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Pradhan SS, R SS, Kanikaram SP, V M DD, Pargaonkar A, Dandamudi RB, Sivaramakrishnan V. Metabolic deregulation associated with aging modulates protein aggregation in the yeast model of Huntington's disease. J Biomol Struct Dyn 2023:1-18. [PMID: 37732342 DOI: 10.1080/07391102.2023.2257322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023]
Abstract
Huntington's disease is associated with increased CAG repeat resulting in an expanded polyglutamine tract in the protein Huntingtin (HTT) leading to its aggregation resulting in neurodegeneration. Previous studies have shown that N-terminal HTT with 46Q aggregated in the stationary phase but not the logarithmic phase in the yeast model of HD. We carried out a metabolomic analysis of logarithmic and stationary phase yeast model of HD expressing different polyQ lengths attached to N-terminal HTT tagged with enhanced green fluorescent protein (EGFP). The results show significant changes in the metabolic profile and deregulated pathways in stationary phase cells compared to logarithmic phase cells. Comparison of metabolic pathways obtained from logarithmic phase 46Q versus 25Q with those obtained for presymptomatic HD patients from our previous study and drosophila model of HD showed considerable overlap. The arginine biosynthesis pathway emerged as one of the key pathways that is common in stationary phase yeast compared to logarithmic phase and HD patients. Treatment of yeast with arginine led to a significant decrease, while transfer to arginine drop-out media led to a significant increase in the size of protein aggregates in both logarithmic and stationary phase yeast model of HD. Knockout of arginine transporters in the endoplasmic reticulum and vacuole led to a significant decrease in mutant HTT aggregation. Overall our results highlight arginine as a critical metabolite that modulates the aggregation of mutant HTT and disease progression in HD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Swaroop R
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Phalguna Kanikaram
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru, Karnataka, India
| | | | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
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Vishweswaraiah S, Yilmaz A, Saiyed N, Khalid A, Koladiya PR, Pan X, Macias S, Robinson AC, Mann D, Green BD, Kerševičiūte I, Gordevičius J, Radhakrishna U, Graham SF. Integrative Analysis Unveils the Correlation of Aminoacyl-tRNA Biosynthesis Metabolites with the Methylation of the SEPSECS Gene in Huntington's Disease Brain Tissue. Genes (Basel) 2023; 14:1752. [PMID: 37761892 PMCID: PMC10530570 DOI: 10.3390/genes14091752] [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: 08/02/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The impact of environmental factors on epigenetic changes is well established, and cellular function is determined not only by the genome but also by interacting partners such as metabolites. Given the significant impact of metabolism on disease progression, exploring the interaction between the metabolome and epigenome may offer new insights into Huntington's disease (HD) diagnosis and treatment. Using fourteen post-mortem HD cases and fourteen control subjects, we performed metabolomic profiling of human postmortem brain tissue (striatum and frontal lobe), and we performed DNA methylome profiling using the same frontal lobe tissue. Along with finding several perturbed metabolites and differentially methylated loci, Aminoacyl-tRNA biosynthesis (adj p-value = 0.0098) was the most significantly perturbed metabolic pathway with which two CpGs of the SEPSECS gene were correlated. This study improves our understanding of molecular biomarker connections and, importantly, increases our knowledge of metabolic alterations driving HD progression.
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Affiliation(s)
- Sangeetha Vishweswaraiah
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (S.V.); (U.R.)
| | - Ali Yilmaz
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
| | - Nazia Saiyed
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
| | - Abdullah Khalid
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
| | - Purvesh R. Koladiya
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
| | - Xiaobei Pan
- Advanced Asset Technology Centre, Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5DL, UK; (X.P.); (S.M.); (B.D.G.)
| | - Shirin Macias
- Advanced Asset Technology Centre, Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5DL, UK; (X.P.); (S.M.); (B.D.G.)
| | - Andrew C. Robinson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Neuroscience, The University of Manchester, Salford Royal Hospital, Salford M6 8HD, UK; (A.C.R.); (D.M.)
| | - David Mann
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Neuroscience, The University of Manchester, Salford Royal Hospital, Salford M6 8HD, UK; (A.C.R.); (D.M.)
| | - Brian D. Green
- Advanced Asset Technology Centre, Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5DL, UK; (X.P.); (S.M.); (B.D.G.)
| | - Ieva Kerševičiūte
- VUGENE, LLC, 625 Kenmoor Ave Suite 301 PMB 96578, Grand Rapids, MI 49546, USA; (I.K.); (J.G.)
| | - Juozas Gordevičius
- VUGENE, LLC, 625 Kenmoor Ave Suite 301 PMB 96578, Grand Rapids, MI 49546, USA; (I.K.); (J.G.)
| | - Uppala Radhakrishna
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (S.V.); (U.R.)
| | - Stewart F. Graham
- Department of Obstetrics and Gynecology, Corewell Health William Beaumont University Hospital, 3601 W. 13 Mile Road, Royal Oak, MI 48073, USA; (S.V.); (U.R.)
- Metabolomics Department, Corewell Health Research Institute, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA; (A.Y.); (N.S.); (A.K.); (P.R.K.)
- Department of Obstetrics and Gynecology, Oakland University-William Beaumont School of Medicine, Rochester, MI 48309, USA
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Burtscher J, Pepe G, Maharjan N, Riguet N, Di Pardo A, Maglione V, Millet GP. Sphingolipids and impaired hypoxic stress responses in Huntington disease. Prog Lipid Res 2023; 90:101224. [PMID: 36898481 DOI: 10.1016/j.plipres.2023.101224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/20/2023] [Accepted: 03/05/2023] [Indexed: 03/11/2023]
Abstract
Huntington disease (HD) is a debilitating, currently incurable disease. Protein aggregation and metabolic deficits are pathological hallmarks but their link to neurodegeneration and symptoms remains debated. Here, we summarize alterations in the levels of different sphingolipids in an attempt to characterize sphingolipid patterns specific to HD, an additional molecular hallmark of the disease. Based on the crucial role of sphingolipids in maintaining cellular homeostasis, the dynamic regulation of sphingolipids upon insults and their involvement in cellular stress responses, we hypothesize that maladaptations or blunted adaptations, especially following cellular stress due to reduced oxygen supply (hypoxia) contribute to the development of pathology in HD. We review how sphingolipids shape cellular energy metabolism and control proteostasis and suggest how these functions may fail in HD and in combination with additional insults. Finally, we evaluate the potential of improving cellular resilience in HD by conditioning approaches (improving the efficiency of cellular stress responses) and the role of sphingolipids therein. Sphingolipid metabolism is crucial for cellular homeostasis and for adaptations following cellular stress, including hypoxia. Inadequate cellular management of hypoxic stress likely contributes to HD progression, and sphingolipids are potential mediators. Targeting sphingolipids and the hypoxic stress response are novel treatment strategies for HD.
