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Machine learning phenomics (MLP) combining deep learning with time-lapse-microscopy for monitoring colorectal adenocarcinoma cells gene expression and drug-response. Sci Rep 2022; 12:8545. [PMID: 35595808 PMCID: PMC9123013 DOI: 10.1038/s41598-022-12364-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 01/31/2022] [Indexed: 11/25/2022] Open
Abstract
High-throughput phenotyping is becoming increasingly available thanks to analytical and bioinformatics approaches that enable the use of very high-dimensional data and to the availability of dynamic models that link phenomena across levels: from genes to cells, from cells to organs, and through the whole organism. The combination of phenomics, deep learning, and machine learning represents a strong potential for the phenotypical investigation, leading the way to a more embracing approach, called machine learning phenomics (MLP). In particular, in this work we present a novel MLP platform for phenomics investigation of cancer-cells response to therapy, exploiting and combining the potential of time-lapse microscopy for cell behavior data acquisition and robust deep learning software architectures for the latent phenotypes extraction. A two-step proof of concepts is designed. First, we demonstrate a strict correlation among gene expression and cell phenotype with the aim to identify new biomarkers and targets for tailored therapy in human colorectal cancer onset and progression. Experiments were conducted on human colorectal adenocarcinoma cells (DLD-1) and their profile was compared with an isogenic line in which the expression of LOX-1 transcript was knocked down. In addition, we also evaluate the phenotypic impact of the administration of different doses of an antineoplastic drug over DLD-1 cells. Under the omics paradigm, proteomics results are used to confirm the findings of the experiments.
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2
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Kolenc Ž, Pirih N, Gretic P, Kunej T. Top Trends in Multiomics Research: Evaluation of 52 Published Studies and New Ways of Thinking Terminology and Visual Displays. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:681-692. [PMID: 34678084 DOI: 10.1089/omi.2021.0160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multiomics study designs have significantly increased understanding of complex biological systems. The multiomics literature is rapidly expanding and so is their heterogeneity. However, the intricacy and fragmentation of omics data are impeding further research. To examine current trends in multiomics field, we reviewed 52 articles from PubMed and Web of Science, which used an integrated omics approach, published between March 2006 and January 2021. From studies, data regarding investigated loci, species, omics type, and phenotype were extracted, curated, and streamlined according to standardized terminology, and summarized in a previously developed graphical summary. Evaluated studies included 21 omics types or applications of omics technology such as genomics, transcriptomics, metabolomics, epigenomics, environmental omics, and pharmacogenomics, species of various phyla including human, mouse, Arabidopsis thaliana, Saccharomyces cerevisiae, and various phenotypes, including cancer and COVID-19. In the analyzed studies, diverse methods, protocols, results, and terminology were used and accordingly, assessment of the studies was challenging. Adoption of standardized multiomics data presentation in the future will further buttress standardization of terminology and reporting of results in systems science. This shall catalyze, we suggest, innovation in both science communication and laboratory medicine by making available scientific knowledge that is easier to grasp, share, and harness toward medical breakthroughs.
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Affiliation(s)
- Živa Kolenc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Pirih
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Petra Gretic
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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3
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Chaby LE, Lasseter HC, Contrepois K, Salek RM, Turck CW, Thompson A, Vaughan T, Haas M, Jeromin A. Cross-Platform Evaluation of Commercially Targeted and Untargeted Metabolomics Approaches to Optimize the Investigation of Psychiatric Disease. Metabolites 2021; 11:609. [PMID: 34564425 PMCID: PMC8466258 DOI: 10.3390/metabo11090609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Metabolomics methods often encounter trade-offs between quantification accuracy and coverage, with truly comprehensive coverage only attainable through a multitude of complementary assays. Due to the lack of standardization and the variety of metabolomics assays, it is difficult to integrate datasets across studies or assays. To inform metabolomics platform selection, with a focus on posttraumatic stress disorder (PTSD), we review platform use and sample sizes in psychiatric metabolomics studies and then evaluate five prominent metabolomics platforms for coverage and performance, including intra-/inter-assay precision, accuracy, and linearity. We found performance was variable between metabolite classes, but comparable across targeted and untargeted approaches. Within all platforms, precision and accuracy were highly variable across classes, ranging from 0.9-63.2% (coefficient of variation) and 0.6-99.1% for accuracy to reference plasma. Several classes had high inter-assay variance, potentially impeding dissociation of a biological signal, including glycerophospholipids, organooxygen compounds, and fatty acids. Coverage was platform-specific and ranged from 16-70% of PTSD-associated metabolites. Non-overlapping coverage is challenging; however, benefits of applying multiple metabolomics technologies must be weighed against cost, biospecimen availability, platform-specific normative levels, and challenges in merging datasets. Our findings and open-access cross-platform dataset can inform platform selection and dataset integration based on platform-specific coverage breadth/overlap and metabolite-specific performance.
