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Dowling P, Trollet C, Negroni E, Swandulla D, Ohlendieck K. How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? Proteomes 2024; 12:4. [PMID: 38250815 PMCID: PMC10801633 DOI: 10.3390/proteomes12010004] [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: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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2
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Ankeny RA, Whittaker AL, Ryan M, Boer J, Plebanski M, Tuke J, Spencer SJ. The power of effective study design in animal Experimentation: Exploring the statistical and ethical implications of asking multiple questions of a data set. Brain Behav Immun 2023:S0889-1591(23)00156-3. [PMID: 37315700 DOI: 10.1016/j.bbi.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/31/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023] Open
Abstract
One of the chief advantages of using highly standardised biological models including model organisms is that multiple variables can be precisely controlled so that the variable of interest is more easily studied. However, such an approach often obscures effects in sub-populations resulting from natural population heterogeneity. Efforts to expand our fundamental understanding of multiple sub-populations are in progress. However, such stratified or personalised approaches require fundamental modifications of our usual study designs that should be implemented in Brain, Behavior and Immunity (BBI) research going forward. Here we explore the statistical feasibility of asking multiple questions (including incorporating sex) within the same experimental cohort using statistical simulations of real data. We illustrate and discuss the large explosion in sample numbers necessary to detect effects with appropriate power for every additional question posed using the same data set. This exploration highlights the strong likelihood of type II errors (false negatives) for standard data and type I errors when dealing with complex genomic data, where studies are too under-powered to appropriately test these interactions. We show this power may differ for males and females in high throughput data sets such as RNA sequencing. We offer a rationale for the use of alternative experimental and statistical strategies based on interdisciplinary insights and discuss the real-world implications of increasing the complexities of our experimental designs, and the implications of not attempting to alter our experimental designs going forward.
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Affiliation(s)
- R A Ankeny
- School of Humanities, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - A L Whittaker
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - M Ryan
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, Australia
| | - J Boer
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria 3083, Australia
| | - M Plebanski
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria 3083, Australia
| | - J Tuke
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, Australia
| | - S J Spencer
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Victoria 3083, Australia.
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3
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Lan X, Peng X, Du T, Xia Z, Gao Q, Tang Q, Yi S, Yang G. Alterations of the Gut Microbiota and Metabolomics Associated with the Different Growth Performances of Macrobrachium rosenbergii Families. Animals (Basel) 2023; 13:ani13091539. [PMID: 37174576 PMCID: PMC10177557 DOI: 10.3390/ani13091539] [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: 04/04/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
To investigate the key gut microbiota and metabolites associated with the growth performance of Macrobrachium rosenbergii families, 16S rRNA sequencing and LC-MS metabolomic methods were used. In this study, 90 M. rosenbergii families were bred to evaluate growth performance. After 92 days of culture, high (H), medium (M), and low (L) experimental groups representing three levels of growth performance, respectively, were collected according to the weight gain and specific growth rate of families. The composition of gut microbiota showed that the relative abundance of Firmicutes, Lachnospiraceae, Lactobacillus, and Blautia were much higher in Group H than those in M and L groups. Meanwhile, compared to the M and L groups, Group H had significantly higher levels of spermidine, adenosine, and creatinine, and lower levels of L-citrulline. Correlation analysis showed that the abundances of Lactobacillus and Blautia were positively correlated with the levels of alpha-ketoglutaric acid and L-arginine. The abundance of Blautia was also positively correlated with the levels of adenosine, taurine, and spermidine. Notably, lots of metabolites related to the metabolism and biosynthesis of arginine, taurine, hypotaurine, and fatty acid were upregulated in Group H. This study contributes to figuring out the landscape of the gut microbiota and metabolites associated with prawn growth performance and provides a basis for selective breeding.
