1
|
Scrima S, Lambrughi M, Tiberti M, Fadda E, Papaleo E. ASM variants in the spotlight: A structure-based atlas for unraveling pathogenic mechanisms in lysosomal acid sphingomyelinase. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167260. [PMID: 38782304 DOI: 10.1016/j.bbadis.2024.167260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 04/30/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
Lysosomal acid sphingomyelinase (ASM), a critical enzyme in lipid metabolism encoded by the SMPD1 gene, plays a crucial role in sphingomyelin hydrolysis in lysosomes. ASM deficiency leads to acid sphingomyelinase deficiency, a rare genetic disorder with diverse clinical manifestations, and the protein can be found mutated in other diseases. We employed a structure-based framework to comprehensively understand the functional implications of ASM variants, integrating pathogenicity predictions with molecular insights derived from a molecular dynamics simulation in a lysosomal membrane environment. Our analysis, encompassing over 400 variants, establishes a structural atlas of missense variants of lysosomal ASM, associating mechanistic indicators with pathogenic potential. Our study highlights variants that influence structural stability or exert local and long-range effects at functional sites. To validate our predictions, we compared them to available experimental data on residual catalytic activity in 135 ASM variants. Notably, our findings also suggest applications of the resulting data for identifying cases suited for enzyme replacement therapy. This comprehensive approach enhances the understanding of ASM variants and provides valuable insights for potential therapeutic interventions.
Collapse
Affiliation(s)
- Simone Scrima
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, 2100 Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, 2100 Copenhagen, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, 2100 Copenhagen, Denmark
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, co. Kildare, Ireland
| | - Elena Papaleo
- Cancer Structural Biology, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, 2100 Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark.
| |
Collapse
|
2
|
Geberhiwot T, Wasserstein M, Wanninayake S, Bolton SC, Dardis A, Lehman A, Lidove O, Dawson C, Giugliani R, Imrie J, Hopkin J, Green J, de Vicente Corbeira D, Madathil S, Mengel E, Ezgü F, Pettazzoni M, Sjouke B, Hollak C, Vanier MT, McGovern M, Schuchman E. Consensus clinical management guidelines for acid sphingomyelinase deficiency (Niemann-Pick disease types A, B and A/B). Orphanet J Rare Dis 2023; 18:85. [PMID: 37069638 PMCID: PMC10108815 DOI: 10.1186/s13023-023-02686-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/02/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Acid Sphingomyelinase Deficiency (ASMD) is a rare autosomal recessive disorder caused by mutations in the SMPD1 gene. This rarity contributes to misdiagnosis, delayed diagnosis and barriers to good care. There are no published national or international consensus guidelines for the diagnosis and management of patients with ASMD. For these reasons, we have developed clinical guidelines that defines standard of care for ASMD patients. METHODS The information contained in these guidelines was obtained through a systematic literature review and the experiences of the authors in their care of patients with ASMD. We adopted the Appraisal of Guidelines for Research and Evaluation (AGREE II) system as method of choice for the guideline development process. RESULTS The clinical spectrum of ASMD, although a continuum, varies substantially with subtypes ranging from a fatal infantile neurovisceral disorder to an adult-onset chronic visceral disease. We produced 39 conclusive statements and scored them according to level of evidence, strengths of recommendations and expert opinions. In addition, these guidelines have identified knowledge gaps that must be filled by future research. CONCLUSION These guidelines can inform care providers, care funders, patients and their carers about best clinical practice and leads to a step change in the quality of care for patients with ASMD with or without enzyme replacement therapy (ERT).
Collapse
Affiliation(s)
- Tarekegn Geberhiwot
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK.
