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Zhang H, Liu Y, Fields L, Shi X, Huang P, Lu H, Schneider AJ, Tang X, Puglielli L, Welham NV, Li L. Single-cell lipidomics enabled by dual-polarity ionization and ion mobility-mass spectrometry imaging. Nat Commun 2023; 14:5185. [PMID: 37626051 PMCID: PMC10457347 DOI: 10.1038/s41467-023-40512-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Single-cell (SC) analysis provides unique insight into individual cell dynamics and cell-to-cell heterogeneity. Here, we utilize trapped ion mobility separation coupled with dual-polarity ionization mass spectrometry imaging (MSI) to enable high-throughput in situ profiling of the SC lipidome. Multimodal SC imaging, in which dual-polarity-mode MSI is used to perform serial data acquisition runs on individual cells, significantly enhanced SC lipidome coverage. High-spatial resolution SC-MSI identifies both inter- and intracellular lipid heterogeneity; this heterogeneity is further explicated by Uniform Manifold Approximation and Projection and machine learning-driven classifications. We characterize SC lipidome alteration in response to stearoyl-CoA desaturase 1 inhibition and, additionally, identify cell-layer specific lipid distribution patterns in mouse cerebellar cortex. This integrated multimodal SC-MSI technology enables high-resolution spatial mapping of intercellular and cell-to-cell lipidome heterogeneity, SC lipidome remodeling induced by pharmacological intervention, and region-specific lipid diversity within tissue.
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Affiliation(s)
- Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Yuan Liu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Xudong Shi
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53792, USA
| | - Penghsuan Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Andrew J Schneider
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Xindi Tang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Nathan V Welham
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53792, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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2
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Kolliari-Turner A, Lima G, Wang G, Malinsky FR, Karanikolou A, Eichhorn G, Tanisawa K, Ospina-Betancurt J, Hamilton B, Kumi PY, Shurlock J, Skiadas V, Twycross-Lewis R, Kilduff L, Martin RP, Ash GI, Potter C, Guppy FM, Seto JT, Fossati C, Pigozzi F, Borrione P, Pitsiladis Y. An observational human study investigating the effect of anabolic androgenic steroid use on the transcriptome of skeletal muscle and whole blood using RNA-Seq. BMC Med Genomics 2023; 16:94. [PMID: 37138349 PMCID: PMC10157927 DOI: 10.1186/s12920-023-01512-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/08/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND The effects of Anabolic Androgenic Steroids (AAS) are largely illustrated through Androgen Receptor induced gene transcription, yet RNA-Seq has yet to be conducted on human whole blood and skeletal muscle. Investigating the transcriptional signature of AAS in blood may aid AAS detection and in muscle further understanding of AAS induced hypertrophy. METHODS Males aged 20-42 were recruited and sampled once: sedentary controls (C), resistance trained lifters (RT) and resistance trained current AAS users (RT-AS) who ceased exposure ≤ 2 or ≥ 10 weeks prior to sampling. RT-AS were sampled twice as Returning Participants (RP) if AAS usage ceased for ≥ 18 weeks. RNA was extracted from whole blood and trapezius muscle samples. RNA libraries were sequenced twice, for validation purposes, on the DNBSEQ-G400RS with either standard or CoolMPS PE100 reagents following MGI protocols. Genes were considered differentially expressed with FDR < 0.05 and a 1.2- fold change. RESULTS Cross-comparison of both standard reagent whole blood (N = 55: C = 7, RT = 20, RT-AS ≤ 2 = 14, RT-AS ≥ 10 = 10, RP = 4; N = 46: C = 6, RT = 17, RT-AS ≤ 2 = 12, RT-AS ≥ 10 = 8, RP = 3) sequencing datasets, showed that no genes or gene sets/pathways were differentially expressed between time points for RP or between group comparisons of RT-AS ≤ 2 vs. C, RT, or RT-AS ≥ 10. Cross-comparison of both muscle (N = 51, C = 5, RT = 17, RT-AS ≤ 2 = 15, RT-AS ≥ 10 = 11, RP = 3) sequencing (one standard & one CoolMPS reagent) datasets, showed one gene, CHRDL1, which has atrophying potential, was upregulated in RP visit two. In both muscle sequencing datasets, nine differentially expressed genes, overlapped with RT-AS ≤ 2 vs. RT and RT-AS ≤ 2 vs. C, but were not differentially expressed with RT vs. C, possibly suggesting they are from acute doping alone. No genes seemed to be differentially expressed in muscle after the long-term cessation of AAS, whereas a previous study found long term proteomic changes. CONCLUSION A whole blood transcriptional signature of AAS doping was not identified. However, RNA-Seq of muscle has identified numerous differentially expressed genes with known impacts on hypertrophic processes that may further our understanding on AAS induced hypertrophy. Differences in training regimens in participant groupings may have influenced results. Future studies should focus on longitudinal sampling pre, during and post-AAS exposure to better control for confounding variables.
