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Andjelkovic M, Klaassen K, Skakic A, Marjanovic I, Kravljanac R, Djordjevic M, Vucetic Tadic B, Kecman B, Pavlovic S, Stojiljkovic M. Characterization of 13 Novel Genetic Variants in Genes Associated with Epilepsy: Implications for Targeted Therapeutic Strategies. Mol Diagn Ther 2024; 28:645-663. [PMID: 39003674 PMCID: PMC11349789 DOI: 10.1007/s40291-024-00720-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Childhood epilepsies are caused by heterogeneous underlying disorders where approximately 40% of the origins of epilepsy can be attributed to genetic factors. The application of next-generation sequencing (NGS) has revolutionized molecular diagnostics and has enabled the identification of disease-causing genes and variants in childhood epilepsies. The objective of this study was to use NGS to identify variants in patients with childhood epilepsy, to expand the variant spectrum and discover potential therapeutic targets. METHODS In our study, 55 children with epilepsy of unknown etiology were analyzed by combining clinical-exome and whole-exome sequencing. Novel variants were characterized using various in silico algorithms for pathogenicity and structure prediction. RESULTS The molecular genetic cause of epilepsy was identified in 28 patients and the overall diagnostic success rate was 50.9%. We identified variants in 22 different genes associated with epilepsy that correlate well with the described phenotype. SCN1A gene variants were found in five unrelated patients, while ALDH7A1 and KCNQ2 gene variants were found twice. In the other 19 genes, variants were found only in a single patient. This includes genes such as ASH1L, CSNK2B, RHOBTB2, and SLC13A5, which have only recently been associated with epilepsy. Almost half of diagnosed patients (46.4%) carried novel variants. Interestingly, we identified variants in ALDH7A1, KCNQ2, PNPO, SCN1A, and SCN2A resulting in gene-directed therapy decisions for 11 children from our study, including four children who all carried novel SCN1A genetic variants. CONCLUSIONS Described novel variants will contribute to a better understanding of the European genetic landscape, while insights into the genotype-phenotype correlation will contribute to a better understanding of childhood epilepsies worldwide. Given the expansion of molecular-based approaches, each newly identified genetic variant could become a potential therapeutic target.
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Affiliation(s)
- Marina Andjelkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Kristel Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Anita Skakic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Irena Marjanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Ruzica Kravljanac
- Institute for Mother and Child Healthcare of Serbia, "Dr Vukan Cupic", Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Maja Djordjevic
- Institute for Mother and Child Healthcare of Serbia, "Dr Vukan Cupic", Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Biljana Vucetic Tadic
- Institute for Mother and Child Healthcare of Serbia, "Dr Vukan Cupic", Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Bozica Kecman
- Institute for Mother and Child Healthcare of Serbia, "Dr Vukan Cupic", Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia.
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Wang Z, Zhao R, Jia X, Li X, Ma L, Fu H. Three novel SLC37A4 variants in glycogen storage disease type 1b and a literature review. J Int Med Res 2023; 51:3000605231216633. [PMID: 38087503 PMCID: PMC10718061 DOI: 10.1177/03000605231216633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
Glycogen storage disease type 1b (GSD1b) is a rare genetic disorder, resulting from mutations in the SLC37A4 gene located on chromosome 11q23.3. Although the SLC37A4 gene has been identified as the pathogenic gene for GSD1b, the complete variant spectrum of this gene remains to be fully elucidated. In this study, we present three patients diagnosed with GSD1b through genetic testing. We detected five variants of the SLC37A4 gene in these three patients, with three of these mutations (p. L382Pfs*15, p. G117fs*28, and p. T312Sfs*13) being novel variants not previously reported in the literature. We also present a literature review and general overview of the currently reported SLC37A4 gene variants. Our study expands the mutation spectrum of SLC37A4, which may help enable genetic testing to facilitate prompt diagnosis, appropriate intervention, and genetic counseling for affected families.
