Department of Genomics of Adaptive Immunity

All publications (show selected)

Dmitriy Chudakov

Dynamics and phenotypes of memory T cell clones in response to anti-viral vaccination

Laboratory of immunosequencing methods,  Laboratory of comparative and functional genomics

Using TCR alpha and beta repertoire sequencing for T-cell subsets, as well as single-cell RNAseq and TCRseq, we track the concentrations and phenotypes of individual T-cell clones in response to primary and secondary yellow fever immunization — the model for acute infection in humans — showing their large diversity. We confirm the secondary response is an order of magnitude weaker, albeit ~10 days faster than the primary one. Estimating the fraction of the T-cell response directed against the single immunodominant epitope, we identify the sequence features of TCRs that define the high precursor frequency of the two major TCR motifs specific for this particular epitope. We also show the consistency of clonal expansion dynamics between bulk alpha and beta repertoires, using a new methodology to reconstruct alpha-beta pairings from clonal trajectories.

MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naïve CD4 T cells.

Group of Structural Organization of T-cell Immunity

We investigated the generation of naïve CD4+ T cells in mice with different MHC-II genetic contexts and found out that the defective selection of CD4+ T cells on the j allelic variant of MHC-II (H2-Aj) was in agreement with the generation of less diverse and more public TCR repertoires. Furthermore, the selection on H2-Aj favored the development of T cells with a higher average number of hydrophobic and aromatic amino acid residues in the middle of TCR-CDR3 loops, which are mostly responsible for antigen recognition. Of note, the association of such amino acid residues in CDR3 and high affinity and cross-reactivity of the corresponding TCRs has been reported previously. We observed CD4+ regulatory T cells (Treg) with even more hydrophobic CDR3 loops, which were efficiently recruited into homeostatic proliferation on the periphery and even restored their number despite the defective thymic selection. This difference in the average number of hydrophobic and aromatic amino acids in the CDR3 middle part between conventional and naive Treg cells was more prominent in the H2-Aj genetic context.

We conducted functional in vitro experiments to measure the suppressive activity of Treg cells selected on distinct MHC-II allelic variants. Treg cells selected on H2-Aj demonstrated more effective suppression of proliferating autologous conventional CD4+ T cells. 

Publications

  1. Logunova NN, Kriukova VV, Shelyakin PV, Egorov ES, Pereverzeva A, Bozhanova NG, Shugay M, Shcherbinin DS, Pogorelyy MV, Merzlyak EM, Zubov VN, Meiler J, Chudakov DM, Apt AS, Britanova OV (2020). MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naïve CD4 T cells. Proc Natl Acad Sci U S A 117 (24), 13659–13669

- two functionally distinct subpopulations of CD8 + memory stem cells described.

- a new approach developed to assess the clonal heterogeneity of tumor-infiltrating T-lymphocytes.

-  stably clonal T cell response was shown to be associated with a response to anti-PD1 immunotherapy.

- the T-cell repertoire of nickel-specific CD4 + T-lymphocytes was characterized.

- the repertoire of gamma-delta T lymphocytes involved in the antitumor response was investigated.

- a comparative analysis of the repertoire of follicular helper T-lymphocytes was carried out.

- a deep comparative study of methods for analyzing the repertoire of T-cell receptors was carried out.

