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Yadav DK, Chang AC, Grooms NWF, Chung SH, Gabel CV. O-GlcNAc signaling increases neuron regeneration through one-carbon metabolism in Caenorhabditis elegans. eLife 2024; 13:e86478. [PMID: 38334260 PMCID: PMC10857789 DOI: 10.7554/elife.86478] [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: 01/28/2023] [Accepted: 11/17/2023] [Indexed: 02/10/2024] Open
Abstract
Cellular metabolism plays an essential role in the regrowth and regeneration of a neuron following physical injury. Yet, our knowledge of the specific metabolic pathways that are beneficial to neuron regeneration remains sparse. Previously, we have shown that modulation of O-linked β-N-acetylglucosamine (O-GlcNAc) signaling, a ubiquitous post-translational modification that acts as a cellular nutrient sensor, can significantly enhance in vivo neuron regeneration. Here, we define the specific metabolic pathway by which O-GlcNAc transferase (ogt-1) loss of function mediates increased regenerative outgrowth. Performing in vivo laser axotomy and measuring subsequent regeneration of individual neurons in C. elegans, we find that glycolysis, serine synthesis pathway (SSP), one-carbon metabolism (OCM), and the downstream transsulfuration metabolic pathway (TSP) are all essential in this process. The regenerative effects of ogt-1 mutation are abrogated by genetic and/or pharmacological disruption of OCM and the SSP linking OCM to glycolysis. Testing downstream branches of this pathway, we find that enhanced regeneration is dependent only on the vitamin B12 independent shunt pathway. These results are further supported by RNA sequencing that reveals dramatic transcriptional changes by the ogt-1 mutation, in the genes involved in glycolysis, OCM, TSP, and ATP metabolism. Strikingly, the beneficial effects of the ogt-1 mutation can be recapitulated by simple metabolic supplementation of the OCM metabolite methionine in wild-type animals. Taken together, these data unearth the metabolic pathways involved in the increased regenerative capacity of a damaged neuron in ogt-1 animals and highlight the therapeutic possibilities of OCM and its related pathways in the treatment of neuronal injury.
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Affiliation(s)
- Dilip Kumar Yadav
- Department of Pharmacology, Physiology and Biophysics, Chobanian & Avedisian School of Medicine, Boston UniversityBostonUnited States
| | - Andrew C Chang
- Department of Pharmacology, Physiology and Biophysics, Chobanian & Avedisian School of Medicine, Boston UniversityBostonUnited States
| | - Noa WF Grooms
- Department of Bioengineering, Northeastern UniversityBostonUnited States
| | - Samuel H Chung
- Department of Bioengineering, Northeastern UniversityBostonUnited States
| | - Christopher V Gabel
- Department of Pharmacology, Physiology and Biophysics, Chobanian & Avedisian School of Medicine, Boston UniversityBostonUnited States
- Neurophotonics Center, Boston UniversityBostonUnited States
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2
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Meng W, Pan H, Sha Y, Zhai X, Xing A, Lingampelly SS, Sripathi SR, Wang Y, Li K. Metabolic Connectome and Its Role in the Prediction, Diagnosis, and Treatment of Complex Diseases. Metabolites 2024; 14:93. [PMID: 38392985 PMCID: PMC10890086 DOI: 10.3390/metabo14020093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
The interconnectivity of advanced biological systems is essential for their proper functioning. In modern connectomics, biological entities such as proteins, genes, RNA, DNA, and metabolites are often represented as nodes, while the physical, biochemical, or functional interactions between them are represented as edges. Among these entities, metabolites are particularly significant as they exhibit a closer relationship to an organism's phenotype compared to genes or proteins. Moreover, the metabolome has the ability to amplify small proteomic and transcriptomic changes, even those from minor genomic changes. Metabolic networks, which consist of complex systems comprising hundreds of metabolites and their interactions, play a critical role in biological research by mediating energy conversion and chemical reactions within cells. This review provides an introduction to common metabolic network models and their construction methods. It also explores the diverse applications of metabolic networks in elucidating disease mechanisms, predicting and diagnosing diseases, and facilitating drug development. Additionally, it discusses potential future directions for research in metabolic networks. Ultimately, this review serves as a valuable reference for researchers interested in metabolic network modeling, analysis, and their applications.
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Affiliation(s)
- Weiyu Meng
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SAR 999078, China
| | - Hongxin Pan
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SAR 999078, China
| | - Yuyang Sha
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SAR 999078, China
| | - Xiaobing Zhai
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SAR 999078, China
| | - Abao Xing
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SAR 999078, China
| | | | - Srinivasa R Sripathi
- Henderson Ocular Stem Cell Laboratory, Retina Foundation of the Southwest, Dallas, TX 75231, USA
| | - Yuefei Wang
- National Key Laboratory of Chinese Medicine Modernization, State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Kefeng Li
- Center for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau SAR 999078, China
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3
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Abdik E, Çakır T. Transcriptome-based biomarker prediction for Parkinson's disease using genome-scale metabolic modeling. Sci Rep 2024; 14:585. [PMID: 38182712 PMCID: PMC10770157 DOI: 10.1038/s41598-023-51034-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease in the world. Identification of PD biomarkers is crucial for early diagnosis and to develop target-based therapeutic agents. Integrative analysis of genome-scale metabolic models (GEMs) and omics data provides a computational approach for the prediction of metabolite biomarkers. Here, we applied the TIMBR (Transcriptionally Inferred Metabolic Biomarker Response) algorithm and two modified versions of TIMBR to investigate potential metabolite biomarkers for PD. To this end, we mapped thirteen post-mortem PD transcriptome datasets from the substantia nigra region onto Human-GEM. We considered a metabolite as a candidate biomarker if its production was predicted to be more efficient by a TIMBR-family algorithm in control or PD case for the majority of the datasets. Different metrics based on well-known PD-related metabolite alterations, PD-associated pathways, and a list of 25 high-confidence PD metabolite biomarkers compiled from the literature were used to compare the prediction performance of the three algorithms tested. The modified algorithm with the highest prediction power based on the metrics was called TAMBOOR, TrAnscriptome-based Metabolite Biomarkers by On-Off Reactions, which was introduced for the first time in this study. TAMBOOR performed better in terms of capturing well-known pathway alterations and metabolite secretion changes in PD. Therefore, our tool has a strong potential to be used for the prediction of novel diagnostic biomarkers for human diseases.
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Affiliation(s)
- Ecehan Abdik
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey.
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4
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Heinken A, El Kouche S, Guéant-Rodriguez RM, Guéant JL. Towards personalized genome-scale modeling of inborn errors of metabolism for systems medicine applications. Metabolism 2024; 150:155738. [PMID: 37981189 DOI: 10.1016/j.metabol.2023.155738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023]
Abstract
Inborn errors of metabolism (IEMs) are a group of more than 1000 inherited diseases that are individually rare but have a cumulative global prevalence of 50 per 100,000 births. Recently, it has been recognized that like common diseases, patients with rare diseases can greatly vary in the manifestation and severity of symptoms. Here, we review omics-driven approaches that enable an integrated, holistic view of metabolic phenotypes in IEM patients. We focus on applications of Constraint-based Reconstruction and Analysis (COBRA), a widely used mechanistic systems biology approach, to model the effects of inherited diseases. Moreover, we review evidence that the gut microbiome is also altered in rare diseases. Finally, we outline an approach using personalized metabolic models of IEM patients for the prediction of biomarkers and tailored therapeutic or dietary interventions. Such applications could pave the way towards personalized medicine not just for common, but also for rare diseases.
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Affiliation(s)
- Almut Heinken
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France.
| | - Sandra El Kouche
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France
| | - Rosa-Maria Guéant-Rodriguez
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France; National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
| | - Jean-Louis Guéant
- Inserm UMRS 1256 NGERE - Nutrition, Genetics, and Environmental Risk Exposure, University of Lorraine, Nancy F-54000, France; National Center of Inborn Errors of Metabolism, University Regional Hospital Center of Nancy, Nancy F-54000, France
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5
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Keizer HG, Brands R, Oosting RS, Seinen W. The Carnitine Palmitoyl-Transferase 2 Cascade Hypothesis for Alzheimer's Disease. J Alzheimers Dis 2024; 97:553-558. [PMID: 38143363 DOI: 10.3233/jad-230991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
Despite decades of intense research, the precise etiology of Alzheimer's disease (AD) remains unclear. In this hypothesis, we present a new perspective on this matter by identifying carnitine palmitoyl transferase-2 (CPT2) as a central target in AD. CPT2 is an enzyme situated within the inner mitochondrial membrane, playing a crucial role in beta-oxidation of fatty acids. It exhibits high sensitivity to hydrogen peroxide. This sensitivity holds relevance for the etiology of AD, as all major risk factors for the disease share a commonality in producing an excess of hydrogen peroxide right at this very mitochondrial membrane. We will explain the high sensitivity of CPT2 to hydrogen peroxide and elucidate how the resulting inhibition of CPT2 can lead to the characteristic phenotype of AD, thus clarifying its central role in the disease's etiology. This insight holds promise for the development of therapies for AD which can be implemented immediately.
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Affiliation(s)
- Hiskias G Keizer
- Alloksys Biotechnology, Wageningen, The Netherlands
- AMRIF Biotechnology, Wageningen, The Netherlands
| | - Ruud Brands
- Alloksys Biotechnology, Wageningen, The Netherlands
- AMRIF Biotechnology, Wageningen, The Netherlands
- Institute for Risk Assessment Sciences (IRAS), Utrecht, The Netherlands
| | - Ronald S Oosting
- Alloksys Biotechnology, Wageningen, The Netherlands
- AMRIF Biotechnology, Wageningen, The Netherlands
| | - Willem Seinen
- Alloksys Biotechnology, Wageningen, The Netherlands
- AMRIF Biotechnology, Wageningen, The Netherlands
- Institute for Risk Assessment Sciences (IRAS), Utrecht, The Netherlands
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6
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Suyama H, Luu LDW, Zhong L, Raftery MJ, Lan R. Integrating proteomic data with metabolic modeling provides insight into key pathways of Bordetella pertussis biofilms. Front Microbiol 2023; 14:1169870. [PMID: 37601354 PMCID: PMC10435875 DOI: 10.3389/fmicb.2023.1169870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023] Open
Abstract
Pertussis, commonly known as whooping cough is a severe respiratory disease caused by the bacterium, Bordetella pertussis. Despite widespread vaccination, pertussis resurgence has been observed globally. The development of the current acellular vaccine (ACV) has been based on planktonic studies. However, recent studies have shown that B. pertussis readily forms biofilms. A better understanding of B. pertussis biofilms is important for developing novel vaccines that can target all aspects of B. pertussis infection. This study compared the proteomic expression of biofilm and planktonic B. pertussis cells to identify key changes between the conditions. Major differences were identified in virulence factors including an upregulation of toxins (adenylate cyclase toxin and dermonecrotic toxin) and downregulation of pertactin and type III secretion system proteins in biofilm cells. To further dissect metabolic pathways that are altered during the biofilm lifestyle, the proteomic data was then incorporated into a genome scale metabolic model using the Integrative Metabolic Analysis Tool (iMAT). The generated models predicted that planktonic cells utilised the glyoxylate shunt while biofilm cells completed the full tricarboxylic acid cycle. Differences in processing aspartate, arginine and alanine were identified as well as unique export of valine out of biofilm cells which may have a role in inter-bacterial communication and regulation. Finally, increased polyhydroxybutyrate accumulation and superoxide dismutase activity in biofilm cells may contribute to increased persistence during infection. Taken together, this study modeled major proteomic and metabolic changes that occur in biofilm cells which helps lay the groundwork for further understanding B. pertussis pathogenesis.