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Affiliation(s)
- Xuan Lan
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xin Peng
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Tingting Du
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Zhenglong Xia
- Jiangsu Shufeng Prawn Breeding Co., Ltd., Gaoyou 225654, China
| | - Quanxin Gao
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Qiongying Tang
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Shaokui Yi
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Guoliang Yang
- Zhejiang Provincial Key Laboratory of Aquatic Resources Conservation and Development, Key Laboratory of Aquatic Animal Genetic Breeding and Nutrition, Chinese Academy of Fishery Sciences, College of Life Sciences, Huzhou University, Huzhou 313000, China
- Jiangsu Shufeng Prawn Breeding Co., Ltd., Gaoyou 225654, China
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Wang D, Gao Y, Li Y, Zhao Y, Du X, Li X, Zhang Y, Liu S, Xu Y. Plasma metabolomics and network pharmacology identified glutamate, glutamine, and arginine as biomarkers of depression under Shuganjieyu capsule treatment. J Pharm Biomed Anal 2023; 232:115419. [PMID: 37146496 DOI: 10.1016/j.jpba.2023.115419] [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: 01/17/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/07/2023]
Abstract
Depression is a psychiatric disorder and confers an enormous burden on society. Mild to moderate forms of depression (MMD) are particularly common. Our previous studies showed that the Shuganjieyu (SGJY) capsule might improve depressive and cognitive symptoms in patients with MMD. However, biomarkers evaluating the efficacy of SGJY and the underlying mechanism remains unclear. The aim of the present study was to discover efficacy biomarkers and explore the underlying mechanisms of SGJY as antidepression treatment. Twenty-three patients with MMD were recruited and administered with SGJY for 8 weeks. Results showed that the content of 19 metabolites changed significantly in the plasma of patients with MMD, among which 8 metabolites improved significantly after SGJY treatment. Network pharmacology analysis showed that 19 active compounds, 102 potential targets, and 73 enzymes were related to the mechanistic action of SGJY. Through a comprehensive analysis, we identified four hub enzymes (GLS2, GLS, GLUL, and ADC), three key differential metabolites (glutamine, glutamate, and arginine), and two shared pathways (alanine, aspartate, and glutamate metabolism; and arginine biosynthesis). Receiver operating characteristic curve (ROC) analysis showed that the three metabolites had a high diagnostic ability. The expression of hub enzymes was validated using RT-qPCR in animal models. Overall, glutamate, glutamine, and arginine may be potential biomarkers for evaluating the efficacy of SGJY. The present study provides a new strategy for pharmacodynamic evaluation and mechanistic study of SGJY, and offers new information for clinical practice and treatment research.
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Affiliation(s)
- Dan Wang
- Basic Medical College, Shanxi Medical University, 030000 Taiyuan, China; Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Yao Gao
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Yaojun Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Yu Zhao
- Basic Medical College, Shanxi Medical University, 030000 Taiyuan, China; Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Xinzhe Du
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Xinrong Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China
| | - Yu Zhang
- Basic Medical College, Shanxi Medical University, 030000 Taiyuan, China
| | - Sha Liu
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, China; Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, 030001 Taiyuan, China.
| | - Yong Xu
- Department of Psychiatry, Taiyuan Central Hospital of Shanxi Medical University, 030032 Taiyuan, China; Department of Psychiatry, First Clinical Medical College of Shanxi Medical University, 030001 Taiyuan, China.
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Qin J, Cheng Q, Cai Z, Zhang L, Xing T, Xu X, Gao F. Gas chromatography-mass spectrometry-based untargeted metabolomics analysis reveals circulating biomarkers related to wooden breast myopathy in broilers: a preliminary study. Poult Sci 2023; 102:102718. [PMID: 37141813 DOI: 10.1016/j.psj.2023.102718] [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: 12/02/2022] [Revised: 04/06/2023] [Accepted: 04/09/2023] [Indexed: 05/06/2023] Open
Abstract
Approaches for the diagnosis of wooden breast (WB) myopathy in live birds are urgently required before applying intervention strategies to reduce occurrence and severity for the poultry industry. The objective of this study was to characterize the serum metabolic profiles in male broilers affected by WB and to identify biomarkers related to this myopathy. Broilers were categorized into normal (CON) and WB groups based on gross scoring and histological evaluation. Gas chromatography-mass spectrometry-based metabolomics, multivariate analysis, and orthogonal partial least squares discriminant analysis revealed a clear separation between CON and WB. A total of 73 significantly different (P < 0.05) metabolites with 17 upregulated and 56 downregulated were identified, which were mainly involved in pathways of alanine, aspartate, and glutamate metabolism, carbohydrate metabolism, and taurine and hypotaurine metabolism. By using the nested cross-validation function of random forest analysis, 9 significantly altered (P < 0.05) metabolites (cerotinic acid, arabitol, phosphoenolpyruvate, terephthalic acid, cis-gondoic acid, N-acetyl-d-glucosamine, 4-hydroxymandelic acid, caffeine, and xanthurenic acid) were identified as biomarkers with an excellent discriminant performance for WB myopathy. Collectively, this study provides new insights for a deeper understanding of the pathogenesis and provides metabolites as biomarkers for diagnostic utilization of WB myopathy.
