Alexander Kel | Institute of Systems Biology (ISB), Ltd/BIOSOFT.RU, Ltd (original) (raw)
Papers by Alexander Kel
The present work aims to identify molecular drivers of short survival in glioblastoma multiforme ... more The present work aims to identify molecular drivers of short survival in glioblastoma multiforme (GBM) using gene regulatory network analysis. We identified five important master regulators-IGFBP2, VEGFA, PDGFA, OSMR and AEBP1 regulating the dysregulated gene networks. Of them, IGFBP2 is found to be highly upregulated in short survivors and has established relevance in glioblastoma pathology. Further investigation on gene regulatory network revealed that FRA-1 transcription factor can be regulated by IGFBP2. FRA-1 is found to be upregulated and impacts overall survival in GBM. It is said to dysregulate at-least 50 downstream genes involved in tumor invasiveness in tumor xenografts making it an important therapeutic target for GBM intervention. We propose that IGFBP2 drives dysregulated gene network responsible for short survival in GBM.
Journal of vascular surgery. Venous and lymphatic disorders, Mar 1, 2022
Biokhimiya, Jun 1, 2014
To fulfill their cell functions, transcription factors (TF) and other DNA binding proteins have t... more To fulfill their cell functions, transcription factors (TF) and other DNA binding proteins have to migrate throughout the nucleus in eukaryotes or the cell in prokaryotes and find their specific binding site on a DNA strand. It is well known that many such proteins easily bind not only to their specific DNA motif, but also to a nonspecific DNA. Thus, it was predicted [1] and then shown in vivo that E. coli lac-repressor is bound to DNA during 90% of its lifetime [2]. Similar results were achieved in the case of some human DNA binding proteins; most of these molecules were also maintained in bound state on chromatin [3]. Due to the fast and sufficient affinity of binding of TF to nonspecific DNA, the question arises whether association of TFs to DNA occurs more promptly than their diffusion-driven distribution throughout the nucleus. If so, the nuclear distribution of proteins will not be homogenous, i.e. TF molecules will be fixed on DNA sites close to the nuclear pores through which they have entered the nucleus (diffusion-limited mode) [4] (figure, panel (a)). Otherwise, if the diffusion of TFs is faster than binding to DNA, protein molecules will find their binding sites after even distribution inside the nucleus (reaction-limited mode) [4] (figure, panel (b)). It is of great interest to calculate using a great deal of biochemical data on specific human TFs what scenario of the two is more appropriate (figure). A recent study has disclosed using next generation sequencing that the human genome is organized in 3D space as a fractal-like structure [5]. If the spatial structure of chromosomes is highly determined
Applied sciences, Feb 28, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
German Conference on Bioinformatics, 1997
German Conference on Bioinformatics, 1996
Journal of Crohn's and Colitis, Jan 16, 2018
Poster presentations different (p = 0.54). A positive correlation was observed between extra-epit... more Poster presentations different (p = 0.54). A positive correlation was observed between extra-epithelial cytokeratin-18 staining and subserosal fibrosis (R 2 =0.66; p = 0.0004). Four members of the miR-200 family were significantly downregulated in fresh whole SCD samples (miR-141, p = 0.002;-200a, p = 0.002;-200c, p = 0.001;-429; p = 0.004). The reduced miRNA expression was localised to the epithelium of SCD samples (p = 0.001-0.015) with only miR-200b downregulated in the submucosa (p = 0.043); no smooth muscle miRNA expression change was found. The miR-200 target ZEB1 was upregulated in SCD compared with NSCD samples (fold change 9.8; p = 0.035; n = 9). A positive correlation was seen between epithelial miR-141 expression and subserosal fibrosis scores in all samples (R 2 =0.75; p = 0.02; n = 6). Conclusions: IHC staining in SCD tissue was consistent with populations of epithelial cells migrating into deeper layers and gaining mesenchymal characteristics, suggestive of EMT. The correlation with fibrosis scores suggests EMT is a functionally relevant mechanism driving fibrosis in CD and occurs independently of inflammation. The miR-200 family are implicated as regulators of this process given the epithelial-specific dysregulation and tissue upregulation of downstream effectors. Functional studies to prove this relationship are warranted.