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Affiliation(s)
- Zhuolin Wang
- Department of Gastroenterology, Hebei Children's Hospital, 133 Jianhua South Street, Shijiazhuang 050031, Hebei Province, China
| | - Ruiqin Zhao
- Department of Gastroenterology, Hebei Children's Hospital, 133 Jianhua South Street, Shijiazhuang 050031, Hebei Province, China
| | - Xiaoyun Jia
- Department of Gastroenterology, Hebei Children's Hospital, 133 Jianhua South Street, Shijiazhuang 050031, Hebei Province, China
| | - Xiaolei Li
- Department of Gastroenterology, Hebei Children's Hospital, 133 Jianhua South Street, Shijiazhuang 050031, Hebei Province, China
| | - Li Ma
- Department of Neonatology, Hebei Children's Hospital, 133 Jianhua South Street, Shijiazhuang 050031, Hebei Province, China
| | - Haiyan Fu
- Department of Gastroenterology, Hebei Children's Hospital, 133 Jianhua South Street, Shijiazhuang 050031, Hebei Province, China
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Crosstalk between Glycogen-Selective Autophagy, Autophagy and Apoptosis as a Road towards Modifier Gene Discovery and New Therapeutic Strategies for Glycogen Storage Diseases. Life (Basel) 2022; 12:life12091396. [PMID: 36143432 PMCID: PMC9504455 DOI: 10.3390/life12091396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
Glycogen storage diseases (GSDs) are rare metabolic monogenic disorders characterized by an excessive accumulation of glycogen in the cell. However, monogenic disorders are not simple regarding genotype–phenotype correlation. Genes outside the major disease-causing locus could have modulatory effect on GSDs, and thus explain the genotype–phenotype inconsistencies observed in these patients. Nowadays, when the sequencing of all clinically relevant genes, whole human exomes, and even whole human genomes is fast, easily available and affordable, we have a scientific obligation to holistically analyze data and draw smarter connections between genotype and phenotype. Recently, the importance of glycogen-selective autophagy for the pathophysiology of disorders of glycogen metabolism have been described. Therefore, in this manuscript, we review the potential role of genes involved in glycogen-selective autophagy as modifiers of GSDs. Given the small number of genes associated with glycogen-selective autophagy, we also include genes, transcription factors, and non-coding RNAs involved in autophagy. A cross-link with apoptosis is addressed. All these genes could be analyzed in GSD patients with unusual discrepancies between genotype and phenotype in order to discover genetic variants potentially modifying their phenotype. The discovery of modifier genes related to glycogen-selective autophagy and autophagy will start a new chapter in understanding of GSDs and enable the usage of autophagy-inducing drugs for the treatment of this group of rare-disease patients.
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Abdulla M, Mohammed N. A Review on Inflammatory Bowel Diseases: Recent Molecular Pathophysiology Advances. Biologics 2022; 16:129-140. [PMID: 36118798 PMCID: PMC9481278 DOI: 10.2147/btt.s380027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/27/2022] [Indexed: 11/24/2022]
Abstract
Inflammatory bowel diseases are considered immune disorders with a complex genetic architecture involving constantly changing endogenous and exogenous factors. The rapid evolution of genomic technologies and the emergence of newly discovered molecular actors are compelling the research community to reevaluate the knowledge and molecular processes. The human intestinal tract contains intestinal human microbiota consisting of commensal, pathogenic, and symbiotic strains leading to immune responses that can contribute and lead to both systemic and intestinal disorders including IBD. In this review, we attempted to highlight some updates of the new IBD features related to genomics, microbiota, new emerging therapies and some major established IBD risk factors.
