Group for Genomic Regulation of Cell Signaling Systems

Department of Genetics and Postgenomic Technologies

Head: Anton Buzdin, D.Sc
bu3din@mail.ru+7(495)727-38-63

www.ibch.ru/gensensor/ggassk.htm

Genome- and Transcriptome Wide Analysis of Gene Expression in Higher Eukaryotes; Identification of Major Molecular Genetic Aspects of Human Speciation; Engineering of human tissue specific gene regulatory sequences; Recovery of new molecular genetic oncom

Our group exists since February 2006 when it had separated from the group supervised by Dr. Yuri Lebedev in the Laboratory of Human Genes Structure and Functions. First of all, the head of the above laboratory, professor Eugene Sverdlov, is our scientific guru.

  1. Functional genomic analysis of human specific DNA
  2. Design of new experimental techniques for large scale functional studies of the complex genomes
  3. Engineering of gene regulatory sequences
  1. Discovery of chimeric retroelements in the mammalian genomes
  2. Development of new experimental techniques for functional genomics
  3. Identification of gene regulatory regions in the human specific DNA
  4. Directed differentiation of several stem cell cultures
NamePositionContacts
Anton Buzdin, D.Scdepart. dir.bu3din@mail.ru+7(495)727-38-63
Andrew Garazhar. f.garazha@gmail.com
Maksim Sorokin, Ph.D.r. f.sorokin.maks@gmail.com
Galina Malahovaj. r. f.galena_vm@mail.ru+7(496)727-38-63
Maria Suntsovaj. r. f.suntsova86@mail.ru
Anastasiya ZabolotnevaPhD stud.a.zabolotneva@gmail.com+7(495)727-38-63
Mihail Potapovres. eng.+7()3306547