Publications

  1. Galletti G, De Simone G, Mazza EMC, Puccio S, Mezzanotte C, Bi TM, Davydov AN, Metsger M, Scamardella E, Alvisi G, De Paoli F, Zanon V, Scarpa A, Camisa B, Colombo FS, Anselmo A, Peano C, Polletti S, Mavilio D, Gattinoni L, Boi SK, Youngblood BA, Jones RE, Baird DM, Gostick E, Llewellyn-Lacey S, Ladell K, Price DA, Chudakov DM, Newell EW, Casucci M, Lugli E (2020). Two subsets of stem-like CD8+ memory T cell progenitors with distinct fate commitments in humans. Nat Immunol ,
  2. Yuzhakova DV, Volchkova LN, Pogorelyy MV, Serebrovskaya EO, Shagina IA, Bryushkova EA, Nakonechnaya TO, Izosimova AV, Zavyalova DS, Karabut MM, Izraelson M, Samoylenko IV, Zagainov VE, Chudakov DM, Zagaynova EV, Sharonov GV (2020). Measuring Intratumoral Heterogeneity of Immune Repertoires. Front Oncol 10, 512
  3. Zhigalova EA, Izosimova AI, Yuzhakova DV, Volchkova LN, Shagina IA, Turchaninova MA, Serebrovskaya EO, Zagaynova EV, Chudakov DM, Sharonov GV (2020). RNA-Seq-Based TCR Profiling Reveals Persistently Increased Intratumoral Clonality in Responders to Anti-PD-1 Therapy. Front Oncol 10, 385
  4. Aparicio-Soto M, Riedel F, Leddermann M, Bacher P, Scheffold A, Kuhl H, Timmermann B, Chudakov DM, Molin S, Worm M, Heine G, Thierse HJ, Luch A, Siewert K (2020). TCRs with segment TRAV9-2 or a CDR3 histidine are overrepresented among nickel-specific CD4+ T cells. Allergy 75 (10), 2574–2586
  5. Janssen A, Villacorta Hidalgo J, Beringer DX, van Dooremalen S, Fernando F, van Diest E, Terrizi AR, Bronsert P, Kock S, Schmitt-Gräff A, Werner M, Heise K, Follo M, Straetemans T, Sebestyen Z, Chudakov DM, Kasatskaya SA, Frenkel FE, Ravens S, Spierings E, Prinz I, Küppers R, Malkovsky M, Fisch P, Kuball J (2020). γδ T-cell Receptors Derived from Breast Cancer-Infiltrating T Lymphocytes Mediate Antitumor Reactivity. Cancer Immunol Res 8 (4), 530–543
  6. Brenna E, Davydov AN, Ladell K, McLaren JE, Bonaiuti P, Metsger M, Ramsden JD, Gilbert SC, Lambe T, Price DA, Campion SL, Chudakov DM, Borrow P, McMichael AJ (2020). CD4 T Follicular Helper Cells in Human Tonsils and Blood Are Clonally Convergent but Divergent from Non-Tfh CD4 Cells. Cell Rep 30 (1), 137–152.e5
  7. Barennes P, Quiniou V, Shugay M, Egorov ES, Davydov AN, Chudakov DM, Uddin I, Ismail M, Oakes T, Chain B, Eugster A, Kashofer K, Rainer PP, Darko S, Ransier A, Douek DC, Klatzmann D, Mariotti-Ferrandiz E (2020). Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nat Biotechnol 39 (2), 236–245
  8. De Simone G, Mazza EMC, Cassotta A, Davydov AN, Kuka M, Zanon V, De Paoli F, Scamardella E, Metsger M, Roberto A, Pilipow K, Colombo FS, Tenedini E, Tagliafico E, Gattinoni L, Mavilio D, Peano C, Price DA, Singh SP, Farber JM, Serra V, Cucca F, Ferrari F, Orrù V, Fiorillo E, Iannacone M, Chudakov DM, Sallusto F, Lugli E (2019). CXCR3 Identifies Human Naive CD8 T Cells with Enhanced Effector Differentiation Potential. J Immunol 203 (12), 3179–3189

SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T cell receptors

Group of Immunosequencing Algorithms

Understanding the hallmarks of the immune response to SARS-CoV-2 is critical for fighting the COVID-19 pandemic. We assessed antibody and T cell reactivity in convalescent COVID-19 patients and healthy donors sampled both prior to and during the pandemic. Healthy donors examined during the pandemic exhibited increased numbers of SARS-CoV-2-specific T cells, but no humoral response. Their probable exposure to the virus resulted in either asymptomatic infection without antibody secretion, or activation of pre-existing immunity. In convalescent patients, we observed a public and diverse T cell response to SARS-CoV-2 epitopes, revealing T cell receptor (TCR) motifs with germline-encoded features. Bulk CD4+ and CD8+ T cell responses to the spike glycoprotein were mediated by groups of homologous TCRs, some of them shared across multiple donors. Overall, our results demonstrate that the T cell response to SARS-CoV-2, including the identified set of TCRs, can serve as a useful biomarker for surveying antiviral immunity.

Formation of the CD4+ and regulatory CD4+ T cell receptor repertoire.

Group of Structural Organization of T-cell Immunity

We studied how different allelic variants of MHC class II shape the TCR repertoires of naive helper and regulatory CD4 + T lymphocytes in two mouse lines. We reveal profound differences in the diversity, convergence, and physicochemical properties of their antigen-interacting regions TCR CDR3 among repertoires of these mouse strains. At the population level, such differences are likely to influence individual susceptibility to infections and autoimmunity.

In our other study, we found that CD4 + lymphocytes with the T memory-like phenotype have been found in the umbilical cord blood and in the embryonic intestine. A rare population of memory CD4+ T cells produce proinflammatory spectrum of cytokines and is characterized by a highly similar TCR repertoires of these cells between different donors, which may indicate the formation of memory in response to similar foreign antigens.