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Affiliation(s)
- Maheeba Abdulla
- Internal Medicine Department, Ibn AlNafees Hospital, Arabian Gulf University, Manama, Bahrain
- Correspondence: Maheeba Abdulla, Consultant Gastroenterologist, Internal Medicine Department, Ibn AlNafees Hospital, Arabian Gulf University, Manama, Bahrain, Email
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Klaassen K, Djordjevic M, Skakic A, Kecman B, Drmanac R, Pavlovic S, Stojiljkovic M. Untreated PKU patients without intellectual disability: SHANK gene family as a candidate modifier. Mol Genet Metab Rep 2021; 29:100822. [PMID: 34900593 PMCID: PMC8639809 DOI: 10.1016/j.ymgmr.2021.100822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/06/2022] Open
Abstract
Phenylketonuria (PKU) is an inborn error of metabolism caused by variants in the phenylalanine hydroxylase (PAH) gene and it is characterized by excessively high levels of phenylalanine in body fluids. PKU is a paradigm for a genetic disease that can be treated and majority of developed countries have a population-based newborn screening. Thus, the combination of early diagnosis and immediate initiation of treatment has resulted in normal intelligence for treated PKU patients. Although PKU is a monogenic disease, decades of research and clinical practice have shown that the correlation between the genotype and corresponding phenotype is not simple at all. Attempts have been made to discover modifier genes for PKU cognitive phenotype but without any success so far. We conducted whole genome sequencing of 4 subjects from unrelated non-consanguineous families who presented with pathogenic mutations in the PAH gene, high blood phenylalanine concentrations and near-normal cognitive development despite no treatment. We used cross sample analysis to select genes common for more than one patient. Thus, the SHANK gene family emerged as the only relevant gene family with variants detected in 3 of 4 analyzed patients. We detected two novel variants, p.Pro1591Ala in SHANK1 and p.Asp18Asn in SHANK2, as well as SHANK2:p.Gly46Ser, SHANK2:p.Pro1388_Phe1389insLeuPro and SHANK3:p.Pro1716Thr variants that were previously described. Computational analysis indicated that the identified variants do not abolish the function of SHANK proteins. However, changes in posttranslational modifications of SHANK proteins could influence functioning of the glutamatergic synapses, cytoskeleton regulation and contribute to maintaining optimal synaptic density and number of dendritic spines. Our findings are linking SHANK gene family and brain plasticity in PKU for the first time. We hypothesize that variant SHANK proteins maintain optimal synaptic density and number of dendritic spines under high concentrations of phenylalanine and could have protective modifying effect on cognitive development of PKU patients.
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Affiliation(s)
- K Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - M Djordjevic
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Belgrade, Serbia.,School of Medicine, University of Belgrade, Belgrade, Serbia
| | - A Skakic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - B Kecman
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Belgrade, Serbia
| | - R Drmanac
- Complete Genomics Incorporated, San Jose, California 95134, USA.,MGI, BGI-Shenzhen, Shenzhen 518083, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - S Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - M Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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6
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Multi-Omics Analysis of Key microRNA-mRNA Metabolic Regulatory Networks in Skeletal Muscle of Obese Rabbits. Int J Mol Sci 2021; 22:ijms22084204. [PMID: 33921578 PMCID: PMC8072691 DOI: 10.3390/ijms22084204] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/10/2021] [Accepted: 04/15/2021] [Indexed: 12/25/2022] Open
Abstract
microRNAs (miRNAs), small non-coding RNA with a length of about 22 nucleotides, are involved in the energy metabolism of skeletal muscle cells. However, their molecular mechanism of metabolism in rabbit skeletal muscle is still unclear. In this study, 16 rabbits, 8 in the control group (CON-G) and 8 in the experimental group (HFD-G), were chosen to construct an obese model induced by a high-fat diet fed from 35 to 70 days of age. Subsequently, 54 differentially expressed miRNAs, 248 differentially expressed mRNAs, and 108 differentially expressed proteins related to the metabolism of skeletal muscle were detected and analyzed with three sequencing techniques (small RNA sequencing, transcriptome sequencing, and tandem mass tab (TMT) protein technology). It was found that 12 miRNAs and 12 core genes (e.g., CRYL1, VDAC3 and APIP) were significantly different in skeletal muscle from rabbits in the two groups. The network analysis showed that seven miRNA-mRNA pairs were involved in metabolism. Importantly, two miRNAs (miR-92a-3p and miR-30a/c/d-5p) regulated three transcription factors (MYBL2, STAT1 and IKZF1) that may be essential for lipid metabolism. These results enhance our understanding of molecular mechanisms associated with rabbit skeletal muscle metabolism and provide a basis for future studies in the metabolic diseases of human obesity.
