Reprogramming human B cells with custom heavy-chain antibodies.
Journal
Nature biomedical engineering
ISSN: 2157-846X
Titre abrégé: Nat Biomed Eng
Pays: England
ID NLM: 101696896
Informations de publication
Date de publication:
22 Jul 2024
22 Jul 2024
Historique:
received:
07
06
2024
accepted:
22
06
2024
medline:
23
7
2024
pubmed:
23
7
2024
entrez:
22
7
2024
Statut:
aheadofprint
Résumé
The immunoglobulin locus of B cells can be reprogrammed by genome editing to produce custom or non-natural antibodies that are not induced by immunization. However, current strategies for antibody reprogramming require complex expression cassettes and do not allow for customization of the constant region of the antibody. Here we show that human B cells can be edited at the immunoglobulin heavy-chain locus to express heavy-chain-only antibodies that support alterations to both the fragment crystallizable domain and the antigen-binding domain, which can be based on both antibody and non-antibody components. Using the envelope protein (Env) from the human immunodeficiency virus as a model antigen, we show that B cells edited to express heavy-chain antibodies to Env support the regulated expression of B cell receptors and antibodies through alternative splicing and that the cells respond to the Env antigen in a tonsil organoid model of immunization. This strategy allows for the reprogramming of human B cells to retain the potential for in vivo amplification while producing molecules with flexibility of composition beyond that of standard antibodies.
Identifiants
pubmed: 39039240
doi: 10.1038/s41551-024-01240-4
pii: 10.1038/s41551-024-01240-4
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : U.S. Department of Health & Human Services | National Institutes of Health (NIH)
ID : AI164561
Organisme : U.S. Department of Health & Human Services | National Institutes of Health (NIH)
ID : AI164556
Organisme : U.S. Department of Health & Human Services | National Institutes of Health (NIH)
ID : MH130178
Organisme : U.S. Department of Health & Human Services | National Institutes of Health (NIH)
ID : HL156274
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Qerqez, A. N., Silva, R. P. & Maynard, J. A. Outsmarting pathogens with antibody engineering. Annu. Rev. Chem. Biomol. Eng. 14, 217–241 (2023).
pubmed: 36917814
pmcid: 10330301
doi: 10.1146/annurev-chembioeng-101121-084508
Carter, P. J. & Rajpal, A. Designing antibodies as therapeutics. Cell 185, 2789–2805 (2022).
pubmed: 35868279
doi: 10.1016/j.cell.2022.05.029
Page, A., Fusil, F. & Cosset, F. L. Towards physiologically and tightly regulated vectored antibody therapies. Cancers 12, 962 (2020).
pubmed: 32295072
pmcid: 7226531
doi: 10.3390/cancers12040962
Zhan, W., Muhuri, M., Tai, P. W. L. & Gao, G. Vectored immunotherapeutics for infectious diseases: can rAAVs be the game changers for fighting transmissible pathogens? Front. Immunol. 12, 673699 (2021).
pubmed: 34046041
pmcid: 8144494
doi: 10.3389/fimmu.2021.673699
Martinez-Navio, J. M. et al. Long-term delivery of an anti-SIV monoclonal antibody with AAV. Front. Immunol. 11, 449 (2020).
pubmed: 32256496
pmcid: 7089924
doi: 10.3389/fimmu.2020.00449
Gardner, M. R. et al. Anti-drug antibody responses impair prophylaxis mediated by AAV-delivered HIV-1 broadly neutralizing antibodies. Mol. Ther. 27, 650–660 (2019).
pubmed: 30704961
pmcid: 6403482
doi: 10.1016/j.ymthe.2019.01.004
Fuchs, S. P., Martinez-Navio, J. M., Rakasz, E. G., Gao, G. & Desrosiers, R. C. Liver-directed but not muscle-directed AAV-antibody gene transfer limits humoral immune responses in rhesus monkeys. Mol. Ther. Methods Clin. Dev. 16, 94–102 (2020).
pubmed: 31890736
doi: 10.1016/j.omtm.2019.11.010
Priddy, F. H. et al. Adeno-associated virus vectored immunoprophylaxis to prevent HIV in healthy adults: a phase 1 randomised controlled trial. Lancet HIV 6, e230–e239 (2019).
pubmed: 30885692
pmcid: 6443625
doi: 10.1016/S2352-3018(19)30003-7
Casazza, J. P. et al. Safety and tolerability of AAV8 delivery of a broadly neutralizing antibody in adults living with HIV: a phase 1, dose-escalation trial. Nat. Med. 28, 1022–1030 (2022).
