1
|
Campana PA, Prasse P, Lienhard M, Thedinga K, Herwig R, Scheffer T. Cancer drug sensitivity estimation using modular deep Graph Neural Networks. NAR Genom Bioinform 2024; 6:lqae043. [PMID: 38680251 PMCID: PMC11055499 DOI: 10.1093/nargab/lqae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/01/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024] Open
Abstract
Computational drug sensitivity models have the potential to improve therapeutic outcomes by identifying targeted drugs components that are tailored to the transcriptomic profile of a given primary tumor. The SMILES representation of molecules that is used by state-of-the-art drug-sensitivity models is not conducive for neural networks to generalize to new drugs, in part because the distance between atoms does not generally correspond to the distance between their representation in the SMILES strings. Graph-attention networks, on the other hand, are high-capacity models that require large training-data volumes which are not available for drug-sensitivity estimation. We develop a modular drug-sensitivity graph-attentional neural network. The modular architecture allows us to separately pre-train the graph encoder and graph-attentional pooling layer on related tasks for which more data are available. We observe that this model outperforms reference models for the use cases of precision oncology and drug discovery; in particular, it is better able to predict the specific interaction between drug and cell line that is not explained by the general cytotoxicity of the drug and the overall survivability of the cell line. The complete source code is available at https://zenodo.org/doi/10.5281/zenodo.8020945. All experiments are based on the publicly available GDSC data.
Collapse
Affiliation(s)
- Pedro A Campana
- University of Potsdam, Department of Computer Science, Potsdam, Germany
| | - Paul Prasse
- University of Potsdam, Department of Computer Science, Potsdam, Germany
| | - Matthias Lienhard
- Max Planck Institute for Molecular Genetics, Department Computational Molecular Biology, Berlin, Germany
| | - Kristina Thedinga
- Max Planck Institute for Molecular Genetics, Department Computational Molecular Biology, Berlin, Germany
| | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Department Computational Molecular Biology, Berlin, Germany
| | - Tobias Scheffer
- University of Potsdam, Department of Computer Science, Potsdam, Germany
| |
Collapse
|
2
|
Arısoy S, Bux K, Herwig R, Şalva E. Development, Evaluation, and Molecular Dynamics Study of Ampicillin-Loaded Chitosan-Hyaluronic Acid Films as a Drug Delivery System. ACS Omega 2024; 9:19805-19815. [PMID: 38737032 PMCID: PMC11079874 DOI: 10.1021/acsomega.3c08076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/08/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024]
Abstract
Periodontitis is an inflammatory periodontal disease defined by the progressive loss of tissues surrounding the tooth. Ampicillin is an antibiotic for managing and treating specific bacterial infections, including periodontitis. Periodontal pockets occur due to periodontal disease progression and act as a natural reservoir that is easily reachable for the insertion of a delivery system, and the amount of drug to be released has a major role in the efficiency of treatment of the disease. Polyelectrolyte complexes (PECs), particularly those based on chitosan and hyaluronic acid combinations, offer a promising avenue to overcome the challenges associated with drug delivery. These complexes are both biodegradable and biocompatible, making them an optimal choice for enabling targeted drug delivery. This study centers on developing and assessing the structure and dynamic attributes of a drug-PEC system encompassing ampicillin and chitosan-hyaluronic acid components, which represents a targeted drug delivery system to better alleviate the periodontitis. To achieve this goal, we conducted experiments including weight and drug content uniformity, swelling ındex, drug release %, FT-IR and SEM analyses, and atomistic molecular dynamics simulations on the drug PECs loaded with ampicillin with varying amounts of hyaluronic acid. All simulations and the experimental analysis suggested that increased HA amount resulted in an increase in drug release % and swelling index. The simulation outcomes provide insights into the nature of the drug and PEC interactions alongside transport properties such as drug diffusion coefficients. These coefficients offer valuable insights into the molecular behavior of ampicillin-PEC drug delivery systems, particularly in the context of their application in periodontitis treatment.
Collapse
Affiliation(s)
- Sema Arısoy
- Faculty
of Pharmacy, Department of Pharmaceutical Technology, Selcuk University, Selcuklu, Konya 42250, Turkey
| | - Khair Bux
- Faculty
of Life Sciences, Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Clifton, Karachi 75600 Pakistan
| | - Ralf Herwig
- Laboratories
PD Dr. R. Herwig, 80337Munich ,Germany
- Heimerer-College, Pristina 10000, Kosovo
| | - Emine Şalva
- Faculty
of Pharmacy, Department of Pharmaceutical Biotechnology, Inonu University, Battalgazi, Malatya 44210, Turkey
| |
Collapse
|
3
|
Springer C, Binsch C, Weide D, Toska L, Cremer AL, Backes H, Scheel AK, Espelage L, Kotzka J, Sill S, Kurowski A, Kim D, Karpinski S, Schnurr TM, Hansen T, Hartwig S, Lehr S, Cames S, Brüning J, Lienhard M, Herwig R, Börno S, Timmermann B, Al-Hasani H, Chadt A. Depletion of TBC1D4 improves the metabolic exercise response by overcoming genetically induced peripheral insulin resistance. Diabetes 2024:db230463. [PMID: 38608276 DOI: 10.2337/db23-0463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
The RabGTPase-activating protein (RabGAP) TBC1D4 (=AS160) represents a key component in the regulation of glucose transport into skeletal muscle and white adipose tissue (WAT) and is therefore crucial during the development of insulin resistance and type-2 diabetes. Increased daily activity has been shown to be associated with improved postprandial hyperglycemia in allele carriers of a loss-of-function variant in the human TBC1D4 gene. Using conventional Tbc1d4-deficient mice (D4KO) fed a high-fat diet (HFD), we show that already a moderate endurance exercise training leads to substantially improved glucose and insulin tolerance and enhanced expression levels of markers for mitochondrial activity and browning in WAT from D4KO animals. Importantly, in vivo and ex vivo analyses of glucose uptake revealed increased glucose clearance in interscapular brown adipose tissue (iBAT) and WAT from trained D4KO mice. Thus, chronic exercise is able to overcome the genetically induced insulin resistance caused by the Tbc1d4-depletion. Gene variants in TBC1D4 may be relevant in future precision medicine as determinants of exercise response.
Collapse
Affiliation(s)
- Christian Springer
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Christian Binsch
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Deborah Weide
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Laura Toska
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Anna Lena Cremer
- Institute for Neuronal Control of Brain Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Heiko Backes
- Institute for Neuronal Control of Brain Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Anna K Scheel
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Lena Espelage
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Jörg Kotzka
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
| | - Sebastian Sill
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Anette Kurowski
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
| | - Daebin Kim
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
| | - Sandra Karpinski
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
| | - Theresia M Schnurr
- Section of Metabolic Genetics, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Section of Metabolic Genetics, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sonja Hartwig
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Stefan Lehr
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Sandra Cames
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Jens Brüning
- Institute for Neuronal Control of Brain Metabolism, Max Planck Institute for Metabolism Research, Cologne, Germany
| | | | - Ralf Herwig
- Max-Planck-Institue for Molecular Genetics, Berlin, Germany
| | - Stefan Börno
- Max-Planck-Institue for Molecular Genetics, Berlin, Germany
| | | | - Hadi Al-Hasani
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| | - Alexandra Chadt
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz-Center for Diabetes Research at the Heinrich Heine University, Medical faculty, Düsseldorf
- German Center for Diabetes Research, Partner Düsseldorf, München-Neuherberg, Germany
| |
Collapse
|
4
|
Mehmood S, Hussain M, Bux K, Hussain Z, Raza Shah M, Ali Jakhrani M, Ali Channar P, Begum I, Saboor R, Yildiz CB, Ali K, Herwig R. Structural dynamics and anti-biofilm screening of novel imidazole derivative to explore their anti-biofilm inhibition mechanism against Pseudomonas Aeruginosa. J Biomol Struct Dyn 2024:1-15. [PMID: 38385459 DOI: 10.1080/07391102.2024.2317983] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The biofilm formation is still prevalent mechanism of developing the drug resistance in the Pseudomonas aeruginosa, gram-negative bacteria, known for its major role in nosocomial, ventilator-associated pneumonia (VAP), lung infections and catheter-associated urinary tract infections. As best of our knowledge, current study first time reports the most potent inhibitors of LasR, a transcriptional activator of biofilm and virulence regulating genes in, Pseudomonas aeruginosa LasR, utilizing newly functionalized imidazoles (5a-d), synthesized via 1,3-dipolar cycloaddition using click approach. The synthesized ligands were characterized through Mass Spectrometry and 1H NMR. The binding potency and mode of biding of ligands. Quantum Mechanical(QM) methods were utilized to investigate the electronic basis, HOMO/LUMO and dipole moment of the geometry of the ligands for their binding potency. Dynamics cross correlation matrix (DCCMs) and protein surface analysis were further utilized to explore the structural dynamics of the protein. Free energy of binding of ligands and protein were further estimated using Molecular Mechanical Energies with the Poisson-Boltzmann surface area (MMPBSA) method. Molecular Docking studies revealed significant negative binding energies (5a - 10.33, 5b -10.09, 5c - 10.11, and 5d -8.33 KJ/mol). HOMO/LUMO and potential energy surface map estimation showed the ligands(5a) with lower energy gaps and larger dipole moments had relatively larger binding potency. The significant change in the structural dynamics of LasR protein due to complex formation with newlyfunctionalized imidazoles ligands. Hydrogen bond surface analysis followed by MMPBSA calculations of free energy of binding further complemented the Molecular docking revelations showing the specifically ligand (5a) having the relatively higher energy of binding(-65.22kj/mol).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shahab Mehmood
- Shaheed Zulfiqar Ali Bhutto Institute of Science and Technology (SZABIST), Pakistan
| | - Mumtaz Hussain
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Khair Bux
- Shaheed Zulfiqar Ali Bhutto Institute of Science and Technology (SZABIST), Pakistan
| | - Zahid Hussain
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Muhammad Raza Shah
- International Center for Chemical and Biological Sciences, H.E.J. Research Institute of Chemistry, Karachi, Pakistan
| | - Mushtaque Ali Jakhrani
- Institute of Chemistry, Shah Abdul Latif University Khairpur mirs, Khairpurmirs, Sindh, Pakistan
| | - Pervaiz Ali Channar
- Department of Basic Sciences and Humanities, Faculty of Information Sciences and Humanities, Dawood University of Engineering and Technology Karachi, Karachi, Pakistan
| | - Irshad Begum
- Department of Chemistry, University of Karachi, Karachi, Pakistan
| | - Rukhsana Saboor
- Department of Pathology, Ghulam Muhammad Mahar Medical College, Sukkur, Pakistan
| | - Cem B Yildiz
- Department of Medicinal and Aromatic Plants, University of Aksaray, Aksaray, Turkey
| | - Kashif Ali
- Shaheed Zulfiqar Ali Bhutto Institute of Science and Technology (SZABIST), Pakistan
| | - Ralf Herwig
- Laboratories PD Dr. R. Herwig, 80337 Munich, Germany and Heimerer-College, Pristina, Kosovo
| |
Collapse
|
5
|
Greilberger J, Erlbacher K, Stiegler P, Wintersteiger R, Herwig R. Different RONS Generation in MTC-SK and NSCL Cells Lead to Varying Antitumoral Effects of Alpha-Ketoglutarate + 5-HMF. Curr Issues Mol Biol 2023; 45:6503-6525. [PMID: 37623229 PMCID: PMC10453038 DOI: 10.3390/cimb45080410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Carbonylated proteins (CPs) serve as specific indicators of increased reactive oxygen and nitrogen species (RONS) production in cancer cells, attributed to the dysregulated mitochondrial energy metabolism known as the Warburg effect. The aim of this study was to investigate the potential of alpha-ketoglutarate (aKG), 5-hydroxymethylfurfural (5-HMF), and their combination as mitochondrial-targeting antioxidants in MTC-SK or NCI-H23 cancer cells. METHODS MTC-SK and NCI-H23 cells were cultured in the absence or presence of varying concentrations (0-500 µg/mL) of aKG, 5-HMF, and the combined aKG + 5-HMF solutions. After 0, 24, 48, and 72 h, mitochondrial activity, cancer cell membrane CP levels, cell growth, and caspase-3 activity were assessed in aliquots of MTC-SK and NCI-H23 cells. RESULTS The mitochondrial activity of MTC-SK cells exhibited a concentration- and time-dependent reduction upon treatment with aKG, 5-HMF, or the combined aKG + 5-HMF. The half-maximal inhibitory concentration (IC50%) for mitochondrial activity was achieved at 500 µg/mL aKG, 200 µg/mL 5-HMF, and 200 µg/mL aKG + 66.7 µg/mL 5-HMF after 72 h. In contrast, NCI-H23 cells showed a minimal reduction (10%) in mitochondrial activity even at the highest combined concentration of aKG + 5-HMF. The CP levels in MTC-SK cells were measured at 8.7 nmol/mg protein, while NCI-H23 cells exhibited CP levels of 1.4 nmol/mg protein. The combination of aKG + 5-HMF led to a decrease in CP levels specifically in MTC-SK cells. The correlation between mitochondrial activity and CP levels in the presence of different concentrations of combined aKG + 5-HMF in MTC-SK cells demonstrated a linear and concentration-dependent decline in CP levels and mitochondrial activity. Conversely, the effect was less pronounced in NCI-H23 cells. Cell growth of MTC-CK cells was reduced to 60% after 48 h and maintained at 50% after 72 h incubation when treated with 500 µg/mL aKG (IC50%). Addition of 500 µg/mL 5-HMF inhibited cell growth completely regardless of the incubation time. The IC50% for 5-HMF on MTC-CK cell growth was calculated at 375 µg/mL after 24 h incubation and 200 µg/mL 5-HMF after 72 h. MTC-SK cells treated with 500 µg/mL aKG + 167 µg/mL 5-HMF showed no cell growth. The calculated IC50% for the combined substances was 250 µg/mL aKG + 83.3 µg/mL 5-HMF (48 h incubation) and 200 µg/mL aKG + 66.7 µg/mL 5-HMF (72 h incubation). None of the tested concentrations of aKG, 5-HMF, or the combined solution had any effect on NCI-H23 cell growth at any incubation time. Caspase-3 activity increased to 21% in MTC-CK cells in the presence of 500 µg/mL aKG, while an increase to 59.6% was observed using 500 µg/mL 5-HMF. The combination of 500 µg/mL aKG + 167.7 µg/mL 5-HMF resulted in a caspase-3 activity of 55.2%. No caspase-3 activation was observed in NCI-H23 cells when treated with aKG, 5-HMF, or the combined solutions. CONCLUSION CPs may serve as potential markers for distinguishing between cancer cells regulated by RONS. The combination of aKG + 5-HMF showed induced cell death in high-RONS-generating cancer cells compared to low-RONS-generating cancer cells.