Blood, Nov 1, 2006
In T-cell acute lymphoblastic leukaemia (T-ALL) alternative t(5;14)(q35;q32.2) forms effect leuke... more In T-cell acute lymphoblastic leukaemia (T-ALL) alternative t(5;14)(q35;q32.2) forms effect leukemic dysregulation of either TLX3 or NKX2-5 homeobox genes at 5q35 by juxtaposition with 3′-BCL11B at 14q32.2. Putative regulatory sequences underlying ectopic homeobox gene activation in t(5;14), and their mode of action have remained poorly understood mainly because breakpoints at 14q32.2 are widely scattered over the ~1 Mbp genomic desert region. We pooled cytogenetic data from t(5;14) cell lines together with published clinical data to refine the BCL11B downstream breakpoint cluster region (bcr). Ectopic homeobox gene dysregulation was investigated by DNA-i(nhibitory-treatments) with 26-mer double-stranded DNA oligo(nucleotide)s directed against putative enhancers using NKX2-5 expression as endpoints. Enhancer targets were provisionally identified from orphan T-cell DNase-I hypersensive sites (DNaseI-HS) located between 3′-BCL11B and VRK1. NKX2-5 downregulation in t(5;14) PEER cells was almost entirely restricted to DNAi targeting enhancers within the distal bcr and was dose- and sequence-dependent. Interestingly, enhancers near 3′-BCL11B regulated that gene only. These data imply that enhancer-promoter distances and/or locations are important for long-range gene regulation. Chromatin immunoprecipation assays showed that the four most effectual NKX2-5 ectopic enhancers were hyperacetylated. These enhancers clustered ~1 Mbp downstream of BCL11B, within a region displaying multiple regulatory stigmata, including a TCRA-enhancer motif, and abyssal sequence-conservation (“5-Way Regulatory Potential”). Paradoxically, although TLX3/NKX2-5 promoter/exon-1 regions were hypo-acetylated, their expression decreased after TSA treatment, implying extrinsic regulation by factor(s) subject to acetylation-control. PU.1 is known to get transcriptionally repressed by TSA and potentially binds TLX3/NKX2-5 upstream promoter regions. Knockdown of PU.1 effected downregulation of both homeobox genes. Moreover, genomic analysis showed preferential enrichment near validated ectopic enhancers of binding sites for the PU.1-cofactor HMGA1, knockdown of which also inhibited NKX2-5 in PEER cells. Analysis of nuclear matrix attachment (NMA) in PEER cells showed enhanced attachment near to the most effectual enhancer cluster which was alleviated by TSA-treatment. Interestingly, the juxtapositional genomic regions of “active” ins(14;5) rearrangements driving NKX2-5 expression exhibited tight NMA, forming structures reminiscent of “active chromatin hubs”. These findings lead us to propose that HMGA1 and PU.1 co-regulate ectopic homeobox gene expression in t(5;14) T-ALL by interactions mediated at the nuclear matrix, possibly mediated by SATB1 binding. Our data document homeobox gene dysregulation by a novel regulatory region at 3′-BCL11B responsive to HDAC-inhibition and highlight a novel class of potential therapeutic target amid “junk” DNA.