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Affiliation(s)
- Lauren E. Chaby
- Cohen Veterans Bioscience, New York, NY 10018, USA; (L.E.C.); (H.C.L.); (A.T.); (T.V.); (M.H.)
| | - Heather C. Lasseter
- Cohen Veterans Bioscience, New York, NY 10018, USA; (L.E.C.); (H.C.L.); (A.T.); (T.V.); (M.H.)
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Reza M. Salek
- International Agency for Research on Cancer, Nutrition and Metabolism Branch, World Health Organisation, 150 Cours Albert Thomas, CEDEX 08, 69372 Lyon, France;
| | - Christoph W. Turck
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, 80804 Munich, Germany;
| | - Andrew Thompson
- Cohen Veterans Bioscience, New York, NY 10018, USA; (L.E.C.); (H.C.L.); (A.T.); (T.V.); (M.H.)
| | - Timothy Vaughan
- Cohen Veterans Bioscience, New York, NY 10018, USA; (L.E.C.); (H.C.L.); (A.T.); (T.V.); (M.H.)
| | - Magali Haas
- Cohen Veterans Bioscience, New York, NY 10018, USA; (L.E.C.); (H.C.L.); (A.T.); (T.V.); (M.H.)
| | - Andreas Jeromin
- Cohen Veterans Bioscience, New York, NY 10018, USA; (L.E.C.); (H.C.L.); (A.T.); (T.V.); (M.H.)
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4
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Braddock M. From Target Identification to Drug Development in Space: Using the Microgravity Assist. Curr Drug Discov Technol 2021; 17:45-56. [PMID: 30648510 DOI: 10.2174/1570163816666190112150014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/21/2018] [Accepted: 12/28/2018] [Indexed: 12/19/2022]
Abstract
The unique nature of microgravity encountered in space provides an opportunity for drug discovery and development that cannot be replicated on Earth. From the production of superior protein crystals to the identification and validation of new drug targets to microarray analyses of transcripts attenuated by microgravity, there are numerous examples which demonstrate the benefit of exploiting the space environment. Moreover, studies conducted on Space Shuttle missions, the International Space Station and other craft have had a direct benefit for drug development programmes such as those directed against reducing bone and muscle loss or increasing bone formation. This review will highlight advances made in both drug discovery and development and offer some future insight into how drug discovery and associated technologies may be further advanced using the microgravity assist.
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Affiliation(s)
- Martin Braddock
- Sherwood Observatory, Mansfield and Sutton Astronomical Society, Coxmoor Road, Sutton-in-Ashfield, Nottinghamshire, NG17 5LF, United Kingdom
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5
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Goswami S, Flores J, Balasubramanian I, Bandyopadhyay S, Joseph I, Bianchi-Smak J, Dhawan P, Mücahit DM, Yu S, Christakos S, Gao N. 1,25-Dihydroxyvitamin D 3 and dietary vitamin D reduce inflammation in mice lacking intestinal epithelial cell Rab11a. J Cell Physiol 2021; 236:8148-8159. [PMID: 34192357 PMCID: PMC9161497 DOI: 10.1002/jcp.30486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/18/2021] [Accepted: 06/15/2021] [Indexed: 12/23/2022]
Abstract
A number of studies have examined the effects of 1,25-dihydroxyvitamin D3 (1,25(OH)2 D3 ) on intestinal inflammation driven by immune cells, while little information is currently available about its impact on inflammation caused by intestinal epithelial cell (IEC) defects. Mice lacking IEC-specific Rab11a a recycling endosome small GTPase resulted in increased epithelial cell production of inflammatory cytokines, notably IL-6 and early onset of enteritis. To determine whether vitamin D supplementation may benefit hosts with epithelial cell-originated mucosal inflammation, we evaluated in vivo effects of injected 1,25(OH)2 D3 or dietary supplement of a high dose of vitamin D on the gut phenotypes of IEC-specific Rab11a knockout mice (Rab11aΔIEC ). 1,25(OH)2 D3 administered at 25 ng, two doses per mouse, by intraperitoneal injection, reduced inflammatory cytokine production in knockout mice compared to vehicle-injected mice. Remarkably, feeding mice with dietary vitamin D supplementation at 20,000 IU/kg spanning fetal and postnatal developmental stages led to improved bodyweights, reduced immune cell infiltration, and decreased inflammatory cytokines. We found that these vitamin D effects were accompanied by decreased NF-κB (p65) in the knockout intestinal epithelia, reduced tissue-resident macrophages, and partial restoration of epithelial morphology. Our study suggests that dietary vitamin D supplementation may prevent and limit intestinal inflammation in hosts with high susceptibility to chronic inflammation.