pubmed: 35411076
pmcid: 9876739
doi: 10.1038/s41591-022-01762-x
Rogers, G. L. & Cannon, P. M. Genome edited B cells: a new frontier in immune cell therapies. Mol. Ther. 29, 3192–3204 (2021).
pubmed: 34563675
pmcid: 8571172
doi: 10.1016/j.ymthe.2021.09.019
Nahmad, A. D. et al. Engineered B cells expressing an anti-HIV antibody enable memory retention, isotype switching and clonal expansion. Nat. Commun. 11, 5851 (2020).
pubmed: 33203857
pmcid: 7673991
doi: 10.1038/s41467-020-19649-1
Huang, D. et al. Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells. Nat. Commun. 11, 5850 (2020).
pubmed: 33203876
pmcid: 7673113
doi: 10.1038/s41467-020-19650-8
Moffett, H. F. et al. B cells engineered to express pathogen-specific antibodies protect against infection. Sci Immunol 4, eaax0644 (2019).
pubmed: 31101673
pmcid: 6913193
doi: 10.1126/sciimmunol.aax0644
Hartweger, H. et al. HIV-specific humoral immune responses by CRISPR/Cas9-edited B cells. J. Exp. Med. 216, 1301–1310 (2019).
pubmed: 30975893
pmcid: 6547862
doi: 10.1084/jem.20190287
Nahmad, A. D. et al. In vivo engineered B cells secrete high titers of broadly neutralizing anti-HIV antibodies in mice. Nat. Biotechnol. 40, 1241–1249 (2022).
pubmed: 35681059
pmcid: 7613293
doi: 10.1038/s41587-022-01328-9
Ou, T. et al. Reprogramming of the heavy-chain CDR3 regions of a human antibody repertoire. Mol. Ther. 30, 184–197 (2022).
pubmed: 34740791
doi: 10.1016/j.ymthe.2021.10.027
Voss, J. E. et al. Reprogramming the antigen specificity of B cells using genome-editing technologies. eLife 8, e42995 (2019).
pubmed: 30648968
pmcid: 6355199
doi: 10.7554/eLife.42995
Greiner, V. et al. CRISPR-mediated editing of the B cell receptor in primary human B cells. iScience 12, 369–378 (2019).
pubmed: 30769282
pmcid: 6374785
doi: 10.1016/j.isci.2019.01.032
Saunders, K. O. Conceptual approaches to modulating antibody effector functions and circulation half-life. Front. Immunol. 10, 1296 (2019).
pubmed: 31231397
pmcid: 6568213
doi: 10.3389/fimmu.2019.01296
Delidakis, G., Kim, J. E., George, K. & Georgiou, G. Improving antibody therapeutics by manipulating the Fc domain: immunological and structural considerations. Annu. Rev. Biomed. Eng. 24, 249–274 (2022).
pubmed: 35363537
pmcid: 9648538
doi: 10.1146/annurev-bioeng-082721-024500
Muyldermans, S. Nanobodies: natural single-domain antibodies. Annu. Rev. Biochem. 82, 775–797 (2013).
pubmed: 23495938
doi: 10.1146/annurev-biochem-063011-092449
Yong Joon Kim, J., Sang, Z., Xiang, Y., Shen, Z. & Shi, Y. Nanobodies: robust miniprotein binders in biomedicine. Adv. Drug Deliv. Rev. 195, 114726 (2023).
pubmed: 36754285
doi: 10.1016/j.addr.2023.114726
Peterson, M. L. Immunoglobulin heavy chain gene regulation through polyadenylation and splicing competition. Wiley Interdiscip. Rev. RNA 2, 92–105 (2011).
pubmed: 21956971
doi: 10.1002/wrna.36
McCoy, L. E. et al. Potent and broad neutralization of HIV-1 by a llama antibody elicited by immunization. J. Exp. Med. 209, 1091–1103 (2012).
pubmed: 22641382
pmcid: 3371729
doi: 10.1084/jem.20112655
Koch, K. et al. Selection of nanobodies with broad neutralizing potential against primary HIV-1 strains using soluble subtype C gp140 envelope trimers. Sci. Rep. 7, 8390 (2017).
