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For: Pushparaj P, Nicoletto A, Sheward DJ, Das H, Castro Dopico X, Perez Vidakovics L, Hanke L, Chernyshev M, Narang S, Kim S, Fischbach J, Ekström S, McInerney G, Hällberg BM, Murrell B, Corcoran M, Karlsson Hedestam GB. Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies. Immunity 2023;56:193-206.e7. [PMID: 36574772 PMCID: PMC9742198 DOI: 10.1016/j.immuni.2022.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/23/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Number Cited by Other Article(s)
1
Darsono A, Giri-Rachman EA, Artarini AA, Chen DV, Lusiany T, Natalia D, Naully PG, Saputra Ismanto H, Pratama D, Ihsanawati, Ono C, Matsuura Y, Tan MI. Construction of a variable fragment (Fv)-immunoglobulin A (IgA) anti-receptor binding domain (RBD) SARS-CoV-2 library based on IgA from Indonesian COVID-19 survivors. Int J Biol Macromol 2025;315:144412. [PMID: 40403817 DOI: 10.1016/j.ijbiomac.2025.144412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 04/14/2025] [Accepted: 05/18/2025] [Indexed: 05/24/2025]
2
Schleich FA, Bale S, Guenaga J, Ozorowski G, Àdori M, Lin X, Castro Dopico X, Wilson R, Chernyshev M, Cotgreave AT, Mandolesi M, Cluff J, Doyle ED, Sewall LM, Lee WH, Zhang S, O'Dell S, Healy BS, Lim D, Lewis VR, Ben-Akiva E, Irvine DJ, Doria-Rose NA, Corcoran M, Carnathan D, Silvestri G, Wilson IA, Ward AB, Karlsson Hedestam GB, Wyatt RT. Vaccination of nonhuman primates elicits a broadly neutralizing antibody lineage targeting a quaternary epitope on the HIV-1 Env trimer. Immunity 2025:S1074-7613(25)00173-6. [PMID: 40339576 DOI: 10.1016/j.immuni.2025.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 02/20/2025] [Accepted: 04/09/2025] [Indexed: 05/10/2025]
3
Peres A, Upadhyay AA, Klein VH, Saha S, Rodriguez OL, Vanwinkle ZM, Karunakaran K, Metz A, Lauer W, Lin MC, Melton T, Granholm L, Polak P, Peterson SM, Peterson EJ, Raju N, Shields K, Schultze S, Ton T, Ericsen A, Lapp SA, Villinger FJ, Ohlin M, Cottrell C, Amara RR, Derdeyn CA, Crotty S, Schief W, Karlsson Hedestam GB, Smith M, Lees W, Watson CT, Yaari G, Bosinger SE. A Broad Survey and Functional Analysis of Immunoglobulin Loci Variation in Rhesus Macaques. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.07.631319. [PMID: 39829807 PMCID: PMC11741282 DOI: 10.1101/2025.01.07.631319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
4
Deng W, Niu X, He P, Yan Q, Liang H, Wang Y, Ning L, Lin Z, Zhang Y, Zhao X, Feng L, Qu L, Chen L. An allelic atlas of immunoglobulin heavy chain variable regions reveals antibody binding epitope preference resilient to SARS-CoV-2 mutation escape. Front Immunol 2025;15:1471396. [PMID: 39840032 PMCID: PMC11746035 DOI: 10.3389/fimmu.2024.1471396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Accepted: 12/04/2024] [Indexed: 01/23/2025]  Open
5
Russell TW, Townsley H, Hellewell J, Gahir J, Shawe-Taylor M, Greenwood D, Hodgson D, Hobbs A, Dowgier G, Penn R, Sanderson T, Stevenson-Leggett P, Bazire J, Harvey R, Fowler AS, Miah M, Smith C, Miranda M, Bawumia P, Mears HV, Adams L, Hatipoglu E, O'Reilly N, Warchal S, Ambrose K, Strange A, Kelly G, Kjar S, Papineni P, Corrah T, Gilson R, Libri V, Kassiotis G, Gamblin S, Lewis NS, Williams B, Swanton C, Gandhi S, Beale R, Wu MY, Bauer DLV, Carr EJ, Wall EC, Kucharski AJ. Real-time estimation of immunological responses against emerging SARS-CoV-2 variants in the UK: a mathematical modelling study. THE LANCET. INFECTIOUS DISEASES 2025;25:80-93. [PMID: 39276782 DOI: 10.1016/s1473-3099(24)00484-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 09/17/2024]