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Affiliation(s)
- Jieyi Qin
- Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingqing Cheng
- Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziyu Cai
- Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Lin Zhang
- Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tong Xing
- Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xinglian Xu
- Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Gao
- Key Laboratory of Animal Origin Food Production and Safety Guarantee of Jiangsu Province, Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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6
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Signorelli M, Tsonaka R, Aartsma-Rus A, Spitali P. Multiomic characterization of disease progression in mice lacking dystrophin. PLoS One 2023; 18:e0283869. [PMID: 37000843 PMCID: PMC10065259 DOI: 10.1371/journal.pone.0283869] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/19/2023] [Indexed: 04/03/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is caused by genetic mutations leading to lack of dystrophin in skeletal muscle. A better understanding of how objective biomarkers for DMD vary across subjects and over time is needed to model disease progression and response to therapy more effectively, both in pre-clinical and clinical research. We present an in-depth characterization of disease progression in 3 murine models of DMD by multiomic analysis of longitudinal trajectories between 6 and 30 weeks of age. Integration of RNA-seq, mass spectrometry-based metabolomic and lipidomic data obtained in muscle and blood samples by Multi-Omics Factor Analysis (MOFA) led to the identification of 8 latent factors that explained 78.8% of the variance in the multiomic dataset. Latent factors could discriminate dystrophic and healthy mice, as well as different time-points. MOFA enabled to connect the gene expression signature in dystrophic muscles, characterized by pro-fibrotic and energy metabolism alterations, to inflammation and lipid signatures in blood. Our results show that omic observations in blood can be directly related to skeletal muscle pathology in dystrophic muscle.
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Affiliation(s)
- Mirko Signorelli
- Mathematical Institute, Leiden University, Leiden, The Netherlands
| | - Roula Tsonaka
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Fortunato F, Ferlini A. Biomarkers in Duchenne Muscular Dystrophy: Current Status and Future Directions. J Neuromuscul Dis 2023; 10:987-1002. [PMID: 37545256 PMCID: PMC10657716 DOI: 10.3233/jnd-221666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2023] [Indexed: 08/08/2023]
Abstract
Duchenne muscular dystrophy is a severe, X-linked disease characterized by decreased muscle mass and function in children. Genetic and biochemical research over the years has led to the characterization of the cause and the pathophysiology of the disease. Moreover, the elucidation of genetic mechanisms underlining Duchenne muscular dystrophy has allowed for the design of innovative personalized therapies.The identification of specific, accurate, and sensitive biomarkers is becoming crucial for evaluating muscle disease progression and response to therapies, disease monitoring, and the acceleration of drug development and related regulatory processes.This review illustrated the up-to-date progress in the development of candidate biomarkers in DMD at the level of proteins, metabolites, micro-RNAs (miRNAs) and genetic modifiers also highlighting the complexity of translating research results to clinical practice.We highlighted the challenges encountered in translating biomarkers into the clinical context and the existing bottlenecks hampering the adoption of biomarkers as surrogate endpoints. These challenges could be overcome by national and international collaborative efforts, multicenter data sharing, definition of public biobanks and patients' registries, and creation of large cohorts of patients. Novel statistical tools/ models suitable to analyze small patient numbers are also required.Finally, collaborations with pharmaceutical companies would greatly benefit biomarker discovery and their translation in clinical trials.