pubmed: 28827559
pmcid: 5566552
doi: 10.1038/s41598-017-08273-7
Singer, P. A. & Williamson, A. R. Cell surface immunoglobulin μ and γ chains of human lymphoid cells are of higher apparent molecular weight than their secreted counterparts. Eur. J. Immunol. 10, 180–186 (1980).
pubmed: 6769679
doi: 10.1002/eji.1830100305
Ford, G. S., Yin, C. H., Barnhart, B., Sztam, K. & Covey, L. R. CD40 ligand exerts differential effects on the expression of Iγ transcripts in subclones of an IgM
pubmed: 9551893
doi: 10.4049/jimmunol.160.2.595
Zhou, T. et al. Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site. Structure 30, 862–875 (2022).
pubmed: 35413243
pmcid: 9177634
doi: 10.1016/j.str.2022.03.012
Luo, X. M. et al. Engineering human hematopoietic stem/progenitor cells to produce a broadly neutralizing anti-HIV antibody after in vitro maturation to human B lymphocytes. Blood 113, 1422–1431 (2009).
pubmed: 19059876
doi: 10.1182/blood-2008-09-177139
Maul, R. W. & Gearhart, P. J. AID and somatic hypermutation. Adv. Immunol. 105, 159–191 (2010).
pubmed: 20510733
pmcid: 2954419
doi: 10.1016/S0065-2776(10)05006-6
Ruckerl, F., Busse, B. & Bachl, J. Episomal vectors to monitor and induce somatic hypermutation in human Burkitt-lymphoma cell lines. Mol. Immunol. 43, 1645–1652 (2006).
pubmed: 16310251
doi: 10.1016/j.molimm.2005.09.011
Vaisman-Mentesh, A., Gutierrez-Gonzalez, M., DeKosky, B. J. & Wine, Y. The molecular mechanisms that underlie the immune biology of anti-drug antibody formation following treatment with monoclonal antibodies. Front. Immunol. 11, 1951 (2020).
pubmed: 33013848
pmcid: 7461797
doi: 10.3389/fimmu.2020.01951
Cohen, Y. Z. et al. Safety, pharmacokinetics, and immunogenicity of the combination of the broadly neutralizing anti-HIV-1 antibodies 3BNC117 and 10-1074 in healthy adults: a randomized, phase 1 study. PLoS ONE 14, e0219142 (2019).
pubmed: 31393868
pmcid: 6687118
doi: 10.1371/journal.pone.0219142
Asaadi, Y., Jouneghani, F. F., Janani, S. & Rahbarizadeh, F. A comprehensive comparison between camelid nanobodies and single chain variable fragments. Biomark. Res. 9, 87 (2021).
pubmed: 34863296
pmcid: 8642758
doi: 10.1186/s40364-021-00332-6
Vincke, C. et al. General strategy to humanize a camelid single-domain antibody and identification of a universal humanized nanobody scaffold. J. Biol. Chem. 284, 3273–3284 (2009).
pubmed: 19010777
doi: 10.1074/jbc.M806889200
Belanger, K. & Tanha, J. High-efficacy, high-manufacturability human VH domain antibody therapeutics from transgenic sources. Protein Eng. Des. Sel. 34, gzab012 (2021).
pubmed: 33991089
doi: 10.1093/protein/gzab012
Sonoda, E., Hochegger, H., Saberi, A., Taniguchi, Y. & Takeda, S. Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair 5, 1021–1029 (2006).
pubmed: 16807135
doi: 10.1016/j.dnarep.2006.05.022
Rogers, G. L. et al. Optimization of AAV6 transduction enhances site-specific genome editing of primary human lymphocytes. Mol. Ther. Methods Clin. Dev. 23, 198–209 (2021).
pubmed: 34703842
pmcid: 8517001
doi: 10.1016/j.omtm.2021.09.003
Hung, K. L. et al. Engineering protein-secreting plasma cells by homology-directed repair in primary human B cells. Mol. Ther. 26, 456–467 (2018).
pubmed: 29273498
doi: 10.1016/j.ymthe.2017.11.012
Sanz, I. et al. Challenges and opportunities for consistent classification of human B cell and plasma cell populations. Front. Immunol. 10, 2458 (2019).
pubmed: 31681331
pmcid: 6813733
doi: 10.3389/fimmu.2019.02458
Schiroli, G. et al. Precise gene editing preserves hematopoietic stem cell function following transient p53-mediated DNA damage response. Cell Stem Cell 24, 551–565 (2019).
