Laboratory of Pharmacogenomics

Maksim L.Filipenko,
Ph.D.
Phone: +7(383)363-51-70
Email

• Development and validation of methods of DNA polymorphism analysis.

- molecular-genetic diagnostics of inherited and multifactorial human diseases, pharmacogenetic studies;
- identification of somatic mutations in tumors and extracellular fluids during human cancer diseases;
- molecular-genetic typing of bacteria (Mycobacterium tuberculosis, Salmonella, Lactobacillus, etc.)

• Design, cloning and expression of recombinant proteins.

- recombinant cytokines and antigens for dendritic cell therapy;
- new enzymes for DNA modification and amplification.

• Systems biology and analysis of genomic and transcriptomic data.

- study of the molecular mechanisms of the emergence of human diseases and drugs action;
- systems biology and bioinformatics of microorganisms.

• Together with Institute of Clinical Immunology SB RAMS we created recombinant plasmids for expression of the artificial protein containing 11 epitopes of tumor-associated antigens for colorectal cancer. Transfection of recombinant plasmids into human dendritic cells allowed us to achieve the stimulation of specific T-helper and cytotoxic T-lymphocyte. [Patent request RF N.2012119658, 2012].
• We identified six most frequent mutations in BRCA1 genes, causing the development of breast cancer in women living in Western Siberian region of Russian Federation. We developed and tested a system of screening of mutations in BRA1 (5382 insC, 300 T>G, 3819del5, 3875del4, 185 delAG, 4153 delA, 2800delAA) and BRCA2 (6174delT, 9318del4 and 1528del4) using «real-time» PCR and subsequent melting curve analysis with high resolution (HRM). It was found that carriers of T allele (rs1050450) of GPX1 gene are protected against sporadic breast cancer. [Ermolenko N. et al., Genetics. 2010].
• We studied the mechanisms of resistance of non-small cell lung cancer cells (NSCLC) to the action of targeted anticancer agents Nutlin-3, tenovin-6 and RITA that activate transcription factor p53. We identified signaling pathways that are activated in the cells resistant to the action of these drugs, and also key regulatory molecules of these signaling pathways (mainly components of Act and NFkB signaling pathways). Key molecules are considered as potential target molecules for complex anticancer therapy were found. [Boyarskikh U.A. et al., Molecular Biology. 2011].
• We established and characterized a representative collection of M.tuberculosis isolates, circulating in different areas of the former CIS (Dymova et al., 2011, BMS). It was shown that some genetic families have an association with multidrug resistance. [Dymova M.A. et al., J.Med.Microbiol. 2011, Dymova et al., MEDLINE.RU. 2012].
• We conducted whole genome sequencing of 10 M.tuberculosis isolates and developed a rapid and efficient method for screening of known and unknown mutations using HRM-PCR analysis of the genes rpoB, katG and pncA, which are responsible for drug resistance to rifampicin, isoniazid, and pyrazinamide, respectively. [Patent request RF N.2012108730/10, 2012].
• We investigated the influence of different genes and non-genetic parameters on the variability of warfarin’s dose among residents of the West Siberian region. It was shown that only polymorphic loci of genes VKORC1 (-1639 G> A) and CYP2C9 (* 3) have a statistically significant effect on a matched dose of warfarin in the studied sample (22.3% of interindividual variability). [Belozerceva L.A. et al., EPMA J. 2012]
• We created the program ProcAnnot (www.platform.genexplain.com/procannot/), which allows to perform annotation of SNPs, obtained by analysing genomes of various prokaryotes. In addition to the mapping of these SNPs in genes and to determination of their synonymy or nonsynonymy, a new program is capable of performation a Gene set enrichment analysis (GSEA) that allows to determine, which pathways are mainly affected by this list of SNP.
• We performed cloning and expression of several thermostable enzymes in E.coli cells: DNA ligase from Pyrococcus abyssi [Zakabunin et al., Molecular Biology. 2011], FEN1 nuclease from Pyrococcus abyssi, RNase HII and endonuclease V from Thermus thermophiles, native and hybrid DNA polymerases from Geobacillus ssp 777 and Thermococcus celer. Derived enzymes are used to develop new methods of the analysis of DNA and RNA.