- Institute of Metabolism and System Research, University of Birmingham, Birmingham, UK.
| | - Melissa Wasserstein
- Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | | | - Andrea Dardis
- Regional Coordinator Centre for Rare Disease, AMC Hospital of Udine, Udine, Italy
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada
| | - Olivier Lidove
- Department of Internal Medicine, Hôpital de La Croix Saint Simon, Paris, France
| | - Charlotte Dawson
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Roberto Giugliani
- BioDiscovery and DR BRASIL Research Group, HCPA, Department of Genetics and PPGBM, UFRGS, INAGEMP, DASA, and Casa Dos Raros, Porto Alegre, Brazil
| | - Jackie Imrie
- International Niemann-Pick Disease Registry, Newcastle, UK
| | - Justin Hopkin
- National Niemann-Pick Disease Foundation, Fort Atkinson, WI, USA
| | - James Green
- International Niemann-Pick Disease Registry, Newcastle, UK
| | | | - Shyam Madathil
- Department of Respiratory Medicine, University Hospital Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Birmingham, UK
| | - Eugen Mengel
- Institute of Clinical Science in LSD, SphinCS, Hochheim, Germany
| | - Fatih Ezgü
- Division of Pediatric Metabolism and Division of Pediatric Genetics, Department of Pediatrics, Gazi University Faculty of Medicine, 06560, Ankara, Turkey
| | - Magali Pettazzoni
- Biochemistry and Molecular Biology and Reference Center for Inherited Metabolic Disorders, Hospices Civils de Lyon, 59 Boulevard Pinel, 69677, Bron Cedex, France
| | - Barbara Sjouke
- Department of Endocrinology and Metabolism, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, F5-169, P.O. Box 22660, 1100 DD, Amsterdam, The Netherlands
| | - Carla Hollak
- Department of Endocrinology and Metabolism, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, F5-169, P.O. Box 22660, 1100 DD, Amsterdam, The Netherlands
| | | | | | - Edward Schuchman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Room 14-20A, New York, NY, 10029, USA
| |
Collapse
|
3
|
Sheth J, Nair A, Jee B. Lysosomal storage disorders: from biology to the clinic with reference to India. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 9:100108. [PMID: 37383036 PMCID: PMC10305895 DOI: 10.1016/j.lansea.2022.100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 06/30/2023]
Abstract
Lysosomal storage disorders (LSDs) are a group of seventy different metabolic storage diseases due to accumulation of substrate mainly in the form of carbohydrate, lipids, proteins, and cellular debris. They occur due to variant in different genes that regulate lysosomal enzymes synthesis, transport, and secretion. In recent years, due to an increased availability of various therapies to treat these disorders, and increased diagnostic tools, there has been an escalated awareness of LSDs. Due to heterogeneous population and various social reasons, India is likely to have a high frequency of LSDs. Therefore, to understand the burden of various LSDs, its molecular spectrum, and understanding the phenotype-genotype correlation, Indian Council of Medical Research (ICMR) and Department of Health Research (DHR), Government of India had set up a task force in the year 2015. It has resulted in identifying common LSDs, and founder variant for some of the storage disorders and molecular spectrum of various LSDs across the country. This review describes in detail the spectrum of LSDs, its molecular epidemiology and prevention in context to Indian population.
Collapse
Affiliation(s)
- Jayesh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad 380015, India
| | - Aadhira Nair
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, Ahmedabad 380015, India
| | - Babban Jee
- Department of Health Research, Ministry of Health and Family Welfare, Government of India, 2nd Floor, IRCS Building, Red Cross Road, New Delhi 110001, India
| |
Collapse
|
4
|
Dursun FE, Özen F. SMPD1 gene variants in patients with β-Thalassemia major. Mol Biol Rep 2023; 50:3355-3363. [PMID: 36725747 PMCID: PMC10042979 DOI: 10.1007/s11033-023-08275-x] [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: 08/22/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023]
Abstract
BACKGROUND β-thalassemia major and Niemann-Pick diseases have similar clinical and laboratory findings. We aimed to investigate the effects of sphingomyelin phosphodiesterase 1 (SMPD1) gene variants on the clinical and laboratory findings in patients with β-thalassemia major. METHODS AND RESULTS This study included 45 patients who were followed up for β-thalassemia major in our clinic. Plasma chitotriosidase, leukocyte acid sphingomyelinase, liver enzymes, ferritin, hemogram, biochemical parameters, SMPD1 gene variant analysis, cardiac T2* MRI, and liver R2 MRI were assessed in all patients. The SMPD1 gene c.132_143del, p.A46_L49del (c.108GCTGGC[4] (p.38AL[4])) (rs3838786) variant was detected in 9 of 45 (20.0%) patients. Plasma chitotriosidase, ferritin, acetyl aminotransferase, and alanine aminotransferase levels were significantly higher in patients with the gene variant than in those without (p < 0.05). Leukocyte acid sphingomyelinase levels were significantly lower in patients with the gene variant than in those without (p < 0.05). CONCLUSION These results imply that the clinical and laboratory findings and some features of disease progression in patients with β-thalassemia major are similar to those of Niemann-Pick disease. They also suggest that SMPD1 gene c.132_143del, p.A46_L49del (c.108GCTGGC[4] (p.38AL[4])) (rs3838786) variant may underlie these clinical findings in patients with β-thalassemia major.