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Du C, Li Z, Wei H, Zhang M, Hu M, Zhang C, Luo X, Liang Y. Clinical analysis and long-term treatment monitoring of 3 patients with glycogen storage disease type Ib. BMC Med Genomics 2021; 14:81. [PMID: 33731098 PMCID: PMC7972195 DOI: 10.1186/s12920-021-00936-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/09/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND To investigate the clinical and genetic characteristics of patients with glycogen storage disease type Ib (GSD Ib). CASE PRESENTATION This report retrospectively analyzed the clinical data of 3 patients with GSD Ib admitted into our hospital, and summarized their onset characteristics, clinical manifestations, related examinations and treatment as well as mutational spectrum. After gene sequencing, the diagnosis of GSD Ib was confirmed in all 3 patients. Five variants of SLC37A4 gene were detected, of which c. 572C > T was the common variant and c. 680G > A was a novel variant. The 3 cases of GSD Ib were mainly affected by liver enlargement, growth retardation, etc., and all had a history of repeated infections. At the onset, patients mainly manifested as mildly elevated alanine-aminotransferase (ALT), accompanied by decreased absolute neutrophil count (ANC), hypertriglyceridemia, and metabolic disorders (hypoglycemia, hyperlactic acidemia, metabolic acidosis, etc.). After long-term treatment by oral uncooked cornstarch, the abnormal liver enzymes gradually returned to normal, and metabolic abnormalities were basically controlled most of the time. With increasing age, ANC of 2 patients decreased progressively, whereas the times of infections was reduced. CONCLUSIONS We reported 3 cases with GSD Ib and a novel SLC37A4 variant. The possibility of GSD type Ib should be kept on alert when a patient suffers recurrent infections, accompanied by hepatomegaly, elevated liver enzymes, hypoglycemia, dyslipidemia, and metabolic disorders.
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Affiliation(s)
- Caiqi Du
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhuoguang Li
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hong Wei
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Min Zhang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Minghui Hu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Cai Zhang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoping Luo
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yan Liang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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8
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Xu Q, Tang H, Duan L, Zuo X, Shi X, Li Y, Zhao H, Zhang H. A novel SLC37A4 missense mutation in GSD-Ib without hepatomegaly causes enhanced leukocytes endoplasmic reticulum stress and apoptosis. Mol Genet Genomic Med 2020; 9:e1568. [PMID: 33280276 PMCID: PMC7963412 DOI: 10.1002/mgg3.1568] [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: 06/23/2020] [Revised: 11/08/2020] [Accepted: 11/16/2020] [Indexed: 11/19/2022] Open
Abstract
Background Glycogen storage disease (GSD) type Ib is an autosomal recessive disease caused by defects of glucose‐6‐phosphate transporter (G6PT), encoded by the SLC37A4 gene. To date, over 100 mutations have been revealed in the SLC37A4 gene. GSD‐Ib patients manifest a metabolic phenotype of impaired blood glucose homeostasis and also carry the additional complications of neutropenia and myeloid dysfunction. Methods Here, we present two daughters with an initial diagnosis of gout in a Chinese consanguineous family. Whole‐exome sequencing was performed to identify the mutations. The mechanism of leukocytopenia was investigated. Results Whole‐exome sequencing analysis of the proband identified a novel homozygous p.P119L mutation in SLC37A4, leading to a diagnosis of GSD‐Ib. We found that the potential pathogenic p.P119L mutation leads to an unusual phenotype characterized by gout at onset, and GSD‐Ib arising from this variant also manifests multiple metabolic abnormalities, leukocytopenia, and anemia, but no hepatomegaly. The leukocytes from the proband showed increased mRNA levels of sXBP‐1, BIP, and CHOP genes in the unfolded protein response pathway, and enhanced Bax mRNA and caspase‐3 activity, which might contribute to leukocytopenia. Conclusion Our findings broaden the variation spectrum of SLC37A4 and suggest no strict genotype–phenotype correlations in GSD‐Ib patients.
