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Kernohan KD, Boycott KM. The expanding diagnostic toolbox for rare genetic diseases. Nat Rev Genet 2024; 25:401-415. [PMID: 38238519 DOI: 10.1038/s41576-023-00683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 05/23/2024]
Abstract
Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
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Affiliation(s)
- Kristin D Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
- Newborn Screening Ontario, CHEO, Ottawa, ON, Canada
| | - Kym M Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada.
- Department of Genetics, CHEO, Ottawa, ON, Canada.
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2
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Li JW, Mao SJ, Chao YQ, Hu CX, Qian YJ, Dai YL, Huang K, Shen Z, Zou CC. Application of tandem mass spectrometry in the screening and diagnosis of mucopolysaccharidoses. Orphanet J Rare Dis 2024; 19:179. [PMID: 38685110 PMCID: PMC11059687 DOI: 10.1186/s13023-024-03195-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Mucopolysaccharidoses (MPSs) are caused by a deficiency in the enzymes needed to degrade glycosaminoglycans (GAGs) in the lysosome. The storage of GAGs leads to the involvement of several systems and even to the death of the patient. In recent years, an increasing number of therapies have increased the treatment options available to patients. Early treatment is beneficial in improving the prognosis, but children with MPSs are often delayed in their diagnosis. Therefore, there is an urgent need to develop a method for early screening and diagnosis of the disease. Tandem mass spectrometry (MS/MS) is an analytical method that can detect multiple substrates or enzymes simultaneously. GAGs are reliable markers of MPSs. MS/MS can be used to screen children at an early stage of the disease, to improve prognosis by treating them before symptoms appear, to evaluate the effectiveness of treatment, and for metabolomic analysis or to find suitable biomarkers. In the future, MS/MS could be used to further identify suitable biomarkers for MPSs for early diagnosis and to detect efficacy.
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Affiliation(s)
- Jing-Wen Li
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Shao-Jia Mao
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yun-Qi Chao
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Chen-Xi Hu
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yan-Jie Qian
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yang-Li Dai
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Ke Huang
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Zheng Shen
- Lab Center, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Chao-Chun Zou
- Department of Endocrinology, the Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China.
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3
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Wurth R, Turgeon C, Stander Z, Oglesbee D. An evaluation of untargeted metabolomics methods to characterize inborn errors of metabolism. Mol Genet Metab 2024; 141:108115. [PMID: 38181458 PMCID: PMC10843816 DOI: 10.1016/j.ymgme.2023.108115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/19/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024]
Abstract
Inborn errors of metabolism (IEMs) encompass a diverse group of disorders that can be difficult to classify due to heterogenous clinical, molecular, and biochemical manifestations. Untargeted metabolomics platforms have become a popular approach to analyze IEM patient samples because of their ability to detect many metabolites at once, accelerating discovery of novel biomarkers, and metabolic mechanisms of disease. However, there are concerns about the reproducibility of untargeted metabolomics research due to the absence of uniform reporting practices, data analyses, and experimental design guidelines. Therefore, we critically evaluated published untargeted metabolomic platforms used to characterize IEMs to summarize the strengths and areas for improvement of this technology as it progresses towards the clinical laboratory. A total of 96 distinct IEMs were collectively evaluated by the included studies. However, most of these IEMs were evaluated by a single untargeted metabolomic method, in a single study, with a limited cohort size (55/96, 57%). The goals of the included studies generally fell into two, often overlapping, categories: detecting known biomarkers from many biochemically distinct IEMs using a single platform, and detecting novel metabolites or metabolic pathways. There was notable diversity in the design of the untargeted metabolomic platforms. Importantly, the majority of studies reported adherence to quality metrics, including the use of quality control samples and internal standards in their experiments, as well as confirmation of at least some of their feature annotations with commercial reference standards. Future applications of untargeted metabolomics platforms to the study of IEMs should move beyond single-subject analyses, and evaluate reproducibility using a prospective, or validation cohort.
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Affiliation(s)
- Rachel Wurth
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, 200 1(st) St SW, Rochester, MN 55905, USA
| | - Coleman Turgeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Zinandré Stander
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN 55905, USA.