Biological processes are fundamentally driven by complex interactions between biomolecules. Integ... more Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated highthroughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research. These essential steps require consistent generation, capture, and distribution of metadata. To ensure transparency, facilitate data harmonization, and maximize reproducibility and usability of life sciences studies, we propose a simple common omics metadata checklist. The proposed checklist is built on the rich ontologies and standards already in use by the life sciences community. The checklist will serve as a common denominator to guide experimental design, capture important parameters, and be used as a standard format for stand-alone data publications. The omics metadata checklist and data publications will create efficient linkages between omics data and knowledge-based life sciences innovation and, importantly, allow for appropriate attribution to data generators and infrastructure science builders in the post-genomics era. We ask that the life sciences community test the proposed omics metadata checklist and data publications and provide feedback for their use and improvement. A Common Omics Metadata Checklist Proposal Modern life science technologies enable rapid and efficient acquisition of omics data. These data comprehensively measure multilayered molecular networks and provide a snapshot of biological processes in a cell, organism, or their communities. Collected on the same sample at the same time, omics data provide information on the functioning of biomolecules and their interactions. Omics studies are essential for the
Новосибирский государственный университет eBooks, 2012
German Conference on Bioinformatics, 1998
Methods in molecular biology, 2017
In this chapter, we present an approach that allows a causal analysis of multiple &qu... more In this chapter, we present an approach that allows a causal analysis of multiple "-omics" data with the help of an "upstream analysis" strategy. The goal of this approach is to identify master regulators in gene regulatory networks as potential drug targets for a pathological process. The data analysis strategy includes a state-of-the-art promoter analysis for potential transcription factor (TF)-binding sites using the TRANSFAC® database combined with an analysis of the upstream signal transduction pathways that control the activity of these TFs. When applied to genes that are associated with a switch to a pathological process, the approach identifies potential key molecules (master regulators) that may exert major control over and maintenance of transient stability of the pathological state. We demonstrate this approach on examples of analysis of multi-omics data sets that contain transcriptomics and epigenomics data in cancer. The results of this analysis helped us to better understand the molecular mechanisms of cancer development and cancer drug resistance. Such an approach promises to be very effective for rapid and accurate identification of cancer drug targets with true potential. The upstream analysis approach is implemented as an automatic workflow in the geneXplain platform ( www.genexplain.com ) using the open-source BioUML framework ( www.biouml.org ).
German Conference on Bioinformatics, 2000
DNA sites bearing the similar functions in different genes often differ significantly by their nu... more DNA sites bearing the similar functions in different genes often differ significantly by their nucleotide sequences. In many cases a set of binding sites can bedivided into subgroups that tend to be bound preferably by a particular member of a transcription factor family. Identification of such subgroups is essential for developing precise methods of binding site recognition in genomic sequences and for understanding peculiarities of transcriptional regulation mechanisms. In order to detect such subgroups in the sets of DNA functional sites it is necessary to create new clusterization methods for revealing common sub-sequences within each subgroup of sites (local consensi and corresponding weight matrixes). Results: We have developed a novel clusterization method for the analysis of the sets of functional sites based on kernel estimation. The method developed has been applied for the analysis of transcription initiation sites in eukaryotic genes. We have revealed two local consensi that correspond to different functional and taxonomic groups of genes.
Journal of Cancer Research and Clinical Oncology, May 8, 2018
Purpose MDM2 inhibitors are promising anticancer agents that induce cell cycle arrest and tumor c... more Purpose MDM2 inhibitors are promising anticancer agents that induce cell cycle arrest and tumor cells death via p53 reactivation. We examined the influence of Mycoplasma hyorhinis infection on sensitivity of human lung carcinoma cells NCI-H292 to MDM2 inhibitor Nutlin-3. In order to unveil possible mechanisms underlying the revealed effect, we investigated gene expression changes and signal transduction networks activated in NCI-H292 cells in response to mycoplasma infection. Methods Sensitivity of NCI-Н292 cells to Nutlin-3 was estimated by resazurin-based cell viability assay. Genome-wide transcriptional profiles of NCI-H292 and NCI-Н292 Myc.h cell lines were determined using Illumina Human HT-12 v3 Expression BeadChip. Search for key transcription factors and key node molecules was performed using the geneXplain platform. Ability for anchorage-independent growth was tested by soft agar colony formation assay. Results NCI-Н292 Myc.h cells were shown to be 1.5-and 5.2-fold more resistant to killing by Nutlin-3 at concentrations of 15 and 30 µM than uninfected NCI-Н292 cells (P < 0.05 and P < 0.001, respectively). Transcriptome analysis revealed differential expression of multiple genes involved in cancer progression and metastasis as well as epithelial-mesenchymal transition (EMT). Moreover, we have shown experimentally that NCI-Н292 Myc.h cells were more capable of growing and dividing without binding to a substrate. The most likely mechanism explaining the observed changes was found to be TLR4and IL-1b-mediated activation of NF-κB pathway. Conclusions Our results provide evidence that mycoplasma infection is an important factor modulating the effect of MDM2 inhibitors on cancer cells and is able to induce EMT-related changes.