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Affiliation(s)
- Johannes Burtscher
- Institute of Sport Sciences, University of Lausanne, 1015 Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, 1005 Lausanne, Switzerland.
| | - Giuseppe Pepe
- IRCCS Neuromed, Via Dell'Elettronica, 86077 Pozzilli, Italy
| | - Niran Maharjan
- Department of Neurology, Center for Experimental Neurology, Inselspital University Hospital, 3010 Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, 3010 Bern, Switzerland
| | | | - Alba Di Pardo
- IRCCS Neuromed, Via Dell'Elettronica, 86077 Pozzilli, Italy
| | | | - Grégoire P Millet
- Institute of Sport Sciences, University of Lausanne, 1015 Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, 1005 Lausanne, Switzerland
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Pradhan SS, Rao KR, Manjunath M, Saiswaroop R, Patnana DP, Phalguna KS, Choudhary B, Sivaramakrishnan V. Vitamin B 6, B 12 and folate modulate deregulated pathways and protein aggregation in yeast model of Huntington disease. 3 Biotech 2023; 13:96. [PMID: 36852176 PMCID: PMC9958225 DOI: 10.1007/s13205-023-03525-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Huntington's disease (HD) is an incurable and progressive neurodegenerative disease affecting the basal ganglia of the brain. HD is caused due to expansion of the polyglutamine tract in the protein Huntingtin resulting in aggregates. The increased PolyQ length results in aggregation of protein Huntingtin leading to neuronal cell death. Vitamin B6, B12 and folate are deficient in many neurodegenerative diseases. We performed an integrated analysis of transcriptomic, metabolomic and cofactor-protein network of vitamin B6, B12 and folate was performed. Our results show considerable overlap of pathways modulated by Vitamin B6, B12 and folate with those obtained from transcriptomic and metabolomic data of HD patients and model systems. Further, in yeast model of HD we showed treatment of B6, B12 or folate either alone or in combination showed impaired aggregate formation. Transcriptomic analysis of yeast model treated with B6, B12 and folate showed upregulation of pathways like ubiquitin mediated proteolysis, autophagy, peroxisome, fatty acid, lipid and nitrogen metabolism. Metabolomic analysis of yeast model shows deregulation of pathways like aminoacyl-tRNA biosynthesis, metabolism of various amino acids, nitrogen metabolism and glutathione metabolism. Integrated transcriptomic and metabolomic analysis of yeast model showed concordance in the pathways obtained. Knockout of Peroxisomal (PXP1 and PEX7) and Autophagy (ATG5) genes in yeast increased aggregates which is mitigated by vitamin B6, B12 and folate treatment. Taken together our results show a role for Vitamin B6, B12 and folate mediated modulation of pathways important for preventing protein aggregation with potential implications for HD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03525-y.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - K. Raksha Rao
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - R. Saiswaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Durga Prasad Patnana
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Kanikaram Sai Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka 560100 India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515134 India
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Zhao H, Wang W, Lin T, Gong L. Serum Metabolomics of Benign Essential Blepharospasm Using Liquid Chromatography and Orbitrap Mass Spectrometry. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6876327. [PMID: 36452462 PMCID: PMC9704060 DOI: 10.1155/2022/6876327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/04/2022] [Accepted: 09/24/2022] [Indexed: 01/19/2024]
Abstract
Background Benign essential blepharospasm (BEB) is a form of focal dystonia that causes excessive involuntary spasms of the eyelids. Currently, the pathogenesis of BEB remains unclear. This study is aimed at investigating the serum metabolites profiles in patients with BEB and healthy control and to identify the mechanism and biomarkers of this disease. Methods 30 patients with BEB and 33 healthy controls were recruited for this study. We conducted the quantitative and nontargeted metabolomics analysis of the serum samples from 63 subjects by using liquid chromatography and Orbitrap mass spectrometry (LC-Orbitrap MS). Multivariate statistical analysis was performed to detect and identify different metabolites between the two groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and receiver operating characteristic (ROC) curve analysis of the altered metabolites were performed. Results A total of 134 metabolites were found and identified. The metabolites belonged to several metabolic pathways including phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, arginine biosynthesis, linoleic acid metabolism, tryptophan metabolism, aminoacyl-tRNA biosynthesis, sphingolipid metabolism, glycosphingolipid biosynthesis, leucine and isoleucine biosynthesis, and vitamin B6 metabolism. Eight metabolites were identified as the potential biomarkers. Conclusions These results demonstrated that serum metabolic profiling of BEB patients was significantly different from healthy controls based on LC-Orbitrap MS. Besides, metabolomics might provide useful information for a better understanding of BEB.