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Affiliation(s)
- Qianyun Xu
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China
| | - Haiyan Tang
- Department of Medical Genetics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Liping Duan
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoxia Zuo
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoliu Shi
- Department of Medical Genetics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yisha Li
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Hongjun Zhao
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China
| | - Huali Zhang
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China.,Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, China.,Sepsis Translational Medicine Key Laboratory of Hunan, Central South University, Changsha, China
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Beyzaei Z, Geramizadeh B, Karimzadeh S. Diagnosis of hepatic glycogen storage disease patients with overlapping clinical symptoms by massively parallel sequencing: a systematic review of literature. Orphanet J Rare Dis 2020; 15:286. [PMID: 33054851 PMCID: PMC7557034 DOI: 10.1186/s13023-020-01573-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 10/05/2020] [Indexed: 12/17/2022] Open
Abstract
Background Glycogen storage diseases (GSDs) with liver involvement are complex disorders with similar manifestations. Currently, the main diagnostic methods such as tissue diagnosis, either histopathology or enzyme assay, are invasive. Meanwhile, GSDs are diseases with significant genetic heterogeneity, and gene-sequencing methods can be more useful. This systematic review aims to review the literature to assess the value of massively parallel sequencing in the diagnosis of GSDs on patients with previously undiagnosed hepatic involvement. Methods Relevant studies identified in the MEDLINE/PubMed, EMBASE, Cochrane Library, Scopus, and Web of Science Core Collection databases up to July 2019 with no time and language restrictions. Publications were included in the review if they analyzed GSDs with hepatic involvement (GSD I, GSD III, GSD IV, GSD VI, GSD IX), using targeted gene sequencing (TGS) or exome sequencing (ES). Results Eleven studies were included in this systematic review. ES demonstrated a 93% diagnostic yield. These methods correctly distinguished all types of pathogenic variants. The diagnostic yield of the TGS method was around 79.7%. Conclusions According to our results, TGS analysis can be considered as the first-line diagnostic method with valuable results and ES can be used to diagnose complex cases of GSD with liver involvement. Overall, these molecular methods are considered as accurate diagnostic tools, which expedite correct diagnosis and treatment with significant cost-effectiveness by reducing unnecessary and inaccurate tests. PROSPERO registration CRD42020139931. Registered 8 January 2020.
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Affiliation(s)
- Zahra Beyzaei
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bita Geramizadeh
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. .,Department of Pathology, Shiraz University of Medical Sciences, Zand St., Shiraz, Iran.
| | - Sara Karimzadeh
- Shiraz Medical School Library, Shiraz University of Medical Sciences, Shiraz, Iran
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Klaassen K, Stankovic B, Zukic B, Kotur N, Gasic V, Pavlovic S, Stojiljkovic M. Functional prediction and comparative population analysis of variants in genes for proteases and innate immunity related to SARS-CoV-2 infection. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 84:104498. [PMID: 32771700 PMCID: PMC7410821 DOI: 10.1016/j.meegid.2020.104498] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 01/12/2023]
Abstract
New coronavirus SARS-CoV-2 is capable to infect humans and cause a novel disease COVID-19. Aiming to understand a host genetic component of COVID-19, we focused on variants in genes encoding proteases and genes involved in innate immunity that could be important for susceptibility and resistance to SARS-CoV-2 infection. Analysis of sequence data of coding regions of FURIN, PLG, PRSS1, TMPRSS11a, MBL2 and OAS1 genes in 143 unrelated individuals from Serbian population identified 22 variants with potential functional effect. In silico analyses (PolyPhen-2, SIFT, MutPred2 and Swiss-Pdb Viewer) predicted that 10 variants could impact the structure and/or function of proteins. These protein-altering variants (p.Gly146Ser in FURIN; p.Arg261His and p.Ala494Val in PLG; p.Asn54Lys in PRSS1; p.Arg52Cys, p.Gly54Asp and p.Gly57Glu in MBL2; p.Arg47Gln, p.Ile99Val and p.Arg130His in OAS1) may have predictive value for inter-individual differences in the response to the SARS-CoV-2 infection. Next, we performed comparative population analysis for the same variants using extracted data from the 1000 Genomes project. Population genetic variability was assessed using delta MAF and Fst statistics. Our study pointed to 7 variants in PLG, TMPRSS11a, MBL2 and OAS1 genes with noticeable divergence in allelic frequencies between populations worldwide. Three of them, all in MBL2 gene, were predicted to be damaging, making them the most promising population-specific markers related to SARS-CoV-2 infection. Comparing allelic frequencies between Serbian and other populations, we found that the highest level of genetic divergence related to selected loci was observed with African, followed by East Asian, Central and South American and South Asian populations. When compared with European populations, the highest divergence was observed with Italian population. In conclusion, we identified 4 variants in genes encoding proteases (FURIN, PLG and PRSS1) and 6 in genes involved in the innate immunity (MBL2 and OAS1) that might be relevant for the host response to SARS-CoV-2 infection.