Current Pharmaceutical Design, Nov 14, 2018
Background: A hallmark of atherosclerosis is its complex pathogenesis, which is dependent on alte... more Background: A hallmark of atherosclerosis is its complex pathogenesis, which is dependent on altered cholesterol metabolism and inflammation. Both arms of pathogenesis involve myeloid cells. Monocytes migrating into the arterial walls interact with modified low-density lipoprotein (LDL) particles, accumulate cholesterol and convert into foam cells, which promote plaque formation and also contribute to inflammation by producing proinflammatory cytokines. A number of studies characterized transcriptomics of macrophages following interaction with modified LDL, and revealed alteration of the expression of genes responsible for inflammatory response and cholesterol metabolism. However, it is still unclear how these two processes are related to each other to contribute to atherosclerotic lesion formation. Methods: We attempted to identify the main mater regulator genes in macrophages treated with atherogenic modified LDL using a bioinformatics approach. Results: We found that most of the identified genes were involved in inflammation, and none of them was implicated in cholesterol metabolism. Among the key identified genes were interleukin (IL)-7, IL-7 receptor, IL-15 and CXCL8. Conclusion: Our results indicate that activation of the inflammatory pathway is the primary response of the immune cells to modified LDL, while the lipid metabolism genes may be a secondary response triggered by inflammatory signalling.
The present work aims to identify molecular drivers of short survival in glioblastoma multiforme ... more The present work aims to identify molecular drivers of short survival in glioblastoma multiforme (GBM) using gene regulatory network analysis. We identified five important master regulators-IGFBP2, VEGFA, PDGFA, OSMR and AEBP1 regulating the dysregulated gene networks. Of them, IGFBP2 is found to be highly upregulated in short survivors and has established relevance in glioblastoma pathology. Further investigation on gene regulatory network revealed that FRA-1 transcription factor can be regulated by IGFBP2. FRA-1 is found to be upregulated and impacts overall survival in GBM. It is said to dysregulate at-least 50 downstream genes involved in tumor invasiveness in tumor xenografts making it an important therapeutic target for GBM intervention. We propose that IGFBP2 drives dysregulated gene network responsible for short survival in GBM.
Journal of vascular surgery. Venous and lymphatic disorders, Mar 1, 2022
Biokhimiya, Jun 1, 2014
To fulfill their cell functions, transcription factors (TF) and other DNA binding proteins have t... more To fulfill their cell functions, transcription factors (TF) and other DNA binding proteins have to migrate throughout the nucleus in eukaryotes or the cell in prokaryotes and find their specific binding site on a DNA strand. It is well known that many such proteins easily bind not only to their specific DNA motif, but also to a nonspecific DNA. Thus, it was predicted [1] and then shown in vivo that E. coli lac-repressor is bound to DNA during 90% of its lifetime [2]. Similar results were achieved in the case of some human DNA binding proteins; most of these molecules were also maintained in bound state on chromatin [3]. Due to the fast and sufficient affinity of binding of TF to nonspecific DNA, the question arises whether association of TFs to DNA occurs more promptly than their diffusion-driven distribution throughout the nucleus. If so, the nuclear distribution of proteins will not be homogenous, i.e. TF molecules will be fixed on DNA sites close to the nuclear pores through which they have entered the nucleus (diffusion-limited mode) [4] (figure, panel (a)). Otherwise, if the diffusion of TFs is faster than binding to DNA, protein molecules will find their binding sites after even distribution inside the nucleus (reaction-limited mode) [4] (figure, panel (b)). It is of great interest to calculate using a great deal of biochemical data on specific human TFs what scenario of the two is more appropriate (figure). A recent study has disclosed using next generation sequencing that the human genome is organized in 3D space as a fractal-like structure [5]. If the spatial structure of chromosomes is highly determined
Applied sciences, Feb 28, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
German Conference on Bioinformatics, 1997
German Conference on Bioinformatics, 1996
Journal of Crohn's and Colitis, Jan 16, 2018
