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Drake C, Wehr MM, Zobl W, Koschmann J, De Lucca D, Kühne BA, Hansen T, Knebel J, Ritter D, Boei J, Vrieling H, Bitsch A, Escher SE. Substantiate a read-across hypothesis by using transcriptome data-A case study on volatile diketones. Front Toxicol 2023; 5:1155645. [PMID: 37206915 PMCID: PMC10188990 DOI: 10.3389/ftox.2023.1155645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
This case study explores the applicability of transcriptome data to characterize a common mechanism of action within groups of short-chain aliphatic α-, β-, and γ-diketones. Human reference in vivo data indicate that the α-diketone diacetyl induces bronchiolitis obliterans in workers involved in the preparation of microwave popcorn. The other three α-diketones induced inflammatory responses in preclinical in vivo animal studies, whereas beta and gamma diketones in addition caused neuronal effects. We investigated early transcriptional responses in primary human bronchiolar (PBEC) cell cultures after 24 h and 72 h of air-liquid exposure. Differentially expressed genes (DEGs) were assessed based on transcriptome data generated with the EUToxRisk gene panel of Temp-O-Seq®. For each individual substance, genes were identified displaying a consistent differential expression across dose and exposure duration. The log fold change values of the DEG profiles indicate that α- and β-diketones are more active compared to γ-diketones. α-diketones in particular showed a highly concordant expression pattern, which may serve as a first indication of the shared mode of action. In order to gain a better mechanistic understanding, the resultant DEGs were submitted to a pathway analysis using ConsensusPathDB. The four α-diketones showed very similar results with regard to the number of activated and shared pathways. Overall, the number of signaling pathways decreased from α-to β-to γ-diketones. Additionally, we reconstructed networks of genes that interact with one another and are associated with different adverse outcomes such as fibrosis, inflammation or apoptosis using the TRANSPATH-database. Transcription factor enrichment and upstream analyses with the geneXplain platform revealed highly interacting gene products (called master regulators, MRs) per case study compound. The mapping of the resultant MRs on the reconstructed networks, visualized similar gene regulation with regard to fibrosis, inflammation and apoptosis. This analysis showed that transcriptome data can strengthen the similarity assessment of compounds, which is of particular importance, e.g., in read-across approaches. It is one important step towards grouping of compounds based on biological profiles.
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Affiliation(s)
- Christina Drake
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
- *Correspondence: Christina Drake,
| | - Matthias M. Wehr
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
| | - Walter Zobl
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
| | | | | | - Britta A. Kühne
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
| | - Tanja Hansen
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
| | - Jan Knebel
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
| | - Detlef Ritter
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
| | - Jan Boei
- Leiden University Medical Center, Leiden, Netherlands
| | | | - Annette Bitsch
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
| | - Sylvia E. Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine, Chemical Safety and Toxicology, Hannover, Germany
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Drake C, Zobl W, Wehr M, Koschmann J, De Luca D, Kühne B, Vrieling H, Boei J, Hansen T, Escher S. P20-07 Transcriptome data to substantiate the assessment of similar mechanism of actions in a context of compound induced pulmonary fibrosis. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Kel A, Boyarskikh U, Stegmaier P, Leskov LS, Sokolov AV, Yevshin I, Mandrik N, Stelmashenko D, Koschmann J, Kel-Margoulis O, Krull M, Martínez-Cardús A, Moran S, Esteller M, Kolpakov F, Filipenko M, Wingender E. Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. BMC Bioinformatics 2019; 20:119. [PMID: 30999858 PMCID: PMC6471696 DOI: 10.1186/s12859-019-2687-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The search for molecular biomarkers of early-onset colorectal cancer (CRC) is an important but still quite challenging and unsolved task. Detection of CpG methylation in human DNA obtained from blood or stool has been proposed as a promising approach to a noninvasive early diagnosis of CRC. Thousands of abnormally methylated CpG positions in CRC genomes are often located in non-coding parts of genes. Novel bioinformatic methods are thus urgently needed for multi-omics data analysis to reveal causative biomarkers with a potential driver role in early stages of cancer. METHODS We have developed a method for finding potential causal relationships between epigenetic changes (DNA methylations) in gene regulatory regions that affect transcription factor binding sites (TFBS) and gene expression changes. This method also considers the topology of the involved signal transduction pathways and searches for positive feedback loops that may cause the carcinogenic aberrations in gene expression. We call this method "Walking pathways", since it searches for potential rewiring mechanisms in cancer pathways due to dynamic changes in the DNA methylation status of important gene regulatory regions ("epigenomic walking"). RESULTS In this paper, we analysed an extensive collection of full genome gene-expression data (RNA-seq) and DNA methylation data of genomic CpG islands (using Illumina methylation arrays) generated from a sample of tumor and normal gut epithelial tissues of 300 patients with colorectal cancer (at different stages of the disease) (data generated in the EU-supported SysCol project). Identification of potential epigenetic biomarkers of DNA methylation was performed using the fully automatic multi-omics analysis web service "My Genome Enhancer" (MGE) (my-genome-enhancer.com). MGE uses the database on gene regulation TRANSFAC®, the signal transduction pathways database TRANSPATH®, and software that employs AI (artificial intelligence) methods for the analysis of cancer-specific enhancers. CONCLUSIONS The identified biomarkers underwent experimental testing on an independent set of blood samples from patients with colorectal cancer. As a result, using advanced methods of statistics and machine learning, a minimum set of 6 biomarkers was selected, which together achieve the best cancer detection potential. The markers include hypermethylated positions in regulatory regions of the following genes: CALCA, ENO1, MYC, PDX1, TCF7, ZNF43.