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Affiliation(s)
- Han Zhao
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, China
- Laboratory of Myopia, NHC Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Fudan University, Shanghai 200000, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, China
| | - Wushuang Wang
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, China
- Laboratory of Myopia, NHC Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Fudan University, Shanghai 200000, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, China
| | - Tong Lin
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, China
- Laboratory of Myopia, NHC Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Fudan University, Shanghai 200000, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, China
| | - Lan Gong
- Department of Ophthalmology, Eye, Ear, Nose, and Throat Hospital of Fudan University, Shanghai 200000, China
- Laboratory of Myopia, NHC Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, Fudan University, Shanghai 200000, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, Shanghai 200000, China
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Pradhan SS, Thota SM, Rajaratnam S, Bhagavatham SKS, Pulukool SK, Rathnakumar S, Phalguna KS, Dandamudi RB, Pargaonkar A, Joseph P, Joshy EV, Sivaramakrishnan V. Integrated multi-omics analysis of Huntington disease identifies pathways that modulate protein aggregation. Dis Model Mech 2022; 15:dmm049492. [PMID: 36052548 PMCID: PMC10655815 DOI: 10.1242/dmm.049492] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Huntington disease (HD) is a neurodegenerative disease associated with polyglutamine expansion in the protein huntingtin (HTT). Although the length of the polyglutamine repeat correlates with age at disease onset and severity, psychological, cognitive and behavioral complications point to the existence of disease modifiers. Mitochondrial dysfunction and metabolic deregulation are both associated with the HD but, despite multi-omics characterization of patients and model systems, their mechanisms have remained elusive. Systems analysis of multi-omics data and its validation by using a yeast model could help to elucidate pathways that modulate protein aggregation. Metabolomics analysis of HD patients and of a yeast model of HD was, therefore, carried out. Our analysis showed a considerable overlap of deregulated metabolic pathways. Further, the multi-omics analysis showed deregulated pathways common in human, mice and yeast model systems, and those that are unique to them. The deregulated pathways include metabolic pathways of various amino acids, glutathione metabolism, longevity, autophagy and mitophagy. The addition of certain metabolites as well as gene knockouts targeting the deregulated metabolic and autophagy pathways in the yeast model system showed that these pathways do modulate protein aggregation. Taken together, our results showed that the modulation of deregulated pathways influences protein aggregation in HD, and has implications for progression and prognosis. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sai S. Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sai M. Thota
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Saiswaroop Rajaratnam
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sai K. S. Bhagavatham
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sujith K. Pulukool
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Sriram Rathnakumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Kanikaram S. Phalguna
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
| | - Rajesh B. Dandamudi
- Department of Chemistry, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh 515 134, India
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru 560048, India
| | - Prasanth Joseph
- Application Division, Agilent Technologies Ltd., Bengaluru 560048, India
| | - E. V. Joshy
- Department of Neurology, Sri Sathya Sai Institute of Higher Medical Sciences, Whitefield, Bengaluru, Karnataka 560066, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India515134
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Phillips GR, Saville JT, Hancock SE, Brown SHJ, Jenner AM, McLean C, Fuller M, Newell KA, Mitchell TW. The long and the short of Huntington’s disease: how the sphingolipid profile is shifted in the caudate of advanced clinical cases. Brain Commun 2021; 4:fcab303. [PMID: 35169703 PMCID: PMC8833324 DOI: 10.1093/braincomms/fcab303] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/27/2021] [Accepted: 12/21/2021] [Indexed: 01/01/2023] Open
Abstract
Huntington’s disease is a devastating neurodegenerative disorder that onsets in late adulthood as progressive and terminal cognitive, psychiatric and motor deficits. The disease is genetic, triggered by a CAG repeat (polyQ) expansion mutation in the Huntingtin gene and resultant huntingtin protein. Although the mutant huntingtin protein is ubiquitously expressed, the striatum degenerates early and consistently in the disease. The polyQ mutation at the N-terminus of the huntingtin protein alters its natural interactions with neural phospholipids in vitro, suggesting that the specific lipid composition of brain regions could influence their vulnerability to interference by mutant huntingtin; however, this has not yet been demonstrated in vivo. Sphingolipids are critical cell signalling molecules, second messengers and membrane components. Despite evidence of sphingolipid disturbance in Huntington’s mouse and cell models, there is limited knowledge of how these lipids are affected in human brain tissue. Using post-mortem brain tissue from five brain regions implicated in Huntington’s disease (control n = 13, Huntington’s n = 13), this study aimed to identify where and how sphingolipid species are affected in the brain of clinically advanced Huntington’s cases. Sphingolipids were extracted from the tissue and analysed using targeted mass spectrometry analysis; proteins were analysed by western blot. The caudate, putamen and cerebellum had distinct sphingolipid changes in Huntington’s brain whilst the white and grey frontal cortex were spared. The caudate of Huntington’s patients had a shifted sphingolipid profile, favouring long (C13–C21) over very-long-chain (C22–C26) ceramides, sphingomyelins and lactosylceramides. Ceramide synthase 1, which synthesizes the long-chain sphingolipids, had a reduced expression in Huntington’s caudate, correlating positively with a younger age at death and a longer CAG repeat length of the Huntington’s patients. The expression of ceramide synthase 2, which synthesizes very-long-chain sphingolipids, was not different in Huntington’s brain. However, there was evidence of possible post-translational modifications in the Huntington’s patients only. Post-translational modifications to ceramide synthase 2 may be driving the distinctive sphingolipid profile shifts of the caudate in advanced Huntington’s disease. This shift in the sphingolipid profile is also found in the most severely affected brain regions of several other neurodegenerative conditions and may be an important feature of region-specific cell dysfunction in neurodegenerative disease.
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Affiliation(s)
- Gabrielle R. Phillips
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Jennifer T. Saville
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia
| | - Sarah E. Hancock
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Simon H. J. Brown
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
- School of Chemistry and Molecular Biosciences, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Andrew M. Jenner
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Catriona McLean
- Department of Anatomical Pathology, Alfred Health and Florey Neuroscience, Parkville, VIC 3052, Australia
| | - Maria Fuller
- Genetics and Molecular Pathology, SA Pathology at Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Kelly A. Newell
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Todd W. Mitchell
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
- School of Medicine, University of Wollongong, Wollongong, NSW 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia
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Identification of potential serum metabolic biomarkers for patient with keratoconus using untargeted metabolomics approach. Exp Eye Res 2021; 211:108734. [PMID: 34428458 DOI: 10.1016/j.exer.2021.108734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/01/2021] [Accepted: 08/17/2021] [Indexed: 11/22/2022]
Abstract
This study aimed to investigate the metabolite differences between patients with keratoconus and control subjects and identify potential serum biomarkers for keratoconus using a non-targeted metabolomics approach. Venous blood samples were obtained from patients with keratoconus (n = 20) as well as from age-, gender- and race-matched control subjects (n = 20). Metabolites extracted from serum were separated and analyzed by liquid chromatography/quadrupole time-of-flight mass spectrometer. Processing of raw data and analysis of the data files was performed using Agilent Mass Hunter Qualitative software. The identified metabolites were subjected to a principal component and hierarchical cluster analysis. Appropriate statistical tests were used to analyze the metabolomic profiling data. Together, the analysis revealed that the dehydroepiandrosterone sulfate from the steroidal hormone synthesis pathway was significantly upregulated in patients with keratoconus (p < 0.05). Also, a combination of eicosanoids from the arachidonic acid pathway, mainly prostaglandin F2α, prostaglandin A2, 16,16-dimethyl prostaglandin E2, and 5-hydroxyeicosatetraenoic acid were collectively up-regulated as a group in keratoconus patients (p < 0.05). On the other hand, glycerophospholipid PS(17:2(9Z,12Z)/20:4(5Z,8Z,11Z,14Z)) was found to be significantly upregulated in the metabolomics profiles of control subjects (p < 0.05). The differently regulated metabolites provide insights into the pathophysiology of keratoconus and could potentially be used as biomarkers for keratoconus to aid in screening for individuals at risk hence, enabling early diagnosis and timely monitoring of disease.
