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Li L, Zhang Y, Zhou J, Wang J, Wang L. Single-cell metabolomics in rare disease: From technology to disease. Intractable Rare Dis Res 2024; 13:99-103. [PMID: 38836176 PMCID: PMC11145402 DOI: 10.5582/irdr.2023.01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 05/12/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024] Open
Abstract
With the development of clinical experience and technology, rare diseases (RDs) are gradually coming into the limelight. As they often lead to poor prognosis, it is urgent to promote the accuracy and rapidity of diagnosis and promote the development of therapeutic drugs. In recent years, with the rapid improvement of single-cell sequencing technology, the advantages of multi-omics combined application in diseases have been continuously explored. Single-cell metabolomics represents a powerful tool for advancing our understanding of rare diseases, particularly metabolic RDs, and transforming clinical practice. By unraveling the intricacies of cellular metabolism at a single-cell resolution, this innovative approach holds the potential to revolutionize diagnosis, treatment, and management strategies, ultimately improving outcomes for RDs patients. Continued research and technological advancements in single-cell metabolomics are essential for realizing its full potential in the field of RDs diagnosis and therapeutics. It is expected that single-cell metabolomics can be better applied to RDs research in the future, for the benefit of patients and society.
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Affiliation(s)
- Lisha Li
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Yiqin Zhang
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Shanghai Key Laboratory Embryo Original Diseases, Shanghai, China
| | - Jing Zhou
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Jing Wang
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Ling Wang
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
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Kanepa A, Fan J, Rots D, Vaska A, Ansone L, Briviba M, Klovins J, Kurjane N, Klavins K. Exploring disease-specific metabolite signatures in hereditary angioedema patients. Front Immunol 2024; 15:1324671. [PMID: 38726011 PMCID: PMC11080650 DOI: 10.3389/fimmu.2024.1324671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Introduction Hereditary angioedema (HAE) is a rare, life-threatening autosomal dominant genetic disorder caused by a deficient and/or dysfunctional C1 esterase inhibitor (C1-INH) (type 1 and type 2) leading to recurrent episodes of edema. This study aims to explore HAE patients' metabolomic profiles and identify novel potential diagnostic biomarkers for HAE. The study also examined distinguishing HAE from idiopathic angioedema (AE). Methods Blood plasma samples from 10 HAE (types 1/2) patients, 15 patients with idiopathic AE, and 20 healthy controls were collected in Latvia and analyzed using LC-MS based targeted metabolomics workflow. T-test and fold change calculation were used to identify metabolites with significant differences between diseases and control groups. ROC analysis was performed to evaluate metabolite based classification model. Results A total of 33 metabolites were detected and quantified. The results showed that isovalerylcarnitine, cystine, and hydroxyproline were the most significantly altered metabolites between the disease and control groups. Aspartic acid was identified as a significant metabolite that could differentiate between HAE and idiopathic AE. The mathematical combination of metabolites (hydroxyproline * cystine)/(creatinine * isovalerylcarnitine) was identified as the diagnosis signature for HAE. Furthermore, glycine/asparagine ratio could differentiate between HAE and idiopathic AE. Conclusion Our study identified isovalerylcarnitine, cystine, and hydroxyproline as potential biomarkers for HAE diagnosis. Identifying new biomarkers may offer enhanced prospects for accurate, timely, and economical diagnosis of HAE, as well as tailored treatment selection for optimal patient care.
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Affiliation(s)
| | - Jingzhi Fan
- Institute of Biomaterials and Bioengineering, Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
| | - Dmitrijs Rots
- Riga Stradiņš University, Riga, Latvia
- Children’s Clinical University Hospital, Riga, Latvia
| | - Annija Vaska
- Institute of Biomaterials and Bioengineering, Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
| | - Laura Ansone
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Monta Briviba
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Natalja Kurjane
- Riga Stradiņš University, Riga, Latvia
- Pauls Stradiņš Clinical University Hospital, Riga, Latvia
| | - Kristaps Klavins
- Institute of Biomaterials and Bioengineering, Faculty of Natural Sciences and Technology, Riga Technical University, Riga, Latvia
- Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
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Panchbudhe SA, Shivkar RR, Banerjee A, Deshmukh P, Maji BK, Kadam CY. Improving newborn screening in India: Disease gaps and quality control. Clin Chim Acta 2024; 557:117881. [PMID: 38521163 DOI: 10.1016/j.cca.2024.117881] [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: 03/01/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
In India, newborn screening (NBS) is essential for detecting health problems in infants. Despite significant progress, significant gaps and challenges persist. India has made great strides in genomics dueto the existence of the National Institute of Biomedical Genomics in West Bengal. The work emphasizes the challenges NBS programs confront with technology, budgetary constraints, insufficient counseling, inequality in illness panels, and a lack of awareness. Advancements in technology, such as genetic testing and next-generation sequencing, are expected to significantly transform the process. The integration of analytical tools, artificial intelligence, and machine learning algorithms could improve the efficiency of newborn screening programs, offering a personalized healthcare approach. It is critical to address gaps in information, inequities in illness incidence, budgetary restrictions, and inadequate counseling. Strengthening national NBS programs requires increased public awareness and coordinated efforts between state and central agencies. Quality control procedures must be used at every level for implementation to be successful. Additional studies endeavor to enhance NBS in India through public education, illness screening expansion, enhanced quality control, government incentive implementation, partnership promotion, and expert training. Improved neonatal health outcomes and the viability of the program across the country will depend heavily on new technology and counseling techniques.
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Affiliation(s)
- Sanjyoti A Panchbudhe
- Shrimati Kashibai Navale Medical College and General Hospital, Narhe, Pune 411041, Maharashtra, India
| | - Rajni R Shivkar
- Shrimati Kashibai Navale Medical College and General Hospital, Narhe, Pune 411041, Maharashtra, India
| | - Arnab Banerjee
- Department of Physiology (UG & PG), Serampore College, 9 William Carey Road, Serampore, Hooghly 712201, West Bengal, India
| | - Paulami Deshmukh
- Shrimati Kashibai Navale Medical College and General Hospital, Narhe, Pune 411041, Maharashtra, India
| | - Bithin Kumar Maji
- Department of Physiology (UG & PG), Serampore College, 9 William Carey Road, Serampore, Hooghly 712201, West Bengal, India
| | - Charushila Y Kadam
- Department of Biochemistry, Sukh Sagar Medical College and Hospital, Jabalpur 482003, Madhya Pradesh, India.
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Tang C, Li L, Chen T, Li Y, Zhu B, Zhang Y, Yin Y, Liu X, Huang C, Miao J, Zhu B, Wang X, Zou H, Han L, Feng J, Huang Y. Newborn Screening for Inborn Errors of Metabolism by Next-Generation Sequencing Combined with Tandem Mass Spectrometry. Int J Neonatal Screen 2024; 10:28. [PMID: 38651393 PMCID: PMC11036227 DOI: 10.3390/ijns10020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
The aim of this study was to observe the outcomes of newborn screening (NBS) in a certain population by using next-generation sequencing (NGS) as a first-tier screening test combined with tandem mass spectrometry (MS/MS). We performed a multicenter study of 29,601 newborns from eight screening centers with NBS via NGS combined with MS/MS. A custom-designed panel targeting the coding region of the 142 genes of 128 inborn errors of metabolism (IEMs) was applied as a first-tier screening test, and expanded NBS using MS/MS was executed simultaneously. In total, 52 genes associated with the 38 IEMs screened by MS/MS were analyzed. The NBS performance of these two methods was analyzed and compared respectively. A total of 23 IEMs were diagnosed via NGS combined with MS/MS. The incidence of IEMs was approximately 1 in 1287. Within separate statistical analyses, the positive predictive value (PPV) for MS/MS was 5.29%, and the sensitivity was 91.3%. However, for genetic screening alone, the PPV for NGS was 70.83%, with 73.91% sensitivity. The three most common IEMs were methylmalonic academia (MMA), primary carnitine deficiency (PCD) and phenylketonuria (PKU). The five genes with the most common carrier frequencies were PAH (1:42), PRODH (1:51), MMACHC (1:52), SLC25A13 (1:55) and SLC22A5 (1:63). Our study showed that NBS combined with NGS and MS/MS improves the performance of screening methods, optimizes the process, and provides accurate diagnoses.
