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Finkelstein MT, Parker Miller E, Erdman MC, Fera D. Analysis of two cooperating antibodies unveils immune pressure imposed on HIV Env to elicit a V3-glycan supersite broadly neutralizing antibody lineage. Front Immunol 2022; 13:962939. [PMID: 36225920 PMCID: PMC9548623 DOI: 10.3389/fimmu.2022.962939] [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: 06/06/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022] Open
Abstract
Elicitation of broadly neutralizing antibodies (bnAbs) is a goal of vaccine design as a strategy for targeting highly divergent strains of HIV-1. Current HIV-1 vaccine design efforts seek to elicit bnAbs by first eliciting their precursors through prime-boost regimens. This requires an understanding of the co-evolution between viruses and antibodies. Towards this goal, we have analyzed two cooperating antibodies, DH475 and DH272, which exerted pressure on the HIV population in an infected donor, called CH848, to evolve in such a way that it became sensitive to the V3-glycan supersite DH270 bnAb lineage. We obtained a 2.90Å crystal structure of DH475 in complex with the Man9 glycan and a negative stain EM model of DH272 in complex with the HIV-1 spike trimer, Env. Coupled with additional modeling studies and biochemical data, our studies reveal that DH475 contacts a V3- and V4-glycan dependent epitope accessible on an open or shed Env and that DH272 makes critical contacts with the V1V2 and V3 loops on HIV-1 Env. Using these data, we suggest a prime-boost regimen that may facilitate the initiation of DH270-like bnAb precursors.
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Affiliation(s)
| | | | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, United States
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2
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Fera D, Lin S, Naagaard D, Chen H, Finkelstein MT, Glatz G, Hayashi S, Hotan Q, Lau B, LeBlanc J, Li K, Parker Miller E, Ye M, Zaidi H. Mapping Allosteric Sites on Protein Kinases Critical in MAPK Signaling. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r3001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Daniela Fera
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Sabrina Lin
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | - Han Chen
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | | | - Scout Hayashi
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Quynn Hotan
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Benjamin Lau
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Julia LeBlanc
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Kevin Li
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | - Ming Ye
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Hussain Zaidi
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
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3
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Finkelstein MT, Erdman MC, Fera D. Characterization of the DH475 cooperating antibody and its interaction with the HIV‐1 spike. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r3277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Daniela Fera
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
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4
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Lin S, Naagaard MD, Pham T, Fera D. Investigating the Interaction Interface between MEK and ERK Kinase. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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5
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Ye M, Hotan Q, Glatz G, Finkelstein MT, Hayashi S, Miller EP, Lau B, Li K, Chen H, LeBlanc J, Zaidi H, Fera D. Biochemical analysis of human ERK2 mutants reveals important residues in MEK1‐ERK2 binding and phosphorylation. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r4202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ming Ye
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Quynn Hotan
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | | | - Scout Hayashi
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Emma P. Miller
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Benjamin Lau
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Kevin Li
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Han Chen
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | - Hussain Zaidi
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Daniela Fera
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
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6
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Parker Miller E, Fera D. Analysis of the interactions between the HIV‐1 Spike and the F7‐22 “cooperating” antibody. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r3084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Daniela Fera
- Chemistry & BiochemistrySwarthmore CollegeSwarthmorePA
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7
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Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW. The biological and clinical significance of emerging SARS-CoV-2 variants. Nat Rev Genet 2021; 22:757-773. [PMID: 34535792 PMCID: PMC8447121 DOI: 10.1038/s41576-021-00408-x] [Citation(s) in RCA: 594] [Impact Index Per Article: 198.0] [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] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The past several months have witnessed the emergence of SARS-CoV-2 variants with novel spike protein mutations that are influencing the epidemiological and clinical aspects of the COVID-19 pandemic. These variants can increase rates of virus transmission and/or increase the risk of reinfection and reduce the protection afforded by neutralizing monoclonal antibodies and vaccination. These variants can therefore enable SARS-CoV-2 to continue its spread in the face of rising population immunity while maintaining or increasing its replication fitness. The identification of four rapidly expanding virus lineages since December 2020, designated variants of concern, has ushered in a new stage of the pandemic. The four variants of concern, the Alpha variant (originally identified in the UK), the Beta variant (originally identified in South Africa), the Gamma variant (originally identified in Brazil) and the Delta variant (originally identified in India), share several mutations with one another as well as with an increasing number of other recently identified SARS-CoV-2 variants. Collectively, these SARS-CoV-2 variants complicate the COVID-19 research agenda and necessitate additional avenues of laboratory, epidemiological and clinical research.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Philip L Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ravindra K Gupta
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | | | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, USA
| | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University, Stanford, CA, USA.
