Chudakov Laboratory

Laboratory research and innovation activities include, among others, development of molecular tools for the basic and biomedical studies, as well development of new methods to identify PCR and sequencing errors and analyze high-throughput sequencing data.  Current focus of interest is the role of clonal T cell and B cell populations in autoimmunity and cancer, DNA technologies and software development for the quantitative analysis of individual T cell receptor and antibody repertoires in health and disease.

The main goal is to understand the architecture of human adaptive immunity organisation in health and disease, in development and aging. Tools: high-throughput profiling of T cell receptor and antibody repertoires with the use of unique molecular identifiers (UMI), followed by advanced bioinformatics analysis.

Supervisor – Dmitry Chudakov

• An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity. Zvyagin IV, Tsvetkov V, Chudakov D, Shugay M; Immunogenetics. 18.11.2019. doi: 10.1007/s00251-019-01139-4.

• Intratumoral immunoglobulin isotypes predict survival in lung adenocarcinoma subtypes. Isaeva O, Sharonov G, Serebrovskaya E, Turchaninova M, Zaretsky A, Shugay M, Chudakov D; J Immunother Cancer. 29.10.2019; 7(1):279. doi: 10.1186/s40425-019-0747-1.

• VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. Bagaev D, Vroomans R, Samir J, Stervbo U, Rius C, Dolton G, Greenshields-Watson A, Attaf M, Egorov E, Zvyagin I, Babel N, Cole D, Godkin A, Sewell A, Kesmir C, Chudakov D, Luciani F, Shugay M.  Nucleic Acids Res.; 07.10.2019; pii: gkz874. doi: 10.1093/nar/gkz874.

• Detecting T cell receptors involved in immune responses from single repertoire snapshots.Pogorelyy M, Minervina A, Shugay M, Chudakov D, Lebedev Y, Mora T, Walczak A. PLoS Biol. 06.2019;17(6):e3000314. doi: 10.1371/journal.pbio.3000314.

• PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice.Weber J, de la Rosa J, Grove C, Schick M, Rad L, Baranov O, Strong A, Pfaus A, Friedrich MJ, Engleitner T, Lersch R, Öllinger R, Grau M, Menendez IG, Martella M, Kohlhofer U, Banerjee R, Turchaninova M, Scherger A, Hoffman G, Hess J, Kuhn L, Ammon T, Kim J, Schneider G, Unger K, Zimber-Strobl U, Heikenwälder M, Schmidt-Supprian M, Yang F, Saur D, Liu P, Steiger K, Chudakov D, Lenz G, Quintanilla-Martinez L, Keller U, Vassiliou G, Cadiñanos J, Bradley A, Rad R. Nat Commun. 29.03.2019;10(1):1415. doi: 10.1038/s41467-019-09180-3.

• Memory CD4⁺T cells are generated in the human fetal intestine. Li N, van Unen V, Abdelaal T, Guo N, Kasatskaya S, Ladell K, McLaren J, Egorov E, Izraelson M, Chuva de Sousa Lopes S, Höllt T, Britanova O, Eggermont J, de Miranda N, Chudakov D, Price D, Lelieveldt B, Koning F Nat Immunol. 21.01.2019;20(3):301-312. doi: 10.1038/s41590-018-0294-9.

• Optimized Peptide-MHC Multimer Protocols for Detection and Isolation of Autoimmune T-Cells. Dolton G, Zervoudi E, Rius C, Wall A, Thomas H, Fuller A, Yeo L, Legut M, Wheeler S, Attaf M, Chudakov D, Choy E, Peakman M, Sewell AK. Front Immunol. 2018 Jun 29;9:1378. doi: 10.3389/fimmu.2018.01378. eCollection 2018.

• Human liver infiltrating γδ T cells are composed of clonally expanded circulating and tissue-resident populations. Hunter S, Willcox C, Davey M, Kasatskaya S, Jeffery H, Chudakov D, Oo Y, Willcox B. J Hepatol. 2018 May 18. pii: S0168-8278(18)32053-1. doi: 10.1016/j.jhep.2018.05.007.