6
Mikelov A, Nefediev G, Tashkeev A, Rodriguez OL, Aguilar Ortmans D, Skatova V, Izraelson M, Davydov AN, Poslavsky S, Rahmouni S, Watson CT, Chudakov D, Boyd SD, Bolotin D. Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR. Genome Res 2024;34:2293-2303. [PMID: 39433438 PMCID: PMC11694755 DOI: 10.1101/gr.278775.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 10/03/2024] [Indexed: 10/23/2024]
7
Mason DM, Reddy ST. Predicting adaptive immune receptor specificities by machine learning is a data generation problem. Cell Syst 2024;15:1190-1197. [PMID: 39701035 DOI: 10.1016/j.cels.2024.11.008] [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: 04/18/2024] [Revised: 06/14/2024] [Accepted: 11/14/2024] [Indexed: 12/21/2024]
8
Cerveira RA, Lenart K, Martin M, Hinchcliff MJ, Hellgren F, Ye K, Geraldo JA, Kreslavsky T, Ols S, Loré K. Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2024;16:100046. [PMID: 40331170 PMCID: PMC12052378 DOI: 10.1016/j.immuno.2024.100046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/08/2025]
9
Konstantinovsky T, Peres A, Polak P, Yaari G. An unbiased comparison of immunoglobulin sequence aligners. Brief Bioinform 2024;25:bbae556. [PMID: 39489605 PMCID: PMC11531861 DOI: 10.1093/bib/bbae556] [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: 06/14/2024] [Revised: 09/11/2024] [Accepted: 10/19/2024] [Indexed: 11/05/2024]  Open
10
Raposo B, Klareskog L, Robinson WH, Malmström V, Grönwall C. The peculiar features, diversity and impact of citrulline-reactive autoantibodies. Nat Rev Rheumatol 2024;20:399-416. [PMID: 38858604 DOI: 10.1038/s41584-024-01124-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/12/2024]
11
Sheward DJ, Pushparaj P, Das H, Greaney AJ, Kim C, Kim S, Hanke L, Hyllner E, Dyrdak R, Lee J, Dopico XC, Dosenovic P, Peacock TP, McInerney GM, Albert J, Corcoran M, Bloom JD, Murrell B, Karlsson Hedestam GB, Hällberg BM. Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies. Cell Rep Med 2024;5:101577. [PMID: 38761799 PMCID: PMC11228396 DOI: 10.1016/j.xcrm.2024.101577] [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: 01/26/2023] [Revised: 12/15/2023] [Accepted: 04/24/2024] [Indexed: 05/20/2024]
12
Tang D, Gueto-Tettay C, Hjortswang E, Ströbaek J, Ekström S, Happonen L, Malmström L, Malmström J. Multimodal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O. Anal Chem 2024;96:9060-9068. [PMID: 38701337 PMCID: PMC11154737 DOI: 10.1021/acs.analchem.4c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
13
Corcoran MM, Karlsson Hedestam GB. Adaptive immune receptor germline gene variation. Curr Opin Immunol 2024;87:102429. [PMID: 38805851 DOI: 10.1016/j.coi.2024.102429] [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: 01/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
14
Zhao X, Gao F. Novel Omicron Variants Enhance Anchored Recognition of TMEM106B: A New Pathway for SARS-CoV-2 Cellular Invasion. J Phys Chem Lett 2024;15:671-680. [PMID: 38206837 DOI: 10.1021/acs.jpclett.3c03296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
15
Yuan M, Feng Z, Lv H, So N, Shen IR, Tan TJC, Teo QW, Ouyang WO, Talmage L, Wilson IA, Wu NC. Widespread impact of immunoglobulin V-gene allelic polymorphisms on antibody reactivity. Cell Rep 2023;42:113194. [PMID: 37777966 PMCID: PMC10636607 DOI: 10.1016/j.celrep.2023.113194] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/07/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023]  Open
16