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8
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Parker Miller E, Finkelstein MT, Erdman MC, Seth PC, Fera D. A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target. Viruses 2021; 13:v13091774. [PMID: 34578355 PMCID: PMC8472920 DOI: 10.3390/v13091774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/29/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Antibodies that can neutralize diverse HIV-1 strains develop in ~10–20% of HIV-1 infected individuals, and their elicitation is a goal of vaccine design. Such antibodies can also serve as therapeutics for those who have already been infected with the virus. Structural characterizations of broadly reactive antibodies in complex with the HIV-1 spike indicate that there are a limited number of sites of vulnerability on the spike. Analysis of their structures can help reveal commonalities that would be useful in vaccine design and provide insights on combinations of antibodies that can be used to minimize the incidence of viral resistance mutations. In this review, we give an update on recent structures determined of the spike in complex with broadly neutralizing antibodies in the context of all epitopes on the HIV-1 spike identified to date.
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Williams WB, Meyerhoff RR, Edwards RJ, Li H, Manne K, Nicely NI, Henderson R, Zhou Y, Janowska K, Mansouri K, Gobeil S, Evangelous T, Hora B, Berry M, Abuahmad AY, Sprenz J, Deyton M, Stalls V, Kopp M, Hsu AL, Borgnia MJ, Stewart-Jones GBE, Lee MS, Bronkema N, Moody MA, Wiehe K, Bradley T, Alam SM, Parks RJ, Foulger A, Oguin T, Sempowski GD, Bonsignori M, LaBranche CC, Montefiori DC, Seaman M, Santra S, Perfect J, Francica JR, Lynn GM, Aussedat B, Walkowicz WE, Laga R, Kelsoe G, Saunders KO, Fera D, Kwong PD, Seder RA, Bartesaghi A, Shaw GM, Acharya P, Haynes BF. Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell 2021; 184:2955-2972.e25. [PMID: 34019795 PMCID: PMC8135257 DOI: 10.1016/j.cell.2021.04.042] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [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: 12/11/2020] [Revised: 03/22/2021] [Accepted: 04/23/2021] [Indexed: 01/03/2023]
Abstract
Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA.
| | - R Ryan Meyerhoff
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - R J Edwards
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | | | | | | | | | - Bhavna Hora
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | | | | | | | | | - Megan Kopp
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | | | - Matthew S Lee
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Naomi Bronkema
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | | | - Thomas Oguin
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Michael Seaman
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - John Perfect
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - Geoffrey M Lynn
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Avidea Technologies, Inc., Baltimore, MD, USA
| | | | | | - Richard Laga
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27705, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA.
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10
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Fera D, Nguyen D, Lin LY, Zhou J, Kibby E, Sia T, Tillis T, Vapuryan N, Xu M, Potluri R, Shin Y, Erler E, Bronkema N, Boehlmer D, Chung C, Burkhard C, Zeng S, Grasso M, Acevedo L, Marmorstein R. Identification and Characterization of a B‐Raf Kinase Alpha Helix Critical for the Activity of MEK Kinase in MAPK Signaling. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.01944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Daniela Fera
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Diep Nguyen
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | - Jeffrey Zhou
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Emily Kibby
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Twan Sia
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Tiara Tillis
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | - Ming‐Ray Xu
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - Rajiv Potluri
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | - YongJoon Shin
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | - Naomi Bronkema
- Chemistry and BiochemistrySwarthmore CollegeSwarthmorePA
| | | | | | | | - Shirley Zeng
- Department of Biochemistry and BiophysicsUniversity of PennsylvaniaPhiladelphiaPA
- Abramson Family Cancer Research InstituteUniversity of PennsylvaniaPhiladelphiaPA
| | - Michael Grasso
- Department of Biochemistry and BiophysicsUniversity of PennsylvaniaPhiladelphiaPA
- Department of ChemistryUniversity of PennsylvaniaPhiladelphiaPA
| | - Lucila Acevedo
- Department of Biochemistry and BiophysicsUniversity of PennsylvaniaPhiladelphiaPA
| | - Ronen Marmorstein
- Department of Biochemistry and BiophysicsUniversity of PennsylvaniaPhiladelphiaPA
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11
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Nguyen D, Lin LY, Zhou JO, Kibby E, Sia TW, Tillis TD, Vapuryan N, Xu MR, Potluri R, Shin Y, Erler EA, Bronkema N, Boehlmer DJ, Chung CD, Burkhard C, Zeng SH, Grasso M, Acevedo LA, Marmorstein R, Fera D. Identification and Characterization of a B-Raf Kinase α-Helix Critical for the Activity of MEK Kinase in MAPK Signaling. Biochemistry 2020; 59:4755-4765. [PMID: 33272017 DOI: 10.1021/acs.biochem.0c00598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the MAPK pathway, an oncogenic V600E mutation in B-Raf kinase causes the enzyme to be constitutively active, leading to aberrantly high phosphorylation levels of its downstream effectors, MEK and ERK kinases. The V600E mutation in B-Raf accounts for more than half of all melanomas and ∼3% of all cancers, and many drugs target the ATP binding site of the enzyme for its inhibition. Because B-Raf can develop resistance against these drugs and such drugs can induce paradoxical activation, drugs that target allosteric sites are needed. To identify other potential drug targets, we generated and kinetically characterized an active form of B-RafV600E expressed using a bacterial expression system. In doing so, we identified an α-helix on B-Raf, found at the B-Raf-MEK interface, that is critical for their interaction and the oncogenic activity of B-RafV600E. We assessed the binding between B-Raf mutants and MEK using pull downs and biolayer interferometry and assessed phosphorylation levels of MEK in vitro and in cells as well as its downstream target ERK to show that mutating certain residues on this α-helix is detrimental to binding and downstream activity. Our results suggest that this B-Raf α-helix binding site on MEK could be a site to target for drug development to treat B-RafV600E-induced melanomas.