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Dong X, Cong S. The emerging roles of long non-coding RNAs in polyglutamine diseases. J Cell Mol Med 2021; 25:8095-8102. [PMID: 34318578 PMCID: PMC8419158 DOI: 10.1111/jcmm.16808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 11/30/2022] Open
Abstract
Polyglutamine (polyQ) diseases are characterized by trinucleotide repeat amplifications within genes, thus resulting in the formation of polyQ peptides, selective neuronal degeneration and possibly death due to neurodegenerative diseases (NDDs). Long non-coding RNAs (lncRNAs), which exceed 200 nucleotides in length, have been shown to play important roles in several pathological processes of NDDs, including polyQ diseases. Some lncRNAs have been consistently identified to be specific to polyQ diseases, and circulating lncRNAs are among the most promising novel candidates in the search for non-invasive biomarkers for the diagnosis and prognosis of polyQ diseases. In this review, we describe the emerging roles of lncRNAs in polyQ diseases and provide an overview of the general biology of lncRNAs, their implications in pathophysiology and their potential roles as future biomarkers and applications for therapy.
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Affiliation(s)
- Xiaoyu Dong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
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Gupta N, Ramakrishnan S, Wajid S. Emerging role of metabolomics in protein conformational disorders. Expert Rev Proteomics 2021; 18:395-410. [PMID: 34227444 DOI: 10.1080/14789450.2021.1948330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Introduction: Metabolomics focuses on interactions among different metabolites associated with various cellular functions in cells, tissues, and organs. In recent years, metabolomics has emerged as a powerful tool to identify perturbed metabolites, pathways influenced by the environment, for protein conformational diseases (PCDs) and also offers wide clinical application.Area Covered: This review provides a brief overview of recent advances in metabolomics as applied to identify metabolic variations in PCDs, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, prion disease, and cardiac amyloidosis. The 'PubMed' and 'Google Scholar' database search methods have been used to screen the published reports with key search terms: metabolomics, biomarkers, and protein conformational disorders.Expert opinion: Metabolomics is the large-scale study of metabolites and is deemed to overwhelm other omics. It plays a crucial role in finding variations in diseases due to protein conformational changes. However, many PCDs are yet to be identified. Metabolomics is still an emerging field; there is a need for new high-resolution analytical techniques and more studies need to be carried out to generate new information.
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Affiliation(s)
- Nimisha Gupta
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
| | | | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
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11
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Muthubharathi BC, Gowripriya T, Balamurugan K. Metabolomics: small molecules that matter more. Mol Omics 2021; 17:210-229. [PMID: 33598670 DOI: 10.1039/d0mo00176g] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics, an analytical study with high-throughput profiling, helps to understand interactions within a biological system. Small molecules, called metabolites or metabolomes with the size of <1500 Da, depict the status of a biological system in a different manner. Currently, we are in need to globally analyze the metabolome and the pathways involved in healthy, as well as diseased conditions, for possible therapeutic applications. Metabolome analysis has revealed high-abundance molecules during different conditions such as diet, environmental stress, microbiota, and disease and treatment states. As a result, it is hard to understand the complete and stable network of metabolites of a biological system. This review helps readers know the available techniques to study metabolomics in addition to other major omics such as genomics, transcriptomics, and proteomics. This review also discusses the metabolomics in various pathological conditions and the importance of metabolomics in therapeutic applications.
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12
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Zafarullah M, Durbin-Johnson B, Fourie ES, Hessl DR, Rivera SM, Tassone F. Metabolomic Biomarkers Are Associated With Area of the Pons in Fragile X Premutation Carriers at Risk for Developing FXTAS. Front Psychiatry 2021; 12:691717. [PMID: 34483988 PMCID: PMC8415564 DOI: 10.3389/fpsyt.2021.691717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/21/2021] [Indexed: 11/22/2022] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late adult-onset neurodegenerative disorder that affects movement and cognition in male and female carriers of a premutation allele (55-200 CGG repeats; PM) in the fragile X mental retardation (FMR1) gene. It is currently unknown how the observed brain changes are associated with metabolic signatures in individuals who develop the disorder over time. The primary objective of this study was to investigate the correlation between longitudinal changes in the brain (area of the pons, midbrain, and MCP width) and the changes in the expression level of metabolic biomarkers of early diagnosis and progression of FXTAS in PM who, as part of an ongoing longitudinal study, emerged into two distinct categories. These included those who developed symptoms of FXTAS (converters, CON) at subsequent visits and those who did not meet the criteria of diagnosis (non-converters, NCON) and were compared to age-matched healthy controls (HC). We assessed CGG repeat allele size by Southern Blot and PCR analysis. Magnetic Resonance Imaging (MRIs) acquisition was obtained on a 3T Siemens Trio scanner and metabolomic profile was obtained by ultra-performance liquid chromatography, accurate mass spectrometer, and an Orbitrap mass analyzer. Our findings indicate that differential metabolite levels are linked with the area of the pons between healthy control and premutation groups. More specifically, we observed a significant association of ceramides and mannonate metabolites with a decreased area of the pons, both at visit 1 (V1) and visit 2 (V2) only in the CON as compared to the NCON group suggesting their potential role in the development of the disorder. In addition, we found a significant correlation of these metabolic signatures with the FXTAS stage at V2 indicating their contribution to the progression and pathogenesis of FXTAS. Interestingly, these metabolites, as part of lipid and sphingolipid lipids pathways, provide evidence of the role that their dysregulation plays in the development of FXTAS and inform us as potential targets for personalized therapeutic development.