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Affiliation(s)
- Sayantani Goswami
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Juan Flores
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Iyshwarya Balasubramanian
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Sheila Bandyopadhyay
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Ivor Joseph
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Jared Bianchi-Smak
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Puneet Dhawan
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
| | - Derya M Mücahit
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Shiyan Yu
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
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6
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Carriot N, Paix B, Greff S, Viguier B, Briand JF, Culioli G. Integration of LC/MS-based molecular networking and classical phytochemical approach allows in-depth annotation of the metabolome of non-model organisms - The case study of the brown seaweed Taonia atomaria. Talanta 2020; 225:121925. [PMID: 33592802 DOI: 10.1016/j.talanta.2020.121925] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/15/2022]
Abstract
Untargeted LC-MS based metabolomics is a useful approach in many research areas such as medicine, systems biology, environmental sciences or even ecology. In such an approach, annotation of metabolomes of non-model organisms remains a significant challenge. In this study, an analytical workflow combining a classical phytochemical approach, using the isolation and the full characterization of the chemical structure of natural products, together with the use of MS/MS-based molecular networking with various levels of restrictiveness was developed. This protocol was applied to the marine brown seaweed Taonia atomaria, a cosmopolitan algal species, and allowed to annotate more than 200 metabolites. First, the algal organic crude extracts were fractionated by flash-chromatography and the chemical structure of eight of the main chemical constituents of this alga were fully characterized by means of spectroscopic methods (1D and 2D NMR, HRMS). These compounds were further used as chemical standards. In a second step, the main fractions of the algal extracts were analyzed by UHPLC-MS/MS and the resulting data were uploaded to the Global Natural Products Social Molecular Networking platform (GNPS) to create several molecular networks (MNs). A first MN (MN-1) was built with restrictive parameters and allowed the creation of clusters composed by nodes with highly similar MS/MS spectra. Then, using database hits and chemical standards as "seed" nodes and/or similarity between MS/MS fragmentation pattern, the main clusters were easily annotated as common glycerolipids and phospholipids, much rare lipids -such as acylglycerylhydroxymethyl-N,N,N-trimethyl-ß-alanines or fulvellic acid derivatives- but also new glycerolipids bearing a terpene moiety. Lastly, the use of less and less constrained MNs allowed to further increase the number of annotated metabolites.
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Affiliation(s)
| | - Benoît Paix
- Université de Toulon, MAPIEM, Toulon, EA 4323, France
| | - Stéphane Greff
- Aix Marseille Université, CNRS, IRD, Avignon Université, Institut Méditerranéen de Biodiversité et d'Ecologie Marine et Continentale (IMBE), Station Marine d'Endoume, Marseille, France
| | - Bruno Viguier
- Université de Toulon, MAPIEM, Toulon, EA 4323, France
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7
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Wang Y, Wang Y, Qian J, Pan X, Li X, Chen F, Hu J, Lü J. Single-cell infrared phenomics: phenotypic screening with infrared microspectroscopy. Chem Commun (Camb) 2020; 56:13237-13240. [PMID: 33030170 DOI: 10.1039/d0cc05721e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We conceptually demonstrate single-cell infrared phenomics as a novel strategy of phenotypic screening with infrared microspectroscopy. Based on this development, the cancer cell HepG2 glycocalyx was first identified as a potential target of protopanaxadiol, an herbal medicine. These findings provide a powerful tool to accurately evaluate the cell stress response and to largely expand the phenotypic screening toolkit for drug discovery.
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Affiliation(s)
- Yadi Wang
- College of Pharmacy, Binzhou Medical University, Yantai 264003, China
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8
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Liessi N, Pedemonte N, Armirotti A, Braccia C. Proteomics and Metabolomics for Cystic Fibrosis Research. Int J Mol Sci 2020; 21:ijms21155439. [PMID: 32751630 PMCID: PMC7432297 DOI: 10.3390/ijms21155439] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/18/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
The aim of this review article is to introduce the reader to the state-of-the-art of the contribution that proteomics and metabolomics sciences are currently providing for cystic fibrosis (CF) research: from the understanding of cystic fibrosis transmembrane conductance regulator (CFTR) biology to biomarker discovery for CF diagnosis. Our work particularly focuses on CFTR post-translational modifications and their role in cellular trafficking as well as on studies that allowed the identification of CFTR molecular interactors. We also show how metabolomics is currently helping biomarker discovery in CF. The most recent advances in these fields are covered by this review, as well as some considerations on possible future scenarios for new applications.