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Pierzynowska K, Deresz P, Węgrzyn G, Gaffke L. Dysregulation of genes coding for proteins involved in metabolic processes in mucopolysaccharidoses, evidenced by a transcriptomic approach. Metab Brain Dis 2023; 38:2133-2144. [PMID: 37195412 PMCID: PMC10349023 DOI: 10.1007/s11011-023-01231-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/07/2023] [Indexed: 05/18/2023]
Abstract
Mucopolysaccharidoses (MPS) are a group of lysosomal storage diseases (LSD) caused by mutations in genes coding for enzymes responsible for degradation of glycosaminoglycans (GAGs). Most types of these severe disorders are characterized by neuronopathic phenotypes. Although lysosomal accumulation of GAGs is the primary metabolic defect in MPS, secondary alterations in biochemical processes are considerable and influence the course of the disease. Early hypothesis suggested that these secondary changes might be due to lysosomal storage-mediated impairment of activities of other enzymes, and subsequent accumulation of various compounds in cells. However, recent studies indicated that expression of hundreds of genes is changed in MPS cells. Therefore, we asked whether metabolic effects observed in MPS are caused primarily by GAG-mediated inhibition of specific biochemical reactions or appear as results of dysregulation of expression of genes coding for proteins involved in metabolic processes. Transcriptomic analyses of 11 types of MPS (using RNA isolated from patient-derived fibroblasts), performed in this study, showed that a battery of the above mentioned genes is dysregulated in MPS cells. Some biochemical pathways might be especially affected by changes in expression of many genes, including GAG metabolism and sphingolipid metabolism which is especially interesting as secondary accumulation of various sphingolipids is one of the best known additional (while significantly enhancing neuropathological effects) metabolic defects in MPS. We conclude that severe metabolic disturbances, observed in MPS cells, can partially arise from changes in the expression of many genes coding for proteins involved in metabolic processes.
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Affiliation(s)
- Karolina Pierzynowska
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Patrycja Deresz
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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5
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Torres CL, Scalco FB, de Oliveira MLC, Peake RWA, Garrett R. Untargeted LC-HRMS metabolomics reveals candidate biomarkers for mucopolysaccharidoses. Clin Chim Acta 2023; 541:117250. [PMID: 36764508 DOI: 10.1016/j.cca.2023.117250] [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: 10/27/2022] [Revised: 12/19/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Mucopolysaccharidoses (MPSs) are inherited genetic diseases caused by an absence or deficiency of lysosomal enzymes responsible for catabolizing glycosaminoglycans (GAGs). Undiagnosed patients, or those without adequate treatment in early life, can be severely and irreversibly affected by the disease. In this study, we applied liquid chromatography-high resolution mass spectrometry (LC-HRMS)-based untargeted metabolomics to identify potential biomarkers for MPS disorders to better understand how MPS may affect the metabolome of patients. METHODS Urine samples from 37 MPS patients (types I, II, III, IV, and VI; untreated and treated with enzyme replacement therapy (ERT)) and 38 controls were analyzed by LC-HRMS. Data were processed by an untargeted metabolomics workflow and submitted to multivariate statistical analyses to reveal significant differences between the MPS and control groups. RESULTS A total of 12 increased metabolites common to all MPS types were identified. Dipeptides, amino acids and derivatives were increased in the MPS group compared to controls. N-acetylgalactosamines 4- or 6-sulfate, important constituents of GAGs, were also elevated in MPS patients, most prominently in those with MPS VI. Notably, treated patients exhibited lower levels of the aforementioned acylaminosugars than untreated patients in all MPS types. CONCLUSIONS Untargeted metabolomics has enabled the detection of metabolites that could improve our understanding of MPS physiopathology. These potential biomarkers can be utilized in screening methods to support diagnosis and ERT monitoring.