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Affiliation(s)
- Kristel Klaassen
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Stojiljkovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
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Pascoal C, Francisco R, Ferro T, Dos Reis Ferreira V, Jaeken J, Videira PA. CDG and immune response: From bedside to bench and back. J Inherit Metab Dis 2020; 43:90-124. [PMID: 31095764 DOI: 10.1002/jimd.12126] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/20/2022]
Abstract
Glycosylation is an essential biological process that adds structural and functional diversity to cells and molecules, participating in physiological processes such as immunity. The immune response is driven and modulated by protein-attached glycans that mediate cell-cell interactions, pathogen recognition and cell activation. Therefore, abnormal glycosylation can be associated with deranged immune responses. Within human diseases presenting immunological defects are congenital disorders of glycosylation (CDG), a family of around 130 rare and complex genetic diseases. In this review, we have identified 23 CDG with immunological involvement, characterized by an increased propensity to-often life-threatening-infection. Inflammatory and autoimmune complications were found in 7 CDG types. CDG natural history(ies) and the mechanisms behind the immunological anomalies are still poorly understood. However, in some cases, alterations in pathogen recognition and intracellular signaling (eg, TGF-β1, NFAT, and NF-κB) have been suggested. Targeted therapies to restore immune defects are only available for PGM3-CDG and SLC35C1-CDG. Fostering research on glycoimmunology may elucidate the involved pathophysiological mechanisms and open new therapeutic avenues, thus improving CDG patients' quality of life.
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Affiliation(s)
- Carlota Pascoal
- Portuguese Association for CDG, Lisbon, Portugal
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Rita Francisco
- Portuguese Association for CDG, Lisbon, Portugal
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Tiago Ferro
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Vanessa Dos Reis Ferreira
- Portuguese Association for CDG, Lisbon, Portugal
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
| | - Jaak Jaeken
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- Center for Metabolic Diseases, Department of Development and Regeneration, UZ and KU Leuven, Leuven, Belgium
| | - Paula A Videira
- Portuguese Association for CDG, Lisbon, Portugal
- CDG & Allies - Professionals and Patient Associations International Network (CDG & Allies - PPAIN), Caparica, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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12
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Nambu R, Muise AM. Advanced Understanding of Monogenic Inflammatory Bowel Disease. Front Pediatr 2020; 8:618918. [PMID: 33553075 PMCID: PMC7862769 DOI: 10.3389/fped.2020.618918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/31/2020] [Indexed: 12/29/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a group of chronic disorders that cause relapsing inflammation in the gastrointestinal tract and comprise three major subgroups of Crohn's disease (CD), ulcerative colitis (UC), and IBD-unclassified (IBDU). Recent advances in genomic technologies have furthered our understanding of IBD pathogenesis. It includes differentiation rare monogenic disorders exhibiting IBD and IBD-like inflammation (monogenic IBD) from patients with the common polygenic form of IBD. Several novel genes responsible for monogenic IBD have been elucidated, and the number of reports has increased due to advancements in molecular functional analysis. Identification of these pathogenic genetic mutations has helped in elucidating the details of the immune response associated with gastrointestinal inflammation and in providing individualized treatments for patients with severe IBD that is often unresponsive to conventional therapy. The majority of monogenic IBD studies have focused on young children diagnosed <6 years of age (very early-onset IBD); however, a recent study revealed high prevalence of monogenic IBD in older children aged >6 years of age as well. Meanwhile, although patients with monogenic IBD generally show co-morbidities and/or extraintestinal manifestation at the time of diagnosis, cases of IBD developing as the initial symptom with unremarkable prodromal symptoms have been reported. It is crucial that the physicians properly match genetic analytical data with clinical diagnosis and/or differential diagnosis. In this review, we summarize the essential clues that may physicians make a correct diagnosis of monogenic disease, including classification, prevalence and clinical phenotype based on available literatures.