Poster presentations different (p = 0.54). A positive correlation was observed between extra-epit... more Poster presentations different (p = 0.54). A positive correlation was observed between extra-epithelial cytokeratin-18 staining and subserosal fibrosis (R 2 =0.66; p = 0.0004). Four members of the miR-200 family were significantly downregulated in fresh whole SCD samples (miR-141, p = 0.002;-200a, p = 0.002;-200c, p = 0.001;-429; p = 0.004). The reduced miRNA expression was localised to the epithelium of SCD samples (p = 0.001-0.015) with only miR-200b downregulated in the submucosa (p = 0.043); no smooth muscle miRNA expression change was found. The miR-200 target ZEB1 was upregulated in SCD compared with NSCD samples (fold change 9.8; p = 0.035; n = 9). A positive correlation was seen between epithelial miR-141 expression and subserosal fibrosis scores in all samples (R 2 =0.75; p = 0.02; n = 6). Conclusions: IHC staining in SCD tissue was consistent with populations of epithelial cells migrating into deeper layers and gaining mesenchymal characteristics, suggestive of EMT. The correlation with fibrosis scores suggests EMT is a functionally relevant mechanism driving fibrosis in CD and occurs independently of inflammation. The miR-200 family are implicated as regulators of this process given the epithelial-specific dysregulation and tissue upregulation of downstream effectors. Functional studies to prove this relationship are warranted.
Blood, Nov 1, 2006
In T-cell acute lymphoblastic leukaemia (T-ALL) alternative t(5;14)(q35;q32.2) forms effect leuke... more In T-cell acute lymphoblastic leukaemia (T-ALL) alternative t(5;14)(q35;q32.2) forms effect leukemic dysregulation of either TLX3 or NKX2-5 homeobox genes at 5q35 by juxtaposition with 3′-BCL11B at 14q32.2. Putative regulatory sequences underlying ectopic homeobox gene activation in t(5;14), and their mode of action have remained poorly understood mainly because breakpoints at 14q32.2 are widely scattered over the ~1 Mbp genomic desert region. We pooled cytogenetic data from t(5;14) cell lines together with published clinical data to refine the BCL11B downstream breakpoint cluster region (bcr). Ectopic homeobox gene dysregulation was investigated by DNA-i(nhibitory-treatments) with 26-mer double-stranded DNA oligo(nucleotide)s directed against putative enhancers using NKX2-5 expression as endpoints. Enhancer targets were provisionally identified from orphan T-cell DNase-I hypersensive sites (DNaseI-HS) located between 3′-BCL11B and VRK1. NKX2-5 downregulation in t(5;14) PEER cells was almost entirely restricted to DNAi targeting enhancers within the distal bcr and was dose- and sequence-dependent. Interestingly, enhancers near 3′-BCL11B regulated that gene only. These data imply that enhancer-promoter distances and/or locations are important for long-range gene regulation. Chromatin immunoprecipation assays showed that the four most effectual NKX2-5 ectopic enhancers were hyperacetylated. These enhancers clustered ~1 Mbp downstream of BCL11B, within a region displaying multiple regulatory stigmata, including a TCRA-enhancer motif, and abyssal sequence-conservation (“5-Way Regulatory Potential”). Paradoxically, although TLX3/NKX2-5 promoter/exon-1 regions were hypo-acetylated, their expression decreased after TSA treatment, implying extrinsic regulation by factor(s) subject to acetylation-control. PU.1 is known to get transcriptionally repressed by TSA and potentially binds TLX3/NKX2-5 upstream promoter regions. Knockdown of PU.1 effected downregulation of both homeobox genes. Moreover, genomic analysis showed preferential enrichment near validated ectopic enhancers of binding sites for the PU.1-cofactor HMGA1, knockdown of which also inhibited NKX2-5 in PEER cells. Analysis of nuclear matrix attachment (NMA) in PEER cells showed enhanced attachment near to the most effectual enhancer cluster which was alleviated by TSA-treatment. Interestingly, the juxtapositional genomic regions of “active” ins(14;5) rearrangements driving NKX2-5 expression exhibited tight NMA, forming structures reminiscent of “active chromatin hubs”. These findings lead us to propose that HMGA1 and PU.1 co-regulate ectopic homeobox gene expression in t(5;14) T-ALL by interactions mediated at the nuclear matrix, possibly mediated by SATB1 binding. Our data document homeobox gene dysregulation by a novel regulatory region at 3′-BCL11B responsive to HDAC-inhibition and highlight a novel class of potential therapeutic target amid “junk” DNA.