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Affiliation(s)
- Marwa Zafarullah
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Sacramento, CA, United States
| | - Blythe Durbin-Johnson
- Division of Biostatistics, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Emily S Fourie
- Center for Mind and Brain, University of California, Davis, Davis, CA, United States.,Department of Psychology, University of California, Davis, Davis, CA, United States
| | - David R Hessl
- MIND Institute, University of California, Davis Medical Center, Sacramento, CA, United States.,Department of Psychiatry and Behavioral Sciences, University of California, Davis Medical Center, Sacramento, CA, United States
| | - Susan M Rivera
- Center for Mind and Brain, University of California, Davis, Davis, CA, United States.,Department of Psychology, University of California, Davis, Davis, CA, United States.,MIND Institute, University of California, Davis Medical Center, Sacramento, CA, United States
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Sacramento, CA, United States.,MIND Institute, University of California, Davis Medical Center, Sacramento, CA, United States
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13
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Akyol S, Yilmaz A, Oh KJ, Ugur Z, Aydas B, McGuinness B, Passmore P, Kehoe PG, Maddens M, Green BD, Graham SF. Evidence that the Kennedy and polyamine pathways are dysregulated in human brain in cases of dementia with Lewy bodies. Brain Res 2020; 1743:146897. [PMID: 32450077 DOI: 10.1016/j.brainres.2020.146897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 01/18/2023]
Abstract
Disruptions of brain metabolism are considered integral to the pathogenesis of dementia, but thus far little is known of how dementia with Lewy bodies (DLB) impacts the brain metabolome. DLB is less well known than other neurodegenerative diseases such as Alzheimer's and Parkinson's disease which is perhaps why it is under-investigated. This exploratory study aimed to address current knowledge gaps in DLB research and search for potentially targetable biochemical pathways for therapeutics. It also aimed to better understand metabolic similarities and differences with other dementias. Combined metabolomic analyses of 1H NMR and tandem mass spectrometry of neocortical post-mortem brain tissue (Brodmann region 7) from autopsy confirmed cases of DLB (n = 15) were compared with age/gender-matched, non-cognitively impaired healthy controls (n = 30). Following correction for multiple comparisons, only 2 metabolites from a total of 219 measured compounds significantly differed. Putrescine was suppressed (55.4%) in DLB and O-phosphocholine was elevated (52.5%). We identified a panel of 5 metabolites (PC aa C38:4, O-Phosphocholine, putrescine, 4-Aminobutyrate, and SM C16:0) capable of accurately discriminating between DLB and control subjects. Deep Learning (DL) provided the best predictive model following 10-fold cross validation (AUROC (95% CI) = 0.80 (0.60-1.0)) with sensitivity and specificity equal to 0.92 and 0.88, respectively. Altered brain levels of putrescine and O-phosphocholine indicate that the Kennedy pathway and polyamine metabolism are perturbed in DLB. These are accompanied by a consistent underlying trend of lipid dysregulation. As yet it is unclear whether these are a cause or consequence of DLB onset.
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Affiliation(s)
- Sumeyya Akyol
- Beaumont Research Institute, Royal Oak, MI 48073, USA
| | - Ali Yilmaz
- Beaumont Research Institute, Royal Oak, MI 48073, USA
| | - Kyung Joon Oh
- Beaumont Research Institute, Royal Oak, MI 48073, USA; Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam-si, Republic of Korea; Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Zafer Ugur
- Beaumont Research Institute, Royal Oak, MI 48073, USA
| | - Buket Aydas
- Departments of Mathematics and Computer Sciences, Albion College, 611 E. Porter St, Albion, MI 49224, USA
| | - Bernadette McGuinness
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Peter Passmore
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Patrick G Kehoe
- Dementia Research Group, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael Maddens
- Oakland University-William Beaumont School of Medicine, Rochester, MI 48309, USA
| | - Brian D Green
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
| | - Stewart F Graham
- Beaumont Research Institute, Royal Oak, MI 48073, USA; Oakland University-William Beaumont School of Medicine, Rochester, MI 48309, USA.
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Abstract
Cerebral palsy (CP), defined as a group of nonprogressive disorders of movement and posture, is the most common cause of severe neurodisability in children. The prevalence of CP is the same across the globe, affecting approximately 17 million people worldwide. Cerebral Palsy is an umbrella term used to describe the disease due to its inherent heterogeneity. For instance, CP has multiple (1) causes; (2) clinical types; (3) patterns of neuropathology on brain imaging and (4) it's associated with several developmental pathologies such as intellectual disability, autism, epilepsy, and visual impairment. Understanding its physiopathology is crucial to developing protective strategies. Despite its importance, there is still insufficient progress in the areas of CP prediction, early diagnosis, treatment, and prevention. Herein we describe the current risk factors and biomarkers used for the diagnosis and prediction of CP. With the advancement in biomarker discovery, we predict that our understanding of the etiopathophysiology of CP will also increase, lending to more opportunities for developing novel treatments and prognosis.