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Affiliation(s)
- Hiroki Suyama
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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7
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Jia D, Wang F, Yu H. Systemic alterations of tricarboxylic acid cycle enzymes in Alzheimer's disease. Front Neurosci 2023; 17:1206688. [PMID: 37575300 PMCID: PMC10413568 DOI: 10.3389/fnins.2023.1206688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Mitochondrial dysfunction, especially tricarboxylic acid (TCA) cycle arrest, is strongly associated with Alzheimer's disease (AD), however, its systemic alterations in the central and peripheral of AD patients are not well defined. Here, we performed an integrated analysis of AD brain and peripheral blood cells transcriptomics to reveal the expression levels of nine TCA cycle enzymes involving 35 genes. The results showed that TCA cycle related genes were consistently down-regulated in the AD brain, whereas 11 genes were increased and 16 genes were decreased in the peripheral system. Pearson analysis of the TCA cycle genes with Aβ, Tau and mini-mental state examination (MMSE) revealed several significant correlated genes, including pyruvate dehydrogenase complex subunit (PDHB), isocitrate dehydrogenase subunits (IDH3B, IDH3G), 2-oxoglutarate dehydrogenase complex subunit (DLD), succinyl-CoA synthetase subunit (SUCLA2), malate dehydrogenase subunit (MDH1). In addition, SUCLA2, MDH1, and PDHB were also uniformly down-regulated in peripheral blood cells, suggesting that they may be candidate biomarkers for the early diagnosis of AD. Taken together, TCA cycle enzymes were systemically altered in AD progression, PDHB, SUCLA2, and MDH1 may be potential diagnostic and therapeutic targets.
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Affiliation(s)
- Dongdong Jia
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
| | - Fangzhou Wang
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Haitao Yu
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu, China
- Department of Fundamental Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
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8
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Costello SM, Cheney AM, Waldum A, Tripet B, Cotrina-Vidal M, Kaufmann H, Norcliffe-Kaufmann L, Lefcort F, Copié V. A Comprehensive NMR Analysis of Serum and Fecal Metabolites in Familial Dysautonomia Patients Reveals Significant Metabolic Perturbations. Metabolites 2023; 13:metabo13030433. [PMID: 36984872 PMCID: PMC10057143 DOI: 10.3390/metabo13030433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Central metabolism has a profound impact on the clinical phenotypes and penetrance of neurological diseases such as Alzheimer’s (AD) and Parkinson’s (PD) diseases, Amyotrophic Lateral Sclerosis (ALS) and Autism Spectrum Disorder (ASD). In contrast to the multifactorial origin of these neurological diseases, neurodevelopmental impairment and neurodegeneration in Familial Dysautonomia (FD) results from a single point mutation in the ELP1 gene. FD patients represent a well-defined population who can help us better understand the cellular networks underlying neurodegeneration, and how disease traits are affected by metabolic dysfunction, which in turn may contribute to dysregulation of the gut–brain axis of FD. Here, 1H NMR spectroscopy was employed to characterize the serum and fecal metabolomes of FD patients, and to assess similarities and differences in the polar metabolite profiles between FD patients and healthy relative controls. Findings from this work revealed noteworthy metabolic alterations reflected in energy (ATP) production, mitochondrial function, amino acid and nucleotide catabolism, neurosignaling molecules, and gut-microbial metabolism. These results provide further evidence for a close interconnection between metabolism, neurodegeneration, and gut microbiome dysbiosis in FD, and create an opportunity to explore whether metabolic interventions targeting the gut–brain–metabolism axis of FD could be used to redress or slow down the progressive neurodegeneration observed in FD patients.
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Affiliation(s)
- Stephanann M. Costello
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Alexandra M. Cheney
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Annie Waldum
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian Tripet
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Maria Cotrina-Vidal
- Department of Neurology, New York University School of Medicine, New York, NY 10017, USA
| | - Horacio Kaufmann
- Department of Neurology, New York University School of Medicine, New York, NY 10017, USA
| | | | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
- Correspondence: ; Tel.: +1-406-994-7244
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Chatterjee G, Negi S, Basu S, Faintuch J, O'Donovan A, Shukla P. Microbiome systems biology advancements for natural well-being. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155915. [PMID: 35568180 DOI: 10.1016/j.scitotenv.2022.155915] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Throughout the years all data from epidemiological, physiological and omics have suggested that the microbial communities play a considerable role in modulating human health. The population of microorganisms residing in the human intestine collectively known as microbiota presents a genetic repertoire that is higher in magnitude than the human genome. They play an essential role in host immunity and neuronal signaling. Rapid enhancement of sequence based screening and development of humanized gnotobiotic model has sparked a great deal of interest among scientists to probe the dynamic interactions of the commensal bacteria. This review focuses on systemic analysis of the gut microbiome to decipher the complexity of the host-microbe intercommunication and gives a special emphasis on the evolution of targeted precision medicine through microbiome engineering. In addition, we have also provided a comprehensive description of how interconnection between metabolism and biochemical reactions in a specific organism can be obtained from a metabolic network or a flux balance analysis and combining multiple datasets helps in the identification of a particular metabolite. The review highlights how genetic modification of the critical components and programming the resident microflora can be employed for targeted precision medicine. Inspite of the ongoing debate on the utility of gut microbiome we have explored on the probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also recapitulates integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet-microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of the disease. Inspite of the ongoing debate on the utility of the gut microbiome we have explored how probable new therapeutic avenues like FMT (Fecal microbiota transplant) can be utilized. This review also summarises integrating human-relevant 3D cellular models coupled with computational models and the metadata obtained from interventional and epidemiological studies may decipher the complex interactome of diet- microbiota-disease pathophysiology. In addition, it will also open new avenues for the development of therapeutics derived from the microbiome or implementation of personalized nutrition. In addition, the identification of biomarkers can also help towards the development of new diagnostic tools and eventually will lead to strategic management of disease.
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Affiliation(s)
| | - Sangeeta Negi
- NMC Biolab, New Mexico Consortium, Los Alamos, NM, USA; Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Supratim Basu
- NMC Biolab, New Mexico Consortium, Los Alamos, NM, USA
| | - Joel Faintuch
- Department of Gastroenterology, Sao Paulo University Medical School, São Paulo, SP 01246-903, Brazil
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Dar MA, Arafah A, Bhat KA, Khan A, Khan MS, Ali A, Ahmad SM, Rashid SM, Rehman MU. Multiomics technologies: role in disease biomarker discoveries and therapeutics. Brief Funct Genomics 2022; 22:76-96. [PMID: 35809340 DOI: 10.1093/bfgp/elac017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/21/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Medical research has been revolutionized after the publication of the full human genome. This was the major landmark that paved the way for understanding the biological functions of different macro and micro molecules. With the advent of different high-throughput technologies, biomedical research was further revolutionized. These technologies constitute genomics, transcriptomics, proteomics, metabolomics, etc. Collectively, these high-throughputs are referred to as multi-omics technologies. In the biomedical field, these omics technologies act as efficient and effective tools for disease diagnosis, management, monitoring, treatment and discovery of certain novel disease biomarkers. Genotyping arrays and other transcriptomic studies have helped us to elucidate the gene expression patterns in different biological states, i.e. healthy and diseased states. Further omics technologies such as proteomics and metabolomics have an important role in predicting the role of different biological molecules in an organism. It is because of these high throughput omics technologies that we have been able to fully understand the role of different genes, proteins, metabolites and biological pathways in a diseased condition. To understand a complex biological process, it is important to apply an integrative approach that analyses the multi-omics data in order to highlight the possible interrelationships of the involved biomolecules and their functions. Furthermore, these omics technologies offer an important opportunity to understand the information that underlies disease. In the current review, we will discuss the importance of omics technologies as promising tools to understand the role of different biomolecules in diseases such as cancer, cardiovascular diseases, neurodegenerative diseases and diabetes. SUMMARY POINTS
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Thanamit K, Hoerhold F, Oswald M, Koenig R. Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis. BMC Bioinformatics 2022; 23:226. [PMID: 35689204 PMCID: PMC9188260 DOI: 10.1186/s12859-022-04742-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Elucidating cellular metabolism led to many breakthroughs in biotechnology, synthetic biology, and health sciences. To date, deriving metabolic fluxes by 13C tracer experiments is the most prominent approach for studying metabolic fluxes quantitatively, often with high accuracy and precision. However, the technique has a high demand for experimental resources. Alternatively, flux balance analysis (FBA) has been employed to estimate metabolic fluxes without labeling experiments. It is less informative but can benefit from the low costs and low experimental efforts and gain flux estimates in experimentally difficult conditions. Methods to integrate relevant experimental data have been emerged to improve FBA flux estimations. Data from transcription profiling is often selected since it is easy to generate at the genome scale, typically embedded by a discretization of differential and non-differential expressed genes coding for the respective enzymes. RESULT We established the novel method Linear Programming based Gene Expression Model (LPM-GEM). LPM-GEM linearly embeds gene expression into FBA constraints. We implemented three strategies to reduce thermodynamically infeasible loops, which is a necessary prerequisite for such an omics-based model building. As a case study, we built a model of B. subtilis grown in eight different carbon sources. We obtained good flux predictions based on the respective transcription profiles when validating with 13C tracer based metabolic flux data of the same conditions. We could well predict the specific carbon sources. When testing the model on another, unseen dataset that was not used during training, good prediction performance was also observed. Furthermore, LPM-GEM outperformed a well-established model building methods. CONCLUSION Employing LPM-GEM integrates gene expression data efficiently. The method supports gene expression-based FBA models and can be applied as an alternative to estimate metabolic fluxes when tracer experiments are inappropriate.
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Affiliation(s)
- Kulwadee Thanamit
- Systems Biology Research Group, Institute for Infectious Diseases and Infection Control (IIMK), Jena University Hospital, Kollegiengasse 10, 07743, Jena, Germany
| | - Franziska Hoerhold
- Systems Biology Research Group, Institute for Infectious Diseases and Infection Control (IIMK), Jena University Hospital, Kollegiengasse 10, 07743, Jena, Germany
| | - Marcus Oswald
- Systems Biology Research Group, Institute for Infectious Diseases and Infection Control (IIMK), Jena University Hospital, Kollegiengasse 10, 07743, Jena, Germany
| | - Rainer Koenig
- Systems Biology Research Group, Institute for Infectious Diseases and Infection Control (IIMK), Jena University Hospital, Kollegiengasse 10, 07743, Jena, Germany.