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Affiliation(s)
- Diep Nguyen
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Linda Yingqi Lin
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Jeffrey O Zhou
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Emily Kibby
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Twan W Sia
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Tiara D Tillis
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Narine Vapuryan
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Ming-Ray Xu
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Rajiv Potluri
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - YongJoon Shin
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Elizabeth A Erler
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Naomi Bronkema
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Daniel J Boehlmer
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Christopher D Chung
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Caroline Burkhard
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Shirley H Zeng
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael Grasso
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lucila A Acevedo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
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12
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Zhou JO, Zaidi HA, Ton T, Fera D. Corrigendum: The Effects of Framework Mutations at the Variable Domain Interface on Antibody Affinity Maturation in an HIV-1 Broadly Neutralizing Antibody Lineage. Front Immunol 2020; 11:620518. [PMID: 33312180 PMCID: PMC7709735 DOI: 10.3389/fimmu.2020.620518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
- Jeffrey O. Zhou
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, United States
| | - Hussain A. Zaidi
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, United States
| | - Therese Ton
- Department of Biology, Swarthmore College, Swarthmore, PA, United States
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, United States
- *Correspondence: Daniela Fera,
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13
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Zhou JO, Zaidi HA, Ton T, Fera D. The Effects of Framework Mutations at the Variable Domain Interface on Antibody Affinity Maturation in an HIV-1 Broadly Neutralizing Antibody Lineage. Front Immunol 2020; 11:1529. [PMID: 32765530 PMCID: PMC7379371 DOI: 10.3389/fimmu.2020.01529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 02/11/2020] [Accepted: 06/10/2020] [Indexed: 11/30/2022] Open
Abstract
Understanding affinity maturation of antibodies that can target many variants of HIV-1 is important for vaccine development. While the antigen-binding site of antibodies is known to mutate throughout the co-evolution of antibodies and viruses in infected individuals, the roles of the mutations in the antibody framework region are not well understood. Throughout affinity maturation, the CH103 broadly neutralizing antibody lineage, from an individual designated CH505, altered the orientation of one of its antibody variable domains. The change in orientation was a response to insertions in the variable loop 5 (V5) of the HIV envelope. In this study, we generated CH103 lineage antibody variants in which residues in the variable domain interface were mutated, and measured the binding to both autologous and heterologous HIV-1 envelopes. Our data show that very few mutations in an early intermediate antibody of the lineage can improve binding toward both autologous and heterologous HIV-1 envelopes. We also crystallized an antibody mutant to show that framework mutations alone can result in a shift in relative orientations of the variable domains. Taken together, our results demonstrate the functional importance of residues located outside the antigen-binding site in affinity maturation.
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Affiliation(s)
- Jeffrey O Zhou
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, United States
| | - Hussain A Zaidi
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, United States
| | - Therese Ton
- Department of Biology, Swarthmore College, Swarthmore, PA, United States
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, United States
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14
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Bajic G, Maron MJ, Caradonna TM, Tian M, Mermelstein A, Fera D, Kelsoe G, Kuraoka M, Schmidt AG. Structure-Guided Molecular Grafting of a Complex Broadly Neutralizing Viral Epitope. ACS Infect Dis 2020; 6:1182-1191. [PMID: 32267676 DOI: 10.1021/acsinfecdis.0c00008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/26/2022]
Abstract
Antigenic variation and viral evolution have thwarted traditional influenza vaccination strategies. The broad protection afforded by a "universal" influenza vaccine may come from immunogens that elicit humoral immune responses targeting conserved epitopes on the viral hemagglutinin (HA), such as the receptor-binding site (RBS). Here, we engineered candidate immunogens that use noncirculating, avian influenza HAs as molecular scaffolds to present the broadly neutralizing RBS epitope from historical, circulating H1 influenzas. These "resurfaced" HAs (rsHAs) remove epitopes potentially targeted by strain-specific responses in immune-experienced individuals. Through structure-guided optimization, we improved two antigenically different scaffolds to bind a diverse panel of pan-H1 and H1/H3 cross-reactive bnAbs with high affinity. Subsequent serological and single germinal center B cell analyses from murine prime-boost immunizations show that the rsHAs are both immunogenic and can augment the quality of elicited RBS-directed antibodies. Our structure-guided, RBS grafting approach provides candidate immunogens for selectively presenting a conserved viral epitope.