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Affiliation(s)
- Nara Liessi
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
| | - Nicoletta Pedemonte
- U.O.C. Genetica Medica, IRCCS Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy;
| | - Andrea Armirotti
- Analytical Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
- Correspondence: ; Tel.: +39-010-2896-938
| | - Clarissa Braccia
- D3PharmaChemistry, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
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9
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Liu AC, Patel K, Vunikili RD, Johnson KW, Abdu F, Belman SK, Glicksberg BS, Tandale P, Fontanez R, Mathew OK, Kasarskis A, Mukherjee P, Subramanian L, Dudley JT, Shameer K. Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses. Brief Bioinform 2020; 21:1182-1195. [PMID: 31190075 PMCID: PMC8179509 DOI: 10.1093/bib/bbz059] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 04/04/2019] [Accepted: 04/18/2019] [Indexed: 12/26/2022] Open
Abstract
Sepsis is a series of clinical syndromes caused by the immunological response to infection. The clinical evidence for sepsis could typically attribute to bacterial infection or bacterial endotoxins, but infections due to viruses, fungi or parasites could also lead to sepsis. Regardless of the etiology, rapid clinical deterioration, prolonged stay in intensive care units and high risk for mortality correlate with the incidence of sepsis. Despite its prevalence and morbidity, improvement in sepsis outcomes has remained limited. In this comprehensive review, we summarize the current landscape of risk estimation, diagnosis, treatment and prognosis strategies in the setting of sepsis and discuss future challenges. We argue that the advent of modern technologies such as in-depth molecular profiling, biomedical big data and machine intelligence methods will augment the treatment and prevention of sepsis. The volume, variety, veracity and velocity of heterogeneous data generated as part of healthcare delivery and recent advances in biotechnology-driven therapeutics and companion diagnostics may provide a new wave of approaches to identify the most at-risk sepsis patients and reduce the symptom burden in patients within shorter turnaround times. Developing novel therapies by leveraging modern drug discovery strategies including computational drug repositioning, cell and gene-therapy, clustered regularly interspaced short palindromic repeats -based genetic editing systems, immunotherapy, microbiome restoration, nanomaterial-based therapy and phage therapy may help to develop treatments to target sepsis. We also provide empirical evidence for potential new sepsis targets including FER and STARD3NL. Implementing data-driven methods that use real-time collection and analysis of clinical variables to trace, track and treat sepsis-related adverse outcomes will be key. Understanding the root and route of sepsis and its comorbid conditions that complicate treatment outcomes and lead to organ dysfunction may help to facilitate identification of most at-risk patients and prevent further deterioration. To conclude, leveraging the advances in precision medicine, biomedical data science and translational bioinformatics approaches may help to develop better strategies to diagnose and treat sepsis in the next decade.
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Affiliation(s)
- Andrew C Liu
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Donald and Barbara School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, USA
| | - Krishna Patel
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Donald and Barbara School of Medicine at Hofstra/Northwell, Northwell Health, Hempstead, NY, USA
| | - Ramya Dhatri Vunikili
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Kipp W Johnson
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
| | - Fahad Abdu
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Stonybrook University, 100 Nicolls Rd, Stony Brook, NY, USA
| | - Shivani Kamath Belman
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Benjamin S Glicksberg
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Pratyush Tandale
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- School of Biotechnology and Bioinformatics, D Y Patil University, Navi Mumbai, India
| | - Roberto Fontanez
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
| | | | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
| | | | | | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Mount Sinai Health System, New York, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
| | - Khader Shameer
- Department of Information Services, Northwell Health, New Hyde Park, NY, USA
- Center for Research Informatics and Innovation, Northwell Health, New Hyde Park, NY, USA
- Institute for Next Generation Healthcare, Mount Sinai Health System, New York, NY, USA
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10