pubmed: 30905619
pmcid: 6458988
doi: 10.1016/j.stem.2019.02.019
Vettermann, C. & Schlissel, M. S. Allelic exclusion of immunoglobulin genes: models and mechanisms. Immunol. Rev. 237, 22–42 (2010).
pubmed: 20727027
pmcid: 2928156
doi: 10.1111/j.1600-065X.2010.00935.x
He, J. S. et al. The distinctive germinal center phase of IgE
pubmed: 24218137
pmcid: 3832920
doi: 10.1084/jem.20131539
Wagar, L. E. et al. Modeling human adaptive immune responses with tonsil organoids. Nat. Med. 27, 125–135 (2021).
pubmed: 33432170
pmcid: 7891554
doi: 10.1038/s41591-020-01145-0
Kastenschmidt, J. M. et al. Influenza vaccine format mediates distinct cellular and antibody responses in human immune organoids. Immunity 56, 1910–1926 (2023).
pubmed: 37478854
pmcid: 10433940
doi: 10.1016/j.immuni.2023.06.019
Chen, W. et al. Exceptionally potent and broadly cross-reactive, bispecific multivalent HIV-1 inhibitors based on single human CD4 and antibody domains. J. Virol. 88, 1125–1139 (2014).
pubmed: 24198429
pmcid: 3911630
doi: 10.1128/JVI.02566-13
Walker, L. M. et al. Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature 477, 466–470 (2011).
pubmed: 21849977
pmcid: 3393110
doi: 10.1038/nature10373
Bates, A. & Power, C. A. David vs. Goliath: the structure, function, and clinical prospects of antibody fragments. Antibodies 8, 28 (2019).
pubmed: 31544834
pmcid: 6640713
doi: 10.3390/antib8020028
Finck, A. V., Blanchard, T., Roselle, C. P., Golinelli, G. & June, C. H. Engineered cellular immunotherapies in cancer and beyond. Nat. Med. 28, 678–689 (2022).
pubmed: 35440724
pmcid: 9305718
doi: 10.1038/s41591-022-01765-8
Hibi, T. & Dosch, H. M. Limiting dilution analysis of the B cell compartment in human bone marrow. Eur. J. Immunol. 16, 139–145 (1986).
pubmed: 2869953
doi: 10.1002/eji.1830160206
Hammarlund, E. et al. Plasma cell survival in the absence of B cell memory. Nat. Commun. 8, 1781 (2017).
pubmed: 29176567
pmcid: 5701209
doi: 10.1038/s41467-017-01901-w
Cheng, R. Y. et al. Ex vivo engineered human plasma cells exhibit robust protein secretion and long-term engraftment in vivo. Nat. Commun. 13, 6110 (2022).
pubmed: 36245034
pmcid: 9573882
doi: 10.1038/s41467-022-33787-8
Davis, C. W. et al. Influenza vaccine-induced human bone marrow plasma cells decline within a year after vaccination. Science 370, 237–241 (2020).
pubmed: 32792465
pmcid: 10155619
doi: 10.1126/science.aaz8432
Monzon-Posadas, W. O. et al. Longitudinal monitoring of mRNA-vaccine-induced immunity against SARS-CoV-2. Front. Immunol. 14, 1066123 (2023).
pubmed: 36742295
pmcid: 9893859
doi: 10.3389/fimmu.2023.1066123
Koike, T., Harada, K., Horiuchi, S. & Kitamura, D. The quantity of CD40 signaling determines the differentiation of B cells into functionally distinct memory cell subsets. eLife 8, e44245 (2019).
pubmed: 31225793
pmcid: 6636905
doi: 10.7554/eLife.44245
Joshi, K. K. et al. Elucidating heavy/light chain pairing preferences to facilitate the assembly of bispecific IgG in single cells. mAbs 11, 1254–1265 (2019).
pubmed: 31286843
pmcid: 6748609
doi: 10.1080/19420862.2019.1640549
Jin, B. K., Odongo, S., Radwanska, M. & Magez, S. NANOBODIES
pubmed: 36983063
pmcid: 10057852
doi: 10.3390/ijms24065994
Hamers-Casterman, C. et al. Naturally occurring antibodies devoid of light chains. Nature 363, 446–448 (1993).
pubmed: 8502296
doi: 10.1038/363446a0
Blanc, M. R. et al. A one-step exclusion-binding procedure for the purification of functional heavy-chain and mammalian-type gamma-globulins from camelid sera. Biotechnol. Appl. Biochem. 54, 207–212 (2009).