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Affiliation(s)
- Goran Bajic
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Max J. Maron
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Timothy M. Caradonna
- Laboratory of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, United States
| | - Ming Tian
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Adam Mermelstein
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina 27710, United States
- Department of Immunology, Duke University, Durham, North Carolina 27710, United States
| | - Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, North Carolina 27710, United States
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, United States
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115, United States
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15
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Zhou JO, Ton T, Morriss JW, Nguyen D, Fera D. Structural Insights from HIV-Antibody Coevolution and Related Immunization Studies. AIDS Res Hum Retroviruses 2018; 34:760-768. [PMID: 29984587 DOI: 10.1089/aid.2018.0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 12/24/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is a rapidly evolving pathogen that causes acquired immunodeficiency syndrome (AIDS) in humans. There are ∼30-35 million people infected with HIV around the world, and ∼25 million have died since the first reported cases in 1981. In addition, each year 2-3 million people become newly infected, and >1 million die of AIDS. An HIV-1 vaccine would help halt an AIDS pandemic, and efforts to develop a vaccine have focused on targeting the HIV-1 envelope, Env, found on the surface of the virus. A number of chronically infected individuals have been shown to produce antibodies, called broadly neutralizing antibodies (bnAbs), that target many strains of HIV-1 by binding to Env, thus suggesting promise for HIV-1 vaccine development. BnAbs take years to develop, and have a number of traits that inhibit their production; thus, a number of researchers are trying to understand the pathways that result in bnAb production, so that they can be elicited more rapidly by vaccination. This review discusses results and implications from two HIV-1-infected individuals studied longitudinally who produced bnAbs against two different sites on HIV-1 Env, and immunization studies that used Envs derived from those individuals.
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Affiliation(s)
- Jeffrey O. Zhou
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania
| | - Therese Ton
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Julia W. Morriss
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Diep Nguyen
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania
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16
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Bonsignori M, Kreider EF, Fera D, Meyerhoff RR, Bradley T, Wiehe K, Alam SM, Aussedat B, Walkowicz WE, Hwang KK, Saunders KO, Zhang R, Gladden MA, Monroe A, Kumar A, Xia SM, Cooper M, Louder MK, McKee K, Bailer RT, Pier BW, Jette CA, Kelsoe G, Williams WB, Morris L, Kappes J, Wagh K, Kamanga G, Cohen MS, Hraber PT, Montefiori DC, Trama A, Liao HX, Kepler TB, Moody MA, Gao F, Danishefsky SJ, Mascola JR, Shaw GM, Hahn BH, Harrison SC, Korber BT, Haynes BF. Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies. Sci Transl Med 2017; 9:9/381/eaai7514. [PMID: 28298420 DOI: 10.1126/scitranslmed.aai7514] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 08/18/2016] [Accepted: 01/31/2017] [Indexed: 12/30/2022]
Abstract
A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs.
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Affiliation(s)
- Mattia Bonsignori
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA. .,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Edward F Kreider
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniela Fera
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - R Ryan Meyerhoff
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Todd Bradley
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Kevin Wiehe
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - S Munir Alam
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Baptiste Aussedat
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - William E Walkowicz
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | | | - Amit Kumar
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brendan W Pier
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia A Jette
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Wilton B Williams
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - John Kappes
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Gift Kamanga
- University of North Carolina Project, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Myron S Cohen
- Departments of Medicine, Epidemiology, and Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Peter T Hraber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Durham, NC 27710, USA.,Department of Surgery, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashley Trama
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Thomas B Kepler
- Department of Microbiology and Department of Mathematics and Statistics, Boston University, Boston, MA 02215, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC 27710, USA.,Department of Immunology, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Pediatrics, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Feng Gao
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Samuel J Danishefsky
- Department of Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - George M Shaw
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen C Harrison
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bette T Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Barton F Haynes
- Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710, USA. .,Duke Human Vaccine Institute, Durham, NC 27710, USA
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17
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Horwitz JA, Bar-On Y, Lu CL, Fera D, Lockhart AAK, Lorenzi JCC, Nogueira L, Golijanin J, Scheid JF, Seaman MS, Gazumyan A, Zolla-Pazner S, Nussenzweig MC. Non-neutralizing Antibodies Alter the Course of HIV-1 Infection In Vivo. Cell 2017; 170:637-648.e10. [PMID: 28757252 DOI: 10.1016/j.cell.2017.06.048] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 11/26/2022]
Abstract
Non-neutralizing antibodies (nnAbs) to HIV-1 show little measurable activity in prevention or therapy in animal models yet were the only correlate of protection in the RV144 vaccine trial. To investigate the role of nnAbs on HIV-1 infection in vivo, we devised a replication-competent HIV-1 reporter virus that expresses a heterologous HA-tag on the surface of infected cells and virions. Anti-HA antibodies bind to, but do not neutralize, the reporter virus in vitro. However, anti-HA protects against infection in humanized mice and strongly selects for nnAb-resistant viruses in an entirely Fc-dependent manner. Similar results were also obtained with tier 2 HIV-1 viruses using a human anti-gp41 nnAb, 246D. While nnAbs are demonstrably less effective than broadly neutralizing antibodies (bNAbs) against HIV-1 in vitro and in vivo, the data show that nnAbs can protect against and alter the course of HIV-1 infection in vivo. PAPERCLIP.