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Affiliation(s)
- Zeynep Alpay Savasan
- Department of Obstetrics and Gynecology, Maternal Fetal Medicine Division, Beaumont Health System, Royal Oak, MI, United States; Oakland University-William Beaumont School of Medicine, Beaumont Health, Royal Oak, MI, United States.
| | - Sun Kwon Kim
- Department of Obstetrics and Gynecology, Maternal Fetal Medicine Division, Beaumont Health System, Royal Oak, MI, United States; Oakland University-William Beaumont School of Medicine, Beaumont Health, Royal Oak, MI, United States
| | - Kyung Joon Oh
- Beaumont Research Institute, Beaumont Health, Royal Oak, MI, United States; Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, South Korea; Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam-si, Gyeonggi-do, South Korea
| | - Stewart F Graham
- Oakland University-William Beaumont School of Medicine, Beaumont Health, Royal Oak, MI, United States; Beaumont Research Institute, Beaumont Health, Royal Oak, MI, United States
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15
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Graham SF, Turkoglu O, Yilmaz A, Ustun I, Ugur Z, Bjorndhal T, Han B, Mandal R, Wishart D, Bahado-Singh RO. Targeted metabolomics highlights perturbed metabolism in the brain of autism spectrum disorder sufferers. Metabolomics 2020; 16:59. [PMID: 32333121 DOI: 10.1007/s11306-020-01685-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders characterized by deficiencies in social interactions and communication, combined with restricted and repetitive behavioral issues. OBJECTIVES As little is known about the etiopathophysiology of ASD and early diagnosis is relatively subjective, we aim to employ a targeted, fully quantitative metabolomics approach to biochemically profile post-mortem human brain with the overall goal of identifying metabolic pathways that may have been perturbed as a result of the disease while uncovering potential central diagnostic biomarkers. METHODS Using a combination of 1H NMR and DI/LC-MS/MS we quantitatively profiled the metabolome of the posterolateral cerebellum from post-mortem human brain harvested from people who suffered with ASD (n = 11) and compared them with age-matched controls (n = 10). RESULTS We accurately identified and quantified 203 metabolites in post-mortem brain extracts and performed a metabolite set enrichment analyses identifying 3 metabolic pathways as significantly perturbed (p < 0.05). These include Pyrimidine, Ubiquinone and Vitamin K metabolism. Further, using a variety of machine-based learning algorithms, we identified a panel of central biomarkers (9-hexadecenoylcarnitine (C16:1) and the phosphatidylcholine PC ae C36:1) capable of discriminating between ASD and controls with an AUC = 0.855 with a sensitivity and specificity equal to 0.80 and 0.818, respectively. CONCLUSION For the first time, we report the use of a multi-platform metabolomics approach to biochemically profile brain from people with ASD and report several metabolic pathways which are perturbed in the diseased brain of ASD sufferers. Further, we identified a panel of biomarkers capable of distinguishing ASD from control brains. We believe that these central biomarkers may be useful for diagnosing ASD in more accessible biomatrices.
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Affiliation(s)
- Stewart F Graham
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA.
- Research Institute, Metabolomics Division, Beaumont Health, Royal Oak, MI, 48073, USA.
| | - Onur Turkoglu
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
| | - Ali Yilmaz
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Research Institute, Metabolomics Division, Beaumont Health, Royal Oak, MI, 48073, USA
| | - Ilyas Ustun
- Wayne State University, Civil and Environmental Engineering, Detroit, MI, USA
| | - Zafer Ugur
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Research Institute, Metabolomics Division, Beaumont Health, Royal Oak, MI, 48073, USA
| | - Trent Bjorndhal
- Department of Biological and Computing Sciences, University of Alberta, Edmonton, AB, Canada
| | - BeomSoo Han
- Department of Biological and Computing Sciences, University of Alberta, Edmonton, AB, Canada
| | - Rupa Mandal
- Department of Biological and Computing Sciences, University of Alberta, Edmonton, AB, Canada
| | - David Wishart
- Department of Biological and Computing Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ray O Bahado-Singh
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
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16
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Nambo-Venegas R, Valdez-Vargas C, Cisneros B, Palacios-González B, Vela-Amieva M, Ibarra-González I, Cerecedo-Zapata CM, Martínez-Cruz E, Cortés H, Reyes-Grajeda JP, Magaña JJ. Altered Plasma Acylcarnitines and Amino Acids Profile in Spinocerebellar Ataxia Type 7. Biomolecules 2020; 10:biom10030390. [PMID: 32138195 PMCID: PMC7175318 DOI: 10.3390/biom10030390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/19/2022] Open
Abstract
Spinocerebellar ataxia type 7 (SCA7), a neurodegenerative disease characterized by cerebellar ataxia and retinal degeneration, is caused by an abnormal CAG repeat expansion in the ATXN7 gene coding region. The onset and severity of SCA7 are highly variable between patients, thus identification of sensitive biomarkers that accurately diagnose the disease and monitoring its progression are needed. With the aim of identified SCA7-specific metabolites with clinical relevance, we report for the first time, to the best of our knowledge, a metabolomics profiling of circulating acylcarnitines and amino acids in SCA7 patients. We identified 21 metabolites with altered levels in SCA7 patients and determined two different sets of metabolites with diagnostic power. The first signature of metabolites (Valine, Leucine, and Tyrosine) has the ability to discriminate between SCA7 patients and healthy controls, while the second one (Methionine, 3-hydroxytetradecanoyl-carnitine, and 3-hydroxyoctadecanoyl-carnitine) possess the capability to differentiate between early-onset and adult-onset patients, as shown by the multivariate model and ROC analyses. Furthermore, enrichment analyses of metabolic pathways suggest alterations in mitochondrial function, energy metabolism, and fatty acid beta-oxidation in SCA7 patients. In summary, circulating SCA7-specific metabolites identified in this study could serve as effective predictors of SCA7 progression in the clinics, as they are sampled in accessible biofluid and assessed by a relatively simple biochemical assay.
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Affiliation(s)
- Rafael Nambo-Venegas
- Laboratory of Chronic Diseases Biochemistry, National Genomics Medicine Institute (INMEGEN), Mexico City 14610, Mexico;
| | - Claudia Valdez-Vargas
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City 14389, Mexico; (C.V.-V.); (H.C.)