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Affiliation(s)
- Clarisse L Torres
- Metabolomics Laboratory, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda B Scalco
- Inborn Error of Metabolism Laboratory, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Maria Lúcia 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
| | - Rafael Garrett
- Metabolomics Laboratory, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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Pančík F, Pakanová Z, Nemčovič M, Květoň F, Šalingová A, Hlavatá A, Kozmon S, Baráth P. Application of MALDI-TOF Mass Spectrometry for Non-invasive Diagnostics of Mucopolysaccharidosis IIIA. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2023. [DOI: 10.1590/2326-4594-jiems-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
| | | | | | | | - Anna Šalingová
- Centre for Inherited Metabolic Disorders, Slovak Republic
| | - Anna Hlavatá
- Comenius University in Bratislava, Slovak Republic
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7
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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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8
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Scerra G, De Pasquale V, Scarcella M, Caporaso MG, Pavone LM, D'Agostino M. Lysosomal positioning diseases: beyond substrate storage. Open Biol 2022; 12:220155. [PMID: 36285443 PMCID: PMC9597170 DOI: 10.1098/rsob.220155] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Lysosomal storage diseases (LSDs) comprise a group of inherited monogenic disorders characterized by lysosomal dysfunctions due to undegraded substrate accumulation. They are caused by a deficiency in specific lysosomal hydrolases involved in cellular catabolism, or non-enzymatic proteins essential for normal lysosomal functions. In LSDs, the lack of degradation of the accumulated substrate and its lysosomal storage impairs lysosome functions resulting in the perturbation of cellular homeostasis and, in turn, the damage of multiple organ systems. A substantial number of studies on the pathogenesis of LSDs has highlighted how the accumulation of lysosomal substrates is only the first event of a cascade of processes including the accumulation of secondary metabolites and the impairment of cellular trafficking, cell signalling, autophagic flux, mitochondria functionality and calcium homeostasis, that significantly contribute to the onset and progression of these diseases. Emerging studies on lysosomal biology have described the fundamental roles of these organelles in a variety of physiological functions and pathological conditions beyond their canonical activity in cellular waste clearance. Here, we discuss recent advances in the knowledge of cellular and molecular mechanisms linking lysosomal positioning and trafficking to LSDs.
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Affiliation(s)
- Gianluca Scerra
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Valeria De Pasquale
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Via Federico Delpino 1, 80137 Naples, Italy
| | - Melania Scarcella
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Maria Gabriella Caporaso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Luigi Michele Pavone
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Massimo D'Agostino
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Naples, Italy
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9
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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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11
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Mak J, Cowan TM. Detecting lysosomal storage disorders by glycomic profiling using liquid chromatography mass spectrometry. Mol Genet Metab 2021; 134:43-52. [PMID: 34474962 PMCID: PMC9069563 DOI: 10.1016/j.ymgme.2021.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUND Urine and plasma biomarker testing for lysosomal storage disorders by liquid chromatography mass spectrometry (LC-MS) currently requires multiple analytical methods to detect the abnormal accumulation of oligosaccharides, mucopolysaccharides, and glycolipids. To improve clinical testing efficiency, we developed a single LC-MS method to simultaneously identify disorders of oligosaccharide, mucopolysaccharide, and glycolipid metabolism with minimal sample preparation. METHODS We created a single chromatographic method for separating free glycans and glycolipids in their native form, using an amide column and high pH conditions. We used this glycomic profiling method both in untargeted analyses of patient and control urines using LC ion-mobility high-resolution MS (biomarker discovery), and targeted analyses of urine, serum, and dried blood spot samples by LC-MS/MS (clinical validation). RESULTS Untargeted glycomic profiling revealed twenty biomarkers that could identify and subtype mucopolysaccharidoses. We incorporated these with known oligosaccharide and glycolipid biomarkers into a rapid test that identifies at least 27 lysosomal storage disorders, including oligosaccharidoses, mucopolysaccharidoses, sphingolipidoses, glycogen storage disorders, and congenital disorders of glycosylation and de-glycosylation. In a validation set containing 115 urine samples from patients with lysosomal storage disorders, all were unambiguously distinguished from normal controls, with correct disease subtyping for 88% (101/115) of cases. Glucosylsphingosine was reliably elevated in dried blood spots from Gaucher disease patients with baseline resolution from galactosylsphingosine. CONCLUSION Glycomic profiling by liquid chromatography mass spectrometry identifies a range of lysosomal storage disorders. This test can be used in clinical evaluations to rapidly focus a diagnosis, as well as to clarify or support additional gene sequencing and enzyme studies.