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Affiliation(s)
- Chengfang Tang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510180, China;
| | - Lixin Li
- Department of Genetic, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang 050090, China;
| | - Ting Chen
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China;
| | - Yulin Li
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan 250001, China; (Y.L.); (H.Z.)
| | - Bo Zhu
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot 750306, China; (B.Z.); (X.W.)
| | - Yinhong Zhang
- Department of Medical Genetics, NHC Key Laboratory of Preconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Yunnan Provincial Clinical Research Center for Birth Defects and Rare Diseases, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, China; (Y.Z.); (B.Z.)
| | - Yifan Yin
- Department of Pediatrics, Chongqing Health Center for Women and Children &Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China; (Y.Y.); (J.M.)
| | - Xiulian Liu
- Neonatal Disease Screening Center, Hainan Women and Children’s Medical Center, Haikou 570206, China; (X.L.); (C.H.)
| | - Cidan Huang
- Neonatal Disease Screening Center, Hainan Women and Children’s Medical Center, Haikou 570206, China; (X.L.); (C.H.)
| | - Jingkun Miao
- Department of Pediatrics, Chongqing Health Center for Women and Children &Women and Children’s Hospital of Chongqing Medical University, Chongqing 401147, China; (Y.Y.); (J.M.)
| | - Baosheng Zhu
- Department of Medical Genetics, NHC Key Laboratory of Preconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, Yunnan Provincial Clinical Research Center for Birth Defects and Rare Diseases, The First People’s Hospital of Yunnan Province/The Affiliated Hospital of Kunming University of Science and Technology, Kunming 650032, China; (Y.Z.); (B.Z.)
| | - Xiaohua Wang
- Department of Genetics, Inner Mongolia Maternity and Child Health Care Hospital, Hohhot 750306, China; (B.Z.); (X.W.)
| | - Hui Zou
- Neonatal Disease Screening Center, Jinan Maternity and Child Health Hospital Affiliated to Shandong First Medical University, Jinan 250001, China; (Y.L.); (H.Z.)
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China;
| | - Jizhen Feng
- Department of Genetic, Shijiazhuang Maternal and Child Health Hospital, Shijiazhuang 050090, China;
| | - Yonglan Huang
- Department of Guangzhou Newborn Screening Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou 510180, China;
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Batagov A, Dalan R, Wu A, Lai W, Tan CS, Eisenhaber F. Generalized metabolic flux analysis framework provides mechanism-based predictions of ophthalmic complications in type 2 diabetes patients. Health Inf Sci Syst 2023; 11:18. [PMID: 37008895 PMCID: PMC10060506 DOI: 10.1007/s13755-023-00218-x] [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: 03/08/2022] [Accepted: 02/19/2023] [Indexed: 03/31/2023] Open
Abstract
Chronic metabolic diseases arise from changes in metabolic fluxes through biomolecular pathways and gene networks accumulated over the lifetime of an individual. While clinical and biochemical profiles present just real-time snapshots of the patients' health, efficient computation models of the pathological disturbance of biomolecular processes are required to achieve individualized mechanistic insights into disease progression. Here, we describe the Generalized metabolic flux analysis (GMFA) for addressing this gap. Suitably grouping individual metabolites/fluxes into pools simplifies the analysis of the resulting more coarse-grain network. We also map non-metabolic clinical modalities onto the network with additional edges. Instead of using the time coordinate, the system status (metabolite concentrations and fluxes) is quantified as function of a generalized extent variable (a coordinate in the space of generalized metabolites) that represents the system's coordinate along its evolution path and evaluates the degree of change between any two states on that path. We applied GMFA to analyze Type 2 Diabetes Mellitus (T2DM) patients from two cohorts: EVAS (289 patients from Singapore) and NHANES (517) from the USA. Personalized systems biology models (digital twins) were constructed. We deduced disease dynamics from the individually parameterized metabolic network and predicted the evolution path of the metabolic health state. For each patient, we obtained an individual description of disease dynamics and predict an evolution path of the metabolic health state. Our predictive models achieve an ROC-AUC in the range 0.79-0.95 (sensitivity 80-92%, specificity 62-94%) in identifying phenotypes at the baseline and predicting future development of diabetic retinopathy and cataract progression among T2DM patients within 3 years from the baseline. The GMFA method is a step towards realizing the ultimate goal to develop practical predictive computational models for diagnostics based on systems biology. This tool has potential use in chronic disease management in medical practice. Supplementary Information The online version contains supplementary material available at 10.1007/s13755-023-00218-x.
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Affiliation(s)
- Arsen Batagov
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Rinkoo Dalan
- Department of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Andrew Wu
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Wenbin Lai
- Mesh Bio Pte. Ltd., 10 Anson Rd, #22-02, 079903 Singapore, Singapore
| | - Colin S. Tan
- Fundus Image Reading Center, National Healthcare Group Eye Institute, Singapore, Singapore
- Tan Tock Seng Hospital, National Healthcare Group Eye Institute, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Science (SBS), Nanyang Technological University, Singapore, Singapore
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Cannet C, Bayat A, Frauendienst-Egger G, Freisinger P, Spraul M, Himmelreich N, Kockaya M, Ahring K, Godejohann M, MacDonald A, Trefz F. Phenylketonuria (PKU) Urinary Metabolomic Phenotype Is Defined by Genotype and Metabolite Imbalance: Results in 51 Early Treated Patients Using Ex Vivo 1H-NMR Analysis. Molecules 2023; 28:4916. [PMID: 37446577 DOI: 10.3390/molecules28134916] [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: 04/24/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
Phenylketonuria (PKU) is a rare metabolic disorder caused by mutations in the phenylalanine hydroxylase gene. Depending on the severity of the genetic mutation, medical treatment, and patient dietary management, elevated phenylalanine (Phe) may occur in blood and brain tissues. Research has recently shown that high Phe not only impacts the central nervous system, but also other organ systems (e.g., heart and microbiome). This study used ex vivo proton nuclear magnetic resonance (1H-NMR) analysis of urine samples from PKU patients (mean 14.9 ± 9.2 years, n = 51) to identify the impact of elevated blood Phe and PKU treatment on metabolic profiles. Our results found that 24 out of 98 urinary metabolites showed a significant difference (p < 0.05) for PKU patients compared to age-matched healthy controls (n = 51) based on an analysis of urinary metabolome. These altered urinary metabolites were related to Phe metabolism, dysbiosis, creatine synthesis or intake, the tricarboxylic acid (TCA) cycle, end products of nicotinamide-adenine dinucleotide degradation, and metabolites associated with a low Phe diet. There was an excellent correlation between the metabolome and genotype of PKU patients and healthy controls of 96.7% in a confusion matrix model. Metabolomic investigations may contribute to a better understanding of PKU pathophysiology.
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Affiliation(s)
| | - Allan Bayat
- Kennedy Centre, Center for PKU, 2600 Glostrup, Denmark
| | | | - Peter Freisinger
- Department of Pediatrics, School of Medicine, University of Tübingen, 72074 Tübingen, Germany
| | | | | | - Musa Kockaya
- Private Pediatric Practice, 68307 Mannheim, Germany
| | | | | | - Anita MacDonald
- Dietetic Department, Birmingham Children's Hospital, Birmingham B4 6NH, UK
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7
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Dai HD, Qiu F, Jackson K, Fruttiger M, Rizzo WB. Untargeted Metabolomic Analysis of Sjögren-Larsson Syndrome Reveals a Distinctive Pattern of Multiple Disrupted Biochemical Pathways. Metabolites 2023; 13:682. [PMID: 37367841 DOI: 10.3390/metabo13060682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
Sjögren-Larsson syndrome (SLS) is a rare inherited neurocutaneous disease characterized by ichthyosis, spastic diplegia or tetraplegia, intellectual disability and a distinctive retinopathy. SLS is caused by bi-allelic mutations in ALDH3A2, which codes for fatty aldehyde dehydrogenase (FALDH) and results in abnormal lipid metabolism. The biochemical abnormalities in SLS are not completely known, and the pathogenic mechanisms leading to symptoms are still unclear. To search for pathways that are perturbed in SLS, we performed untargeted metabolomic screening in 20 SLS subjects along with age- and sex-matched controls. Of 823 identified metabolites in plasma, 121 (14.7%) quantitatively differed in the overall SLS cohort from controls; 77 metabolites were decreased and 44 increased. Pathway analysis pointed to disrupted metabolism of sphingolipids, sterols, bile acids, glycogen, purines and certain amino acids such as tryptophan, aspartate and phenylalanine. Random forest analysis identified a unique metabolomic profile that had a predictive accuracy of 100% for discriminating SLS from controls. These results provide new insight into the abnormal biochemical pathways that likely contribute to disease in SLS and may constitute a biomarker panel for diagnosis and future therapeutic studies.