- Department of Genetics and Molecular Biology, Center of Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | - Bulmaro Cisneros
- Department of Genetics and Molecular Biology, Center of Research and Advanced Studies (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | | | - Marcela Vela-Amieva
- Laboratory of Inborn errors of metabolism, National Pediatrics Institute (INP), Mexico City 04530, Mexico;
| | | | - César M. Cerecedo-Zapata
- Rehabilitation and Special Education Center of Veracruz (CRISVER-DIF), Xalapa 91097, Veracruz, Mexico; (C.M.C.-Z.)
| | - Emilio Martínez-Cruz
- Rehabilitation and Special Education Center of Veracruz (CRISVER-DIF), Xalapa 91097, Veracruz, Mexico; (C.M.C.-Z.)
| | - Hernán Cortés
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City 14389, Mexico; (C.V.-V.); (H.C.)
| | - Juan P. Reyes-Grajeda
- Laboratory of Chronic Diseases Biochemistry, National Genomics Medicine Institute (INMEGEN), Mexico City 14610, Mexico;
- Correspondence: (J.P.R.-G.); or (J.J.M.); Tel.: +52-55-5350-1900 (ext. 1192) (J.P.R.-G.); +52-55- 5999-1000 (ext. 14708) (J.J.M.)
| | - Jonathan J. Magaña
- Laboratory of Genomic Medicine, Department of Genetics, National Rehabilitation Institute (INR-LGII), Mexico City 14389, Mexico; (C.V.-V.); (H.C.)
- Correspondence: (J.P.R.-G.); or (J.J.M.); Tel.: +52-55-5350-1900 (ext. 1192) (J.P.R.-G.); +52-55- 5999-1000 (ext. 14708) (J.J.M.)
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17
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Chen K, Baluya D, Tosun M, Li F, Maletic-Savatic M. Imaging Mass Spectrometry: A New Tool to Assess Molecular Underpinnings of Neurodegeneration. Metabolites 2019; 9:metabo9070135. [PMID: 31295847 PMCID: PMC6681116 DOI: 10.3390/metabo9070135] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/19/2019] [Accepted: 06/26/2019] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases are prevalent and devastating. While extensive research has been done over the past decades, we are still far from comprehensively understanding what causes neurodegeneration and how we can prevent it or reverse it. Recently, systems biology approaches have led to a holistic examination of the interactions between genome, metabolome, and the environment, in order to shed new light on neurodegenerative pathogenesis. One of the new technologies that has emerged to facilitate such studies is imaging mass spectrometry (IMS). With its ability to map a wide range of small molecules with high spatial resolution, coupled with the ability to quantify them at once, without the need for a priori labeling, IMS has taken center stage in current research efforts in elucidating the role of the metabolome in driving neurodegeneration. IMS has already proven to be effective in investigating the lipidome and the proteome of various neurodegenerative diseases, such as Alzheimer's, Parkinson's, Huntington's, multiple sclerosis, and amyotrophic lateral sclerosis. Here, we review the IMS platform for capturing biological snapshots of the metabolic state to shed more light on the molecular mechanisms of the diseased brain.
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Affiliation(s)
- Kevin Chen
- Department of Biosciences, Rice University, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Dodge Baluya
- Chemical Imaging Research Core at MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
| | - Mehmet Tosun
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mirjana Maletic-Savatic
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
- Department of Neuroscience and Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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Urrutia NL. Adult-onset Huntington disease: An update. Nursing 2019; 49:36-43. [PMID: 31219985 DOI: 10.1097/01.nurse.0000559914.46449.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Appropriate nursing-care strategies depend on the early recognition of Huntington disease (HD) to prioritize a plan of care. This article offers perspective on the clinical presentation, prognosis, diagnosis, and management of adult-onset HD.
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Affiliation(s)
- Nancy L Urrutia
- Nancy L. Urrutia is a nurse educator in the Cleveland, Ohio metropolitan area
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19
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Dong X, Cong S. The Emerging Role of microRNAs in Polyglutamine Diseases. Front Mol Neurosci 2019; 12:156. [PMID: 31275113 PMCID: PMC6593396 DOI: 10.3389/fnmol.2019.00156] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/04/2019] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding molecules that regulate a large amount of post-transcriptional repressor genes by recognizing semi-complementary target sequences that are normally located in the 3' UTR of the mRNA. Altered expression of miRNA has been related to several pathological processes, including polyglutamine (Poly Q) diseases. Specific expression patterns in the circulating fluids and brain parenchyma have been speculated as potential biomarkers for Poly Q disease diagnosis and prognosis. Several miRNAs have been consistently identified in diseases including Huntington's disease (HD) and spinocerebellar ataxia (SCA). In our review, we describe the emerging role of miRNAs in Poly Q diseases and provide an overview on general miRNA biology, implications in pathophysiology, and their potential roles as future biomarkers and applications for therapy.
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Affiliation(s)
| | - Shuyan Cong
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
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20
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Zhang Q, Yin X, Wang H, Wu X, Li X, Li Y, Zhang X, Fu C, Li H, Qiu Y. Fecal Metabolomics and Potential Biomarkers for Systemic Lupus Erythematosus. Front Immunol 2019; 10:976. [PMID: 31130958 PMCID: PMC6509220 DOI: 10.3389/fimmu.2019.00976] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/16/2019] [Indexed: 01/03/2023] Open
Abstract
The role of metabolomics in autoimmune diseases has been a rapidly expanding area in researches over the last decade, while its pathophysiologic impact on systemic lupus erythematosus (SLE) remains poorly elucidated. In this study, we analyzed the metabolic profiling of fecal samples from SLE patients and healthy controls based on ultra-high-performance liquid chromatography equipped with mass spectrometry for exploring the potential biomarkers of SLE. The results showed that 23 differential metabolites and 5 perturbed pathways were identified between the two groups, including aminoacyl-tRNA biosynthesis, thiamine metabolism, nitrogen metabolism, tryptophan metabolism, and cyanoamino acid metabolism. In addition, logistic regression and ROC analysis were used to establish a diagnostic model for distinguishing SLE patients from healthy controls. The combined model of fecal PG 27:2 and proline achieved an area under the ROC curve of 0.846, and had a good diagnostic efficacy. In the present study, we analyzed the correlations between fecal metabolic perturbations and SLE pathogenesis. In summary, we firstly illustrate the comprehensive metabolic profiles of feces in SLE patients, suggesting that the fecal metabolites could be used as the potential non-invasive biomarkers for SLE.