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12
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Genome-Scale Metabolic Model Analysis of Metabolic Differences between Lauren Diffuse and Intestinal Subtypes in Gastric Cancer. Cancers (Basel) 2022; 14:cancers14092340. [PMID: 35565469 PMCID: PMC9104812 DOI: 10.3390/cancers14092340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 01/01/2023] Open
Abstract
Gastric cancer (GC) is one of the most lethal cancers worldwide; it has a high mortality rate, particularly in East Asia. Recently, genetic events (e.g., mutations and copy number alterations) and molecular signaling associated with histologically different GC subtypes (diffuse and intestinal) have been elucidated. However, metabolic differences among the histological GC subtypes have not been studied systematically. In this study, we utilized transcriptome-based genome-scale metabolic models (GEMs) to identify differential metabolic pathways between Lauren diffuse and intestinal subtypes. We found that diverse metabolic pathways, including cholesterol homeostasis, xenobiotic metabolism, fatty acid metabolism, the MTORC1 pathway, and glycolysis, were dysregulated between the diffuse and intestinal subtypes. Our study provides an overview of the metabolic differences between the two subtypes, possibly leading to an understanding of metabolism in GC heterogeneity.
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Hassan M, Awan FM, Naz A, deAndrés-Galiana EJ, Alvarez O, Cernea A, Fernández-Brillet L, Fernández-Martínez JL, Kloczkowski A. Innovations in Genomics and Big Data Analytics for Personalized Medicine and Health Care: A Review. Int J Mol Sci 2022; 23:4645. [PMID: 35563034 PMCID: PMC9104788 DOI: 10.3390/ijms23094645] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/06/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
Big data in health care is a fast-growing field and a new paradigm that is transforming case-based studies to large-scale, data-driven research. As big data is dependent on the advancement of new data standards, technology, and relevant research, the future development of big data applications holds foreseeable promise in the modern day health care revolution. Enormously large, rapidly growing collections of biomedical omics-data (genomics, proteomics, transcriptomics, metabolomics, glycomics, etc.) and clinical data create major challenges and opportunities for their analysis and interpretation and open new computational gateways to address these issues. The design of new robust algorithms that are most suitable to properly analyze this big data by taking into account individual variability in genes has enabled the creation of precision (personalized) medicine. We reviewed and highlighted the significance of big data analytics for personalized medicine and health care by focusing mostly on machine learning perspectives on personalized medicine, genomic data models with respect to personalized medicine, the application of data mining algorithms for personalized medicine as well as the challenges we are facing right now in big data analytics.
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Affiliation(s)
- Mubashir Hassan
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore 54590, Pakistan;
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Faryal Mehwish Awan
- Department of Medical Lab Technology, The University of Haripur, Haripur 22620, Pakistan;
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore 54590, Pakistan;
| | - Enrique J. deAndrés-Galiana
- Group of Inverse Problems, Optimization and Machine Learning, University of Oviedo, 33003 Oviedo, Spain; (E.J.d.-G.); (J.L.F.-M.)
| | - Oscar Alvarez
- DeepBioInsights, 38311 La Florida, Spain; (O.A.); (A.C.); (L.F.-B.)
| | - Ana Cernea
- DeepBioInsights, 38311 La Florida, Spain; (O.A.); (A.C.); (L.F.-B.)
| | | | - Juan Luis Fernández-Martínez
- Group of Inverse Problems, Optimization and Machine Learning, University of Oviedo, 33003 Oviedo, Spain; (E.J.d.-G.); (J.L.F.-M.)
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43205, USA
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14
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Collin CB, Gebhardt T, Golebiewski M, Karaderi T, Hillemanns M, Khan FM, Salehzadeh-Yazdi A, Kirschner M, Krobitsch S, Kuepfer L. Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation. J Pers Med 2022; 12:jpm12020166. [PMID: 35207655 PMCID: PMC8879572 DOI: 10.3390/jpm12020166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
The future development of personalized medicine depends on a vast exchange of data from different sources, as well as harmonized integrative analysis of large-scale clinical health and sample data. Computational-modelling approaches play a key role in the analysis of the underlying molecular processes and pathways that characterize human biology, but they also lead to a more profound understanding of the mechanisms and factors that drive diseases; hence, they allow personalized treatment strategies that are guided by central clinical questions. However, despite the growing popularity of computational-modelling approaches in different stakeholder communities, there are still many hurdles to overcome for their clinical routine implementation in the future. Especially the integration of heterogeneous data from multiple sources and types are challenging tasks that require clear guidelines that also have to comply with high ethical and legal standards. Here, we discuss the most relevant computational models for personalized medicine in detail that can be considered as best-practice guidelines for application in clinical care. We define specific challenges and provide applicable guidelines and recommendations for study design, data acquisition, and operation as well as for model validation and clinical translation and other research areas.
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Affiliation(s)
- Catherine Bjerre Collin
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N Copenhagen, Denmark; (C.B.C.); (T.K.)
| | - Tom Gebhardt
- Department of Systems Biology and Bioinformatics, University of Rostock, 18057 Rostock, Germany; (T.G.); (M.H.); (F.M.K.)
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies gGmbH, 69118 Heidelberg, Germany;
| | - Tugce Karaderi
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N Copenhagen, Denmark; (C.B.C.); (T.K.)
- Center for Health Data Science, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 N Copenhagen, Denmark
| | - Maximilian Hillemanns
- Department of Systems Biology and Bioinformatics, University of Rostock, 18057 Rostock, Germany; (T.G.); (M.H.); (F.M.K.)
| | - Faiz Muhammad Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, 18057 Rostock, Germany; (T.G.); (M.H.); (F.M.K.)
| | | | - Marc Kirschner
- Forschungszentrum Jülich GmbH, Project Management Jülich, 52425 Jülich, Germany; (M.K.); (S.K.)
| | - Sylvia Krobitsch
- Forschungszentrum Jülich GmbH, Project Management Jülich, 52425 Jülich, Germany; (M.K.); (S.K.)
| | | | - Lars Kuepfer
- Institute for Systems Medicine with Focus on Organ Interaction, University Hospital RWTH Aachen, 52074 Aachen, Germany
- Correspondence: ; Tel.: +49-241-8085900
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15
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Bayraktar A, Lam S, Altay O, Li X, Yuan M, Zhang C, Arif M, Turkez H, Uhlén M, Shoaie S, Mardinoglu A. Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis. Int J Mol Sci 2021; 22:11556. [PMID: 34768988 PMCID: PMC8584243 DOI: 10.3390/ijms222111556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
The complex pathology of Alzheimer's disease (AD) emphasises the need for comprehensive modelling of the disease, which may lead to the development of efficient treatment strategies. To address this challenge, we analysed transcriptome data of post-mortem human brain samples of healthy elders and individuals with late-onset AD from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) and Mayo Clinic (MayoRNAseq) studies in the AMP-AD consortium. In this context, we conducted several bioinformatics and systems medicine analyses including the construction of AD-specific co-expression networks and genome-scale metabolic modelling of the brain in AD patients to identify key genes, metabolites and pathways involved in the progression of AD. We identified AMIGO1 and GRPRASP2 as examples of commonly altered marker genes in AD patients. Moreover, we found alterations in energy metabolism, represented by reduced oxidative phosphorylation and ATPase activity, as well as the depletion of hexanoyl-CoA, pentanoyl-CoA, (2E)-hexenoyl-CoA and numerous other unsaturated fatty acids in the brain. We also observed that neuroprotective metabolites (e.g., vitamins, retinoids and unsaturated fatty acids) tend to be depleted in the AD brain, while neurotoxic metabolites (e.g., β-alanine, bilirubin) were more abundant. In summary, we systematically revealed the key genes and pathways related to the progression of AD, gained insight into the crucial mechanisms of AD and identified some possible targets that could be used in the treatment of AD.
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Affiliation(s)
- Abdulahad Bayraktar
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK; (A.B.); (S.L.); (S.S.)
| | - Simon Lam
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK; (A.B.); (S.L.); (S.S.)
| | - Ozlem Altay
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (O.A.); (X.L.); (M.Y.); (C.Z.); (M.A.); (M.U.)
| | - Xiangyu Li
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (O.A.); (X.L.); (M.Y.); (C.Z.); (M.A.); (M.U.)
| | - Meng Yuan
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (O.A.); (X.L.); (M.Y.); (C.Z.); (M.A.); (M.U.)
| | - Cheng Zhang
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (O.A.); (X.L.); (M.Y.); (C.Z.); (M.A.); (M.U.)
| | - Muhammad Arif
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (O.A.); (X.L.); (M.Y.); (C.Z.); (M.A.); (M.U.)
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Ataturk University, Erzurum 25240, Turkey;
| | - Mathias Uhlén
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (O.A.); (X.L.); (M.Y.); (C.Z.); (M.A.); (M.U.)
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK; (A.B.); (S.L.); (S.S.)
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (O.A.); (X.L.); (M.Y.); (C.Z.); (M.A.); (M.U.)
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK; (A.B.); (S.L.); (S.S.)
- Science for Life Laboratory, KTH–Royal Institute of Technology, SE-17121 Stockholm, Sweden; (O.A.); (X.L.); (M.Y.); (C.Z.); (M.A.); (M.U.)
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16
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Esvap E, Ulgen KO. Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome. ACS Synth Biol 2021; 10:2121-2137. [PMID: 34402617 DOI: 10.1021/acssynbio.1c00140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A genome-scale metabolic model (GEM) represents metabolic pathways of an organism in a mathematical form and can be built using biochemistry and genome annotation data. GEMs are invaluable for understanding organisms since they analyze the metabolic capabilities and behaviors quantitatively and can predict phenotypes. The development of high-throughput data collection techniques led to an immense increase in omics data such as metagenomics, which expand our knowledge on the human microbiome, but this also created a need for systematic analysis of these data. In recent years, GEMs have also been reconstructed for microbial species, including human gut microbiota, and methods for the analysis of microbial communities have been developed to examine the interaction between the organisms or the host. The purpose of this review is to provide a comprehensive guide for the applications of GEMs in microbial community analysis. Starting with GEM repositories, automatic GEM reconstruction tools, and quality control of models, this review will give insights into microbe-microbe and microbe-host interaction predictions and optimization of microbial community models. Recent studies that utilize microbial GEMs and personalized models to infer the influence of microbiota on human diseases such as inflammatory bowel diseases (IBD) or Parkinson's disease are exemplified. Being powerful system biology tools for both species-level and community-level analysis of microbes, GEMs integrated with omics data and machine learning techniques will be indispensable for studying the microbiome and their effects on human physiology as well as for deciphering the mechanisms behind human diseases.