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Affiliation(s)
- Ryusuke Nambu
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada.,SickKids Inflammatory Bowel Disease Center, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Gastroenterology and Hepatology, Saitama Children's Medical Center, Saitama, Japan
| | - Aleixo M Muise
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada.,SickKids Inflammatory Bowel Disease Center, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Pediatrics, Institute of Medical Science and Biochemistry, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
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13
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Sperb-Ludwig F, Pinheiro FC, Bettio Soares M, Nalin T, Ribeiro EM, Steiner CE, Ribeiro Valadares E, Porta G, Fishinger Moura de Souza C, Schwartz IVD. Glycogen storage diseases: Twenty-seven new variants in a cohort of 125 patients. Mol Genet Genomic Med 2019; 7:e877. [PMID: 31508908 PMCID: PMC6825860 DOI: 10.1002/mgg3.877] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/07/2019] [Accepted: 07/08/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Hepatic glycogen storage diseases (GSDs) are a group of rare genetic disorders in which glycogen cannot be metabolized to glucose in the liver because of enzyme deficiencies along the glycogenolytic pathway. GSDs are well-recognized diseases that can occur without the full spectrum, and with overlapping in symptoms. METHODS We analyzed a cohort of 125 patients with suspected hepatic GSD through a next-generation sequencing (NGS) gene panel in Ion Torrent platform. New variants were analyzed by pathogenicity prediction tools. RESULTS Twenty-seven new variants predicted as pathogenic were found between 63 variants identified. The most frequent GSD was type Ia (n = 53), followed by Ib (n = 23). The most frequent variants were p.Arg83Cys (39 alleles) and p.Gln347* (14 alleles) in G6PC gene, and p.Leu348Valfs (21 alleles) in SLC37A4 gene. CONCLUSIONS The study presents the largest cohort ever analyzed in Brazilian patients with hepatic glycogenosis. We determined the clinical utility of NGS for diagnosis. The molecular diagnosis of hepatic GSDs enables the characterization of diseases with similar clinical symptoms, avoiding hepatic biopsy and having faster results.
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Affiliation(s)
- Fernanda Sperb-Ludwig
- Post‐Graduation Program in Genetics and Molecular BiologyUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Laboratory of Basic Research and Advanced Investigations in Neurosciences (BRAIN)Hospital de Clínicas de Porto AlegrePorto AlegreBrazil
| | - Franciele Cabral Pinheiro
- Post‐Graduation Program in Genetics and Molecular BiologyUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Laboratory of Basic Research and Advanced Investigations in Neurosciences (BRAIN)Hospital de Clínicas de Porto AlegrePorto AlegreBrazil
| | - Malu Bettio Soares
- Laboratory of Basic Research and Advanced Investigations in Neurosciences (BRAIN)Hospital de Clínicas de Porto AlegrePorto AlegreBrazil
| | - Tatiele Nalin
- Post‐Graduation Program in Genetics and Molecular BiologyUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | | | | | - Eugênia Ribeiro Valadares
- Departamento de Propedêutica ComplementarFaculdade de Medicina da Universidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Gilda Porta
- Hospital Infantil Menino JesusSão PauloBrazil
| | | | - Ida Vanessa Doederlein Schwartz
- Post‐Graduation Program in Genetics and Molecular BiologyUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Laboratory of Basic Research and Advanced Investigations in Neurosciences (BRAIN)Hospital de Clínicas de Porto AlegrePorto AlegreBrazil
- Medical Genetics ServiceHospital de Clínicas de Porto AlegrePorto AlegreBrazil
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14
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Sarajlija A, Djordjevic M, Kecman B, Skakic A, Pavlovic S, Pasic S, Stojiljkovic M. Impact of genotype on neutropenia in a large cohort of Serbian patients with glycogen storage disease type Ib. Eur J Med Genet 2019; 63:103767. [PMID: 31536830 DOI: 10.1016/j.ejmg.2019.103767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 09/12/2019] [Accepted: 09/15/2019] [Indexed: 01/30/2023]
Abstract
BACKGROUND Glycogen storage disease type Ib (GSD-Ib) is an inherited metabolic disorder caused by autosomal recessive mutations in SLC37A4 coding for the glucose-6-phosphate transporter. Neutropenia represents major feature of GSD-Ib along with metabolic disturbances. Previous research in GSD-Ib patients did not reveal significant genotype-phenotype correlation. Our objective was to explore the frequency and severity of neutropenia and it's complications in relation to genotype of GSD-Ib patients. METHODS We estimated cumulative incidence of neutropenia and severe neutropenia, relation of genotype to absolute neutrophil count (ANC), and dynamics of ANC during serious bacterial infections (SBI) in a cohort of Serbian GSD Ib patients. Impact of genotype on GSD Ib-related inflammatory bowel disease (IBD) was also assessed. RESULTS Absolute neutrophil count (ANC) < 1500/mm3 was present in all 33 patients, with severe neutropenia (ANC<500/mm3) occurring in 60.6% of patients. The median age at neutropenia onset was 24 months, while severe neutropenia developed at median of 4.5 years. The ANC was elevated during 90.5% episodes of SBI. Genotypes c.81T>A/c.785G>A and c.81T>A/c.1042_1043delCT are associated with earlier onset of neutropenia. Patients carrying c.785G>A mutation express a higher capacity for ANC increase during SBI. Inflammatory bowel disease was diagnosed in 8 patients (24.2% of total) with median age of onset at 7 years. Risk for IBD occurrence was not significantly affected by gender, genotype and severity of neutropenia. CONCLUSIONS We may conclude that certain mutations in SLC37A4 influence the risk for severe neutropenia occurrence but also affect the capacity to increase ANC during SBI.