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Affiliation(s)
- Fernanda Fortunato
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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8
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Gegner HM, Naake T, Dugourd A, Müller T, Czernilofsky F, Kliewer G, Jäger E, Helm B, Kunze-Rohrbach N, Klingmüller U, Hopf C, Müller-Tidow C, Dietrich S, Saez-Rodriguez J, Huber W, Hell R, Poschet G, Krijgsveld J. Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis. Front Mol Biosci 2022; 9:961448. [PMID: 36605986 PMCID: PMC9808085 DOI: 10.3389/fmolb.2022.961448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
Metabolomic and proteomic analyses of human plasma and serum samples harbor the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures. To better understand the impact of pre-analytical factors that are relevant to implementing a unified proteomic and metabolomic approach in a clinical setting, we assessed the influence of temperature, sitting times, and centrifugation speed on the plasma and serum metabolomes and proteomes from six healthy volunteers. We used targeted metabolic profiling (497 metabolites) and data-independent acquisition (DIA) proteomics (572 proteins) on the same samples generated with well-defined pre-analytical conditions to evaluate criteria for pre-analytical SOPs for plasma and serum samples. Time and temperature showed the strongest influence on the integrity of plasma and serum proteome and metabolome. While rapid handling and low temperatures (4°C) are imperative for metabolic profiling, the analyzed proteomics data set showed variability when exposed to temperatures of 4°C for more than 2 h, highlighting the need for compromises in a combined analysis. We formalized a quality control scoring system to objectively rate sample stability and tested this score using external data sets from other pre-analytical studies. Stringent and harmonized standard operating procedures (SOPs) are required for pre-analytical sample handling when combining proteomics and metabolomics of clinical samples to yield robust and interpretable data on a longitudinal scale and across different clinics. To ensure an adequate level of practicability in a clinical routine for metabolomics and proteomics studies, we suggest keeping blood samples up to 2 h on ice (4°C) prior to snap-freezing as a compromise between stability and operability. Finally, we provide the methodology as an open-source R package allowing the systematic scoring of proteomics and metabolomics data sets to assess the stability of plasma and serum samples.
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Affiliation(s)
- Hagen M. Gegner
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, Germany
| | - Thomas Naake
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Aurélien Dugourd
- Bioquant, Faculty of Medicine, Institute for Computational Biomedicine, University of Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Torsten Müller
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany,Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felix Czernilofsky
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Georg Kliewer
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany,Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evelyn Jäger
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Barbara Helm
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina Kunze-Rohrbach
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, Germany
| | - Ursula Klingmüller
- Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Carsten Müller-Tidow
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Sascha Dietrich
- Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Bioquant, Faculty of Medicine, Institute for Computational Biomedicine, University of Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, University of Heidelberg, Heidelberg, Germany,*Correspondence: Jeroen Krijgsveld, ; Gernot Poschet,
| | - Jeroen Krijgsveld
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany,Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany,*Correspondence: Jeroen Krijgsveld, ; Gernot Poschet,
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9
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Abstract
PURPOSE OF REVIEW This review highlights the key studies investigating various types of biomarkers in Duchenne muscular dystrophy (DMD). RECENT FINDINGS Several proteomic and metabolomic studies have been undertaken in both human DMD patients and animal models of DMD that have identified potential biomarkers in DMD. Although there have been a number of proteomic and metabolomic studies that have identified various potential biomarkers in DMD, more definitive studies still need to be undertaken in DMD patients to firmly correlate these biomarkers with diagnosis, disease progression, and monitoring the effects of novel treatment strategies being developed.
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Affiliation(s)
- Theo Lee-Gannon
- Division of Cardiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Xuan Jiang
- Division of Cardiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
- UT Southwestern Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Tara C Tassin
- Division of Cardiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
- UT Southwestern Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Pradeep P A Mammen
- Division of Cardiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
- UT Southwestern Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
- Heart Failure, Ventricular Assist Device & Heart Transplant Program, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
- Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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10
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Huang Z, Wang C. A Review on Differential Abundance Analysis Methods for Mass Spectrometry-Based Metabolomic Data. Metabolites 2022; 12:305. [PMID: 35448492 PMCID: PMC9032534 DOI: 10.3390/metabo12040305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 12/04/2022] Open
Abstract
This review presents an overview of the statistical methods on differential abundance (DA) analysis for mass spectrometry (MS)-based metabolomic data. MS has been widely used for metabolomic abundance profiling in biological samples. The high-throughput data produced by MS often contain a large fraction of zero values caused by the absence of certain metabolites and the technical detection limits of MS. Various statistical methods have been developed to characterize the zero-inflated metabolomic data and perform DA analysis, ranging from simple tests to more complex models including parametric, semi-parametric, and non-parametric approaches. In this article, we discuss and compare DA analysis methods regarding their assumptions and statistical modeling techniques.