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Affiliation(s)
- Elif Esvap
- Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
| | - Kutlu O. Ulgen
- Department of Chemical Engineering, Bogazici University, 34342 Istanbul, Turkey
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17
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Elmaleh DR, Downey MA, Kundakovic L, Wilkinson JE, Neeman Z, Segal E. New Approaches to Profile the Microbiome for Treatment of Neurodegenerative Disease. J Alzheimers Dis 2021; 82:1373-1401. [PMID: 34219718 DOI: 10.3233/jad-210198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Progressive neurodegenerative diseases represent some of the largest growing treatment challenges for public health in modern society. These diseases mainly progress due to aging and are driven by microglial surveillance and activation in response to changes occurring in the aging brain. The lack of efficacious treatment options for Alzheimer's disease (AD), as the focus of this review, and other neurodegenerative disorders has encouraged new approaches to address neuroinflammation for potential treatments. Here we will focus on the increasing evidence that dysbiosis of the gut microbiome is characterized by inflammation that may carry over to the central nervous system and into the brain. Neuroinflammation is the common thread associated with neurodegenerative diseases, but it is yet unknown at what point and how innate immune function turns pathogenic for an individual. This review will address extensive efforts to identify constituents of the gut microbiome and their neuroactive metabolites as a peripheral path to treatment. This approach is still in its infancy in substantive clinical trials and requires thorough human studies to elucidate the metabolic microbiome profile to design appropriate treatment strategies for early stages of neurodegenerative disease. We view that in order to address neurodegenerative mechanisms of the gut, microbiome and metabolite profiles must be determined to pre-screen AD subjects prior to the design of specific, chronic titrations of gut microbiota with low-dose antibiotics. This represents an exciting treatment strategy designed to balance inflammatory microglial involvement in disease progression with an individual's manifestation of AD as influenced by a coercive inflammatory gut.
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Affiliation(s)
- David R Elmaleh
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,AZTherapies, Inc., Boston, MA, USA
| | | | | | - Jeremy E Wilkinson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ziv Neeman
- Department of Radiology, Emek Medical Center, Afula, Israel.,Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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18
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Hampel H, Nisticò R, Seyfried NT, Levey AI, Modeste E, Lemercier P, Baldacci F, Toschi N, Garaci F, Perry G, Emanuele E, Valenzuela PL, Lucia A, Urbani A, Sancesario GM, Mapstone M, Corbo M, Vergallo A, Lista S. Omics sciences for systems biology in Alzheimer's disease: State-of-the-art of the evidence. Ageing Res Rev 2021; 69:101346. [PMID: 33915266 DOI: 10.1016/j.arr.2021.101346] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/06/2021] [Accepted: 04/22/2021] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is characterized by non-linear, genetic-driven pathophysiological dynamics with high heterogeneity in biological alterations and disease spatial-temporal progression. Human in-vivo and post-mortem studies point out a failure of multi-level biological networks underlying AD pathophysiology, including proteostasis (amyloid-β and tau), synaptic homeostasis, inflammatory and immune responses, lipid and energy metabolism, oxidative stress. Therefore, a holistic, systems-level approach is needed to fully capture AD multi-faceted pathophysiology. Omics sciences - genomics, epigenomics, transcriptomics, proteomics, metabolomics, lipidomics - embedded in the systems biology (SB) theoretical and computational framework can generate explainable readouts describing the entire biological continuum of a disease. Such path in Neurology is encouraged by the promising results of omics sciences and SB approaches in Oncology, where stage-driven pathway-based therapies have been developed in line with the precision medicine paradigm. Multi-omics data integrated in SB network approaches will help detect and chart AD upstream pathomechanistic alterations and downstream molecular effects occurring in preclinical stages. Finally, integrating omics and neuroimaging data - i.e., neuroimaging-omics - will identify multi-dimensional biological signatures essential to track the clinical-biological trajectories, at the subpopulation or even individual level.
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19
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Marcucci V, Kleiman J. Biomarkers and Their Implications in Alzheimer’s Disease: A Literature Review. EXPLORATORY RESEARCH AND HYPOTHESIS IN MEDICINE 2021; 000:000-000. [DOI: 10.14218/erhm.2021.00016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Csaban D, Pentelenyi K, Toth-Bencsik R, Illes A, Grosz Z, Gezsi A, Molnar MJ. The Role of the Rare Variants in the Genes Encoding the Alpha-Ketoglutarate Dehydrogenase in Alzheimer's Disease. Life (Basel) 2021; 11:321. [PMID: 33917565 PMCID: PMC8067443 DOI: 10.3390/life11040321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 12/17/2022] Open
Abstract
There is increasing evidence that several mitochondrial abnormalities are present in the brains of patients with Alzheimer's disease (AD). Decreased alpha-ketoglutarate dehydrogenase complex (αKGDHc) activity was identified in some patients with AD. The αKGDHc is a key enzyme in the Krebs cycle. This enzyme is very sensitive to the harmful effect of reactive oxygen species, which gives them a critical role in the Alzheimer and mitochondrial disease research area. Previously, several genetic risk factors were described in association with AD. Our aim was to analyze the associations of rare damaging variants in the genes encoding αKGDHc subunits and AD. The three genes (OGDH, DLST, DLD) encoding αKGDHc subunits were sequenced from different brain regions of 11 patients with histologically confirmed AD and the blood of further 35 AD patients. As a control group, we screened 134 persons with whole-exome sequencing. In all subunits, a one-one rare variant was identified with unknown significance based on American College of Medical Genetics and Genomics (ACMG) classification. Based on the literature research and our experience, R263H mutation in the DLD gene seems likely to be pathogenic. In the different cerebral areas, the αKGDHc mutational profile was the same, indicating the presence of germline variants. We hypothesize that the heterozygous missense R263H in the DLD gene may have a role in AD as a mild genetic risk factor.
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Affiliation(s)
- Dora Csaban
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, H-1082 Budapest, Hungary; (D.C.); (Z.G.)
| | - Klara Pentelenyi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, H-1082 Budapest, Hungary; (D.C.); (Z.G.)
| | - Renata Toth-Bencsik
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, H-1082 Budapest, Hungary; (D.C.); (Z.G.)
| | - Anett Illes
- PentaCore Laboratory Budapest, H-1094 Budapest, Hungary
| | - Zoltan Grosz
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, H-1082 Budapest, Hungary; (D.C.); (Z.G.)
| | - Andras Gezsi
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, H-1117 Budapest, Hungary
| | - Maria Judit Molnar
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, H-1082 Budapest, Hungary; (D.C.); (Z.G.)
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21
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Towards the routine use of in silico screenings for drug discovery using metabolic modelling. Biochem Soc Trans 2021; 48:955-969. [PMID: 32369553 PMCID: PMC7329353 DOI: 10.1042/bst20190867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
Currently, the development of new effective drugs for cancer therapy is not only hindered by development costs, drug efficacy, and drug safety but also by the rapid occurrence of drug resistance in cancer. Hence, new tools are needed to study the underlying mechanisms in cancer. Here, we discuss the current use of metabolic modelling approaches to identify cancer-specific metabolism and find possible new drug targets and drugs for repurposing. Furthermore, we list valuable resources that are needed for the reconstruction of cancer-specific models by integrating various available datasets with genome-scale metabolic reconstructions using model-building algorithms. We also discuss how new drug targets can be determined by using gene essentiality analysis, an in silico method to predict essential genes in a given condition such as cancer and how synthetic lethality studies could greatly benefit cancer patients by suggesting drug combinations with reduced side effects.
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22
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Rawls KD, Dougherty BV, Vinnakota KC, Pannala VR, Wallqvist A, Kolling GL, Papin JA. Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model. Toxicol Appl Pharmacol 2021; 412:115390. [PMID: 33387578 PMCID: PMC7859602 DOI: 10.1016/j.taap.2020.115390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/02/2020] [Accepted: 12/26/2020] [Indexed: 12/12/2022]
Abstract
The kidneys are metabolically active organs with importance in several physiological tasks such as the secretion of soluble wastes into the urine and synthesizing glucose and oxidizing fatty acids for energy in fasting (non-fed) conditions. Once damaged, the metabolic capability of the kidneys becomes altered. Here, we define metabolic tasks in a computational modeling framework to capture kidney function in an update to the iRno network reconstruction of rat metabolism using literature-based evidence. To demonstrate the utility of iRno for predicting kidney function, we exposed primary rat renal proximal tubule epithelial cells to four compounds with varying levels of nephrotoxicity (acetaminophen, gentamicin, 2,3,7,8-tetrachlorodibenzodioxin, and trichloroethylene) for six and twenty-four hours, and collected transcriptomics and metabolomics data to measure the metabolic effects of compound exposure. For the transcriptomics data, we observed changes in fatty acid metabolism and amino acid metabolism, as well as changes in existing markers of kidney function such as Clu (clusterin). The iRno metabolic network reconstruction was used to predict alterations in these same pathways after integrating transcriptomics data and was able to distinguish between select compound-specific effects on the proximal tubule epithelial cells. Genome-scale metabolic network reconstructions with coupled omics data can be used to predict changes in metabolism as a step towards identifying novel metabolic biomarkers of kidney function and dysfunction.
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Affiliation(s)
- Kristopher D Rawls
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Bonnie V Dougherty
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Kalyan C Vinnakota
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, MD 20817, USA
| | - Venkat R Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, MD 20817, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA
| | - Glynis L Kolling
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
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24
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Shao Y, Ouyang Y, Li T, Liu X, Xu X, Li S, Xu G, Le W. Alteration of Metabolic Profile and Potential Biomarkers in the Plasma of Alzheimer's Disease. Aging Dis 2020; 11:1459-1470. [PMID: 33269100 PMCID: PMC7673846 DOI: 10.14336/ad.2020.0217] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/17/2020] [Indexed: 12/23/2022] Open
Abstract
The expending of elderly population worldwide has resulted in a dramatic rise in the incidence of chronic diseases such as Alzheimer's disease (AD). Inadequate understanding of the mechanisms underlying AD has hampered the development of efficient tools for definitive diagnosis and curative interventions. Previous studies have attempted to discover reliable biomarkers of AD, but these biomarkers can only be measured through invasive (neuropathological markers in cerebrospinal fluid) or expensive (positron emission tomography scanning or magnetic resonance imaging) techniques. Metabolomics is a high-throughput technology that can detect and catalog large numbers of small metabolites and may be a useful tool for characterization of AD and identification of biomarkers. In this study, we used ultra-performance liquid chromatography-mass spectrometry based untargeted metabolomics to measure the concentrations of plasma metabolites in a cohort of subjects with AD (n=44) and cognitively normal controls (Ctrl, n=94). The AD group showed marked reductions in levels of polyunsaturated fatty acids, acyl-carnitines, degradation products of tryptophan, and elevated levels of bile acids compared to the Ctrl group. We then validated the results using an independent cohort that included subjects with AD (n=30), mild cognitive impairment (MCI, n=13), healthy controls (n=43), and non-AD neurological disease controls (NDC, n=31). We identified five metabolites comprising cholic acid, chenodeoxycholic acid, allocholic acid, indolelactic acid, and tryptophan that were able to distinguish patients with AD from both Ctrl and NDC with satisfactory sensitivity and specificity. The concentrations of these metabolites were significantly correlated with disease severity. Our results also suggested that altered bile acid profiles in AD and MCI might indicate early risk for the development of AD. These findings may allow for development of new approaches for diagnosis of AD and may provide novel insights into AD pathogenesis.
