Laboratory of comparative and functional genomics

Department of Genomics of Adaptive Immunity

Head: Yuri Lebedev, D.Sc, professor

Human genome, genome evolution and variability, retroelements, regulation of gene expression, transcriptome of human lymphocytes, autoimmune diseases

The laboratory was formed early in 2006 and was joined by those of young scientists and PhD students from Laboratory of structure and functions of human genes (LSFHG, laboratory head — academician E.D. Sverdlov) who studied retroposon’s impact on human genome evolution and functioning. On March 2009, Laboratory of comparative and functional genomics includes: laboratory head Y.B. Lebedev, D.Sci., researchers I.Z. Mamedov, Ph.D. and A.L. Amosova, Ph.D., junior researcher S.V. Ustyugova, Ph.D., PhD students A.V. Chkalina, I.V. Zvyagin, A.Y. Komkov, and three undergraduate students from Moscow State University who work on their bachelor’s theses. Ongoing laboratory projects are supported by the Institute, by Russ. Acad. Sci. Presidium programs, by RFBR grants and by other grants, including:

  • Studies of human genome variability and genetic basis of inherited diseases;
  • New approach to identification and selective suppression of expanded T-cell clones in patients with autoimmune and oncological diseases;
  • Role of retroposon’s insertional polymorphism in oncological diseases;
  • Large-scale functional analysis of human specific and polymorphic retroelement insertions;
  • Advanced molecular-genetic markers and their application for people genetic services and records;
  • Molecular-genetic analysis of eneolithic/bronze age inhabitants of Thrace valley and South-Russian steppe.

The laboratory carries out a wide range of molecular genetic research applying newly developed techniques and approaches to comparative analysis of genomic DNAs and cDNA pools of various origins. Ongoing research includes the following directions:

  1. genetics of distinct types of autoimmune diseases associated with clonal T-cell expansion; comparative transcriptome analysis of various subpopulations of peripheral blood lymphocytes;
  2. transposable elements impact on the eukaryotic genome evolution; investigation of genomic variability of individuals and within human population forming by retroelements activity; studies on the interaction between species-specific and polymorphic retroelements and gene expression systems;
  3. development of new aproaches for analysis of individual T-cell repertoires;
  4. studying of clonal diversity dynamic of human T- and B-lymphocytes in normal state and during development of autoimmune or oncological diseases.
Yuri Lebedev, D.Sc, professordepart.
Il'gar Mamedov, Ph.D.s. r.
Ivan Zvyagin, Ph.D.s. r.
Alexander Komkov, Ph.D.r.
Svetlana Ustjugova, Ph.D.j. r.
Ekaterina KomechPhD
Mikhail PogorelyyPhD
Anastasia MinervinaPhD
Anastasiia SychevaPhD

Selected publications

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

    The risk of AS is associated with genomic variants related to antigen presentation and specific cytokine signalling pathways, suggesting the involvement of cellular immunity in disease initiation/progression. The aim of the present study was to explore the repertoire of TCR sequences in healthy donors and AS patients to uncover AS-linked TCR variants.

  2. Sycheva A.L., Pogorelyy M.V. (2017). Quantitative profiling reveals minor changes of T cell receptor repertoire in response to subunit inactivated influenza vaccine. Vaccine , [+]

    under review

  3. Zvyagin I.V., Mamedov I.Z., Tatarinova O.V., Komech E.A., Kurnikova E.E., Boyakova E.V., Brilliantova V., Shelikhova L.N., Balashov D.N., Shugay M., Sycheva A.L., Kasatskaya S.A., Lebedev Y.B., Maschan A.A., Maschan M.A., Chudakov D.M. (2016). Tracking T-cell immune reconstitution after TCRαβ/CD19-depleted hematopoietic cells transplantation in children. Leukemia , [+]