Selected publications

  1. Sorokin M, Kholodenko R, Suntsova M, Malakhova G, Garazha A, Kholodenko I, Poddubskaya E, Lantsov D, Stilidi I, Arhiri P, Osipov A, Buzdin A (2018). Oncobox bioinformatical platform for selecting potentially effective combinations of target cancer drugs using high-throughput gene expression data. Cancers (Basel) 10 (10),
  2. Nikitin D, Penzar D, Garazha A, Sorokin M, Tkachev V, Borisov N, Poltorak A, Prassolov V, Buzdin AA (2018). Profiling of human molecular pathways affected by retrotransposons at the level of regulation by transcription factor proteins. Front Immunol 9 (0), 30
  3. Buzdin A, Sorokin M, Garazha A, Sekacheva M, Kim E, Zhukov N, Wang Y, Li X, Kar S, Hartmann C, Samii A, Giese A, Borisov N (2018). Molecular pathway activation – New type of biomarkers for tumor morphology and personalized selection of target drugs. Semin Cancer Biol  (0),
  4. Sorokin M, Kholodenko R, Grekhova A, Suntsova M, Pustovalova M, Vorobyeva N, Kholodenko I, Malakhova G, Garazha A, Nedoluzhko A, Vasilov R, Poddubskaya E, Kovalchuk O, Adamyan L, Prassolov V, Allina D, Kuzmin D, Ignatev K, Osipov A, Buzdin A (2018). Acquired resistance to tyrosine kinase inhibitors may be linked with the decreased sensitivity to X-ray irradiation. Oncotarget 9 (4), 5111–5124
  5. Larkin B, Ilyukha V, Sorokin M, Buzdin A, Vannier E, Poltorak A (2017). Cutting edge: Activation of sting in t cells induces type i IFN responses and cell death. J Immunol 199 (2), 397–402
  6. Wirsching A, Melloul E, Lezhnina K, Buzdin AA, Ogunshola OO, Borger P, Clavien PA, Lesurtel M (2017). Temporary portal vein embolization is as efficient as permanent portal vein embolization in mice. Surgery 162 (1), 68–81
  7. Buzdin AA, Prassolov V, Garazha AV (2017). Friends-Enemies: Endogenous retroviruses are major transcriptional regulators of human DNA. Front Chem 5 (0), 35
  8. Garazha A, Suntsova M, Buzdin A (2017). Structural and functional coevolution of human endogenous retroviruses with our genome.  (0), 479–485
  9. Petrov I, Suntsova M, Ilnitskaya E, Roumiantsev S, Sorokin M, Garazha A, Spirin P, Lebedev T, Gaifullin N, Larin S, Kovalchuk O, Konovalov D, Prassolov V, Roumiantsev A, Buzdin A (2017). Gene expression and molecular pathway activation signatures of MYCN-amplified neuroblastomas. Oncotarget 8 (48), 83768–83780
  10. Alexandrova E, Nassa G, Corleone G, Buzdin A, Aliper AM, Terekhanova N, Shepelin D, Zhavoronkov A, Tamm M, Milanesi L, Miglino N, Weisz A, Borger P (2016). Large-scale profiling of signalling pathways reveals an asthma specific signature in bronchial smooth muscle cells. Oncotarget 7 (18), 25150–25161
  11. Petrov I, Suntsova M, Mutorova O, Sorokin M, Garazha A, Ilnitskaya E, Spirin P, Larin S, Zhavoronkov A, Kovalchuk O, Prassolov V, Roumiantsev A, Buzdin A (2016). Molecular pathway activation features of pediatric acute myeloid leukemia (AML) and acute lymphoblast leukemia (ALL) cells. Aging (Albany NY) 8 (11), 2936–2947
  12. Shepelin D, Korzinkin M, Vanyushina A, Aliper A, Borisov N, Vasilov R, Zhukov N, Sokov D, Prassolov V, Gaifullin N, Zhavoronkov A, Bhullar B, Buzdin A (2016). Molecular pathway activation features linked with transition from normal skin to primary and metastatic melanomas in human. Oncotarget 7 (1), 656–670
  13. Aliper A, Belikov AV, Garazha A, Jellen L, Artemov A, Suntsova M, Ivanova A, Venkova L, Borisov N, Buzdin A, Mamoshina P, Putin E, Swick AG, Moskalev A, Zhavoronkov A (2016). In search for geroprotectors: In silico screening and in vitro validation of signalome-level mimetics of young healthy state. Aging (Albany NY) 8 (9), 2127–2152
  14. Suntsova M, Garazha A, Ivanova A, Kaminsky D, Zhavoronkov A, Buzdin A (2015). Molecular functions of human endogenous retroviruses in health and disease. Cell Mol Life Sci 72 (19), 3653–3675
  15. Artemov A, Aliper A, Korzinkin M, Lezhnina K, Jellen L, Zhukov N, Roumiantsev S, Gaifullin N, Zhavoronkov A, Borisov N, Buzdin A (2015). A method for predicting target drug efficiency in cancer based on the analysis of signaling pathway activation. Oncotarget 6 (30), 29347–29356
  16. Venkova L, Aliper A, Suntsova M, Kholodenko R, Shepelin D, Borisov N, Malakhova G, Vasilov R, Roumiantsev S, Zhavoronkov A, Buzdin A (2015). Combinatorial high-throughput experimental and bioinformatic approach identifies molecular pathways linked with the sensitivity to anticancer target drugs. Oncotarget 6 (29), 27227–27238