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Affiliation(s)
- Yaping Shao
- Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
- Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
| | - Yang Ouyang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianbai Li
- Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
- Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
| | - Xinyao Liu
- Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
- Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
| | - Xiaojiao Xu
- Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
- Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
| | - Song Li
- Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
- Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Weidong Le
- Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
- Liaoning Provincial Key Laboratory for Research on the Pathogenic Mechanisms of Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China.
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Moolamalla STR, Vinod PK. Genome-scale metabolic modelling predicts biomarkers and therapeutic targets for neuropsychiatric disorders. Comput Biol Med 2020; 125:103994. [PMID: 32980779 DOI: 10.1016/j.compbiomed.2020.103994] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 01/06/2023]
Abstract
Distinguishing neuropsychiatric disorders is challenging due to the overlap in symptoms and genetic risk factors. People suffering from these disorders face personal and professional challenges. Understanding the dysregulation of brain metabolism under disease condition can aid in effective diagnosis and in developing treatment strategies based on the metabolism. In this study, we reconstructed the metabolic network of three major neuropsychiatric disorders, schizophrenia (SCZ), bipolar disorder (BD) and major depressive disorder (MDD) using transcriptomic data and constrained based modelling approach. We integrated brain transcriptomic data from six independent studies with a recent comprehensive genome-scale metabolic model Recon3D. The analysis of the reconstructed network revealed the flux-level alterations in the peroxisome-mitochondria-golgi axis in neuropsychiatric disorders. We also extracted reporter metabolites and pathways that distinguish these three neuropsychiatric disorders. We found differences with respect to fatty acid oxidation, aromatic and branched chain amino acid metabolism, bile acid synthesis, glycosaminoglycans synthesis and modifications, and phospholipid metabolism. Further, we predicted network perturbations that transform the disease metabolic state to a healthy metabolic state for each disorder. These analyses provide local and global views of the metabolic changes in SCZ, BD and MDD, which may have clinical implications.
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Affiliation(s)
- S T R Moolamalla
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - P K Vinod
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.
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26
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Valcárcel LV, Torrano V, Tobalina L, Carracedo A, Planes FJ. rMTA: robust metabolic transformation analysis. Bioinformatics 2020; 35:4350-4355. [PMID: 30923806 DOI: 10.1093/bioinformatics/btz231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION The development of computational tools exploiting -omics data and high-quality genome-scale metabolic networks for the identification of novel drug targets is a relevant topic in Systems Medicine. Metabolic Transformation Algorithm (MTA) is one of these tools, which aims to identify targets that transform a disease metabolic state back into a healthy state, with potential application in any disease where a clear metabolic alteration is observed. RESULTS Here, we present a robust extension to MTA (rMTA), which additionally incorporates a worst-case scenario analysis and minimization of metabolic adjustment to evaluate the beneficial effect of gene knockouts. We show that rMTA complements MTA in the different datasets analyzed (gene knockout perturbations in different organisms, Alzheimer's disease and prostate cancer), bringing a more accurate tool for predicting therapeutic targets. AVAILABILITY AND IMPLEMENTATION rMTA is freely available on The Cobra Toolbox: https://opencobra.github.io/cobratoolbox/latest/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luis V Valcárcel
- Tecnun, University of Navarra, San Sebastián 20018, Spain
- Area de Hemato-Oncología, IDISNA, Centro de Investigación Médica Aplicada (CIMA), University of Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen University, Aachen D-52074, Germany
| | - Verónica Torrano
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen University, Aachen D-52074, Germany
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
| | - Luis Tobalina
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen University, Aachen D-52074, Germany
| | - Arkaitz Carracedo
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen University, Aachen D-52074, Germany
- CIC bioGUNE, Bizkaia Technology Park, Derio, Spain
- Ikerbasque, Basque foundation for science, Bilbao, Spain
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), Bilbao E-48080, Spain
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27
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Hampel H, Vergallo A, Afshar M, Akman-Anderson L, Arenas J, Benda N, Batrla R, Broich K, Caraci F, Cuello AC, Emanuele E, Haberkamp M, Kiddle SJ, Lucía A, Mapstone M, Verdooner SR, Woodcock J, Lista S. Blood-based systems biology biomarkers for next-generation clinical trials in Alzheimer's disease
. DIALOGUES IN CLINICAL NEUROSCIENCE 2020. [PMID: 31636492 PMCID: PMC6787542 DOI: 10.31887/dcns.2019.21.2/hhampel] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD)-a complex disease showing multiple pathomechanistic alterations-is triggered by nonlinear dynamic interactions of genetic/epigenetic and environmental risk factors, which, ultimately, converge into a biologically heterogeneous disease. To tackle the burden of AD during early preclinical stages, accessible blood-based biomarkers are currently being developed. Specifically, next-generation clinical trials are expected to integrate positive and negative predictive blood-based biomarkers into study designs to evaluate, at the individual level, target druggability and potential drug resistance mechanisms. In this scenario, systems biology holds promise to accelerate validation and qualification for clinical trial contexts of use-including proof-of-mechanism, patient selection, assessment of treatment efficacy and safety rates, and prognostic evaluation. Albeit in their infancy, systems biology-based approaches are poised to identify relevant AD "signatures" through multifactorial and interindividual variability, allowing us to decipher disease pathophysiology and etiology. Hopefully, innovative biomarker-drug codevelopment strategies will be the road ahead towards effective disease-modifying drugs.
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Affiliation(s)
- Harald Hampel
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Andrea Vergallo
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Mohammad Afshar
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Leyla Akman-Anderson
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Joaquín Arenas
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Norbert Benda
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Richard Batrla
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Karl Broich
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Filippo Caraci
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - A Claudio Cuello
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Enzo Emanuele
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Marion Haberkamp
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Steven J Kiddle
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Alejandro Lucía
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Mark Mapstone
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Steven R Verdooner
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Janet Woodcock
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
| | - Simone Lista
- Author affiliations: AXA Research Fund & Sorbonne University Chair, Paris, France; Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Paris, France; Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Paris, France; Institute of Memory and Alzheimer's Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Paris, France (Harald Hampel, Andrea Vergallo, Simone Lista); Ariana Pharma, Paris, France (Mohammad Afshar); NeuroVision Imaging, Inc., Sacramento, California, USA (Leyla Akman-Anderson, Steven R. Verdooner); Research Institute of Hospital 12 de Octubre (i+12), Madrid, Spain (Joaquín Arenas, Alejandro Lucía); Biostatistics and Special Pharmacokinetics Unit/Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Norbert Benda); Roche Diagnostics International, Rotkreuz, Switzerland (Richard Batrla); Head and President, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Karl Broich); Department of Drug Sciences, University of Catania, Catania, Italy; IRCCS Associazione Oasi Maria S.S., Institute for Research on Mental Retardation and Brain Aging, Troina, Enna, Italy (Filippo Caraci); Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada; Department of Neurology and Neurosurgery, McGill University, Montreal, Canada; Department of Anatomy and Cell Biology, McGill University, Montreal, Canada (A. Claudio Cuello); 2E Science, Robbio, Pavia, Italy (Enzo Emanuele); Neurology/Psychiatry/Ophthalmology Unit, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany (Marion Haberkamp); MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK (Steven J. Kiddle); Universidad Europea de Madrid (Sports Science Department), Madrid, Spain (Alejandro Lucía); Department of Neurology, University of California Irvine School of Medicine, Irvine, California, USA (Mark Mapstone); Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA (Janet Woodcock). Address for correspondence: Professor Harald Hampel, MD, PhD, Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, 47 boulevard de l'hôpital, F-75013, Paris, France.
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Sigmarsdóttir Þ, McGarrity S, Rolfsson Ó, Yurkovich JT, Sigurjónsson ÓE. Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine. Front Bioeng Biotechnol 2020; 8:239. [PMID: 32296688 PMCID: PMC7136564 DOI: 10.3389/fbioe.2020.00239] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Mesenchymal stem cells are a promising source for externally grown tissue replacements and patient-specific immunomodulatory treatments. This promise has not yet been fulfilled in part due to production scaling issues and the need to maintain the correct phenotype after re-implantation. One aspect of extracorporeal growth that may be manipulated to optimize cell growth and differentiation is metabolism. The metabolism of MSCs changes during and in response to differentiation and immunomodulatory changes. MSC metabolism may be linked to functional differences but how this occurs and influences MSC function remains unclear. Understanding how MSC metabolism relates to cell function is however important as metabolite availability and environmental circumstances in the body may affect the success of implantation. Genome-scale constraint based metabolic modeling can be used as a tool to fill gaps in knowledge of MSC metabolism, acting as a framework to integrate and understand various data types (e.g., genomic, transcriptomic and metabolomic). These approaches have long been used to optimize the growth and productivity of bacterial production systems and are being increasingly used to provide insights into human health research. Production of tissue for implantation using MSCs requires both optimized production of cell mass and the understanding of the patient and phenotype specific metabolic situation. This review considers the current knowledge of MSC metabolism and how it may be optimized along with the current and future uses of genome scale constraint based metabolic modeling to further this aim.
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Affiliation(s)
- Þóra Sigmarsdóttir
- The Blood Bank, Landspitali – The National University Hospital of Iceland, Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
| | - Sarah McGarrity
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Óttar Rolfsson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Ólafur E. Sigurjónsson
- The Blood Bank, Landspitali – The National University Hospital of Iceland, Reykjavik, Iceland
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
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Rawls K, Dougherty BV, Papin J. Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects. Methods Mol Biol 2020; 2088:315-330. [PMID: 31893380 DOI: 10.1007/978-1-0716-0159-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The drug development pipeline has stalled because of the difficulty in identifying new drug targets while minimizing off-target effects. Computational methods, such as the use of metabolic network reconstructions, may provide a cost-effective platform to test new hypotheses for drug targets and prevent off-target effects. Here, we summarize available methods to identify drug targets and off-target effects using either reaction-centric, gene-centric, or metabolite-centric approaches with genome-scale metabolic network reconstructions.
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Affiliation(s)
- Kristopher Rawls
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Bonnie V Dougherty
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Jason Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
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Chu SH, Huang M, Kelly RS, Benedetti E, Siddiqui JK, Zeleznik OA, Pereira A, Herrington D, Wheelock CE, Krumsiek J, McGeachie M, Moore SC, Kraft P, Mathé E, Lasky-Su J. Integration of Metabolomic and Other Omics Data in Population-Based Study Designs: An Epidemiological Perspective. Metabolites 2019; 9:E117. [PMID: 31216675 PMCID: PMC6630728 DOI: 10.3390/metabo9060117] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 12/30/2022] Open
Abstract
It is not controversial that study design considerations and challenges must be addressed when investigating the linkage between single omic measurements and human phenotypes. It follows that such considerations are just as critical, if not more so, in the context of multi-omic studies. In this review, we discuss (1) epidemiologic principles of study design, including selection of biospecimen source(s) and the implications of the timing of sample collection, in the context of a multi-omic investigation, and (2) the strengths and limitations of various techniques of data integration across multi-omic data types that may arise in population-based studies utilizing metabolomic data.