    αβT-cell-depleted allogeneic hematopoietic cell transplantation holds promise for the safe and accessible therapy of both malignant and non-malignant blood disorders. Here we employed molecular barcoding normalized T-cell receptor (TCR) profiling to quantitatively track T-cell immune reconstitution after TCRαβ-/CD19-depleted transplantation in children. We demonstrate that seemingly early reconstitution of αβT-cell counts 2 months after transplantation is based on only several hundred rapidly expanded clones originating from non-depleted graft cells. In further months, frequency of these hyperexpanded clones declines, and after 1 year the observed T-cell counts and TCRβ diversity are mostly provided by the newly produced T cells. We also demonstrate that high TCRβ diversity at day 60 observed for some of the patients is determined by recipient T cells and intrathymic progenitors that survived conditioning regimen. Our results indicate that further efforts on optimization of TCRαβ-/CD19-depleted transplantation protocols should be directed toward providing more efficient T-cell defense in the first months after transplantation.Leukemia advance online publication, 9 December 2016; doi:10.1038/leu.2016.321.

  4. Nazarov V.I., Minervina A.A., Komkov A.Y., Pogorelyy M.V., Maschan M.A., Olshanskaya Y.V., Zvyagin I.V., Chudakov D.M., Lebedev Y.B., Mamedov I.Z. (2016). Reliability of immune receptor rearrangements as genetic markers for minimal residual disease monitoring. Bone marrow transplantation , ID:1532
  5. Nazarov V.I., Pogorelyy M.V., Komech E.A., Zvyagin I.V., Bolotin D.A., Shugay M., Chudakov D.M., Lebedev Y.B., Mamedov I.Z. (2015). tcR: an R package for T cell receptor repertoire advanced data analysis. BMC Bioinformatics 16, 175 [+]

    The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is required for the rational analysis of massive data generated by next-generation sequencing.

  6. Kurnosov A.A., Ustyugova S.V., Nazarov V.I., Minervina A.A., Komkov A.Y., Shugay M., Pogorelyy M.V., Khodosevich K.V., Mamedov I.Z., Lebedev Y.B. (2014). The evidence for increased L1 activity in the site of human adult brain neurogenesis. PLoS ONE 10 (2), e0117854 [+]

    Retroelement activity is a common source of polymorphisms in human genome. The mechanism whereby retroelements contribute to the intraindividual genetic heterogeneity by inserting into the DNA of somatic cells is gaining increasing attention. Brain tissues are suspected to accumulate genetic heterogeneity as a result of the retroelements somatic activity. This study aims to expand our understanding of the role retroelements play in generating somatic mosaicism of neural tissues. Whole-genome Alu and L1 profiling of genomic DNA extracted from the cerebellum, frontal cortex, subventricular zone, dentate gyrus, and the myocardium revealed hundreds of somatic insertions in each of the analyzed tissues. Interestingly, the highest concentration of such insertions was detected in the dentate gyrus-the hotspot of adult neurogenesis. Insertions of retroelements and their activity could produce genetically diverse neuronal subsets, which can be involved in hippocampal-dependent learning and memory.

  7. Bolotin D.A., Shugay M., Mamedov I.Z., Putintseva E.V., Turchaninova M.A., Zvyagin I.V., Britanova O.V., Chudakov D.M. (2013). MiTCR: software for T-cell receptor sequencing data analysis. Nat. Methods 10 (9), 813–4 ID:886
  8. Bolotin D.A., Mamedov I.Z., Britanova O.V., Zvyagin I.V., Shagin D., Ustyugova S.V., Turchaninova M.A., Lukyanov S., Lebedev Y.B., Chudakov D.M. (2012). Next generation sequencing for TCR repertoire profiling: platform-specific features and correction algorithms. European journal of immunology , [+]

    The T-cell receptor (TCR) repertoire is a mirror of the human immune system that reflects processes caused by infections, cancer, autoimmunity, and aging. Next generation sequencing (NGS) is becoming a powerful tool for deep TCR profiling; yet, questions abound regarding the methodological approaches for sample preparation and correct data interpretation. Accumulated PCR and sequencing errors along with library preparation bottlenecks and uneven PCR efficiencies lead to information loss, biased quantification, and generation of huge artificial TCR diversity. Here, we compare Illumina, 454, and Ion Torrent platforms for individual TCR profiling, evaluate the rate and character of errors, and propose advanced platform-specific algorithms to correct massive sequencing data. These developments are applicable to a wide variety of NGS applications. We demonstrate that advanced correction allows the removal of the majority of artificial TCR diversity with concomitant rescue of most of the sequencing information. Thus, this correction enhances the accuracy of clonotype identification and quantification as well as overall TCR diversity measurements.