Biological processes are fundamentally driven by complex interactions between biomolecules. Integ... more Biological processes are fundamentally driven by complex interactions between biomolecules. Integrated highthroughput omics studies enable multifaceted views of cells, organisms, or their communities. With the advent of new post-genomics technologies, omics studies are becoming increasingly prevalent; yet the full impact of these studies can only be realized through data harmonization, sharing, meta-analysis, and integrated research. These essential steps require consistent generation, capture, and distribution of metadata. To ensure transparency, facilitate data harmonization, and maximize reproducibility and usability of life sciences studies, we propose a simple common omics metadata checklist. The proposed checklist is built on the rich ontologies and standards already in use by the life sciences community. The checklist will serve as a common denominator to guide experimental design, capture important parameters, and be used as a standard format for stand-alone data publications. The omics metadata checklist and data publications will create efficient linkages between omics data and knowledge-based life sciences innovation and, importantly, allow for appropriate attribution to data generators and infrastructure science builders in the post-genomics era. We ask that the life sciences community test the proposed omics metadata checklist and data publications and provide feedback for their use and improvement. A Common Omics Metadata Checklist Proposal Modern life science technologies enable rapid and efficient acquisition of omics data. These data comprehensively measure multilayered molecular networks and provide a snapshot of biological processes in a cell, organism, or their communities. Collected on the same sample at the same time, omics data provide information on the functioning of biomolecules and their interactions. Omics studies are essential for the
Новосибирский государственный университет eBooks, 2012
German Conference on Bioinformatics, 1998
Methods in molecular biology, 2017
In this chapter, we present an approach that allows a causal analysis of multiple &amp;qu... more In this chapter, we present an approach that allows a causal analysis of multiple &amp;quot;-omics&amp;quot; data with the help of an &amp;quot;upstream analysis&amp;quot; strategy. The goal of this approach is to identify master regulators in gene regulatory networks as potential drug targets for a pathological process. The data analysis strategy includes a state-of-the-art promoter analysis for potential transcription factor (TF)-binding sites using the TRANSFAC® database combined with an analysis of the upstream signal transduction pathways that control the activity of these TFs. When applied to genes that are associated with a switch to a pathological process, the approach identifies potential key molecules (master regulators) that may exert major control over and maintenance of transient stability of the pathological state. We demonstrate this approach on examples of analysis of multi-omics data sets that contain transcriptomics and epigenomics data in cancer. The results of this analysis helped us to better understand the molecular mechanisms of cancer development and cancer drug resistance. Such an approach promises to be very effective for rapid and accurate identification of cancer drug targets with true potential. The upstream analysis approach is implemented as an automatic workflow in the geneXplain platform ( www.genexplain.com ) using the open-source BioUML framework ( www.biouml.org ).