  17. Moskalev A, Chernyagina E, de Magalhães JP, Barardo D, Thoppil H, Shaposhnikov M, Budovsky A, Fraifeld VE, Garazha A, Tsvetkov V, Bronovitsky E, Bogomolov V, Scerbacov A, Kuryan O, Gurinovich R, Jellen LC, Kennedy B, Mamoshina P, Dobrovolskaya E, Aliper A, Kaminsky D, Zhavoronkov A (2015). Geroprotectors.org: A new, structured and curated database of current therapeutic interventions in aging and age-related disease. Aging (Albany NY) 7 (9), 616–628
  18. Spirin PV, Lebedev TD, Orlova NN, Gornostaeva AS, Prokofjeva MM, Nikitenko NA, Dmitriev SE, Buzdin AA, Borisov NM, Aliper AM, Garazha AV, Rubtsov PM, Stocking C, Prassolov VS (2014). Silencing AML1-ETO gene expression leads to simultaneous activation of both pro-apoptotic and proliferation signaling. Leukemia 28 (11), 2222–2228
  19. Borisov NM, Terekhanova NV, Aliper AM, Venkova LS, Smirnov PY, Roumiantsev S, Korzinkin MB, Zhavoronkov AA, Buzdin AA (2014). Signaling pathways activation profiles make better markers of cancer than expression of individual genes. Oncotarget 5 (20), 10198–10205
  20. Buzdin AA, Zhavoronkov AA, Korzinkin MB, Venkova LS, Zenin AA, Smirnov PY, Borisov NM (2014). Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data. Front Genet 5 (0), 55
  21. Aliper AM, Frieden-Korovkina VP, Buzdin A, Roumiantsev SA, Zhavoronkov A (2014). A role for G-CSF and GM-CSF in nonmyeloid cancers. Cancer Med 3 (4), 737–746
  22. Aliper AM, Frieden-Korovkina VP, Buzdin A, Roumiantsev SA, Zhavoronkov A (2014). Interactome analysis of myeloid-derived suppressor cells in murine models of colon and breast cancer. Oncotarget 5 (22), 11345–11353
  23. Zhavoronkov A, Buzdin AA, Garazha AV, Borisov NM, Moskalev AA (2014). Signaling pathway cloud regulation for in silico screening and ranking of the potential geroprotective drugs. Front Genet 5 (0), 49
  24. Lezhnina K, Kovalchuk O, Zhavoronkov AA, Korzinkin MB, Zabolotneva AA, Shegay PV, Sokov DG, Gaifullin NM, Rusakov IG, Aliper AM, Roumiantsev SA, Alekseev BY, Borisov NM, Buzdin AA (2014). Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways. Oncotarget 5 (19), 9022–9032
  25. Zabolotneva AA, Zhavoronkov AA, Shegay PV, Gaifullin NM, Alekseev BY, Roumiantsev SA, Garazha AV, Kovalchuk O, Aravin A, Buzdin AA (2013). A systematic experimental evaluation of microRNA markers of human bladder cancer. Front Genet 4 (0), 247
  26. Jones RB, Song H, Xu Y, Garrison KE, Buzdin AA, Anwar N, Hunter DV, Mujib S, Mihajlovic V, Martin E, Lee E, Kuciak M, Raposo RAS, Bozorgzad A, Meiklejohn DA, Ndhlovu LC, Nixon DF, Ostrowski MA (2013). LINE-1 retrotransposable element DNA accumulates in HIV-1- infected cells. J Virol 87 (24), 13307–13320
  27. Suntsova M, Gogvadze EV, Salozhin S, Gaifullin N, Eroshkin F, Dmitriev SE, Martynova N, Kulikov K, Malakhova G, Tukhbatova G, Bolshakov AP, Ghilarov D, Garazha A, Aliper A, Cantor CR, Solokhin Y, Roumiantsev S, Balaban P, Zhavoronkov A, Buzdin A (2013). Human-specific endogenous retroviral insert serves as an enhancer for the schizophrenia-linked gene PRODH. Proc Natl Acad Sci U S A 110 (48), 19472–19477
  28. Zabolotneva AA, Zhavoronkov A, Garazha AV, Roumiantsev SA, Buzdin AA (2013). Characteristic patterns of microrna expression in human bladder cancer. Front Genet 3 (0), 310
  29. Alexandrova EA, Olovnikov IA, Malakhova GV, Zabolotneva AA, Suntsova MV, Dmitriev SE, Buzdin AA (2012). Sense transcripts originated from an internal part of the human retrotransposon LINE-1 5' UTR. Gene 511 (1), 46–53
  30. Zabolotneva AA, Bantysh O, Suntsova MV, Efimova N, Malakhova GV, Schumann GG, Gayfullin NM, Buzdin AA (2012). Transcriptional regulation of human-specific SVAF1retrotransposons by cis-regulatory MAST2 sequences. Gene 505 (1), 128–136
  31. Baskaev K, Garazha A, Gaifullin N, Suntsova MV, Zabolotneva AA, Buzdin AA (2012). NMETR: Technique for facile recovery of hypomethylation genomic tags. Gene 498 (1), 75–80
  32. Peletskaya E, Andrake M, Gustchina A, Merkel G, Alexandratos J, Zhou D, Bojja RS, Satoh T, Potapov M, Kogon A, Potapov V, Wlodawer A, Skalka AM (2011). Localization of asv integrase-dna contacts by site-directed crosslinking and their structural analysis. PLoS One 6 (12), e27751
  33. Zabolotneva A, Tkachev V, Filatov F, Buzdin A (2010). How many antiviral small interfering RNAs may be encoded by the mammalian genomes? Biol Direct 5 (0), 62
  34. Kuzmin D, Gogvadze E, Kholodenko R, Grzela DP, Mityaev M, Vinogradova T, Kopantzev E, Malakhova G, Suntsova M, Sokov D, Ivics Z, Buzdin A (2010). Novel strong tissue specific promoter for gene expression in human germ cells. BMC Biotechnol 10 (0), 58