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Affiliation(s)
- Su H Chu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Mengna Huang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Elisa Benedetti
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Jalal K Siddiqui
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Alexandre Pereira
- Department of Genetics and Molecular Medicine, University of Sao Paulo Medical School, Sao Paulo 01246-903, Brazil.
| | - David Herrington
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA.
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden.
| | - Jan Krumsiek
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Steven C Moore
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA.
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.
| | - Ewy Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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31
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Lin CN, Huang CC, Huang KL, Lin KJ, Yen TC, Kuo HC. A metabolomic approach to identifying biomarkers in blood of Alzheimer's disease. Ann Clin Transl Neurol 2019; 6:537-545. [PMID: 30911577 PMCID: PMC6414491 DOI: 10.1002/acn3.726] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/20/2018] [Accepted: 12/31/2018] [Indexed: 01/28/2023] Open
Abstract
Objective This study aims to identify metabolites with altered levels of expression in patients with early and progressive stages of Alzheimer's disease (AD). Methods All participants of the study underwent genetic screening and were diagnosed using both neuropsychological assessment and amyloid imaging before metabolome analysis. According to these assessments, the patients were classified as normal (n = 15), with mild cognitive impairment (n = 10), and with AD (n = 15). Results Using a targeted metabolomic approach, we found that plasma levels of C3, C5, and C5‐DC acylcarnitines, arginine, phenylalanine, creatinine, symmetric dimethylarginine (SDMA) and phosphatidylcholine ae C38:2 were significantly altered in patients with early and progressive stages of AD. We created a predictive model based on the decision tree that included three main parameters: age, arginine and C5 plasma concentrations. The model distinguished AD patients from other participants with 60% sensitivity and 86.7% specificity. For healthy controls, the sensitivity was 85.7% and specificity was 61.5%. Multivariate ROC analysis to develop a decision tree showed that our model reached moderate diagnostic power in differentiating between older adults who are cognitively normal (AUC = 0.77) and those with AD (AUC = 0.72). Interpretation The plasma levels of arginine and valeryl carnitine, together with subject age, are promising as biomarkers for the diagnosis of AD in older adults.
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Affiliation(s)
- Chia-Ni Lin
- Department of Laboratory Medicine Chang Gung Memorial Hospital Taoyuan Taiwan.,Department of Medical Biotechnology and Laboratory Science College of Medicine Chang Gung University Taoyuan Taiwan
| | - Chin-Chang Huang
- Department of Neurology Chang Gung Memorial Hospital at Linkou Medical Center Chang Gung University College of Medicine Taoyuan Taiwan
| | - Kuo-Lun Huang
- Department of Neurology Chang Gung Memorial Hospital at Linkou Medical Center Chang Gung University College of Medicine Taoyuan Taiwan
| | - Kun-Ju Lin
- Molecular Imaging Center and Department of Nuclear Medicine Chang Gung Memorial Hospital Taoyuan Taiwan.,Department of Medical Imaging and Radiological Sciences Healthy Aging Research Center Chang Gung University Taoyuan Taiwan
| | - Tzu-Chen Yen
- Molecular Imaging Center and Department of Nuclear Medicine Chang Gung Memorial Hospital Taoyuan Taiwan.,Department of Medical Imaging and Radiological Sciences Healthy Aging Research Center Chang Gung University Taoyuan Taiwan
| | - Hung-Chou Kuo
- Department of Neurology Chang Gung Memorial Hospital at Linkou Medical Center Chang Gung University College of Medicine Taoyuan Taiwan
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32
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Madav Y, Wairkar S, Prabhakar B. Recent therapeutic strategies targeting beta amyloid and tauopathies in Alzheimer's disease. Brain Res Bull 2019; 146:171-184. [PMID: 30634016 DOI: 10.1016/j.brainresbull.2019.01.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/13/2018] [Accepted: 01/03/2019] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) has been a global concern for years due to its severe implications that affects the quality of life of the patients. The available line of therapy for treating Alzheimer's includes acetylcholinesterase inhibitors, NMDA(N-methyl-D-aspartate) antagonists and their combination which gives only symptomatic relief rather than treating the root cause of AD. Senile plaques and neurofibrillary tangles are the characteristic features underlying Alzheimer's pathology. Several attempts have been made towards exploring the niceties of these hallmarks and targeting various aspects of amyloid and tau pathology at different stages to eliminate the ultimate cause. Approaches targeting cleavage and formation of toxic amyloid fragments by secretases, aggregation of amyloid monofilaments, and immunotherapy against amyloid deposits has been extensively studied to treat amyloid pathology. Similarly, for tau pathology, tau hyperphosphorylation, microtubule stabilization, anti-tau immunotherapy has been explored. This article focuses on AD pathology and current pharmacotherapy, precisely for amyloid and tau. Furthermore, preclinical and clinical studies along with potential leads discovered under these approaches have also been included in this article. However, despite extensive research in drug development, overcoming clinical barrier still remain a major challenge for Alzheimer's pharmacotherapy.
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Affiliation(s)
- Yamini Madav
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKMs NMIMS, V.L.Mehta Road, Vile Parle (W), Mumbai, Maharashtra, 400056, India
| | - Sarika Wairkar
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKMs NMIMS, V.L.Mehta Road, Vile Parle (W), Mumbai, Maharashtra, 400056, India
| | - Bala Prabhakar
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKMs NMIMS, V.L.Mehta Road, Vile Parle (W), Mumbai, Maharashtra, 400056, India.
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33
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McGarrity S, Anuforo Ó, Halldórsson H, Bergmann A, Halldórsson S, Palsson S, Henriksen HH, Johansson PI, Rolfsson Ó. Metabolic systems analysis of LPS induced endothelial dysfunction applied to sepsis patient stratification. Sci Rep 2018; 8:6811. [PMID: 29717213 PMCID: PMC5931560 DOI: 10.1038/s41598-018-25015-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/13/2018] [Indexed: 12/24/2022] Open
Abstract
Endothelial dysfunction contributes to sepsis outcome. Metabolic phenotypes associated with endothelial dysfunction are not well characterised in part due to difficulties in assessing endothelial metabolism in situ. Here, we describe the construction of iEC2812, a genome scale metabolic reconstruction of endothelial cells and its application to describe metabolic changes that occur following endothelial dysfunction. Metabolic gene expression analysis of three endothelial subtypes using iEC2812 suggested their similar metabolism in culture. To mimic endothelial dysfunction, an in vitro sepsis endothelial cell culture model was established and the metabotypes associated with increased endothelial permeability and glycocalyx loss after inflammatory stimuli were quantitatively defined through metabolomics. These data and transcriptomic data were then used to parametrize iEC2812 and investigate the metabotypes of endothelial dysfunction. Glycan production and increased fatty acid metabolism accompany increased glycocalyx shedding and endothelial permeability after inflammatory stimulation. iEC2812 was then used to analyse sepsis patient plasma metabolome profiles and predict changes to endothelial derived biomarkers. These analyses revealed increased changes in glycan metabolism in sepsis non-survivors corresponding to metabolism of endothelial dysfunction in culture. The results show concordance between endothelial health and sepsis survival in particular between endothelial cell metabolism and the plasma metabolome in patients with sepsis.
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Affiliation(s)
- Sarah McGarrity
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | - Ósk Anuforo
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | - Haraldur Halldórsson
- Medical Department, University of Iceland, Sturlugata 8, Reykjavik, Iceland
- Landspitali, Læknagarður, Hringbraut, Reykjavik, Iceland
| | - Andreas Bergmann
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | | | - Sirus Palsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
| | | | - Pär Ingemar Johansson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland
- Rigshospitalet, Blegdamsvej 9, 2100, Kobenhavn O, Denmark
| | - Óttar Rolfsson
- Center for Systems Biology, University of Iceland, Sturlugata 8, Reykjavik, Iceland.
- Medical Department, University of Iceland, Sturlugata 8, Reykjavik, Iceland.
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34
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Siddiqui JK, Baskin E, Liu M, Cantemir-Stone CZ, Zhang B, Bonneville R, McElroy JP, Coombes KR, Mathé EA. IntLIM: integration using linear models of metabolomics and gene expression data. BMC Bioinformatics 2018; 19:81. [PMID: 29506475 PMCID: PMC5838881 DOI: 10.1186/s12859-018-2085-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/21/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. For this reason, these data are increasingly collected in large (> 100 participants) cohorts, thereby driving a need for the development of user-friendly and open-source methods/tools for their integration. Of note, clinical/translational studies typically provide snapshot (e.g. one time point) gene and metabolite profiles and, oftentimes, most metabolites measured are not identified. Thus, in these types of studies, pathway/network approaches that take into account the complexity of transcript-metabolite relationships may neither be applicable nor readily uncover novel relationships. With this in mind, we propose a simple linear modeling approach to capture disease-(or other phenotype) specific gene-metabolite associations, with the assumption that co-regulation patterns reflect functionally related genes and metabolites. RESULTS The proposed linear model, metabolite ~ gene + phenotype + gene:phenotype, specifically evaluates whether gene-metabolite relationships differ by phenotype, by testing whether the relationship in one phenotype is significantly different from the relationship in another phenotype (via a statistical interaction gene:phenotype p-value). Statistical interaction p-values for all possible gene-metabolite pairs are computed and significant pairs are then clustered by the directionality of associations (e.g. strong positive association in one phenotype, strong negative association in another phenotype). We implemented our approach as an R package, IntLIM, which includes a user-friendly R Shiny web interface, thereby making the integrative analyses accessible to non-computational experts. We applied IntLIM to two previously published datasets, collected in the NCI-60 cancer cell lines and in human breast tumor and non-tumor tissue, for which transcriptomic and metabolomic data are available. We demonstrate that IntLIM captures relevant tumor-specific gene-metabolite associations involved in known cancer-related pathways, including glutamine metabolism. Using IntLIM, we also uncover biologically relevant novel relationships that could be further tested experimentally. CONCLUSIONS IntLIM provides a user-friendly, reproducible framework to integrate transcriptomic and metabolomic data and help interpret metabolomic data and uncover novel gene-metabolite relationships. The IntLIM R package is publicly available in GitHub ( https://github.com/mathelab/IntLIM ) and includes a user-friendly web application, vignettes, sample data and data/code to reproduce results.
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Affiliation(s)
- Jalal K Siddiqui
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Elizabeth Baskin
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Mingrui Liu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Carmen Z Cantemir-Stone
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Bofei Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA.,Biomedical Engineering Undegraduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Russell Bonneville
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA.,Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Joseph P McElroy
- Center for Biostatistics, The Ohio State University, Columbus, OH, USA
| | - Kevin R Coombes
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Ewy A Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA.