Collapse
Affiliation(s)
- Joachim Greilberger
- Institut für Laborwissenschaften Dr. Greilberger, Schwarzl Medical Center, 8301 Lassnitzhoehe, Austria
| | | | - Philipp Stiegler
- Division of Transplantation Surgery, Medical University of Graz, 8010 Graz, Austria
| | - Reinhold Wintersteiger
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz, 8010 Graz, Austria
| | - Ralf Herwig
- Laboratories PD Dr. R. Herwig, 80337 Munich, Germany
- Heimerer-College, 10000 Pristina, Kosovo
| |
Collapse
|
6
|
Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MR, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. bioRxiv 2023:2023.07.25.550582. [PMID: 37546854 PMCID: PMC10402094 DOI: 10.1101/2023.07.25.550582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
Collapse
Affiliation(s)
- Francisco J. Pardo-Palacios
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- These authors contributed equally to this work
| | - Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Fairlie Reese
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- These authors contributed equally to this work
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- These authors contributed equally to this work
| | - Jane E. Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Maite De María
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Matthew S. Adams
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Gabriela Balderrama-Gutierrez
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Amit K. Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Jose M. Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain
- These authors contributed equally to this work
| | - Cindy E. Liang
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Marcus Jerryd Meade
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- These authors contributed equally to this work
| | - David A. Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Andrey D. Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- These authors contributed equally to this work
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Hamed Bostan
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Ashley M. Brooks
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Muhammed Hasan Çelik
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei R,M. Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Saber Hafezqorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Joseph Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian Liang Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Matthias Lienhard
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alla Mikheenko
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Dennis Mulligan
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andre D. Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alison D. Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Changqing Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Brandon Y. Wong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | | | - Luis Ferrández-Peral
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA
| | | | | | | | | | | | | | - Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nedka G. Panayotova
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | | | - Eric Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Enrique Sapena
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Melissa Laird Smith
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hazuki Takahashi
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
| | | | - Piero Carninci
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
- Human Technopole, Milano, Italy
| | - Nancy D. Denslow
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Hagen U. Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA
| | - Barbara J. Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- Center for Public Health Genomics
- UVA Cancer Center, University of Virginia, Charlottesville, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Angela N. Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| |
Collapse
|
7
|
Lienhard M, van den Beucken T, Timmermann B, Hochradel M, Börno S, Caiment F, Vingron M, Herwig R. IsoTools: a flexible workflow for long-read transcriptome sequencing analysis. Bioinformatics 2023; 39:btad364. [PMID: 37267159 PMCID: PMC10287928 DOI: 10.1093/bioinformatics/btad364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 06/04/2023] Open
Abstract
MOTIVATION Long-read transcriptome sequencing (LRTS) has the potential to enhance our understanding of alternative splicing and the complexity of this process requires the use of versatile computational tools, with the ability to accommodate various stages of the workflow with maximum flexibility. RESULTS We introduce IsoTools, a Python-based LRTS analysis framework that offers a wide range of functionality for transcriptome reconstruction and quantification of transcripts. Furthermore, we integrate a graph-based method for identifying alternative splicing events and a statistical approach based on the beta-binomial distribution for detecting differential events. To demonstrate the effectiveness of our methods, we applied IsoTools to PacBio LRTS data of human hepatocytes treated with the histone deacetylase inhibitor valproic acid. Our results indicate that LRTS can provide valuable insights into alternative splicing, particularly in terms of complex and differential splicing patterns, in comparison to short-read RNA-seq. AVAILABILITY AND IMPLEMENTATION IsoTools is available on GitHub and PyPI, and its documentation, including tutorials, CLI, and API references, can be found at https://isotools.readthedocs.io/.
Collapse
Affiliation(s)
- Matthias Lienhard
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Twan van den Beucken
- Department of Toxicogenomics, Maastricht University, Maastricht 6229ER, The Netherlands
| | - Bernd Timmermann
- Sequencing Core Unit, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Myriam Hochradel
- Sequencing Core Unit, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Stefan Börno
- Sequencing Core Unit, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht 6229ER, The Netherlands
| | - Martin Vingron
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| |
Collapse
|
8
|
Binsch C, Barbosa DM, Hansen-Dille G, Hubert M, Hodge SM, Kolasa M, Jeruschke K, Weiß J, Springer C, Gorressen S, Fischer JW, Lienhard M, Herwig R, Börno S, Timmermann B, Cremer AL, Backes H, Chadt A, Al-Hasani H. Deletion of Tbc1d4/As160 abrogates cardiac glucose uptake and increases myocardial damage after ischemia/reperfusion. Cardiovasc Diabetol 2023; 22:17. [PMID: 36707786 PMCID: PMC9881301 DOI: 10.1186/s12933-023-01746-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Type 2 Diabetes mellitus (T2DM) is a major risk factor for cardiovascular disease and associated with poor outcome after myocardial infarction (MI). In T2DM, cardiac metabolic flexibility, i.e. the switch between carbohydrates and lipids as energy source, is disturbed. The RabGTPase-activating protein TBC1D4 represents a crucial regulator of insulin-stimulated glucose uptake in skeletal muscle by controlling glucose transporter GLUT4 translocation. A human loss-of-function mutation in TBC1D4 is associated with impaired glycemic control and elevated T2DM risk. The study's aim was to investigate TBC1D4 function in cardiac substrate metabolism and adaptation to MI. METHODS Cardiac glucose metabolism of male Tbc1d4-deficient (D4KO) and wild type (WT) mice was characterized using in vivo [18F]-FDG PET imaging after glucose injection and ex vivo basal/insulin-stimulated [3H]-2-deoxyglucose uptake in left ventricular (LV) papillary muscle. Mice were subjected to cardiac ischemia/reperfusion (I/R). Heart structure and function were analyzed until 3 weeks post-MI using echocardiography, morphometric and ultrastructural analysis of heart sections, complemented by whole heart transcriptome and protein measurements. RESULTS Tbc1d4-knockout abolished insulin-stimulated glucose uptake in ex vivo LV papillary muscle and in vivo cardiac glucose uptake after glucose injection, accompanied by a marked reduction of GLUT4. Basal cardiac glucose uptake and GLUT1 abundance were not changed compared to WT controls. D4KO mice showed mild impairments in glycemia but normal cardiac function. However, after I/R D4KO mice showed progressively increased LV endsystolic volume and substantially increased infarction area compared to WT controls. Cardiac transcriptome analysis revealed upregulation of the unfolded protein response via ATF4/eIF2α in D4KO mice at baseline. Transmission electron microscopy revealed largely increased extracellular matrix (ECM) area, in line with decreased cardiac expression of matrix metalloproteinases of D4KO mice. CONCLUSIONS TBC1D4 is essential for insulin-stimulated cardiac glucose uptake and metabolic flexibility. Tbc1d4-deficiency results in elevated cardiac endoplasmic reticulum (ER)-stress response, increased deposition of ECM and aggravated cardiac damage following MI. Hence, impaired TBC1D4 signaling contributes to poor outcome after MI.
Collapse
Affiliation(s)
- C. Binsch
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - D. M. Barbosa
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - G. Hansen-Dille
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - M. Hubert
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - S. M. Hodge
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - M. Kolasa
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - K. Jeruschke
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - J. Weiß
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - C. Springer
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany
| | - S. Gorressen
- grid.411327.20000 0001 2176 9917Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany
| | - J. W. Fischer
- grid.411327.20000 0001 2176 9917Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Düsseldorf, Germany
| | - M. Lienhard
- grid.419538.20000 0000 9071 0620Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - R. Herwig
- grid.419538.20000 0000 9071 0620Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - S. Börno
- grid.419538.20000 0000 9071 0620Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - B. Timmermann
- grid.419538.20000 0000 9071 0620Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - A. L. Cremer
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Cologne, Germany
| | - H. Backes
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Cologne, Germany
| | - A. Chadt
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany ,grid.452622.5German Center for Diabetes Research, Partner Düsseldorf, Munich-Neuherberg, Germany
| | - H. Al-Hasani
- grid.429051.b0000 0004 0492 602XMedical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz-Center for Diabetes Research at Heinrich Heine University Düsseldorf, Auf’m Hennekamp 65, 40225 Düsseldorf, Germany ,grid.452622.5German Center for Diabetes Research, Partner Düsseldorf, Munich-Neuherberg, Germany
| |
Collapse
|
9
|
Bouabid C, Rabhi S, Thedinga K, Barel G, Tnani H, Rabhi I, Benkahla A, Herwig R, Guizani-Tabbane L. Host M-CSF induced gene expression drives changes in susceptible and resistant mice-derived BMdMs upon Leishmania major infection. Front Immunol 2023; 14:1111072. [PMID: 37187743 PMCID: PMC10175952 DOI: 10.3389/fimmu.2023.1111072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Leishmaniases are a group of diseases with different clinical manifestations. Macrophage-Leishmania interactions are central to the course of the infection. The outcome of the disease depends not only on the pathogenicity and virulence of the parasite, but also on the activation state, the genetic background, and the underlying complex interaction networks operative in the host macrophages. Mouse models, with mice strains having contrasting behavior in response to parasite infection, have been very helpful in exploring the mechanisms underlying differences in disease progression. We here analyzed previously generated dynamic transcriptome data obtained from Leishmania major (L. major) infected bone marrow derived macrophages (BMdMs) from resistant and susceptible mouse. We first identified differentially expressed genes (DEGs) between the M-CSF differentiated macrophages derived from the two hosts, and found a differential basal transcriptome profile independent of Leishmania infection. These host signatures, in which 75% of the genes are directly or indirectly related to the immune system, may account for the differences in the immune response to infection between the two strains. To gain further insights into the underlying biological processes induced by L. major infection driven by the M-CSF DEGs, we mapped the time-resolved expression profiles onto a large protein-protein interaction (PPI) network and performed network propagation to identify modules of interacting proteins that agglomerate infection response signals for each strain. This analysis revealed profound differences in the resulting responses networks related to immune signaling and metabolism that were validated by qRT-PCR time series experiments leading to plausible and provable hypotheses for the differences in disease pathophysiology. In summary, we demonstrate that the host's gene expression background determines to a large degree its response to L. major infection, and that the gene expression analysis combined with network propagation is an effective approach to help identifying dynamically altered mouse strain-specific networks that hold mechanistic information about these contrasting responses to infection.
Collapse
Affiliation(s)
- Cyrine Bouabid
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- Faculty of Sciences of Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Sameh Rabhi
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Kristina Thedinga
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gal Barel
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hedia Tnani
- Laboratory de BioInformatic, BioMathematic and BioStatistic (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Imen Rabhi
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- Higher Institute of Biotechnology at Sidi-Thabet (ISBST), Biotechnopole Sidi-Thabet- University of Manouba, Sidi-Thabet, Tunisia
| | - Alia Benkahla
- Laboratory de BioInformatic, BioMathematic and BioStatistic (BIMS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ralf Herwig
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lamia Guizani-Tabbane
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules (PMBB), Institut Pasteur de Tunis, Tunis, Tunisia
- *Correspondence: Lamia Guizani-Tabbane,
| |
Collapse
|
10
|
Hoehe MR, Herwig R. Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes. Methods Mol Biol 2023; 2590:237-272. [PMID: 36335503 DOI: 10.1007/978-1-0716-2819-5_15] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Many methods for haplotyping have materialized, but their application on a significant scale has been rare to date. Here we summarize analyses that were carried out in 1092 genomes from the 1000 Genomes Consortium and validated in an unprecedented number of 184 PGP genomes that have been experimentally haplotype-resolved by application of the Long-Fragment Read (LFR) technology. These analyses provided first insights into the diplotypic nature of human genomes and its potential functional implications. Thus, protein-changing variants were not randomly distributed between the two homologues of 18,121 autosomal protein-coding genes but occurred significantly more frequently in cis than in trans configurations in virtually each of the 1276 phased genomes. This resulted in global cis/trans ratios of ~60:40, establishing "cis abundance" as a universal characteristic of diploid human genomes. This phenomenon was based on two different classes of genes, a larger one exhibiting cis configurations of protein-changing variants in excess, so-called "cis-abundant" genes, and a smaller one of "trans-abundant" genes. These two gene classes, which together constitute a common diplotypic exome, were further functionally distinguished by means of gene ontology (GO) and pathway enrichment analysis. Moreover, they were distinguishable in terms of their effects on the human interactome, where they constitute distinct cis and trans modules, as shown with network propagation on a large integrated protein-protein interaction network. These analyses, recently performed with updated database and analysis tools, further consolidated the characterization of cis- and trans-abundant genes while expanding previous results. In this chapter, we present the key results along with the materials and methods to motivate readers to investigate these findings independently and gain further insights into the diplotypic nature of genes and genomes.