  35. Gogvadze E, Stukacheva E, Buzdin A, Sverdlov E (2009). Human-specific modulation of transcriptional activity provided by endogenous retroviral insertions. J Virol 83 (12), 6098–6105
  36. Ghilarov DA, Buzdin AA (2009). Endogenous retroviral sequences control the transcription of many host genes in eukaryotes.  (0), 35–63
  37. Gogvadze E, Buzdin A (2009). Retroelements and their impact on genome evolution and functioning. Cell Mol Life Sci 66 (23), 3727–3742
  38. Gogvadze E, Barbisan C, Lebrun MH, Buzdin A (2007). Tripartite chimeric pseudogene from the genome of rice blast fungus Magnaporthe grisea suggests double template jumps during long interspersed nuclear element (LINE) reverse transcription. BMC Genomics 8 (0), 360
  39. Buzdin A, Gogvadze E, Lebrun MH (2007). Chimeric retrogenes suggest a role for the nucleolus in LINE amplification. FEBS Lett 581 (16), 2877–2882
  40. Kholodenko R, Kholodenko I, Sorokin V, Tolmazova A, Sazonova O, Buzdin A (2007). Anti-apoptotic effect of retinoic acid on retinal progenitor cells mediated by a protein kinase A-dependent mechanism. Cell Res 17 (2), 151–162
  41. Buzdin AA (2007). DNA hybridization in solution for mutation detection.  (0), 211–239
  42. Buzdin AA (2007). Nucleic acids hybridization: Potentials and limitationS.  (0), 1–28
  43. Buzdin AA, Lukyanov SA (2007). Stem-loop oligonucleotides as hybridization probes and their practical use in molecular biology and biomedicine.  (0), 85–96
  44. Lukyanov SA, Lukyanov KA, Gurskaya NG, Bogdanova EA, Buzdin AA (2007). Selective suppression of polymerase chain reaction and its most popular applications.  (0), 29–51
  45. Buzdin AA (2007). Current attempts to improve the specificity of nucleic acids hybridization.  (0), 241–264
  46. Buzdin AA (2007). Coincidence cloning: Robust technique for isolation of common sequences.  (0), 187–210
  47. Lukyanov SA, Rebrikov D, Buzdin AA (2007). Suppression subtractive hybridization.  (0), 53–84
  48. Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E (2006). At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription. J Virol 80 (21), 10752–10762
  49. Buzdin A, Kovalskaya-Alexandrova E, Gogvadze E, Sverdlov E (2006). GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats. Nucleic Acids Res 34 (9), e67
  50. Kholodenko IV, Buzdin AA, Kholodenko RV, Baibikova JA, Sorokin VF, Yarygin VN, Sverdlov ED (2006). Mouse retinal progenitor cell (RPC) cocultivation with retinal pigment epithelial cell culture affects features of RPC differentiation. Biochemistry (Mosc) 71 (7), 767–774
  51. Kovalskaya E, Buzdin A, Gogvadze E, Vinogradova T, Sverdlov E (2006). Functional human endogenous retroviral LTR transcription start sites are located between the R and U5 regions. Virology 346 (2), 373–378
  52. Buzdin AA (2004). Retroelements and formation of chimeric retrogenes. Cell Mol Life Sci 61 (16), 2046–2059
  53. Chalaya T, Gogvadze E, Buzdin A, Kovalskaya E, Sverdlov ED (2004). Improving specificity of DNA hybridization-based methods. Nucleic Acids Res 32 (16), e130
  54. Buzdin A, Gogvadze E, Kovalskaya E, Volchkov P, Ustyugova S, Illarionova A, Fushan A, Vinogradova T, Sverdlov E (2003). The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination. Nucleic Acids Res 31 (15), 4385–4390
  55. 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 (56), 527–533
  56. 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), 149–156
  57. Mamedov I, Batrak A, Buzdin A, Arzumanyan E, Lebedev Y, Sverdlov ED (2002). Genome-wide comparison of differences in the integration sites of interspersed repeats between closely related genomes. Nucleic Acids Res 30 (14), e71
  58. Buzdin A, Ustyugova S, Gogvadze E, Vinogradova T, Lebedev Y, Sverdlov E (2002). A new family of chimeric retrotranscripts formed by a full copy of U6 small nuclear RNA fused to the 3′ terminus of L1. Genomics 80 (4), 402–406
  59. 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), 413–422

Anton Buzdin

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 51, office. 663
  • Phone: +7(495)727-38-63
  • E-mail: bu3din@mail.ru

New methods of estimation of evolutional rate of molecular pathways (2017-12-11)

We showed that transcription factor binding sites in the vicinities of gene promoters, that colocalize with the transposable elements, may serve as the markers of the evolutional rate ofmolecular pathways. We found that in human ancestral lineage the most quickly evolving pathways were linked with immunity and response to pathogens, as well as for metabolism of fats and catabolism of heterocyclic molecules, and for formation of perception organs.