  9. Britanova O.V., Bochkova A.G., Staroverov D.B., Fedorenko D.A., Bolotin D.A., Mamedov I.Z., Turchaninova M.A., Putintseva E.V., Kotlobay A.A., Lukyanov S., Novik A.A., Lebedev Y.B., Chudakov D.M. (2012). First autologous hematopoietic SCT for ankylosing spondylitis: a case report and clues to understanding the therapy. Bone marrow transplantation , ID:732
  10. Mamedov I.Z., Britanova O.V., Bolotin D.A., Chkalina A.V., Staroverov D.B., Zvyagin I.V., Kotlobay A.A., Turchaninova M.A., Fedorenko D.A., Novik A.A., Sharonov G.V., Lukyanov S., Chudakov D.M., Lebedev Y.B. (2011). Quantitative tracking of T cell clones after haematopoietic stem cell transplantation. EMBO Mol Med 3 (4), 201–7 [+]

    Autologous haematopoietic stem cell transplantation is highly efficient for the treatment of systemic autoimmune diseases, but its consequences for the immune system remain poorly understood. Here, we describe an optimized RNA-based technology for unbiased amplification of T cell receptor beta-chain libraries and use it to perform the first detailed, quantitative tracking of T cell clones during 10 months after transplantation. We show that multiple clones survive the procedure, contribute to the immune response to activated infections, and form a new skewed and stable T cell receptor repertoire.

  11. Zvyagin I.V., Mamedov I.Z., Britanova O.V., Staroverov D.B., Nasonov E.L., Bochkova A.G., Chkalina A.V., Kotlobay A.A., Korostin D.O., Rebrikov D.V., Lukyanov S., Lebedev Y.B., Chudakov D.M. (2010). Contribution of functional KIR3DL1 to ankylosing spondylitis. Cellular & molecular immunology , [+]

    Increasing evidence points to a role for killer immunoglobulin-like receptors (KIRs) in the development of autoimmune diseases. In particular, a positive association of KIR3DS1 (activating receptor) and a negative association of KIR3DL1 (inhibitory receptor) alleles with ankylosing spondylitis (AS) have been reported by several groups. However, none of the studies analyzed these associations in the context of functionality of polymorphic KIR3DL1. To better understand how the KIR3DL1/3DS1 genes determine susceptibility to AS, we analyzed the frequencies of alleles and genotypes encoding functional (KIR3DL1*F) and non-functional (KIR3DL1*004) receptors. We genotyped 83 AS patients and 107 human leukocyte antigen (HLA)-B27-positive healthy controls from the Russian Caucasian population using a two-stage sequence-specific primer PCR, which distinguishes KIR3DS1, KIR3DL1*F and KIR3DL1*004 alleles. For the patients carrying two functional KIR3DL1 alleles, those alleles were additionally genotyped to identify KIR3DL1*005 and KIR3DL1*007 alleles, which are functional but are expressed at low levels. KIR3DL1 was negatively associated with AS at the expense of KIR3DL1*F but not of KIR3DL1*004. This finding indicates that the inhibitory KIR3DL1 receptor protects against the development of AS and is not simply a passive counterpart of the segregating KIR3DS1 allele encoding the activating receptor. However, analysis of genotype frequencies indicates that the presence of KIR3DS1 is a more important factor for AS susceptibility than the absence of KIR3DL1*F. The activation of either natural killer (NK) or T cells via the KIR3DS1 receptor can be one of the critical events in AS development, while the presence of the functional KIR3DL1 receptor has a protective effect. Nevertheless, even individuals with a genotype that carried two inhibitory KIR3DL1 alleles expressed at high levels could develop AS.Cellular & Molecular Immunology advance online publication, 6 September 2010; doi:10.1038/cmi.2010.42.