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Affiliation(s)
- Zhengyan Huang
- Everest Clinical Research Corporation, Little Falls, NJ 07424, USA
| | - Chi Wang
- Markey Cancer Center, Department of Internal Medicine, University of Kentucky, Lexington, KY 40536, USA
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11
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Ohlendieck K, Swandulla D. Complexity of skeletal muscle degeneration: multi-systems pathophysiology and organ crosstalk in dystrophinopathy. Pflugers Arch 2021; 473:1813-1839. [PMID: 34553265 PMCID: PMC8599371 DOI: 10.1007/s00424-021-02623-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Duchenne muscular dystrophy is a highly progressive muscle wasting disorder due to primary abnormalities in one of the largest genes in the human genome, the DMD gene, which encodes various tissue-specific isoforms of the protein dystrophin. Although dystrophinopathies are classified as primary neuromuscular disorders, the body-wide abnormalities that are associated with this disorder and the occurrence of organ crosstalk suggest that a multi-systems pathophysiological view should be taken for a better overall understanding of the complex aetiology of X-linked muscular dystrophy. This article reviews the molecular and cellular effects of deficiency in dystrophin isoforms in relation to voluntary striated muscles, the cardio-respiratory system, the kidney, the liver, the gastrointestinal tract, the nervous system and the immune system. Based on the establishment of comprehensive biomarker signatures of X-linked muscular dystrophy using large-scale screening of both patient specimens and genetic animal models, this article also discusses the potential usefulness of novel disease markers for more inclusive approaches to differential diagnosis, prognosis and therapy monitoring that also take into account multi-systems aspects of dystrophinopathy. Current therapeutic approaches to combat muscular dystrophy are summarised.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Co. Kildare, Maynooth, W23F2H6, Ireland.
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Co. Kildare, Maynooth, W23F2H6, Ireland.
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, 53115, Bonn, Germany.
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12
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Alonso-Jiménez A, Fernández-Simón E, Natera-de Benito D, Ortez C, García C, Montiel E, Belmonte I, Pedrosa I, Segovia S, Piñol-Jurado P, Carrasco-Rozas A, Suárez-Calvet X, Jimenez-Mallebrera C, Nascimento A, Llauger J, Nuñez-Peralta C, Montesinos P, Alonso-Pérez J, Gallardo E, Illa I, Díaz-Manera J. Platelet Derived Growth Factor-AA Correlates With Muscle Function Tests and Quantitative Muscle Magnetic Resonance in Dystrophinopathies. Front Neurol 2021; 12:659922. [PMID: 34177765 PMCID: PMC8226260 DOI: 10.3389/fneur.2021.659922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022] Open
Abstract
Introduction: Duchenne (DMD) and Becker (BMD) muscular dystrophy are X-linked muscular disorders produced by mutations in the DMD gene which encodes the protein dystrophin. Both diseases are characterized by progressive involvement of skeletal, cardiac, and respiratory muscles. As new treatment strategies become available, reliable biomarkers and outcome measures that can monitor disease progression are needed for clinical trials. Methods: We collected clinical and functional data and blood samples from 19 DMD patients, 13 BMD patients, and 66 healthy controls (8 pediatric and 58 adult controls), and blood samples from 15 patients with dysferlinopathy (DYSF) and studied the serum concentration of 4 growth factors involved in the process of muscle fibrosis. We correlated the serum concentration of these growth factors with several muscle function tests, spirometry results and fat fraction identified by quantitative Dixon muscle MRI. Results: We found significant differences in the serum concentration of Platelet Derived Growth Factor-AA (PDGF-AA) between DMD patients and pediatric controls, in Connective Tissue Growth Factor (CTGF) between BMD patients and adult controls, and in and Transforming Growth Factor- β1 (TGF-β1) between BMD and DYSF patients. PDGF-AA showed a good correlation with several muscle function tests for both DMD and BMD patients and with thigh fat fraction in BMD patients. Moreover, PDGF-AA levels were increased in muscle biopsies of patients with DMD and BMD as was demonstrated by immunohistochemistry and Real-Time PCR studies. Conclusion: Our study suggests that PDGF-AA should be further investigated in a larger cohort of DMD and BMD patients because it might be a good biomarker candidate to monitor the progression of these diseases.