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Affiliation(s)
- Hongying Daisy Dai
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Fang Qiu
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | | | - Marcus Fruttiger
- UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - William B Rizzo
- Department of Pediatrics and Child Health Research Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Children's Hospital & Medical Center, Omaha, NE 68114, USA
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Cannet C, Frauendienst-Egger G, Freisinger P, Götz H, Götz M, Himmelreich N, Kock V, Spraul M, Bus C, Biskup S, Trefz F. Ex vivo proton spectroscopy ( 1 H-NMR) analysis of inborn errors of metabolism: Automatic and computer-assisted analyses. NMR IN BIOMEDICINE 2023; 36:e4853. [PMID: 36264537 DOI: 10.1002/nbm.4853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/29/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
There are about 1500 genetic metabolic diseases. A small number of treatable diseases are diagnosed by newborn screening programs, which are continually being developed. However, most diseases can only be diagnosed based on clinical symptoms or metabolic findings. The main biological fluids used are urine, plasma and, in special situations, cerebrospinal fluid. In contrast to commonly used methods such as gas chromatography and high performance liquid chromatography mass spectrometry, ex vivo proton spectroscopy (1 H-NMR) is not yet used in routine clinical practice, although it has been recommended for more than 30 years. Automatic analysis and improved NMR technology have also expanded the applications used for the diagnosis of inborn errors of metabolism. We provide a mini-overview of typical applications, especially in urine but also in plasma, used to diagnose common but also rare genetic metabolic diseases with 1 H-NMR. The use of computer-assisted diagnostic suggestions can facilitate interpretation of the profiles. In a proof of principle, to date, 182 reports of 59 different diseases and 500 reports of healthy children are stored. The percentage of correct automatic diagnoses was 74%. Using the same 1 H-NMR profile-targeted analysis, it is possible to apply an untargeted approach that distinguishes profile differences from healthy individuals. Thus, additional conditions such as lysosomal storage diseases or drug interferences are detectable. Furthermore, because 1 H-NMR is highly reproducible and can detect a variety of different substance categories, the metabolomic approach is suitable for monitoring patient treatment and revealing additional factors such as nutrition and microbiome metabolism. Besides the progress in analytical techniques, a multiomics approach is most effective to combine metabolomics with, for example, whole exome sequencing, to also diagnose patients with nondetectable metabolic abnormalities in biological fluids. In this mini review we also provide our own data to demonstrate the role of NMR in a multiomics platform in the field of inborn errors of metabolism.
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Affiliation(s)
| | - Georg Frauendienst-Egger
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | - Peter Freisinger
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | | | | | | | - Vanessa Kock
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | | | - Christine Bus
- CEGAT, Tübingen, Germany and Human Genetics Institute, Tübingen, Germany
| | - Saskia Biskup
- CEGAT, Tübingen, Germany and Human Genetics Institute, Tübingen, Germany
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9
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de Moraes MBM, de Souza HMR, de Oliveira MLC, Peake RWA, Scalco FB, Garrett R. Combined targeted and untargeted high-resolution mass spectrometry analyses to investigate metabolic alterations in pompe disease. Metabolomics 2023; 19:29. [PMID: 36988742 DOI: 10.1007/s11306-023-01989-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/05/2023] [Indexed: 03/30/2023]
Abstract
INTRODUCTION Pompe disease is a rare, lysosomal disorder, characterized by intra-lysosomal glycogen accumulation due to an impaired function of α-glucosidase enzyme. The laboratory testing for Pompe is usually performed by enzyme activity, genetic test, or urine glucose tetrasaccharide (Glc4) screening by HPLC. Despite being a good preliminary marker, the Glc4 is not specific for Pompe. OBJECTIVE The purpose of the present study was to develop a simple methodology using liquid chromatography-high resolution mass spectrometry (LC-HRMS) for targeted quantitative analysis of Glc4 combined with untargeted metabolic profiling in a single analytical run to search for complementary biomarkers in Pompe disease. METHODS We collected 21 urine specimens from 13 Pompe disease patients and compared their metabolic signatures with 21 control specimens. RESULTS Multivariate statistical analyses on the untargeted profiling data revealed Glc4, creatine, sorbitol/mannitol, L-phenylalanine, N-acetyl-4-aminobutanal, N-acetyl-L-aspartic acid, and 2-aminobenzoic acid as significantly altered in Pompe disease. This panel of metabolites increased sample class prediction (Pompe disease versus control) compared with a single biomarker. CONCLUSION This study has demonstrated the potential of combined acquisition methods in LC-HRMS for Pompe disease investigation, allowing for routine determination of an established biomarker and discovery of complementary candidate biomarkers that may increase diagnostic accuracy, or improve the risk stratification of patients with disparate clinical phenotypes.
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Affiliation(s)
- Mariana B M de Moraes
- Metabolomics Laboratory, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Horácio Macedo 1281, Rio de Janeiro, RJ, 21941-598, Brazil
| | - Hygor M R de Souza
- Metabolomics Laboratory, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Horácio Macedo 1281, Rio de Janeiro, RJ, 21941-598, Brazil
- Institute of Chemistry, Fluminense Federal University, Niterói, RJ, Brazil
| | - Maria L C de Oliveira
- Inborn Error of Metabolism Laboratory, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Roy W A Peake
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fernanda B Scalco
- Inborn Error of Metabolism Laboratory, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rafael Garrett
- Metabolomics Laboratory, Institute of Chemistry, Federal University of Rio de Janeiro, Av. Horácio Macedo 1281, Rio de Janeiro, RJ, 21941-598, Brazil.
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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He X, Kuang J, Lai J, Huang J, Wang Y, Lan G, Xie Y, Shi X. A retrospective analysis of MS/MS screening for IEM in high-risk areas. BMC Med Genomics 2023; 16:57. [PMID: 36927542 PMCID: PMC10021976 DOI: 10.1186/s12920-023-01483-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
Inborn errors of metabolism (IEM) can lead to severe motor and neurological developmental disorders and even disability and death in children due to untimely treatment. In this study, we used tandem mass spectrometry (MS/MS) for primary screening and recall of those with positive primary screening for rescreening. Further diagnosis was based on biochemical tests, imaging and clinical presentation as well as accurate genetic testing using multi-gene panel with high-throughput sequencing of 130 IEM-related genes. The screening population was 16,207 newborns born between July 1, 2019, and December 31, 2021. Based on the results, 8 newborns were diagnosed with IEM, constituting a detection rate of 1:2,026. Phenylketonuria was the most common form of IEM. In addition, seven genes associated with IEM were detected in these eight patients. All eight patients received standardized treatment starting in the neonatal period, and the follow-up results showed good growth and development. Therefore, our study suggests that MS/MS rescreening for IEM pathogenic variants in high-risk areas, combined with a sequencing validation strategy, can be highly effective in the early detection of affected children. This strategy, combined with early intervention, can be effective in preventing neonatal morbidity and improving population quality.
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Affiliation(s)
- Xiao He
- Department of Pediatrics, The Second Nanning People's Hospital, Nanning, 530031, Guangxi, China
| | - Juan Kuang
- Department of Pediatrics, The Second Nanning People's Hospital, Nanning, 530031, Guangxi, China
| | - Jiahong Lai
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, Guangdong, China
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China
| | - Jingxiong Huang
- Department of Pediatrics, The Second Nanning People's Hospital, Nanning, 530031, Guangxi, China
| | - Yijin Wang
- Department of Pediatrics, The Second Nanning People's Hospital, Nanning, 530031, Guangxi, China
| | - Guofeng Lan
- Department of Pediatrics, The Second Nanning People's Hospital, Nanning, 530031, Guangxi, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China.
- Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, Guangdong, China.
| | - Xuekai Shi
- Department of Pediatrics, The Second Nanning People's Hospital, Nanning, 530031, Guangxi, China.
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11
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Men S, Liu S, Zheng Q, Yang S, Mao H, Wang Z, Gu Y, Tang X, Wang L. Incidence and genetic variants of inborn errors of metabolism identified through newborn screening: A 7-year study in eastern coastal areas of China. Mol Genet Genomic Med 2023:e2152. [PMID: 36787440 DOI: 10.1002/mgg3.2152] [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: 07/19/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND The incidence of inborn errors of metabolism (IEM) varies across countries and areas. Currently, there are no studies on IEM using newborn screening (NBS) in eastern coastal areas of China. We aimed to estimate the incidence and genetic variants of IEM and understand the spectrum of diseases caused by IEM and variants among them in this area. METHODS The NBS performed by tandem mass spectrometry (MS/MS) from 2016 to 2021 was retrospectively reviewed. Heel blood was collected from all newborns 72 h after birth. Targeted massively parallel sequencing was performed for genetic analysis. RESULTS Among 245,194 newborns, 95 were diagnosed with IEM, the overall incidence observed was-IEM: 1/2581; amino acid metabolism disorder: 1/4715; organic acid metabolism disorder: 1/11676; and fatty acid metabolism disorder: 1/11145. The incidence of different IEM was in the range of 1/245194 to 1/6452. Phenylketonuria (PKU, 1/7211) was the most common IEM, followed by methylmalonic acidemia (MMA, 1/27244), short-chain acyl-CoA dehydrogenase deficiency (SCADD, 1/30649), and citrin deficiency (CD, 1/35028). For genetic variants, the common hotspot variants found were-PAH gene for PKU: c.728G > A, c.442-1G > A, c.611A > G, c.721C > T; PTS gene for non-classical PKU: c.259C > T; MMACHC gene for MMA: c.658_660delAAG, c.609G > A; MMUT gene for MMA: c.1663G > A; ACADS gene for SCADD: c.1031A > G and c.1130C > T; and SLC25A13 gene for CD: c.1638_1660dup, c.852_855del. CONCLUSION This study displayed the diseases and varied spectrum of IEM in eastern coastal areas of China. Implementing NBS for IEM by MS/MS combined with massively parallel sequencing can offer an improved plan for NBS to detect IEM.
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Affiliation(s)
- Shuai Men
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
| | - Shuang Liu
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
| | - Qin Zheng
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
| | - Shuting Yang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
| | - Huafen Mao
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
| | - Zhiwei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
| | - Ying Gu
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
| | - Xinxin Tang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, People's Republic of China
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12
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Leal AF, Fnu N, Benincore-Flórez E, Herreño-Pachón AM, Echeverri-Peña OY, Alméciga-Díaz CJ, Tomatsu S. The landscape of CRISPR/Cas9 for inborn errors of metabolism. Mol Genet Metab 2023; 138:106968. [PMID: 36525790 DOI: 10.1016/j.ymgme.2022.106968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 12/03/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022]
Abstract
Since its discovery as a genome editing tool, the clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9) system has opened new horizons in the diagnosis, research, and treatment of genetic diseases. CRISPR/Cas9 can rewrite the genome at any region with outstanding precision to modify it and further instructions for gene expression. Inborn Errors of Metabolism (IEM) are a group of more than 1500 diseases produced by mutations in genes encoding for proteins that participate in metabolic pathways. IEM involves small molecules, energetic deficits, or complex molecules diseases, which may be susceptible to be treated with this novel tool. In recent years, potential therapeutic approaches have been attempted, and new models have been developed using CRISPR/Cas9. In this review, we summarize the most relevant findings in the scientific literature about the implementation of CRISPR/Cas9 in IEM and discuss the future use of CRISPR/Cas9 to modify epigenetic markers, which seem to play a critical role in the context of IEM. The current delivery strategies of CRISPR/Cas9 are also discussed.
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Affiliation(s)
- Andrés Felipe Leal
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá, Colombia; Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Nidhi Fnu
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA; University of Delaware, Newark, DE, USA
| | | | | | - Olga Yaneth Echeverri-Peña
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Carlos Javier Alméciga-Díaz
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Shunji Tomatsu
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, USA; University of Delaware, Newark, DE, USA; Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA.
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13
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Hertzog A, Selvanathan A, Devanapalli B, Ho G, Bhattacharya K, Tolun AA. A narrative review of metabolomics in the era of "-omics": integration into clinical practice for inborn errors of metabolism. Transl Pediatr 2022; 11:1704-1716. [PMID: 36345452 PMCID: PMC9636448 DOI: 10.21037/tp-22-105] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Traditional targeted metabolomic investigations identify a pre-defined list of analytes in samples and have been widely used for decades in the diagnosis and monitoring of inborn errors of metabolism (IEMs). Recent technological advances have resulted in the development and maturation of untargeted metabolomics: a holistic, unbiased, analytical approach to detecting metabolic disturbances in human disease. We aim to provide a summary of untargeted metabolomics [focusing on tandem mass spectrometry (MS-MS)] and its application in the field of IEMs. METHODS Data for this review was identified through a literature search using PubMed, Google Scholar, and personal repositories of articles collected by the authors. Findings are presented within several sections describing the metabolome, the current use of targeted metabolomics in the diagnostic pathway of patients with IEMs, the more recent integration of untargeted metabolomics into clinical care, and the limitations of this newly employed analytical technique. KEY CONTENT AND FINDINGS Untargeted metabolomic investigations are increasingly utilized in screening for rare disorders, improving understanding of cellular and subcellular physiology, discovering novel biomarkers, monitoring therapy, and functionally validating genomic variants. Although the untargeted metabolomic approach has some limitations, this "next generation metabolic screening" platform is becoming increasingly affordable and accessible. CONCLUSIONS When used in conjunction with genomics and the other promising "-omic" technologies, untargeted metabolomics has the potential to revolutionize the diagnostics of IEMs (and other rare disorders), improving both clinical and health economic outcomes.
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Affiliation(s)
- Ashley Hertzog
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Beena Devanapalli
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Gladys Ho
- Sydney Genome Diagnostics, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Adviye Ayper Tolun
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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14
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Trofimova AV, Reddy KM. Imaging of Inherited Metabolic and Endocrine Disorders. Clin Perinatol 2022; 49:657-673. [PMID: 36113928 DOI: 10.1016/j.clp.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
"Inherited metabolic disorders represent a large group of disorders of which approximately 25% present in neonatal period with acute metabolic decompensation, rapid clinical deterioration, and often nonspecific imaging findings. Neonatal onset signifies the profound severity of the metabolic abnormality compared with cases with later presentation and necessitates rapid diagnosis and urgent therapeutic measures in an attempt to decrease the extent of brain injury and prevent grave neurologic sequela or death. Here, the authors discuss classification and clinical and imaging findings in a spectrum of metabolic and endocrine disorders with neonatal presentation."
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Affiliation(s)
- Anna V Trofimova
- Children's Healthcare of Atlanta, Radiology Department, 1405 Clifton Road NE, Atlanta, GA 30322, USA; Emory University, Department of Radiology and Imaging Sciences, 1364 Clifton Road NE, Atlanta, GA, 30322, USA.
| | - Kartik M Reddy
- Children's Healthcare of Atlanta, Radiology Department, 1405 Clifton Road NE, Atlanta, GA 30322, USA; Emory University, Department of Radiology and Imaging Sciences, 1364 Clifton Road NE, Atlanta, GA, 30322, USA
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15
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Understanding Inborn Errors of Metabolism through Metabolomics. Metabolites 2022; 12:metabo12050398. [PMID: 35629902 PMCID: PMC9143820 DOI: 10.3390/metabo12050398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/14/2022] [Accepted: 04/25/2022] [Indexed: 12/10/2022] Open
Abstract
Inborn errors of metabolism (IEMs) are rare diseases caused by a defect in a single enzyme, co-factor, or transport protein. For most IEMs, no effective treatment is available and the exact disease mechanism is unknown. The application of metabolomics and, more specifically, tracer metabolomics in IEM research can help to elucidate these disease mechanisms and hence direct novel therapeutic interventions. In this review, we will describe the different approaches to metabolomics in IEM research. We will discuss the strengths and weaknesses of the different sample types that can be used (biofluids, tissues or cells from model organisms; modified cell lines; and patient fibroblasts) and when each of them is appropriate to use.
