Department of Genomics and Postgenomic Technologies

All publications (show selected)

Sergei Lukyanov

  • Russia, Moscow, Ul. Miklukho-Maklaya 16/10 — On the map
  • IBCh RAS, build. 54, office. 636
  • Phone: +7(499)724-80-66
  • E-mail: luk@ibch.ru

The discovery of four genes of the Noggin family in lampreys is consistent with the hypothesis of two rounds of genomic duplications in vertebrate ancestors

Laboratory of molecular bases of embryogenesis

Researchers from the Laboratory of Molecular Bases of Embryogenesis, in the co-operation with a colleague from the Severtsov Institute of Ecology and Evolution, described for the first time four genes of the Noggin family in the oldest representatives of vertebrates - lampreys, and compared their structure, expression and some functional features with those of the known genes of this family in other vertebrates. The Noggin genes encode secreted factors that regulate many important processes in embryogenesis. As a result, it was concluded that the entire set of the data obtained is in the best agreement with the hypothesis of two successive rounds of duplications of the ancestral genome of invertebrates that occurred at the earliest stage of vertebrate evolution, i.e. about 550 millions years ago, in Paleozoic Era.

Small RNA MTS1338 of Mycobacterium tuberculosis acts as a bacterial virulence factor modulating immune response to infection

Laboratory of regulatory transcriptomics

Small noncoding RNA MTS1338 is present only in the genomes of pathogenic mycobacteria of the tuberculosis complex, and is highly expressed during infection. We demonstrated that MTS1338 provides mycobacterial resistance to oxidative stress, arrests maturation of phagolysosomes, and simulates immune response by activating pro-inflammatory cytokines synthesis. The MTS1338 knock-out mutant strain showed a significant attenuation of M. tuberculosis upon infection of mice. Thus, the small noncoding RNA MTS1338 is a new M. tuberculosis virulence factor providing intracellular survival of mycobacteria.

New mechanism of regulation of the embryonic cells stem status

Department of metabolism and redox biology,  Laboratory of molecular bases of embryogenesis

 

Researchers from the Laboratory of Molecular Bases of Embryogenesis IBCh RAS, in technical cooperation with colleagues from the Department of Metabolism and Redox Biology IBCh RAS, the Laboratory of Genomics and Epigenomics of Vertebrates in the Federal Center "Fundamentals of Biotechnology" RAS, as well as with colleagues from the Cell Motility Group of the Institute of Protein Research RAS, discovered a previously unknown mechanism of the regulation of the activity of genes that determine the pluripotent status of the embryonic stem cells. This mechanism is based on the ability of the cytoskeletal protein Zyxin to displace mRNA of pluripotency genes from complexes with the mRNA-stabilizing protein Ybx1, which accelerates the degradation of these mRNAs. The authors suggest that this mechanism helps to coordinate the processes of morphogenesis and cell differentiation in embryogenesis.

 

The key factor of pancreatic embryogenesis PDX1 reduces the metastatic potential of pancreatic cancer cells

Laboratory of human genes structure and functions

Metastasis is the main cause of death in patients with pancreatic adenocarcinoma (PDAC). We studied in vitro the effect of key regulator of pancreas development, PDX1, on the rate of proliferation and mobility of pancreatic cancer cell line PANC-1. The study of growth kinetics showed that the expression of PDX1 significantly increases the GFP-labeled PANC-1 cells growth rate. The effect of PDX1 on the migratory ability was assessed using wound healing and Transwell assays. PDX1 ectopic expression resulted in slowing down the wound healing rate and reduced the migration rate compared to control cells. In order to evaluate the possible effect of PDX1 expression on PANC-1 cells metastatic ability, an in vivo Danio rerio embryos model was used in collaboration with the Laboratory of Protein Engineering of the Institute of Molecular Genetics of the Russian Academy of Sciences. GFP-labeled control and expressing PDX1 PANC-1 cells were injected into the yolk sac area of two-day Danio rerio embryos and after 48 hours the distribution of cells in organisms was analyzed. In 50% of Danio rerio embryos, the control cells without PDX expression migrated to the vessels of the head and tail. The migration of PDX1-containing cells was significantly reduced and was observed in only 12.5% of embryos. When the expression of PDX1 was suppressed using siRNA, migrated cells were detected in 40% of embryos. This may indicate that the expression of the PDX1 gene suppresses the metastasis of cancer cells.

Novel modulator of FGF and ADP signaling, c-Answer, regulates regeneration and brain development in the cold-blooded animals, but lacks in the warm-blooded, including human.

Laboratory of molecular bases of embryogenesis

Earlier the hypothesis was proposed in the laboratory of the Molecular Bases of Embryogenesis (IBCH RUS) that the loss in warm-blooded animals of the ability to regenerate limbs and, as a compensation, the progressive development of the brain may be associated with the loss of some genes by the warm-blooded ancestors. Now we developed a new bioinformatics method which allows one to reveal genes that appeared or disappeared at a certain stage of evolution. Using this method, a previously unknown modulator of FGF and ADP signaling, the transmembrane protein c-Answer was revealed, which stimulates regeneration and affects brain development in cold-blooded animals, but has disappeared in warm-blooded animals, including humans. The effectiveness of the new bioinformatics method was also confirmed by finding genes specific only for short-lived mammals.