Collapse
Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| |
Collapse
|
11
|
Thomalla D, Beckmann L, Grimm C, Oliverio M, Meder L, Herling C, Nieper P, Feldmann T, Merkel O, Lorsy E, da Palma Guerreiro A, von Jan J, Kisis I, Wasserburger E, Claasen J, Faitschuk-Meyer E, Altmüller J, Nürnberg P, Yang TP, Lienhard M, Herwig R, Kreuzer KA, Pallasch C, Büttner R, Schäfer S, Hartley J, Abken H, Peifer M, Kashkar H, Knittel G, Eichhorst B, Ullrich R, Herling M, Reinhardt H, Hallek M, Schweiger M, Frenzel L. Deregulation and epigenetic modification of BCL2-family genes cause resistance to venetoclax in hematologic malignancies. Blood 2022; 140:2113-2126. [PMID: 35704690 PMCID: PMC10653032 DOI: 10.1182/blood.2021014304] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 06/01/2022] [Indexed: 11/20/2022] Open
Abstract
The BCL2 inhibitor venetoclax has been approved to treat different hematological malignancies. Because there is no common genetic alteration causing resistance to venetoclax in chronic lymphocytic leukemia (CLL) and B-cell lymphoma, we asked if epigenetic events might be involved in venetoclax resistance. Therefore, we employed whole-exome sequencing, methylated DNA immunoprecipitation sequencing, and genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 screening to investigate venetoclax resistance in aggressive lymphoma and high-risk CLL patients. We identified a regulatory CpG island within the PUMA promoter that is methylated upon venetoclax treatment, mediating PUMA downregulation on transcript and protein level. PUMA expression and sensitivity toward venetoclax can be restored by inhibition of methyltransferases. We can demonstrate that loss of PUMA results in metabolic reprogramming with higher oxidative phosphorylation and adenosine triphosphate production, resembling the metabolic phenotype that is seen upon venetoclax resistance. Although PUMA loss is specific for acquired venetoclax resistance but not for acquired MCL1 resistance and is not seen in CLL patients after chemotherapy-resistance, BAX is essential for sensitivity toward both venetoclax and MCL1 inhibition. As we found loss of BAX in Richter's syndrome patients after venetoclax failure, we defined BAX-mediated apoptosis to be critical for drug resistance but not for disease progression of CLL into aggressive diffuse large B-cell lymphoma in vivo. A compound screen revealed TRAIL-mediated apoptosis as a target to overcome BAX deficiency. Furthermore, antibody or CAR T cells eliminated venetoclax resistant lymphoma cells, paving a clinically applicable way to overcome venetoclax resistance.
Collapse
MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- bcl-2-Associated X Protein/metabolism
- Drug Resistance, Neoplasm/genetics
- Apoptosis Regulatory Proteins/genetics
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/therapeutic use
- Lymphoma, Large B-Cell, Diffuse/pathology
- Hematologic Neoplasms/drug therapy
- Hematologic Neoplasms/genetics
- Epigenesis, Genetic
Collapse
Affiliation(s)
- D. Thomalla
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - L. Beckmann
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - C. Grimm
- Institute for Translational Epigenetics, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - M. Oliverio
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - L. Meder
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - C.D. Herling
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Clinic of Hematology, Cellular Therapy and Hemostaseology, University of Leipzig, Leipzig, Germany
| | - P. Nieper
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
| | - T. Feldmann
- Institute for Translational Epigenetics, Medical Faculty, University of Cologne, Cologne, Germany
| | - O. Merkel
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - E. Lorsy
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - A. da Palma Guerreiro
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - J. von Jan
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
| | - I. Kisis
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
| | - E. Wasserburger
- Institute for Translational Epigenetics, Medical Faculty, University of Cologne, Cologne, Germany
| | - J. Claasen
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - J. Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - P. Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - T.-P. Yang
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Center of Integrated Oncology Cologne-Bonn, Medical Faculty, Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - M. Lienhard
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - R. Herwig
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - K.-A. Kreuzer
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - C.P. Pallasch
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - R. Büttner
- Department of Pathology, University of Cologne, Cologne, Germany
| | - S.C. Schäfer
- Department of Pathology, University of Cologne, Cologne, Germany
- Institut für Pathologie im Medizin Campus Bodensee, Friedrichshafen, Germany
| | - J. Hartley
- RCI, Regensburg Center for Interventional Immunology, University Hospital of Regensburg, Regensburg, Germany
| | - H. Abken
- RCI, Regensburg Center for Interventional Immunology, University Hospital of Regensburg, Regensburg, Germany
| | - M. Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Center of Integrated Oncology Cologne-Bonn, Medical Faculty, Department of Translational Genomics, University of Cologne, Cologne, Germany
| | - H. Kashkar
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Molecular Immunologie, University of Cologne, Cologne, Germany
| | - G. Knittel
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University Duisburg-Essen, German Cancer Consortium (DKTK Partner Site Essen), Essen, Germany
| | - B. Eichhorst
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
| | - R.T. Ullrich
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - M. Herling
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Clinic of Hematology, Cellular Therapy and Hemostaseology, University of Leipzig, Leipzig, Germany
| | - H.C. Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University Duisburg-Essen, German Cancer Consortium (DKTK Partner Site Essen), Essen, Germany
| | - M. Hallek
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - M.R. Schweiger
- Institute for Translational Epigenetics, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - L.P. Frenzel
- Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| |
Collapse
|
12
|
Prasse P, Iversen P, Lienhard M, Thedinga K, Herwig R, Scheffer T. Pre-Training on In Vitro and Fine-Tuning on Patient-Derived Data Improves Deep Neural Networks for Anti-Cancer Drug-Sensitivity Prediction. Cancers (Basel) 2022; 14:cancers14163950. [PMID: 36010942 PMCID: PMC9406038 DOI: 10.3390/cancers14163950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Large-scale databases that report the inhibitory capacities of many combinations of candidate drug compounds and cultivated cancer cell lines have driven the development of preclinical drug-sensitivity models based on machine learning. However, cultivated cell lines have devolved from human cancer cells over years or even decades under selective pressure in culture conditions. Moreover, models that have been trained on in vitro data cannot account for interactions with other types of cells. Drug-response data that are based on patient-derived cell cultures, xenografts, and organoids, on the other hand, are not available in the quantities that are needed to train high-capacity machine-learning models. We found that pre-training deep neural network models of drug sensitivity on in vitro drug-sensitivity databases before fine-tuning the model parameters on patient-derived data improves the models’ accuracy and improves the biological plausibility of the features, compared to training only on patient-derived data. From our experiments, we can conclude that pre-trained models outperform models that have been trained on the target domains in the vast majority of cases.
Collapse
Affiliation(s)
- Paul Prasse
- Department of Computer Science, University of Potsdam, 14476 Potsdam, Germany
- Correspondence:
| | - Pascal Iversen
- Department of Computer Science, University of Potsdam, 14476 Potsdam, Germany
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Kristina Thedinga
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Tobias Scheffer
- Department of Computer Science, University of Potsdam, 14476 Potsdam, Germany
| |
Collapse
|
13
|
Herwig R, Erlbacher K, Ibrahimagic A, Kacar M, Brajshori N, Beqiri P, Greilberger J. Vitamin D-Dimer: A Possible Biomolecule Modulator in Cytotoxic and Phagocytosis Processes? Biomedicines 2022; 10:biomedicines10081785. [PMID: 35892685 PMCID: PMC9331816 DOI: 10.3390/biomedicines10081785] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Vitamin D3 complexed to deglycosylated vitamin D binding protein (VitD-dgVDBP) is a water-soluble vitamin D dimeric compound (VitD-dgVDBP). It is not clear how VitD-dgVDBP affects circulating monocytes, macrophages, other immune cell systems, including phagocytosis and apoptosis, and the generation of reactive oxygen species (ROS) compared to dgVDBP. Methods: Flow cytometry was used to measure superoxide anion radical (O2*−) levels and macrophage activity in the presence of VitD-dgVDBP or dgVDBP. VitD-dgVDBP was incubated with normal human lymphocytes (nPBMCs), and several clusters of determination (CDs) were estimated. dgVDBP and VitD-dgVDBP apoptosis was estimated on malignant prostatic cells. Results: The macrophage activity was 2.8-fold higher using VitD-dgVDBP (19.8·106 counts) compared to dgVDBP (7.0·106 counts), but O2*− production was 1.8-fold lower in favor of VitD-dgVDBP (355·103 counts) compared to dgVDBP (630·106 counts). The calculated ratio of the radical/macrophage activity was 5-fold lower compared to that of dgVDBP. Only VitD-dgVDBP activated caspase-3 (8%), caspase-9 (13%), and cytochrome-C (11%) on prostatic cancer cells. PE-Cy7-labeled VitD-dgVDBP was found to bind to cytotoxic suppressor cells, monocytes/macrophages, dendritic and natural killer cells (CD8+), and helper cells (CD4+). After 12 h of co-incubation of nPBMCs with VitD-dgVDBP, significant activation and expression were measured for CD16++/CD16 (0.6 ± 0.1% vs. 0.4 ± 0.1%, p < 0.05), CD45k+ (96.0 ± 6.0% vs. 84.7 ± 9.5%, p < 0.05), CD85k+ (24.3 ± 13.2% vs. 3.8 ± 3.2%, p < 0.05), and CD85k+/CD123+ (46.8 ± 8.1% vs. 3.5 ± 3.7%, p < 0.001) compared to the control experiment. No significant difference was found using CD3+, CD4+, CD8+, CD4/CD8, CD4/CD8, CD16+, CD16++, CD14+, or CD123+. A significant decline in CD14+/CD16+ was obtained in the presence of VitD-dgVDBP (0.7 ± 0.2% vs. 3.1 ± 1.7%; p < 0.01). Conclusion: The newly developed water-soluble VitD3 form VitD-dgVDBP affected cytotoxic suppressor cells by activating the low radical-dependent CD16 pathway and seemed to induce apoptosis in malignant prostatic cells.
Collapse
Affiliation(s)
- Ralf Herwig
- Laboratories PD Dr. R. Herwig, 80337 Munich, Germany; (R.H.); (K.E.)
- Heimerer-College, 10000 Pristina, Kosovo; (N.B.); (P.B.)
| | | | - Amela Ibrahimagic
- Department of Speech and Language Pathology and Audiology, Faculty of Education and Rehabilitation, University of Tuzla, 75000 Tuzla, Bosnia and Herzegovina;
| | - Mehtap Kacar
- Department of Physiology, Faculty of Medicine, Yeditepe University, Ataşehir, 34755 İstanbul, Turkey;
- Department of Pathophysiology, Health Sciences Institute, Yeditepe University, Ataşehir, 34755 İstanbul, Turkey
| | | | - Petrit Beqiri
- Heimerer-College, 10000 Pristina, Kosovo; (N.B.); (P.B.)
| | - Joachim Greilberger
- Institut fuer Laborwissenschaften, 8301 Lassnitzhoehe, Austria
- Division of Medicinal Chemistry, Otto-Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, 8010 Graz, Austria
- Correspondence:
| |
Collapse
|
14
|
Kuhn T, Kaiser K, Lebek S, Altenhofen D, Knebel B, Herwig R, Rasche A, Pelligra A, Görigk S, Khuong JMA, Vogel H, Schürmann A, Blüher M, Chadt A, Al-Hasani H. Comparative genomic analyses of multiple backcross mouse populations suggest SGCG as a novel potential obesity-modifier gene. Hum Mol Genet 2022; 31:4019-4033. [PMID: 35796564 DOI: 10.1093/hmg/ddac150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/10/2022] [Accepted: 07/01/2022] [Indexed: 11/14/2022] Open
Abstract
To nominate novel disease genes for obesity and type 2 diabetes (T2D), we recently generated two mouse backcross populations of the T2D-susceptible New Zealand Obese (NZO/HI) mouse strain and two genetically different, lean and T2D-resistant strains, 129P2/OlaHsd and C3HeB/FeJ. Comparative linkage analysis of our two female backcross populations identified seven novel body fat-associated quantitative trait loci (QTL). Only the locus Nbw14 (NZO body weight on chromosome 14) showed linkage to obesity-related traits in both backcross populations, indicating that the causal gene variant is likely specific for the NZO strain as NZO allele carriers in both crosses displayed elevated body weight and fat mass. To identify candidate genes for Nbw14, we used a combined approach of gene expression and haplotype analysis to filter for NZO-specific gene variants in gonadal white adipose tissue (gWAT), defined as the main QTL-target tissue. Only two genes, Arl11 and Sgcg, fulfilled our candidate criteria. In addition, expression QTL analysis revealed cis-signals for both genes within the Nbw14 locus. Moreover, retroviral overexpression of Sgcg in 3 T3-L1 adipocytes resulted in increased insulin-stimulated glucose uptake. In humans, mRNA levels of SGCG correlated with BMI and body fat mass exclusively in diabetic subjects, suggesting that SGCG may present a novel marker for metabolically unhealthy obesity. In conclusion, our comparative-cross analysis could substantially improve the mapping resolution of the obesity locus Nbw14. Future studies will shine light on the mechanism by which Sgcg may protect from the development of obesity.