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16
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Fernández-Eulate G, Carreau C, Benoist JF, Lamari F, Rucheton B, Shor N, Nadjar Y. Diagnostic approach in adult-onset neurometabolic diseases. J Neurol Neurosurg Psychiatry 2022; 93:413-421. [PMID: 35140137 PMCID: PMC8921565 DOI: 10.1136/jnnp-2021-328045] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/02/2022] [Indexed: 12/31/2022]
Abstract
Neurometabolic diseases are a group of individually rare but numerous and heterogeneous genetic diseases best known to paediatricians. The more recently reported adult forms may present with phenotypes strikingly different from paediatric ones and may mimic other more common neurological disorders in adults. Furthermore, unlike most neurogenetic diseases, many neurometabolic diseases are treatable, with both conservative and more recent innovative therapeutics. However, the phenotypical complexity of this group of diseases and the growing number of specialised biochemical tools account for a significant diagnostic delay and underdiagnosis. We reviewed all series and case reports of patients with a confirmed neurometabolic disease and a neurological onset after the age of 10 years, with a focus on the 36 treatable ones, and classified these diseases according to their most relevant clinical manifestations. The biochemical diagnostic approach of neurometabolic diseases lays on the use of numerous tests studying a set of metabolites, an enzymatic activity or the function of a given pathway; and therapeutic options aim to restore the enzyme activity or metabolic function, limit the accumulation of toxic substrates or substitute the deficient products. A quick diagnosis of a treatable neurometabolic disease can have a major impact on patients, leading to the stabilisation of the disease and cease of repeated diagnostic investigations, and allowing for familial screening. For the aforementioned, in addition to an exhaustive and clinically meaningful review of these diseases, we propose a simplified diagnostic approach for the neurologist with the aim to help determine when to suspect a neurometabolic disease and how to proceed in a rational manner. We also discuss the place of next-generation sequencing technologies in the diagnostic process, for which deep phenotyping of patients (both clinical and biochemical) is necessary for improving their diagnostic yield.
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Affiliation(s)
- Gorka Fernández-Eulate
- Neuro-Metabolism Unit, Reference Center for Lysosomal Diseases, Neurology Department, Pitié-Salpêtrière University Hospital, APHP, Paris, France.,Reference Center for Neuromuscular Diseases, Neuro-myology Department, Pitié-Salpêtrière University Hospital, APHP, Paris, France
| | - Christophe Carreau
- Neurology Department, Saint-Louis University Hospital, APHP, Paris, France
| | - Jean-François Benoist
- Metabolic Biochemistry Laboratory, Necker Enfants Malades University Hospital, APHP, Paris-Saclay University, Paris, France
| | - Foudil Lamari
- Department of Biochemistry of Neurometabolic Diseases, Pitié-Salpêrière University Hospital, APHP, Paris, Fance
| | - Benoit Rucheton
- Department of Biochemistry of Neurometabolic Diseases, Pitié-Salpêrière University Hospital, APHP, Paris, Fance
| | - Natalia Shor
- Neuroradiology Department, Pitié-Salpêtrière University Hospital, APHP, Sorbonne University, Paris, France
| | - Yann Nadjar
- Neuro-Metabolism Unit, Reference Center for Lysosomal Diseases, Neurology Department, Pitié-Salpêtrière University Hospital, APHP, Paris, France
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17
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Altered Plasma Mitochondrial Metabolites in Persistently Symptomatic Individuals after a GBCA-Assisted MRI. TOXICS 2022; 10:toxics10020056. [PMID: 35202243 PMCID: PMC8879776 DOI: 10.3390/toxics10020056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 12/22/2022]
Abstract
Despite the impressive safety of gadolinium (Gd)-based contrast agents (GBCAs), a small number of patients report the onset of new, severe, ongoing symptoms after even a single exposure—a syndrome termed Gadolinium Deposition Disease (GDD). Mitochondrial dysfunction and oxidative stress have been repeatedly implicated by animal and in vitro studies as mechanisms of Gd/GBCA-related toxicity, and as pathogenic in other diseases with similarities in presentation. Here, we aimed to molecularly characterize and explore potential metabolic associations with GDD symptoms. Detailed clinical phenotypes were systematically obtained for a small cohort of individuals (n = 15) with persistent symptoms attributed to a GBCA-enhanced MRI and consistent with provisional diagnostic criteria for GDD. Global untargeted mass spectroscopy-based metabolomics analyses were performed on plasma samples and examined for relevance with both single marker and pathways approaches. In addition to GDD criteria, frequently reported symptoms resembled those of patients with known mitochondrial-related diseases. Plasma differences compared to a healthy, asymptomatic reference cohort were suggested for 45 of 813 biochemicals. A notable proportion of these are associated with mitochondrial function and related disorders, including nucleotide and energy superpathways, which were over-represented. Although early evidence, coincident clinical and biochemical indications of potential mitochondrial involvement in GDD are remarkable in light of preclinical models showing adverse Gd/GBCA effects on multiple aspects of mitochondrial function. Further research on the potential contributory role of these markers and pathways in persistent symptoms attributed to GBCA exposure is recommended.
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18
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Neumann E, Schreeck F, Herberg J, Jacqz Aigrain E, Maitland-van der Zee AH, Pérez-Martínez A, Hawcutt DB, Schaeffeler E, Rane A, de Wildt SN, Schwab M. How paediatric drug development and use could benefit from OMICs: a c4c expert group white paper. Br J Clin Pharmacol 2022; 88:5017-5033. [PMID: 34997627 DOI: 10.1111/bcp.15216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/01/2022] Open
Abstract
The safety and efficacy of pharmacotherapy in children, particularly preterms, neonates, and infants, is limited by a paucity of good quality data from prospective clinical drug trials. A specific challenge is the establishment of valid biomarkers. OMICs technologies may support these efforts, by complementary information about targeted and non-targeted molecules through systematic characterization and quantitation of biological samples. OMICs technologies comprise at least genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics in addition to the patient's phenotype. OMICs technologies are in part hypothesis-generating allowing an in depth understanding of disease pathophysiology and pharmacological mechanisms. Application of OMICs technologies in paediatrics faces major challenges before routine adoption. First, developmental processes need to be considered, including a sub-division into specific age groups as developmental changes clearly impact OMICs data. Second, compared to the adult population, the number of patients is limited as well as type and amount of necessary biomaterial, especially in neonates and preterms. Thus, advanced trial designs and biostatistical methods, non-invasive biomarkers, innovative biobanking concepts including data and samples from healthy children, as well as analytical approaches (e.g. liquid biopsies) should be addressed to overcome these obstacles. The ultimate goal is to link OMICs technologies with innovative analysis tools, like artificial intelligence at an early stage. The use of OMICs data based on a feasible approach will contribute to identify complex phenotypes and subpopulations of patients to improve development of medicines for children with potential economic advantages.