Publications

  1. Rubanov LI, Zaraisky AG, Shilovsky GA, Seliverstov AV, Zverkov OA, Lyubetsky VA (2019). Screening for mouse genes lost in mammals with long lifespans. BioData Min 12 (1), 20
  2. Korotkova DD, Lyubetsky VA, Ivanova AS, Rubanov LI, Seliverstov AV, Zverkov OA, Martynova NY, Nesterenko AM, Tereshina MB, Peshkin L, Zaraisky AG (2019). Bioinformatics Screening of Genes Specific for Well-Regenerating Vertebrates Reveals c-answer, a Regulator of Brain Development and Regeneration. Cell Rep 29 (4), 1027–1040.e6

A new class of antisense oligonucleotides – phosphoryl guanidine oligo-2′-O-methylribonucleotides - specifically inhibits target genes expression in intracellular Mycobacteria

Laboratory of regulatory transcriptomics

Phosphoryl guanidine oligo-2′-O-methylribonucleotides (2′-OMe PGOs) are a novel type of uncharged RNA analogues. We demonstrated that antisense 2′-OMe PGO inhibits the growth of Mycobacterium smegmatis and downregulates target gene expression at both transcriptional and translational levels. 2′-OMe PGO penetrates into intracellular mycobacteria residing in macrophages without exerting toxic effects on eukaryotic cells, and inhibits the transcription of the target gene in M. smegmatis-infected macrophages. So, these novel oligonucleotide derivatives have a potential as antisense therapeutic agents against tuberculosis, especially its drug-resistant forms

Coincidence of functional epigenetic marks and transposable elements enables measuring transcriptional regulation evolution rates of genes and molecular pathways

Group for Genomic Regulation of Cell Signaling Systems

We developed bioinformatic method RetroSpect that enables measuring rates of evolution of transcriptional regulation of genes and molecular pathways based on coincidences of functional genomic epigenetic marks and transposable elements. We applied Retrospect to quantitative data on genomic distribution of transcription factor binding sites and histone marks: H3K4me1, H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3. The analysis of public databases demonstrated that the most strongly evolving processes (termed RRE-enriched) are connected with regulation of microRNAs, olfaction, fertilization, immune response, fatty acids metabolism and detoxication. In contrast, the most slowly evolving processes (RRE-deficient) dealt with protein translation, RNA transcription, maintaining chromatin structure and molecular signaling.

Publications

  1. Nikitin D, Kolosov N, Murzina A, Pats K, Zamyatin A, Tkachev V, Sorokin M, Kopylov P, Buzdin A (2019). Retroelement-Linked H3K4me1 Histone Tags Uncover Regulatory Evolution Trends of Gene Enhancers and Feature Quickly Evolving Molecular Processes in Human Physiology. Cells 8 (10),
  2. Igolkina AA, Zinkevich A, Karandasheva KO, Popov AA, Selifanova MV, Nikolaeva D, Tkachev V, Penzar D, Nikitin DM, Buzdin A (2019). H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks. Cells 8 (9),
  3. Nikitin D, Garazha A, Sorokin M, Penzar D, Tkachev V, Markov A, Gaifullin N, Borger P, Poltorak A, Buzdin A (2019). Correction: Nikitin, D., et al. Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution. 2019, , 130. Cells 8 (8),
  4. Nikitin D, Garazha A, Sorokin M, Penzar D, Tkachev V, Markov A, Gaifullin N, Borger P, Poltorak A, Buzdin A (2019). Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution. Cells 8 (2), 130

Ras-dva small GTPases lost during evolution of amniotes regulate regeneration in anamniotes

Laboratory of molecular bases of embryogenesis

Anamniotes — fishes and amphibians — have an amazing ability to regenerate organs. For example, limbs, tail, heart, eyes and brain. Unfortunately, in the course of evolution, amniotes — reptiles, birds, and mammals — lost their ability to efficient regeneration. We assumed that the loss of regenerative capacity is associated with the loss of some genes responsible for the formation of the wound blastema - a group of actively dividing dedifferentiated cells that guarantee regeneration. In confirmation of this, we showed that amniotes lacks the genes of small GTPases of Ras-dva family, which are responsible for the formation of the regeneration blastema in fish and amphibians, and, consequently, for one of the mechanisms of regeneration.

Novel antitumor combination based on a binary system of vectors for the tumor-specific expression of the killer gene FCU1

Laboratory of human genes structure and functions

Despite advances in cancer treatment, cancer remains the second leading cause of death after cardiovascular diseases. Therefore, the search for new effective and low-toxic approaches to the treatment of cancer is an extremely important challenge. Cancer gene therapy, which is based on the delivery to a tumor of genes causing growth inhibition or death of cancer cells, is one of the promising directions. A gene-therapeutic complex was created in which a modified binary cre-loxP system and the artificial promoter PhTSurv269 created by us earlier were used to control the expression of the suicidal FCU1 gene. Under the conditions of a mouse adenocarcinoma model, a high therapeutic potential of the complex under study was demonstrated.