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Affiliation(s)
- Joshua A Horwitz
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Laboratory of Structural Cell Biology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA; Whelan Laboratory, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Yotam Bar-On
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ching-Lan Lu
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Daniela Fera
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Ainsley A K Lockhart
- Laboratory of Mucosal Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Johannes F Scheid
- Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center/Harvard Medical School, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Susan Zolla-Pazner
- Zolla-Pazner Laboratory, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave, New York, NY 10065, USA.
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18
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Easterhoff D, Moody MA, Fera D, Cheng H, Ackerman M, Wiehe K, Saunders KO, Pollara J, Vandergrift N, Parks R, Kim J, Michael NL, O’Connell RJ, Excler JL, Robb ML, Vasan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Nitayaphan S, Sinangil F, Tartaglia J, Phogat S, Kepler TB, Alam SM, Liao HX, Ferrari G, Seaman MS, Montefiori DC, Tomaras GD, Harrison SC, Haynes BF. Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial. PLoS Pathog 2017; 13:e1006182. [PMID: 28235027 PMCID: PMC5342261 DOI: 10.1371/journal.ppat.1006182] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/08/2017] [Accepted: 01/12/2017] [Indexed: 12/13/2022] Open
Abstract
The canary pox vector and gp120 vaccine (ALVAC-HIV and AIDSVAX B/E gp120) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy. Although the vaccine Env AE.A244 gp120 is antigenic for the unmutated common ancestor of V1V2 broadly neutralizing antibody (bnAbs), no plasma bnAb activity was induced. The RV305 (NCT01435135) HIV-1 clinical trial was a placebo-controlled randomized double-blinded study that assessed the safety and efficacy of vaccine boosting on B cell repertoires. HIV-1-uninfected RV144 vaccine recipients were reimmunized 6–8 years later with AIDSVAX B/E gp120 alone, ALVAC-HIV alone, or a combination of ALVAC-HIV and AIDSVAX B/E gp120 in the RV305 trial. Env-specific post-RV144 and RV305 boost memory B cell VH mutation frequencies increased from 2.9% post-RV144 to 6.7% post-RV305. The vaccine was well tolerated with no adverse events reports. While post-boost plasma did not have bnAb activity, the vaccine boosts expanded a pool of envelope CD4 binding site (bs)-reactive memory B cells with long third heavy chain complementarity determining regions (HCDR3) whose germline precursors and affinity matured B cell clonal lineage members neutralized the HIV-1 CRF01 AE tier 2 (difficult to neutralize) primary isolate, CNE8. Electron microscopy of two of these antibodies bound with near-native gp140 trimers showed that they recognized an open conformation of the Env trimer. Although late boosting of RV144 vaccinees expanded a novel pool of neutralizing B cell clonal lineages, we hypothesize that boosts with stably closed trimers would be necessary to elicit antibodies with greater breadth of tier 2 HIV-1 strains. Trial Registration: ClinicalTrials.gov NCT01435135 Developing a successful HIV-1 vaccine remains a high global health priority. Several HIV-1 vaccine trials have been performed with only the RV144 vaccine trial showing vaccine efficacy, albeit modest. No broadly neutralizing antibody activity was identified in RV144 and inducing sterilizing immunity against a complex pathogen like HIV-1 remains a major challenge. Here we characterize the B cell responses after RV144 vaccine-recipients received two additional boosts severals years after the conclusion of the RV144 vaccine trial. Delayed and repetitive boosting of RV144 vaccine-recipients was capable of increasing somatic hypermutation of the Env-reactive antibodies and expanding subdominant pools of neutralizing B cell clonal lineages. These data are pertinent to HIV-1 vaccine-regimen design.