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Affiliation(s)
- Eva Neumann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Filippa Schreeck
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Jethro Herberg
- Department of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Evelyne Jacqz Aigrain
- Pediatric Pharmacology and Pharmacogenetics, Hopital Universitaire Saint-Louis, Paris, France.,Clinical Investigation Center CIC1426, Hôpital Robert Debre, Paris, France.,Pharmacology, University of Paris, Paris, France
| | | | - Antonio Pérez-Martínez
- Institute for Health Research (IdiPAZ), La Paz University Hospital, Madrid, Spain.,Pediatric Onco-Hematology Department, La Paz University Hospital, Madrid, Spain.,Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, UK.,NIHR Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, UK
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Anders Rane
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Saskia N de Wildt
- Department of Pharmacology and Toxicology, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands.,Intensive Care and Department of Paediatric Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany.,Departments of Clinical Pharmacology, and of Biochemistry and Pharmacy, University of Tuebingen, Tuebingen, Germany
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19
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Blakebrough-Hall C, Hick P, Mahony TJ, González LA. Factors associated with bovine respiratory disease case fatality in feedlot cattle. J Anim Sci 2022; 100:skab361. [PMID: 34894141 PMCID: PMC8796815 DOI: 10.1093/jas/skab361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Bovine respiratory disease (BRD) is the primary cause of morbidity and mortality in cattle feedlots. There is a need to understand what animal health and production factors are associated with increased mortality risk due to BRD. The aim of the present study was to explore factors associated with BRD case fatality in feedlot cattle. Four pens totaling 898 steers were monitored daily for visual signs of BRD such as difficult breathing and coughing, and animals exhibiting signs of BRD were taken to the hospital shed for further examination and clinical measures. Blood samples were obtained at feedlot entry and at time of first BRD pull from animals diagnosed with BRD (n = 121) and those that died due to BRD confirmed by postmortem examination (n = 16; 13.2% case fatality rate). Mixed-effects linear regression models were used to estimate differences in animal health and production factors and the relative concentrations of 34 identified blood metabolites between animals that survived versus those that died. Generalized linear mixed-effects models were used to obtain the odds of being seronegative (at both feedlot entry and first BRD pull) to 5 BRD viruses and having a positive nasal swab result at the time of first pull in died and survived animals. Animals that died from BRD had lower average daily gain (ADG), reduced weight at first BRD pull, higher visual BRD scores and received more treatments for BRD compared with animals that survived BRD (P < 0.05). The odds of being seronegative for bovine viral diarrhea virus 1 (BVDV-1) were 5.66 times higher for animals that died compared with those that survived (P = 0.013). The odds of having a positive bovine coronavirus nasal swab result were 13.73 times higher in animals that died versus those that survived (P = 0.007). Animals that died from BRD had higher blood concentrations of α glucose chain, β-hydroxybutyrate, leucine, phenylalanine, and pyruvate compared with those that survived (P < 0.05). Animals that died from BRD had lower concentrations of acetate, citrate, and glycine compared with animals that survived (P < 0.05). The results of the current study suggest that ADG to first BRD pull, weight at first BRD pull, visual BRD score, the number of BRD treatments, seronegativity to BVDV-1, virus positive to BCoV nasal swab, and that certain blood metabolites are associated with BRD case fatality risk. The ability of these measures to predict the risk of death due to BRD needs further research.
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Affiliation(s)
- Claudia Blakebrough-Hall
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Camden, NSW 2570, Australia
| | - Paul Hick
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camden, NSW 2570, Australia
| | - T J Mahony
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, QLD 4072, Australia
| | - Luciano A González
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Camden, NSW 2570, Australia
- Sydney Institute of Agriculture, University of Sydney, Biomedical Building, Australian Technology Park, NSW 2015, Australia
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20
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Mukherjee S, Kotnis A, Ray SK, Vaidyanathan K, Singh S, Mittal R. Current Scenario of Clinical Diagnosis to Identify Inborn Errors of Metabolism with Precision Profiling for Expanded Screening in Infancy in a Resource-limited Setting. Curr Pediatr Rev 2022; 19:34-47. [PMID: 35379152 DOI: 10.2174/1573396318666220404113732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/18/2022] [Accepted: 02/15/2022] [Indexed: 01/28/2023]
Abstract
Inborn errors of metabolism (IEM) are a diverse collection of abnormalities that cause a variety of morbidities and mortality in children and are classified as uncommon genetic diseases. Early and accurate detection of the condition can save a patient's life. By aiding families as they navigate the experience of having a child with an IEM, healthcare practitioners have the chance to reduce the burden of negative emotional consequences. New therapeutic techniques, such as enzyme replacement and small chemical therapies, organ transplantation, and cellular and gene-based therapies using whole-genome sequencing, have become available in addition to traditional medical intake and cofactor treatments. In the realm of metabolic medicine and metabolomics, the twentyfirst century is an exciting time to be alive. The availability of metabolomics and genomic analysis has led to the identification of a slew of novel diseases. Due to the rarity of individual illnesses, obtaining high-quality data for these treatments in clinical trials and real-world settings has proven difficult. Guidelines produced using standardized techniques have helped enhance treatment delivery and clinical outcomes over time. This article gives a comprehensive description of IEM and how to diagnose it in patients who have developed clinical signs early or late. The appropriate use of standard laboratory outcomes in the preliminary patient assessment is also emphasized that can aid in the ordering of specific laboratory tests to confirm a suspected diagnosis, in addition, to begin treatment as soon as possible in a resource limiting setting where genomic analysis or newborn screening facility is not available.
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Affiliation(s)
- Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
| | - Ashwin Kotnis
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
| | | | - Kannan Vaidyanathan
- Department of Biochemistry, Amrita Institute of Medical Science & Research Center, Kochi, Kerala-682041, India
| | - Snighdha Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
| | - Rishabh Mittal
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
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21
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Mukherjee S, Ray SK. Inborn Errors of Metabolism Screening in Neonates: Current Perspective with Diagnosis and Therapy. Curr Pediatr Rev 2022; 18:274-285. [PMID: 35379134 DOI: 10.2174/1573396318666220404194452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022]
Abstract
Inborn errors of metabolism (IEMs) are rare hereditary or acquired disorders resulting from an enzymatic deformity in biochemical and metabolic pathways influencing proteins, fats, carbohydrate metabolism, or hampered some organelle function. Even though individual IEMs are uncommon, together, they represent a diverse class of genetic diseases, with new issues and disease mechanisms being portrayed consistently. IEM includes the extraordinary multifaceted nature of the fundamental pathophysiology, biochemical diagnosis, molecular level investigation, and complex therapeutic choices. However, due to the molecular, biochemical, and clinical heterogeneity of IEM, screening alone will not detect and diagnose all illnesses included in newborn screening programs. Early diagnosis prevents the emergence of severe clinical symptoms in the majority of IEM cases, lowering morbidity and death. The appearance of IEM disease can vary from neonates to adult people, with the more serious conditions showing up in juvenile stages along with significant morbidity as well as mortality. Advances in understanding the physiological, biochemical, and molecular etiologies of numerous IEMs by means of modalities, for instance, the latest molecular-genetic technologies, genome engineering knowledge, entire exome sequencing, and metabolomics, have prompted remarkable advancement in detection and treatment in modern times. In this review, we analyze the biochemical basis of IEMs, clinical manifestations, the present status of screening, ongoing advances, and efficiency of diagnosis in treatment for IEMs, along with prospects for further exploration as well as innovation.
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Affiliation(s)
- Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
| | - Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh-462020, India
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22
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Odom JD, Sutton VR. Metabolomics in Clinical Practice: Improving Diagnosis and Informing Management. Clin Chem 2021; 67:1606-1617. [PMID: 34633032 DOI: 10.1093/clinchem/hvab184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/17/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Metabolomics is the study of small molecules to simultaneously identify multiple low molecular weight molecules in a system. Broadly speaking, metabolomics can be subdivided into targeted and untargeted types of analysis, each type having advantages and drawbacks. Targeted metabolomics can quantify analytes but only looks for known or expected analytes related to particular disease(s), whereas untargeted metabolomics is typically nonquantitative but can detect thousands of analytes from an agnostic or nonhypothesis driven perspective, allowing for novel discoveries. CONTENT One application of metabolomics is the study of inborn errors of metabolism (IEM). The biochemical hallmark of IEMs is decreased concentrations of analytes distal to the enzymatic defect and buildup of analytes proximal to the defect. Metabolomics can detect these changes with one test and is effective in screening for and diagnosis of IEMs. Metabolomics has also been used to study many nonmetabolic diseases such as autism spectrum disorder, various cancers, and multiple congenital anomalies syndromes. Metabolomics has led to the discovery of many novel biomarkers of disease. Recent publications demonstrate how metabolomics can be useful clinically in the diagnosis and management of patients, as well as for research and clinical discovery. SUMMARY Metabolomics has proved to be a useful tool clinically for screening and diagnostic purposes and from a research perspective for the detection of novel biomarkers. In the future, metabolomics will likely become a routine part of the evaluation for many diseases as either a supplementary test or it may simply replace historical analyses that require several individual tests and sample types.