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Brocker CN, Velenosi T, Flaten HK, McWilliams G, McDaniel K, Shelton SK, Saben J, Krausz KW, Gonzalez FJ, Monte AA. Metabolomic profiling of metoprolol hypertension treatment reveals altered gut microbiota-derived urinary metabolites. Hum Genomics 2020; 14:10. [PMID: 32160915 PMCID: PMC7066769 DOI: 10.1186/s40246-020-00260-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/28/2020] [Indexed: 11/17/2022] Open
Abstract
Introduction Metoprolol succinate is a long-acting beta-blocker prescribed for the management of hypertension (HTN) and other cardiovascular diseases. Metabolomics, the study of end-stage metabolites of upstream biologic processes, yield insight into mechanisms of drug effectiveness and safety. Our aim was to determine metabolomic profiles associated with metoprolol effectiveness for the treatment of hypertension. Methods We performed a prospective pragmatic trial (NCT02293096) that enrolled patients between 30 and 80 years with uncontrolled HTN. Patients were started on metoprolol succinate at a dose based upon systolic blood pressure (SBP). Urine and blood pressure measurements were collected weekly. Individuals with a 10% decline in SBP or heart rate (HR) were considered responsive. Genotype for the CYP2D6 enzyme, the primary metabolic pathway for metoprolol, was evaluated for each subject. Unbiased metabolomic analyses were performed on urine samples using UPLC-QTOF mass spectrometry. Results Urinary metoprolol metabolite ratios are indicative of patient CYP2D6 genotypes. Patients taking metoprolol had significantly higher urinary levels of many gut microbiota-dependent metabolites including hydroxyhippuric acid, hippuric acid, and methyluric acid. Urinary metoprolol metabolite profiles of normal metabolizer (NM) patients more closely correlate to ultra-rapid metabolizer (UM) patients than NM patients. Metabolites did not predict either 10% SBP or HR decline. Conclusion In summary, urinary metabolites predict CYP2D6 genotype in hypertensive patients taking metoprolol. Metoprolol succinate therapy affects the microbiome-derived metabolites.
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Affiliation(s)
- Chad N Brocker
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Velenosi
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hania K Flaten
- Department of Emergency Medicine & Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Glenn McWilliams
- Department of Emergency Medicine & Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kyle McDaniel
- Department of Emergency Medicine & Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shelby K Shelton
- Department of Emergency Medicine & Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jessica Saben
- Department of Emergency Medicine & Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kristopher W Krausz
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Frank J Gonzalez
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew A Monte
- Department of Emergency Medicine & Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA. .,Rocky Mountain Poison & Drug Center, Denver Health and Hospital Authority, Denver, CO, USA. .,Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, 12401 E 17th Ave, Aurora, CO, 80045, USA.
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11
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Fioranelli M, Sepehri A, Roccia MG, Linda C, Rossi C, Dawodo A, Vojvodic P, Lotti J, Barygina V, Vojvodic A, Wollina U, Tirant M, Van TN, Lotti T. Clinical Applications of System Regulation Medicine. Open Access Maced J Med Sci 2019; 7:3053-3060. [PMID: 31850122 PMCID: PMC6910802 DOI: 10.3889/oamjms.2019.775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 12/04/2022] Open
Abstract
Increasing incidence and poor outcome of chronic non-communicable diseases in western population would require a paradigm shift in the treatments. Guidelines-based medical approaches continue to be the standard rule in clinical practice, although only less than 15% of them are based on high-quality research. For each person who benefits from the 10 best-selling drugs in the USA, a number between 4 and 25 has no one beneficial effect. The reductionist linear medicine method does not offer solutions in the non-manifest preclinical stage of the disease when it would still be possible to reverse the pathological progression and the axiom “a drug, a target, a symptom” are still inconclusive. Needs additional tools to address these challenges. System Medicine considers the disease as a dysregulation of the biological networks that changes throughout the evolution of the pathological process and with the comorbidities development. The strength of the networks indicates their ability to withstand dysregulations during the perturbation phases, returning to the state of stability. The treatment of dysregulated networks before the symptomatological manifestation emerges offers the possibility of treating and preventing pathologies in the preclinical phase and potentially reversing the pathological process, stopping it or preventing comorbidities. Furthermore, treating shared networks instead of individual phenotypic symptoms can reduce drug use, offering a solution to the problem of ineffective drug use.