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Affiliation(s)
- Alicia Alonso-Jiménez
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Neurology Department, Neuromuscular Reference Center, University Hospital of Antwerp, Antwerp, Belgium
| | - Esther Fernández-Simón
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,John Walton Muscular Dystrophy Research Centre, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Neuropediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Neuropediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carme García
- Rehabilitation and Physiotherapy Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elena Montiel
- Rehabilitation and Physiotherapy Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Izaskun Belmonte
- Rehabilitation and Physiotherapy Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Irene Pedrosa
- Rehabilitation and Physiotherapy Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sonia Segovia
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Patricia Piñol-Jurado
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,John Walton Muscular Dystrophy Research Centre, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ana Carrasco-Rozas
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Xavier Suárez-Calvet
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Cecilia Jimenez-Mallebrera
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,Neuromuscular Unit, Neuropediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain.,Departamento de Genética, Microbiología y Estadística, Universidad de Barcelona, Barcelona, Spain
| | - Andrés Nascimento
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,Neuromuscular Unit, Neuropediatrics Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Jaume Llauger
- Radiology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Claudia Nuñez-Peralta
- Radiology Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Jorge Alonso-Pérez
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Eduard Gallardo
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Isabel Illa
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain
| | - Jordi Díaz-Manera
- Neuromuscular Disorders Unit, Neurology Department, Hospital de la Santa Creu i Sant Pau, Departament de Medicina. Universitat Autònoma de Barcelona, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Barcelona, Spain.,John Walton Muscular Dystrophy Research Centre, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
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13
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Signorelli M, Ebrahimpoor M, Veth O, Hettne K, Verwey N, García‐Rodríguez R, Tanganyika‐deWinter CL, Lopez Hernandez LB, Escobar Cedillo R, Gómez Díaz B, Magnusson OT, Mei H, Tsonaka R, Aartsma‐Rus A, Spitali P. Peripheral blood transcriptome profiling enables monitoring disease progression in dystrophic mice and patients. EMBO Mol Med 2021; 13:e13328. [PMID: 33751844 PMCID: PMC8033515 DOI: 10.15252/emmm.202013328] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/13/2022] Open
Abstract
DMD is a rare disorder characterized by progressive muscle degeneration and premature death. Therapy development is delayed by difficulties to monitor efficacy non-invasively in clinical trials. In this study, we used RNA-sequencing to describe the pathophysiological changes in skeletal muscle of 3 dystrophic mouse models. We show how dystrophic changes in muscle are reflected in blood by analyzing paired muscle and blood samples. Analysis of repeated blood measurements followed the dystrophic signature at five equally spaced time points over a period of seven months. Treatment with two antisense drugs harboring different levels of dystrophin recovery identified genes associated with safety and efficacy. Evaluation of the blood gene expression in a cohort of DMD patients enabled the comparison between preclinical models and patients, and the identification of genes associated with physical performance, treatment with corticosteroids and body measures. The presented results provide evidence that blood RNA-sequencing can serve as a tool to evaluate disease progression in dystrophic mice and patients, as well as to monitor response to (dystrophin-restoring) therapies in preclinical drug development and in clinical trials.
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Affiliation(s)
- Mirko Signorelli
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenThe Netherlands
| | - Mitra Ebrahimpoor
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenThe Netherlands
| | - Olga Veth
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Kristina Hettne
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Nisha Verwey
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | | | | | - Luz B Lopez Hernandez
- Departamento de Medicina GenómicaUniversidad Autónoma de GuadalajaraGuadalajaraMexico
- Centro Médico Nacional "20 de Noviembre", ISSSTECiudad de MéxicoMexico
| | | | - Benjamín Gómez Díaz
- Sociedad Mexicana de la Distrofia Muscular A.C INR‐LGIICiudad de MéxicoMexico
| | | | - Hailiang Mei
- Sequencing Analysis Support CoreLeiden University Medical CenterLeidenThe Netherlands
| | - Roula Tsonaka
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenThe Netherlands
| | | | - Pietro Spitali
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
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14
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Ebrahimpoor M, Spitali P, Goeman JJ, Tsonaka R. Pathway testing for longitudinal metabolomics. Stat Med 2021; 40:3053-3065. [PMID: 33768548 PMCID: PMC8252476 DOI: 10.1002/sim.8957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/19/2021] [Accepted: 03/04/2021] [Indexed: 01/12/2023]
Abstract
We propose a top‐down approach for pathway analysis of longitudinal metabolite data. We apply a score test based on a shared latent process mixed model which can identify pathways with differentially progressing metabolites. The strength of our approach is that it can handle unbalanced designs, deals with potential missing values in the longitudinal markers, and gives valid results even with small sample sizes. Contrary to bottom‐up approaches, correlations between metabolites are explicitly modeled leveraging power gains. For large pathway sizes, a computationally efficient solution is proposed based on pseudo‐likelihood methodology. We demonstrate the advantages of the proposed method in identification of differentially expressed pathways through simulation studies. Finally, longitudinal metabolite data from a mice experiment is analyzed to demonstrate our methodology.