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Affiliation(s)
- John D Odom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Baylor Genetics Laboratory, Houston, TX
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23
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Furlani IL, da Cruz Nunes E, Canuto GAB, Macedo AN, Oliveira RV. Liquid Chromatography-Mass Spectrometry for Clinical Metabolomics: An Overview. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:179-213. [PMID: 34628633 DOI: 10.1007/978-3-030-77252-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Metabolomics is a discipline that offers a comprehensive analysis of metabolites in biological samples. In the last decades, the notable evolution in liquid chromatography and mass spectrometry technologies has driven an exponential progress in LC-MS-based metabolomics. Targeted and untargeted metabolomics strategies are important tools in health and medical science, especially in the study of disease-related biomarkers, drug discovery and development, toxicology, diet, physical exercise, and precision medicine. Clinical and biological problems can now be understood in terms of metabolic phenotyping. This overview highlights the current approaches to LC-MS-based metabolomics analysis and its applications in the clinical research.
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Affiliation(s)
- Izadora L Furlani
- Núcleo de Pesquisa em Cromatografia (Separare), Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Estéfane da Cruz Nunes
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Gisele A B Canuto
- Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil
| | - Adriana N Macedo
- Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Regina V Oliveira
- Núcleo de Pesquisa em Cromatografia (Separare), Department of Chemistry, Federal University of São Carlos, São Carlos, SP, Brazil.
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24
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Liu H, Zhu J, Li Q, Wang D, Wan K, Yuan Z, Zhang J, Zou L, He X, Miao J. Untargeted metabolomic analysis of urine samples for diagnosis of inherited metabolic disorders. Funct Integr Genomics 2021; 21:645-653. [PMID: 34585279 DOI: 10.1007/s10142-021-00804-w] [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: 04/21/2021] [Revised: 08/07/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
Metabolomics has become an important tool for clinical research, especially for analyzing inherited metabolic disorders (IMDs). The purpose of this study was to explore the performance of metabolomics in diagnosing IMDs using an untargeted metabolomic approach. A total of 40 urine samples were collected: 20 samples from healthy children and 20 from pediatric patients, of whom 13 had confirmed IMDs and seven had suspected IMDs. Samples were analyzed by Orbitrap mass spectrometry in positive and negative mode alternately, coupled with ultra-high liquid chromatography. Raw data were processed using Compound Discovery 2.0 ™ and then exported for partial least squares discriminant analysis (PLS-DA) by SIMCA-P 14.1. After comparing with m/zCloud and chemSpider libraries, compounds with similarity above 80% were selected and normalized for subsequent relative quantification analysis. The uncommon compounds discovered were analyzed based on the Kyoto Encyclopedia of Genes and Genomes to explore their possible metabolic pathways. All IMDs patients were successfully distinguished from controls in the PLS-DA. Untargeted metabolomics revealed a broader metabolic spectrum in patients than what is observed using routine chromatographic methods for detecting IMDs. Higher levels of certain compounds were found in all 13 confirmed IMD patients and 5 of 7 suspected IMD patients. Several potential novel markers emerged after relative quantification. Untargeted metabolomics may be able to diagnose IMDs from urine and may deepen insights into the disease by revealing changes in various compounds such as amino acids, acylcarnitines, organic acids, and nucleosides. Such analyses may identify biomarkers to improve the study and treatment of IMDs.
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Affiliation(s)
- Hao Liu
- Newborn Screening Center, Chongqing Health Center for Women and Children, Longshan Road 120th, Yubei District, Chongqing, 401147, People's Republic of China.,Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Jiang Zhu
- Chongqing Key Laboratory of Child Nutrition and Health, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Qiu Li
- Chongqing Key Laboratory of Child Nutrition and Health, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Dongjuan Wang
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Kexing Wan
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Zhaojian Yuan
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Juan Zhang
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Lin Zou
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Xiaoyan He
- Center for Clinical Molecular Medicine, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Zhongshan Road 2nd, Yuzhong District, Chongqing, 400014, People's Republic of China.
| | - Jingkun Miao
- Newborn Screening Center, Chongqing Health Center for Women and Children, Longshan Road 120th, Yubei District, Chongqing, 401147, People's Republic of China.
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25
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Barbosa-Gouveia S, Vázquez-Mosquera ME, González-Vioque E, Álvarez JV, Chans R, Laranjeira F, Martins E, Ferreira AC, Avila-Alvarez A, Couce ML. Utility of Gene Panels for the Diagnosis of Inborn Errors of Metabolism in a Metabolic Reference Center. Genes (Basel) 2021; 12:1262. [PMID: 34440436 PMCID: PMC8391361 DOI: 10.3390/genes12081262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 11/28/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have been proposed as a first-line test for the diagnosis of inborn errors of metabolism (IEM), a group of genetically heterogeneous disorders with overlapping or nonspecific phenotypes. Over a 3-year period, we prospectively analyzed 311 pediatric patients with a suspected IEM using four targeted gene panels. The rate of positive diagnosis was 61.86% for intermediary metabolism defects, 32.84% for complex molecular defects, 19% for hypoglycemic/hyperglycemic events, and 17% for mitochondrial diseases, and a conclusive molecular diagnosis was established in 2-4 weeks. Forty-one patients for whom negative results were obtained with the mitochondrial diseases panel underwent subsequent analyses using the NeuroSeq panel, which groups all genes from the individual panels together with genes associated with neurological disorders (1870 genes in total). This achieved a diagnostic rate of 32%. We next evaluated the utility of a tool, Phenomizer, for differential diagnosis, and established a correlation between phenotype and molecular findings in 39.3% of patients. Finally, we evaluated the mutational architecture of the genes analyzed by determining z-scores, loss-of-function observed/expected upper bound fraction (LOEUF), and haploinsufficiency (HI) scores. In summary, targeted gene panels for specific groups of IEMs enabled rapid and effective diagnosis, which is critical for the therapeutic management of IEM patients.
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Affiliation(s)
- Sofia Barbosa-Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, IDIS-Health Research Institute of Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), European Reference Network for Hereditary Metabolic Disorders (MetabERN), Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (S.B.-G.); (M.E.V.-M.); (J.V.Á.); (R.C.)
| | - María E. Vázquez-Mosquera
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, IDIS-Health Research Institute of Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), European Reference Network for Hereditary Metabolic Disorders (MetabERN), Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (S.B.-G.); (M.E.V.-M.); (J.V.Á.); (R.C.)
| | - Emiliano González-Vioque
- Department of Clinical Biochemistry, Puerta de Hierro-Majadahonda University Hospital, 28222 Majadahonda, Spain;
| | - José V. Álvarez
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, IDIS-Health Research Institute of Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), European Reference Network for Hereditary Metabolic Disorders (MetabERN), Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (S.B.-G.); (M.E.V.-M.); (J.V.Á.); (R.C.)
| | - Roi Chans
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, IDIS-Health Research Institute of Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), European Reference Network for Hereditary Metabolic Disorders (MetabERN), Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (S.B.-G.); (M.E.V.-M.); (J.V.Á.); (R.C.)
| | - Francisco Laranjeira
- Biochemical Genetics Unit, Centro de Genética Médica Doutor Jacinto Magalhães, 4050-466 Porto, Portugal;
| | - Esmeralda Martins
- Centro Materno-Infantil do Norte, Centro Hospitalar Universitário do Porto (CHUP), Coordinator of the Centro de Referência de Doenças Hereditárias do Metabolismo do CHUP, 4050-466 Porto, Portugal;
| | - Ana Cristina Ferreira
- Hospital D. Estefânia, Centro Hospitalar de Lisboa Central (CHLC), Coordinator of the Centro de Referência de Doenças Hereditárias do Metabolismo do CHLC, 1169-050 Lisboa, Portugal;
| | - Alejandro Avila-Alvarez
- Neonatology Unit, Pediatrics Department, Complexo Hospitalario Universitario de A Coruña, SERGAS, 15006 A Coruña, Spain;
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, IDIS-Health Research Institute of Santiago de Compostela, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), European Reference Network for Hereditary Metabolic Disorders (MetabERN), Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (S.B.-G.); (M.E.V.-M.); (J.V.Á.); (R.C.)