1. Weiner A.S., Boyarskikh U.A., Voronina E.N., Mishukova O.V., Filipenko M.L. Methylenetetrahydrofolate reductase C677T and methionine synthase A2756G polymorphisms influence on leukocyte genomic DNA methylation level. Gene. 2014. 533(1), 168-172.
2. Weiner AS, Boyarskikh UA, Voronina EN, Tupikin AE, Korolkova OV, Morozov IV, Filipenko ML. Polymorphisms in folate-metabolizing genes and risk of idiopathic male infertility: a study on a Russian population and a meta-analysis. Fertil Steril. 2014. 101(1), 87-94.
3. Oskina N.A., Boyarskikh U.A., Lazarev A.F., Petrova V.D., Ganov D.I., Tonacheva O.G., Lifshits G.I., Filipenko M.L. A replication study examining association of rs6983267, rs10090154, and rs1447295 common single nucleotide polymorphisms in 8q24 region with prostate cancer in Siberians. Urol Oncol. 2014. 32(1):37. e7-12.
4. Zarebska A, Ahmetov II, Sawczyn S, Weiner AS, Kaczmarczyk M, Ficek K, Maciejewska-Karlowska A, Sawczuk M, Leonska-Duniec A, Klocek T, Voronina EN, Boyarskikh UA, Filipenko ML, Cieszczyk P. Association of the MTHFR 1298A>C (rs1801131) polymorphism with speed and strength sports in Russian and Polish athletes. J Sports Sci. 2014. 32(4), 375-382.
5. Smagin D.A., Boyarskikh U.A., Bondar N.P., Filipenko M.L., Kudryavtseva N.N. Reduction of serotonergic gene expression in the raphe nuclei of the midbrain under positive fighting experience in male mice. Advances in Bioscience and Biotechnology. 2013. 4(10), 36-44.
6. Sokolova E.A., Malkova N.A., Korobko D.S., Rozhdestvenskii A.S., Kakulya A.V., Khanokh E.V., Delov R.A., Platonov F.A., Popova T.Y., Aref Eva E.G., Zagorskaya N.N., Alifirova V.M., Titova M.A., Smagina I.V., Chaninova S.A., Popovtseva A.V., Puzyrev V.P., Kulakova O.G., Tsareva E.Y., Favorova O.O., Shchur S.G., Lashch N.Y., Popova N.F., Popova E.V., Gusev E.I., Boyko A.N., Aulchenko Y.S., Filipenko M.L. Association of SNPs of CD40 Gene with Multiple Sclerosis in Russians. PloS ONE. 2013. 8(4), e61032.
7. Boyarskikh U.A., Bondar N.P., Filipenko M.L., Kudryavtseva N.N. Downregulation of serotonergic gene expression in the raphe nuclei of the midbrain under chronic social defeat stress in male mice. Molecular Neurobiology. 2013. 48(1), 13-21.
8. Gordeeva L.A., Voronina E.N., Sokolova E.A., Ermolenko N.A., Gareeva J.V., Sutulina I.M., Simonova T.A., Filipenko M.L., Glushkov A.N. Association GSTT1, GSTM1, and GSTP1 (Ile105Val) genetic polymorphisms in mothers with risk of congenital malformations in their children in Western Siberia: a case-control study. Prenatal diagnosis. 2013. 33(11), 1095–1101.
9. Kushnir A.V., Ilina E.N., Malakhova M.V., Priputnevich T.V., Filipenko M.L. Multiple-locus variable number tandem repeat analysis of Neisseria gonorrhoeae isolates in Russia. Infect. Genet. Evol. 2013 14, 8-14.
10. KushnirA.V., Muminov T.A., Bayev A.I., Khrapov E.A., Filipenko M.L. Molecular characterization of Neisseria gonorrhoeae isolates in Almaty, Kazakhstan, by VNTR analysis, Opa-typing and NG-MAST. Infect. Genet. Evol. 2012. 12(3), 570-576.
11. Battulin NR, Khabarova AA, Boyarskikh UA, Menzorov AG, Filipenko ML, Serov OL. Reprogramming somatic cells by fusion with embryonic stem cells does not cause silencing of the Dlk1-Dio3 region in mice. World J Stem Cells. 2012. 4(8), 87-93.
12. Weiner AS, Boyarskih UA,Voronina EN, Selezneva IA, Sinkina TV, Lazarev AF, Petrova VD, Filipenko ML. Polymorphisms in the folate-metabolizing genes MTR, MTRR, and CBS and breast cancer risk. Cancer Epidemiology, 2012. 36(2), e95-e100.
13. Yatsenko OP, Silkov AN, Khrapov EA, Filipenko ML, Kozlov VA, Sennikov SV. Tissue-specific expression of splice variants of human IL-4 and IL-6 gene mRNA. Bull Exp Biol Med. 2012. 152(3), 329-332.
14. Gabdoulline R., Eckweiler D., Kel A.E., Stegmaier P. 3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. Nucleic Acids Res. 2012. 40(1), 180-185.
15. Surovtseva M.N., Sokolova E.A., Voronina E.N., Pronin S.V., Filipenko M.L. Association of the 54-nucleotide repeat polymorphism of hPer3 with opioid dependence in residents of the West Siberian region. Psychiatr Genet. 2012. 22(6), 309-310.
16. Vayner A.S., Gordeeva L.A., Voronina E.N., Boyarskikh U.A., Shabaldin A.V., Filipenko M.L. Polymorphisms in folate-metabolizing genes and risk of having an offspring with congenital anomalies in the West Siberian region of Russia: a case-control study. Prenatal diagnosis. 2012. 32(11), 1041-1048.
17. Belozertseva L.A., Voronina E.N., Kokh N.V., Tsvetovskaya G.A., Momot A.P., Lifshits G.I., Filipenko M.L., Shevela A.I., Vlassov V.V. Personalized approach of medication by indirect anticoagulants tailored to the patient-Russian context: what are the prospects? The Epma J. 2012. 3(1), 10.
18. Oskina N.А., Boyarskikh U.А., Lazarev А.F., Petrova V.D., Ganov D.I., Tonacheva О.G., Lifshits G.I., Filipenko М.L. The chromosomal region 8q24 is associated with increased risk of prostate cancer in the Siberian region of Russia, a meta-analysis. Molecular Biology. 2012. 46(2), 234. [Article in Russian]
19. Jurik S.А., Filipenko М.L., Khrapov Е.А., Semenihin V.I. Identification of streptococcus thermophilus, which are used in starter cultures in production of hard cheeses. Doklady Akademii Nauk. 2012. 3, 45-47. [Article in Russian]
20. Weiner А.S., Nagaicev V.М., Korolkova О.V., Vostrikov V.V., Osadchuk L.V., Pechkovskiy E.V., Malinovskaya I.S., Filipenko М.L. Polymorphic locus rs3088232 of BRDT gene is associated with the risk of idiopathic male infertility in a sample of residents of the West Siberian region of Russia. Bulletin of Siberian medicine. 2012. 3, 18-22. [Article in Russian]
21. Afoniushkin V.N., Malaheeeva L.I., Dudareva Е.V., Filipenko М.L. Epizooties of bacterial endocarditis. Aviculture. 2012. 9, 41-44. [Article in Russian]
22. Osadchii S.A., Shubin V.G., Kozlova L.P., Varlamenko V.S., Filipenko M.L., Boyarskikh U.A. Improvement of Ways to Obtain Ethidium Bromide and Synthesis of Ethidium Ethyl Sulfate, a New Fluorescent Dye for Detection of Nucleic Acids. Russian Journal of Applied Chemistry. 2011. 84(9), 1541-1548.