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35
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Zhang B, Hu S, Baskin E, Patt A, Siddiqui JK, Mathé EA. RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites. Metabolites 2018; 8:E16. [PMID: 29470400 PMCID: PMC5876005 DOI: 10.3390/metabo8010016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 01/04/2023] Open
Abstract
The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be checked multiple times a year and RaMP will be updated accordingly.
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Affiliation(s)
- Bofei Zhang
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Senyang Hu
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Elizabeth Baskin
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Andrew Patt
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
- Biomedical Engineering Graduate Program, The Ohio State University, Columbus, OH 43210, USA.
| | - Jalal K Siddiqui
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Ewy A Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
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36
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Aramillo Irizar P, Schäuble S, Esser D, Groth M, Frahm C, Priebe S, Baumgart M, Hartmann N, Marthandan S, Menzel U, Müller J, Schmidt S, Ast V, Caliebe A, König R, Krawczak M, Ristow M, Schuster S, Cellerino A, Diekmann S, Englert C, Hemmerich P, Sühnel J, Guthke R, Witte OW, Platzer M, Ruppin E, Kaleta C. Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly. Nat Commun 2018; 9:327. [PMID: 29382830 PMCID: PMC5790807 DOI: 10.1038/s41467-017-02395-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Disease epidemiology during ageing shows a transition from cancer to degenerative chronic disorders as dominant contributors to mortality in the old. Nevertheless, it has remained unclear to what extent molecular signatures of ageing reflect this phenomenon. Here we report on the identification of a conserved transcriptomic signature of ageing based on gene expression data from four vertebrate species across four tissues. We find that ageing-associated transcriptomic changes follow trajectories similar to the transcriptional alterations observed in degenerative ageing diseases but are in opposite direction to the transcriptomic alterations observed in cancer. We confirm the existence of a similar antagonism on the genomic level, where a majority of shared risk alleles which increase the risk of cancer decrease the risk of chronic degenerative disorders and vice versa. These results reveal a fundamental trade-off between cancer and degenerative ageing diseases that sheds light on the pronounced shift in their epidemiology during ageing. Ageing is associated with a pronounced shift in mortality from cancer to degenerative diseases. Here, the authors show that in concordance with this shift, conserved transcriptional alterations during ageing across four vertebrates align with degenerative diseases but are opposite to those in cancer.
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Affiliation(s)
- Peer Aramillo Irizar
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Sascha Schäuble
- Jena University Language and Information Engineering Lab, Friedrich-Schiller-University Jena, D-07743, Jena, Germany.,GerontoSys JenAge Consortium, D-07745, Jena, Germany
| | - Daniela Esser
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Marco Groth
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Genome Analysis Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Christiane Frahm
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Steffen Priebe
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Mario Baumgart
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biology of Ageing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Nils Hartmann
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Genetics Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Shiva Marthandan
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Imageing Facility, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Uwe Menzel
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Jule Müller
- Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Silvio Schmidt
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, D-07747, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, D-07745, Jena, Germany
| | - Amke Caliebe
- Institute for Medical Informatics and Statistics, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, D-07747, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, D-07745, Jena, Germany
| | - Michael Krawczak
- Institute for Medical Informatics and Statistics, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Michael Ristow
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach/Zürich, CH-8603, Switzerland
| | - Stefan Schuster
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Department of Bioinformatics, Friedrich-Schiller-University Jena, D-07743, Jena, Germany
| | - Alessandro Cellerino
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biology of Ageing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany.,Laboratory of Neurobiology, Scuola Normale Superiore, University of Pisa, I-56100, Pisa, Italy
| | - Stephan Diekmann
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Biology Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Christoph Englert
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Genetics Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany.,Faculty of Biology and Pharmacy, Friedrich-Schiller-University Jena, D-07743, Jena, Germany
| | - Peter Hemmerich
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Imageing Facility, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Jürgen Sühnel
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biocomputing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Reinhard Guthke
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Otto W Witte
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Matthias Platzer
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Genome Analysis Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Eytan Ruppin
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany. .,GerontoSys JenAge Consortium, D-07745, Jena, Germany.
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Nday CM, Eleftheriadou D, Jackson G. Shared pathological pathways of Alzheimer's disease with specific comorbidities: current perspectives and interventions. J Neurochem 2018; 144:360-389. [PMID: 29164610 DOI: 10.1111/jnc.14256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) belongs to one of the most multifactorial, complex and heterogeneous morbidity-leading disorders. Despite the extensive research in the field, AD pathogenesis is still at some extend obscure. Mechanisms linking AD with certain comorbidities, namely diabetes mellitus, obesity and dyslipidemia, are increasingly gaining importance, mainly because of their potential role in promoting AD development and exacerbation. Their exact cognitive impairment trajectories, however, remain to be fully elucidated. The current review aims to offer a clear and comprehensive description of the state-of-the-art approaches focused on generating in-depth knowledge regarding the overlapping pathology of AD and its concomitant ailments. Thorough understanding of associated alterations on a number of molecular, metabolic and hormonal pathways, will contribute to the further development of novel and integrated theranostics, as well as targeted interventions that may be beneficial for individuals with age-related cognitive decline.
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Affiliation(s)
- Christiane M Nday
- Department of Chemical Engineering, Laboratory of Inorganic Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Despoina Eleftheriadou
- Department of Chemical Engineering, Laboratory of Inorganic Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Graham Jackson
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, South Africa
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38
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Huang X, Liu H, Li X, Guan L, Li J, Tellier LCAM, Yang H, Wang J, Zhang J. Revealing Alzheimer's disease genes spectrum in the whole-genome by machine learning. BMC Neurol 2018; 18:5. [PMID: 29320986 PMCID: PMC5763548 DOI: 10.1186/s12883-017-1010-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/21/2017] [Indexed: 11/23/2022] Open
Abstract
Background Alzheimer’s disease (AD) is an important, progressive neurodegenerative disease, with a complex genetic architecture. A key goal of biomedical research is to seek out disease risk genes, and to elucidate the function of these risk genes in the development of disease. For this purpose, expanding the AD-associated gene set is necessary. In past research, the prediction methods for AD related genes has been limited in their exploration of the target genome regions. We here present a genome-wide method for AD candidate genes predictions. Methods We present a machine learning approach (SVM), based upon integrating gene expression data with human brain-specific gene network data, to discover the full spectrum of AD genes across the whole genome. Results We classified AD candidate genes with an accuracy and the area under the receiver operating characteristic (ROC) curve of 84.56% and 94%. Our approach provides a supplement for the spectrum of AD-associated genes extracted from more than 20,000 genes in a genome wide scale. Conclusions In this study, we have elucidated the whole-genome spectrum of AD, using a machine learning approach. Through this method, we expect for the candidate gene catalogue to provide a more comprehensive annotation of AD for researchers. Electronic supplementary material The online version of this article (10.1186/s12883-017-1010-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoyan Huang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.,BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Hankui Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xinming Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liping Guan
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jiankang Li
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Laurent Christian Asker M Tellier
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.,Department of Biology, Bioinformatics, University of Copenhagen, Copenhagen, Denmark
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jianguo Zhang
- BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China. .,Shenzhen Key Lab of Neurogenomics, BGI-Shenzhen, Shenzhen, 518120, China.
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Özcan E, Çakır T. Genome-Scale Brain Metabolic Networks as Scaffolds for the Systems Biology of Neurodegenerative Diseases: Mapping Metabolic Alterations. ADVANCES IN NEUROBIOLOGY 2018; 21:195-217. [PMID: 30334223 DOI: 10.1007/978-3-319-94593-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Systems-based investigation of diseases requires integrated analysis of cellular networks and high-throughput data of gene products. The use of genome-scale metabolic networks for such integration has led to the elucidation of cellular mechanisms for several cell types from microorganisms to plants. It has become easier and cheaper to generate high-throughput data over years in the form of transcriptome, proteome and metabolome. This has tremendously improved the quality and quantity of information extracted from such data enabling the documentation of active pathways and reactions in cell metabolism. A number of omics-based datasets for several neurodegenerative diseases are now available in public repositories. This increases the potential of using genome-scale brain metabolic networks as a scaffold for this type of data to map metabolic alterations for the purpose of elucidating disease mechanisms and for the diagnosis and treatment of such disorders. This chapter first reviews omics data collected for neurodegenerative diseases to map their effect on metabolism. Later, the potential for genome-scale metabolic modeling of such data is reviewed and discussed in light of recently reconstructed brain metabolic networks at genome-scale.
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Affiliation(s)
- Emrah Özcan
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey.
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Abstract
Proteomics and lipidomics are powerful tools to the large-scale study of proteins and lipids, respectively. Several methods can be employed with particular benefits and limitations in the study of human brain. This is a review of the rationale use of current techniques with particular attention to limitations and pitfalls inherent to each one of the techniques, and more importantly, to their use in the study of post-mortem brain tissue. These aspects are cardinal to avoid false interpretations, errors and unreal expectancies. Other points are also stressed as exemplified in the analysis of human neurodegenerative diseases which are manifested by disease-, region-, and stage-specific modifications commonly in the context of aging. Information about certain altered protein clusters and proteins oxidatively damaged is summarized for Alzheimer and Parkinson diseases.
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Affiliation(s)
- Isidro Ferrer
- Pathologic Anatomy Service, Institute of Neuropathology, Bellvitge University Hospital; Department of Pathology and Experimental Therapeutics, Faculty of Medicine, University of Barcelona; and Network Center of Biomedical Research on Neurodegenerative Diseases, Institute Carlos III; Hospitalet de Llobregat, Llobregat, Spain.
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Fenech M. Vitamins Associated with Brain Aging, Mild Cognitive Impairment, and Alzheimer Disease: Biomarkers, Epidemiological and Experimental Evidence, Plausible Mechanisms, and Knowledge Gaps. Adv Nutr 2017; 8:958-970. [PMID: 29141977 PMCID: PMC5682999 DOI: 10.3945/an.117.015610] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The key to preventing brain aging, mild cognitive impairment (MCI), and Alzheimer disease (AD) via vitamin intake is first to understand molecular mechanisms, then to deduce relevant biomarkers, and subsequently to test the level of evidence for the impact of vitamins in the relevant pathways and their modulation of dementia risk. This narrative review infers information on mechanisms from gene and metabolic defects associated with MCI and AD, and assesses the role of vitamins using recent results from animal and human studies. Current evidence suggests that all known vitamins and some "quasi-vitamins" are involved as cofactors or influence ≥1 of the 6 key sets of pathways or pathologies associated with MCI or AD, relating to 1) 1-carbon metabolism, 2) DNA damage and repair, 3) mitochondrial function and glucose metabolism, 4) lipid and phospholipid metabolism and myelination, 5) neurotransmitter synthesis and synaptogenesis, and 6) amyloidosis and Tau protein phosphorylation. The contemporary level of evidence for each of the vitamins varies considerably, but it is notable that B vitamins are involved as cofactors in all of the core pathways or pathologies and, together with vitamins C and E, are consistently associated with a protective role against dementia. Outcomes from recent studies indicate that the efficacy and safety of supplementation with vitamins to prevent MCI and the early stages of AD will most likely depend on 1) which pathways are defective, 2) which vitamins are deficient and could correct the relevant metabolic defects, and 3) the modulating impact of nutrient-nutrient and nutrient-genotype interaction. More focus on a precision nutrition approach is required to realize the full potential of vitamin therapy in preventing dementia and to avoid causing harm.