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Affiliation(s)
- Alexander Kel
- Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, 630090, Russia. .,Biosoft.ru, Ltd, Novosibirsk, 630090, Russia. .,geneXplain GmbH, 38302, Wolfenbüttel, Germany.
| | - Ulyana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, 630090, Russia
| | | | | | | | | | | | | | | | | | | | - Anna Martínez-Cardús
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, Barcelona, Spain
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908, Barcelona, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029, Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08010, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Fedor Kolpakov
- Biosoft.ru, Ltd, Novosibirsk, 630090, Russia.,Institute of Computational Technologies SB RAS, Novosibirsk, 630090, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, 630090, Russia
| | - Edgar Wingender
- geneXplain GmbH, 38302, Wolfenbüttel, Germany.,Institute of Bioinformatics, University Medical Center Göttingen (UMG), Göttingen, 37077, Germany
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Koschmann J. Bioinformatic pipelines to predict respiratory toxicity and reduce animal testing. Toxicol Lett 2017. [DOI: 10.1016/j.toxlet.2017.07.394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Niehof M, Hildebrandt T, Danov O, Arndt K, Koschmann J, Dahlmann F, Hansen T, Sewald K. RNA isolation from precision-cut lung slices (PCLS) from different species. BMC Res Notes 2017; 10:121. [PMID: 28274266 PMCID: PMC5343379 DOI: 10.1186/s13104-017-2447-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 03/01/2017] [Indexed: 11/10/2022] Open
Abstract
Background Functional 3D organ models such as precision-cut lung slices (PCLS) have recently captured the attention of biomedical research. To enable wider implementation in research and development, these new biologically relevant organ models are being constantly refined. A very important issue is to improve the preparation of high-quality RNA (ribonucleic acid) from PCLS for drug discovery and development of new therapies. Gene expression analysis at different levels is used as an important experimental readout. Genome-wide analysis using microarrays is mostly applied for biomarker selection in disease models or in comprehensive toxicological studies. Specific biomarker testing by reverse transcriptase quantitative polymerase chain reaction (RTqPCR) is often used in efficacy studies. Both applications require high-quality RNA as starting material for the generation of reliable data. Additionally, a small number of slices should be sufficient for satisfactory RNA isolation to allow as many experimental conditions as possible to be covered with a given tissue sample. Unfortunately, the vast amount of agarose in PCLS impedes RNA extraction according to the standard procedures. Results We established an optimized protocol for RNA isolation from PCLS from humans, rats, mice, marmosets, and rhesus macaques based on the separation of lysis and precipitation steps and a magnetic-bead cleanup procedure. The resulting RNA is of high purity and possesses a high degree of integrity. There are no contaminations affecting RTqPCR efficiency or any enzymatic step in sample preparation for microarray analysis. Conclusions In summary, we isolated RNA from PCLS from different species that is well suited for RTqPCR and for microarray analysis as downstream applications.
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Affiliation(s)
- Monika Niehof
- Division of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Excellence Cluster REBIRTH, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany.
| | - Tobias Hildebrandt
- Immunology and Respiratory, Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim am Rhein, Germany
| | - Olga Danov
- Division of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Excellence Cluster REBIRTH, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
| | - Kirsten Arndt
- Immunology and Respiratory, Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim am Rhein, Germany
| | | | - Franziska Dahlmann
- Division of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Excellence Cluster REBIRTH, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany.,Pathology Unit, German Primate Center GmbH, Leibniz-Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
| | - Tanja Hansen
- Division of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Excellence Cluster REBIRTH, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
| | - Katherina Sewald
- Division of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Excellence Cluster REBIRTH, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
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Kel AE, Stegmaier P, Valeev T, Koschmann J, Poroikov V, Kel-Margoulis OV, Wingender E. Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. EuPA Open Proteom 2016; 13:1-13. [PMID: 29900117 PMCID: PMC5988513 DOI: 10.1016/j.euprot.2016.09.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 09/05/2016] [Accepted: 09/08/2016] [Indexed: 11/25/2022]
Abstract
Upstream analysis strategy for multi-omics data is proposed. Drug targets are predicted by search for TFBS and analysis of signaling network. Methotrexate resistance data include transcriptomics, proteomics and epigenomics. Predicted targets are: TGFalpha, IGFBP7, alpha9-integrin. Predicted drugs are: zardaverine, divalproex and human metabolite nicotinamide N-oxide.
