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Cottrell CA, Hu X, Lee JH, Skog P, Luo S, Flynn CT, McKenney KR, Hurtado J, Kalyuzhniy O, Liguori A, Willis JR, Landais E, Raemisch S, Chen X, Baboo S, Himansu S, Diedrich JK, Duan H, Cheng C, Schiffner T, Bader DLV, Kulp DW, Tingle R, Georgeson E, Eskandarzadeh S, Alavi N, Lu D, Sincomb T, Kubitz M, Mullen TM, Yates JR, Paulson JC, Mascola JR, Alt FW, Briney B, Sok D, Schief WR. Heterologous prime-boost vaccination drives early maturation of HIV broadly neutralizing antibody precursors in humanized mice. Sci Transl Med 2024; 16:eadn0223. [PMID: 38753806 DOI: 10.1126/scitranslmed.adn0223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
A protective HIV vaccine will likely need to induce broadly neutralizing antibodies (bnAbs). Vaccination with the germline-targeting immunogen eOD-GT8 60mer adjuvanted with AS01B was found to induce VRC01-class bnAb precursors in 97% of vaccine recipients in the IAVI G001 phase 1 clinical trial; however, heterologous boost immunizations with antigens more similar to the native glycoprotein will be required to induce bnAbs. Therefore, we designed core-g28v2 60mer, a nanoparticle immunogen to be used as a first boost after eOD-GT8 60mer priming. We found, using a humanized mouse model approximating human conditions of VRC01-class precursor B cell diversity, affinity, and frequency, that both protein- and mRNA-based heterologous prime-boost regimens induced VRC01-class antibodies that gained key mutations and bound to near-native HIV envelope trimers lacking the N276 glycan. We further showed that VRC01-class antibodies induced by mRNA-based regimens could neutralize pseudoviruses lacking the N276 glycan. These results demonstrated that heterologous boosting can drive maturation toward VRC01-class bnAb development and supported the initiation of the IAVI G002 phase 1 trial testing mRNA-encoded nanoparticle prime-boost regimens.
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Affiliation(s)
- Christopher A Cottrell
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Therapeutics, Cambridge, MA 02139, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patrick Skog
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sai Luo
- HHMI, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Claudia T Flynn
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katherine R McKenney
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan Hurtado
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan R Willis
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sebastian Raemisch
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabyasachi Baboo
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Jolene K Diedrich
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hongying Duan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Torben Schiffner
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel L V Bader
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Tingle
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erik Georgeson
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nushin Alavi
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Danny Lu
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Troy Sincomb
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tina-Marie Mullen
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frederick W Alt
- HHMI, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Bryan Briney
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Development, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Therapeutics, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
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2
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Wang X, Cottrell CA, Hu X, Ray R, Bottermann M, Villavicencio PM, Yan Y, Xie Z, Warner JE, Ellis-Pugh JR, Kalyuzhniy O, Liguori A, Willis JR, Menis S, Rämisch S, Eskandarzadeh S, Kubitz M, Tingle R, Phelps N, Groschel B, Himansu S, Carfi A, Kirsch KH, Weldon SR, Nair U, Schief WR, Batista FD. mRNA-LNP prime boost evolves precursors toward VRC01-like broadly neutralizing antibodies in preclinical humanized mouse models. Sci Immunol 2024; 9:eadn0622. [PMID: 38753808 DOI: 10.1126/sciimmunol.adn0622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/09/2024] [Indexed: 05/18/2024]
Abstract
Germline-targeting (GT) protein immunogens to induce VRC01-class broadly neutralizing antibodies (bnAbs) to the CD4-binding site of the HIV envelope (Env) have shown promise in clinical trials. Here, we preclinically validated a lipid nanoparticle-encapsulated nucleoside mRNA (mRNA-LNP) encoding eOD-GT8 60mer as a soluble self-assembling nanoparticle in mouse models. In a model with three humanized B cell lineages bearing distinct VRC01-precursor B cell receptors (BCRs) with similar affinities for eOD-GT8, all lineages could be simultaneously primed and undergo diversification and affinity maturation without exclusionary competition. Boosts drove precursor B cell participation in germinal centers; the accumulation of somatic hypermutations, including in key VRC01-class positions; and affinity maturation to boost and native-like antigens in two of the three precursor lineages. We have preclinically validated a prime-boost regimen of soluble self-assembling nanoparticles encoded by mRNA-LNP, demonstrating that multiple lineages can be primed, boosted, and diversified along the bnAb pathway.