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Affiliation(s)
- Adrijan Sarajlija
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Department of Metabolism and Clinical Genetics, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
| | - Maja Djordjevic
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Department of Metabolism and Clinical Genetics, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Bozica Kecman
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Department of Metabolism and Clinical Genetics, Belgrade, Serbia
| | - Anita Skakic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Srdjan Pasic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia; Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Department of Immunology, Belgrade, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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15
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Chou JY, Cho JH, Kim GY, Mansfield BC. Molecular biology and gene therapy for glycogen storage disease type Ib. J Inherit Metab Dis 2018; 41:1007-1014. [PMID: 29663270 DOI: 10.1007/s10545-018-0180-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/01/2018] [Accepted: 03/26/2018] [Indexed: 12/15/2022]
Abstract
Glycogen storage disease type Ib (GSD-Ib) is caused by a deficiency in the ubiquitously expressed glucose-6-phosphate (G6P) transporter (G6PT or SLC37A4). The primary function of G6PT is to translocate G6P from the cytoplasm into the lumen of the endoplasmic reticulum (ER). Inside the ER, G6P is hydrolyzed to glucose and phosphate by either the liver/kidney/intestine-restricted glucose-6-phosphatase-α (G6Pase-α) or the ubiquitously expressed G6Pase-β. A deficiency in G6Pase-α causes GSD type Ia (GSD-Ia) and a deficiency in G6Pase-β causes GSD-I-related syndrome (GSD-Irs). In gluconeogenic organs, functional coupling of G6PT and G6Pase-α is required to maintain interprandial blood glucose homeostasis. In myeloid tissues, functional coupling of G6PT and G6Pase-β is required to maintain neutrophil homeostasis. Accordingly, GSD-Ib is a metabolic and immune disorder, manifesting impaired glucose homeostasis, neutropenia, and neutrophil dysfunction. A G6pt knockout mouse model is being exploited to delineate the pathophysiology of GSD-Ib and develop new clinical treatment options, including gene therapy. The safety and efficacy of several G6PT-expressing recombinant adeno-associated virus pseudotype 2/8 vectors have been examined in murine GSD-Ib. The results demonstrate that the liver-directed gene transfer and expression safely corrects metabolic abnormalities and prevents hepatocellular adenoma (HCA) development. However, a second vector system may be required to correct myeloid and renal dysfunction in GSD-Ib. These findings are paving the way to a safe and efficacious gene therapy for entering clinical trials.
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Affiliation(s)
- Janice Y Chou
- Section on Cellular Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 10, Room 8N240C, NIH 10 Center Drive, Bethesda, MD, 20892-1830, USA.
| | - Jun-Ho Cho
- Section on Cellular Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 10, Room 8N240C, NIH 10 Center Drive, Bethesda, MD, 20892-1830, USA
| | - Goo-Young Kim
- Section on Cellular Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 10, Room 8N240C, NIH 10 Center Drive, Bethesda, MD, 20892-1830, USA
| | - Brian C Mansfield
- Section on Cellular Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Building 10, Room 8N240C, NIH 10 Center Drive, Bethesda, MD, 20892-1830, USA
- Foundation Fighting Blindness, Columbia, MD, 21046, USA
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