsha
- Mahatma Gandhi-Doerenkamp Center, Bharathidasan University, Tiruchirappalli, India
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Sridharan S, Mohankumar K, Jeepipalli SPK, Sankaramourthy D, Ronsard L, Subramanian K, Thamilarasan M, Raja K, Chandra VK, Sadras SR. Neuroprotective effect of Valeriana wallichii rhizome extract against the neurotoxin MPTP in C57BL/6 mice. Neurotoxicology 2015; 51:172-83. [PMID: 26522450 DOI: 10.1016/j.neuro.2015.10.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 10/20/2015] [Accepted: 10/26/2015] [Indexed: 01/08/2023]
Abstract
Oxidative stress and inflammation are some of the contributing factors for dopaminergic neurodegeneration in Parkinson's disease (PD). Though Valeriana wallichii D.C. is known for its nervine activities its effect against PD is yet to be studied. This is the first report on the antioxidant and anti-inflammatory effect of V. wallichii rhizome extract (VWE) in MPTP induced PD mice. GC-MS analysis of VWE indicated the presence of phytoconstituents like isovaleric acid and acacetin. PD induced mice were treated orally with three different doses (50, 100 and 200mg/kg body weight (BW)) of VWE for 14 days and their behavioural changes were studied on days 0, 8, 13 and 21. The levels of striatal dopamine, mid brain tyrosine hydroxylase positive (TH(+)) cell count, TH protein expression, reactive oxygen species (ROS), lipid peroxidation (LPO), antioxidants and inflammatory cytokines were analysed. Mid brain glial fibrillary acidic protein (GFAP) expression was assessed by immunohistochemistry and western blotting. Also mid brain histopathological analysis was performed. VWE treatment significantly recuperated the altered behavioural test scores, striatal dopamine levels, mid brain TH(+) cell count and TH protein levels, increased GFAP expression and the histopathological changes observed in PD mice. Similarly, diminished levels of antioxidants, elevated levels of ROS, LPO and inflammatory cytokines were also significantly ameliorated following VWE treatment. The effective dose of VWE was found to be 200mg/kg BW. Conclusively, V. wallichii rhizome extract has the potential to mitigate oxidative stress and inflammatory damage in PD.
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Affiliation(s)
- Subhashree Sridharan
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Kumaravel Mohankumar
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Syam Praveen Kumar Jeepipalli
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Divya Sankaramourthy
- Department of Pharmacology, Mother Theresa Post Graduate and Research Institute of Health Sciences, Puducherry 605006, India
| | - Larance Ronsard
- Virology Laboratory-II, National Institute of Immunology, New Delhi, Delhi 110067, India
| | - Kavimani Subramanian
- Department of Pharmacology, Mother Theresa Post Graduate and Research Institute of Health Sciences, Puducherry 605006, India
| | - Manivasagam Thamilarasan
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar 608002, India
| | - Kumar Raja
- Department of Pathology, Rajiv Gandhi Institute of Veterinary Education and Research, Puducherry 605009, India
| | - Varshney Khub Chandra
- Department of Pathology, Rajiv Gandhi Institute of Veterinary Education and Research, Puducherry 605009, India
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
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Ronsard L, Ramachandran VG, Banerjea AC. Functional characterization of HIV-1 Tat exon-1 variants from North India and their implications on HIV-1 transactivation and TAR interaction. BMC Infect Dis 2014. [PMCID: PMC4080451 DOI: 10.1186/1471-2334-14-s3-p81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Mohankumar K, Pajaniradje S, Sridharan S, Singh VK, Ronsard L, Banerjea AC, Benson CS, Coumar MS, Rajagopalan R. Mechanism of apoptotic induction in human breast cancer cell, MCF-7, by an analog of curcumin in comparison with curcumin – An in vitro and in silico approach. Chem Biol Interact 2014; 210:51-63. [DOI: 10.1016/j.cbi.2013.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/20/2013] [Accepted: 12/16/2013] [Indexed: 11/30/2022]
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Ronsard L, Lata S, Singh J, Ramachandran VG, Das S, Banerjea AC. Molecular and genetic characterization of natural HIV-1 Tat Exon-1 variants from North India and their functional implications. PLoS One 2014; 9:e85452. [PMID: 24465566 PMCID: PMC3900424 DOI: 10.1371/journal.pone.0085452] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 11/27/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Designing an ideal vaccine against HIV-1 has been difficult due to enormous genetic variability as a result of high replication rate and lack of proofreading activity of reverse transcriptase leading to emergence of genetic variants and recombinants. Tat transactivates HIV-1 LTR, resulting in a remarkable increase in viral gene expression, and plays a vital role in pathogenesis. The aim of this study was to characterize the genetic variations of Tat exon-1 from HIV-1 infected patients from North India. METHODS Genomic DNA was isolated from PBMCs and Tat exon-1 was PCR amplified with specific primers followed by cloning, sequencing and sequence analyses using bioinformatic tools for predicting HIV-1 subtypes, recombination events, conservation of domains and phosphorylation sites, and LTR transactivation by luciferase assay. RESULTS Phylogenetic analysis of Tat exon-1 variants (n = 120) revealed sequence similarity with South African Tat C sequences and distinct geographical relationships were observed for B/C recombinants. Bootscan analysis of our variants showed 90% homology to Tat C and 10% to B/C recombinants with a precise breakpoint. Natural substitutions were observed with high allelic frequencies which may be beneficial for virus. High amino acid conservation was observed in Tat among Anti Retroviral Therapy (ART) recipients. Barring few changes, most of the functional domains, predicted motifs and phosphorylation sites were well conserved in most of Tat variants. dN/dS analysis revealed purifying selection, implying the importance of functional conservation of Tat exon-1. Our Indian Tat C variants and B/C recombinants showed differential LTR transactivation. CONCLUSIONS The possible role of Tat exon-1 variants in shaping the current HIV-1 epidemic in North India was highlighted. Natural substitutions across conserved functional domains were observed and provided evidence for the emergence of B/C recombinants within the ORF of Tat exon-1. These events are likely to have implications for viral pathogenesis and vaccine formulations.