Collapse
Affiliation(s)
- Fadime Ersoy Dursun
- Department of Hematology, Prof. Dr. Süleyman Yalçın City Hospital, Eğitim mah, Dr. Erkin Cd. No:161/1, 34722, Kadıköy, İstanbul, Turkey.
| | - Filiz Özen
- Department of Medical Genetics, Prof. Dr. Süleyman Yalçın City Hospital, Kadıköy, İstanbul, Turkey
| |
Collapse
|
5
|
Deshpande D, Gupta SK, Sarma AS, Ranganath P, Jain S JMN, Sheth J, Mistri M, Gupta N, Kabra M, Phadke SR, Girisha KM, Dua Puri R, Aggarwal S, Datar C, Mandal K, Tilak P, Muranjan M, Bijarnia-Mahay S, Rama Devi A R, Tayade NB, Ranjan A, Dalal AB. Functional characterization of novel variants in SMPD1 in Indian patients with acid sphingomyelinase deficiency. Hum Mutat 2021; 42:1336-1350. [PMID: 34273913 DOI: 10.1002/humu.24263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/29/2021] [Accepted: 07/15/2021] [Indexed: 02/03/2023]
Abstract
Pathogenic variations in SMPD1 lead to acid sphingomyelinase deficiency (ASMD), that is, Niemann-Pick disease (NPD) type A and B (NPA, NPB), which is a recessive lysosomal storage disease. The knowledge of variant spectrum in Indian patients is crucial for early and accurate NPD diagnosis and genetic counseling of families. In this study, we recruited 40 unrelated pediatric patients manifesting symptoms of ASMD and subnormal ASM enzyme activity. Variations in SMPD1 were studied using Sanger sequencing for all exons, followed by interpretation of variants based on American College of Medical Genetics and Genomics & Association for Molecular Pathology (ACMG/AMP) criteria. We identified 18 previously unreported variants and 21 known variants, including missense, nonsense, deletions, duplications, and splice site variations with disease-causing potential. Eight missense variants were functionally characterized using in silico molecular dynamic simulation and in vitro transient transfection in HEK293T cells, followed by ASM enzyme assay, immunoblot, and immunofluorescence studies. All the variants showed reduced ASM activity in transfected cells confirming their disease-causing potential. The study provides data for efficient prenatal diagnosis and genetic counseling of families with NPD type A and B.