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Affiliation(s)
- Justin Mak
- Clinical Biochemical Genetics Laboratory, Stanford Health Care, United States of America.
| | - Tina M Cowan
- Clinical Biochemical Genetics Laboratory, Stanford Health Care, United States of America; Department of Pathology, Stanford University Medical Center, United States of America
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12
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Ługowska A, Baydakova G, Ilyushkina A, Zakharova E, Mierzewska H, Szymańska K, Wierzba J, Kubalska J, Graban A, Kmieć T, Perkowska-Sumiła B, Tylki-Szymańska A, Bednarska-Makaruk M. Elevated Dipeptidyl Peptidase IV (DPP-IV) Activity in Plasma from Patients with Various Lysosomal Diseases. Diagnostics (Basel) 2021; 11:320. [PMID: 33669444 PMCID: PMC7920438 DOI: 10.3390/diagnostics11020320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 01/21/2023] Open
Abstract
Increased activity of dipeptidyl peptidase IV (DPP-IV) was reported earlier in patients with different types of mucopolysaccharidoses. DPP-IV (also known as CD26 lymphocyte T surface antigen) is a transmembrane protein showing protease activity. This enzyme displays various functions in the organism and plays an important role in multiple processes like glucose metabolism, nociception, cell-adhesion, psychoneuroendocrine regulation, immune response and cardiovascular adaptation. In order to evaluate DPP-IV in lysosomal storage diseases (LSD), we examined its activity in plasma samples from 307 patients affected with 24 different LSDs and in 75 control persons. Our results revealed elevated DPP-IV activity especially in individuals affected with mucolipidosis II/III, alpha-mannosidosis, and mucopolysaccharidoses types III, II, and I (p < 0.05). In other LSDs the DPP-IV activity was still significantly increased, but to a lesser extent. In patients with Gaucher disease, ceroid lipofuscinosis type 1 (CLN1), Niemann-Pick disease type C and A, Krabbe and Pompe diseases, gangliosidosis GM2 and metachromatic leukodystrophy discreet or no changes in DPP-IV activity were observed. DPP-IV may serve as a first-tier diagnostic procedure or additional biochemical analysis in recognizing patients with some LSDs. DPP-IV may become an object of basic research for a better understanding of LSDs.
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Affiliation(s)
- Agnieszka Ługowska
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland; (J.K.); (M.B.-M.)
| | - Galina Baydakova
- Research Centre for Medical Genetics, Federal State Budgetary Institution, 115478 Moscow, Russia; (G.B.); (A.I.); (E.Z.)
| | - Alex Ilyushkina
- Research Centre for Medical Genetics, Federal State Budgetary Institution, 115478 Moscow, Russia; (G.B.); (A.I.); (E.Z.)
| | - Ekaterina Zakharova
- Research Centre for Medical Genetics, Federal State Budgetary Institution, 115478 Moscow, Russia; (G.B.); (A.I.); (E.Z.)
| | - Hanna Mierzewska
- Department of Child and Adolescent Neurology, Institute of Mother and Child, 01-211 Warsaw, Poland;
| | - Krystyna Szymańska
- Mossakowski Medical Research Center, Department of Experimental and Clinical Neuropathology, Polish Academy of Sciences, 02-106 Warsaw, Poland;
| | - Jolanta Wierzba
- Department of Internal and Pediatric Nursing, Institute of Nursing and Midwifery, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Jolanta Kubalska
- Department of Genetics, Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland; (J.K.); (M.B.-M.)
| | - Ałła Graban
- 1st Department of Neurology, Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland;
| | - Tomasz Kmieć
- Department of Neurology and Epileptology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland;
| | - Barbara Perkowska-Sumiła
- Department of Pediatrics, Nutrition and Metabolic Diseases, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (B.P.-S.); (A.T.-S.)
| | - Anna Tylki-Szymańska
- Department of Pediatrics, Nutrition and Metabolic Diseases, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (B.P.-S.); (A.T.-S.)
