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Lomakin YA, Ovchinnikova LA, Terekhov SS, Dzhelad SS, Yaroshevich I, Mamedov I, Smirnova A, Grigoreva T, Eliseev IE, Filimonova IN, Mokrushina YA, Abrikosova V, Rubtsova MP, Kostin NN, Simonova MA, Bobik TV, Aleshenko NL, Alekhin AI, Boitsov VM, Zhang H, Smirnov IV, Rubtsov YP, Gabibov AG. Two-dimensional high-throughput on-cell screening of immunoglobulins against broad antigen repertoires. Commun Biol 2024; 7:842. [PMID: 38987383 PMCID: PMC11237129 DOI: 10.1038/s42003-024-06500-2] [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: 10/31/2023] [Accepted: 06/24/2024] [Indexed: 07/12/2024] Open
Abstract
Identifying high-affinity antibodies in human serum is challenging due to extremely low number of circulating B cells specific to the desired antigens. Delays caused by a lack of information on the immunogenic proteins of viral origin hamper the development of therapeutic antibodies. We propose an efficient approach allowing for enrichment of high-affinity antibodies against pathogen proteins with simultaneous epitope mapping, even in the absence of structural information about the pathogenic immunogens. To screen therapeutic antibodies from blood of recovered donors, only pathogen transcriptome is required to design an antigen polypeptide library, representing pathogen proteins, exposed on the bacteriophage surface. We developed a two-dimensional screening approach enriching lentiviral immunoglobulin libraries from the convalescent or vaccinated donors against bacteriophage library expressing the overlapping set of polypeptides covering the spike protein of SARS-CoV-2. This platform is suitable for pathogen-specific immunoglobulin enrichment and allows high-throughput selection of therapeutic human antibodies.
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Affiliation(s)
- Yakov A Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia.
| | - Leyla A Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Stanislav S Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Samir S Dzhelad
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Igor Yaroshevich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Ilgar Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Anastasia Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Tatiana Grigoreva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Igor E Eliseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Ioanna N Filimonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Yuliana A Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Victoria Abrikosova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Maria P Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Nikita N Kostin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Maria A Simonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Tatiana V Bobik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Natalia L Aleshenko
- Federal State Budgetary Scientific Institution «Petrovsky National Research Centre of Surgery» (FSBSI «Petrovsky NRCS»), Moscow, Russia
| | - Alexander I Alekhin
- Federal State Budgetary Scientific Institution «Petrovsky National Research Centre of Surgery» (FSBSI «Petrovsky NRCS»), Moscow, Russia
| | - Vitali M Boitsov
- Saint Petersburg National Research Academic University of the Russian Academy of Sciences, 194021, Saint Petersburg, Russia
| | - Hongkai Zhang
- College of Life Science, Nankai University, Tianjin, People's Republic of China
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Endocrinology Research Centre, Ministry of Health of Russia, 117036, Moscow, Russia
| | - Yuri P Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Blokhin National Medical Research Center of Oncology, Ministry of Health, Moscow, Russia
| | - Alexander G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia.
- Faculty of Biology and Biotechnology, HSE University, 101000, Moscow, Russia.
- Faculty of Medicine, Lomonosov Moscow State University, 119192, Moscow, Russia.
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Sørensen CV, Hofmann N, Rawat P, Sørensen FV, Ljungars A, Greiff V, Laustsen AH, Jenkins TP. ExpoSeq: simplified analysis of high-throughput sequencing data from antibody discovery campaigns. BIOINFORMATICS ADVANCES 2024; 4:vbae020. [PMID: 38425781 PMCID: PMC10902677 DOI: 10.1093/bioadv/vbae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/08/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
Summary High-throughput sequencing (HTS) offers a modern, fast, and explorative solution to unveil the full potential of display techniques, like antibody phage display, in molecular biology. However, a significant challenge lies in the processing and analysis of such data. Furthermore, there is a notable absence of open-access user-friendly software tools that can be utilized by scientists lacking programming expertise. Here, we present ExpoSeq as an easy-to-use tool to explore, process, and visualize HTS data from antibody discovery campaigns like an expert while only requiring a beginner's knowledge. Availability and implementation The pipeline is distributed via GitHub and PyPI, and it can either be installed as a package with pip or the user can choose to clone the repository.
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Affiliation(s)
- Christoffer V Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Nils Hofmann
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, NO-0316 Oslo, Norway
| | | | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, NO-0316 Oslo, Norway
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
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