pubmed: 19824883
doi: 10.1042/BA20090208
Daley-Bauer, L. P. et al. Contributions of conventional and heavy-chain IgG to immunity in fetal, neonatal, and adult alpacas. Clin. Vaccine Immunol. 17, 2007–2015 (2010).
pubmed: 20926693
pmcid: 3008178
doi: 10.1128/CVI.00287-10
Llewellyn, G. N. et al. Comparison of SARS-CoV-2 entry inhibitors based on ACE2 receptor or engineered Spike-binding peptides. J. Virol. 97, e0068423 (2023).
pubmed: 37555663
doi: 10.1128/jvi.00684-23
Laursen, N. S. et al. Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin. Science 362, 598–602 (2018).
pubmed: 30385580
pmcid: 6241527
doi: 10.1126/science.aaq0620
Smith, P., DiLillo, D. J., Bournazos, S., Li, F. & Ravetch, J. V. Mouse model recapitulating human Fcγ receptor structural and functional diversity. Proc. Natl Acad. Sci. USA 109, 6181–6186 (2012).
pubmed: 22474370
pmcid: 3341029
doi: 10.1073/pnas.1203954109
Zalevsky, J. et al. Enhanced antibody half-life improves in vivo activity. Nat. Biotechnol. 28, 157–159 (2010).
pubmed: 20081867
pmcid: 2855492
doi: 10.1038/nbt.1601
Yu, J. et al. A rational approach to enhancing antibody Fc homodimer formation for robust production of antibody mixture in a single cell line. J. Biol. Chem. 292, 17885–17896 (2017).
pubmed: 28878018
doi: 10.1074/jbc.M116.771188
Vamva, E. et al. A lentiviral vector B cell gene therapy platform for the delivery of the anti-HIV-1 eCD4-Ig-knob-in-hole-reversed immunoadhesin. Mol. Ther. Methods Clin. Dev. 28, 366–384 (2023).
pubmed: 36879849
pmcid: 9984920
doi: 10.1016/j.omtm.2023.02.004
Irrgang, P. et al. Class switch toward noninflammatory, spike-specific IgG4 antibodies after repeated SARS-CoV-2 mRNA vaccination. Sci. Immunol. 8, eade2798 (2023).
pubmed: 36548397
doi: 10.1126/sciimmunol.ade2798
Roco, J. A. et al. Class-switch recombination occurs infrequently in germinal centers. Immunity 51, 337–350 (2019).
pubmed: 31375460
pmcid: 6914312
doi: 10.1016/j.immuni.2019.07.001
Wardemann, H. et al. Predominant autoantibody production by early human B cell precursors. Science 301, 1374–1377 (2003).
pubmed: 12920303
doi: 10.1126/science.1086907
Casellas, R. et al. Igκ allelic inclusion is a consequence of receptor editing. J. Exp. Med. 204, 153–160 (2007).
pubmed: 17210730
pmcid: 2118438
doi: 10.1084/jem.20061918
Pelanda, R. Dual immunoglobulin light chain B cells: Trojan horses of autoimmunity? Curr. Opin. Immunol. 27, 53–59 (2014).
pubmed: 24549093
doi: 10.1016/j.coi.2014.01.012
Sirac, C., Carrion, C., Duchez, S., Comte, I. & Cogne, M. Light chain inclusion permits terminal B cell differentiation and does not necessarily result in autoreactivity. Proc. Natl Acad. Sci. USA 103, 7747–7752 (2006).
pubmed: 16682638
pmcid: 1472516
doi: 10.1073/pnas.0509121103
Velez, M. G. et al. Ig allotypic inclusion does not prevent B cell development or response. J. Immunol. 179, 1049–1057 (2007).
pubmed: 17617597
doi: 10.4049/jimmunol.179.2.1049
Makdasi, E. & Eilat, D. L chain allelic inclusion does not increase autoreactivity in lupus-prone New Zealand Black/New Zealand White mice. J. Immunol. 190, 1472–1480 (2013).
pubmed: 23319731
doi: 10.4049/jimmunol.1202331
Peterson, J. N. et al. Elevated detection of dual antibody B cells identifies lupus patients with B cell-reactive VH4-34 autoantibodies. Front. Immunol. 13, 795209 (2022).