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Affiliation(s)
- David Easterhoff
- Duke University, Durham, North Carolina, United States of America
- * E-mail: (DE); (BFH)
| | - M. Anthony Moody
- Duke University, Durham, North Carolina, United States of America
| | - Daniela Fera
- Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hao Cheng
- Dartmouth College, Hanover, New Hampshire, United States of America
| | | | - Kevin Wiehe
- Duke University, Durham, North Carolina, United States of America
| | | | - Justin Pollara
- Duke University, Durham, North Carolina, United States of America
| | | | - Rob Parks
- Duke University, Durham, North Carolina, United States of America
| | - Jerome Kim
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Nelson L. Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | | | - Jean-Louis Excler
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Merlin L. Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sandhya Vasan
- U.S. Army Medical Directorate, AFRIMS, Bangkok, Thailand
| | | | | | | | | | - Faruk Sinangil
- GSID, South San Francisco, California, United States of America
| | - James Tartaglia
- Sanofi Pasteur, Swiftwater, Pennsylvania, United States of America
| | - Sanjay Phogat
- Sanofi Pasteur, Swiftwater, Pennsylvania, United States of America
| | - Thomas B. Kepler
- Boston University, Boston, Massachusetts, United States of America
| | - S. Munir Alam
- Duke University, Durham, North Carolina, United States of America
| | - Hua-Xin Liao
- Duke University, Durham, North Carolina, United States of America
| | - Guido Ferrari
- Duke University, Durham, North Carolina, United States of America
| | - Michael S. Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | - Stephen C. Harrison
- Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Barton F. Haynes
- Duke University, Durham, North Carolina, United States of America
- * E-mail: (DE); (BFH)
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19
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Bradley T, Fera D, Bhiman J, Eslamizar L, Lu X, Anasti K, Zhang R, Sutherland LL, Scearce RM, Bowman CM, Stolarchuk C, Lloyd KE, Parks R, Eaton A, Foulger A, Nie X, Karim SSA, Barnett S, Kelsoe G, Kepler TB, Alam SM, Montefiori DC, Moody MA, Liao HX, Morris L, Santra S, Harrison SC, Haynes BF. Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site. Cell Rep 2015; 14:43-54. [PMID: 26725118 DOI: 10.1016/j.celrep.2015.12.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/20/2015] [Accepted: 12/04/2015] [Indexed: 12/13/2022] Open
Abstract
Antibodies that neutralize autologous transmitted/founder (TF) HIV occur in most HIV-infected individuals and can evolve to neutralization breadth. Autologous neutralizing antibodies (nAbs) against neutralization-resistant (Tier-2) viruses are rarely induced by vaccination. Whereas broadly neutralizing antibody (bnAb)-HIV-Envelope structures have been defined, the structures of autologous nAbs have not. Here, we show that immunization with TF mutant Envs gp140 oligomers induced high-titer, V5-dependent plasma neutralization for a Tier-2 autologous TF evolved mutant virus. Structural analysis of autologous nAb DH427 revealed binding to V5, demonstrating the source of narrow nAb specificity and explaining the failure to acquire breadth. Thus, oligomeric TF Envs can elicit autologous nAbs to Tier-2 HIVs, but induction of bnAbs will require targeting of precursors of B cell lineages that can mature to heterologous neutralization.
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Affiliation(s)
- Todd Bradley
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Daniela Fera
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jinal Bhiman
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2131, South Africa
| | - Leila Eslamizar
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ruijung Zhang
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Richard M Scearce
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cindy M Bowman
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Christina Stolarchuk
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaoyan Nie
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Salim S Abdool Karim
- Center for AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa; Columbia University, New York, NY 10032, USA
| | - Susan Barnett
- Novartis Vaccines and Diagnostics, Inc., Cambridge, MA 02139, USA
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - S Munir Alam
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa; Center for AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2131, South Africa
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Stephen C Harrison
- Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Departments of Medicine, Surgery and Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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20
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Malecka KA, Fera D, Schultz DC, Hodawadekar S, Reichman M, Donover PS, Murphy ME, Marmorstein R. Identification and characterization of small molecule human papillomavirus E6 inhibitors. ACS Chem Biol 2014; 9:1603-12. [PMID: 24854633 PMCID: PMC4145632 DOI: 10.1021/cb500229d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [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] [Indexed: 01/21/2023]
Abstract
Cervical cancer is the sixth most common cancer in women worldwide and the leading cause of women's death in developing countries. Nearly all cervical cancers are associated with infection of the human papillomavirus (HPV). This sexually transmitted pathogen disrupts the cell cycle via two oncoproteins: E6 and E7. Cells respond to E7-mediated degradation of pRB by upregulating the p53 tumor suppressor pathway. However, E6 thwarts this response by binding to the cellular E6-Associating Protein (E6AP) and targeting p53 for degradation. These two virus-facilitated processes pave the way for cellular transformation. Prophylactic HPV vaccines are available, but individuals already infected with HPV lack drug-based therapeutic options. To fill this void, we sought to identify small molecule inhibitors of the E6-E6AP interaction. We designed an ELISA-based high throughput assay to rapidly screen compound libraries, and hits were confirmed in several orthogonal biochemical and cell-based assays. Over 88,000 compounds were screened; 30 had in vitro potencies in the mid-nanomolar to mid-micromolar range and were classified as validated hits. Seven of these hits inhibited p53 degradation in cell lines with HPV-integrated genomes. Two compounds of similar scaffold successfully blocked p53 degradation and inhibited cell proliferation in cells stably transfected with E6. Together, these studies suggest that small molecules can successfully block E6-dependent p53 degradation and restore p53 activity. The compounds identified here constitute attractive starting points for further medicinal chemistry efforts and development into beneficial therapeutics.