  12. Shagina I., Bogdanova E., Mamedov I., Lebedev Y., Lukyanov S., Shagin D. (2010). Normalization of genomic DNA using duplex-specific nuclease. BioTechniques 48 (6), 351–355 [+]

    An application of duplex-specific nuclease (DSN) normalization technology to whole-genome shotgun sequencing of genomes with a large proportion of repetitive DNA is described. The method uses a thermostable DSN from the Kamchatka crab that specifically hydrolyzes dsDNA. In model experiments on human genomic DNA, we demonstrated that DSN normalization of double-stranded DNA formed during C0t analysis is effective against abundant repetitive sequences with high sequence identity, while retaining highly divergent repeats and coding regions at baseline levels. Thus, DSN normalization applied to C0t analysis can be used to eliminate evolutionarily young repetitive elements from genomic DNA before sequencing, and should prove invaluable in studies of large eukaryotic genomes, such as those of higher plants.

  13. Mamedov I.Z., Shagina I.A., Kurnikova M.A., Novozhilov S.N., Shagin D.A., Lebedev Y.B. (2010). A new set of markers for human identification based on 32 polymorphic Alu insertions. EJHG , [+]

    A number of genetic systems for human genetic identification based on short tandem repeats or single nucleotide polymorphisms are widely used for crime detection, kinship studies and in analysis of victims of mass disasters. Here, we have developed a new set of 32 molecular genetic markers for human genetic identification based on polymorphic retroelement insertions. Allele frequencies were determined in a group of 90 unrelated individuals from four genetically distant populations of the Russian Federation. The mean match probability and probability of paternal exclusion, calculated based on population data, were 5.53 x 10(-14) and 99.784%, respectively. The developed system is cheap and easy to use as compared to all previously published methods. The application of fluorescence-based methods for allele discrimination allows to use the human genetic identification set in automatic and high-throughput formats.European Journal of Human Genetics advance online publication, 24 February 2010; doi:10.1038/ejhg.2010.22.

  14. Mamedov I.Z., Britanova O.V., Chkalina A.V., Staroverov D.B., Amosova A.L., Mishin A.S., Kurnikova M.A., Zvyagin I.V., Mutovina Z.Y., Gordeev A.V., Khaidukov S.V., Sharonov G.V., Shagin D.A., Chudakov D.M., Lebedev Y.B. (2009). Individual characterization of stably expanded T cell clones in ankylosing spondylitis patients. Autoimmunity 42 (6), 525–36 [+]

    Ankylosing spondylitis (AS) is commonly characterized by clonal expansions of T cells. However, these clonal populations are poorly studied and their role in disease initiation and progression remains unclear. Here, we performed mass sequencing of TCR V beta libraries to search for the expanded T cell clones for two AS patients. A number of clones comprising more than 5% of the corresponding TCR V beta family were identified in both patients. For the first time, expanded clones were shown to be stably abundant in blood samples of AS patients for the prolonged period (1.5 and 2.5 years for two patients, correspondingly). These clones were individually characterized in respect to their differentiation status using fluorescent cell sorting with CD27, CD28, and CD45RA markers followed by quantitative identification of each clone within corresponding fraction using real time PCR analysis. Stable clones differed in phenotype and several were shown to belong to the proinflammatory CD27 - /CD28 - population. Their potentially cytotoxic status was confirmed by staining with perforin-specific antibodies. Search for the TCR V beta CRD3 sequences homologous to the identified clones revealed close matches with the previously reported T cell clones from AS and reactive arthritis patients, thus supporting their role in the disease and proposing consensus TCR V beta CDR3 motifs for AS. Interestingly, these motifs were also found to have homology with earlier reported virus-specific CDR3 variants, indicating that viral infections could play role in development of AS.

  15. Lebedev Y.B., Amosova A.L., Mamedov I.Z., Fisunov G.Y., Sverdlov E.D. (2007). Most recent AluY insertions in human gene introns reduce the content of the primary transcripts in a cell type specific manner. Gene 390 (1-2), 122–9 [+]

    New strategy for large-scale functional analysis of polymorphic retroelements is described. Inhibitory effect of dimorphic Alu on human gene expression was discovered. Cell type specificity of the inhibitory effect was observed in heterozygous cell lines.