Collapse
Affiliation(s)
- Tanja Kuhn
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Katharina Kaiser
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Sandra Lebek
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Delsi Altenhofen
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Birgit Knebel
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, D-14195, Germany
| | - Axel Rasche
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, D-14195, Germany
| | - Angela Pelligra
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Sarah Görigk
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Jenny Minh-An Khuong
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Heike Vogel
- German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany.,Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, D-14558, Germany
| | - Annette Schürmann
- German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany.,Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, D-14558, Germany
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, D-04103, Germany
| | - Alexandra Chadt
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| | - Hadi Al-Hasani
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Heinrich Heine University, Medical Faculty, Duesseldorf, D-40225, Germany.,German Center for Diabetes Research (DZD), Munich-Neuherberg, D-85764, Germany
| |
Collapse
|
15
|
Thedinga K, Herwig R. Gradient tree boosting and network propagation for the identification of pan-cancer survival networks. STAR Protoc 2022; 3:101353. [PMID: 35509973 PMCID: PMC9059156 DOI: 10.1016/j.xpro.2022.101353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Cancer survival prediction is typically done with uninterpretable machine learning techniques, e.g., gradient tree boosting. Therefore, additional steps are needed to infer biological plausibility of the predictions. Here, we describe a protocol that combines pan-cancer survival prediction with XGBoost tree-ensemble learning and subsequent propagation of the learned feature weights on protein interaction networks. This protocol is based on TCGA transcriptome data of 8,024 patients from 25 cancer types but can easily be adapted to cancer patient data from other sources. For complete details on the use and execution of this protocol, please refer to Thedinga and Herwig (2022). Efficient pan-cancer survival prediction with XGBoost Network propagation with NetCore improves biological plausibility of features Combined approach identifies pan-cancer survival networks
Collapse
|
16
|
Nguyen N, Lienhard M, Herwig R, Kleinjans J, Jennen D. Epirubicin Alters DNA Methylation Profiles Related to Cardiotoxicity. FRONT BIOSCI-LANDMRK 2022; 27:173. [DOI: 10.31083/j.fbl2706173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/06/2022]
|
17
|
Prasse P, Iversen P, Lienhard M, Thedinga K, Bauer C, Herwig R, Scheffer T. Matching anticancer compounds and tumor cell lines by neural networks with ranking loss. NAR Genom Bioinform 2022; 4:lqab128. [PMID: 35047818 PMCID: PMC8759564 DOI: 10.1093/nargab/lqab128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/03/2021] [Accepted: 12/29/2021] [Indexed: 12/24/2022] Open
Abstract
Computational drug sensitivity models have the potential to improve therapeutic outcomes by identifying targeted drug components that are likely to achieve the highest efficacy for a cancer cell line at hand at a therapeutic dose. State of the art drug sensitivity models use regression techniques to predict the inhibitory concentration of a drug for a tumor cell line. This regression objective is not directly aligned with either of these principal goals of drug sensitivity models: We argue that drug sensitivity modeling should be seen as a ranking problem with an optimization criterion that quantifies a drug's inhibitory capacity for the cancer cell line at hand relative to its toxicity for healthy cells. We derive an extension to the well-established drug sensitivity regression model PaccMann that employs a ranking loss and focuses on the ratio of inhibitory concentration and therapeutic dosage range. We find that the ranking extension significantly enhances the model's capability to identify the most effective anticancer drugs for unseen tumor cell profiles based in on in-vitro data.
Collapse
Affiliation(s)
- Paul Prasse
- To whom correspondence should be addressed. Tel: +49 331 977 3829;
| | | | - Matthias Lienhard
- Dep. Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kristina Thedinga
- Dep. Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Ralf Herwig
- Dep. Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tobias Scheffer
- University of Potsdam, Department of Computer Science, Potsdam, Germany
| |
Collapse
|
18
|
Ibrahimagić A, Patković N, Herwig R. Autism Spectrum Disorders Child Language and Communication Skills and Its Impact on Parental Emotions and Stress. Psychiatr Danub 2022; 34:530. [PMID: 36257000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- Amela Ibrahimagić
- Faculty of Education and Rehabilitation, University of Tuzla, Bosnia and Herzegovina,
| | | | | |
Collapse
|
19
|
Kamburov A, Herwig R. ConsensusPathDB 2022: molecular interactions update as a resource for network biology. Nucleic Acids Res 2021; 50:D587-D595. [PMID: 34850110 PMCID: PMC8728246 DOI: 10.1093/nar/gkab1128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/21/2021] [Accepted: 11/04/2021] [Indexed: 01/01/2023] Open
Abstract
Molecular interactions are key drivers of biological function. Providing interaction resources to the research community is important since they allow functional interpretation and network-based analysis of molecular data. ConsensusPathDB (http://consensuspathdb.org) is a meta-database combining interactions of diverse types from 31 public resources for humans, 16 for mice and 14 for yeasts. Using ConsensusPathDB, researchers commonly evaluate lists of genes, proteins and metabolites against sets of molecular interactions defined by pathways, Gene Ontology and network neighborhoods and retrieve complex molecular neighborhoods formed by heterogeneous interaction types. Furthermore, the integrated protein–protein interaction network is used as a basis for propagation methods. Here, we present the 2022 update of ConsensusPathDB, highlighting content growth, additional functionality and improved database stability. For example, the number of human molecular interactions increased to 859 848 connecting 200 499 unique physical entities such as genes/proteins, metabolites and drugs. Furthermore, we integrated regulatory datasets in the form of transcription factor–, microRNA– and enhancer–gene target interactions, thus providing novel functionality in the context of overrepresentation and enrichment analyses. We specifically emphasize the use of the integrated protein–protein interaction network as a scaffold for network inferences, present topological characteristics of the network and discuss strengths and shortcomings of such approaches.
Collapse
Affiliation(s)
- Atanas Kamburov
- R&D Digital Technologies Department, Bayer AG, Berlin 13353, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| |
Collapse
|
20
|
Greilberger J, Greilberger M, Wintersteiger R, Zangger K, Herwig R. Alpha-Ketoglutarate: A Potential Inner Mitochondrial and Cytosolic Protector against Peroxynitrite and Peroxynitrite-Induced Nitration? Antioxidants (Basel) 2021; 10:antiox10091501. [PMID: 34573133 PMCID: PMC8468307 DOI: 10.3390/antiox10091501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/25/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 01/02/2023] Open
Abstract
The generation of peroxynitrite (ONOO-) is associated with several diseases, including atherosclerosis, hypertension, neurodegeneration, cancer, inflammation, and sepsis. Alpha-ketoglutarate (αKG) is a known potential highly antioxidative agent for radical oxidative species such as peroxides. The question arises as to whether αKG is also a potential scavenger of ONOO- and a potential protector against ONOO--mediated nitration of proteins. NMR studies of 1 mM αKG in 100 mM phosphate-buffered saline at pH 7.4 and pH 6.0 were carried out in the presence or absence of a final concentration of 2 mM ONOO-. An ONOO--luminol-induced chemiluminescence reaction was used to measure the scavenging function of several concentrations of αKG; quantification of αKG was performed via spectrophotometric enzymatic assay of αKG in the absence or presence of 0, 1, or 2 mM ONOO-. The nitration of tyrosine residues on proteins was measured on ONOO--treated bovine serum albumin (BSA) in the presence or absence of 0-24 mM αKG by an ELISA technique using a specific anti-IgG against nitro-tyrosine. The addition of ONOO- to αKG led to the formation of succinic acid and nitrite at pH 7.0, but not at pH 6.0, as αKG was stable against ONOO-. The absorbance of enzymatically estimated αKG at the time point of 30 min was significantly lower in favour of ONOO- (1 mM: 0.21 ± 0.03, 2 mM: 0.12 ± 0.05 vs. 0 mM: 0.32 ± 0.02; p < 0.001). The luminol technique showed an inverse logarithmic correlation of the ONOO- and αKG concentrations (y = -2 × 105 ln(x) + 1 × 106; r2 = 0.99). The usage of 4 mM αKG showed a significant reduction by nearly half in the chemiluminescence signal (284,456 ± 29,293 cps, p < 0.001) compared to the control (474,401 ± 18,259); for 20 and 200 mM αKG, there were further reductions to 163,546 ± 26,196 cps (p < 0.001) and 12,658 ± 1928 cps (p < 0.001). Nitrated tyrosine residues were estimated using the ELISA technique. A negative linear correlation was obtained by estimating nitrated tyrosine residues in the presence of αKG (r2 = 0.94): a reduction by half of nitrated tyrosine was estimated using 12 mM αKG compared to the control (326.1 ± 39.6 nmol vs. 844.5 ± 128.4 nmol; p < 0.001).
Collapse
Affiliation(s)
- Joachim Greilberger
- Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Division of Physiological Chemistry, Medical University of Graz, 8010 Graz, Austria
- Schwarzl Medical Center, Institute of Scientific Laboratory, 8301 Graz, Austria;
- Correspondence:
| | - Michaela Greilberger
- Schwarzl Medical Center, Institute of Scientific Laboratory, 8301 Graz, Austria;
| | - Reinhold Wintersteiger
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz, 8010 Graz, Austria;
| | - Klaus Zangger
- Institute of Chemistry, Organic and Bioorganic Chemistry, University of Graz, 8010 Graz, Austria;
| | - Ralf Herwig
- German Medical Center, Department of Urology Surgery, Dubai 665664, United Arab Emirates;
| |
Collapse
|
21
|
Pacholewska A, Grimm C, Herling CD, Lienhard M, Königs A, Timmermann B, Altmüller J, Mücke O, Reinhardt HC, Plass C, Herwig R, Hallek M, Schweiger MR. Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients. Int J Mol Sci 2021; 22:ijms22179337. [PMID: 34502260 PMCID: PMC8431484 DOI: 10.3390/ijms22179337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in splicing factor genes have a severe impact on the survival of cancer patients. Splicing factor 3b subunit 1 (SF3B1) is one of the most frequently mutated genes in chronic lymphocytic leukemia (CLL); patients carrying these mutations have a poor prognosis. Since the splicing machinery and the epigenome are closely interconnected, we investigated whether these alterations may affect the epigenomes of CLL patients. While an overall hypomethylation during CLL carcinogenesis has been observed, the interplay between the epigenetic stage of the originating B cells and SF3B1 mutations, and the subsequent effect of the mutations on methylation alterations in CLL, have not been investigated. We profiled the genome-wide DNA methylation patterns of 27 CLL patients with and without SF3B1 mutations and identified local decreases in methylation levels in SF3B1mut CLL patients at 67 genomic regions, mostly in proximity to telomeric regions. These differentially methylated regions (DMRs) were enriched in gene bodies of cancer-related signaling genes, e.g., NOTCH1, HTRA3, and BCL9L. In our study, SF3B1 mutations exclusively emerged in two out of three epigenetic stages of the originating B cells. However, not all the DMRs could be associated with the methylation programming of B cells during development, suggesting that mutations in SF3B1 cause additional epigenetic aberrations during carcinogenesis.
Collapse
Affiliation(s)
- Alicja Pacholewska
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Christina Grimm
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Carmen D. Herling
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; (M.L.); (R.H.)
| | - Anja Königs
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany;
| | - Oliver Mücke
- German Cancer Research Center, Cancer Epigenomics, 69120 Heidelberg, Germany; (O.M.); (C.P.)
| | - Hans Christian Reinhardt
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- West German Cancer Center Essen, Department of Hematology and Stem Cell Transplantation, University Hospital Essen, 45147 Essen, Germany
| | - Christoph Plass
- German Cancer Research Center, Cancer Epigenomics, 69120 Heidelberg, Germany; (O.M.); (C.P.)
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; (M.L.); (R.H.)
| | - Michael Hallek
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German CLL Study Group, Department I of Internal Medicine, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (C.D.H.); (H.C.R.); (M.H.)
| | - Michal R. Schweiger
- Institute for Translational Epigenetics, Faculty of Medicine, University Hospital Cologne, 50931 Cologne, Germany; (A.P.); (C.G.); (A.K.)
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Correspondence:
| |
Collapse
|
22
|
Bauer C, Herwig R, Lienhard M, Prasse P, Scheffer T, Schuchhardt J. Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types. J Transl Med 2021; 19:274. [PMID: 34174885 PMCID: PMC8236166 DOI: 10.1186/s12967-021-02941-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/13/2021] [Indexed: 12/09/2022] Open
Abstract
Background There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually. Methods In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data. Results We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: https://knowledgebase.microdiscovery.de/heatmap. Conclusions Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02941-z.
Collapse
Affiliation(s)
- Chris Bauer
- MicroDiscovery GmbH, Marienburger Straße 1, 10405, Berlin, Germany.
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Paul Prasse
- Department of Informatics, University of Potsdam, August-Bebel-Str. 89, 14482, Potsdam, Germany
| | - Tobias Scheffer
- Department of Informatics, University of Potsdam, August-Bebel-Str. 89, 14482, Potsdam, Germany
| | | |
Collapse
|
23
|
Rehman SU, Schallschmidt T, Rasche A, Knebel B, Stermann T, Altenhofen D, Herwig R, Schürmann A, Chadt A, Al-Hasani H. Alternative exon splicing and differential expression in pancreatic islets reveals candidate genes and pathways implicated in early diabetes development. Mamm Genome 2021; 32:153-172. [PMID: 33880624 PMCID: PMC8128753 DOI: 10.1007/s00335-021-09869-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/03/2021] [Indexed: 12/29/2022]
Abstract
Type 2 diabetes (T2D) has a strong genetic component. Most of the gene variants driving the pathogenesis of T2D seem to target pancreatic β-cell function. To identify novel gene variants acting at early stage of the disease, we analyzed whole transcriptome data to identify differential expression (DE) and alternative exon splicing (AS) transcripts in pancreatic islets collected from two metabolically diverse mouse strains at 6 weeks of age after three weeks of high-fat-diet intervention. Our analysis revealed 1218 DE and 436 AS genes in islets from NZO/Hl vs C3HeB/FeJ. Whereas some of the revealed genes present well-established markers for β-cell failure, such as Cd36 or Aldh1a3, we identified numerous DE/AS genes that have not been described in context with β-cell function before. The gene Lgals2, previously associated with human T2D development, was DE as well as AS and localizes in a quantitative trait locus (QTL) for blood glucose on Chr.15 that we reported recently in our N2(NZOxC3H) population. In addition, pathway enrichment analysis of DE and AS genes showed an overlap of only half of the revealed pathways, indicating that DE and AS in large parts influence different pathways in T2D development. PPARG and adipogenesis pathways, two well-established metabolic pathways, were overrepresented for both DE and AS genes, probably as an adaptive mechanism to cope for increased cellular stress. Our results provide guidance for the identification of novel T2D candidate genes and demonstrate the presence of numerous AS transcripts possibly involved in islet function and maintenance of glucose homeostasis.