German Conference on Bioinformatics, 2000
DNA sites bearing the similar functions in different genes often differ significantly by their nu... more DNA sites bearing the similar functions in different genes often differ significantly by their nucleotide sequences. In many cases a set of binding sites can bedivided into subgroups that tend to be bound preferably by a particular member of a transcription factor family. Identification of such subgroups is essential for developing precise methods of binding site recognition in genomic sequences and for understanding peculiarities of transcriptional regulation mechanisms. In order to detect such subgroups in the sets of DNA functional sites it is necessary to create new clusterization methods for revealing common sub-sequences within each subgroup of sites (local consensi and corresponding weight matrixes). Results: We have developed a novel clusterization method for the analysis of the sets of functional sites based on kernel estimation. The method developed has been applied for the analysis of transcription initiation sites in eukaryotic genes. We have revealed two local consensi that correspond to different functional and taxonomic groups of genes.
Journal of Cancer Research and Clinical Oncology, May 8, 2018
Purpose MDM2 inhibitors are promising anticancer agents that induce cell cycle arrest and tumor c... more Purpose MDM2 inhibitors are promising anticancer agents that induce cell cycle arrest and tumor cells death via p53 reactivation. We examined the influence of Mycoplasma hyorhinis infection on sensitivity of human lung carcinoma cells NCI-H292 to MDM2 inhibitor Nutlin-3. In order to unveil possible mechanisms underlying the revealed effect, we investigated gene expression changes and signal transduction networks activated in NCI-H292 cells in response to mycoplasma infection. Methods Sensitivity of NCI-Н292 cells to Nutlin-3 was estimated by resazurin-based cell viability assay. Genome-wide transcriptional profiles of NCI-H292 and NCI-Н292 Myc.h cell lines were determined using Illumina Human HT-12 v3 Expression BeadChip. Search for key transcription factors and key node molecules was performed using the geneXplain platform. Ability for anchorage-independent growth was tested by soft agar colony formation assay. Results NCI-Н292 Myc.h cells were shown to be 1.5-and 5.2-fold more resistant to killing by Nutlin-3 at concentrations of 15 and 30 µM than uninfected NCI-Н292 cells (P < 0.05 and P < 0.001, respectively). Transcriptome analysis revealed differential expression of multiple genes involved in cancer progression and metastasis as well as epithelial-mesenchymal transition (EMT). Moreover, we have shown experimentally that NCI-Н292 Myc.h cells were more capable of growing and dividing without binding to a substrate. The most likely mechanism explaining the observed changes was found to be TLR4and IL-1b-mediated activation of NF-κB pathway. Conclusions Our results provide evidence that mycoplasma infection is an important factor modulating the effect of MDM2 inhibitors on cancer cells and is able to induce EMT-related changes.
Current Pharmaceutical Design, Nov 14, 2018
Background: A hallmark of atherosclerosis is its complex pathogenesis, which is dependent on alte... more Background: A hallmark of atherosclerosis is its complex pathogenesis, which is dependent on altered cholesterol metabolism and inflammation. Both arms of pathogenesis involve myeloid cells. Monocytes migrating into the arterial walls interact with modified low-density lipoprotein (LDL) particles, accumulate cholesterol and convert into foam cells, which promote plaque formation and also contribute to inflammation by producing proinflammatory cytokines. A number of studies characterized transcriptomics of macrophages following interaction with modified LDL, and revealed alteration of the expression of genes responsible for inflammatory response and cholesterol metabolism. However, it is still unclear how these two processes are related to each other to contribute to atherosclerotic lesion formation. Methods: We attempted to identify the main mater regulator genes in macrophages treated with atherogenic modified LDL using a bioinformatics approach. Results: We found that most of the identified genes were involved in inflammation, and none of them was implicated in cholesterol metabolism. Among the key identified genes were interleukin (IL)-7, IL-7 receptor, IL-15 and CXCL8. Conclusion: Our results indicate that activation of the inflammatory pathway is the primary response of the immune cells to modified LDL, while the lipid metabolism genes may be a secondary response triggered by inflammatory signalling.