  16. Mamedov I.Z., Arzumanyan E.S., Amosova A.L., Lebedev Y.B., Sverdlov E.D. (2005). Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach. Nucleic Acids Res. 33 (2), e16 [+]

    A new experimental technique for genome-wide detection of integration sites of polymorphic retroelements (REs) is described. Efficiency of the technique was demonstrated by discovering large subset of dimorphic AluY elements undetectable by available bioinformatic approaches.

  17. Buzdin A., Ustyugova S., Gogvadze E., Lebedev Y., Hunsmann G., Sverdlov E. (2003). Genome-wide targeted search for human specific and polymorphic L1 integrations. Hum. Genet. 112 (5-6), 527–33 [+]

    An efficient application of original method of subtractive genomic DNA hybridization to identification of species-specific LINE insertions.

  18. Buzdin A., Ustyugova S., Khodosevich K., Mamedov I., Lebedev Y., Hunsmann G., Sverdlov E. (2003). Human-specific subfamilies of HERV-K (HML-2) long terminal repeats: three master genes were active simultaneously during branching of hominoid lineages. Genomics 81 (2), 149–56 [+]

    Complete structural analysis of human specific LTRs. Multiple endogenous retroviral retropositions in course of human speciation were confirmed at the very first time.

  19. Mamedov I., Batrak A., Buzdin A., Arzumanyan E., Lebedev Y., Sverdlov E.D. (2002). Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes. Nucleic Acids Res. 30 (14), e71 [+]

    New whole-genome approach to comparison of LTR distribution in genomes of related species was presented. The eleven LTR insertions distinguishing human genome from chimpanzee ones were described at the first time.

  20. Buzdin A., Khodosevich K., Mamedov I., Vinogradova T., Lebedev Y., Hunsmann G., Sverdlov E. (2002). A technique for genome-wide identification of differences in the interspersed repeats integrations between closely related genomes and its application to detection of human-specific integrations of HERV-K LTRs. Genomics 79 (3), 413–22 [+]

    We have developed a method of targeted genomic difference analysis (TGDA) for genomewide detection of interspersed repeat integration site differences between closely related genomes. The method includes a whole-genome amplification of the flanks adjacent to target interspersed repetitive elements in both genomic DNAs under comparison, and subtractive hybridization (SH) of the selected amplicons. The potential of TGDA was demonstrated by the detection of differences in the integration sites of human endogenous retroviruses K (HERV-K) and related solitary long terminal repeats (LTRs) between the human and chimpanzee genomes. Of 55 randomly sequenced clones from a library enriched with human-specific integration (HSI) sites, 33 (60%) represented HSIs. All the human-specific (Hs) LTRs belong to two related evolutionarily young groups, suggesting simultaneous activity of two master genes in the hominid lineage. No deletion/insertion polymorphism was detected for the LTR HSIs for 25 unrelated caucasoid individuals. We also discuss the possible research applications for TGDA research.

  21. Lebedev Y.B., Belonovitch O.S., Zybrova N.V., Khil P.P., Kurdyukov S.G., Vinogradova T.V., Hunsmann G., Sverdlov E.D. (2000). Differences in HERV-K LTR insertions in orthologous loci of humans and great apes. Gene 247 (1-2), 265–77 [+]

    The classification of the long terminal repeats (LTRs) of the human endogenous retrovirus HERV-K (HML-2) family was refined according to diagnostic differences between the LTR sequences. The mutation rate was estimated to be approximately equal for LTRs belonging to different families and branches of human endogenous retroviruses (HERVs). An average mutation rate value was calculated based on differences between LTRs of the same HERV and was found to be 0.13% per million years (Myr). Using this value, the ages of different LTR groups belonging to the LTR HML-2 subfamily were found to vary from 3 to 50Myr. Orthologous potential LTR-containing loci from different primate species were PCR amplified using primers corresponding to the genomic sequences flanking LTR integration sites. This allowed us to calculate the phylogenetic times of LTR integrations in primate lineages in the course of the evolution and to demonstrate that they are in good agreement with the LTR ages calculated from the mutation rates. Human-specific integrations for some very young LTRs were demonstrated. The possibility of LTRs and HERVs involvement in the evolution of primates is discussed.


Yuri Lebedev

T cell immune response to the flu vaccination (2017-11-22)

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.