• The human Vδ2⁺ T-cell compartment comprises distinct innate-like Vγ9⁺ and adaptive Vγ9^-subsets.  Davey M, Willcox C, Hunter S, Kasatskaya S, Remmerswaal E, Salim M, Mohammed F, Bemelman F, Chudakov D, Oo Y, Willcox B. Nat Commun. 2018 May 2;9(1):1760. doi: 10.1038/s41467-018-04076-0.

• Method for identification of condition-associated public antigen receptor sequences. Pogorelyy M, Minervina A, Chudakov D, Mamedov I, Lebedev Y, Mora T, Walczak A. Elife. 2018 Mar 13;7. pii: e33050. doi: 10.7554/eLife.33050.

• CD8+ T cells with characteristic T cell receptor beta motif are detected in blood and expanded in synovial fluid of ankylosing spondylitis patients. Komech E, Pogorelyy M, Egorov E, Britanova O, Rebrikov D, Bochkova A, Shmidt E, Shostak N, Shugay M, Lukyanov S, Mamedov I, Lebedev Y, Chudakov D, Zvyagin I. Rheumatology (Oxford). 2018 Feb 22. doi: 10.1093

• Comparative analysis of murine T-cell receptor repertoires. Izraelson M, Nakonechnaya T, Moltedo B, Egorov E, Kasatskaya S, Putintseva E, Mamedov I, Staroverov D, Shemiakina I, Zakharova M, Davydov A, Bolotin D, Shugay M, Chudakov D, Rudensky A, Britanova O. Immunology. 2018 Feb;153(2):133-144. doi: 10.1111/imm.12857

• VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Shugay M, Bagaev D, Zvyagin I, Vroomans R, Crawford J, Dolton G, Komech E, Sycheva L, Koneva A, Egorov E, Eliseev A, Van Dyk E, Dash P, Attaf M, Rius C, Ladell K, McLaren J, Matthews K, Clemens E, Douek D, Luciani F, van Baarle D, Kedzierska K, Kesmir C, Thomas P, Price D, Sewell A, Chudakov D. Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427. doi: 10.1093/nar/gkx760. PMID: 28977646

• Quantitative profiling reveals minor changes of T cell receptor repertoire in response to subunit inactivated influenza vaccine. Sycheva A, Pogorelyy M, Komech E, Minervina A, Zvyagin I, Staroverov D, Chudakov D, Lebedev Y, Mamedov I. Vaccine. 2018 Mar 14;36(12):1599-1605. doi: 10.1016/j.vaccine.2018.02.027. Epub 2018 Feb 15.PMID:29454515

• A high-throughput assay for quantitative measurement of PCR errors.Shagin D, Shagina I, Zaretsky A, Barsova E, Kelmanson I, Lukyanov S, Chudakov D, Shugay M. Sci Rep. 2017 Jun 2;7(1):2718. doi: 10.1038/s41598-017-02727-8. PubMed PMID: 28578414

• MAGERI: Computational pipeline for molecular-barcoded targeted resequencing. Shugay M, Zaretsky A, Shagin D, Shagina I, Volchenkov I, Shelenkov A, Lebedin M, Bagaev D, Lukyanov S, Chudakov D. PLoS Comput Biol. 2017 May 5;13(5):e1005480. doi: 10.1371/journal.pcbi.1005480. eCollection 2017 May. PubMed PMID: 28475621; PubMed Central PMCID: PMC5419444

• Antigen receptor repertoire profiling from RNA-seq data. Bolotin D, Poslavsky S, Davydov A, Frenkel F, Fanchi L, Zolotareva O, Hemmers S, Putintseva E, Obraztsova A, Shugay M, Ataullakhanov R, Rudensky A, Schumacher T, Chudakov D. Nat Biotechnol. 2017Oct 11;35(10):908-911. doi: 10.1038/nbt.3979. No abstract available. PMID:29020005

• Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries. Shagin D, Turchaninova M, Shagina I, Shugay M, Zaretsky A, Zueva O, Bolotin D, Lukyanov S, Chudakov D. BMC Genomics. 2017 Jun 5;18(1):440. doi: 10.1186/s12864-017-3815-2.PMID:28583065