Jones RP, Ponomarenko A. COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality. Infect Dis Rep 2023;15:600-634. [PMID: 37888139 PMCID: PMC10606787 DOI: 10.3390/idr15050058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023]  Open
17
Sokal A, Barba-Spaeth G, Hunault L, Fernández I, Broketa M, Meola A, Fourati S, Azzaoui I, Vandenberghe A, Lagouge-Roussey P, Broutin M, Roeser A, Bouvier-Alias M, Crickx E, Languille L, Fournier M, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Canoui-Poitrine F, Pirenne F, Megret J, Pawlotsky JM, Fillatreau S, Reynaud CA, Weill JC, Rey FA, Bruhns P, Mahévas M, Chappert P. SARS-CoV-2 Omicron BA.1 breakthrough infection drives late remodeling of the memory B cell repertoire in vaccinated individuals. Immunity 2023;56:2137-2151.e7. [PMID: 37543032 DOI: 10.1016/j.immuni.2023.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 08/07/2023]
18
Peres A, Lees WD, Rodriguez OL, Lee NY, Polak P, Hope R, Kedmi M, Collins AM, Ohlin M, Kleinstein S, Watson C, Yaari G. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Res 2023;51:e86. [PMID: 37548401 PMCID: PMC10484671 DOI: 10.1093/nar/gkad603] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]  Open
19
Bedi R, Bayless NL, Glanville J. Challenges and Progress in Designing Broad-Spectrum Vaccines Against Rapidly Mutating Viruses. Annu Rev Biomed Data Sci 2023;6:419-441. [PMID: 37196356 DOI: 10.1146/annurev-biodatasci-020722-041304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
20
Yamamoto S, Yamayoshi S, Ito M, Sakai-Tagawa Y, Nakachi I, Baba R, Kamimoto S, Ogura T, Hagiwara S, Kato H, Nakajima H, Uwamino Y, Yagi K, Sugaya N, Nagai H, Saito M, Adachi E, Koga M, Tsutsumi T, Duong C, Okuda M, Murakami J, Furusawa Y, Ujie M, Iwatsuki-Horimoto K, Yotsuyanagi H, Kawaoka Y. Differences among epitopes recognized by neutralizing antibodies induced by SARS-CoV-2 infection or COVID-19 vaccination. iScience 2023;26:107208. [PMID: 37448563 PMCID: PMC10290734 DOI: 10.1016/j.isci.2023.107208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/21/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]  Open
21
Troelnikov A, Armour B, Putty T, Aggarwal A, Akerman A, Milogiannakis V, Chataway T, King J, Turville SG, Gordon TP, Wang JJ. Immunoglobulin repertoire restriction characterizes the serological responses of patients with predominantly antibody deficiency. J Allergy Clin Immunol 2023;152:290-301.e7. [PMID: 36965845 DOI: 10.1016/j.jaci.2023.02.033] [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: 08/22/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 03/27/2023]
22
Yuan M, Feng Z, Lv H, So N, Shen IR, Tan TJ, WenTeo Q, Ouyang WO, Talmage L, Wilson IA, Wu NC. Widespread impact of immunoglobulin V gene allelic polymorphisms on antibody reactivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543969. [PMID: 37333077 PMCID: PMC10274783 DOI: 10.1101/2023.06.06.543969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
23
Pushparaj P, Nicoletto A, Castro Dopico X, Sheward DJ, Kim S, Ekström S, Murrell B, Corcoran M, Karlsson Hedestam GB. Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses. FRONTIERS IN VIROLOGY 2023;3:1128253. [PMID: 37041983 PMCID: PMC7614418 DOI: 10.3389/fviro.2023.1128253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
24
Narang S, Kaduk M, Chernyshev M, Karlsson Hedestam GB, Corcoran MM. Adaptive immune receptor genotyping using the corecount program. Front Immunol 2023;14:1125884. [PMID: 37114042 PMCID: PMC10126697 DOI: 10.3389/fimmu.2023.1125884] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/27/2023] [Indexed: 04/29/2023]  Open
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