Collapse
Affiliation(s)
- Sayeed Ur Rehman
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Tanja Schallschmidt
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Axel Rasche
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Birgit Knebel
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Torben Stermann
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Delsi Altenhofen
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annette Schürmann
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,German Institute of Human Nutrition, Potsdam, Germany
| | - Alexandra Chadt
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Duesseldorf, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Hadi Al-Hasani
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich Heine University, Medical Faculty, Duesseldorf, Germany. .,German Center for Diabetes Research (DZD), München-Neuherberg, Germany.
| |
Collapse
|
24
|
Klymenko O, Brecklinghaus T, Dille M, Springer C, de Wendt C, Altenhofen D, Binsch C, Knebel B, Scheller J, Hardt C, Herwig R, Chadt A, Pfluger PT, Al-Hasani H, Kabra DG. Histone deacetylase 5 regulates interleukin 6 secretion and insulin action in skeletal muscle. Mol Metab 2020; 42:101062. [PMID: 32771698 PMCID: PMC7481569 DOI: 10.1016/j.molmet.2020.101062] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Physical exercise training is associated with increased glucose uptake in skeletal muscle and improved glycemic control. HDAC5, a class IIa histone deacetylase, has been shown to regulate transcription of the insulin-responsive glucose transporter GLUT4 in cultured muscle cells. In this study, we analyzed the contribution of HDAC5 to the transcriptional network in muscle and the beneficial effect of muscle contraction and regular exercise on glucose metabolism. METHODS HDAC5 knockout mice (KO) and wild-type (WT) littermates were trained for 8 weeks on treadmills, metabolically phenotyped, and compared to sedentary controls. Hdac5-deficient skeletal muscle and cultured Hdac5-knockdown (KD) C2C12 myotubes were utilized for studies of gene expression and glucose metabolism. Chromatin immunoprecipitation (ChIP) studies were conducted to analyze Il6 promoter activity using H3K9ac and HDAC5 antibodies. RESULTS Global transcriptome analysis of Hdac5 KO gastrocnemius muscle demonstrated activation of the IL-6 signaling pathway. Accordingly, knockdown of Hdac5 in C2C12 myotubes led to higher expression and secretion of IL-6 with enhanced insulin-stimulated activation of AKT that was reversed by Il6 knockdown. Moreover, Hdac5-deficient myotubes exhibited enhanced glucose uptake, glycogen synthesis, and elevated expression levels of the glucose transporter GLUT4. Transcription of Il6 was further enhanced by electrical pulse stimulation in Hdac5-deficient C2C12 myotubes. ChIP identified a ∼1 kb fragment of the Il6 promoter that interacts with HDAC5 and demonstrated increased activation-associated histone marker AcH3K9 in Hdac5-deficient muscle cells. Exercise intervention of HDAC5 KO mice resulted in improved systemic glucose tolerance as compared to WT controls. CONCLUSIONS We identified HDAC5 as a negative epigenetic regulator of IL-6 synthesis and release in skeletal muscle. HDAC5 may exert beneficial effects through two different mechanisms, transcriptional control of genes required for glucose disposal and utilization, and HDAC5-dependent IL-6 signaling cross-talk to improve glucose uptake in muscle in response to exercise.
Collapse
Affiliation(s)
- Oleksiy Klymenko
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Tim Brecklinghaus
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Matthias Dille
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Christian Springer
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany
| | - Christian de Wendt
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany
| | - Delsi Altenhofen
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany
| | - Christian Binsch
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany
| | - Birgit Knebel
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany
| | - Jürgen Scheller
- Institute of Biochemistry and Molecular Biology II, Heinrich Heine University, Medical faculty, Düsseldorf, Germany
| | - Christopher Hardt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra Chadt
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Paul T Pfluger
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany; Research Unit Neurobiology of Diabetes, Helmholtz Zentrum München, 85764, Neuherberg, Germany; TUM School of Medicine, Technical University of Munich, 81675, München, Germany
| | - Hadi Al-Hasani
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany.
| | - Dhiraj G Kabra
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Medical faculty, Düsseldorf, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| |
Collapse
|
25
|
Barel G, Herwig R. NetCore: a network propagation approach using node coreness. Nucleic Acids Res 2020; 48:e98. [PMID: 32735660 PMCID: PMC7515737 DOI: 10.1093/nar/gkaa639] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/22/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
We present NetCore, a novel network propagation approach based on node coreness, for phenotype–genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves improved re-ranking of genes after propagation. Furthermore, NetCore implements a semi-supervised approach to identify phenotype-associated network modules, which anchors the identification of novel candidate genes at known genes associated with the phenotype. We evaluated NetCore on gene sets from 11 different GWAS traits and showed improved performance compared to the standard degree-based network propagation using cross-validation. Furthermore, we applied NetCore to identify disease genes and modules for Schizophrenia GWAS data and pan-cancer mutation data. We compared the novel approach to existing network propagation approaches and showed the benefits of using NetCore in comparison to those. We provide an easy-to-use implementation, together with a high confidence PPI network extracted from ConsensusPathDB, which can be applied to various types of genomics data in order to obtain a re-ranking of genes and functionally relevant network modules.
Collapse
Affiliation(s)
- Gal Barel
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| |
Collapse
|
26
|
Farrall AL, Lienhard M, Grimm C, Kuhl H, Sluka SHM, Caparros M, Forejt J, Timmermann B, Herwig R, Herrmann BG, Morkel M. PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/β-Catenin Response to Suppress Apc Min-Triggered Intestinal Tumor Formation. Cancer Res 2020; 81:38-49. [PMID: 33154092 DOI: 10.1158/0008-5472.can-20-1480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/26/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Genetic predisposition affects the penetrance of tumor-initiating mutations, such as APC mutations that stabilize β-catenin and cause intestinal tumors in mice and humans. However, the mechanisms involved in genetically predisposed penetrance are not well understood. Here, we analyzed tumor multiplicity and gene expression in tumor-prone Apc Min/+ mice on highly variant C57BL/6J (B6) and PWD/Ph (PWD) genetic backgrounds. (B6 × PWD) F1 APC Min offspring mice were largely free of intestinal adenoma, and several chromosome substitution (consomic) strains carrying single PWD chromosomes on the B6 genetic background displayed reduced adenoma numbers. Multiple dosage-dependent modifier loci on PWD chromosome 5 each contributed to tumor suppression. Activation of β-catenin-driven and stem cell-specific gene expression in the presence of Apc Min or following APC loss remained moderate in intestines carrying PWD chromosome 5, suggesting that PWD variants restrict adenoma initiation by controlling stem cell homeostasis. Gene expression of modifier candidates and DNA methylation on chromosome 5 were predominantly cis controlled and largely reflected parental patterns, providing a genetic basis for inheritance of tumor susceptibility. Human SNP variants of several modifier candidates were depleted in colorectal cancer genomes, suggesting that similar mechanisms may also affect the penetrance of cancer driver mutations in humans. Overall, our analysis highlights the strong impact that multiple genetic variants acting in networks can exert on tumor development. SIGNIFICANCE: These findings in mice show that, in addition to accidental mutations, cancer risk is determined by networks of individual gene variants.
Collapse
Affiliation(s)
- Alexandra L Farrall
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | | | - Christina Grimm
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecophysiology and Aquaculture, Berlin, Germany
| | | | - Marta Caparros
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jiri Forejt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Prague, Czech Republic
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.
| |
Collapse
|
27
|
Herwig R, Panhofer P. Cavernous Venous Insufficiency: An Underestimated Vascular Disease Causing Erectile Dysfunction Resistant to Medical Treatment. Eur J Vasc Endovasc Surg 2020; 61:518. [PMID: 33127242 DOI: 10.1016/j.ejvs.2020.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/17/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022]
Affiliation(s)
- Ralf Herwig
- Department of Urology and Andrology, Medicent Medical Centre, Baden, Austria; German Medical Centre, Dubai, United Arab Emirates.
| | - Peter Panhofer
- Medical Faculty, Sigmund Freud University, Vienna, Austria; MedOstWest Centre, Vienna, Austria
| |
Collapse
|
28
|
Greilberger J, Herwig R. Vitamin D - Deglycosylated Vitamin D Binding Protein Dimer: Positive Synergistic Effects on Recognition, Activation, Phagocytosis and Oxidative Stress on Macrophages. Clin Lab 2020; 66. [PMID: 32013346 DOI: 10.7754/clin.lab.2019.191121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND We have recently shown positive effects in the quality of life in autism and amyloid lateral sclerosis patients using a newly developed 25-OH vitamin D deglycosylated vitamin D binding protein complex (VitD~dgVDBP) by reducing oxidative stress. The question arises whether this reduction of oxidative stress was due to a synergistic effect of the dimer in the recognition and activation of phagocytosis on macrophages combined with a lower oxidative burst compared to the VitD free proteins, namely vitamin D binding protein (VDBP: Gc Protein) and deglycosylated dgVDBP (GcMAF). METHODS VDBP sandwich ELISA of equal protein concentration of VDBP, dgVDBP, and VitD~dgVDBP (1 µg/ mL by BCA protein technique) was used to identify immune affinity to polyclonal antibodies raised against human VDBP. The 25(OH) vitamin D levels of VDBP, dgVDBP and VitD~dgVDBP were estimated by a competitive immune assay using a monoclonal antibody. Macrophage phagocytosis and oxidative burst in absence or presence of 400 pg/mL VDBP, 400 pg/mL dgVDBP, and 400 pg/mL VitD~dgVDBP was measured. RESULTS The recognition of the antibody against VDBP protein was significantly more than 4-fold higher for VitD~dgVDBP (769.2 +/- 35.1%) compared to dgVDBP (186.5 +/- 16.8 %; p < 0.01) and 7-fold higher to VDBP (100 +/- 11.4 %; p < 0.001). 25(OH) vitamin D levels of VDBP (20.7 nmol/mg; p < 0.001) and dgVDBP (28.8 +/- 3.9 nmol/mL; p < 0.001) was significantly lower than of VitD~dgVDBP (324.0 +/- 12.8 nmol/mL). The calculated VitD/ protein ratio showed significantly higher results in favor of VitD~dgVDBP (1.01 +/- 0.12) compared to dgVDBP (0.06 +/- 0.03; p < 0.001) and VDBP (0.05 +/- 0.01; p < 0.001). The estimation of macrophage phagocytosis rate of VitD~dgVDBP (5,864.3 +/- 742.2 cps) was significantly higher compared to dgVDBP (2,789.6 +/- 102.7 cps; p < 0.01) and VDBP (1,134.3 +/- 135.9 cps) whereas the production of macrophage superoxide anion radicals showed significantly higher levels of dgVDBP (255.3 +/- 14.5 cps) in comparison to VDBP (148.6 +/- 24.7 cps, p < 0.01) and VitD~dgVDBP (142.3 +/- 20.0 cps; p < 0.001). Linear regression between VDBP antibody affinity and macrophage phagocytosis of VDBP, dgVDBP and VitD~dgVDBP resulted in a correlation coefficient of r = 0.95 in favor of VitD~dgVDBP. CONCLUSIONS VitD~dgVDBP (Il-42) showed higher macrophage activation and lower oxidative burst than VitD free dgVDBP (GcMaf) and VDBP (Gc) which may result from a synergistic effect by presenting protein bound Vitamin D better to macrophages.
Collapse
|
29
|
Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T. Significant abundance of cis configurations of coding variants in diploid human genomes. Nucleic Acids Res 2019; 47:2981-2995. [PMID: 30698752 PMCID: PMC6451136 DOI: 10.1093/nar/gkz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function.
Collapse
Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Qing Mao
- Complete Genomics, Inc., San Jose, CA 95112, USA
| | - Brock A Peters
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - Radoje Drmanac
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Huebsch
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| |
Collapse
|
30
|
Weibl P, Herwig R. Superficial penile cancer treated with complete excision of the glans epithelium and coverage with a tissue sealant matrix (TachoSil®). Cent European J Urol 2019; 72:204-208. [PMID: 31482031 PMCID: PMC6715082 DOI: 10.5173/ceju.2019.1626] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/31/2018] [Accepted: 06/17/2019] [Indexed: 11/22/2022] Open
Abstract
Introduction The aim of our work was to demonstrate the feasibility and clinical outcomes after partial excision of the epithelial and subepithelial layer of the glans with subsequent tissue sealant matrix coverage (TachoSil®). Material and methods We enrolled 11 consecutive patients with superficial penile cancer. Under the microscopic guidance, the tumor in the glans area was excised continuously with a minimal lateral margin of 5 mm. The cosmetic result was accessed using a 5-graded scale ranging from very dissatisfied to very satisfied. Results The median patient's age at the presentation was 46 years (range 38-53). Histopathological examination of the specimen confirmed squamous cell carcinoma and tumor-free surgical margins were obtained in all cases. Overall, the tumors were TaG1 in 3 patients, TaG2 in 1 patient, TisG1 in 2 patients, TisG2 in 2 patient, T1aG1 in 2 patients, and T1aG2 in 1 patient. All patients had clinically negative lymph-node status - cN0 (confirmed by aabdominopelvic computed tomography (CT) scan with contrast). During the follow-up of 6 to 36 months (median 18), local recurrence occurred in 1 patient with carcinoma in situ six months after surgery, which was managed by a second glans-preserving surgery without recurrence. The others showed no signs of local recurrence or metastasis during the period of observation. Conclusions These preliminary data suggests that glans-preserving surgical technique using TachoSil® as a defect coverage is technically feasible, functionally safe and cosmetically satisfying. However, well-designed prospective-randomized trial is warranted, to further confirm the clinical utility of our approach.