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Affiliation(s)
| | - Daniela Fera
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - David C. Schultz
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | | | - Melvin Reichman
- Lankenau
Institute for Medical Research, Chemical Genomics Center, Wynnewood, Pennsylvania 19096, United States
| | - Preston S. Donover
- Lankenau
Institute for Medical Research, Chemical Genomics Center, Wynnewood, Pennsylvania 19096, United States
| | - Maureen E. Murphy
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
| | - Ronen Marmorstein
- The Wistar Institute, Philadelphia, Pennsylvania 19104, United States
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Fera D, Marmorstein R. Different regions of the HPV-E7 and Ad-E1A viral oncoproteins bind competitively but through distinct mechanisms to the CH1 transactivation domain of p300. Biochemistry 2012; 51:9524-34. [PMID: 23121466 DOI: 10.1021/bi3011863] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
p300 is a transcriptional coactivator that participates in many important processes in the cell, including proliferation, differentiation, and apoptosis. The viral oncoproteins, adenovirus (Ad) E1A and human papillomavirus (HPV) E7, have been implicated in binding to p300. The Ad-E1A-p300 interaction has been shown to result in the induction of cellular proliferation, epigenetic reprogramming, and cellular transformation and cancer. The HPV-E7-p300 interaction, on the other hand, is not well understood. p300 contains three zinc-binding domains, CH1-CH3, and studies have shown that Ad-E1A can bind to the p300 CH1 and CH3 domains whereas E7 can bind to the CH1 domain and to a lesser extent to the CH2 and CH3 domains. Here we address how high-risk HPV16-E7 and Ad5-E1A, which have different structures, can both bind the p300 CH1 domain. Using pull-down, gel filtration, and analytical ultracentrifugation studies, we show that the N-terminus and CR1 domains of Ad5-E1A and the CR1 and CR2 domains of HPV16-E7 bind to the p300 CH1 domain competitively and with midnanomolar and low micromolar dissociation constants, respectively. We also show that Ad5-E1A can form a ternary complex with the p300 CH1 domain and the retinoblastoma pRb transcriptional repressor, whereas HPV16-E7 cannot. These studies suggest that the HPV16-E7 and Ad5-E1A viral oncoproteins bind to the same p300 CH1 domain to disrupt p300 function by distinct mechanisms.
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Affiliation(s)
- Daniela Fera
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA
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Fera D, Schultz DC, Hodawadekar S, Reichman M, Donover PS, Melvin J, Troutman S, Kissil J, Huryn DM, Marmorstein R. Identification and characterization of small molecule antagonists of pRb inactivation by viral oncoproteins. Chem Biol 2012; 19:518-28. [PMID: 22520758 PMCID: PMC3334872 DOI: 10.1016/j.chembiol.2012.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 01/21/2012] [Accepted: 03/01/2012] [Indexed: 11/23/2022]
Abstract
The retinoblastoma protein pRb is essential for regulating many cellular activities through its binding and inhibition of E2F transcription activators, and pRb inactivation leads to many cancers. pRb activity can be perturbed by viral oncoproteins including human papillomavirus (HPV) that share an LxCxE motif. Because there are no treatments for existing HPV infection leading to nearly all cervical cancers and other cancers to a lesser extent, we screened for compounds that inhibit the ability of HPV-E7 to disrupt pRb/E2F complexes. This lead to the identification of thiadiazolidinedione compounds that bind to pRb with mid-high nanomolar dissociation constants, are competitive with the binding of viral oncoproteins containing an LxCxE motif, and are selectively cytotoxic in HPV-positive cells alone and in mice. These inhibitors provide a promising scaffold for the development of therapies to treat HPV-mediated pathologies.