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Affiliation(s)
- Xuesong Wang
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Christopher A Cottrell
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Inc., Cambridge, MA 02139, USA
| | - Rashmi Ray
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Maria Bottermann
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Yu Yan
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Zhenfei Xie
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - John E Warner
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sebastian Rämisch
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Tingle
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bettina Groschel
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | - Kathrin H Kirsch
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Stephanie R Weldon
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Usha Nair
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - William R Schief
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, Scripps Research Institute, La Jolla, CA 92037, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
- Moderna Inc., Cambridge, MA 02139, USA
| | - Facundo D Batista
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Hu J, Luo S, Tian M, Ye AY. TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing. BMC Bioinformatics 2024; 25:154. [PMID: 38637756 PMCID: PMC11025179 DOI: 10.1186/s12859-024-05775-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, 'N's. PCR duplicates introduced in library preparation are conventionally removed in genomics studies, and several deduplication tools have been developed for this purpose. Two identical reads may appear different due to ambiguous bases and the existing tools cannot address 'N's correctly or efficiently. RESULTS Here we proposed and implemented TrieDedup, which uses the trie (prefix tree) data structure to compare and store sequences. TrieDedup can handle ambiguous base 'N's, and efficiently deduplicate at the level of raw sequences. We also reduced its memory usage by approximately 20% by implementing restrictedDict in Python. We benchmarked the performance of the algorithm and showed that TrieDedup can deduplicate reads up to 270-fold faster than pairwise comparison at a cost of 32-fold higher memory usage. CONCLUSIONS The TrieDedup algorithm may facilitate PCR deduplication, barcode or UMI assignment, and repertoire diversity analysis of large-scale high-throughput sequencing datasets with its ultra-fast algorithm that can account for ambiguous bases due to sequencing errors.
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Affiliation(s)
- Jianqiao Hu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Sai Luo
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
- School of Basic Medical Science, Tsinghua University, Beijing, China
| | - Ming Tian
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Adam Yongxin Ye
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
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4
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Qiu Y, Yi X, Tang X, Wei Y, Zhang B, Duan S, Wang S, Sun X. Differential analysis of immunoglobulin gene expression pattern in chickens of distinct breeds and developmental periods. J Anim Sci 2024; 102:skae111. [PMID: 38651250 PMCID: PMC11107122 DOI: 10.1093/jas/skae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/20/2024] [Indexed: 04/25/2024] Open
Abstract
Immunoglobulin is an essential component of the body's defense against pathogens, aiding in the recognition and clearance of foreign antigens. Research concerning immunoglobulin gene and its diversity of expression across different breeds within the same species is relatively scarce. In this study, we employed RACE (Rapid Amplification of cDNA Ends) technology, prepared DNA libraries, performed high-throughput sequencing, and conducted related bioinformatics analysis to analyze the differences in immunoglobulin gene diversity and expression at different periods in Hy-line brown hens, Lueyang black-bone chickens, and Beijing-You chickens. The study found that the composition of chicken immunoglobulin genes is relatively simple, with both the light chain and heavy chain having a functional V gene. Additionally, the mechanisms of immunoglobulin diversity generation tended to be consistent among different breeds and periods of chickens, primarily relying on abundant junctional diversity, somatic hypermutation (SHM), and gene conversion (GCV) to compensate for the limitations of low-level V(D)J recombination. As the age increased, the junctional diversity of IgH and IgL tended to diversify and showed similar expression patterns among different breeds. In the three chicken breeds, the predominant types of mutations observed in IGHV and IGLV SHM were A to G and G to A transitions. Specifically, IGLV exhibited a preference for A to G mutations, whereas IGHV displayed a bias toward G to A mutations. The regions at the junctions between framework regions (FR) and complementarity-determining regions (CDR) and within the CDR regions themselves are typically prone to mutations. The locations of GCV events in IGLV and IGHV do not show significant differences, and replacement segments are concentrated in the central regions of FR1, CDR, and FR2. Importantly, gene conversion events are not random occurrences. Additionally, our investigation revealed that CDRH3 in chickens of diverse breeds and periods the potential for diversification through the incorporation of cysteine. This study demonstrates that the diversity of immunoglobulin expression tends to converge among Hy-line brown hens, Lueyang black-bone chickens, and Beijing-You chickens, indicating that the immunoglobulin gene expression mechanisms in different breeds of chickens do not exhibit significant differences due to selective breeding.