Collapse
Affiliation(s)
- Peter Weibl
- Landesklinikum Korneuburg - Teaching Hospital, Department of Urology, Korneuburg, Austria
| | - Ralf Herwig
- Department of Reconstructive Urology, Andrology and Mens's Health, Vienna Urology Foundation, Vienna, Austria
| |
Collapse
|
31
|
Hu H, Kahrizi K, Musante L, Fattahi Z, Herwig R, Hosseini M, Oppitz C, Abedini SS, Suckow V, Larti F, Beheshtian M, Lipkowitz B, Akhtarkhavari T, Mehvari S, Otto S, Mohseni M, Arzhangi S, Jamali P, Mojahedi F, Taghdiri M, Papari E, Soltani Banavandi MJ, Akbari S, Tonekaboni SH, Dehghani H, Ebrahimpour MR, Bader I, Davarnia B, Cohen M, Khodaei H, Albrecht B, Azimi S, Zirn B, Bastami M, Wieczorek D, Bahrami G, Keleman K, Vahid LN, Tzschach A, Gärtner J, Gillessen-Kaesbach G, Varaghchi JR, Timmermann B, Pourfatemi F, Jankhah A, Chen W, Nikuei P, Kalscheuer VM, Oladnabi M, Wienker TF, Ropers HH, Najmabadi H. Genetics of intellectual disability in consanguineous families. Mol Psychiatry 2019; 24:1027-1039. [PMID: 29302074 DOI: 10.1038/s41380-017-0012-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 01/17/2023]
Abstract
Autosomal recessive (AR) gene defects are the leading genetic cause of intellectual disability (ID) in countries with frequent parental consanguinity, which account for about 1/7th of the world population. Yet, compared to autosomal dominant de novo mutations, which are the predominant cause of ID in Western countries, the identification of AR-ID genes has lagged behind. Here, we report on whole exome and whole genome sequencing in 404 consanguineous predominantly Iranian families with two or more affected offspring. In 219 of these, we found likely causative variants, involving 77 known and 77 novel AR-ID (candidate) genes, 21 X-linked genes, as well as 9 genes previously implicated in diseases other than ID. This study, the largest of its kind published to date, illustrates that high-throughput DNA sequencing in consanguineous families is a superior strategy for elucidating the thousands of hitherto unknown gene defects underlying AR-ID, and it sheds light on their prevalence.
Collapse
Affiliation(s)
- Hao Hu
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Guangzhou Women and Children's Medical Center, 510623, Guangzhou, China
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Luciana Musante
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ralf Herwig
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Cornelia Oppitz
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Vanessa Suckow
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Farzaneh Larti
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sabine Otto
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Payman Jamali
- Shahrood Genetic Counseling Center, Welfare Office, Semnan, 36156, Iran
| | - Faezeh Mojahedi
- Mashhad Medical Genetic Counseling Center, Mashhad, 91767, Iran
| | - Maryam Taghdiri
- Shiraz Genetic Counseling Center, Welfare Office, Shiraz, Iran
| | - Elaheh Papari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | | | - Saeide Akbari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Seyed Hassan Tonekaboni
- Pediatric Neurology Research Center, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, 15468, Iran
| | - Hossein Dehghani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Mohammad Reza Ebrahimpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Ingrid Bader
- Kinderzentrum München, Technische Universität München, 81377, München, Germany
| | - Behzad Davarnia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Monika Cohen
- Children's Center Munich, 81377, Munich, Germany
| | - Hossein Khodaei
- Meybod Genetics Research Center, Welfare Organization, Yazd, 89651, Iran
| | - Beate Albrecht
- Institute of Human Genetics, University Hospital Essen, 45122, Essen, Germany
| | - Sarah Azimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Birgit Zirn
- Genetikum Counseling Center, 70173, Stuttgart, Germany
| | - Milad Bastami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Dagmar Wieczorek
- Institute of Human Genetics and Anthropology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Gholamreza Bahrami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Krystyna Keleman
- IMP-Research Institute of Molecular Pathology, 1030, Vienna, Austria.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Leila Nouri Vahid
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Andreas Tzschach
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany.,Institute of Clinical Genetics, Technische Universität Dresden, Dresden, Germany
| | - Jutta Gärtner
- University Medical Center, Georg August University Göttingen, 37075, Göttingen, Germany
| | | | | | - Bernd Timmermann
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | | | - Aria Jankhah
- Shiraz Genetic Counseling Center, Shiraz, 71346, Iran
| | - Wei Chen
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, 13125, Berlin, Germany
| | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran
| | - Thomas F Wienker
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Hans-Hilger Ropers
- Max-Planck-Institute for Molecular Genetics, 14195, Berlin, Germany. .,Institute of Human Genetics, University Medicine, Mainz, Germany.
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19857, Iran. .,Kariminejad - Najmabadi Pathology & Genetics Centre, Tehran, 14667-13713, Iran.
| |
Collapse
|
32
|
Greilberger J, Greilberger M, Petek T, Philipp S, Bettina L, Reichl H, Kamel A, Herwig R. Effective Increase of Serum Vitamin D3 by IV Application of a Cholecalciferol-N-Acetyl-Galactosamine-Stabilized Dimer: a Clinical Murine Trial Study. Clin Lab 2019; 65. [PMID: 31115209 DOI: 10.7754/clin.lab.2019.181114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Pre-clinical toxicology studies of human Gc-protein (vitamin D binding protein) are of special interest as to the transport of vitamin D and its biological activities. We have demonstrated that the oral application of a special dimeric vitamin D complex reduces oxidative stress and increases the quality of life in autistic children. Therefore, safety and toxic effects of two dimeric cholecalciferol-N-acetyl-galactosamine-albumin complexes were evaluated in increasing intravenous (iv.) vitamin D levels administered in a pre-clinical trial in mice over a 5-week period. METHODS Over a period of 5 weeks, two times a week, mice received iv. administration of one of the following: (a) 1.2 IE of vitamin D-N-acetyl-galactosamine-albumin (Vitamin D3 NAGA, ImmunoD® group), (b) 1.2 IE of vitamin-D-poly-N-acetyl-galactosamine-albumin (Poly-Nac group), or (c) isotonic saline solution (sham group). Before and after the trial, red and white blood cell panels (RBS, WBC and platelets) were determined. Furthermore, vitamin D levels, electrolytes, and C-reactive protein levels were measured directly before sacrificing. RESULTS No toxic effects were observed during iv. injection with dimeric vitamin D complexes, neither in the sham group, nor in the two treatment groups. Vitamin D levels increased significantly within 5 weeks in the Poly-Nac group (26.6 ± 8.8 ng/mL; p = 0.001) compared to the sham group (3.1 ± 0.9 ng/mL), and the Poly-Nac group to the ImmunoD group (7.0 ± 3.6 ng/mL; p = 0.003). A significant increase of vitamin D was also obtained in favor of the ImmunoD group compared to the sham (p = 0.03). Electrolytes (K, Na, Cl, Mg, Ca) and C-reactive protein showed no significant differences after administration in all three mice groups. Also, no significant differences were observed between these three groups in the WBC and RBC blood panels. CONCLUSIONS The two dimeric vitamin D complexes used in this pre-clinical study showed no side or toxic effects after iv. administration in mice, but a sole increase in vitamin D levels without any change in electrolytes or blood cells. Therefore, we assume this newly developed composition to be safe in oral or iv.-administration and further pre-clinical studies can be conducted to evaluate the value in treatment of various diseases related to vitamin D deficiencies.
Collapse
|
33
|
Abstract
Toxicogenomics is the study of the molecular effects of chemical, biological and physical agents in biological systems, with the aim of elucidating toxicological mechanisms, building predictive models and improving diagnostics. The vast majority of toxicogenomics data has been generated at the transcriptome level, including RNA-seq and microarrays, and large quantities of drug-treatment data have been made publicly available through databases and repositories. Besides the identification of differentially expressed genes (DEGs) from case-control studies or drug treatment time series studies, bioinformatics methods have emerged that infer gene expression data at the molecular network and pathway level in order to reveal mechanistic information. In this work we describe different resources and tools that have been developed by us and others that relate gene expression measurements with known pathway information such as over-representation and gene set enrichment analyses. Furthermore, we highlight approaches that integrate gene expression data with molecular interaction networks in order to derive network modules related to drug toxicity. We describe the two main parts of the approach, i.e., the construction of a suitable molecular interaction network as well as the conduction of network propagation of the experimental data through the interaction network. In all cases we apply methods and tools to publicly available rat in vivo data on anthracyclines, an important class of anti-cancer drugs that are known to induce severe cardiotoxicity in patients. We report the results and functional implications achieved for four anthracyclines (doxorubicin, epirubicin, idarubicin, and daunorubicin) and compare the information content inherent in the different computational approaches.
Collapse
Affiliation(s)
| | - Ralf Herwig
- Department Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| |
Collapse
|
34
|
Verheijen M, Lienhard M, Schrooders Y, Clayton O, Nudischer R, Timmermann B, Boerno S, Selevsek N, Schlapbach R, Gmuender H, Gotta S, Herwig R, Kleinjans J, Caiment F. DMSO-induced drastic changes in cellular processes and epigenetic landscape in vitro. Toxicol Lett 2018. [DOI: 10.1016/j.toxlet.2018.06.927] [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: 11/15/2022]
|
35
|
Grasse S, Lienhard M, Frese S, Kerick M, Steinbach A, Grimm C, Hussong M, Rolff J, Becker M, Dreher F, Schirmer U, Boerno S, Ramisch A, Leschber G, Timmermann B, Grohé C, Lüders H, Vingron M, Fichtner I, Klein S, Odenthal M, Büttner R, Lehrach H, Sültmann H, Herwig R, Schweiger MR. Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance. Genome Med 2018; 10:55. [PMID: 30029672 PMCID: PMC6054719 DOI: 10.1186/s13073-018-0562-1] [Citation(s) in RCA: 31] [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] [Received: 03/25/2018] [Accepted: 06/21/2018] [Indexed: 12/31/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is the most common cause of cancer-related deaths worldwide and is primarily treated with radiation, surgery, and platinum-based drugs like cisplatin and carboplatin. The major challenge in the treatment of NSCLC patients is intrinsic or acquired resistance to chemotherapy. Molecular markers predicting the outcome of the patients are urgently needed. Methods Here, we employed patient-derived xenografts (PDXs) to detect predictive methylation biomarkers for platin-based therapies. We used MeDIP-Seq to generate genome-wide DNA methylation profiles of 22 PDXs, their parental primary NSCLC, and their corresponding normal tissues and complemented the data with gene expression analyses of the same tissues. Candidate biomarkers were validated with quantitative methylation-specific PCRs (qMSP) in an independent cohort. Results Comprehensive analyses revealed that differential methylation patterns are highly similar, enriched in PDXs and lung tumor-specific when comparing differences in methylation between PDXs versus primary NSCLC. We identified a set of 40 candidate regions with methylation correlated to carboplatin response and corresponding inverse gene expression pattern even before therapy. This analysis led to the identification of a promoter CpG island methylation of LDL receptor-related protein 12 (LRP12) associated with increased resistance to carboplatin. Validation in an independent patient cohort (n = 35) confirmed that LRP12 methylation status is predictive for therapeutic response of NSCLC patients to platin therapy with a sensitivity of 80% and a specificity of 84% (p < 0.01). Similarly, we find a shorter survival time for patients with LRP12 hypermethylation in the TCGA data set for NSCLC (lung adenocarcinoma). Conclusions Using an epigenome-wide sequencing approach, we find differential methylation patterns from primary lung cancer and PDX-derived cancers to be very similar, albeit with a lower degree of differential methylation in primary tumors. We identify LRP12 DNA methylation as a powerful predictive marker for carboplatin resistance. These findings outline a platform for the identification of epigenetic therapy resistance biomarkers based on PDX NSCLC models. Electronic supplementary material The online version of this article (10.1186/s13073-018-0562-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sabrina Grasse
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Matthias Lienhard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Martin Kerick
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Present Address: Department of Cell Biology and Immunology, Institute for Parasitology and Biomedicine, Granada, Spain
| | - Anne Steinbach
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Department of Biology, Chemistry and Pharmacy, Free University Berlin, Berlin, Germany
| | - Christina Grimm
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Michelle Hussong
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, CMMC, Cologne, Germany
| | - Jana Rolff
- Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Michael Becker
- Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Felix Dreher
- Alacris Theranostics GmbH Berlin, Berlin, Germany
| | - Uwe Schirmer
- Cancer Genome Research Group, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Translational Lung Research, Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anna Ramisch
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Iduna Fichtner
- Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
| | - Sebastian Klein
- Institute of Pathology, University of Cologne, Cologne, Germany.,Else Kröner Forschungskolleg Clonal Evolution in Cancer, University Hospital Cologne, Weyertal 115b, 50931, Cologne, Germany
| | | | | | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Alacris Theranostics GmbH Berlin, Berlin, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Translational Lung Research, Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michal R Schweiger
- Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany. .,Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Center for Molecular Medicine Cologne, CMMC, Cologne, Germany.