Collapse
Affiliation(s)
- Dipti Deshpande
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shailesh Kumar Gupta
- Laboratory of Computational and Functional Genomics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Asodu Sandeep Sarma
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Prajnya Ranganath
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Jamal Md Nurul Jain S
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Jayesh Sheth
- Institute of Human Genetics, FRIGE House, Ahmedabad, Gujarat, India
| | - Mehul Mistri
- Institute of Human Genetics, FRIGE House, Ahmedabad, Gujarat, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, AIIMS, New Delhi, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Ratna Dua Puri
- Institute of Medical Genetics & Genomics, Sir Ganga Ram hospital, New Delhi, India
| | - Shagun Aggarwal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.,Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, Telangana, India
| | - Chaitanya Datar
- Bharati Hospital and Research Center, Pune, Maharashtra, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Preetha Tilak
- Division of Human Genetics, St. John's National Academy of Health, Science, Bangalore, Karnataka, India
| | - Mamta Muranjan
- Genetic Clinic, Department of Pediatrics, Seth GS Medical College & KEM Hospital, Mumbai, India
| | | | | | - Naresh B Tayade
- Life Care Hospital, Amravati, India.,Dr. Panjabarao Deshmukh Medical College Amravati, India
| | - Akash Ranjan
- Laboratory of Computational and Functional Genomics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India
| | - Ashwin B Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.,Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| |
Collapse
|
6
|
In Silico Analysis of the Molecular-Level Impact of SMPD1 Variants on Niemann-Pick Disease Severity. Int J Mol Sci 2021; 22:ijms22094516. [PMID: 33925997 PMCID: PMC8123603 DOI: 10.3390/ijms22094516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/10/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022] Open
Abstract
Sphingomyelin phosphodiesterase (SMPD1) is a key enzyme in the sphingolipid metabolism. Genetic SMPD1 variants have been related to the Niemann-Pick lysosomal storage disorder, which has different degrees of phenotypic severity ranging from severe symptomatology involving the central nervous system (type A) to milder ones (type B). They have also been linked to neurodegenerative disorders such as Parkinson and Alzheimer. In this paper, we leveraged structural, evolutionary and stability information on SMPD1 to predict and analyze the impact of variants at the molecular level. We developed the SMPD1-ZooM algorithm, which is able to predict with good accuracy whether variants cause Niemann-Pick disease and its phenotypic severity; the predictor is freely available for download. We performed a large-scale analysis of all possible SMPD1 variants, which led us to identify protein regions that are either robust or fragile with respect to amino acid variations, and show the importance of aromatic-involving interactions in SMPD1 function and stability. Our study also revealed a good correlation between SMPD1-ZooM scores and in vitro loss of SMPD1 activity. The understanding of the molecular effects of SMPD1 variants is of crucial importance to improve genetic screening of SMPD1-related disorders and to develop personalized treatments that restore SMPD1 functionality.
Collapse
|
7
|
Hu J, Maegawa GHB, Zhan X, Gao X, Wang Y, Xu F, Qiu W, Han L, Gu X, Zhang H. Clinical, biochemical, and genotype-phenotype correlations of 118 patients with Niemann-Pick disease Types A/B. Hum Mutat 2021; 42:614-625. [PMID: 33675270 DOI: 10.1002/humu.24192] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 11/08/2022]
Abstract
Niemann-Pick disease Types A and B (NPA/B) are autosomal recessive disorders caused by variants in the sphingomyelin phosphodiesterase-1 (SMPD1) gene. This study aimed to describe and characterize a cohort of 118 patients diagnosed with NPA/B based on clinical, biochemical, and molecular findings, and to identify sound correlations between laboratory findings and clinical presentations. Decreased peripheral leukocyte acid sphingomyelinase activity levels and increased plasma 7-ketocholesterol levels were significantly correlated with disease onset and severity of the clinical course. We identified 92 different sequence SMPD1 variants, including 41 novel variants, in 118 NPA/B patients (19 NPA, 24 intermediate type, 75 NPB). The most prevalent mutation was p.Arg602His, which accounted for 9.3% of the alleles. Patients homozygous for p.Arg602His or p.Asn522Ser showed a late-onset form of the NPB phenotype. The homozygous SMPD1 variant p.Tyr500His correlated with the early-onset NPB clinical form. Additionally, homozygous variants p.His284SerfsX18, p.Phe465Ser, and p.Ser486Arg were associated with the neuronopathic NPA clinical form. The homozygous variant p.Arg3AlafsX74 was associated with the intermediate clinical form. Our study contributes to the understanding of the natural history of NPA/B and assists in the development of efficacious treatments for patients afflicted with this devastating lysosomal storage disorder.