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13
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Douglas TD, Newby LK, Eckstrand J, Wixted D, Singh RH. Lipid changes in the metabolome of a single case study with maple syrup urine disease (MSUD) after five days of improved diet adherence of controlled branched-chain amino acids (BCAA). Mol Genet Metab Rep 2020; 25:100651. [PMID: 33088714 PMCID: PMC7567947 DOI: 10.1016/j.ymgmr.2020.100651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/19/2020] [Indexed: 11/19/2022] Open
Abstract
Background Distinguishing systemic metabolic disruptions in maple syrup urine disease (MSUD) beyond amino acid pathways is under-investigated, yet important to understanding disease pathology and treatment options. Methods An adolescent female (15 years) with MSUD without liver transplant, attended 2 study visits, 5 days apart. Medical diet adherence was determined based on her 3-day diet records and plasma branched-chain amino acid (BCAA) concentrations at both study visits. Plasma from a single age- and sex-matched control (MURDOCK Study, Duke University) and the case patient were analyzed with UPLC/MS/MS for intensity (m/z), annotated, and normalized against a median of 1 (Metabolon, Morrisville NC). Differences between case/control and 5-day comparisons were defined as ≥ ǀ 0.5 ǀ. Results 434 lipid metabolites were identified across samples; 90 (20.7%) were higher and 120 (27.6%) lower in the MSUD case at baseline compared with control. By study visit 2, plasma BCAA had declined, while 48 (53%) of elevated lipids and 14 (11.7%) of lower lipid values had moved to within ǀ 0.5 ǀ of control. Most shifts towards control by day 5 were seen in long-chain fatty acid intermediates (42%) and acylcarnitines (32%). Although androgenic (28%) and bile acid (23%) metabolites increased towards control, neither reached control level by day 5. Discussion This comparative metabolomics study in a single MSUD case and healthy control suggests intrinsic differences in MSUD lipid metabolism potentially influenced by therapeutic diet. Findings suggest influences on hormone regulation, fatty acid oxidation, and bile acid synthesis, but further studies are needed to confirm an association between MSUD and lipid dysregulation. Synopsis Within 5 days of improved dietary adherence, a single MSUD case experienced substantial changes in lipid markers potentially related to changes in plasma branched-chain amino acids.
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Affiliation(s)
- Teresa D. Douglas
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Corresponding author.
| | - L. Kristin Newby
- Duke Clinical and Translational Science Institute (CTSI), Duke University School of Medicine, Durham, NC, USA
| | - Julie Eckstrand
- Duke Clinical and Translational Science Institute (CTSI), Duke University School of Medicine, Durham, NC, USA
| | - Douglas Wixted
- Duke Clinical and Translational Science Institute (CTSI), Duke University School of Medicine, Durham, NC, USA
| | - Rani H. Singh
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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14
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Novel biomarkers for lysosomal storage disorders: Metabolomic and proteomic approaches. Clin Chim Acta 2020; 509:195-209. [PMID: 32561345 DOI: 10.1016/j.cca.2020.06.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 12/20/2022]
Abstract
Lysosomal storage disorders (LSDs) are characterized by the accumulation of specific disease substrates inside the lysosomes of various cells, eventually leading to the deterioration of cellular function and multisystem organ damage. With the continuous discovery and validation of novel and advanced therapies for most LSDs, there is an urgent need to discover more versatile and clinically relevant biomarkers. The utility of these biomarkers should ideally extend beyond the screening and diagnosis of LSDs to the evaluation of disease severity and monitoring of therapy. Metabolomic and proteomic approaches provide the means to the discovery and validation of such novel biomarkers. This is achieved mainly through the application of various mass spectrometric techniques to common and easily accessible biological samples, such as plasma, urine and dried blood spots. In this review, we tried to summarize the complexity of the lysosomal disorders phenotypes, their current diagnostic and therapeutic approaches, the various techniques supporting metabolomic and proteomic studies and finally we tried to explore the newly discovered biomarkers for most LSDs and their reported clinical values.