| |
Collapse
|
36
|
Binsch C, Barbosa D, Jeruschke K, Weiß J, Hubert M, Hansen G, Gorressen S, Fischer JW, Lienhard M, Herwig R, Chadt A, Al-Hasani H. Deletion von TBC1D4/AS160 erhöht den Myokardschaden nach Ischämie/Reperfusion und verschlechtert den kardialen Substratmetabolismus. DIABETOL STOFFWECHS 2018. [DOI: 10.1055/s-0038-1641777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- C Binsch
- Deutsches Diabetes-Zentrum (DDZ), Institut für Klinische Biochemie und Pathobiochemie, Düsseldorf, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), München-Neuherberg, Germany
| | - D Barbosa
- Deutsches Diabetes-Zentrum (DDZ), Institut für Klinische Biochemie und Pathobiochemie, Düsseldorf, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), München-Neuherberg, Germany
| | - K Jeruschke
- Deutsches Diabetes-Zentrum (DDZ), Institut für Klinische Biochemie und Pathobiochemie, Düsseldorf, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), München-Neuherberg, Germany
| | - J Weiß
- Deutsches Diabetes-Zentrum (DDZ), Institut für Klinische Biochemie und Pathobiochemie, Düsseldorf, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), München-Neuherberg, Germany
| | - M Hubert
- Deutsches Diabetes-Zentrum (DDZ), Institut für Klinische Biochemie und Pathobiochemie, Düsseldorf, Germany
| | - G Hansen
- Deutsches Diabetes-Zentrum (DDZ), Institut für Klinische Biochemie und Pathobiochemie, Düsseldorf, Germany
| | - S Gorressen
- Heinrich-Heine-Universität Düsseldorf, Institut für Pharmakologie und Klinische Pharmakologie, Düsseldorf, Germany
| | - JW Fischer
- Heinrich-Heine-Universität Düsseldorf, Institut für Pharmakologie und Klinische Pharmakologie, Düsseldorf, Germany
| | - M Lienhard
- Max-Planck-Institut für molekulare Genetik, Berlin, Germany
| | - R Herwig
- Max-Planck-Institut für molekulare Genetik, Berlin, Germany
| | - A Chadt
- Deutsches Diabetes-Zentrum (DDZ), Institut für Klinische Biochemie und Pathobiochemie, Düsseldorf, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), München-Neuherberg, Germany
| | - H Al-Hasani
- Deutsches Diabetes-Zentrum (DDZ), Institut für Klinische Biochemie und Pathobiochemie, Düsseldorf, Germany
- Deutsches Zentrum für Diabetesforschung (DZD), München-Neuherberg, Germany
| |
Collapse
|
37
|
Abstract
The computational prediction of compound effects from molecular data is an important task in hazard and risk assessment and pivotal for judging the safety of any drug, chemical or cosmetic compound. In particular, the identification of such compound effects at the level of molecular interaction networks can be helpful for the construction of adverse outcome pathways (AOPs). AOPs emerged as a guiding concept for toxicity prediction, because of the inherent mechanistic information of such networks. In fact, integrating molecular interactions in transcriptome analysis and observing expression changes in closely interacting genes might allow identifying the key molecular initiating events of compound toxicity.In this work we describe a computational approach that is suitable for the identification of such network modules from transcriptomics data, which is the major molecular readout of toxicogenomics studies. The approach is composed of different tools (1) for primary data analysis, i.e., the biostatistical quantification of the gene expression changes, (2) for functional annotation and prioritization of genes using literature mining, as well as (3) for the construction of an interaction network that consists of interactions with high confidence and the identification of predictive modules from these networks. We describe the different steps of the approach and demonstrate its performance with public data on drugs that induce hepatic and cardiac toxicity.
Collapse
Affiliation(s)
- C Hardt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195, Berlin, Germany
| | - C Bauer
- MicroDiscovery GmbH, Marienburgerstr. 1, D-10405, Berlin, Germany
| | - J Schuchhardt
- MicroDiscovery GmbH, Marienburgerstr. 1, D-10405, Berlin, Germany
| | - R Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195, Berlin, Germany.
| |
Collapse
|
38
|
Kuepfer L, Clayton O, Thiel C, Cordes H, Nudischer R, Blank LM, Baier V, Heymans S, Caiment F, Roth A, Fluri DA, Kelm JM, Castell J, Selevsek N, Schlapbach R, Keun H, Hynes J, Sarkans U, Gmuender H, Herwig R, Niederer S, Schuchhardt J, Segall M, Kleinjans J. A model-based assay design to reproduce in vivo patterns of acute drug-induced toxicity. Arch Toxicol 2017; 92:553-555. [PMID: 28852801 PMCID: PMC5773653 DOI: 10.1007/s00204-017-2041-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/10/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Lars Kuepfer
- Institute of Applied Microbiology, RWTH, Aachen, Germany.
| | - Olivia Clayton
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Henrik Cordes
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | - Ramona Nudischer
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Lars M Blank
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | - Vanessa Baier
- Institute of Applied Microbiology, RWTH, Aachen, Germany
| | - Stephane Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands.,Department of Cardiovascular Sciences, Leuven University, Leuven, Belgium
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| | - Adrian Roth
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | | | - José Castell
- Instituto de Investigación Sanitaria. Hospital Universitario La Fe, Valencia, Spain
| | - Nathalie Selevsek
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Hector Keun
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | | | - Ugis Sarkans
- European Molecular Biology Laboratory, Cambridge, UK
| | | | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Steven Niederer
- Department of Imaging Sciences and BioMedical Engineering, King's College London, London, UK
| | | | | | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, Netherlands
| |
Collapse
|
39
|
Lienhard M, Grasse S, Rolff J, Frese S, Schirmer U, Becker M, Börno S, Timmermann B, Chavez L, Sültmann H, Leschber G, Fichtner I, Schweiger MR, Herwig R. QSEA-modelling of genome-wide DNA methylation from sequencing enrichment experiments. Nucleic Acids Res 2017; 45:e44. [PMID: 27913729 PMCID: PMC5389680 DOI: 10.1093/nar/gkw1193] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/17/2016] [Indexed: 12/22/2022] Open
Abstract
Genome-wide enrichment of methylated DNA followed by sequencing (MeDIP-seq) offers a reasonable compromise between experimental costs and genomic coverage. However, the computational analysis of these experiments is complex, and quantification of the enrichment signals in terms of absolute levels of methylation requires specific transformation. In this work, we present QSEA, Quantitative Sequence Enrichment Analysis, a comprehensive workflow for the modelling and subsequent quantification of MeDIP-seq data. As the central part of the workflow we have developed a Bayesian statistical model that transforms the enrichment read counts to absolute levels of methylation and, thus, enhances interpretability and facilitates comparison with other methylation assays. We suggest several calibration strategies for the critical parameters of the model, either using additional data or fairly general assumptions. By comparing the results with bisulfite sequencing (BS) validation data, we show the improvement of QSEA over existing methods. Additionally, we generated a clinically relevant benchmark data set consisting of methylation enrichment experiments (MeDIP-seq), BS-based validation experiments (Methyl-seq) as well as gene expression experiments (RNA-seq) derived from non-small cell lung cancer patients, and show that the workflow retrieves well-known lung tumour methylation markers that are causative for gene expression changes, demonstrating the applicability of QSEA for clinical studies. QSEA is implemented in R and available from the Bioconductor repository 3.4 (www.bioconductor.org/packages/qsea).
Collapse
Affiliation(s)
- Matthias Lienhard
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| | - Sabrina Grasse
- Functional Epigenomics, University Hospital Cologne, Cologne 50937, Germany
| | - Jana Rolff
- Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany
| | - Steffen Frese
- Department of Thoracic Surgery, ELK Berlin Chest Hospital, Berlin 13125, Germany
| | - Uwe Schirmer
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany
| | - Michael Becker
- Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| | - Lukas Chavez
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany
| | - Gunda Leschber
- Department of Thoracic Surgery, ELK Berlin Chest Hospital, Berlin 13125, Germany
| | - Iduna Fichtner
- Experimental Pharmacology & Oncology Berlin-Buch GmbH, Berlin 13125, Germany
| | - Michal R Schweiger
- Functional Epigenomics, University Hospital Cologne, Cologne 50937, Germany.,Department of Vertebrate Genomics, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin 14195, Germany
| |
Collapse
|
40
|
Hardt C, Beber ME, Rasche A, Kamburov A, Hebels DG, Kleinjans JC, Herwig R. ToxDB: pathway-level interpretation of drug-treatment data. Database (Oxford) 2016; 2016:baw052. [PMID: 27074805 PMCID: PMC4830474 DOI: 10.1093/database/baw052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/17/2016] [Indexed: 01/05/2023]
Abstract
Motivation: Extensive drug treatment gene expression data have been generated in order to identify biomarkers that are predictive for toxicity or to classify compounds. However, such patterns are often highly variable across compounds and lack robustness. We and others have previously shown that supervised expression patterns based on pathway concepts rather than unsupervised patterns are more robust and can be used to assess toxicity for entire classes of drugs more reliably. Results: We have developed a database, ToxDB, for the analysis of the functional consequences of drug treatment at the pathway level. We have collected 2694 pathway concepts and computed numerical response scores of these pathways for 437 drugs and chemicals and 7464 different experimental conditions. ToxDB provides functionalities for exploring these pathway responses by offering tools for visualization and differential analysis allowing for comparisons of different treatment parameters and for linking this data with toxicity annotation and chemical information. Database URL:http://toxdb.molgen.mpg.de
Collapse
Affiliation(s)
- C Hardt
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr, 73, D-14195 Berlin, Germany
| | - M E Beber
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr, 73, D-14195 Berlin, Germany
| | - A Rasche
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr, 73, D-14195 Berlin, Germany
| | - A Kamburov
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr, 73, D-14195 Berlin, Germany
| | - D G Hebels
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, Md 6200, The Netherlands Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute, Maastricht University, Universiteitssingel 40, Maastricht, Er 6229, The Netherlands
| | - J C Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, Md 6200, The Netherlands
| | - R Herwig
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr, 73, D-14195 Berlin, Germany
| |
Collapse
|
41
|
Broecker F, Hardt C, Herwig R, Timmermann B, Kerick M, Wunderlich A, Schweiger MR, Borsig L, Heikenwalder M, Lehrach H, Moelling K. Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line. FEBS J 2016; 283:1669-88. [PMID: 26919036 DOI: 10.1111/febs.13694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 01/20/2016] [Accepted: 02/23/2016] [Indexed: 01/06/2023]
Abstract
UNLABELLED Deletions at the C-terminus of the proto-oncogene protein c-Src kinase are found in the viral oncogene protein v-Src as well as in some advanced human colon cancers. They are associated with increased kinase activity and cellular invasiveness. Here, we analyzed the mRNA expression signature of a constitutively active C-terminal mutant of c-Src, c-Src(mt), in comparison with its wild-type protein, c-Src(wt), in the human non-transformed breast epithelial cell line MCF-10A. We demonstrated previously that the mutant altered migratory and metastatic properties. Genome-wide transcriptome analysis revealed that c-Src(mt) de-regulated the expression levels of approximately 430 mRNAs whose gene products are mainly involved in the cellular processes of migration and adhesion, apoptosis and protein synthesis. 82.9% of these genes have previously been linked to cellular migration, while the others play roles in RNA transport and splicing processes, for instance. Consistent with the transcriptome data, cells expressing c-Src(mt), but not those expressing c-Src(wt), showed the capacity to metastasize into the lungs of mice in vivo. The mRNA expression profile of c-Src(mt)-expressing cells shows significant overlap with that of various primary human tumor samples, possibly reflecting elevated Src activity in some cancerous cells. Expression of c-Src(mt) led to elevated migratory potential. We used this model system to analyze the transcriptional changes associated with an invasive cellular phenotype. These genes and pathways de-regulated by c-Src(mt) may provide suitable biomarkers or targets of therapeutic approaches for metastatic cells. DATABASE This project was submitted to the National Center for Biotechnology Information BioProject under ID PRJNA288540. The Illumina RNA-Seq reads are available in the National Center for Biotechnology Information Sequence Read Archive under study ID SRP060008 with accession numbers SRS977414 for MCF-10A cells, SRS977717 for mock cells, SRS978053 for c-Src(wt) cells and SRS978046 for c-Src(mt) cells.