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Affiliation(s)
- Larance Ronsard
- Virology Laboratory, National Institute of Immunology, New Delhi, India
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Sneh Lata
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Jyotsna Singh
- Virology Laboratory, National Institute of Immunology, New Delhi, India
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | | | - Shukla Das
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Akhil C. Banerjea
- Virology Laboratory, National Institute of Immunology, New Delhi, India
- * E-mail: ,
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Lata S, Ronsard L, Sood V, Dar SA, Ramachandran VG, Das S, Banerjea AC. Effect on HIV-1 gene expression, Tat-Vpr interaction and cell apoptosis by natural variants of HIV-1 Tat exon 1 and Vpr from Northern India. PLoS One 2013; 8:e82128. [PMID: 24367500 PMCID: PMC3868622 DOI: 10.1371/journal.pone.0082128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/18/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Since HIV-1 Tat and Vpr genes are involved in promoter transactivation, apoptosis, etc, we carried out studies to find out nature and extent of natural variation in the two genes from seropositive patients from Northern India and determined their functional implications. METHODS HIV-1 tat exon 1 and vpr were amplified from the genomic DNA isolated from the blood of HIV-1 infected individuals using specific primers by Polymerase Chain reaction (PCR) and subjected to extensive genetic analysis (CLUSTAL W, Simplot etc). Their expression was monitored by generating myc fusion clones. Tat exon 1 and Vpr variants were co-transfected with the reporter gene construct (LTR-luc) and their transactivation potential was monitored by measuring luciferase activity. Apoptosis and cell cycle analysis was done by Propidium Iodide (PI) staining followed by FACS. RESULTS Exon 1 of tat was amplified from 21 samples and vpr was amplified from 16 samples. One of the Tat exon 1 variants showed phylogenetic relatedness to subtype B & C and turned out to be a unique recombinant. Two of the Vpr variants were B/C/D recombinants. These natural variations were found to have no impact on the stability of Tat and Vpr. These variants differed in their ability to transactivate B LTR and C LTR promoters. B/C recombinant Tat showed better co-operative interaction with Vpr. B/C/D recombination in Vpr was found to have no effect on its co-operativity with Tat. Recombinant Tat (B/C) induced more apoptosis than wild type B and C Tat. The B/C/D recombination in Vpr did not affect its G2 arrest induction potential but reduced its apoptosis induction ability. CONCLUSIONS Extensive sequence and region-specific variations were observed in Tat and Vpr genes from HIV-1 infected individuals from Northern India. These variations have functional implications & therefore important for the pathogenicity of virus.
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Affiliation(s)
- Sneh Lata
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Larance Ronsard
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Vikas Sood
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Sajad A. Dar
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Vishnampettai G. Ramachandran
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
- * E-mail: (VGR); (ACB)
| | - Shukla Das
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Delhi, India
| | - Akhil C. Banerjea
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
- * E-mail: (VGR); (ACB)
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Verma S, Ronsard L, Kapoor R, Banerjea AC. Genetic characterization of natural variants of Vpu from HIV-1 infected individuals from Northern India and their impact on virus release and cell death. PLoS One 2013; 8:e59283. [PMID: 23555649 PMCID: PMC3610703 DOI: 10.1371/journal.pone.0059283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 02/13/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genetic studies reveal that vpu is one of the most variable regions in HIV-1 genome. Functional studies have been carried out mostly with Vpu derived from laboratory adapted subtype B pNL 4-3 virus. The rationale of this study was to characterize genetic variations that are present in the vpu gene from HIV-1 infected individuals from North-India (Punjab/Haryana) and determine their functional relevance. METHODS Functionally intact vpu gene variants were PCR amplified from genomic DNA of HIV-1 infected individuals. These variants were then subjected to genetic analysis and unique representative variants were cloned under CMV promoter containing expression vector as well as into pNL 4-3 HIV-1 virus for intracellular expression studies. These variants were characterized with respect to their ability to promote virus release as well as cell death. RESULTS Based on phylogenetic analysis and extensive polymorphisms with respect to consensus Vpu B and C, we were able to arbitrarily assign variants into two major groups (B and C). The group B variants always showed significantly higher virus release activity and exhibited moderate levels of cell death. On the other hand, group C variants displayed lower virus release activity but greater cell death potential. Interestingly, Vpu variants with a natural S61A mutation showed greater intracellular stability. These variants also exhibited significant reduction in their intracellular ubiquitination and caused greater virus release. Another group C variant that possessed a non-functional β-TrcP binding motif due to two critical serine residues (S52 and S56) being substituted with isoleucine residues, showed reduced virus release activity but modest cytotoxic activity. CONCLUSIONS The natural variations exhibited by our Vpu variants involve extensive polymorphism characterized by substitution and deletions that contribute toward positive selection. We identified two major groups and an extremely rare β-TrcP binding motif mutant that show widely varying biological activities with potential implications for conferring subtype-specific pathogenesis.
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Affiliation(s)
- Sachin Verma
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Larance Ronsard
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Richa Kapoor
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
| | - Akhil C. Banerjea
- Laboratory of Virology, National Institute of Immunology, New Delhi, India
- * E-mail:
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