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De Pasquale V, Caterino M, Costanzo M, Fedele R, Ruoppolo M, Pavone LM. Targeted Metabolomic Analysis of a Mucopolysaccharidosis IIIB Mouse Model Reveals an Imbalance of Branched-Chain Amino Acid and Fatty Acid Metabolism. Int J Mol Sci 2020; 21:ijms21124211. [PMID: 32545699 PMCID: PMC7352355 DOI: 10.3390/ijms21124211] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Mucopolysaccharidoses (MPSs) are inherited disorders of the glycosaminoglycan (GAG) metabolism. The defective digestion of GAGs within the intralysosomal compartment of affected patients leads to a broad spectrum of clinical manifestations ranging from cardiovascular disease to neurological impairment. The molecular mechanisms underlying the progression of the disease downstream of the genetic mutation of genes encoding for lysosomal enzymes still remain unclear. Here, we applied a targeted metabolomic approach to a mouse model of PS IIIB, using a platform dedicated to the diagnosis of inherited metabolic disorders, in order to identify amino acid and fatty acid metabolic pathway alterations or the manifestations of other metabolic phenotypes. Our analysis highlighted an increase in the levels of branched-chain amino acids (BCAAs: Val, Ile, and Leu), aromatic amino acids (Tyr and Phe), free carnitine, and acylcarnitines in the liver and heart tissues of MPS IIIB mice as compared to the wild type (WT). Moreover, Ala, Met, Glu, Gly, Arg, Orn, and Cit amino acids were also found upregulated in the liver of MPS IIIB mice. These findings show a specific impairment of the BCAA and fatty acid catabolism in the heart of MPS IIIB mice. In the liver of affected mice, the glucose-alanine cycle and urea cycle resulted in being altered alongside a deregulation of the BCAA metabolism. Thus, our data demonstrate that an accumulation of BCAAs occurs secondary to lysosomal GAG storage, in both the liver and the heart of MPS IIIB mice. Since BCAAs regulate the biogenesis of lysosomes and autophagy mechanisms through mTOR signaling, impacting on lipid metabolism, this condition might contribute to the progression of the MPS IIIB disease.
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Affiliation(s)
- Valeria De Pasquale
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (M.C.); (L.M.P.)
| | - Marianna Caterino
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (M.C.); (L.M.P.)
- CEINGE—Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy;
| | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (M.C.); (L.M.P.)
- CEINGE—Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy;
| | - Roberta Fedele
- CEINGE—Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy;
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (M.C.); (L.M.P.)
- CEINGE—Biotecnologie Avanzate s.c.ar.l., 80145 Naples, Italy;
- Correspondence: ; Tel.: +39-081-3737850
| | - Luigi Michele Pavone
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; (V.D.P.); (M.C.); (M.C.); (L.M.P.)
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Heon-Roberts R, Nguyen ALA, Pshezhetsky AV. Molecular Bases of Neurodegeneration and Cognitive Decline, the Major Burden of Sanfilippo Disease. J Clin Med 2020; 9:jcm9020344. [PMID: 32012694 PMCID: PMC7074161 DOI: 10.3390/jcm9020344] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022] Open
Abstract
The mucopolysaccharidoses (MPS) are a group of diseases caused by the lysosomal accumulation of glycosaminoglycans, due to genetic deficiencies of enzymes involved in their degradation. MPS III or Sanfilippo disease, in particular, is characterized by early-onset severe, progressive neurodegeneration but mild somatic involvement, with patients losing milestones and previously acquired skills as the disease progresses. Despite being the focus of extensive research over the past years, the links between accumulation of the primary molecule, the glycosaminoglycan heparan sulfate, and the neurodegeneration seen in patients have yet to be fully elucidated. This review summarizes the current knowledge on the molecular bases of neurological decline in Sanfilippo disease. It emerges that this deterioration results from the dysregulation of multiple cellular pathways, leading to neuroinflammation, oxidative stress, impaired autophagy and defects in cellular signaling. However, many important questions about the neuropathological mechanisms of the disease remain unanswered, highlighting the need for further research in this area.
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Affiliation(s)
- Rachel Heon-Roberts
- Division of Medical Genetics, CHU Ste-Justine Research Centre, Montreal, QC H3T 1C5, Canada; (R.H.-R.); (A.L.A.N.)
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada
| | - Annie L. A. Nguyen
- Division of Medical Genetics, CHU Ste-Justine Research Centre, Montreal, QC H3T 1C5, Canada; (R.H.-R.); (A.L.A.N.)