1. Sennikov S.V., Filippenko M.L., Kurilin V.V., Kulikova E.V., Khrapov E.A., Shevchenko Ju.A., Shorokhov R.V., Jakushenko V.K., Sokolov A.V. Recombinant plasmid DNA pCI-UB-POLYEPI containing epitopes of tumour-associated antigens for colorectal cancer and method of its application for stimulation of specific antitumour immune response against colorectal cancer cells. Patent RF N.2507265, 2014.
2. Filipenko M.L., Dymova M.A., Bojarskikh U.A., Khrapov E.A., Petrenko T.I., Al'khovik O.I. Method of detecting rifampicin-resistant isolates of Mycobacterium tuberculosis. Patent RF N.2485177, 2013.

Partner integration project of the Presidium of SB RAS

• N.46 «The study of mechanisms for preserving populations of mobile and stationary members of the intestine microbiota in animals and humans, and the development of technologies for medical impact on mobile enteropathogenic forms of bacteria» (2012-2014)

Programs of the Presidium of RAS N.5 “Basic Science for Medicine”

• N.43 «Development of a new method for the rapid identification of drug resistance of mycobacteria to the six major antituberculosis drugs using melting curve analysis of PCR products with high resolution» (2013-2015)

N.6 «Molecular and cell biology»

• N.16 «Identification of key regulatory target genes of varicose veins transformation through modern integrated methods of bioinformatic and experimental analysis of the complete transcriptome» (2013-2015)

• Real-time thermocycler CFX384 (Bio-Rad);
• real-time thermocycler CFX96 (Bio-Rad);
• pyrosequencer (QIAGEN);
• centrifuge Avanti J-26 XP I (Beckman Coulter);
• chromatograph DuoFlow (Bio-Rad);
• automated System Biomek2000 (Beckman Coulter);
• microbiological boxing, certified according to 3-4 biosafety group.