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Affiliation(s)
- Massimo Fioranelli
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Alireza Sepehri
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Maria Grazia Roccia
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Cota Linda
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Chiara Rossi
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Amos Dawodo
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Petar Vojvodic
- Clinic for Psychiatric Disorders "Dr. Laza Lazarevic", Belgrade, Serbia
| | - Jacopo Lotti
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Victoria Barygina
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Aleksandra Vojvodic
- Department of Dermatology and Venereology, Military Medical Academy, Belgrade, Serbia
| | - Uwe Wollina
- Department of Dermatology and Allergology, Städtisches Klinikum Dresden, Dresden, Germany
| | | | - Thuong Nguyen Van
- Vietnam National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - Torello Lotti
- Department of Dermatology, University of G. Marconi, Rome, Italy
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12
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Katsila T, Balasopoulou A, Tsagaraki I, Patrinos GP. Pharmacomicrobiomics informs clinical pharmacogenomics. Pharmacogenomics 2019; 20:731-739. [PMID: 31368841 DOI: 10.2217/pgs-2019-0027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: Microbiota-host-xenobiotics interactions in humans become of prime interest when clinical pharmacogenomics is to be implemented. Despite the advent of technology, information still needs to be translated into knowledge for optimum patient stratification and disease management. Material & methods: Herein, we mined metagenomic, pharmacometagenomic and pharmacomicrobiomic datasets to map microbiota-host-drugs networks. Results: Datasets were multifaceted and voluminous. Interoperability, data sparsity and scarcity remain a challenge. Mapping microbiota-host-drugs networks allowed the prediction of drug response/toxicity and modulation of the microbiota-host-drugs interplay. Conclusion: Our approach triangulated microbiota, host and drug networks revealing the need for contextual data and open science via microattribution to accelerate knowledge growth. Our findings may serve as a data storehouse for a user-friendly query system, coupled with databanks and databases.
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Affiliation(s)
- Theodora Katsila
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece.,Institute of Chemical Biology, National Hellenic Research Centre, Athens, Greece
| | - Angeliki Balasopoulou
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
| | - Ioanna Tsagaraki
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece
| | - George P Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras, Greece.,Department of Pathology, College of Medicine & Health Sciences, Al Ain, United Arab Emirates.,Zayed Center of Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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13
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Nguyen A, Moussallieh FM, Mackay A, Cicek AE, Coca A, Chenard MP, Weingertner N, Lhermitte B, Letouzé E, Guérin E, Pencreach E, Jannier S, Guenot D, Namer IJ, Jones C, Entz-Werlé N. Characterization of the transcriptional and metabolic responses of pediatric high grade gliomas to mTOR-HIF-1α axis inhibition. Oncotarget 2017; 8:71597-71617. [PMID: 29069732 PMCID: PMC5641075 DOI: 10.18632/oncotarget.16500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 01/16/2017] [Indexed: 12/12/2022] Open
Abstract
Pediatric high grade glioma (pHGGs), including sus-tentorial and diffuse intrinsic pontine gliomas, are known to have a very dismal prognosis. For instance, even an increased knowledge on molecular biology driving this brain tumor entity, there is no treatment able to cure those patients. Therefore, we were focusing on a translational pathway able to increase the cell resistance to treatment and to reprogram metabolically tumor cells, which are, then, adapting easily to a hypoxic microenvironment. To establish, the crucial role of the hypoxic pathways in pHGGs, we, first, assessed their protein and transcriptomic deregulations in a pediatric cohort of pHGGs and in pHGG's cell lines, cultured in both normoxic and hypoxic conditions. Secondly, based on the concept of a bi-therapy targeting in pHGGs mTORC1 (rapamycin) and HIF-1α (irinotecan), we hypothesized that the balanced expressions between RAS/ERK, PI3K/AKT and HIF-1α/HIF-2α/MYC proteins or genes may provide a modulation of the cell response to this double targeting. Finally, we could evidence three protein, genomic and metabolomic profiles of response to rapamycin combined with irinotecan. The pattern of highly sensitive cells to mTOR/HIF-1α targeting was linked to a MYC/ERK/HIF-1α over-expression and the cell resistance to a major hyper-expression of HIF-2α.