- Department of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Alexey V. Pshezhetsky
- Division of Medical Genetics, CHU Ste-Justine Research Centre, Montreal, QC H3T 1C5, Canada; (R.H.-R.); (A.L.A.N.)
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 0C7, Canada
- Department of Paediatrics, University of Montreal, Montreal, QC H3T 1C5, Canada
- Correspondence: ; Tel.: +1-(514)-345-4931 (ext. 2736)
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17
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Ismail IT, Showalter MR, Fiehn O. Inborn Errors of Metabolism in the Era of Untargeted Metabolomics and Lipidomics. Metabolites 2019; 9:metabo9100242. [PMID: 31640247 PMCID: PMC6835511 DOI: 10.3390/metabo9100242] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/30/2022] Open
Abstract
Inborn errors of metabolism (IEMs) are a group of inherited diseases with variable incidences. IEMs are caused by disrupting enzyme activities in specific metabolic pathways by genetic mutations, either directly or indirectly by cofactor deficiencies, causing altered levels of compounds associated with these pathways. While IEMs may present with multiple overlapping symptoms and metabolites, early and accurate diagnosis of IEMs is critical for the long-term health of affected subjects. The prevalence of IEMs differs between countries, likely because different IEM classifications and IEM screening methods are used. Currently, newborn screening programs exclusively use targeted metabolic assays that focus on limited panels of compounds for selected IEM diseases. Such targeted approaches face the problem of false negative and false positive diagnoses that could be overcome if metabolic screening adopted analyses of a broader range of analytes. Hence, we here review the prospects of using untargeted metabolomics for IEM screening. Untargeted metabolomics and lipidomics do not rely on predefined target lists and can detect as many metabolites as possible in a sample, allowing to screen for many metabolic pathways simultaneously. Examples are given for nontargeted analyses of IEMs, and prospects and limitations of different metabolomics methods are discussed. We conclude that dedicated studies are needed to compare accuracy and robustness of targeted and untargeted methods with respect to widening the scope of IEM diagnostics.
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Affiliation(s)
- Israa T Ismail
- National Liver Institute, Menoufia University, Shebeen El Kom 55955, Egypt.
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
| | - Megan R Showalter
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, University of California Davis, Davis, CA 95616, USA.
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18
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Shafaat M, Hashemi M, Majd A, Abiri M, Zeinali S. Genetic testing of Mucopolysaccharidoses disease using multiplex PCR- based panels of STR markers: in silico analysis of novel mutations. Metab Brain Dis 2019; 34:1447-1455. [PMID: 31236806 DOI: 10.1007/s11011-019-00434-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/13/2019] [Indexed: 12/22/2022]
Abstract
The Mucopolysaccharidoses (MPS) are group of inherited metabolic diseases caused by the deficiency of enzymes required to degrade glycosaminoglycans (GAGs) in the lysosomes. GAGs are sulfated polysaccharides involving repeating disaccharides, uronic acid and hexosamines including chondroitin sulfate (CS), dermatan sulfate (DS), heparan sulfate (HS) and keratan sulfate (KS). Hyaluronan is excluded in terms of being non-sulfated in the GAG family. Different types of mutations have been identified as the causative agent in all types of MPS. Herein, we planned to investigate the pathogenic mutations in different types of MPS including type I (IDUA gene), IIIA (SGSH) and IIIB (NAGLU) in the eight Iranian patients. Autozygosity mapping was performed to identify the potential pathogenic variants in these 8 patients indirectly with the clinical diagnosis of MPSs. so three panels of STR (Short Tandem Repeat) markres flanking IDUA, SGSH and NAGLU genes were selected for multiplex PCR amplification. Then in each family candidate gene was sequenced to identify the pathogenic mutation. Our study showed two novel mutations c.469 T > C and c.903C > G in the IDUA gene, four recurrent mutations: c.1A > C in IDUA, c.220C > T, c.1298G > A in SGSH gene and c.457G > A in the NAGLU gene. The c.1A > C in IDUA was the most common mutation in our study. In silico analysis were performed as well to predict the pathogenicity of the novel variants.