Publications

  1. Li N, van Unen V, Abdelaal T, Guo N, Kasatskaya SA, Ladell K, McLaren JE, Egorov ES, Izraelson M, Chuva de Sousa Lopes SM, Höllt T, Britanova OV, Eggermont J, de Miranda NFCC, Chudakov DM, Price DA, Lelieveldt BPF, Koning F (2019). Memory CD4 T cells are generated in the human fetal intestine. Nat Immunol 20 (3), 301–312

A new approach to the functional analysis of sequencing data for T-lymphocyte repertoires

Laboratory of immunosequencing methods,  Group of Immunosequencing Algorithms,  Laboratory of comparative and functional genomics

In order to extract clinically relevant information from large high-throughput sequencing of TCR repertoires we create a new statistical approach - Antigen-specific Lymphocyte Identification by Clustering of Expanded sequences (ALICE) /fig a/. We applied our algorithm to distinguish naïve from the effector memory cells in available TCR beta repertoires /fig b/, to identify reactive T-cell clones in mixed lymphocyte reaction (MLR) assay /fig c, d/, to fractionate TCR repertoires of patients with autoimmune disease or ones being under cancer immunotherapy, or subject to an acute viral infection. In summary, implementation of ALICE facilitate the identification of TCR variants associated with diseases and conditions, which can be used for diagnostics and rational vaccine design.

Study of the role of tumor-infiltrating B-lymphocytes

Laboratory of immunosequencing methods

- For the first time, the association of the isotype composition of antibodies and B-cell receptors in the tumor environment and the prognosis of patient survival associated with the presence of certain driver mutations is shown.

- The role of tumor-infiltrating B-lymphocytes was first systemically characterized through the prism of the analysis of repertoires of antibodies and B-cell receptors.

Joint work with Privolzhsky Research Medical University.

 

Publications:

1) Isaeva OI, Sharonov GV, Serebrovskaya EO, Turchaninova MA, Zaretsky AR, Shugay M, Chudakov DM (2019). Intratumoral immunoglobulin isotypes predict survival in lung adenocarcinoma subtypes. J Immunother Cancer 7 (1), 279

2) Sharonov GV, Serebrovskaya EO, Yuzhakova DV, Britanova OV, Chudakov DM (2020). B cells, plasma cells and antibody repertoires in the tumour microenvironment. Nature Rev. Immunology, in press.

 

Clonal profiling of T cell response to antiviral vaccination

Laboratory of comparative and functional genomics

T cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed an experimental approach with a statistical framework to detect TCR clone proliferation and contraction from longitudinal repertoire data. We applied this framework to data from three pairs of identical twins immunized with the yellow fever vaccine. We identified 600 to 1,700 responding TCRs in each donor and validated them using three independent assays. While the responding TCRs were mostly private, albeit with higher overlap between twins, they could be well-predicted using a classifier based on sequence similarity. Our method can also be applied to samples obtained postinfection, making it suitable for systematic discovery of new infection-specific TCRs in the clinic.

Photoswitchable red fluorescent proteins for nanoscopy of live cells

Laboratory of immunosequencing methods,  Laboratory of genetically encoded molecular tools

We developed new reversibly photoswitchable red fluorescent proteins based on FusionRed. These proteins, rsFusionRed1, 2 and 3, can be switched OFF and ON and by orange and green light, respectively. This photoswitching behavior allows to avoid illumination by phototoxic violet and blue light, which is commonly used for other photoswitchable proteins. Due to high brightness, high photostability, rapid photoswitching and low phototoxic excitation wavelengths rsFusionReds represent excellent tags for nanoscale imaging of living cells.

Publications

  1. Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA, Verkhusha VV, Mishin AS, Testa I (2018). Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nat Methods 15 (8), 601–604

Investigation of T-cell receptors and antibody repertoires in health and disease 

T cell immune response to the flu vaccination

Laboratory of comparative and functional genomics

Deep quantitative T cell receptors profiling of peripheral lymphocytes have been performed to investigate T cell impact on the human immune response to the trivalent subunit influenza vaccine. Besides the fact that the flu vaccination does not lead to a significant rebuilding of T-lymphocytes repertoire, we founded small oligoclonal subpopulation bearing T cell memory phenotype. The subpopulation appears at 45th day after vaccine administration and then decreases its proportion of T cell clones in the repertoire. These “new memory” T cell clones suggest a potential for recruitment of a limited number of new T cells after each seasonal influenza vaccination.