We present an “upstream analysis” strategy for causal analysis of multiple “-omics” data. It analyzes promoters using the TRANSFAC database, combines it with an analysis of the upstream signal transduction pathways and identifies master regulators as potential drug targets for a pathological process. We applied this approach to a complex multi-omics data set that contains transcriptomics, proteomics and epigenomics data. We identified the following potential drug targets against induced resistance of cancer cells towards chemotherapy by methotrexate (MTX): TGFalpha, IGFBP7, alpha9-integrin, and the following chemical compounds: zardaverine and divalproex as well as human metabolites such as nicotinamide N-oxide.
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Affiliation(s)
- Alexander E Kel
- Institute of Chemical Biology and Fundamental Medicine, SBRAS, Novosibirsk, Russia.,Biosoft.ru, Ltd, Novosibirsk, Russia.,geneXplain GmbH, D-38302 Wolfenbüttel, Germany
| | | | - Tagir Valeev
- Biosoft.ru, Ltd, Novosibirsk, Russia.,A.P. Ershov Institute of Informatics Systems, SB RAS, Novosibirsk, Russia
| | | | | | | | - Edgar Wingender
- geneXplain GmbH, D-38302 Wolfenbüttel, Germany.,Institute of Bioinformatics, University Medical Center Göttingen, D-37077 Göttingen, Germany
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Koschmann J, Machens F, Becker M, Niemeyer J, Schulze J, Bülow L, Stahl DJ, Hehl R. Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis. Plant Physiol 2012; 160:178-91. [PMID: 22744985 PMCID: PMC3440196 DOI: 10.1104/pp.112.198259] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 06/26/2012] [Indexed: 05/03/2023]
Abstract
A combination of bioinformatic tools, high-throughput gene expression profiles, and the use of synthetic promoters is a powerful approach to discover and evaluate novel cis-sequences in response to specific stimuli. With Arabidopsis (Arabidopsis thaliana) microarray data annotated to the PathoPlant database, 732 different queries with a focus on fungal and oomycete pathogens were performed, leading to 510 up-regulated gene groups. Using the binding site estimation suite of tools, BEST, 407 conserved sequence motifs were identified in promoter regions of these coregulated gene sets. Motif similarities were determined with STAMP, classifying the 407 sequence motifs into 37 families. A comparative analysis of these 37 families with the AthaMap, PLACE, and AGRIS databases revealed similarities to known cis-elements but also led to the discovery of cis-sequences not yet implicated in pathogen response. Using a parsley (Petroselinum crispum) protoplast system and a modified reporter gene vector with an internal transformation control, 25 elicitor-responsive cis-sequences from 10 different motif families were identified. Many of the elicitor-responsive cis-sequences also drive reporter gene expression in an Agrobacterium tumefaciens infection assay in Nicotiana benthamiana. This work significantly increases the number of known elicitor-responsive cis-sequences and demonstrates the successful integration of a diverse set of bioinformatic resources combined with synthetic promoter analysis for data mining and functional screening in plant-pathogen interaction.
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Affiliation(s)
- Jeannette Koschmann
- Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.K., F.M., M.B., J.N., L.B., R.H.); Institut für Pflanzenbiologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.S.); and KWS SAAT AG, 37555 Einbeck, Germany (D.J.S.)
| | - Fabian Machens
- Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.K., F.M., M.B., J.N., L.B., R.H.); Institut für Pflanzenbiologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.S.); and KWS SAAT AG, 37555 Einbeck, Germany (D.J.S.)
| | - Marlies Becker
- Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.K., F.M., M.B., J.N., L.B., R.H.); Institut für Pflanzenbiologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.S.); and KWS SAAT AG, 37555 Einbeck, Germany (D.J.S.)
| | - Julia Niemeyer
- Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.K., F.M., M.B., J.N., L.B., R.H.); Institut für Pflanzenbiologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.S.); and KWS SAAT AG, 37555 Einbeck, Germany (D.J.S.)
| | - Jutta Schulze
- Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.K., F.M., M.B., J.N., L.B., R.H.); Institut für Pflanzenbiologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.S.); and KWS SAAT AG, 37555 Einbeck, Germany (D.J.S.)
| | - Lorenz Bülow
- Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.K., F.M., M.B., J.N., L.B., R.H.); Institut für Pflanzenbiologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.S.); and KWS SAAT AG, 37555 Einbeck, Germany (D.J.S.)
| | - Dietmar J. Stahl
- Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.K., F.M., M.B., J.N., L.B., R.H.); Institut für Pflanzenbiologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.S.); and KWS SAAT AG, 37555 Einbeck, Germany (D.J.S.)
| | - Reinhard Hehl
- Institut für Genetik, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.K., F.M., M.B., J.N., L.B., R.H.); Institut für Pflanzenbiologie, Technische Universität Braunschweig, 38106 Braunschweig, Germany (J.S.); and KWS SAAT AG, 37555 Einbeck, Germany (D.J.S.)
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