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26
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Allen J, Zareen Z, Doyle S, Whitla L, Afzal Z, Stack M, Franklin O, Green A, James A, Leahy TR, Quinn S, Elnazir B, Russell J, Paran S, Kiely P, Roche EF, McDonnell C, Baker L, Hensey O, Gibson L, Kelly S, McDonald D, Molloy EJ. Multi-Organ Dysfunction in Cerebral Palsy. Front Pediatr 2021; 9:668544. [PMID: 34434904 PMCID: PMC8382237 DOI: 10.3389/fped.2021.668544] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/15/2021] [Indexed: 11/20/2022] Open
Abstract
Cerebral Palsy (CP) describes a heterogenous group of non-progressive disorders of posture or movement, causing activity limitation, due to a lesion in the developing brain. CP is an umbrella term for a heterogenous condition and is, therefore, descriptive rather than a diagnosis. Each case requires detailed consideration of etiology. Our understanding of the underlying cause of CP has developed significantly, with areas such as inflammation, epigenetics and genetic susceptibility to subsequent insults providing new insights. Alongside this, there has been increasing recognition of the multi-organ dysfunction (MOD) associated with CP, in particular in children with higher levels of motor impairment. Therefore, CP should not be seen as an unchanging disorder caused by a solitary insult but rather, as a condition which evolves over time. Assessment of multi-organ function may help to prevent complications in later childhood or adulthood. It may also contribute to an improved understanding of the etiology and thus may have an implication in prevention, interventional methods and therapies. MOD in CP has not yet been quantified and a scoring system may prove useful in allowing advanced clinical planning and follow-up of children with CP. Additionally, several biomarkers hold promise in assisting with long-term monitoring. Clinicians should be aware of the multi-system complications that are associated with CP and which may present significant diagnostic challenges given that many children with CP communicate non-verbally. A step-wise, logical, multi-system approach is required to ensure that the best care is provided to these children. This review summarizes multi-organ dysfunction in children with CP whilst highlighting emerging research and gaps in our knowledge. We identify some potential organ-specific biomarkers which may prove useful in developing guidelines for follow-up and management of these children throughout their lifespan.
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Affiliation(s)
- John Allen
- Discipline of Pediatrics, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Trinity Research in Childhood Centre, Trinity College Dublin, Dublin, Ireland.,Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland
| | | | - Samantha Doyle
- Department of Clinical Genetics, Birmingham Women's Hospital, Birmingham, United Kingdom
| | - Laura Whitla
- Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Zainab Afzal
- Discipline of Pediatrics, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Maria Stack
- Children's Health Ireland at Crumlin, Dublin, Ireland.,Children's Health Ireland at Temple St. Dublin, Dublin, Ireland
| | - Orla Franklin
- Children's Health Ireland at Crumlin, Dublin, Ireland.,Children's Health Ireland at Temple St. Dublin, Dublin, Ireland
| | - Andrew Green
- Children's Health Ireland at Crumlin, Dublin, Ireland.,Children's Health Ireland at Temple St. Dublin, Dublin, Ireland
| | - Adam James
- Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Timothy Ronan Leahy
- Discipline of Pediatrics, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Shoana Quinn
- Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland
| | - Basil Elnazir
- Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland
| | - John Russell
- Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Sri Paran
- Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Patrick Kiely
- Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Edna Frances Roche
- Discipline of Pediatrics, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Trinity Research in Childhood Centre, Trinity College Dublin, Dublin, Ireland.,Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland
| | - Ciara McDonnell
- Discipline of Pediatrics, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Trinity Research in Childhood Centre, Trinity College Dublin, Dublin, Ireland.,Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland.,Children's Health Ireland at Temple St. Dublin, Dublin, Ireland
| | - Louise Baker
- Children's Health Ireland at Temple St. Dublin, Dublin, Ireland
| | | | - Louise Gibson
- Department of Paediatrics, Cork University Hospital, Cork, Ireland
| | - Stephanie Kelly
- Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland
| | - Denise McDonald
- Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland
| | - Eleanor J Molloy
- Discipline of Pediatrics, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Trinity Research in Childhood Centre, Trinity College Dublin, Dublin, Ireland.,Children's Health Ireland (CHI) at Tallaght, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland.,Department of Neonatology, The Coombe Women and Infants University Hospital, Dublin, Ireland
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27
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Saigusa D, Matsukawa N, Hishinuma E, Koshiba S. Identification of biomarkers to diagnose diseases and find adverse drug reactions by metabolomics. Drug Metab Pharmacokinet 2020; 37:100373. [PMID: 33631535 DOI: 10.1016/j.dmpk.2020.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Abstract
Metabolomics has been widely used for investigating the biological functions of disease expression and has the potential to discover biomarkers in circulating biofluids or tissue extracts that reflect in phenotypic changes. Metabolic profiling has advantages because of the use of unbiased techniques, including multivariate analysis, and has been applied in pharmacological studies to predict therapeutic and adverse reactions of drugs, which is called pharmacometabolomics (PMx). Nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics has contributed to the discovery of recent disease biomarkers; however, the optimal strategy for the study purpose must be selected from many established protocols, methodologies and analytical platforms. Additionally, information on molecular localization in tissue is essential for further functional analyses related to therapeutic and adverse effects of drugs in the process of drug development. MS imaging (MSI) is a promising technology that can visualize molecules on tissue surfaces without labeling and thus provide localized information. This review summarizes recent uses of MS-based global and wide-targeted metabolomics technologies and the advantages of the MSI approach for PMx and highlights the PMx technique for the biomarker discovery of adverse drug effects.
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Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Eiji Hishinuma
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
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28
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Li S, Liu J, Zhou J, Wang Y, Jin F, Chen X, Yang J, Chen Z. Urinary Metabolomic Profiling Reveals Biological Pathways and Predictive Signatures Associated with Childhood Asthma. J Asthma Allergy 2020; 13:713-724. [PMID: 33376359 PMCID: PMC7755329 DOI: 10.2147/jaa.s281198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/20/2020] [Indexed: 12/16/2022] Open
Abstract
Background Despite considerable efforts, the pathogenic mechanisms of asthma are still incompletely understood, due to its heterogeneous nature. However, metabolomics can offer a global view of a biological system, making it a valuable tool for further elucidation of mechanisms and biomarker discovery in asthma. Methods GC-MS-based metabolomic analysis was conducted for comparison of urine metabolic profiles between asthmatic children (n=30) and healthy controls (n=30). Results An orthogonal projections to latent structures discriminant-analysis model revealed a clear separation of the asthma and control groups (R 2 x =0.137, R 2 y =0.947, Q 2=0.82). A total of 20 differential metabolites were identified as discriminant factors, of which eleven were significantly increased and nine decreased in the asthma group compared to the control group. Pathway-enrichment analysis based on these differential metabolites indicated that sphingolipid metabolism, protein biosynthesis, and citric acid cycle were strongly associated with asthma. Among the identified metabolites, 2-hydroxybutanoic acid showed excellent discriminatory performance for distinguishing asthma from healthy controls, with an AUC of 0.969. Conclusion Our study revealed significant changes in the urine metabolome of asthma patients. Several perturbed pathways (eg, sphingolipid metabolism and citric acid cycle) may be related to asthma pathogenesis, and 2-hydroxybutanoic acid could serve as a potential biomarker for asthma diagnosis.
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Affiliation(s)
- Shuxian Li
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China
| | - Jinling Liu
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China
| | - Junfen Zhou
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China.,Department of Pediatrics, Wenling Maternal and Child Health Care Hospital, Wenling, Zhejiang 317500, China
| | - Yingshuo Wang
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China
| | - Fang Jin
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China
| | - Xiaoyang Chen
- Developmental and Behavioral Department, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China
| | - Jun Yang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310013, China.,Department of Toxicology, Hangzhou Normal University School of Public Health, Hangzhou, Zhejiang 310016, China
| | - Zhimin Chen
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China
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