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Affiliation(s)
- Alexander Kolliari-Turner
- School of Sport and Heath Sciences, University of Brighton Welkin House, 30 Carlisle Road, Eastbourne, BN20 7SN UK
- Centre for Stress and Age-Related Disease, University of Brighton, Brighton, UK
| | - Giscard Lima
- School of Sport and Heath Sciences, University of Brighton Welkin House, 30 Carlisle Road, Eastbourne, BN20 7SN UK
- Muscle Research, Murdoch Children’s Research Institute, Parkville, VIC Australia
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Rome, Italy
| | - Guan Wang
- School of Sport and Heath Sciences, University of Brighton Welkin House, 30 Carlisle Road, Eastbourne, BN20 7SN UK
- Centre for Regenerative Medicine and Devices, University of Brighton, Brighton, UK
| | - Fernanda Rossell Malinsky
- School of Sport and Heath Sciences, University of Brighton Welkin House, 30 Carlisle Road, Eastbourne, BN20 7SN UK
| | - Antonia Karanikolou
- School of Sport and Heath Sciences, University of Brighton Welkin House, 30 Carlisle Road, Eastbourne, BN20 7SN UK
| | - Gregor Eichhorn
- School of Sport and Heath Sciences, University of Brighton Welkin House, 30 Carlisle Road, Eastbourne, BN20 7SN UK
- Environmental Extremes Laboratory, University of Brighton, Eastbourne, UK
| | - Kumpei Tanisawa
- Faculty of Sport Sciences, Waseda University, Tokorozawa, Japan
| | | | - Blair Hamilton
- School of Sport and Heath Sciences, University of Brighton Welkin House, 30 Carlisle Road, Eastbourne, BN20 7SN UK
- Centre for Stress and Age-Related Disease, University of Brighton, Brighton, UK
- The Gender Identity Clinic, Tavistock and Portman NHS Foundation Trust, London, UK
| | - Paulette Y.O. Kumi
- Centre for Sports and Exercise Medicine, William Harvey Research Institute, Queen Mary University of London, London, UK
| | | | - Vasileios Skiadas
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Richard Twycross-Lewis
- School of Engineering and Materials Science, Queen Mary University of London, London, UK
- St Mary’s University, Twickenham, London, UK
| | - Liam Kilduff
- Applied Sports, Technology, Exercise, and Medicine Research Centre (A-STEM), Faculty of Science and Engineering, Swansea University, Swansea, Wales
| | - Renan Paulo Martin
- Department of Biophysics, Federal University of Sao Paulo, Sao Paulo, Brazil
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Garrett I. Ash
- Veterans Affairs Connecticut Healthcare System, West Haven, CT USA
- Center for Medical Informatics, Yale University, New Haven, CT USA
| | | | - Fergus M. Guppy
- Centre for Stress and Age-Related Disease, University of Brighton, Brighton, UK
- Institute for Life and Earth Sciences, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Edinburgh, UK
| | - Jane T. Seto
- Muscle Research, Murdoch Children’s Research Institute, Parkville, VIC Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Chiara Fossati
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Rome, Italy
| | - Fabio Pigozzi
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Rome, Italy
| | - Paolo Borrione
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Rome, Italy
| | - Yannis Pitsiladis
- School of Sport and Heath Sciences, University of Brighton Welkin House, 30 Carlisle Road, Eastbourne, BN20 7SN UK
- Centre for Stress and Age-Related Disease, University of Brighton, Brighton, UK
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Kern F, Kuhn T, Ludwig N, Simon M, Gröger L, Fabis N, Aparicio-Puerta E, Salhab A, Fehlmann T, Hahn O, Engel A, Wagner V, Koch M, Winek K, Soreq H, Nazarenko I, Fuhrmann G, Wyss-Coray T, Meese E, Keller V, Laschke MW, Keller A. Ageing-associated small RNA cargo of extracellular vesicles. RNA Biol 2023; 20:482-494. [PMID: 37498213 PMCID: PMC10376918 DOI: 10.1080/15476286.2023.2234713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 07/28/2023] Open
Abstract
Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.