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Affiliation(s)
- Mitra Ebrahimpoor
- Medical Statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Pietro Spitali
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Medical Statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Roula Tsonaka
- Medical Statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
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15
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Koutsoulidou A, Phylactou LA. Circulating Biomarkers in Muscular Dystrophies: Disease and Therapy Monitoring. Mol Ther Methods Clin Dev 2020; 18:230-239. [PMID: 32637452 PMCID: PMC7327849 DOI: 10.1016/j.omtm.2020.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Muscular dystrophies are a group of inherited disorders that primarily affect the muscle tissues. Across the muscular dystrophies, symptoms commonly compromise the quality of life in all areas of functioning. It is well noted that muscular dystrophies need reliable and measurable biomarkers that will monitor the progress of the disease and evaluate the potential therapeutic approaches. In this review, we analyze the current findings regarding the development of blood-based circulating biomarkers for different types of muscular dystrophies. We emphasize those muscular dystrophies that gained particular interest for the development of biomarkers, including Duchenne muscular dystrophy, Becker muscular dystrophy, myotonic dystrophy types 1 and 2, Ullrich congenital muscular dystrophy, congenital muscular dystrophy type 1A, Facioscapulohumeral muscular dystrophy, and limb-girdle muscular dystrophy types 2A, 2B, 2C, and 2D, recently renamed as limb-girdle muscular dystrophy R1 calpain3-related, R2 dysferlin-related, R5 γ-sarcoglycan-related, and R3 α-sarcoglycan-related. This review highlights the up-to-date progress in the development of biomarkers at the level of proteins, lipids, and metabolites, as well as microRNAs (miRNAs) that currently are the main potential biomarker candidates in muscular dystrophies.
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Affiliation(s)
- Andrie Koutsoulidou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus.,Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus
| | - Leonidas A Phylactou
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus.,Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus
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16
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Al-Khalili Szigyarto C. Duchenne Muscular Dystrophy: recent advances in protein biomarkers and the clinical application. Expert Rev Proteomics 2020; 17:365-375. [PMID: 32713262 DOI: 10.1080/14789450.2020.1773806] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Early biomarker discovery studies have praised the value of their emerging results, predicting an unprecedented impact on health care. Biomarkers are expected to provide tests with increased specificity and sensitivity compared to existing measures, improve the decision-making process, and accelerate the development of therapies. For rare disorders, like Duchenne Muscular Dystrophy (DMD) such biomarkers can assist the development of therapies, therefore also helping to find a cure for the disease. AREA COVERED State-of-the-art technologies have been used to identify blood biomarkers for DMD and efforts have been coordinated to develop and promote translation of biomarkers for clinical practice. Biomarker translation to clinical practice is however, adjoined by challenges related to the complexity of the disease, involving numerous biological processes, and the limited sample resources. This review highlights the current progress on the development of biomarkers, describing the proteomics technologies used, the most promising findings and the challenges encountered. EXPERT OPINION Strategies for effective use of samples combined with orthogonal proteomics methods for protein quantification are essential for translating biomarkers to the patient's bed side. Progress is achieved only if strong evidence is provided that the biomarker constitutes a reliable indicator of the patient's health status for a specific context of use.
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Affiliation(s)
- Cristina Al-Khalili Szigyarto
- Science for Life Laboratory, KTH - Royal Institute of Technology , Solna, Sweden.,School of Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology , Stockholm, Sweden
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