Collapse
Affiliation(s)
- Jiayue Hu
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gustavo H B Maegawa
- Departments of Pediatrics Genetics and Metabolism, Neuroscience, Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Xia Zhan
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaolan Gao
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feng Xu
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjuan Qiu
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lianshu Han
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefan Gu
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huiwen Zhang
- Pediatric Endocrinology and Genetic, Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
8
|
Chung HY, Claus RA. Keep Your Friends Close, but Your Enemies Closer: Role of Acid Sphingomyelinase During Infection and Host Response. Front Med (Lausanne) 2021; 7:616500. [PMID: 33553211 PMCID: PMC7859284 DOI: 10.3389/fmed.2020.616500] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022] Open
Abstract
Breakdown of the inert and constitutive membrane building block sphingomyelin to the highly active lipid mediator ceramide by extracellularly active acid sphingomyelinase is tightly regulated during stress response and opens the gate for invading pathogens, triggering the immune response, development of remote organ failure, and tissue repair following severe infection. How do one enzyme and one mediator manage all of these affairs? Under physiological conditions, the enzyme is located in the lysosomes and takes part in the noiseless metabolism of sphingolipids, but following stress the protein is secreted into circulation. When secreted, acid sphingomyelinase (ASM) is able to hydrolyze sphingomyelin present at the outer leaflet of membranes to ceramide. Its generation troubles the biophysical context of cellular membranes resulting in functional assembly and reorganization of proteins and receptors, also embedded in highly conserved response mechanisms. As a consequence of cellular signaling, not only induction of cell death but also proliferation, differentiation, and fibrogenesis are affected. Here, we discuss the current state of the art on both the impact and function of the enzyme during host response and damage control. Also, the potential role of lysosomotropic agents as functional inhibitors of this upstream alarming cascade is highlighted.
Collapse
Affiliation(s)
- Ha-Yeun Chung
- Section Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Jena, Germany.,Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Ralf A Claus
- Department for Anaesthesiology and Intensive Care, Jena University Hospital, Jena, Germany
| |
Collapse
|
9
|
Angural A, Spolia A, Mahajan A, Verma V, Sharma A, Kumar P, Dhar MK, Pandita KK, Rai E, Sharma S. Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir - India. Front Genet 2020; 11:415. [PMID: 32425985 PMCID: PMC7203485 DOI: 10.3389/fgene.2020.00415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Rare diseases (RDs) are the clinical conditions affecting a few percentage of individuals in a general population compared to other diseases. Limited clinical information and a lack of reliable epidemiological data make their timely diagnosis and therapeutic management difficult. Emerging Next-Generation DNA Sequencing technologies have enhanced our horizons on patho-physiological understanding of many of the RDs and ushered us into an era of diagnostic and therapeutic research related to this ignored health challenge. Unfortunately, relevant research is meager in developing countries which lack a reliable estimate of the exact burden of most of the RDs. India is to be considered as the "Pandora's Box of genetic disorders." Owing to its huge population heterogeneity and high inbreeding or endogamy rates, a higher burden of rare recessive genetic diseases is expected and supported by the literature findings that endogamy is highly detrimental to health as it enhances the degree of homozygosity of recessive alleles in the general population. The population of a low resource region Jammu and Kashmir (J&K) - India, is highly inbred. Some of its population groups variably practice consanguinity. In context with the region's typical geographical topography, highly inbred population structure and unique but heterogeneous gene pool, a huge burden of known and uncharacterized genetic disorders is expected. Unfortunately, many suspected cases of genetic disorders remain undiagnosed or misdiagnosed due to lack of appropriate clinical as well as diagnostic resources in the region, causing patients to face a huge psycho-socio-economic crisis and many a time suffer life-long with their ailment. In this review, the major challenges associated with RDs are highlighted in general and an account on the methods that can be adopted for conducting fruitful molecular genetic studies in genetically vulnerable and low resource regions is also provided, with an example of a region like J&K - India.