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Affiliation(s)
- Mehdi Shafaat
- Department of Biology, Faculty of Science, North Tehran Branch of Islamic Azad University, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ahmad Majd
- Department of Biology, Faculty of Science, North Tehran Branch of Islamic Azad University, Tehran, Iran
| | - Maryam Abiri
- Department of Medical Genetics and Molecular biology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St, Tehran, Iran.
- Dr. Zeinali's Medical Genetics Lab, Kawsar Human Genetics Center, No. 41 Majlesi St., Vali Asr St., Postal Code, Tehran, 1595645513, Iran.
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Tebani A, Abily-Donval L, Schmitz-Afonso I, Piraud M, Ausseil J, Zerimech F, Pilon C, Pereira T, Marret S, Afonso C, Bekri S. Analysis of Mucopolysaccharidosis Type VI through Integrative Functional Metabolomics. Int J Mol Sci 2019; 20:ijms20020446. [PMID: 30669586 PMCID: PMC6359186 DOI: 10.3390/ijms20020446] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/12/2022] Open
Abstract
Metabolic phenotyping is poised as a powerful and promising tool for biomarker discovery in inherited metabolic diseases. However, few studies applied this approach to mcopolysaccharidoses (MPS). Thus, this innovative functional approach may unveil comprehensive impairments in MPS biology. This study explores mcopolysaccharidosis VI (MPS VI) or Maroteaux–Lamy syndrome (OMIM #253200) which is an autosomal recessive lysosomal storage disease caused by the deficiency of arylsulfatase B enzyme. Urine samples were collected from 16 MPS VI patients and 66 healthy control individuals. Untargeted metabolomics analysis was applied using ultra-high-performance liquid chromatography combined with ion mobility and high-resolution mass spectrometry. Furthermore, dermatan sulfate, amino acids, carnitine, and acylcarnitine profiles were quantified using liquid chromatography coupled to tandem mass spectrometry. Univariate analysis and multivariate data modeling were used for integrative analysis and discriminant metabolites selection. Pathway analysis was done to unveil impaired metabolism. The study revealed significant differential biochemical patterns using multivariate data modeling. Pathway analysis revealed that several major amino acid pathways were dysregulated in MPS VI. Integrative analysis of targeted and untargeted metabolomics data with in silico results yielded arginine-proline, histidine, and glutathione metabolism being the most affected. This study is one of the first metabolic phenotyping studies of MPS VI. The findings might shed light on molecular understanding of MPS pathophysiology to develop further MPS studies to enhance diagnosis and treatments of this rare condition.
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Affiliation(s)
- Abdellah Tebani
- Department of Metabolic Biochemistry, Rouen University Hospital, 76000 Rouen, France.
- Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France.
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Lenaig Abily-Donval
- Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France.
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Rouen University Hospital, 76031 Rouen, France.
| | | | - Monique Piraud
- Service de Biochimie et Biologie Moléculaire Grand Est, Unité des Maladies Héréditaires du Métabolisme et Dépistage Néonatal, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, 69002 Lyon, France.
| | - Jérôme Ausseil
- INSERM U1088, Laboratoire de Biochimie Métabolique, Centre de Biologie Humaine, CHU Sud, 80054 Amiens CEDEX, France.
| | - Farid Zerimech
- Laboratoire de Biochimie et Biologie Moléculaire, Université de Lille et Pôle de Biologie Pathologie Génétique du CHRU de Lille, 59000 Lille, France.
| | - Carine Pilon
- Department of Metabolic Biochemistry, Rouen University Hospital, 76000 Rouen, France.
| | - Tony Pereira
- Department of Pharmacology, Rouen University Hospital, 76000 Rouen, France.
| | - Stéphane Marret
- Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France.
- Department of Neonatal Pediatrics, Intensive Care and Neuropediatrics, Rouen University Hospital, 76031 Rouen, France.
| | - Carlos Afonso
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, COBRA, 76000 Rouen, France.
| | - Soumeya Bekri
- Department of Metabolic Biochemistry, Rouen University Hospital, 76000 Rouen, France.
- Normandie University, UNIROUEN, CHU Rouen, INSERM U1245, 76000 Rouen, France.
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