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Affiliation(s)
- Aurélia Nguyen
- Laboratory EA 3430, Progression Tumorale et Micro-Environnement, Approches Translationnelles et Epidémiologie, University of Strasbourg, Strasbourg, France
| | | | - Alan Mackay
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - A Ercument Cicek
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.,Computer Engineering Department, Bilkent University, Cankaya, Ankara, Turkey
| | - Andres Coca
- Department of Neurosurgery, University Hospital of Strasbourg, Strasbourg, France
| | - Marie Pierre Chenard
- Department of Pathology, University Hospital of Strasbourg, Strasbourg, France.,Centre de Ressources Biologiques, University Hospital of Strasbourg, Strasbourg, France
| | - Noelle Weingertner
- Department of Pathology, University Hospital of Strasbourg, Strasbourg, France
| | - Benoit Lhermitte
- Department of Pathology, University Hospital of Strasbourg, Strasbourg, France
| | - Eric Letouzé
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer, Paris, France
| | - Eric Guérin
- Laboratory EA 3430, Progression Tumorale et Micro-Environnement, Approches Translationnelles et Epidémiologie, University of Strasbourg, Strasbourg, France
| | - Erwan Pencreach
- Laboratory EA 3430, Progression Tumorale et Micro-Environnement, Approches Translationnelles et Epidémiologie, University of Strasbourg, Strasbourg, France
| | - Sarah Jannier
- Laboratory EA 3430, Progression Tumorale et Micro-Environnement, Approches Translationnelles et Epidémiologie, University of Strasbourg, Strasbourg, France.,Department of Pediatric Onco-hematology, University Hospital of Strasbourg, Strasbourg, France
| | - Dominique Guenot
- Laboratory EA 3430, Progression Tumorale et Micro-Environnement, Approches Translationnelles et Epidémiologie, University of Strasbourg, Strasbourg, France
| | - Izzie Jacques Namer
- Department of Nuclear Medicine, University Hospital of Strasbourg, Strasbourg, France
| | - Chris Jones
- Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Natacha Entz-Werlé
- Laboratory EA 3430, Progression Tumorale et Micro-Environnement, Approches Translationnelles et Epidémiologie, University of Strasbourg, Strasbourg, France.,Department of Pediatric Onco-hematology, University Hospital of Strasbourg, Strasbourg, France
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14
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The Use of Omic Technologies Applied to Traditional Chinese Medicine Research. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:6359730. [PMID: 28250795 PMCID: PMC5307000 DOI: 10.1155/2017/6359730] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 12/28/2022]
Abstract
Natural products represent one of the most important reservoirs of structural and chemical diversity for the generation of leads in the drug development process. A growing number of researchers have shown interest in the development of drugs based on Chinese herbs. In this review, the use and potential of omic technologies as powerful tools in the modernization of traditional Chinese medicine are discussed. The analytical combination from each omic approach is crucial for understanding the working mechanisms of cells, tissues, organs, and organisms as well as the mechanisms of disease. Gradually, omic approaches have been introduced in every stage of the drug development process to generate high-quality Chinese medicine-based drugs. Finally, the future picture of the use of omic technologies is a promising tool and arena for further improvement in the modernization of traditional Chinese medicine.
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15
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Rodrigues KT, Cieslarová Z, Tavares MFM, Simionato AVC. Strategies Involving Mass Spectrometry Combined with Capillary Electrophoresis in Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:99-141. [DOI: 10.1007/978-3-319-47656-8_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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16
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Maslov D, Balashova E, Lokhov P, Archakov A. Pharmacometabonomics – the novel way to personalized drug therapy. ACTA ACUST UNITED AC 2017; 63:115-123. [DOI: 10.18097/pbmc20176302115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review is devoted to pharmacometabonomics - a new branch of science focused on personalization of drug therapy through the comprehensive analysis of metabolites of patient's biological fluids. It considers the history of pharmacometabonomic, positioning to other “-omic” sciences, and system approach, realized by this science, in determination of individual therapeutic dose of the drugs and also a technical implementation of pharmacometabonomic based on direct mass spectrometry of blood plasma metabolites. Special attention is paid to a comparative analysis of pharmacometabonomics and other main approaches to personalized therapy in the clinic, such as pharmacogenetics and therapeutic drug monitoring. Finally, prospects of pharmacometabonomics applications in clinical practice were also discussed.
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Affiliation(s)
- D.L. Maslov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - P.G. Lokhov
- Institute of Biomedical Chemistry, Moscow, Russia
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17
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Abstract
Precision medicine is an emerging approach for prevention and treatment of diseases considering individuals’ uniqueness. Omics provide one step forward toward advanced precision medicine and include technologies such as genomics, proteomics and metabolomics generating valuable data through characterization of entire biological systems. With the aid of omics, a major shift has been started to occur in understanding of diseases followed by potential fundamental changes in medical care strategies. This short review aims at providing some examples of current omics that are applied in the field of pain in terms of new biomarkers for diagnosis of different pain types, stratification of patients and new therapeutic targets. Implementation of omics would most likely offer breakthrough in the future of pain management.