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Affiliation(s)
- Michael Fenech
- CSIRO Health and Biosecurity, Genome Health and Personalised Nutrition, Adelaide, South Australia, Australia
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42
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Biomedical applications of cell- and tissue-specific metabolic network models. J Biomed Inform 2017; 68:35-49. [DOI: 10.1016/j.jbi.2017.02.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 02/21/2017] [Accepted: 02/23/2017] [Indexed: 12/17/2022]
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Aurich MK, Fleming RMT, Thiele I. MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models. Front Physiol 2016; 7:327. [PMID: 27536246 PMCID: PMC4971542 DOI: 10.3389/fphys.2016.00327] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/18/2016] [Indexed: 11/13/2022] Open
Abstract
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. This computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community.
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Affiliation(s)
- Maike K Aurich
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
| | - Ronan M T Fleming
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg Esch-sur-Alzette, Luxembourg
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Cristofano A, Sapere N, La Marca G, Angiolillo A, Vitale M, Corbi G, Scapagnini G, Intrieri M, Russo C, Corso G, Di Costanzo A. Serum Levels of Acyl-Carnitines along the Continuum from Normal to Alzheimer's Dementia. PLoS One 2016; 11:e0155694. [PMID: 27196316 PMCID: PMC4873244 DOI: 10.1371/journal.pone.0155694] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 05/03/2016] [Indexed: 01/07/2023] Open
Abstract
This study aimed to determine the serum levels of free L-carnitine, acetyl-L-carnitine and 34 acyl-L-carnitine in healthy subjects and in patients with or at risk of Alzheimer’s disease. Twenty-nine patients with probable Alzheimer’s disease, 18 with mild cognitive impairment of the amnestic type, 24 with subjective memory complaint and 46 healthy subjects were enrolled in the study, and the levels of carnitine and acyl-carnitines were measured by tandem mass spectrometry. The concentrations of acetyl-L-carnitine progressively decreased passing from healthy subjects group (mean±SD, 5.6±1.3 μmol/L) to subjective memory complaint (4.3±0.9 μmol/L), mild cognitive impairment (4.0±0.53 μmol/L), up to Alzheimer’s disease (3.5±0.6 μmol/L) group (p<0.001). The differences were significant for the comparisons: healthy subjects vs. subjective memory complaint, mild cognitive impairment or Alzheimer’s disease group; and subjective memory complaint vs. Alzheimer’s disease group. Other acyl-carnitines, such as malonyl-, 3-hydroxyisovaleryl-, hexenoyl-, decanoyl-, dodecanoyl-, dodecenoyl-, myristoyl-, tetradecenoyl-, hexadecenoyl-, stearoyl-, oleyl- and linoleyl-L-carnitine, showed a similar decreasing trend, passing from healthy subjects to patients at risk of or with Alzheimer’s disease. These results suggest that serum acetyl-L-carnitine and other acyl-L-carnitine levels decrease along the continuum from healthy subjects to subjective memory complaint and mild cognitive impairment subjects, up to patients with Alzheimer’s disease, and that the metabolism of some acyl-carnitines is finely connected among them. These findings also suggest that the serum levels of acetyl-L-carnitine and other acyl-L-carnitines could help to identify the patients before the phenotype conversion to Alzheimer’s disease and the patients who would benefit from the treatment with acetyl-L-carnitine. However, further validation on a larger number of samples in a longitudinal study is needed before application to clinical practice.
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Affiliation(s)
- Adriana Cristofano
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Nadia Sapere
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Giancarlo La Marca
- Newborn Screening, Biochemistry and Pharmacology Laboratories, Clinic of Pediatric Neurology, Meyer University Children’s Hospital, Florence, Italy
- Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence, Florence, Italy
| | - Antonella Angiolillo
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Michela Vitale
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Graziamaria Corbi
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Giovanni Scapagnini
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Mariano Intrieri
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Claudio Russo
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Gaetano Corso
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
- * E-mail: (ADC); (GC)
| | - Alfonso Di Costanzo
- Centre for Research and Training in Medicine for Aging, Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
- * E-mail: (ADC); (GC)
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McGarrity S, Halldórsson H, Palsson S, Johansson PI, Rolfsson Ó. Understanding the Causes and Implications of Endothelial Metabolic Variation in Cardiovascular Disease through Genome-Scale Metabolic Modeling. Front Cardiovasc Med 2016; 3:10. [PMID: 27148541 PMCID: PMC4834436 DOI: 10.3389/fcvm.2016.00010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/03/2016] [Indexed: 01/04/2023] Open
Abstract
High-throughput biochemical profiling has led to a requirement for advanced data interpretation techniques capable of integrating the analysis of gene, protein, and metabolic profiles to shed light on genotype-phenotype relationships. Herein, we consider the current state of knowledge of endothelial cell (EC) metabolism and its connections to cardiovascular disease (CVD) and explore the use of genome-scale metabolic models (GEMs) for integrating metabolic and genomic data. GEMs combine gene expression and metabolic data acting as frameworks for their analysis and, ultimately, afford mechanistic understanding of how genetic variation impacts metabolism. We demonstrate how GEMs can be used to investigate CVD-related genetic variation, drug resistance mechanisms, and novel metabolic pathways in ECs. The application of GEMs in personalized medicine is also highlighted. Particularly, we focus on the potential of GEMs to identify metabolic biomarkers of endothelial dysfunction and to discover methods of stratifying treatments for CVDs based on individual genetic markers. Recent advances in systems biology methodology, and how these methodologies can be applied to understand EC metabolism in both health and disease, are thus highlighted.
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Affiliation(s)
- Sarah McGarrity
- Center for Systems Biology, University of Iceland , Reykjavik , Iceland
| | - Haraldur Halldórsson
- Department of Pharmacology and Toxicology, School of Health Sciences, University of Iceland , Reykjavik , Iceland
| | - Sirus Palsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland; Sinopia Biosciences Inc., San Diego, CA, USA
| | - Pär I Johansson
- Section for Transfusion Medicine, Capital Region Blood Bank, Rigshospitalet, University of Copenhagen , Copenhagen , Denmark
| | - Óttar Rolfsson
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland; Department of Biochemistry and Molecular Biology, School of Health Sciences, University of Iceland, Reykjavik, Iceland
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Perera MTPR, Higdon R, Richards DA, Silva MA, Murphy N, Kolker E, Mirza DF. Biomarker differences between cadaveric grafts used in human orthotopic liver transplantation as identified by coulometric electrochemical array detection (CEAD) metabolomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:767-77. [PMID: 25353146 DOI: 10.1089/omi.2014.0094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Metabolomics in systems biology research unravels intracellular metabolic changes by high throughput methods, but such studies focusing on liver transplantation (LT) are limited. Microdialysate samples of liver grafts from donors after circulatory death (DCD; n=13) and brain death (DBD; n=27) during cold storage and post-reperfusion phase were analyzed through coulometric electrochemical array detection (CEAD) for identification of key metabolomics changes. Metabolite peak differences between the graft types at cold phase, post-reperfusion trends, and in failed allografts, were identified against reference chromatograms. In the cold phase, xanthine, uric acid, and kynurenine were overexpressed in DCD by 3-fold, and 3-nitrotyrosine (3-NT) and 4-hydroxy-3-methoxymandelic acid (HMMA) in DBD by 2-fold (p<0.05). In both grafts, homovanillic acid and methionine increased by 20%-30% with each 100 min increase in cold ischemia time (p<0.05). Uric acid expression was significantly different in DCD post-reperfusion. Failed allografts had overexpression of reduced glutathione and kynurenine (cold phase) and xanthine (post-reperfusion) (p<0.05). This differential expression of metabolites between graft types is a novel finding, meanwhile identification of overexpression of kynurenine in DCD grafts and in failed allografts is unique. Further studies should examine kynurenine as a potential biomarker predicting graft function, its causation, and actions on subsequent clinical outcomes.
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Affiliation(s)
- M Thamara P R Perera
- 1 The Liver Unit, Queen Elizabeth Hospital Birmingham , Edgbaston, Birmingham, United Kingdom
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Eddy JA, Funk CC, Price ND. Fostering synergy between cell biology and systems biology. Trends Cell Biol 2015; 25:440-5. [PMID: 26013981 DOI: 10.1016/j.tcb.2015.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/25/2015] [Accepted: 04/28/2015] [Indexed: 01/05/2023]
Abstract
In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship.
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Affiliation(s)
- James A Eddy
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Cory C Funk
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Nathan D Price
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA.
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48
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Heinken A, Thiele I. Systems biology of host-microbe metabolomics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:195-219. [PMID: 25929487 PMCID: PMC5029777 DOI: 10.1002/wsbm.1301] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/25/2015] [Accepted: 04/01/2015] [Indexed: 12/15/2022]
Abstract
The human gut microbiota performs essential functions for host and well‐being, but has also been linked to a variety of disease states, e.g., obesity and type 2 diabetes. The mammalian body fluid and tissue metabolomes are greatly influenced by the microbiota, with many health‐relevant metabolites being considered ‘mammalian–microbial co‐metabolites’. To systematically investigate this complex host–microbial co‐metabolism, a systems biology approach integrating high‐throughput data and computational network models is required. Here, we review established top‐down and bottom‐up systems biology approaches that have successfully elucidated relationships between gut microbiota‐derived metabolites and host health and disease. We focus particularly on the constraint‐based modeling and analysis approach, which enables the prediction of mechanisms behind metabolic host–microbe interactions on the molecular level. We illustrate that constraint‐based models are a useful tool for the contextualization of metabolomic measurements and can further our insight into host–microbe interactions, yielding, e.g., in potential novel drugs and biomarkers. WIREs Syst Biol Med 2015, 7:195–219. doi: 10.1002/wsbm.1301 For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article.
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Affiliation(s)
- Almut Heinken
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belval, Luxembourg
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Oberhardt MA, Gianchandani EP. Genome-scale modeling and human disease: an overview. Front Physiol 2015; 5:527. [PMID: 25667572 PMCID: PMC4304257 DOI: 10.3389/fphys.2014.00527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022] Open
Affiliation(s)
- Matthew A Oberhardt
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, School of Computer Sciences, and Sackler School of Medicine, Tel Aviv University Tel Aviv, Israel
| | - Erwin P Gianchandani
- Division of Computer and Network Systems, United States National Science Foundation Arlington, VA, USA
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