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Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Department for Clinical Bioinformatics, Saarbrücken, Germany
| | - Thomas Kuhn
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Biogenic Nanotherapeutics Group (BION), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
- Center for Human and Molecular Biology, Saarland University, Homburg, Germany
| | - Martin Simon
- Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
| | - Laura Gröger
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Natalie Fabis
- Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany
| | - Ernesto Aparicio-Puerta
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Abdulrahman Salhab
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
| | - Annika Engel
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Viktoria Wagner
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Marcus Koch
- INM - Leibniz Institute for New Materials, Saarbrücken, Germany
| | - Katarzyna Winek
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hermona Soreq
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Irina Nazarenko
- Faculty of Medicine, Institute for Infection Prevention and Control; Medical Center - University of Freiburg, Freiburg, Germany
| | - Gregor Fuhrmann
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Biogenic Nanotherapeutics Group (BION), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Verena Keller
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
| | - Matthias W Laschke
- Institute for Clinical and Experimental Surgery, Saarland University, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz-Centre for Infection Research (HZI), Department for Clinical Bioinformatics, Saarbrücken, Germany
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
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Keller A, Gröger L, Tschernig T, Solomon J, Laham O, Schaum N, Wagner V, Kern F, Schmartz GP, Li Y, Borcherding A, Meier C, Wyss-Coray T, Meese E, Fehlmann T, Ludwig N. miRNATissueAtlas2: an update to the human miRNA tissue atlas. Nucleic Acids Res 2021; 50:D211-D221. [PMID: 34570238 PMCID: PMC8728130 DOI: 10.1093/nar/gkab808] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/26/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Small non-coding RNAs (sncRNAs) are pervasive regulators of physiological and pathological processes. We previously developed the human miRNA Tissue Atlas, detailing the expression of miRNAs across organs in the human body. Here, we present an updated resource containing sequencing data of 188 tissue samples comprising 21 organ types retrieved from six humans. Sampling the organs from the same bodies minimizes intra-individual variability and facilitates the making of a precise high-resolution body map of the non-coding transcriptome. The data allow shedding light on the organ- and organ system-specificity of piwi-interacting RNAs (piRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs) and other non-coding RNAs. As use case of our resource, we describe the identification of highly specific ncRNAs in different organs. The update also contains 58 samples from six tissues of the Tabula Muris collection, allowing to check if the tissue specificity is evolutionary conserved between Homo sapiens and Mus musculus. The updated resource of 87 252 non-coding RNAs from nine non-coding RNA classes for all organs and organ systems is available online without any restrictions (https://www.ccb.uni-saarland.de/tissueatlas2).
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Affiliation(s)
- Andreas Keller
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurobiology, Stanford University, CA 94305, USA
| | - Laura Gröger
- Center for Human and Molecular Biology, Junior Research Group Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Thomas Tschernig
- Institute for Anatomy, Saarland University, 66421 Homburg, Germany
| | - Jeffrey Solomon
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Omar Laham
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nicholas Schaum
- Department of Neurology and Neurobiology, Stanford University, CA 94305, USA
| | - Viktoria Wagner
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Georges Pierre Schmartz
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Yongping Li
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Carola Meier
- Institute for Anatomy, Saarland University, 66421 Homburg, Germany
| | - Tony Wyss-Coray
- Department of Neurology and Neurobiology, Stanford University, CA 94305, USA
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Center for Human and Molecular Biology, Junior Research Group Human Genetics, Saarland University, 66421 Homburg, Germany
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Fehlmann T, Kern F, Laham O, Backes C, Solomon J, Hirsch P, Volz C, Müller R, Keller A. miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale. Nucleic Acids Res 2021; 49:W397-W408. [PMID: 33872372 PMCID: PMC8262700 DOI: 10.1093/nar/gkab268] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 01/19/2023] Open
Abstract
Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Omar Laham
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jeffrey Solomon
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Pascal Hirsch
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Carsten Volz
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
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