Collapse
Affiliation(s)
- Felix Broecker
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,University of Zurich, Switzerland
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Martin Kerick
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | - Lubor Borsig
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Switzerland
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München, Germany.,Institute of Virology, Helmholtz Zentrum Munich, Germany.,Department Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Dahlem Centre for Genome Research and Medical Systems Biology, Berlin, Germany.,Alacris Theranostics GmbH, Berlin, Germany
| | - Karin Moelling
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,University of Zurich, Switzerland
| |
Collapse
|
42
|
Herwig R, Gmuender H, Corvi R, Bloch KM, Brandenburg A, Castell J, Ceelen L, Chesne C, Doktorova TY, Jennen D, Jennings P, Limonciel A, Lock EA, McMorrow T, Phrakonkham P, Radford R, Slattery C, Stierum R, Vilardell M, Wittenberger T, Yildirimman R, Ryan M, Rogiers V, Kleinjans J. Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective. Arch Toxicol 2015; 90:2215-2229. [PMID: 26525393 DOI: 10.1007/s00204-015-1617-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 01/29/2023]
Abstract
The assessment of the carcinogenic potential of chemicals with alternative, human-based in vitro systems has become a major goal of toxicogenomics. The central read-out of these assays is the transcriptome, and while many studies exist that explored the gene expression responses of such systems, reports on robustness and reproducibility, when testing them independently in different laboratories, are still uncommon. Furthermore, there is limited knowledge about variability induced by the data analysis protocols. We have conducted an inter-laboratory study for testing chemical carcinogenicity evaluating two human in vitro assays: hepatoma-derived cells and hTERT-immortalized renal proximal tubule epithelial cells, representing liver and kidney as major target organs. Cellular systems were initially challenged with thirty compounds, genome-wide gene expression was measured with microarrays, and hazard classifiers were built from this training set. Subsequently, each system was independently established in three different laboratories, and gene expression measurements were conducted using anonymized compounds. Data analysis was performed independently by two separate groups applying different protocols for the assessment of inter-laboratory reproducibility and for the prediction of carcinogenic hazard. As a result, both workflows came to very similar conclusions with respect to (1) identification of experimental outliers, (2) overall assessment of robustness and inter-laboratory reproducibility and (3) re-classification of the unknown compounds to the respective toxicity classes. In summary, the developed bioinformatics workflows deliver accurate measures for inter-laboratory comparison studies, and the study can be used as guidance for validation of future carcinogenicity assays in order to implement testing of human in vitro alternatives to animal testing.
Collapse
Affiliation(s)
- R Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany.
| | - H Gmuender
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - R Corvi
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), Institute for Health and Consumer Protection (IHCP), European Commission Joint Research Centre, TP 126, Via E. Fermi 2749, 21027, Ispra, Italy
| | - K M Bloch
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - A Brandenburg
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - J Castell
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Valencia, Av. Blasco Ibanez 15, 46010, Valencia, Spain
| | - L Ceelen
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - C Chesne
- Biopredic International, Parc d'affaires de la Bretèche, Bldg. A4, 35760, St Gregoire, France
| | - T Y Doktorova
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - D Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - P Jennings
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - A Limonciel
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - E A Lock
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - T McMorrow
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - P Phrakonkham
- European Union Reference Laboratory for Alternatives to Animal Testing (EURL ECVAM), Institute for Health and Consumer Protection (IHCP), European Commission Joint Research Centre, TP 126, Via E. Fermi 2749, 21027, Ispra, Italy
| | - R Radford
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - C Slattery
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - R Stierum
- Department of Risk Analysis for Products in Development, Netherlands Organisation for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE, Zeist, The Netherlands
| | - M Vilardell
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany
| | - T Wittenberger
- Genedata AG, Margarethenstrasse 38, 4053, Basel, Switzerland
| | - R Yildirimman
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestr. 73, 14195, Berlin, Germany
| | - M Ryan
- Conway Institute, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - V Rogiers
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - J Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| |
Collapse
|
43
|
Hendrickx DM, Aerts HJWL, Caiment F, Clark D, Ebbels TMD, Evelo CT, Gmuender H, Hebels DGAJ, Herwig R, Hescheler J, Jennen DGJ, Jetten MJA, Kanterakis S, Keun HC, Matser V, Overington JP, Pilicheva E, Sarkans U, Segura-Lepe MP, Sotiriadou I, Wittenberger T, Wittwehr C, Zanzi A, Kleinjans JCS. diXa: a data infrastructure for chemical safety assessment. Bioinformatics 2015; 31:1505-7. [PMID: 25505093 PMCID: PMC4410652 DOI: 10.1093/bioinformatics/btu827] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/26/2014] [Accepted: 12/08/2014] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The field of toxicogenomics (the application of '-omics' technologies to risk assessment of compound toxicities) has expanded in the last decade, partly driven by new legislation, aimed at reducing animal testing in chemical risk assessment but mainly as a result of a paradigm change in toxicology towards the use and integration of genome wide data. Many research groups worldwide have generated large amounts of such toxicogenomics data. However, there is no centralized repository for archiving and making these data and associated tools for their analysis easily available. RESULTS The Data Infrastructure for Chemical Safety Assessment (diXa) is a robust and sustainable infrastructure storing toxicogenomics data. A central data warehouse is connected to a portal with links to chemical information and molecular and phenotype data. diXa is publicly available through a user-friendly web interface. New data can be readily deposited into diXa using guidelines and templates available online. Analysis descriptions and tools for interrogating the data are available via the diXa portal. AVAILABILITY AND IMPLEMENTATION http://www.dixa-fp7.eu CONTACT d.hendrickx@maastrichtuniversity.nl; info@dixa-fp7.eu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Diana M Hendrickx
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Hugo J W L Aerts
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Florian Caiment
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Dominic Clark
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Timothy M D Ebbels
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Chris T Evelo
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Hans Gmuender
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Dennie G A J Hebels
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Ralf Herwig
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Jürgen Hescheler
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Danyel G J Jennen
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Marlon J A Jetten
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Stathis Kanterakis
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Hector C Keun
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Vera Matser
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - John P Overington
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Ekaterina Pilicheva
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Ugis Sarkans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Marcelo P Segura-Lepe
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Isaia Sotiriadou
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Timo Wittenberger
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Clemens Wittwehr
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Antonella Zanzi
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| | - Jos C S Kleinjans
- Department of Toxicogenomics, School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, 02215, MA, USA, European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SD, UK, Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, South Kensington, London SW7 2AZ, UK, Department of Bioinformatics - BiGCaT, Maastricht University, 6200 MD Maastricht, The Netherlands, Genedata AG, CH-4053 Basel, Switzerland, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne, Cologne 50931, Germany and European Commission, Joint Research Centre, 21027 Ispra VA, Italy
| |
Collapse
|
44
|
Herwig R, Sansalone S. Venous leakage treatment revisited: pelvic venoablation using aethoxysclerol under air block technique and Valsalva maneuver. ACTA ACUST UNITED AC 2015; 87:1-4. [PMID: 25847887 DOI: 10.4081/aiua.2015.1.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 04/01/2015] [Indexed: 11/23/2022]
Abstract
OBJECTIVE We evaluated the effectiveness of pelvic vein embolization with aethoxysclerol in aero-block technique for the treatment of impotence due to venous leakage in men using sildenafil for intercourse. The aim of the procedure was to reduce the use of sildenafil. METHODS A total of 96 patients with veno-occlusive dysfunction, severe enough for the need of PDE5 inhibitors for vaginal penetration, underwent pelvic venoablation with aethoxysclerol. The mean patient age was 53.5 years. Venous leaks were identified by Color Doppler Ultrasound after intracavernous alprostadil injection. Under local anesthesia a 20-gauge needle was inserted into the deep dorsal penile vein. The pelvic venogram was obtained through deep dorsal venography. Aethoxysclerol 3% as sclerosing agent was injected after air-block under Valsalva manoeuver. Success was defined as the ability to achieve vaginal insertion without the aid of any drugs, vasoactive injections, penile prosthesis, or vacuum device. Additionally, a pre- and post- therapy IIEF score and a digital overnight spontaneous erections protocol (OSEP) with the NEVA™-system was performed. RESULTS At 3 month follow-up 77 out of 96 patients (80.21%) reported to have erections sufficient for vaginal insertion without the use of any drug or additional device. Four (4.17%) patients did not report any improvement. Follow up with color Doppler ultrasound revealed a new or persistent venous leakage in 8 (8.33%) of the patients. No serious complications occurred. CONCLUSIONS Our new pelvic venoablation technique using aethoxysclerol in air-block technique was effective, minimally invasive, and cost-effective. All patients were able to perform sexual intercourse without the previously used dosage of PDE5 inhibitor. This new method may help in patients with contra-indications against PDE5 inhibitors, in patients who cannot afford the frequent usage of expensive oral medication or those who do not fully respond to PDE5-inhibitors.
Collapse
Affiliation(s)
- Ralf Herwig
- Vienna International Medical Clinic, Department of Urology.
| | | |
Collapse
|
45
|
Abstract
The development of novel high-throughput technologies has opened up the opportunity to deeply characterize patient tissues at various molecular levels and has given rise to a paradigm shift in medicine towards personalized therapies. Computational analysis plays a pivotal role in integrating the various genome data and understanding the cellular response to a drug. Based on that data, molecular models can be constructed that incorporate the known downstream effects of drug-targeted receptor molecules and that predict optimal therapy decisions. In this article, we describe the different steps in the conceptual framework of computational modeling. We review resources that hold information on molecular pathways that build the basis for constructing the model interaction maps, highlight network analysis concepts that have been helpful in identifying predictive disease patterns, and introduce the basic concepts of kinetic modeling. Finally, we illustrate this framework with selected studies related to the modeling of important target pathways affected by drugs.
Collapse
Affiliation(s)
- Ralf Herwig
- Max Planck Institute for Molecular Genetics, Department Vertebrate Genomics, Berlin, Germany
| |
Collapse
|
46
|
|
47
|
Reiner G, Dreher F, Drungowski M, Hoeltig D, Bertsch N, Selke M, Willems H, Gerlach GF, Probst I, Tuemmler B, Waldmann KH, Herwig R. Pathway deregulation and expression QTLs in response to Actinobacillus pleuropneumoniae infection in swine. Mamm Genome 2014; 25:600-17. [DOI: 10.1007/s00335-014-9536-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/10/2014] [Indexed: 11/27/2022]
|
48
|
Abstract
The computational prediction of alternative splicing from high-throughput sequencing data is inherently difficult and necessitates robust statistical measures because the differential splicing signal is overlaid by influencing factors such as gene expression differences and simultaneous expression of multiple isoforms amongst others. In this work we describe ARH-seq, a discovery tool for differential splicing in case–control studies that is based on the information-theoretic concept of entropy. ARH-seq works on high-throughput sequencing data and is an extension of the ARH method that was originally developed for exon microarrays. We show that the method has inherent features, such as independence of transcript exon number and independence of differential expression, what makes it particularly suited for detecting alternative splicing events from sequencing data. In order to test and validate our workflow we challenged it with publicly available sequencing data derived from human tissues and conducted a comparison with eight alternative computational methods. In order to judge the performance of the different methods we constructed a benchmark data set of true positive splicing events across different tissues agglomerated from public databases and show that ARH-seq is an accurate, computationally fast and high-performing method for detecting differential splicing events.
Collapse
Affiliation(s)
- Axel Rasche
- Max-Planck-Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Matthias Lienhard
- Max-Planck-Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Marie-Laure Yaspo
- Max-Planck-Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Hans Lehrach
- Max-Planck-Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Ralf Herwig
- Max-Planck-Institute for Molecular Genetics, Department of Vertebrate Genomics, Ihnestrasse 63-73, 14195 Berlin, Germany
| |
Collapse
|
49
|
Toepker M, Kuehas F, Kienzl D, Herwig R, Spazierer E, Krauss B, Weber M, Seitz C, Ringl H. Dual Energy Computerized Tomography with a Split Bolus—A 1-Stop Shop for Patients with Suspected Urinary Stones? J Urol 2014; 191:792-7. [DOI: 10.1016/j.juro.2013.10.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Michael Toepker
- Department of Radiology, Medical University Vienna, Vienna General Hospital, Vienna, Austria
| | - Franklin Kuehas
- Department of Urology, Medical University Vienna, Vienna General Hospital, Vienna, Austria
| | - Daniela Kienzl
- Department of Radiology, Medical University Vienna, Vienna General Hospital, Vienna, Austria
| | - Ralf Herwig
- Department of Urology, Medical University Vienna, Vienna General Hospital, Vienna, Austria
| | - Elisa Spazierer
- Department of Radiology, Medical University Vienna, Vienna General Hospital, Vienna, Austria
| | | | - Michael Weber
- Department of Radiology, Medical University Vienna, Vienna General Hospital, Vienna, Austria
| | - Christian Seitz
- Department of Urology, Medical University Vienna, Vienna General Hospital, Vienna, Austria
| | - Helmut Ringl
- Department of Radiology, Medical University Vienna, Vienna General Hospital, Vienna, Austria
| |
Collapse
|
50
|
Hebels DGA, Jetten MJA, Aerts HJW, Herwig R, Theunissen DHJ, Gaj S, van Delft JH, Kleinjans JCS. Evaluation of database-derived pathway development for enabling biomarker discovery for hepatotoxicity. Biomark Med 2014; 8:185-200. [DOI: 10.2217/bmm.13.154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Current testing models for predicting drug-induced liver injury are inadequate, as they basically under-report human health risks. We present here an approach towards developing pathways based on hepatotoxicity-associated gene groups derived from two types of publicly accessible hepatotoxicity databases, in order to develop drug-induced liver injury biomarker profiles. One human liver ‘omics-based and four text-mining-based databases were explored for hepatotoxicity-associated gene lists. Over-representation analysis of these gene lists with a hepatotoxicant-exposed primary human hepatocytes data set showed that human liver ‘omics gene lists performed better than text-mining gene lists and the results of the latter differed strongly between databases. However, both types of databases contained gene lists demonstrating biomarker potential. Visualizing those in pathway format may aid in interpreting the biomolecular background. We conclude that exploiting existing and openly accessible databases in a dedicated manner seems promising in providing venues for translational research in toxicology and biomarker development.
Collapse
Affiliation(s)
- Dennie GA Hebels
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Marlon JA Jetten
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Hugo JW Aerts
- Department or Biostatistics & Computational Biology, Dana–Farber Cancer Institute, Harvard School of Public Health, 44 Binney Street, Boston, MA 02115, USA
| | - Ralf Herwig
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Daniël HJ Theunissen
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Stan Gaj
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Joost H van Delft
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Jos CS Kleinjans
- Department of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| |
Collapse
|