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Affiliation(s)
- Parisa Gazerani
- Department of Health Science & Technology, Faculty of Medicine, Aalborg University, Frederik Bajers Vej 7A2-A2-208, 9220 Aalborg East, Denmark
| | - Hye Sook Han Vinterhøj
- Department of Health Science & Technology, Faculty of Medicine, Aalborg University, Frederik Bajers Vej 7A2-A2-208, 9220 Aalborg East, Denmark
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18
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Abstract
The exponential growth of the Internet of Things and the global popularity and remarkable decline in cost of the mobile phone is driving the digital transformation of medical practice. The rapidly maturing digital, non-medical world of mobile (wireless) devices, cloud computing and social networking is coalescing with the emerging digital medical world of omics data, biosensors and advanced imaging which offers the increasingly realistic prospect of personalized medicine. Described as a potential “seismic” shift from the current “healthcare” model to a “wellness” paradigm that is predictive, preventative, personalized and participatory, this change is based on the development of increasingly sophisticated biosensors which can track and measure key biochemical variables in people. Additional key drivers in this shift are metabolomic and proteomic signatures, which are increasingly being reported as pre-symptomatic, diagnostic and prognostic of toxicity and disease. These advancements also have profound implications for toxicological evaluation and safety assessment of pharmaceuticals and environmental chemicals. An approach based primarily on human in vivo and high-throughput in vitro human cell-line data is a distinct possibility. This would transform current chemical safety assessment practice which operates in a human “data poor” to a human “data rich” environment. This could also lead to a seismic shift from the current animal-based to an animal-free chemical safety assessment paradigm.
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Affiliation(s)
- George D Loizou
- Health Risks, Health and Safety Laboratory, Health and Safety Executive Buxton, UK
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19
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Ahuja NK, Nimgaonkar A. Precision Bariatrics: Toward a New Paradigm of Personalized Devices in Obesity Therapeutics. Obes Surg 2016; 26:1642-5. [PMID: 27067911 DOI: 10.1007/s11695-016-2180-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The prevalence and complexity of obesity and its associated metabolic complications highlight the importance of building a rigorous investigative framework for the development of novel weight loss therapies. Device-based interventions in particular constitute a market poised for rapid expansion in the coming years. Optimizing outcomes for this new class of therapies requires attention to an evolving taxonomy of subdivisions within the broader obesity phenotype and a means for stratifying patients toward maximally effective interventions. Extant bariatric devices implicitly prioritize anatomic variables as surrogates for physiology, a somewhat arbitrary assumption that merits empiric validation. Utilizing the governing principles of systems biology and recent innovations in clinical trial design, a robust and precise research infrastructure can and should be developed to more effectively mitigate this contemporary epidemic.
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Affiliation(s)
- Nitin K Ahuja
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Blalock Suite 412, Baltimore, MD, 21287, USA.
| | - Ashish Nimgaonkar
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, 1830 E. Monument Street, Suite 424, Baltimore, MD, 21205, USA.,Center for Bioengineering Innovation & Design, Johns Hopkins University, 3400 N. Charles Street, Clark Hall, Suite 200, Baltimore, MD, 21218, USA
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20
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Beebe K, Kennedy AD. Sharpening Precision Medicine by a Thorough Interrogation of Metabolic Individuality. Comput Struct Biotechnol J 2016; 14:97-105. [PMID: 26929792 PMCID: PMC4744241 DOI: 10.1016/j.csbj.2016.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/07/2016] [Accepted: 01/10/2016] [Indexed: 12/24/2022] Open
Abstract
Precision medicine is an active component of medical practice today, but aspirations are to both broaden its reach to a greater diversity of individuals and improve its “precision” by enhancing the ability to define even more disease states in combination with associated treatments. Given complexity of human phenotypes, much work is required. In this review, we deconstruct this challenge at a high level to define what is needed to move closer toward these aspirations. In the context of the variables that influence the diverse array of phenotypes across human health and disease – genetics, epigenetics, environmental influences, and the microbiome – we detail the factors behind why an individual's biochemical (metabolite) composition is increasingly regarded as a key element to precisely defining phenotypes. Although an individual's biochemical (metabolite) composition is generally regarded, and frequently shown, to be a surrogate to the phenotypic state, we review how metabolites (and therefore an individual's metabolic profile) are also functionally related to the myriad of phenotypic influencers like genetics and the microbiota. We describe how using the technology to comprehensively measure an individual's biochemical profile – metabolomics – is integrative to defining individual phenotypes and how it is currently being deployed in efforts to continue to elaborate on human health and disease in large population studies. Finally, we summarize instances where metabolomics is being used to assess individual health in instances where signatures (i.e. biomarkers) have been defined. Untargeted biochemical profiling has the potential to phenotype individuals where genetic associations do not seem to show penetrance Metabolomics can be leveraged with other ‘omics data to discern phenotype information that is driven by environmental, microbiota, or epigenetic factors. Tracking the biochemical profile of individuals may help discern effectiveness or response to treatment or disease progression.
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