Collapse
Affiliation(s)
- Arshia Angural
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Akshi Spolia
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankit Mahajan
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Vijeshwar Verma
- Bioinformatics Infrastructure Facility, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankush Sharma
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
| | - Parvinder Kumar
- Institute of Human Genetics, University of Jammu, Jammu, India
| | | | - Kamal Kishore Pandita
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
- Independent Researcher, Health Clinic, Jammu, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| |
Collapse
|
10
|
Al-Eitan L, Alqa'qa' K, Amayreh W, Aljamal H, Khasawneh R, Al-Zoubi B, Okour I, Haddad A, Haddad Y, Haddad H. Novel mutations in the SMPD1 gene in Jordanian children with Acid sphingomyelinase deficiency (Niemann-Pick types A and B). Gene 2020; 747:144683. [PMID: 32311413 DOI: 10.1016/j.gene.2020.144683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 01/13/2023]
Abstract
Acid sphingomyelinase (ASM) deficiency (ASMD) is a spectrum that includes Niemann-Pick disease (NPD) types A (NPD A) and B (NPD B). ASMD is characterized by intracellular accumulation of unesterified cholesterol and gangliosides within the endosomal-lysosomal system. It is caused by different mutations in SMPD1 gene that result in reduction or complete absence of acid sphingomyelinase activity in the cells. Herein, four unrelated consanguineous families with two NPD A and three NPD B patients were assessed for their genotypes via sequencing of the SMPD1 gene and their acid sphingomyelinase enzymatic activity. Among the eight identified mutations, three were novel and reported for the first time in Jordanian families (c.120_131delGCTGGCGCTGGC or c.132_143delGCTGGCGCTGGC, c.1758T > G, and c.1344T > A). All the patients displayed ASM activity lower than 1.3 µmol/l/h (P < 0.001). Genotyping and enzymatic assessment might play a significant role in disease identification in people at risk to facilitate genetic counseling in the future.
Collapse
Affiliation(s)
- Laith Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Kifah Alqa'qa'
- Department of Pediatrics, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Wajdi Amayreh
- Department of Pediatrics, Metabolic Genetics Clinic, Queen Rania Al-Abdullah Children's Hospital, King Hussein Medical Centre, Amman 11855, Jordan
| | - Hanan Aljamal
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Rame Khasawneh
- Department of Pathology, Division of Molecular Genetic Pathology, King Hussein Medical Center, Amman 11733, Jordan
| | - Batool Al-Zoubi
- Princess Haya Biotechnology Center, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Israa Okour
- Princess Haya Biotechnology Center, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Amany Haddad
- Princess Haya Biotechnology Center, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Brno 61300, Czech Republic; Central European Institute of Technology, Brno University of Technology, Brno 61200, Czech Republic
| | - Hazem Haddad
- Princess Haya Biotechnology Center, Jordan University of Science and Technology, Irbid 22110, Jordan
| |
Collapse
|
11
|
Perveen S, Gupta N, Kumar M, Kaur P, Chowdhury MR, Kabra M. Spectrum of amyloglucosidase mutations in Asian Indian patients with Glycogen storage disease type III. Am J Med Genet A 2020; 182:1190-1200. [PMID: 32222031 DOI: 10.1002/ajmg.a.61547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 11/11/2022]
Abstract
Glycogen storage disease type III (GSD III) is a rare autosomal recessive inborn error of glycogen degradation pathway due to deficiency or reduced activity of glycogen debranching enzyme (GDE) that results in accumulation of abnormal glycogen in the liver, muscle, and heart. The cardinal hallmarks are hepatomegaly, fasting hypoglycemia, seizures, growth retardation, progressive skeletal myopathy, and cardiomyopathy in few. To date, 258 mutations in amyloglucosidase (AGL) gene have been identified worldwide. However, the mutation spectrum in the Asian Indian region is yet to be well characterized. We investigated 24 patients of Asian origin from 21 unrelated families with a provisional diagnosis of GSD III based on clinical and biochemical criteria. Molecular diagnosis was assessed by bidirectional sequencing and the impact of novel missense variants on the tertiary (three-dimensional) structure of GDE was evaluated by molecular modeling approach. Eighteen different pathogenic variants were identified, out of which 78% were novel. Novel variants included five nonsense, three small duplications and two small deletions, a splice site variant, and three missense variants. Variations in Exons 4, 14, 19, 24, 27, and 33 accounted for 61% of the total pathogenic variants identified and Allele p.Gly798Alafs*3 showed a high allele frequency of 11%. Molecular modeling study of novel pathogenic missense variants indicated the probable underlying molecular mechanism of adverse impact of variations on the structure and catalytic function of human GDE. Our study is the first large study on GSD III from the Asian subcontinent, which further expands the mutation spectrum of AGL.
Collapse
Affiliation(s)
- Shama Perveen
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhumita R Chowdhury
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
12
|
Bhattacherjee A, Ranganath P, Pasumarthi D, Dalal AB. Identification and in-silico analysis of a novel disease-causing variant in the GUSB gene for Mucopolysaccharidosis VII presenting as non-immune fetal hydrops. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|