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Affiliation(s)
- Daniela Fera
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David C. Schultz
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Santosh Hodawadekar
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Melvin Reichman
- The Lankenau Institute for Medical Research, Chemical Genomics Center, Wynnewood, PA 19096, USA
| | - Preston Scott Donover
- The Lankenau Institute for Medical Research, Chemical Genomics Center, Wynnewood, PA 19096, USA
| | - Jason Melvin
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott Troutman
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Joseph Kissil
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Donna M. Huryn
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Program in Gene Expression and Regulation, The Wistar Institute, Philadelphia, PA 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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Yi C, Troutman S, Fera D, Stemmer-Rachamimov A, Avila JL, Christian N, Persson NL, Shimono A, Speicher DW, Marmorstein R, Holmgren L, Kissil JL. A tight junction-associated Merlin-angiomotin complex mediates Merlin's regulation of mitogenic signaling and tumor suppressive functions. Cancer Cell 2011; 19:527-40. [PMID: 21481793 PMCID: PMC3075552 DOI: 10.1016/j.ccr.2011.02.017] [Citation(s) in RCA: 197] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 10/20/2010] [Accepted: 02/22/2011] [Indexed: 01/12/2023]
Abstract
The Merlin/NF2 tumor suppressor restrains cell growth and tumorigenesis by controlling contact-dependent inhibition of proliferation. We have identified a tight-junction-associated protein complex comprising Merlin, Angiomotin, Patj, and Pals1. We demonstrate that Angiomotin functions downstream of Merlin and upstream of Rich1, a small GTPase Activating Protein, as a positive regulator of Rac1. Merlin, through competitive binding to Angiomotin, releases Rich1 from the Angiomotin-inhibitory complex, allowing Rich1 to inactivate Rac1, ultimately leading to attenuation of Rac1 and Ras-MAPK pathways. Patient-derived Merlin mutants show diminished binding capacities to Angiomotin and are unable to dissociate Rich1 from Angiomotin or inhibit MAPK signaling. Depletion of Angiomotin in Nf2(-/-) Schwann cells attenuates the Ras-MAPK signaling pathway, impedes cellular proliferation in vitro and tumorigenesis in vivo.
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Affiliation(s)
- Chunling Yi
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Scott Troutman
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Daniela Fera
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Jacqueline L. Avila
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Neepa Christian
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Nathalie Luna Persson
- Department of Oncology-Pathology, Cancer Center Karolinska Institutet, SE-17176 Stockholm, Sweden
| | - Akihiko Shimono
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117456
| | - David W. Speicher
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Ronen Marmorstein
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lars Holmgren
- Department of Oncology-Pathology, Cancer Center Karolinska Institutet, SE-17176 Stockholm, Sweden
| | - Joseph L. Kissil
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
- Corresponding author. ; Phone: 1-215-898-3874
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Abstract
BACKGROUND The proliferation of structural and functional studies of RNA has revealed an increasing range of RNA's structural repertoire. Toward the objective of systematic cataloguing of RNA's structural repertoire, we have recently described the basis of a graphical approach for organizing RNA secondary structures, including existing and hypothetical motifs. DESCRIPTION We now present an RNA motif database based on graph theory, termed RAG for RNA-As-Graphs, to catalogue and rank all theoretically possible, including existing, candidate and hypothetical, RNA secondary motifs. The candidate motifs are predicted using a clustering algorithm that classifies RNA graphs into RNA-like and non-RNA groups. All RNA motifs are filed according to their graph vertex number (RNA length) and ranked by topological complexity. CONCLUSIONS RAG's quantitative cataloguing allows facile retrieval of all classes of RNA secondary motifs, assists identification of structural and functional properties of user-supplied RNA sequences, and helps stimulate the search for novel RNAs based on predicted candidate motifs.
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Affiliation(s)
- Daniela Fera
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
| | - Namhee Kim
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
| | - Nahum Shiffeldrim
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
| | - Julie Zorn
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
| | - Uri Laserson
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
| | - Hin Hark Gan
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Room 1001, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
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Abstract
MOTIVATION Understanding RNA's structural diversity is vital for identifying novel RNA structures and pursuing RNA genomics initiatives. By classifying RNA secondary motifs based on correlations between conserved RNA secondary structures and functional properties, we offer an avenue for predicting novel motifs. Although several RNA databases exist, no comprehensive schemes are available for cataloguing the range and diversity of RNA's structural repertoire. RESULTS Our RNA-As-Graphs (RAG) database describes and ranks all mathematically possible (including existing and candidate) RNA secondary motifs on the basis of graphical enumeration techniques. We represent RNA secondary structures as two-dimensional graphs (networks), specifying the connectivity between RNA secondary structural elements, such as loops, bulges, stems and junctions. We archive RNA tree motifs as 'tree graphs' and other RNAs, including pseudoknots, as general 'dual graphs'. All RNA motifs are catalogued by graph vertex number (a measure of sequence length) and ranked by topological complexity. The RAG inventory immediately suggests candidates for novel RNA motifs, either naturally occurring or synthetic, and thereby might stimulate the prediction and design of novel RNA motifs. AVAILABILITY The database is accessible on the web at http://monod.biomath.nyu.edu/rna
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Affiliation(s)
- Hin Hark Gan
- Department of Chemistry, New York University, New York, NY 10003, USA
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