Publications

  1. Bezborodova OA, Alekseenko IV, Nemtsova ER, Pankratov AA, Filyukova OB, Yakubovskaya RI, Kostina MB, Potapov VK, Sverdlov ED (2018). The Antitumor Efficacy of a Complex Based on Two-Vector System for Coexpression of the Suicide Gene Fcu1 and Cre Recombinase. Dokl Biochem Biophys 483 (1), 326–328

PIWIL2 functions in testicular germ cell tumors development

Laboratory of human genes structure and functions

PIWILs, highly evolutionary conserved proteins, are involved in many cellular processes including carcinogenesis. They function in combination with short non-coding RNAs (piRNAs), determining genomes stability, preventing expression and transposition of mobile elements. We studied functions of the PIWI/piRNA system in germ testicular cells, as well as in testicular germ cell tumors development, and showed predominant expression of short 60 kDa PIWIL2 isoform. Herewith, there is no piRNA biogenesis in tumor cells, and the short PIWIL2 isoform suppresses the expression of young LINE and SINE transposon families post-transcriptionally, which can provide advantages for tumor growth by maintaining the stability of its genome.

PIWIL2 functions in testicular germ cell tumors development

Laboratory of regulatory transcriptomics

PIWILs, highly evolutionary conserved proteins, are involved in many cellular processes including carcinogenesis. They function in combination with short non-coding RNAs (piRNAs), determining genomes stability, preventing expression and transposition of mobile elements. We studied functions of the PIWI/piRNA system in germ testicular cells, as well as in testicular germ cell tumors development, and showed predominant expression of short 60 kDa PIWIL2 isoform. Herewith, there is no piRNA biogenesis in tumor cells, and the short PIWIL2 isoform suppresses the expression of young LINE and SINE transposon families post-transcriptionally, which can provide advantages for tumor growth by maintaining the stability of its genome.

New methods of estimation of evolutional rate of molecular pathways

Group for Genomic Regulation of Cell Signaling Systems

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. 

The discovery and study of the function of the homeobox gene Anf / Hesx1 in lampreys confirms its key role in the appearance of the telencephalon in vertebrates

Laboratory of molecular bases of embryogenesis

An important feature of vertebrates, including humans, is the presence of a unique part of the forebrain, called the telencephalon, which has no homologs in invertebrates. Previously, we discovered a  monogenic class of homeobox genes Anf / Hesx1, which is also  absent in all invertebrates but plays a key role in regulation of the telencephalon development  in vertebrates. However, until recently, the Anf / Hesx1 gene was not found in the most ancient group of vertebrate - in jawless fishes (extant lampreys and myxins), while the telencephalon in these animals was described and their genomes were sequenced. Now we have shown for the first time that Anf / Hesx1 is still present in lampreys, in which it also regulate development of the telencephalon. The obtained data confirm the hypothesis, which we have formulated earlier, that the emergence of the telencephalon in evolution was associated with the appearance of the homeobox gene Anf / Hesx1.

A novel approach to design of tumor-specific promoters. Construction and analysis of a combinatorial library of chimeric promoters which consist of random combinations of promoter modules

Laboratory of human genes structure and functions

The research of transcription promoters active in cancer cells but not in normal cells is important in understanding the processes of carcinogenesis and embryogenesis. The revealing or the  de novo design of highly specific “cancer” promoters has also a great practical interest in design of vectors which are restricted in their toxic effect by tumors and not damage healthy tissues in anticancer gene therapy. In the continuation of our previous studies (Alekseenko et al, 2012, Kashkin et al, 2015), in this work, for the first time, a combinatorial library of chimeric promoters was created by random combining fragments of cancer-specific promoters of human genes to search for new promoters with prescribed functions. The library of chimeric promoters was inserted into lentiviral vector with CopGFP reporter gene. A431 cells was transduced with the library and sorted for selection of fluorescent cells which may contain active chimeric promoters. It was shown that most of the selected cells really contained active and cancer-specific promoters. The analysis of random clones demonstrated that the combinations of the fragments in the chimeric promoters are non-casual. Some of the chimeric promoters manifest high promoter activity and cancer specificity. Further analysis of most frequent modules in chimeric promoters must expand the conception of the nature of tumor-specific promoter activity and should allow to design purposefully more active and specific promoters.

The secreted factor Ag1 missing in higher vertebrates regulates fins regeneration in Danio rerio.

Laboratory of molecular bases of embryogenesis

Using the model of the Danio rerio caudal fin regeneration, it is established that the secreted protein Ag1 is required for regeneration. It is shown that the caudal amputation induces rapid activation of the expression of Ag1 in cells of the wound epithelium. However, inhibition of the Ag1 mRNA translation causes a retardation of the regeneration. The results of this work are important because Ag1 presents in genomes of only the lower, well regenerating vertebrates, including fish and amphibians, but not in higher vertebrates, which cannot effectively regenerate limbs. The data obtained indicate that a reduction of the regeneration capabilities in higher vertebrates, including humans, could be attributed to the disappearance of some genes important for regeneration, in particular, Ag1.