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Affiliation(s)
- Yanbo Qiu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Yanpei Wei
- College of Grassland Agriculture, Northwest A&F University, Shaanxi, China
| | - Beibei Zhang
- College of Grassland Agriculture, Northwest A&F University, Shaanxi, China
| | - Shunan Duan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi, China
| | - Xiuzhu Sun
- College of Grassland Agriculture, Northwest A&F University, Shaanxi, China
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5
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Hutchinson GB, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. Cell Rep 2023; 42:113552. [PMID: 38096058 PMCID: PMC10801709 DOI: 10.1016/j.celrep.2023.113552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/28/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses elicited by next-generation vaccines. Here, we use computational protein design to generate a nanoparticle vaccine platform based on the receptor-binding domain (RBD) of influenza hemagglutinin (HA) that enables precise control of antigen conformation and spacing. HA RBDs are presented as either monomers or native-like closed trimers that are connected to the underlying nanoparticle by a rigid linker that is modularly extended to precisely control antigen spacing. Nanoparticle immunogens with decreased spacing between trimeric RBDs elicit antibodies with improved hemagglutination inhibition and neutralization potency as well as binding breadth across diverse H1 HAs. Our "trihead" nanoparticle immunogen platform provides insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used in next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Geoffrey B Hutchinson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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6
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Haynes BF, Wiehe K, Alam SM, Weissman D, Saunders KO. Progress with induction of HIV broadly neutralizing antibodies in the Duke Consortia for HIV/AIDS Vaccine Development. Curr Opin HIV AIDS 2023; 18:300-308. [PMID: 37751363 PMCID: PMC10552807 DOI: 10.1097/coh.0000000000000820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
PURPOSE OF REVIEW Design of an HIV vaccine that can induce broadly neutralizing antibodies (bnAbs) is a major goal. However, HIV bnAbs are not readily made by the immune system. Rather HIV bnAbs are disfavored by a number of virus and host factors. The purpose of the review is to discuss recent progress made in the design and use of immunogens capable of inducing HIV bnAbs in the Duke Consortia for HIV/AIDS Vaccine Development. RECENT FINDINGS New immunogens capable of binding with high affinity to unmutated common ancestors (UCAs) of bnAb B cell lineages have been designed and strategies for stabilization of HIV Env in its prefusion state are being developed. Success is starting to be translated from preclinical studies of UCA-targeting immunogens in animals, to success of initiating bnAb lineages in humans. SUMMARY Recent progress has been made in both immunogen design and in achieving bnAb B cell lineage induction in animal models and now in human clinical trials. With continued progress, a practical HIV/AIDS vaccine may be possible. However, host constraints on full bnAb maturation remain as potential roadblocks for full maturation of some types of bnAbs.
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Affiliation(s)
- Barton F. Haynes
- Duke Human Vaccine Institute, Departments of Medicine and Immunology
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - S. Munir Alam
- Duke Human Vaccine Institute, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Drew Weissman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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7
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Martin TM, Robinson ST, Huang Y. Discovery medicine - the HVTN's iterative approach to developing an HIV-1 broadly neutralizing vaccine. Curr Opin HIV AIDS 2023; 18:290-299. [PMID: 37712873 PMCID: PMC10552837 DOI: 10.1097/coh.0000000000000821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
PURPOSE OF REVIEW In the past two decades, there has been an explosion in the discovery of HIV-1 broadly neutralizing antibodies (bnAbs) and associated vaccine strategies to induce them. This abundance of approaches necessitates a system that accurately and expeditiously identifies the most promising regimens. We herein briefly review the background science of bnAbs, provide a description of the first round of phase 1 discovery medicine studies, and suggest an approach to integrate these into a comprehensive HIV-1-neutralizing vaccine. RECENT FINDINGS With recent preclinical success including induction of early stage bnAbs in mouse knockin models and rhesus macaques, successful priming of VRC01-class bnAbs with eOD-GT8 in a recent study in humans, and proof-of-concept that intravenous infusion of VRC01 prevents sexual transmission of virus in humans, the stage is set for a broad and comprehensive bnAb vaccine program. Leveraging significant advances in protein nanoparticle science, mRNA technology, adjuvant development, and B-cell and antibody analyses, the HVTN has reconfigured its HIV-1 vaccine strategy by developing the Discovery Medicine Program to test promising vaccine candidates targeting six key epitopes. SUMMARY The HVTN Discovery Medicine program is testing multiple HIV-1-neutralizing vaccine candidates.
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Affiliation(s)
- Troy M Martin
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
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8
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Ellis D, Dosey A, Boyoglu-Barnum S, Park YJ, Gillespie R, Syeda H, Tsybovsky Y, Murphy M, Pettie D, Matheson N, Chan S, Ueda G, Fallas JA, Carter L, Graham BS, Veesler D, Kanekiyo M, King NP. Antigen spacing on protein nanoparticles influences antibody responses to vaccination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541980. [PMID: 37292995 PMCID: PMC10245855 DOI: 10.1101/2023.05.23.541980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Immunogen design approaches aim to control the specificity and quality of antibody responses to enable the creation of next-generation vaccines with improved potency and breadth. However, our understanding of the relationship between immunogen structure and immunogenicity is limited. Here we use computational protein design to generate a self-assembling nanoparticle vaccine platform based on the head domain of influenza hemagglutinin (HA) that enables precise control of antigen conformation, flexibility, and spacing on the nanoparticle exterior. Domain-based HA head antigens were presented either as monomers or in a native-like closed trimeric conformation that prevents exposure of trimer interface epitopes. These antigens were connected to the underlying nanoparticle by a rigid linker that was modularly extended to precisely control antigen spacing. We found that nanoparticle immunogens with decreased spacing between closed trimeric head antigens elicited antibodies with improved hemagglutination inhibition (HAI) and neutralization potency as well as binding breadth across diverse HAs within a subtype. Our "trihead" nanoparticle immunogen platform thus enables new insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used to generate next-generation vaccines against influenza and other viruses.
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Affiliation(s)
- Daniel Ellis
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally: Daniel Ellis and Annie Dosey
| | - Annie Dosey
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- These authors contributed equally: Daniel Ellis and Annie Dosey
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Rebecca Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hubza Syeda
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Vaccine Research Center Electron Microscopy Unit, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Michael Murphy
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Deleah Pettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Nick Matheson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorge A. Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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