pubmed: 35185888
pmcid: 8854503
doi: 10.3389/fimmu.2022.795209
Rogers, G. L., Chen, H. Y., Morales, H. & Cannon, P. M. Homologous recombination-based genome editing by clade F AAVs is inefficient in the absence of a targeted DNA break. Mol. Ther. 27, 1726–1736 (2019).
pubmed: 31540849
pmcid: 6822228
doi: 10.1016/j.ymthe.2019.08.019
Lock, M. et al. Characterization of a recombinant adeno-associated virus type 2 Reference Standard Material. Hum. Gene Ther. 21, 1273–1285 (2010).
pubmed: 20486768
pmcid: 2957240
doi: 10.1089/hum.2009.223
Rogers, G. L. et al. Unique roles of TLR9- and MyD88-dependent and -independent pathways in adaptive immune responses to AAV-mediated gene transfer. J. Innate Immun. 7, 302–314 (2015).
pubmed: 25612611
pmcid: 4417066
doi: 10.1159/000369273
Tatiossian, K. J. et al. Rational selection of CRISPR–Cas9 guide RNAs for homology-directed genome editing. Mol. Ther. 29, 1057–1069 (2021).
pubmed: 33160457
doi: 10.1016/j.ymthe.2020.10.006
Llewellyn, G. N. et al. Humanized mouse model of HIV-1 latency with enrichment of latent virus in PD-1
pubmed: 30842333
pmcid: 6498059
doi: 10.1128/JVI.02086-18
Sarzotti-Kelsoe, M. et al. Optimization and validation of the TZM-bl assay for standardized assessments of neutralizing antibodies against HIV-1. J. Immunol. Methods 409, 131–146 (2014).
pubmed: 24291345
doi: 10.1016/j.jim.2013.11.022
Korbie, D. J. & Mattick, J. S. Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat. Protoc. 3, 1452–1456 (2008).
pubmed: 18772872
doi: 10.1038/nprot.2008.133
Conant, D. et al. Inference of CRISPR edits from Sanger trace data. CRISPR J. 5, 123–130 (2022).
pubmed: 35119294
doi: 10.1089/crispr.2021.0113
Hill, J. T. et al. Poly peak parser: method and software for identification of unknown indels using sanger sequencing of polymerase chain reaction products. Dev. Dyn. 243, 1632–1636 (2014).
pubmed: 25160973
pmcid: 4525701
doi: 10.1002/dvdy.24183
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Philos. Trans. R Soc. Lond B 370, 20130624 (2015).
doi: 10.1098/rstb.2013.0624
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G. & Neufeld, J. D. PANDAseq: paired-end assembler for illumina sequences. BMC Bioinform. 13, 31 (2012).
doi: 10.1186/1471-2105-13-31
Morgan, M. et al. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 25, 2607–2608 (2009).
pubmed: 19654119
pmcid: 2752612
doi: 10.1093/bioinformatics/btp450
Pagès, H., Aboyoun, P., Gentleman, R. & DebRoy, S. Biostrings: efficient manipulation of biological strings. R package version 2.62.0 https://bioconductor.org/packages/Biostrings (2021).
Schauberger, P. & Walker, A. openxlsx: read, write and edit xlsx files. R package version 4.2.5.1 https://CRAN.R-project.org/package=openxlsx (2022).
Fields, B., Moeskjaer, S., Friman, V. P., Andersen, S. U. & Young, J. P. W. MAUI-seq: metabarcoding using amplicons with unique molecular identifiers to improve error correction. Mol. Ecol. Resour. 21, 703–720 (2021).
pubmed: 33171018
doi: 10.1111/1755-0998.13294
Karst, S. M. et al. High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nat. Methods 18, 165–169 (2021).
pubmed: 33432244
doi: 10.1038/s41592-020-01041-y
Rogozin, I. B. & Diaz, M. Cutting edge: DGYW/WRCH is a better predictor of mutability at G:C bases in Ig hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered process. J. Immunol. 172, 3382–3384 (2004).
pubmed: 15004135
doi: 10.4049/jimmunol.172.6.3382
Wagih, O. ggseqlogo: A ‘ggplot2’ extension for drawing publication-ready sequence logos. R package version 0.1 https://CRAN.R-project.org/package=ggseqlogo (2017).
Abhinandan, K. R. & Martin, A. C. Analyzing the ‘degree of humanness’ of antibody sequences. J. Mol. Biol. 369, 852–862 (2007).
pubmed: 17442342
doi: 10.1016/j.jmb.2007.02.100