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Affiliation(s)
- Qiong Zhang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaofeng Yin
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haifang Wang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xing Wu
- Longsee Biomedical Corporation, Guangzhou, China
| | - Xin Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yao Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaohe Zhang
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chen Fu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haixia Li
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yurong Qiu
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Huayin Medical Laboratory Center Co., Ltd., Guangzhou, China
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Alterations in the tyrosine and phenylalanine pathways revealed by biochemical profiling in cerebrospinal fluid of Huntington's disease subjects. Sci Rep 2019; 9:4129. [PMID: 30858393 PMCID: PMC6411723 DOI: 10.1038/s41598-019-40186-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/06/2019] [Indexed: 02/07/2023] Open
Abstract
Huntington’s disease (HD) is a severe neurological disease leading to psychiatric symptoms, motor impairment and cognitive decline. The disease is caused by a CAG expansion in the huntingtin (HTT) gene, but how this translates into the clinical phenotype of HD remains elusive. Using liquid chromatography mass spectrometry, we analyzed the metabolome of cerebrospinal fluid (CSF) from premanifest and manifest HD subjects as well as control subjects. Inter-group differences revealed that the tyrosine metabolism, including tyrosine, thyroxine, L-DOPA and dopamine, was significantly altered in manifest compared with premanifest HD. These metabolites demonstrated moderate to strong associations to measures of disease severity and symptoms. Thyroxine and dopamine also correlated with the five year risk of onset in premanifest HD subjects. The phenylalanine and the purine metabolisms were also significantly altered, but associated less to disease severity. Decreased levels of lumichrome were commonly found in mutated HTT carriers and the levels correlated with the five year risk of disease onset in premanifest carriers. These biochemical findings demonstrates that the CSF metabolome can be used to characterize molecular pathogenesis occurring in HD, which may be essential for future development of novel HD therapies.
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Alpay Savasan Z, Yilmaz A, Ugur Z, Aydas B, Bahado-Singh RO, Graham SF. Metabolomic Profiling of Cerebral Palsy Brain Tissue Reveals Novel Central Biomarkers and Biochemical Pathways Associated with the Disease: A Pilot Study. Metabolites 2019; 9:metabo9020027. [PMID: 30717353 PMCID: PMC6409919 DOI: 10.3390/metabo9020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 12/17/2022] Open
Abstract
Cerebral palsy (CP) is one of the most common causes of motor disability in childhood, with complex and heterogeneous etiopathophysiology and clinical presentation. Understanding the metabolic processes associated with the disease may aid in the discovery of preventive measures and therapy. Tissue samples (caudate nucleus) were obtained from post-mortem CP cases (n = 9) and age- and gender-matched control subjects (n = 11). We employed a targeted metabolomics approach using both 1H NMR and direct injection liquid chromatography-tandem mass spectrometry (DI/LC-MS/MS). We accurately identified and quantified 55 metabolites using 1H NMR and 186 using DI/LC-MS/MS. Among the 222 detected metabolites, 27 showed significant concentration changes between CP cases and controls. Glycerophospholipids and urea were the most commonly selected metabolites used to develop predictive models capable of discriminating between CP and controls. Metabolomics enrichment analysis identified folate, propanoate, and androgen/estrogen metabolism as the top three significantly perturbed pathways. We report for the first time the metabolomic profiling of post-mortem brain tissue from patients who died from cerebral palsy. These findings could help to further investigate the complex etiopathophysiology of CP while identifying predictive, central biomarkers of CP.
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Affiliation(s)
- Zeynep Alpay Savasan
- Department of Obstetrics and Gynecology, Maternal Fetal Medicine Division, Beaumont Health System, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA.
- Oakland University-William Beaumont School of Medicine, Beaumont Health, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA.
| | - Ali Yilmaz
- Beaumont Research Institute, Beaumont Health, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA.
| | - Zafer Ugur
- Beaumont Research Institute, Beaumont Health, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA.
| | - Buket Aydas
- Departments of Mathematics and Computer Sciences, Albion College, 611 E. Porter St., Albion, MI 49224, USA.
| | - Ray O Bahado-Singh
- Department of Obstetrics and Gynecology, Maternal Fetal Medicine Division, Beaumont Health System, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA.
- Oakland University-William Beaumont School of Medicine, Beaumont Health, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA.
| | - Stewart F Graham
- Oakland University-William Beaumont School of Medicine, Beaumont Health, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA.
- Beaumont Research Institute, Beaumont Health, 3811 W. 13 Mile Road, Royal Oak, MI 48073, USA.
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23
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Combinational Biomarkers for Atrial Fibrillation Derived from Atrial Appendage and Plasma Metabolomics Analysis. Sci Rep 2018; 8:16930. [PMID: 30446671 PMCID: PMC6240090 DOI: 10.1038/s41598-018-34930-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 10/18/2018] [Indexed: 02/06/2023] Open
Abstract
Atrial fibrillation (AF) is one of the most common types of arrhythmias and often leads to clinical complications. The objectives of this study were to offer insights into the metabolites of AF and to determine biomarkers for AF diagnosis or prediction. Sixty atrial appendage samples (AF group: 30; non-AF group: 30) and 163 plasma samples (AF group: 48; non-AF group: 115) from 49 AF patients and 116 non-AF patients were subjected to liquid chromatography positive ion electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) metabolomics analysis. Consequently, 24 metabolites in atrial appendage samples and 24 metabolites in plasma samples were found to reflect metabolic differences between AF and non-AF patients (variable importance in projection (VIP) ≥ 1, P ≤ 0.05). Five identical metabolites including creatinine, D-glutamic acid, choline, hypoxanthine, and niacinamide (VIP ≥ 1.5, P < 0.01, FDR < 0.05) in atrial appendage and plasma samples were considered prominent features of AF patients, and the D-glutamine and D-glutamate metabolic pathway was also identified as a feature of AF patients. Finally, in plasma samples, the combination of D-glutamic acid, creatinine, and choline had an AUC value of 0.927 (95% CI: 0.875-0.979, P < 0.001) and displayed 90.5% sensitivity and 83.3% specificity; this group of metabolites was thus defined as a combinational biomarker for the recognition of AF and non-AF patients.
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